################# wgEncodeOpenChrom... {Dnase, Faire, Chip} composites' hg19 submissions ############### 2010-06-23 UTA ChIP for hg19 June Freeze ======================================== select id,name,status,user_id from projects where status = "loaded" and user_id = 17 and name like "%UTA%" order by id; +------+----------------------------------+--------+---------+ | id | name | status | user_id | +------+----------------------------------+--------+---------+ | 1229 | DNCT UTA c-Myc GM12878 20100528 | loaded | 17 | | 1478 | DNCT UTA PolII GM12878 20100615 | loaded | 17 | | 1490 | DNCT UTA CTCF GM12891 20100615 | loaded | 17 | | 1491 | DNCT UTA CTCF GM12892 20100615 | loaded | 17 | | 1499 | DNCT UTA CTCF HeLa-S3 20100615 | loaded | 17 | | 1500 | DNCT UTA CTCF H1-hESC 20100615 | loaded | 17 | | 1501 | DNCT UTA c-Myc HeLa-S3 20100615 | loaded | 17 | | 1504 | DNCT UTA c-Myc H1_hESC 20100615 | loaded | 17 | | 1505 | DNCT UTA PolII HeLa-S3 20100615 | loaded | 17 | | 1516 | DNCT UTA CTCF GM19238 20100615 | loaded | 17 | | 1517 | DNCT UTA CTCF HepG2 20100615 | loaded | 17 | | 1518 | DNCT UTA Input GM12878 20100615 | loaded | 17 | | 1525 | DNCT UTA CTCF GM19239 20100615 | loaded | 17 | | 1526 | DNCT UTA CTCF PolII 20100615 | loaded | 17 | | 1527 | DNCT UTA c-Myc HepG2 20100616 | loaded | 17 | | 1536 | DNCT UTA CTCF GM19240 20100615 | loaded | 17 | | 1537 | DNCT UTA CTCF HUVEC 20100616 | loaded | 17 | | 1538 | DNCT UTA CTCF K562 20100616 | loaded | 17 | | 1539 | DNCT UTA CTCF NHEK 20100616 | loaded | 17 | | 1540 | DNCT UTA PolII HUVEC 20100616 | loaded | 17 | | 1541 | DNCT UTA PolII K562 20100616 | loaded | 17 | | 1542 | DNCT UTA c-Myc HUVEC 20100616 | loaded | 17 | | 1543 | DNCT UTA c-Myc K562 20100616 | loaded | 17 | | 1580 | DNCT UTA CTCF MCF-7 20100617 | loaded | 17 | | 1606 | DNCT UTA Input K562 200100617 | loaded | 17 | | 1607 | DNCT UTA Input HUVEC 200100617 | loaded | 17 | | 1608 | DNCT UTA Input HepG2 200100617 | loaded | 17 | | 1609 | DNCT UTA Input HeLa-S3 200100617 | loaded | 17 | | 1652 | DNCT UTA PolII ProgFib 20100618 | loaded | 17 | | 1657 | DNCT UTA CTCF ProgFib 20100619 | loaded | 17 | | 1832 | DNCT UTA Input ProgFib 20100621 | loaded | 17 | | 1833 | DNCT UTA PolII H1_hESC 20100621 | loaded | 17 | | 1834 | DNCT UTA Input MCF-7 20100621 | loaded | 17 | +------+----------------------------------+--------+---------+ 33 rows in set (0.00 sec) # load up the trackDb... rm /cluster/home/tdreszer/kent/src/hg/makeDb/trackDb/human/hg19/testing/tmp.ra cat 1229/out/trackDb.ra >> /cluster/home/tdreszer/kent/src/hg/makeDb/trackDb/human/hg19/testing/tmp.ra cat 1478/out/trackDb.ra >> /cluster/home/tdreszer/kent/src/hg/makeDb/trackDb/human/hg19/testing/tmp.ra cat 1490/out/trackDb.ra >> /cluster/home/tdreszer/kent/src/hg/makeDb/trackDb/human/hg19/testing/tmp.ra cat 1491/out/trackDb.ra >> /cluster/home/tdreszer/kent/src/hg/makeDb/trackDb/human/hg19/testing/tmp.ra cat 1499/out/trackDb.ra >> /cluster/home/tdreszer/kent/src/hg/makeDb/trackDb/human/hg19/testing/tmp.ra cat 1500/out/trackDb.ra >> /cluster/home/tdreszer/kent/src/hg/makeDb/trackDb/human/hg19/testing/tmp.ra cat 1501/out/trackDb.ra >> /cluster/home/tdreszer/kent/src/hg/makeDb/trackDb/human/hg19/testing/tmp.ra cat 1504/out/trackDb.ra >> /cluster/home/tdreszer/kent/src/hg/makeDb/trackDb/human/hg19/testing/tmp.ra cat 1505/out/trackDb.ra >> /cluster/home/tdreszer/kent/src/hg/makeDb/trackDb/human/hg19/testing/tmp.ra cat 1516/out/trackDb.ra >> /cluster/home/tdreszer/kent/src/hg/makeDb/trackDb/human/hg19/testing/tmp.ra cat 1517/out/trackDb.ra >> /cluster/home/tdreszer/kent/src/hg/makeDb/trackDb/human/hg19/testing/tmp.ra cat 1518/out/trackDb.ra >> /cluster/home/tdreszer/kent/src/hg/makeDb/trackDb/human/hg19/testing/tmp.ra cat 1525/out/trackDb.ra >> /cluster/home/tdreszer/kent/src/hg/makeDb/trackDb/human/hg19/testing/tmp.ra cat 1526/out/trackDb.ra >> /cluster/home/tdreszer/kent/src/hg/makeDb/trackDb/human/hg19/testing/tmp.ra cat 1527/out/trackDb.ra >> /cluster/home/tdreszer/kent/src/hg/makeDb/trackDb/human/hg19/testing/tmp.ra cat 1536/out/trackDb.ra >> /cluster/home/tdreszer/kent/src/hg/makeDb/trackDb/human/hg19/testing/tmp.ra cat 1537/out/trackDb.ra >> /cluster/home/tdreszer/kent/src/hg/makeDb/trackDb/human/hg19/testing/tmp.ra cat 1538/out/trackDb.ra >> /cluster/home/tdreszer/kent/src/hg/makeDb/trackDb/human/hg19/testing/tmp.ra cat 1539/out/trackDb.ra >> /cluster/home/tdreszer/kent/src/hg/makeDb/trackDb/human/hg19/testing/tmp.ra cat 1540/out/trackDb.ra >> /cluster/home/tdreszer/kent/src/hg/makeDb/trackDb/human/hg19/testing/tmp.ra cat 1541/out/trackDb.ra >> /cluster/home/tdreszer/kent/src/hg/makeDb/trackDb/human/hg19/testing/tmp.ra cat 1542/out/trackDb.ra >> /cluster/home/tdreszer/kent/src/hg/makeDb/trackDb/human/hg19/testing/tmp.ra cat 1543/out/trackDb.ra >> /cluster/home/tdreszer/kent/src/hg/makeDb/trackDb/human/hg19/testing/tmp.ra cat 1580/out/trackDb.ra >> /cluster/home/tdreszer/kent/src/hg/makeDb/trackDb/human/hg19/testing/tmp.ra cat 1606/out/trackDb.ra >> /cluster/home/tdreszer/kent/src/hg/makeDb/trackDb/human/hg19/testing/tmp.ra cat 1607/out/trackDb.ra >> /cluster/home/tdreszer/kent/src/hg/makeDb/trackDb/human/hg19/testing/tmp.ra cat 1608/out/trackDb.ra >> /cluster/home/tdreszer/kent/src/hg/makeDb/trackDb/human/hg19/testing/tmp.ra cat 1609/out/trackDb.ra >> /cluster/home/tdreszer/kent/src/hg/makeDb/trackDb/human/hg19/testing/tmp.ra cat 1652/out/trackDb.ra >> /cluster/home/tdreszer/kent/src/hg/makeDb/trackDb/human/hg19/testing/tmp.ra cat 1657/out/trackDb.ra >> /cluster/home/tdreszer/kent/src/hg/makeDb/trackDb/human/hg19/testing/tmp.ra cat 1832/out/trackDb.ra >> /cluster/home/tdreszer/kent/src/hg/makeDb/trackDb/human/hg19/testing/tmp.ra cat 1833/out/trackDb.ra >> /cluster/home/tdreszer/kent/src/hg/makeDb/trackDb/human/hg19/testing/tmp.ra cat 1834/out/trackDb.ra >> /cluster/home/tdreszer/kent/src/hg/makeDb/trackDb/human/hg19/testing/tmp.ra cd /cluster/home/tdreszer/kent/src/hg/makeDb/trackDb/human/hg19/testing/ raToLines tmp.ra tmp.txt grep compositeTrack tmp.txt > tmpC.txt grep view=Peaks tmp.txt > tmpP.txt grep view=Base tmp.txt > tmpB.txt grep view=Signal tmp.txt > tmpS.txt wl tmp?.txt 26 tmpB.txt 33 tmpC.txt 26 tmpP.txt 33 tmpS.txt 118 total wl tmp.txt 118 tmp.txt # No replicates e tmpP.txt tmpS.txt tmpB.txt # Fix view references linesToRa tmpP.txt tmpP.ra linesToRa tmpS.txt tmpS.ra linesToRa tmpB.txt tmpB.ra e tmpP.ra tmpS.ra tmpB.ra cd .. cp ../hg18/wgEncodeChromatinMap.ra wgEncodeOpenChromChip.ra cp ../hg18/wgEncodeChromatinMap.html wgEncodeOpenChromChip.html e wgEncodeOpenChromChip.html wgEncodeUwHistone.html # mark it as preliminary e trackDb.wgEncode.ra # include wgEncodeOpenChromChip.ra e wgEncodeOpenChromChip.ra # add tmpP.ra tmpS.ra tmpB.ra make DBS=hg19 # till working git add wgEncodeOpenChromChip.ra wgEncodeOpenChromChip.html trackDb.wgEncode.ra git commit; pull; push # now metadata mdbUpdate hg19 1229/out/mdb.txt mdbUpdate hg19 1478/out/mdb.txt mdbUpdate hg19 1490/out/mdb.txt mdbUpdate hg19 1491/out/mdb.txt mdbUpdate hg19 1499/out/mdb.txt mdbUpdate hg19 1500/out/mdb.txt mdbUpdate hg19 1501/out/mdb.txt mdbUpdate hg19 1504/out/mdb.txt mdbUpdate hg19 1505/out/mdb.txt mdbUpdate hg19 1516/out/mdb.txt mdbUpdate hg19 1517/out/mdb.txt mdbUpdate hg19 1518/out/mdb.txt mdbUpdate hg19 1525/out/mdb.txt mdbUpdate hg19 1526/out/mdb.txt mdbUpdate hg19 1527/out/mdb.txt mdbUpdate hg19 1536/out/mdb.txt mdbUpdate hg19 1537/out/mdb.txt mdbUpdate hg19 1538/out/mdb.txt mdbUpdate hg19 1539/out/mdb.txt mdbUpdate hg19 1540/out/mdb.txt mdbUpdate hg19 1541/out/mdb.txt mdbUpdate hg19 1542/out/mdb.txt mdbUpdate hg19 1543/out/mdb.txt mdbUpdate hg19 1580/out/mdb.txt mdbUpdate hg19 1606/out/mdb.txt mdbUpdate hg19 1607/out/mdb.txt mdbUpdate hg19 1608/out/mdb.txt mdbUpdate hg19 1609/out/mdb.txt mdbUpdate hg19 1652/out/mdb.txt mdbUpdate hg19 1657/out/mdb.txt mdbUpdate hg19 1832/out/mdb.txt mdbUpdate hg19 1833/out/mdb.txt mdbUpdate hg19 1834/out/mdb.txt Using table named 'hg19.metaDb_tdreszer'. Read 2 metadata objects from hg19 Affected 38 row(s) in hg19.metaDb_tdreszer # Now update dates cd /cluster/home/tdreszer/kent/src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/testing mdbPrint hg18 -table=metaDb -vars="composite=wgEncodeChromatinMap dataType=ChIPseq" -updDb=hg19 -updMdb=metaDb_tdreszer -updSelect="grant,dataType,cell,antibody,view,replicate" -updVars="dateSubmitted,dateUnrestricted" > utaDates.txt objects:250 vars:4729 mdbPrint hg19 -vars="composite=wgEncodeOpenChromChip" -updDb=hg19 -updMdb=metaDb_tdreszer -updSelect="subId" -updVars="dateSubmitted" > utaResub.txt objects:144 vars:2526 e utaDates.txt # Add origAssembly=hg18, change select /grant,dataType/composite=wgEncodeOpenChromChip/ chmod 755 uta*.txt ./utaDates.txt Affected 2 row(s) in hg19.metaDb_tdreszer Affected 0 row(s) in hg19.metaDb_tdreszer ... e utaResub.txt # Add select origAssembly=hg18, change dateSubmitted to dateResubmitted ./utaResub.txt Affected 5 row(s) in hg19.metaDb_tdreszer Affected 0 row(s) in hg19.metaDb_tdreszer # not remapped! ... cd .. mdbPrint hg19 -vars="composite=wgEncodeOpenChromChip" > wgEncodeOpenChromChip.ra Using table named 'hg19.metaDb_tdreszer'. objects:144 vars:2670 mdbUpdate hg19 -table=metaDb wgEncodeOpenChromChip.ra Read 144 metadata objects from hg19 Affected 2670 row(s) in hg19.metaDb e makefile # add wgEncodeOpenChromChip.ra git add makefile wgEncodeOpenChromChip.ra git commit -m "Metadata for UTA Open Chrom ChIPseq June 2010 freeze" git pull; git push make alpha DBS=hg19 # Now downloads: cd /usr/local/apache/htdocs-hgdownload/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip e preamble.html ../wgEncodeUwHistone/preamble.html encodeDownloadsPage.pl -db=hg19 index.html # Mark as displayed: /cluster/data/encode/pipeline/bin/encodeStatus.pl 1229 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 1478 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 1490 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 1491 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 1499 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 1500 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 1501 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 1504 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 1505 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 1516 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 1517 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 1518 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 1525 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 1526 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 1527 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 1536 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 1537 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 1538 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 1539 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 1540 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 1541 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 1542 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 1543 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 1580 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 1606 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 1607 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 1608 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 1609 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 1652 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 1657 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 1832 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 1833 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 1834 displayed select id,name,status,user_id from projects where status = "loaded" and user_id = 17 and name like "%UTA%" order by id; Empty set (0.00 sec) 2010-06-24 Duke DNase for hg19 June Freeze ========================================== select id,name,status,user_id from projects where status = "loaded" and user_id = 17 and name like "%Duke%" order by id; +------+---------------------------------------------+--------+---------+ | id | name | status | user_id | +------+---------------------------------------------+--------+---------+ | 1412 | DNCT Duke DNaseHS Chorion 20100614 | loaded | 17 | | 1479 | DNCT Duke DNaseHS Medullo 20100615 | loaded | 17 | | 1487 | DNCT Duke DNaseHS GM12891 20100615 | loaded | 17 | | 1488 | DNCT Duke DNaseHS GM12892 20100615 | loaded | 17 | | 1489 | DNCT Duke DNaseHS GM19238 20100615 | loaded | 17 | | 1494 | DNCT Duke DNaseHS GM12878 20100615 | loaded | 17 | | 1495 | DNCT Duke DNaseHS H1-hESC 20100615 | loaded | 17 | | 1498 | DNCT Duke DNaseHS HeLa-S3 20100615 | loaded | 17 | | 1506 | DNCT Duke DNaseHS GM19239 20100615 | loaded | 17 | | 1507 | DNCT Duke DNaseHS GM18507 20100615 | loaded | 17 | | 1509 | DNCT Duke DNaseHS GM19240 20100615 | loaded | 17 | | 1519 | DNCT Duke DNaseHS H9ES 20100615 | loaded | 17 | | 1528 | DNCT Duke DNaseHS HepG2 20100616 | loaded | 17 | | 1532 | DNCT Duke DNaseHS HUVEC 20100616 | loaded | 17 | | 1533 | DNCT Duke DNaseHS NHEK 20100616 | loaded | 17 | | 1534 | DNCT Duke DNaseHS K562 20100616 | loaded | 17 | | 1535 | DNCT Duke DNaseHS LHSR androgen 20100616 | loaded | 17 | | 1544 | DNCT Duke DNaseHS HeLa-S3 IFNa4h 20100616 | loaded | 17 | | 1545 | DNCT Duke DNaseHS MCF-7 20100616 | loaded | 17 | | 1575 | DNCT Duke DNaseHS LHSR 20100616 | loaded | 17 | | 1650 | DNCT Duke DNaseHS ProgFib 20100618 | loaded | 17 | | 1651 | DNCT Duke DNaseHS FibroP 20100618 | loaded | 17 | | 1653 | DNCT Duke DNaseHS Fibrobl 20100618 | loaded | 17 | | 1654 | DNCT Duke DNaseHS HSMM 20100618 | loaded | 17 | | 1655 | DNCT Duke DNaseHS Myometr 20100618 | loaded | 17 | | 1656 | DNCT Duke DNaseHS PanIslets 20100618 | loaded | 17 | | 1678 | DNCT Duke DNaseHS AoSMC 20100619 | loaded | 17 | | 1679 | DNCT Duke DNaseHS HSMMtube 20100619 | loaded | 17 | +------+---------------------------------------------+--------+---------+ 28 rows in set (0.00 sec) # load up the trackDb... rm /cluster/home/tdreszer/kent/src/hg/makeDb/trackDb/human/hg19/testing/tmp.ra cat 1412/out/trackDb.ra >> /cluster/home/tdreszer/kent/src/hg/makeDb/trackDb/human/hg19/testing/tmp.ra cat 1479/out/trackDb.ra >> /cluster/home/tdreszer/kent/src/hg/makeDb/trackDb/human/hg19/testing/tmp.ra cat 1487/out/trackDb.ra >> /cluster/home/tdreszer/kent/src/hg/makeDb/trackDb/human/hg19/testing/tmp.ra cat 1488/out/trackDb.ra >> /cluster/home/tdreszer/kent/src/hg/makeDb/trackDb/human/hg19/testing/tmp.ra cat 1489/out/trackDb.ra >> /cluster/home/tdreszer/kent/src/hg/makeDb/trackDb/human/hg19/testing/tmp.ra cat 1494/out/trackDb.ra >> /cluster/home/tdreszer/kent/src/hg/makeDb/trackDb/human/hg19/testing/tmp.ra cat 1495/out/trackDb.ra >> /cluster/home/tdreszer/kent/src/hg/makeDb/trackDb/human/hg19/testing/tmp.ra cat 1498/out/trackDb.ra >> /cluster/home/tdreszer/kent/src/hg/makeDb/trackDb/human/hg19/testing/tmp.ra cat 1506/out/trackDb.ra >> /cluster/home/tdreszer/kent/src/hg/makeDb/trackDb/human/hg19/testing/tmp.ra cat 1507/out/trackDb.ra >> /cluster/home/tdreszer/kent/src/hg/makeDb/trackDb/human/hg19/testing/tmp.ra cat 1509/out/trackDb.ra >> /cluster/home/tdreszer/kent/src/hg/makeDb/trackDb/human/hg19/testing/tmp.ra cat 1519/out/trackDb.ra >> /cluster/home/tdreszer/kent/src/hg/makeDb/trackDb/human/hg19/testing/tmp.ra cat 1528/out/trackDb.ra >> /cluster/home/tdreszer/kent/src/hg/makeDb/trackDb/human/hg19/testing/tmp.ra cat 1532/out/trackDb.ra >> /cluster/home/tdreszer/kent/src/hg/makeDb/trackDb/human/hg19/testing/tmp.ra cat 1533/out/trackDb.ra >> /cluster/home/tdreszer/kent/src/hg/makeDb/trackDb/human/hg19/testing/tmp.ra cat 1534/out/trackDb.ra >> /cluster/home/tdreszer/kent/src/hg/makeDb/trackDb/human/hg19/testing/tmp.ra cat 1535/out/trackDb.ra >> /cluster/home/tdreszer/kent/src/hg/makeDb/trackDb/human/hg19/testing/tmp.ra cat 1544/out/trackDb.ra >> /cluster/home/tdreszer/kent/src/hg/makeDb/trackDb/human/hg19/testing/tmp.ra cat 1545/out/trackDb.ra >> /cluster/home/tdreszer/kent/src/hg/makeDb/trackDb/human/hg19/testing/tmp.ra cat 1575/out/trackDb.ra >> /cluster/home/tdreszer/kent/src/hg/makeDb/trackDb/human/hg19/testing/tmp.ra cat 1650/out/trackDb.ra >> /cluster/home/tdreszer/kent/src/hg/makeDb/trackDb/human/hg19/testing/tmp.ra cat 1651/out/trackDb.ra >> /cluster/home/tdreszer/kent/src/hg/makeDb/trackDb/human/hg19/testing/tmp.ra cat 1653/out/trackDb.ra >> /cluster/home/tdreszer/kent/src/hg/makeDb/trackDb/human/hg19/testing/tmp.ra cat 1654/out/trackDb.ra >> /cluster/home/tdreszer/kent/src/hg/makeDb/trackDb/human/hg19/testing/tmp.ra cat 1655/out/trackDb.ra >> /cluster/home/tdreszer/kent/src/hg/makeDb/trackDb/human/hg19/testing/tmp.ra cat 1656/out/trackDb.ra >> /cluster/home/tdreszer/kent/src/hg/makeDb/trackDb/human/hg19/testing/tmp.ra cat 1678/out/trackDb.ra >> /cluster/home/tdreszer/kent/src/hg/makeDb/trackDb/human/hg19/testing/tmp.ra cat 1679/out/trackDb.ra >> /cluster/home/tdreszer/kent/src/hg/makeDb/trackDb/human/hg19/testing/tmp.ra cd /cluster/home/tdreszer/kent/src/hg/makeDb/trackDb/human/hg19/testing/ raToLines tmp.ra tmp.txt grep compositeTrack tmp.txt > tmpC.txt grep view=Peaks tmp.txt > tmpP.txt grep view=Base tmp.txt > tmpB.txt grep view=Signal tmp.txt > tmpS.txt wl tmp?.txt 28 tmpB.txt 28 tmpC.txt 28 tmpP.txt 28 tmpS.txt 112 total wl tmp.txt 112 tmp.txt # No replicates e tmpP.txt tmpS.txt tmpB.txt # Fix view references linesToRa tmpP.txt tmpP.ra linesToRa tmpS.txt tmpS.ra linesToRa tmpB.txt tmpB.ra e tmpP.ra tmpS.ra tmpB.ra cd .. cp ../hg18/wgEncodeChromatinMap.ra wgEncodeOpenChromDnase.ra cp wgEncodeOpenChromChip.html wgEncodeOpenChromDnase.html e trackDb.wgEncode.ra # include wgEncodeOpenChromDnase.ra e wgEncodeOpenChromDnase.ra # add tmpP.ra tmpS.ra tmpB.ra make DBS=hg19 # till working git add wgEncodeOpenChromDnase.ra wgEncodeOpenChromDnase.html trackDb.wgEncode.ra git commit; pull; push # now metadata mdbUpdate hg19 1412/out/mdb.txt mdbUpdate hg19 1479/out/mdb.txt mdbUpdate hg19 1487/out/mdb.txt mdbUpdate hg19 1488/out/mdb.txt mdbUpdate hg19 1489/out/mdb.txt mdbUpdate hg19 1494/out/mdb.txt mdbUpdate hg19 1495/out/mdb.txt mdbUpdate hg19 1498/out/mdb.txt mdbUpdate hg19 1506/out/mdb.txt mdbUpdate hg19 1507/out/mdb.txt mdbUpdate hg19 1509/out/mdb.txt mdbUpdate hg19 1519/out/mdb.txt mdbUpdate hg19 1528/out/mdb.txt mdbUpdate hg19 1532/out/mdb.txt mdbUpdate hg19 1533/out/mdb.txt mdbUpdate hg19 1534/out/mdb.txt mdbUpdate hg19 1535/out/mdb.txt mdbUpdate hg19 1544/out/mdb.txt mdbUpdate hg19 1545/out/mdb.txt mdbUpdate hg19 1575/out/mdb.txt mdbUpdate hg19 1650/out/mdb.txt mdbUpdate hg19 1651/out/mdb.txt mdbUpdate hg19 1653/out/mdb.txt mdbUpdate hg19 1654/out/mdb.txt mdbUpdate hg19 1655/out/mdb.txt mdbUpdate hg19 1656/out/mdb.txt mdbUpdate hg19 1678/out/mdb.txt mdbUpdate hg19 1679/out/mdb.txt Read 6 metadata objects from hg19 Affected 99 row(s) in hg19.metaDb_tdreszer ... # Add treatement=None mdbPrint hg19 -vars="composite=wgEncodeOpenChromDnase treatment!=" -countObjs 137 objects mdbPrint hg19 -vars="composite=wgEncodeOpenChromDnase treatment=" -countObjs 15 objects mdbPrint hg19 -vars="composite=wgEncodeOpenChromDnase" -countObjs 152 objects mdbUpdate hg19 -vars="composite=wgEncodeOpenChromDnase treatment!=" -setVars="treatment=None" Using table named 'hg19.metaDb_tdreszer'. Affected 137 row(s) in hg19.metaDb_tdreszer # Now update dates cd /cluster/home/tdreszer/kent/src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/testing mdbPrint hg18 -table=metaDb -vars="composite=wgEncodeChromatinMap dataType=DNase%" -updDb=hg19 -updMdb=metaDb_tdreszer -updSelect="grant,dataType,cell,treatment,antibody,view,replicate" -updVars="dateSubmitted,dateUnrestricted" > dukeDates.txt objects:223 vars:3767 mdbPrint hg19 -vars="composite=wgEncodeOpenChromDnase" -updDb=hg19 -updMdb=metaDb_tdreszer -updSelect="subId" -updVars="dateSubmitted" > dukeResub.txt objects:152 vars:2650 e dukeDates.txt # Add origAssembly=hg18, change select /grant,dataType/composite=wgEncodeOpenChromChip/ chmod 755 duke*.txt ./dukeDates.txt Affected 2 row(s) in hg19.metaDb_tdreszer Affected 0 row(s) in hg19.metaDb_tdreszer ... e dukeResub.txt # Add select origAssembly=hg18, change dateSubmitted to dateResubmitted ./dukeResub.txt Affected 5 row(s) in hg19.metaDb_tdreszer ... cd .. mdbPrint hg19 -vars="composite=wgEncodeOpenChromDnase" > wgEncodeOpenChromDnase.ra mdbUpdate hg19 -table=metaDb wgEncodeOpenChromDnase.ra Read 152 metadata objects from hg19 Affected 2802 row(s) in hg19.metaDb e makefile # add wgEncodeOpenChromDnase.ra git add makefile wgEncodeOpenChromDnase.ra git commit -m "Metadata for Open Chrom Duke DNase June 2010 freeze" git pull; git push make alpha DBS=hg19 # Now downloads: cd /usr/local/apache/htdocs-hgdownload/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase e preamble.html ../wgEncodeOpenChromChip/preamble.html encodeDownloadsPage.pl -db=hg19 index.html encodeDownloadsPage.pl -db=hg19 -checksum index.html . & # Mark as displayed: /cluster/data/encode/pipeline/bin/encodeStatus.pl 1412 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 1479 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 1487 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 1488 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 1489 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 1494 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 1495 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 1498 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 1506 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 1507 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 1509 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 1519 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 1528 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 1532 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 1533 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 1534 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 1535 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 1544 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 1545 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 1575 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 1650 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 1651 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 1653 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 1654 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 1655 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 1656 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 1678 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 1679 displayed select id,name,status,user_id from projects where status = "loaded" and user_id = 17 and name like "%Duke%" order by id; Empty set (0.00 sec) 2010-06-24 UNC FAIRE for hg19 June Freeze ========================================= select id,name,status,user_id from projects where status = "loaded" and user_id = 17 and name like "%Duke%" order by id; +------+--------------------------------------------+--------+---------+ | id | name | status | user_id | +------+--------------------------------------------+--------+---------+ | 1480 | DNCT UNC FAIRE-Seq GM12878 20100615 | loaded | 17 | | 1496 | DNCT UNC FAIRE-Seq H1-hESC 20100615 | loaded | 17 | | 1497 | DNCT UNC FAIRE-Seq HeLa-S3 20100615 | loaded | 17 | | 1508 | DNCT UNC FAIRE-Seq GM19239 20100615 | loaded | 17 | | 1513 | DNCT UNC FAIRE-Seq GM18507 20100615 | loaded | 17 | | 1515 | DNCT UNC FAIRE-Seq HepG2 20100615 | loaded | 17 | | 1529 | DNCT UNC FAIRE-Seq HUVEC 20100616 | loaded | 17 | | 1530 | DNCT UNC FAIRE-Seq NHEK 20100616 | loaded | 17 | | 1531 | DNCT UNC FAIRE-Seq K562 20100616 | loaded | 17 | | 1546 | DNCT UNC FAIRE-Seq PanIslets 20100616 | loaded | 17 | | 1547 | DNCT UNC FAIRE-Seq LHSR 20100616 | loaded | 17 | | 1574 | DNCT UNC FAIRE-Seq NHBE 20100616 | loaded | 17 | | 1610 | DNCT UNC FAIRE-Seq LHSR androgen 20100617 | loaded | 17 | | 1611 | DNCT UNC FAIRE-Seq HeLa-S3 IFNa4h 20100617 | loaded | 17 | | 1612 | DNCT UNC FAIRE-Seq HeLa-S3 IFNg4h 20100617 | loaded | 17 | +------+--------------------------------------------+--------+---------+ 15 rows in set (0.00 sec) # load up the trackDb... rm /cluster/home/tdreszer/kent/src/hg/makeDb/trackDb/human/hg19/testing/tmp.ra cat 1480/out/trackDb.ra >> /cluster/home/tdreszer/kent/src/hg/makeDb/trackDb/human/hg19/testing/tmp.ra cat 1496/out/trackDb.ra >> /cluster/home/tdreszer/kent/src/hg/makeDb/trackDb/human/hg19/testing/tmp.ra cat 1497/out/trackDb.ra >> /cluster/home/tdreszer/kent/src/hg/makeDb/trackDb/human/hg19/testing/tmp.ra cat 1508/out/trackDb.ra >> /cluster/home/tdreszer/kent/src/hg/makeDb/trackDb/human/hg19/testing/tmp.ra cat 1513/out/trackDb.ra >> /cluster/home/tdreszer/kent/src/hg/makeDb/trackDb/human/hg19/testing/tmp.ra cat 1515/out/trackDb.ra >> /cluster/home/tdreszer/kent/src/hg/makeDb/trackDb/human/hg19/testing/tmp.ra cat 1529/out/trackDb.ra >> /cluster/home/tdreszer/kent/src/hg/makeDb/trackDb/human/hg19/testing/tmp.ra cat 1530/out/trackDb.ra >> /cluster/home/tdreszer/kent/src/hg/makeDb/trackDb/human/hg19/testing/tmp.ra cat 1531/out/trackDb.ra >> /cluster/home/tdreszer/kent/src/hg/makeDb/trackDb/human/hg19/testing/tmp.ra cat 1546/out/trackDb.ra >> /cluster/home/tdreszer/kent/src/hg/makeDb/trackDb/human/hg19/testing/tmp.ra cat 1547/out/trackDb.ra >> /cluster/home/tdreszer/kent/src/hg/makeDb/trackDb/human/hg19/testing/tmp.ra cat 1574/out/trackDb.ra >> /cluster/home/tdreszer/kent/src/hg/makeDb/trackDb/human/hg19/testing/tmp.ra cat 1610/out/trackDb.ra >> /cluster/home/tdreszer/kent/src/hg/makeDb/trackDb/human/hg19/testing/tmp.ra cat 1611/out/trackDb.ra >> /cluster/home/tdreszer/kent/src/hg/makeDb/trackDb/human/hg19/testing/tmp.ra cat 1612/out/trackDb.ra >> /cluster/home/tdreszer/kent/src/hg/makeDb/trackDb/human/hg19/testing/tmp.ra cd /cluster/home/tdreszer/kent/src/hg/makeDb/trackDb/human/hg19/testing/ raToLines tmp.ra tmp.txt grep compositeTrack tmp.txt > tmpC.txt grep view=Peaks tmp.txt > tmpP.txt grep view=Base tmp.txt > tmpB.txt grep view=Signal tmp.txt > tmpS.txt wl tmp?.txt 15 tmpB.txt 15 tmpC.txt 15 tmpP.txt 15 tmpS.txt 60 total wl tmp.txt 60 tmp.txt # No replicates e tmpP.txt tmpS.txt tmpB.txt # Fix view references linesToRa tmpP.txt tmpP.ra linesToRa tmpS.txt tmpS.ra linesToRa tmpB.txt tmpB.ra e tmpP.ra tmpS.ra tmpB.ra cd .. cp wgEncodeOpenChromDnase.ra wgEncodeOpenChromFaire.ra cp wgEncodeOpenChromDnase.html wgEncodeOpenChromFaire.html e trackDb.wgEncode.ra # include wgEncodeOpenChromFaire.ra e wgEncodeOpenChromFaire.ra # add tmpP.ra tmpS.ra tmpB.ra make DBS=hg19 # till working git add wgEncodeOpenChromFaire.ra wgEncodeOpenChromFaire.html trackDb.wgEncode.ra git commit; pull; push # now metadata mdbUpdate hg19 1480/out/mdb.txt mdbUpdate hg19 1496/out/mdb.txt mdbUpdate hg19 1497/out/mdb.txt mdbUpdate hg19 1508/out/mdb.txt mdbUpdate hg19 1513/out/mdb.txt mdbUpdate hg19 1515/out/mdb.txt mdbUpdate hg19 1529/out/mdb.txt mdbUpdate hg19 1530/out/mdb.txt mdbUpdate hg19 1531/out/mdb.txt mdbUpdate hg19 1546/out/mdb.txt mdbUpdate hg19 1547/out/mdb.txt mdbUpdate hg19 1574/out/mdb.txt mdbUpdate hg19 1610/out/mdb.txt mdbUpdate hg19 1611/out/mdb.txt mdbUpdate hg19 1612/out/mdb.txt # Now update dates cd /cluster/home/tdreszer/kent/src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/testing mdbPrint hg18 -table=metaDb -vars="composite=wgEncodeChromatinMap dataType=FAIRE%" -updDb=hg19 -updMdb=metaDb_tdreszer -updSelect="grant,dataType,cell,treatment,antibody,view,replicate" -updVars="dateSubmitted,dateUnrestricted" > uncDates.txt objects:142 vars:2412 mdbPrint hg19 -vars="composite=wgEncodeOpenChromFaire" -updDb=hg19 -updMdb=metaDb_tdreszer -updSelect="subId" -updVars="dateSubmitted" > uncResub.txt e uncDates.txt # Add origAssembly=hg18, change select /grant,dataType/composite=wgEncodeOpenChromChip/ chmod 755 unc*.txt ./uncDates.txt Affected 2 row(s) in hg19.metaDb_tdreszer Affected 0 row(s) in hg19.metaDb_tdreszer ... e uncResub.txt # Add select origAssembly=hg18, change dateSubmitted to dateResubmitted ./uncResub.txt Affected 5 row(s) in hg19.metaDb_tdreszer ... cd .. mdbPrint hg19 -vars="composite=wgEncodeOpenChromFaire" > wgEncodeOpenChromFaire.ra Using table named 'hg19.metaDb_tdreszer'. objects:76 vars:1338 mdbUpdate hg19 -table=metaDb wgEncodeOpenChromFaire.ra Read 76 metadata objects from hg19 Affected 1338 row(s) in hg19.metaDb e makefile # add wgEncodeOpenChromFaire.ra git add makefile wgEncodeOpenChromFaire.ra git commit -m "Metadata for Open Chrom UNC FAIRE ChIPseq June 2010 freeze" git pull; git push make alpha DBS=hg19 # Now downloads: cd /usr/local/apache/htdocs-hgdownload/goldenPath/hg19/encodeDCC/wgEncodeOpenChromFaire e preamble.html ../wgEncodeOpenChromChip/preamble.html encodeDownloadsPage.pl -db=hg19 index.html encodeDownloadsPage.pl -db=hg19 -checksum index.html . & # Mark as displayed: /cluster/data/encode/pipeline/bin/encodeStatus.pl 1480 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 1496 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 1497 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 1508 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 1513 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 1515 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 1529 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 1530 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 1531 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 1546 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 1547 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 1574 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 1610 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 1611 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 1612 displayed select id,name,status,user_id from projects where status = "loaded" and user_id = 17 and name like "%FAIRE%" order by id; Empty set (0.00 sec) 2010-07-26 Including hg18 mdb update here ========================================= ### UW Chip cd ../../wgEncodeUwChIPSeq/release1 grep parentTable fileDb.ra > ~/kent/src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/testing/uwChip.txt grep metadata ../../../wgEncodeUwChIPSeq.ra >> uwChip.txt mdbUpdate hg18 -table=tmpMdb -recreate uwChip.txt cp ../wgEncodeUwChIPSeq.ra uwChipMdb.ra mdbUpdate hg18 -table=tmpMdb uwChipMdb.ra -test -verbose=2 > uwChipUpd.txt 2>&1 grep update uwChipUpd.txt | grep -v Requesting > uwChipUpd2.txt update tmpMdb set varType = 'txt', val = '304' where obj = 'wgEncodeUwChIPSeqHotspotsRep1Helas3Ctcf' and var = 'subId'; update tmpMdb set varType = 'txt', val = 'ENCODE July 2009 Freeze' where obj = 'wgEncodeUwChIPSeqHotspotsRep1K562Ctcf' and var = 'dataVersion'; grep -v subId uwChipUpd2.txt | grep -v Freeze > uwChipUpd3.txt update tmpMdb set varType = 'txt', val = 'Hotspot-v5.0' where obj = 'wgEncodeUwChIPSeqHotspotsRep1Gm06990Ctcf' and var = 'labVersion'; update tmpMdb set varType = 'txt', val = 'Hotspot-v5.0' where obj = 'wgEncodeUwChIPSeqHotspotsRep1Gm12878Ctcf' and var = 'labVersion'; update tmpMdb set varType = 'txt', val = 'Hotspot-v5.0' where obj = 'wgEncodeUwChIPSeqHotspotsRep1Gm12878H3k4me3' and var = 'labVersion'; update tmpMdb set varType = 'txt', val = 'Hotspot-v5.0' where obj = 'wgEncodeUwChIPSeqHotspotsRep1Hek293Ctcf' and var = 'labVersion'; update tmpMdb set varType = 'txt', val = 'Hotspot-v5.0' where obj = 'wgEncodeUwChIPSeqHotspotsRep1Helas3Ctcf' and var = 'labVersion'; update tmpMdb set varType = 'txt', val = 'Hotspot-v5.0' where obj = 'wgEncodeUwChIPSeqHotspotsRep1K562Ctcf' and var = 'labVersion'; update tmpMdb set varType = 'txt', val = 'Hotspot-v5.0' where obj = 'wgEncodeUwChIPSeqHotspotsRep1K562H3k4me3' and var = 'labVersion'; update tmpMdb set varType = 'txt', val = 'Hotspot-v5.0' where obj = 'wgEncodeUwChIPSeqHotspotsRep2Hepg2Ctcf' and var = 'labVersion'; update tmpMdb set varType = 'txt', val = 'ENCODE July 2009 Freeze' where obj = 'wgEncodeUwChIPSeqHotspotsRep1Gm06990Ctcf' and var = 'dataVersion'; update tmpMdb set varType = 'txt', val = 'Hotspot-v5.0' where obj = 'wgEncodeUwChIPSeqHotspotsRep1Gm06990Ctcf' and var = 'labVersion'; update tmpMdb set varType = 'txt', val = '298' where obj = 'wgEncodeUwChIPSeqHotspotsRep1Gm06990Ctcf' and var = 'subId'; update tmpMdb set varType = 'txt', val = 'ENCODE July 2009 Freeze' where obj = 'wgEncodeUwChIPSeqHotspotsRep1Gm12878Ctcf' and var = 'dataVersion'; update tmpMdb set varType = 'txt', val = 'Hotspot-v5.0' where obj = 'wgEncodeUwChIPSeqHotspotsRep1Gm12878Ctcf' and var = 'labVersion'; update tmpMdb set varType = 'txt', val = '301' where obj = 'wgEncodeUwChIPSeqHotspotsRep1Gm12878Ctcf' and var = 'subId'; update tmpMdb set varType = 'txt', val = 'ENCODE July 2009 Freeze' where obj = 'wgEncodeUwChIPSeqHotspotsRep1Gm12878H3k4me3' and var = 'dataVersion'; update tmpMdb set varType = 'txt', val = 'Hotspot-v5.0' where obj = 'wgEncodeUwChIPSeqHotspotsRep1Gm12878H3k4me3' and var = 'labVersion'; update tmpMdb set varType = 'txt', val = '302' where obj = 'wgEncodeUwChIPSeqHotspotsRep1Gm12878H3k4me3' and var = 'subId'; update tmpMdb set varType = 'txt', val = 'ENCODE July 2009 Freeze' where obj = 'wgEncodeUwChIPSeqHotspotsRep1Hek293Ctcf' and var = 'dataVersion'; update tmpMdb set varType = 'txt', val = 'Hotspot-v5.0' where obj = 'wgEncodeUwChIPSeqHotspotsRep1Hek293Ctcf' and var = 'labVersion'; update tmpMdb set varType = 'txt', val = '303' where obj = 'wgEncodeUwChIPSeqHotspotsRep1Hek293Ctcf' and var = 'subId'; update tmpMdb set varType = 'txt', val = 'ENCODE July 2009 Freeze' where obj = 'wgEncodeUwChIPSeqHotspotsRep1Helas3Ctcf' and var = 'dataVersion'; update tmpMdb set varType = 'txt', val = 'Hotspot-v5.0' where obj = 'wgEncodeUwChIPSeqHotspotsRep1Helas3Ctcf' and var = 'labVersion'; update tmpMdb set varType = 'txt', val = '304' where obj = 'wgEncodeUwChIPSeqHotspotsRep1Helas3Ctcf' and var = 'subId'; update tmpMdb set varType = 'txt', val = 'ENCODE July 2009 Freeze' where obj = 'wgEncodeUwChIPSeqHotspotsRep1K562Ctcf' and var = 'dataVersion'; update tmpMdb set varType = 'txt', val = 'Hotspot-v5.0' where obj = 'wgEncodeUwChIPSeqHotspotsRep1K562Ctcf' and var = 'labVersion'; update tmpMdb set varType = 'txt', val = '307' where obj = 'wgEncodeUwChIPSeqHotspotsRep1K562Ctcf' and var = 'subId'; update tmpMdb set varType = 'txt', val = 'ENCODE July 2009 Freeze' where obj = 'wgEncodeUwChIPSeqHotspotsRep1K562H3k4me3' and var = 'dataVersion'; update tmpMdb set varType = 'txt', val = 'Hotspot-v5.0' where obj = 'wgEncodeUwChIPSeqHotspotsRep1K562H3k4me3' and var = 'labVersion'; update tmpMdb set varType = 'txt', val = '308' where obj = 'wgEncodeUwChIPSeqHotspotsRep1K562H3k4me3' and var = 'subId'; update tmpMdb set varType = 'txt', val = 'ENCODE July 2009 Freeze' where obj = 'wgEncodeUwChIPSeqHotspotsRep2Hepg2Ctcf' and var = 'dataVersion'; update tmpMdb set varType = 'txt', val = 'Hotspot-v5.0' where obj = 'wgEncodeUwChIPSeqHotspotsRep2Hepg2Ctcf' and var = 'labVersion'; update tmpMdb set varType = 'txt', val = '406' where obj = 'wgEncodeUwChIPSeqHotspotsRep2Hepg2Ctcf' and var = 'subId'; update tmpMdb set varType = 'txt', val = 'ENCODE July 2009 Freeze' where obj = 'wgEncodeUwChIPSeqRawSignalRep1Gm06990Ctcf' and var = 'dataVersion'; update tmpMdb set varType = 'txt', val = '298' where obj = 'wgEncodeUwChIPSeqRawSignalRep1Gm06990Ctcf' and var = 'subId'; update tmpMdb set varType = 'txt', val = 'ENCODE July 2009 Freeze' where obj = 'wgEncodeUwChIPSeqRawSignalRep1Gm12878Ctcf' and var = 'dataVersion'; update tmpMdb set varType = 'txt', val = '301' where obj = 'wgEncodeUwChIPSeqRawSignalRep1Gm12878Ctcf' and var = 'subId'; update tmpMdb set varType = 'txt', val = 'ENCODE July 2009 Freeze' where obj = 'wgEncodeUwChIPSeqRawSignalRep1Gm12878H3k4me3' and var = 'dataVersion'; update tmpMdb set varType = 'txt', val = '302' where obj = 'wgEncodeUwChIPSeqRawSignalRep1Gm12878H3k4me3' and var = 'subId'; update tmpMdb set varType = 'txt', val = 'ENCODE July 2009 Freeze' where obj = 'wgEncodeUwChIPSeqRawSignalRep1Hek293Ctcf' and var = 'dataVersion'; update tmpMdb set varType = 'txt', val = '303' where obj = 'wgEncodeUwChIPSeqRawSignalRep1Hek293Ctcf' and var = 'subId'; update tmpMdb set varType = 'txt', val = 'ENCODE July 2009 Freeze' where obj = 'wgEncodeUwChIPSeqRawSignalRep1Helas3Ctcf' and var = 'dataVersion'; update tmpMdb set varType = 'txt', val = '304' where obj = 'wgEncodeUwChIPSeqRawSignalRep1Helas3Ctcf' and var = 'subId'; update tmpMdb set varType = 'txt', val = 'ENCODE July 2009 Freeze' where obj = 'wgEncodeUwChIPSeqRawSignalRep1K562Ctcf' and var = 'dataVersion'; update tmpMdb set varType = 'txt', val = '307' where obj = 'wgEncodeUwChIPSeqRawSignalRep1K562Ctcf' and var = 'subId'; update tmpMdb set varType = 'txt', val = 'ENCODE July 2009 Freeze' where obj = 'wgEncodeUwChIPSeqRawSignalRep1K562H3k4me3' and var = 'dataVersion'; update tmpMdb set varType = 'txt', val = '308' where obj = 'wgEncodeUwChIPSeqRawSignalRep1K562H3k4me3' and var = 'subId'; update tmpMdb set varType = 'txt', val = 'ENCODE July 2009 Freeze' where obj = 'wgEncodeUwChIPSeqRawSignalRep2Hepg2Ctcf' and var = 'dataVersion'; update tmpMdb set varType = 'txt', val = '406' where obj = 'wgEncodeUwChIPSeqRawSignalRep2Hepg2Ctcf' and var = 'subId'; rm tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwChIPSeqHotspotsRep1Gm06990Ctcf -var=dataVersion -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwChIPSeqHotspotsRep1Gm06990Ctcf -var=labVersion -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwChIPSeqHotspotsRep1Gm06990Ctcf -var=subId -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwChIPSeqHotspotsRep1Gm12878Ctcf -var=dataVersion -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwChIPSeqHotspotsRep1Gm12878Ctcf -var=labVersion -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwChIPSeqHotspotsRep1Gm12878Ctcf -var=subId -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwChIPSeqHotspotsRep1Gm12878H3k4me3 -var=dataVersion -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwChIPSeqHotspotsRep1Gm12878H3k4me3 -var=labVersion -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwChIPSeqHotspotsRep1Gm12878H3k4me3 -var=subId -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwChIPSeqHotspotsRep1Hek293Ctcf -var=dataVersion -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwChIPSeqHotspotsRep1Hek293Ctcf -var=labVersion -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwChIPSeqHotspotsRep1Hek293Ctcf -var=subId -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwChIPSeqHotspotsRep1Helas3Ctcf -var=dataVersion -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwChIPSeqHotspotsRep1Helas3Ctcf -var=labVersion -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwChIPSeqHotspotsRep1Helas3Ctcf -var=subId -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwChIPSeqHotspotsRep1K562Ctcf -var=dataVersion -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwChIPSeqHotspotsRep1K562Ctcf -var=labVersion -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwChIPSeqHotspotsRep1K562Ctcf -var=subId -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwChIPSeqHotspotsRep1K562H3k4me3 -var=dataVersion -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwChIPSeqHotspotsRep1K562H3k4me3 -var=labVersion -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwChIPSeqHotspotsRep1K562H3k4me3 -var=subId -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwChIPSeqHotspotsRep2Hepg2Ctcf -var=dataVersion -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwChIPSeqHotspotsRep2Hepg2Ctcf -var=labVersion -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwChIPSeqHotspotsRep2Hepg2Ctcf -var=subId -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwChIPSeqRawSignalRep1Gm06990Ctcf -var=dataVersion -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwChIPSeqRawSignalRep1Gm06990Ctcf -var=subId -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwChIPSeqRawSignalRep1Gm12878Ctcf -var=dataVersion -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwChIPSeqRawSignalRep1Gm12878Ctcf -var=subId -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwChIPSeqRawSignalRep1Gm12878H3k4me3 -var=dataVersion -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwChIPSeqRawSignalRep1Gm12878H3k4me3 -var=subId -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwChIPSeqRawSignalRep1Hek293Ctcf -var=dataVersion -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwChIPSeqRawSignalRep1Hek293Ctcf -var=subId -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwChIPSeqRawSignalRep1Helas3Ctcf -var=dataVersion -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwChIPSeqRawSignalRep1Helas3Ctcf -var=subId -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwChIPSeqRawSignalRep1K562Ctcf -var=dataVersion -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwChIPSeqRawSignalRep1K562Ctcf -var=subId -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwChIPSeqRawSignalRep1K562H3k4me3 -var=dataVersion -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwChIPSeqRawSignalRep1K562H3k4me3 -var=subId -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwChIPSeqRawSignalRep2Hepg2Ctcf -var=dataVersion -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwChIPSeqRawSignalRep2Hepg2Ctcf -var=subId -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwChIPSeqHotspotsRep1Gm06990Ctcf -var=dataVersion -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwChIPSeqHotspotsRep1Gm06990Ctcf -var=labVersion -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwChIPSeqHotspotsRep1Gm06990Ctcf -var=subId -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwChIPSeqHotspotsRep1Gm12878Ctcf -var=dataVersion -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwChIPSeqHotspotsRep1Gm12878Ctcf -var=labVersion -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwChIPSeqHotspotsRep1Gm12878Ctcf -var=subId -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwChIPSeqHotspotsRep1Gm12878H3k4me3 -var=dataVersion -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwChIPSeqHotspotsRep1Gm12878H3k4me3 -var=labVersion -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwChIPSeqHotspotsRep1Gm12878H3k4me3 -var=subId -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwChIPSeqHotspotsRep1Hek293Ctcf -var=dataVersion -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwChIPSeqHotspotsRep1Hek293Ctcf -var=labVersion -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwChIPSeqHotspotsRep1Hek293Ctcf -var=subId -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwChIPSeqHotspotsRep1Helas3Ctcf -var=dataVersion -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwChIPSeqHotspotsRep1Helas3Ctcf -var=labVersion -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwChIPSeqHotspotsRep1Helas3Ctcf -var=subId -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwChIPSeqHotspotsRep1K562Ctcf -var=dataVersion -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwChIPSeqHotspotsRep1K562Ctcf -var=labVersion -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwChIPSeqHotspotsRep1K562Ctcf -var=subId -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwChIPSeqHotspotsRep1K562H3k4me3 -var=dataVersion -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwChIPSeqHotspotsRep1K562H3k4me3 -var=labVersion -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwChIPSeqHotspotsRep1K562H3k4me3 -var=subId -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwChIPSeqHotspotsRep2Hepg2Ctcf -var=dataVersion -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwChIPSeqHotspotsRep2Hepg2Ctcf -var=labVersion -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwChIPSeqHotspotsRep2Hepg2Ctcf -var=subId -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwChIPSeqRawSignalRep1Gm06990Ctcf -var=dataVersion -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwChIPSeqRawSignalRep1Gm06990Ctcf -var=subId -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwChIPSeqRawSignalRep1Gm12878Ctcf -var=dataVersion -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwChIPSeqRawSignalRep1Gm12878Ctcf -var=subId -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwChIPSeqRawSignalRep1Gm12878H3k4me3 -var=dataVersion -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwChIPSeqRawSignalRep1Gm12878H3k4me3 -var=subId -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwChIPSeqRawSignalRep1Hek293Ctcf -var=dataVersion -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwChIPSeqRawSignalRep1Hek293Ctcf -var=subId -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwChIPSeqRawSignalRep1Helas3Ctcf -var=dataVersion -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwChIPSeqRawSignalRep1Helas3Ctcf -var=subId -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwChIPSeqRawSignalRep1K562Ctcf -var=dataVersion -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwChIPSeqRawSignalRep1K562Ctcf -var=subId -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwChIPSeqRawSignalRep1K562H3k4me3 -var=dataVersion -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwChIPSeqRawSignalRep1K562H3k4me3 -var=subId -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwChIPSeqRawSignalRep2Hepg2Ctcf -var=dataVersion -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwChIPSeqRawSignalRep2Hepg2Ctcf -var=subId -line >> tmp.txt sort < tmp.txt > uwChipChanges.txt mdbUpdate hg18 -table=metaDb_tdreszer uwChip.txt -test -verbose=2 > uwChipFix.txt 2>&1 grep update uwChipFix.txt | grep -v Requesting > uwChipFix2.txt mdbPrint hg18 -vars="composite=wgEncodeUwChIPSeq" > ../wgEncodeUwChIPSeq.ra hgswl hg18 update metaDb_tdreszer set varType = 'txt', val = 'ENCODE Sep 2009 Freeze' where obj = 'wgEncodeUwChIPSeqHotspotsRep1Gm06990Ctcf' and var = 'dataVersion'; update metaDb_tdreszer set varType = 'txt', val = 'Hotspot-v5.1' where obj = 'wgEncodeUwChIPSeqHotspotsRep1Gm06990Ctcf' and var = 'labVersion'; update metaDb_tdreszer set varType = 'txt', val = '520' where obj = 'wgEncodeUwChIPSeqHotspotsRep1Gm06990Ctcf' and var = 'subId'; update metaDb_tdreszer set varType = 'txt', val = 'ENCODE Sep 2009 Freeze' where obj = 'wgEncodeUwChIPSeqHotspotsRep1Gm12878Ctcf' and var = 'dataVersion'; update metaDb_tdreszer set varType = 'txt', val = 'Hotspot-v5.1' where obj = 'wgEncodeUwChIPSeqHotspotsRep1Gm12878Ctcf' and var = 'labVersion'; update metaDb_tdreszer set varType = 'txt', val = '690' where obj = 'wgEncodeUwChIPSeqHotspotsRep1Gm12878Ctcf' and var = 'subId'; update metaDb_tdreszer set varType = 'txt', val = 'ENCODE Sep 2009 Freeze' where obj = 'wgEncodeUwChIPSeqHotspotsRep1Gm12878H3k4me3' and var = 'dataVersion'; update metaDb_tdreszer set varType = 'txt', val = 'Hotspot-v5.1' where obj = 'wgEncodeUwChIPSeqHotspotsRep1Gm12878H3k4me3' and var = 'labVersion'; update metaDb_tdreszer set varType = 'txt', val = '699' where obj = 'wgEncodeUwChIPSeqHotspotsRep1Gm12878H3k4me3' and var = 'subId'; update metaDb_tdreszer set varType = 'txt', val = 'ENCODE Sep 2009 Freeze' where obj = 'wgEncodeUwChIPSeqHotspotsRep1Hek293Ctcf' and var = 'dataVersion'; update metaDb_tdreszer set varType = 'txt', val = 'Hotspot-v5.1' where obj = 'wgEncodeUwChIPSeqHotspotsRep1Hek293Ctcf' and var = 'labVersion'; update metaDb_tdreszer set varType = 'txt', val = '626' where obj = 'wgEncodeUwChIPSeqHotspotsRep1Hek293Ctcf' and var = 'subId'; update metaDb_tdreszer set varType = 'txt', val = 'ENCODE Sep 2009 Freeze' where obj = 'wgEncodeUwChIPSeqHotspotsRep1Helas3Ctcf' and var = 'dataVersion'; update metaDb_tdreszer set varType = 'txt', val = 'Hotspot-v5.1' where obj = 'wgEncodeUwChIPSeqHotspotsRep1Helas3Ctcf' and var = 'labVersion'; update metaDb_tdreszer set varType = 'txt', val = '691' where obj = 'wgEncodeUwChIPSeqHotspotsRep1Helas3Ctcf' and var = 'subId'; update metaDb_tdreszer set varType = 'txt', val = 'ENCODE Sep 2009 Freeze' where obj = 'wgEncodeUwChIPSeqHotspotsRep2Hepg2Ctcf' and var = 'dataVersion'; update metaDb_tdreszer set varType = 'txt', val = 'Hotspot-v5.1' where obj = 'wgEncodeUwChIPSeqHotspotsRep2Hepg2Ctcf' and var = 'labVersion'; update metaDb_tdreszer set varType = 'txt', val = '608' where obj = 'wgEncodeUwChIPSeqHotspotsRep2Hepg2Ctcf' and var = 'subId'; update metaDb_tdreszer set varType = 'txt', val = 'ENCODE Sep 2009 Freeze' where obj = 'wgEncodeUwChIPSeqHotspotsRep1K562Ctcf' and var = 'dataVersion'; update metaDb_tdreszer set varType = 'txt', val = 'Hotspot-v5.1' where obj = 'wgEncodeUwChIPSeqHotspotsRep1K562Ctcf' and var = 'labVersion'; update metaDb_tdreszer set varType = 'txt', val = '659' where obj = 'wgEncodeUwChIPSeqHotspotsRep1K562Ctcf' and var = 'subId'; update metaDb_tdreszer set varType = 'txt', val = 'ENCODE Sep 2009 Freeze' where obj = 'wgEncodeUwChIPSeqHotspotsRep1K562H3k4me3' and var = 'dataVersion'; update metaDb_tdreszer set varType = 'txt', val = 'Hotspot-v5.1' where obj = 'wgEncodeUwChIPSeqHotspotsRep1K562H3k4me3' and var = 'labVersion'; update metaDb_tdreszer set varType = 'txt', val = '660' where obj = 'wgEncodeUwChIPSeqHotspotsRep1K562H3k4me3' and var = 'subId'; update metaDb_tdreszer set varType = 'txt', val = 'ENCODE Sep 2009 Freeze' where obj = 'wgEncodeUwChIPSeqRawSignalRep1Gm06990Ctcf' and var = 'dataVersion'; update metaDb_tdreszer set varType = 'txt', val = '520' where obj = 'wgEncodeUwChIPSeqRawSignalRep1Gm06990Ctcf' and var = 'subId'; update metaDb_tdreszer set varType = 'txt', val = 'ENCODE Sep 2009 Freeze' where obj = 'wgEncodeUwChIPSeqRawSignalRep1Gm12878Ctcf' and var = 'dataVersion'; update metaDb_tdreszer set varType = 'txt', val = '690' where obj = 'wgEncodeUwChIPSeqRawSignalRep1Gm12878Ctcf' and var = 'subId'; update metaDb_tdreszer set varType = 'txt', val = 'ENCODE Sep 2009 Freeze' where obj = 'wgEncodeUwChIPSeqRawSignalRep1Gm12878H3k4me3' and var = 'dataVersion'; update metaDb_tdreszer set varType = 'txt', val = '699' where obj = 'wgEncodeUwChIPSeqRawSignalRep1Gm12878H3k4me3' and var = 'subId'; update metaDb_tdreszer set varType = 'txt', val = 'ENCODE Sep 2009 Freeze' where obj = 'wgEncodeUwChIPSeqRawSignalRep1Hek293Ctcf' and var = 'dataVersion'; update metaDb_tdreszer set varType = 'txt', val = '626' where obj = 'wgEncodeUwChIPSeqRawSignalRep1Hek293Ctcf' and var = 'subId'; update metaDb_tdreszer set varType = 'txt', val = 'ENCODE Sep 2009 Freeze' where obj = 'wgEncodeUwChIPSeqRawSignalRep1Helas3Ctcf' and var = 'dataVersion'; update metaDb_tdreszer set varType = 'txt', val = '691' where obj = 'wgEncodeUwChIPSeqRawSignalRep1Helas3Ctcf' and var = 'subId'; update metaDb_tdreszer set varType = 'txt', val = 'ENCODE Sep 2009 Freeze' where obj = 'wgEncodeUwChIPSeqRawSignalRep2Hepg2Ctcf' and var = 'dataVersion'; update metaDb_tdreszer set varType = 'txt', val = '608' where obj = 'wgEncodeUwChIPSeqRawSignalRep2Hepg2Ctcf' and var = 'subId'; update metaDb_tdreszer set varType = 'txt', val = 'ENCODE Sep 2009 Freeze' where obj = 'wgEncodeUwChIPSeqRawSignalRep1K562Ctcf' and var = 'dataVersion'; update metaDb_tdreszer set varType = 'txt', val = '659' where obj = 'wgEncodeUwChIPSeqRawSignalRep1K562Ctcf' and var = 'subId'; update metaDb_tdreszer set varType = 'txt', val = 'ENCODE Sep 2009 Freeze' where obj = 'wgEncodeUwChIPSeqRawSignalRep1K562H3k4me3' and var = 'dataVersion'; update metaDb_tdreszer set varType = 'txt', val = '660' where obj = 'wgEncodeUwChIPSeqRawSignalRep1K562H3k4me3' and var = 'subId'; ### UW DNase cd ../../wgEncodeUwDnaseSeq/release3 grep parentTable fileDb.ra > ~/kent/src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/testing/uwDnase.txt grep metadata ../../../wgEncodeUwDnaseSeq.ra >> uwDnase.txt mdbUpdate hg18 -table=tmpMdb -recreate uwDnase.txt cp ../wgEncodeUwDnaseSeq.ra uwDnaseMdb.ra mdbUpdate hg18 -table=tmpMdb uwDnaseMdb.ra -test -verbose=2 > uwDnaseUpd.txt 2>&1 grep update uwDnaseUpd.txt | grep -v Requesting > uwDnaseUpd2.txt rm tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwDnaseSeqAlignmentsRep1Bjtert -var=cell -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwDnaseSeqAlignmentsRep2Bjtert -var=cell -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwDnaseSeqHotspotsRep1Gm12878 -var=dateSubmitted -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwDnaseSeqHotspotsRep1Gm12878 -var=dateUnrestricted -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwDnaseSeqHotspotsRep1Helas3 -var=dateSubmitted -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwDnaseSeqHotspotsRep1Helas3 -var=dateUnrestricted -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwDnaseSeqHotspotsRep1Hrcepic -var=dateSubmitted -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwDnaseSeqHotspotsRep1Hrcepic -var=dateUnrestricted -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwDnaseSeqHotspotsRep1Hre -var=dateSubmitted -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwDnaseSeqHotspotsRep1Hre -var=dateUnrestricted -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwDnaseSeqHotspotsRep2Bjtert -var=dateSubmitted -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwDnaseSeqHotspotsRep2Bjtert -var=dateUnrestricted -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwDnaseSeqHotspotsRep2Caco2 -var=dateSubmitted -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwDnaseSeqHotspotsRep2Caco2 -var=dateUnrestricted -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwDnaseSeqHotspotsRep2Helas3 -var=dateSubmitted -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwDnaseSeqHotspotsRep2Helas3 -var=dateUnrestricted -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwDnaseSeqHotspotsRep2Hrcepic -var=dateSubmitted -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwDnaseSeqHotspotsRep2Hrcepic -var=dateUnrestricted -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwDnaseSeqHotspotsRep2Hre -var=dateSubmitted -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwDnaseSeqHotspotsRep2Hre -var=dateUnrestricted -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwDnaseSeqPeaksRep1Gm12878 -var=dateSubmitted -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwDnaseSeqPeaksRep1Gm12878 -var=dateUnrestricted -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwDnaseSeqPeaksRep1Helas3 -var=dateSubmitted -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwDnaseSeqPeaksRep1Helas3 -var=dateUnrestricted -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwDnaseSeqPeaksRep1Hrcepic -var=dateSubmitted -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwDnaseSeqPeaksRep1Hrcepic -var=dateUnrestricted -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwDnaseSeqPeaksRep1Hre -var=dateSubmitted -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwDnaseSeqPeaksRep1Hre -var=dateUnrestricted -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwDnaseSeqPeaksRep2Bjtert -var=dateSubmitted -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwDnaseSeqPeaksRep2Bjtert -var=dateUnrestricted -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwDnaseSeqPeaksRep2Caco2 -var=dateSubmitted -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwDnaseSeqPeaksRep2Caco2 -var=dateUnrestricted -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwDnaseSeqPeaksRep2Helas3 -var=dateSubmitted -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwDnaseSeqPeaksRep2Helas3 -var=dateUnrestricted -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwDnaseSeqPeaksRep2Hrcepic -var=dateSubmitted -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwDnaseSeqPeaksRep2Hrcepic -var=dateUnrestricted -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwDnaseSeqPeaksRep2Hre -var=dateSubmitted -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwDnaseSeqPeaksRep2Hre -var=dateUnrestricted -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwDnaseSeqRawDataRep1Bjtert -var=cell -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwDnaseSeqRawDataRep2Bjtert -var=cell -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwDnaseSeqRawSignalRep1Gm12878 -var=dateSubmitted -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwDnaseSeqRawSignalRep1Gm12878 -var=dateUnrestricted -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwDnaseSeqRawSignalRep1Helas3 -var=dateSubmitted -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwDnaseSeqRawSignalRep1Helas3 -var=dateUnrestricted -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwDnaseSeqRawSignalRep1Hrcepic -var=dateSubmitted -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwDnaseSeqRawSignalRep1Hrcepic -var=dateUnrestricted -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwDnaseSeqRawSignalRep1Hre -var=dateSubmitted -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwDnaseSeqRawSignalRep1Hre -var=dateUnrestricted -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwDnaseSeqRawSignalRep2Bjtert -var=dateSubmitted -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwDnaseSeqRawSignalRep2Bjtert -var=dateUnrestricted -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwDnaseSeqRawSignalRep2Caco2 -var=dateSubmitted -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwDnaseSeqRawSignalRep2Caco2 -var=dateUnrestricted -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwDnaseSeqRawSignalRep2Helas3 -var=dateSubmitted -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwDnaseSeqRawSignalRep2Helas3 -var=dateUnrestricted -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwDnaseSeqRawSignalRep2Hrcepic -var=dateSubmitted -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwDnaseSeqRawSignalRep2Hrcepic -var=dateUnrestricted -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwDnaseSeqRawSignalRep2Hre -var=dateSubmitted -line >> tmp.txt mdbPrint hg18 -table=tmpMdb -obj=wgEncodeUwDnaseSeqRawSignalRep2Hre -var=dateUnrestricted -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwDnaseSeqAlignmentsRep1Bjtert -var=cell -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwDnaseSeqAlignmentsRep2Bjtert -var=cell -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwDnaseSeqHotspotsRep1Gm12878 -var=dateSubmitted -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwDnaseSeqHotspotsRep1Gm12878 -var=dateUnrestricted -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwDnaseSeqHotspotsRep1Helas3 -var=dateSubmitted -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwDnaseSeqHotspotsRep1Helas3 -var=dateUnrestricted -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwDnaseSeqHotspotsRep1Hrcepic -var=dateSubmitted -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwDnaseSeqHotspotsRep1Hrcepic -var=dateUnrestricted -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwDnaseSeqHotspotsRep1Hre -var=dateSubmitted -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwDnaseSeqHotspotsRep1Hre -var=dateUnrestricted -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwDnaseSeqHotspotsRep2Bjtert -var=dateSubmitted -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwDnaseSeqHotspotsRep2Bjtert -var=dateUnrestricted -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwDnaseSeqHotspotsRep2Caco2 -var=dateSubmitted -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwDnaseSeqHotspotsRep2Caco2 -var=dateUnrestricted -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwDnaseSeqHotspotsRep2Helas3 -var=dateSubmitted -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwDnaseSeqHotspotsRep2Helas3 -var=dateUnrestricted -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwDnaseSeqHotspotsRep2Hrcepic -var=dateSubmitted -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwDnaseSeqHotspotsRep2Hrcepic -var=dateUnrestricted -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwDnaseSeqHotspotsRep2Hre -var=dateSubmitted -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwDnaseSeqHotspotsRep2Hre -var=dateUnrestricted -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwDnaseSeqPeaksRep1Gm12878 -var=dateSubmitted -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwDnaseSeqPeaksRep1Gm12878 -var=dateUnrestricted -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwDnaseSeqPeaksRep1Helas3 -var=dateSubmitted -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwDnaseSeqPeaksRep1Helas3 -var=dateUnrestricted -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwDnaseSeqPeaksRep1Hrcepic -var=dateSubmitted -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwDnaseSeqPeaksRep1Hrcepic -var=dateUnrestricted -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwDnaseSeqPeaksRep1Hre -var=dateSubmitted -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwDnaseSeqPeaksRep1Hre -var=dateUnrestricted -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwDnaseSeqPeaksRep2Bjtert -var=dateSubmitted -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwDnaseSeqPeaksRep2Bjtert -var=dateUnrestricted -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwDnaseSeqPeaksRep2Caco2 -var=dateSubmitted -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwDnaseSeqPeaksRep2Caco2 -var=dateUnrestricted -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwDnaseSeqPeaksRep2Helas3 -var=dateSubmitted -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwDnaseSeqPeaksRep2Helas3 -var=dateUnrestricted -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwDnaseSeqPeaksRep2Hrcepic -var=dateSubmitted -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwDnaseSeqPeaksRep2Hrcepic -var=dateUnrestricted -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwDnaseSeqPeaksRep2Hre -var=dateSubmitted -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwDnaseSeqPeaksRep2Hre -var=dateUnrestricted -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwDnaseSeqRawDataRep1Bjtert -var=cell -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwDnaseSeqRawDataRep2Bjtert -var=cell -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwDnaseSeqRawSignalRep1Gm12878 -var=dateSubmitted -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwDnaseSeqRawSignalRep1Gm12878 -var=dateUnrestricted -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwDnaseSeqRawSignalRep1Helas3 -var=dateSubmitted -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwDnaseSeqRawSignalRep1Helas3 -var=dateUnrestricted -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwDnaseSeqRawSignalRep1Hrcepic -var=dateSubmitted -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwDnaseSeqRawSignalRep1Hrcepic -var=dateUnrestricted -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwDnaseSeqRawSignalRep1Hre -var=dateSubmitted -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwDnaseSeqRawSignalRep1Hre -var=dateUnrestricted -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwDnaseSeqRawSignalRep2Bjtert -var=dateSubmitted -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwDnaseSeqRawSignalRep2Bjtert -var=dateUnrestricted -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwDnaseSeqRawSignalRep2Caco2 -var=dateSubmitted -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwDnaseSeqRawSignalRep2Caco2 -var=dateUnrestricted -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwDnaseSeqRawSignalRep2Helas3 -var=dateSubmitted -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwDnaseSeqRawSignalRep2Helas3 -var=dateUnrestricted -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwDnaseSeqRawSignalRep2Hrcepic -var=dateSubmitted -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwDnaseSeqRawSignalRep2Hrcepic -var=dateUnrestricted -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwDnaseSeqRawSignalRep2Hre -var=dateSubmitted -line >> tmp.txt mdbPrint hg18 -table=metaDb -obj=wgEncodeUwDnaseSeqRawSignalRep2Hre -var=dateUnrestricted -line >> tmp.txt sort < tmp.txt > uwDnaseChanges.txt ### UW DGF cd ../../wgEncodeUwDGF/release1 grep parentTable fileDb.ra > ~/kent/src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/testing/uwDgf.txt grep metadata ../../../wgEncodeUwDGF.ra >> uwDfg.txt mdbUpdate hg18 -table=tmpMdb -recreate uwDgf.txt cp ../wgEncodeUwDGF.ra uwDgfMdb.ra mdbUpdate hg18 -table=tmpMdb uwDgfMdb.ra -test -verbose=2 > uwDgfUpd.txt 2>&1 grep update uwDgfUpd.txt | grep -v Requesting > uwDgfUpd2.txt wl uwDgfUpd2.txt 0 ### Broad cd ../../wgEncodeBroadChipSeq/release3/ grep parentTable fileDb.ra > ~/kent/src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/testing/broad.txt grep metadata ../../../wgEncodeBroadChipSeq.ra >> broad.txt mdbUpdate hg18 -table=tmpMdb -recreate broad.txt cp ../wgEncodeBroadChipSeq.ra broadMdb.ra mdbUpdate hg18 -table=tmpMdb broadMdb.ra -test -verbose=2 > broadUpd.txt 2>&1 grep update broadUpd.txt | grep -v Requesting > broadUpd2.txt wl broadUpd2.txt 0 broadUpd2.txt grep -v inputType broadUpd.txt | grep -v setType > broadUpd2.txt grep -v Requesting broadUpd2.txt | grep -v select > broadUpd3.txt wl broadUpd3.txt 2 broadUpd3.txt m broadUpd3.txt Read 549 metadata objects from hg18 Command would affected 1098 row(s) in hg18.tmpMdb ### OpenChrom cd ../../wgEncodeChromatinMap/release3/ grep parentTable fileDb.ra > ~/kent/src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/testing/openChrom.txt grep metadata ../../../wgEncodeChromatinMap.ra >> openChrom.txt mdbUpdate hg18 -table=tmpMdb -recreate openChrom.txt cp ../wgEncodeChromatinMap.ra openChromMdb.ra mdbUpdate hg18 -table=tmpMdb openChromMdb.ra -test -verbose=2 > openChromUpd.txt 2>&1 grep update openChromUpd.txt | grep -v Requesting > openChromUpd2.txt wl openChromUpd2.txt 143 openChromUpd2.txt update tmpMdb set varType = 'txt', val = 'wgEncodeChromatinMap' where obj = 'wgEncodeDukeDNaseSeqPeaksH9es' and var = 'composite'; grep -v composite openChromUpd2.txt | wl 1 update tmpMdb set varType = 'txt', val = 'Crawford' where obj = 'wgEncodeUtaChIPseqPeaksHelas3CtcfV3' and var = 'grant'; 2011-01-10 Fastq's added ======================== select id,name,status,user_id from projects where status = "loaded" and user_id = 17; +------+---------------------------+--------+---------+ | id | name | status | user_id | +------+---------------------------+--------+---------+ | 3141 | DNCT UTA Fastq's 20101221 | loaded | 17 | | 3153 | DNCT UNC Fastq's 20101221 | loaded | 17 | +------+---------------------------+--------+---------+ cd ~/kent/src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/testing/ cp /hive/groups/encode/dcc/pipeline/encpipeline_prod/3141/out/mdb.txt . cat /hive/groups/encode/dcc/pipeline/encpipeline_prod/3153/out/mdb.txt >> mdb.txt e mdb.txt # dateSubmitted to dateResubmitted dateUnrestricted/submitted toprevious metadata project=wgEncode grant=Crawford lab=UT-A(Iyer) dataType=ChipSeq cell=HepG2 antibody=Pol2 setType=exp controlId=HepG2/Input view=RawData replicate=1 origAssembly=hg18 dataVersion="ENCODE Jan 2011 Freeze" subId=3141 dateSubmitted=2009-09-29 dateUnrestricted=2010-06-29 dateResubmitted=2010-12-23 composite=wgEncodeOpenChromChip fileName=wgEncodeOpenChromChipHepg2Pol2RawDataRep1.fastq.gz metadata project=wgEncode grant=Crawford lab=UT-A(Iyer) dataType=ChipSeq cell=MCF-7 antibody=c-Myc setType=exp controlId=MCF-7/Input view=RawData replicate=1 origAssembly=hg18 dataVersion="ENCODE Jan 2011 Freeze" subId=3141 dateSubmitted=2009-12-28 dateUnrestricted=2010-09-28 dateResubmitted=2010-12-23 composite=wgEncodeOpenChromChip fileName=wgEncodeOpenChromChipMcf7CmycRawDataRep1.fastq.gz metadata project=wgEncode grant=Crawford lab=UT-A(Iyer) dataType=ChipSeq cell=HeLa-S3 antibody=Pol2 setType=exp controlId=HeLa-S3/Input view=RawData replicate=2 origAssembly=hg18 dataVersion="ENCODE Jan 2011 Freeze" subId=3141 dateSubmitted=2009-12-28 dateUnrestricted=2010-09-28 dateResubmitted=2010-12-23 composite=wgEncodeOpenChromChip fileName=wgEncodeOpenChromChipHelas3Pol2RawDataRep2.fastq.gz metadata project=wgEncode grant=Crawford lab=UT-A(Iyer) dataType=ChipSeq cell=MCF-7 antibody=c-Myc setType=exp controlId=MCF-7/Input view=RawData replicate=2 origAssembly=hg18 dataVersion="ENCODE Jan 2011 Freeze" subId=3141 dateResubmitted=2010-12-23 composite=wgEncodeOpenChromChip fileName=wgEncodeOpenChromChipMcf7CmycRawDataRep2.fastq.gz metadata project=wgEncode grant=Crawford lab=UNC(Lieb) dataType=FaireSeq cell=PanIslets treatment=None view=RawData replicate=1 origAssembly=hg18 dataVersion="ENCODE Jan 2011 Freeze" subId=3153 dateResubmitted=2010-12-31 composite=wgEncodeOpenChromFaire fileName=wgEncodeOpenChromFairePanisletsRawDataRep1.fastq.gz metadata project=wgEncode grant=Crawford lab=UNC(Lieb) dataType=FaireSeq cell=GM12878 treatment=None view=RawData replicate=1 origAssembly=hg18 dataVersion="ENCODE Jan 2011 Freeze" subId=3153 dateResubmitted=2010-12-31 composite=wgEncodeOpenChromFaire fileName=wgEncodeOpenChromFaireGm12878RawDataRep1.fastq.gz metadata project=wgEncode grant=Crawford lab=UNC(Lieb) dataType=FaireSeq cell=GM18507 treatment=None view=RawData replicate=1 origAssembly=hg18 dataVersion="ENCODE Jan 2011 Freeze" subId=3153 dateResubmitted=2010-12-31 composite=wgEncodeOpenChromFaire fileName=wgEncodeOpenChromFaireGm18507RawDataRep1.fastq.gz metadata project=wgEncode grant=Crawford lab=UNC(Lieb) dataType=FaireSeq cell=GM19239 treatment=None view=RawData replicate=1 origAssembly=hg18 dataVersion="ENCODE Jan 2011 Freeze" subId=3153 dateResubmitted=2010-12-31 composite=wgEncodeOpenChromFaire fileName=wgEncodeOpenChromFaireGm19239RawDataRep1.fastq.gz metadata project=wgEncode grant=Crawford lab=UNC(Lieb) dataType=FaireSeq cell=H1-hESC treatment=None view=RawData replicate=1 origAssembly=hg18 dataVersion="ENCODE Jan 2011 Freeze" subId=3153 dateResubmitted=2010-12-31 composite=wgEncodeOpenChromFaire fileName=wgEncodeOpenChromFaireH1hescRawDataRep1.fastq.gz metadata project=wgEncode grant=Crawford lab=UNC(Lieb) dataType=FaireSeq cell=HeLa-S3 treatment=IFNa4h view=RawData replicate=1 origAssembly=hg18 dataVersion="ENCODE Jan 2011 Freeze" subId=3153 dateResubmitted=2010-12-31 composite=wgEncodeOpenChromFaire fileName=wgEncodeOpenChromFaireHelas3Ifna4hRawDataRep1.fastq.gz metadata project=wgEncode grant=Crawford lab=UNC(Lieb) dataType=FaireSeq cell=HeLa-S3 treatment=IFNg4h view=RawData replicate=1 origAssembly=hg18 dataVersion="ENCODE Jan 2011 Freeze" subId=3153 dateResubmitted=2010-12-31 composite=wgEncodeOpenChromFaire fileName=wgEncodeOpenChromFaireHelas3Ifng4hRawDataRep1.fastq.gz metadata project=wgEncode grant=Crawford lab=UNC(Lieb) dataType=FaireSeq cell=HeLa-S3 treatment=None view=RawData replicate=1 origAssembly=hg18 dataVersion="ENCODE Jan 2011 Freeze" subId=3153 dateResubmitted=2010-12-31 composite=wgEncodeOpenChromFaire fileName=wgEncodeOpenChromFaireHelas3RawDataRep1.fastq.gz metadata project=wgEncode grant=Crawford lab=UNC(Lieb) dataType=FaireSeq cell=HepG2 treatment=None view=RawData replicate=1 origAssembly=hg18 dataVersion="ENCODE Jan 2011 Freeze" subId=3153 dateResubmitted=2010-12-31 composite=wgEncodeOpenChromFaire fileName=wgEncodeOpenChromFaireHepg2RawDataRep1.fastq.gz metadata project=wgEncode grant=Crawford lab=UNC(Lieb) dataType=FaireSeq cell=HUVEC treatment=None view=RawData replicate=1 origAssembly=hg18 dataVersion="ENCODE Jan 2011 Freeze" subId=3153 dateResubmitted=2010-12-31 composite=wgEncodeOpenChromFaire fileName=wgEncodeOpenChromFaireHuvecRawDataRep1.fastq.gz metadata project=wgEncode grant=Crawford lab=UNC(Lieb) dataType=FaireSeq cell=K562 treatment=None view=RawData replicate=1 origAssembly=hg18 dataVersion="ENCODE Jan 2011 Freeze" subId=3153 dateResubmitted=2010-12-31 composite=wgEncodeOpenChromFaire fileName=wgEncodeOpenChromFaireK562RawDataRep1.fastq.gz metadata project=wgEncode grant=Crawford lab=UNC(Lieb) dataType=FaireSeq cell=LHSR treatment=androgen view=RawData replicate=1 origAssembly=hg18 dataVersion="ENCODE Jan 2011 Freeze" subId=3153 dateResubmitted=2010-12-31 composite=wgEncodeOpenChromFaire fileName=wgEncodeOpenChromFaireLhsrAndroRawDataRep1.fastq.gz metadata project=wgEncode grant=Crawford lab=UNC(Lieb) dataType=FaireSeq cell=LHSR treatment=None view=RawData replicate=1 origAssembly=hg18 dataVersion="ENCODE Jan 2011 Freeze" subId=3153 dateResubmitted=2010-12-31 composite=wgEncodeOpenChromFaire fileName=wgEncodeOpenChromFaireLhsrRawDataRep1.fastq.gz metadata project=wgEncode grant=Crawford lab=UNC(Lieb) dataType=FaireSeq cell=NHBE treatment=None view=RawData replicate=1 origAssembly=hg18 dataVersion="ENCODE Jan 2011 Freeze" subId=3153 dateResubmitted=2010-12-31 composite=wgEncodeOpenChromFaire fileName=wgEncodeOpenChromFaireNhbeRawDataRep1.fastq.gz metadata project=wgEncode grant=Crawford lab=UNC(Lieb) dataType=FaireSeq cell=NHEK treatment=None view=RawData replicate=1 origAssembly=hg18 dataVersion="ENCODE Jan 2011 Freeze" subId=3153 dateResubmitted=2010-12-31 composite=wgEncodeOpenChromFaire fileName=wgEncodeOpenChromFaireNhekRawDataRep1.fastq.gz metadata project=wgEncode grant=Crawford lab=UNC(Lieb) dataType=FaireSeq cell=GM12878 treatment=None view=RawData replicate=2 origAssembly=hg18 dataVersion="ENCODE Jan 2011 Freeze" subId=3153 dateResubmitted=2010-12-31 composite=wgEncodeOpenChromFaire fileName=wgEncodeOpenChromFaireGm12878RawDataRep2.fastq.gz metadata project=wgEncode grant=Crawford lab=UNC(Lieb) dataType=FaireSeq cell=GM18507 treatment=None view=RawData replicate=2 origAssembly=hg18 dataVersion="ENCODE Jan 2011 Freeze" subId=3153 dateResubmitted=2010-12-31 composite=wgEncodeOpenChromFaire fileName=wgEncodeOpenChromFaireGm18507RawDataRep2.fastq.gz metadata project=wgEncode grant=Crawford lab=UNC(Lieb) dataType=FaireSeq cell=GM19239 treatment=None view=RawData replicate=2 origAssembly=hg18 dataVersion="ENCODE Jan 2011 Freeze" subId=3153 dateResubmitted=2010-12-31 composite=wgEncodeOpenChromFaire fileName=wgEncodeOpenChromFaireGm19239RawDataRep2.fastq.gz metadata project=wgEncode grant=Crawford lab=UNC(Lieb) dataType=FaireSeq cell=H1-hESC treatment=None view=RawData replicate=2 origAssembly=hg18 dataVersion="ENCODE Jan 2011 Freeze" subId=3153 dateResubmitted=2010-12-31 composite=wgEncodeOpenChromFaire fileName=wgEncodeOpenChromFaireH1hescRawDataRep2.fastq.gz metadata project=wgEncode grant=Crawford lab=UNC(Lieb) dataType=FaireSeq cell=HeLa-S3 treatment=IFNa4h view=RawData replicate=2 origAssembly=hg18 dataVersion="ENCODE Jan 2011 Freeze" subId=3153 dateResubmitted=2010-12-31 composite=wgEncodeOpenChromFaire fileName=wgEncodeOpenChromFaireHelas3Ifna4hRawDataRep2.fastq.gz metadata project=wgEncode grant=Crawford lab=UNC(Lieb) dataType=FaireSeq cell=HeLa-S3 treatment=IFNg4h view=RawData replicate=2 origAssembly=hg18 dataVersion="ENCODE Jan 2011 Freeze" subId=3153 dateResubmitted=2010-12-31 composite=wgEncodeOpenChromFaire fileName=wgEncodeOpenChromFaireHelas3Ifng4hRawDataRep2.fastq.gz metadata project=wgEncode grant=Crawford lab=UNC(Lieb) dataType=FaireSeq cell=HeLa-S3 treatment=None view=RawData replicate=2 origAssembly=hg18 dataVersion="ENCODE Jan 2011 Freeze" subId=3153 dateResubmitted=2010-12-31 composite=wgEncodeOpenChromFaire fileName=wgEncodeOpenChromFaireHelas3RawDataRep2.fastq.gz metadata project=wgEncode grant=Crawford lab=UNC(Lieb) dataType=FaireSeq cell=HepG2 treatment=None view=RawData replicate=2 origAssembly=hg18 dataVersion="ENCODE Jan 2011 Freeze" subId=3153 dateResubmitted=2010-12-31 composite=wgEncodeOpenChromFaire fileName=wgEncodeOpenChromFaireHepg2RawDataRep2.fastq.gz metadata project=wgEncode grant=Crawford lab=UNC(Lieb) dataType=FaireSeq cell=HUVEC treatment=None view=RawData replicate=2 origAssembly=hg18 dataVersion="ENCODE Jan 2011 Freeze" subId=3153 dateResubmitted=2010-12-31 composite=wgEncodeOpenChromFaire fileName=wgEncodeOpenChromFaireHuvecRawDataRep2.fastq.gz metadata project=wgEncode grant=Crawford lab=UNC(Lieb) dataType=FaireSeq cell=K562 treatment=None view=RawData replicate=2 origAssembly=hg18 dataVersion="ENCODE Jan 2011 Freeze" subId=3153 dateResubmitted=2010-12-31 composite=wgEncodeOpenChromFaire fileName=wgEncodeOpenChromFaireK562RawDataRep2.fastq.gz metadata project=wgEncode grant=Crawford lab=UNC(Lieb) dataType=FaireSeq cell=LHSR treatment=androgen view=RawData replicate=2 origAssembly=hg18 dataVersion="ENCODE Jan 2011 Freeze" subId=3153 dateResubmitted=2010-12-31 composite=wgEncodeOpenChromFaire fileName=wgEncodeOpenChromFaireLhsrAndroRawDataRep2.fastq.gz metadata project=wgEncode grant=Crawford lab=UNC(Lieb) dataType=FaireSeq cell=LHSR treatment=None view=RawData replicate=2 origAssembly=hg18 dataVersion="ENCODE Jan 2011 Freeze" subId=3153 dateResubmitted=2010-12-31 composite=wgEncodeOpenChromFaire fileName=wgEncodeOpenChromFaireLhsrRawDataRep2.fastq.gz metadata project=wgEncode grant=Crawford lab=UNC(Lieb) dataType=FaireSeq cell=NHBE treatment=None view=RawData replicate=2 origAssembly=hg18 dataVersion="ENCODE Jan 2011 Freeze" subId=3153 dateResubmitted=2010-12-31 composite=wgEncodeOpenChromFaire fileName=wgEncodeOpenChromFaireNhbeRawDataRep2.fastq.gz metadata project=wgEncode grant=Crawford lab=UNC(Lieb) dataType=FaireSeq cell=NHEK treatment=None view=RawData replicate=2 origAssembly=hg18 dataVersion="ENCODE Jan 2011 Freeze" subId=3153 dateResubmitted=2010-12-31 composite=wgEncodeOpenChromFaire fileName=wgEncodeOpenChromFaireNhekRawDataRep2.fastq.gz metadata project=wgEncode grant=Crawford lab=UNC(Lieb) dataType=FaireSeq cell=HeLa-S3 treatment=None view=RawData replicate=3 origAssembly=hg18 dataVersion="ENCODE Jan 2011 Freeze" subId=3153 dateResubmitted=2010-12-31 composite=wgEncodeOpenChromFaire fileName=wgEncodeOpenChromFaireHelas3RawDataRep3.fastq.gz metadata project=wgEncode grant=Crawford lab=UNC(Lieb) dataType=FaireSeq cell=HepG2 treatment=None view=RawData replicate=3 origAssembly=hg18 dataVersion="ENCODE Jan 2011 Freeze" subId=3153 dateResubmitted=2010-12-31 composite=wgEncodeOpenChromFaire fileName=wgEncodeOpenChromFaireHepg2RawDataRep3.fastq.gz metadata project=wgEncode grant=Crawford lab=UNC(Lieb) dataType=FaireSeq cell=K562 treatment=None view=RawData replicate=3 origAssembly=hg18 dataVersion="ENCODE Jan 2011 Freeze" subId=3153 dateResubmitted=2010-12-31 composite=wgEncodeOpenChromFaire fileName=wgEncodeOpenChromFaireK562RawDataRep3.fastq.gz # use mdbPrint -upd to get dates from hg18: mdbPrint hg18 -vars="grant=Crawford dataType=ChipSeq cell=HepG2 antibody=Pol2 view=RawData replicate=1" -updDb=hg19 -updMdb=metaDb_tdreszer -updSelect=grant,dataType,cell,antibody,setType,view,replicate -updVars=dateSubmitted,dateUnrestricted >> crawford.txt mdbPrint hg18 -vars="grant=Crawford dataType=ChipSeq cell=MCF-7 antibody=c-Myc setType=exp view=RawData replicate=1" -updDb=hg19 -updMdb=metaDb_tdreszer -updSelect=grant,dataType,cell,antibody,setType,view,replicate -updVars=dateSubmitted,dateUnrestricted >> crawford.txt mdbPrint hg18 -vars="grant=Crawford dataType=ChipSeq cell=HeLa-S3 antibody=Pol2 setType=exp view=RawData replicate=2" -updDb=hg19 -updMdb=metaDb_tdreszer -updSelect=grant,dataType,cell,antibody,setType,view,replicate -updVars=dateSubmitted,dateUnrestricted >> crawford.txt mdbPrint hg18 -vars="grant=Crawford dataType=ChipSeq cell=MCF-7 antibody=c-Myc setType=exp view=RawData replicate=2" -updDb=hg19 -updMdb=metaDb_tdreszer -updSelect=grant,dataType,cell,antibody,setType,view,replicate -updVars=dateSubmitted,dateUnrestricted >> crawford.txt mdbPrint hg18 -vars="grant=Crawford dataType=FaireSeq cell=PanIslets view=RawData" -updDb=hg19 -updMdb=metaDb_tdreszer -updSelect=grant,dataType,cell,view,replicate -updVars=dateSubmitted,dateUnrestricted >> crawford.txt mdbPrint hg18 -vars="grant=Crawford dataType=FaireSeq cell=GM12878 view=RawData replicate=1 submittedDataVersion=V2%" -updDb=hg19 -updMdb=metaDb_tdreszer -updSelect=grant,dataType,cell,view,replicate -updVars=dateSubmitted,dateUnrestricted >> crawford.txt mdbPrint hg18 -vars="grant=Crawford dataType=FaireSeq cell=GM18507 view=RawData replicate=1" -updDb=hg19 -updMdb=metaDb_tdreszer -updSelect=grant,dataType,cell,view,replicate -updVars=dateSubmitted,dateUnrestricted >> crawford.txt mdbPrint hg18 -vars="grant=Crawford dataType=FaireSeq cell=GM19239 view=RawData replicate=1" -updDb=hg19 -updMdb=metaDb_tdreszer -updSelect=grant,dataType,cell,view,replicate -updVars=dateSubmitted,dateUnrestricted >> crawford.txt mdbPrint hg18 -vars="grant=Crawford dataType=FaireSeq cell=H1-hESC view=RawData replicate=1" -updDb=hg19 -updMdb=metaDb_tdreszer -updSelect=grant,dataType,cell,view,replicate -updVars=dateSubmitted,dateUnrestricted >> crawford.txt mdbPrint hg18 -vars="grant=Crawford dataType=FaireSeq cell=HeLa-S3 treatment=IFNa4h view=RawData replicate=1" -updDb=hg19 -updMdb=metaDb_tdreszer -updSelect=grant,dataType,cell,treatment,view,replicate -updVars=dateSubmitted,dateUnrestricted >> crawford.txt mdbPrint hg18 -vars="grant=Crawford dataType=FaireSeq cell=HeLa-S3 treatment=IFNg4h view=RawData replicate=1" -updDb=hg19 -updMdb=metaDb_tdreszer -updSelect=grant,dataType,cell,treatment,view,replicate -updVars=dateSubmitted,dateUnrestricted >> crawford.txt mdbPrint hg18 -vars="grant=Crawford dataType=FaireSeq cell=HeLa-S3 view=RawData replicate=1 submittedDataVersion=V2%" -updDb=hg19 -updMdb=metaDb_tdreszer -updSelect=grant,dataType,cell,view,replicate -updVars=dateSubmitted,dateUnrestricted >> crawford.txt mdbPrint hg18 -vars="grant=Crawford dataType=FaireSeq cell=HepG2 view=RawData replicate=1 submittedDataVersion=V2%" -updDb=hg19 -updMdb=metaDb_tdreszer -updSelect=grant,dataType,cell,view,replicate -updVars=dateSubmitted,dateUnrestricted >> crawford.txt mdbPrint hg18 -vars="grant=Crawford dataType=FaireSeq cell=HUVEC view=RawData replicate=1" -updDb=hg19 -updMdb=metaDb_tdreszer -updSelect=grant,dataType,cell,view,replicate -updVars=dateSubmitted,dateUnrestricted >> crawford.txt mdbPrint hg18 -vars="grant=Crawford dataType=FaireSeq cell=K562 view=RawData replicate=1 submittedDataVersion=V2%" -updDb=hg19 -updMdb=metaDb_tdreszer -updSelect=grant,dataType,cell,view,replicate -updVars=dateSubmitted,dateUnrestricted >> crawford.txt mdbPrint hg18 -vars="grant=Crawford dataType=FaireSeq cell=LHSR treatment=androgen view=RawData replicate=1" -updDb=hg19 -updMdb=metaDb_tdreszer -updSelect=grant,dataType,cell,treatment,view,replicate -updVars=dateSubmitted,dateUnrestricted >> crawford.txt mdbPrint hg18 -vars="grant=Crawford dataType=FaireSeq cell=LHSR treatment!= view=RawData replicate=1" -updDb=hg19 -updMdb=metaDb_tdreszer -updSelect=grant,dataType,cell,view,replicate -updVars=dateSubmitted,dateUnrestricted >> crawford.txt mdbPrint hg18 -vars="grant=Crawford dataType=FaireSeq cell=NHBE view=RawData replicate=1" -updDb=hg19 -updMdb=metaDb_tdreszer -updSelect=grant,dataType,cell,view,replicate -updVars=dateSubmitted,dateUnrestricted >> crawford.txt mdbPrint hg18 -vars="grant=Crawford dataType=FaireSeq cell=NHEK view=RawData replicate=1" -updDb=hg19 -updMdb=metaDb_tdreszer -updSelect=grant,dataType,cell,view,replicate -updVars=dateSubmitted,dateUnrestricted >> crawford.txt mdbPrint hg18 -vars="grant=Crawford dataType=FaireSeq cell=GM12878 view=RawData replicate=2 submittedDataVersion=V2%" -updDb=hg19 -updMdb=metaDb_tdreszer -updSelect=grant,dataType,cell,view,replicate -updVars=dateSubmitted,dateUnrestricted >> crawford.txt mdbPrint hg18 -vars="grant=Crawford dataType=FaireSeq cell=GM18507 view=RawData replicate=2" -updDb=hg19 -updMdb=metaDb_tdreszer -updSelect=grant,dataType,cell,view,replicate -updVars=dateSubmitted,dateUnrestricted >> crawford.txt mdbPrint hg18 -vars="grant=Crawford dataType=FaireSeq cell=GM19239 view=RawData replicate=2" -updDb=hg19 -updMdb=metaDb_tdreszer -updSelect=grant,dataType,cell,view,replicate -updVars=dateSubmitted,dateUnrestricted >> crawford.txt mdbPrint hg18 -vars="grant=Crawford dataType=FaireSeq cell=H1-hESC view=RawData replicate=2" -updDb=hg19 -updMdb=metaDb_tdreszer -updSelect=grant,dataType,cell,view,replicate -updVars=dateSubmitted,dateUnrestricted >> crawford.txt mdbPrint hg18 -vars="grant=Crawford dataType=FaireSeq cell=HeLa-S3 treatment=IFNa4h view=RawData replicate=2" -updDb=hg19 -updMdb=metaDb_tdreszer -updSelect=grant,dataType,cell,treatment,view,replicate -updVars=dateSubmitted,dateUnrestricted >> crawford.txt mdbPrint hg18 -vars="grant=Crawford dataType=FaireSeq cell=HeLa-S3 treatment=IFNg4h view=RawData replicate=2" -updDb=hg19 -updMdb=metaDb_tdreszer -updSelect=grant,dataType,cell,treatment,view,replicate -updVars=dateSubmitted,dateUnrestricted >> crawford.txt mdbPrint hg18 -vars="grant=Crawford dataType=FaireSeq cell=HeLa-S3 view=RawData replicate=2 submittedDataVersion=V2%" -updDb=hg19 -updMdb=metaDb_tdreszer -updSelect=grant,dataType,cell,view,replicate -updVars=dateSubmitted,dateUnrestricted >> crawford.txt mdbPrint hg18 -vars="grant=Crawford dataType=FaireSeq cell=HepG2 view=RawData replicate=2 submittedDataVersion=V2%" -updDb=hg19 -updMdb=metaDb_tdreszer -updSelect=grant,dataType,cell,view,replicate -updVars=dateSubmitted,dateUnrestricted >> crawford.txt mdbPrint hg18 -vars="grant=Crawford dataType=FaireSeq cell=HUVEC view=RawData replicate=2" -updDb=hg19 -updMdb=metaDb_tdreszer -updSelect=grant,dataType,cell,view,replicate -updVars=dateSubmitted,dateUnrestricted >> crawford.txt mdbPrint hg18 -vars="grant=Crawford dataType=FaireSeq cell=K562 view=RawData replicate=2 submittedDataVersion=V2%" -updDb=hg19 -updMdb=metaDb_tdreszer -updSelect=grant,dataType,cell,view,replicate -updVars=dateSubmitted,dateUnrestricted >> crawford.txt mdbPrint hg18 -vars="grant=Crawford dataType=FaireSeq cell=LHSR treatment=androgen view=RawData replicate=2" -updDb=hg19 -updMdb=metaDb_tdreszer -updSelect=grant,dataType,cell,treatment,view,replicate -updVars=dateSubmitted,dateUnrestricted >> crawford.txt mdbPrint hg18 -vars="grant=Crawford dataType=FaireSeq cell=LHSR treatment!= view=RawData replicate=2" -updDb=hg19 -updMdb=metaDb_tdreszer -updSelect=grant,dataType,cell,view,replicate -updVars=dateSubmitted,dateUnrestricted >> crawford.txt mdbPrint hg18 -vars="grant=Crawford dataType=FaireSeq cell=NHBE view=RawData replicate=2" -updDb=hg19 -updMdb=metaDb_tdreszer -updSelect=grant,dataType,cell,view,replicate -updVars=dateSubmitted,dateUnrestricted >> crawford.txt mdbPrint hg18 -vars="grant=Crawford dataType=FaireSeq cell=NHEK view=RawData replicate=2" -updDb=hg19 -updMdb=metaDb_tdreszer -updSelect=grant,dataType,cell,view,replicate -updVars=dateSubmitted,dateUnrestricted >> crawford.txt mdbPrint hg18 -vars="grant=Crawford dataType=FaireSeq cell=HeLa-S3 view=RawData replicate=3 submittedDataVersion=V2%" -updDb=hg19 -updMdb=metaDb_tdreszer -updSelect=grant,dataType,cell,view,replicate -updVars=dateSubmitted,dateUnrestricted >> crawford.txt mdbPrint hg18 -vars="grant=Crawford dataType=FaireSeq cell=HepG2 view=RawData replicate=3 submittedDataVersion=V2%" -updDb=hg19 -updMdb=metaDb_tdreszer -updSelect=grant,dataType,cell,view,replicate -updVars=dateSubmitted,dateUnrestricted >> crawford.txt mdbPrint hg18 -vars="grant=Crawford dataType=FaireSeq cell=K562 view=RawData replicate=3 submittedDataVersion=V2%" -updDb=hg19 -updMdb=metaDb_tdreszer -updSelect=grant,dataType,cell,view,replicate -updVars=dateSubmitted,dateUnrestricted >> crawford.txt mdbUpdate hg19 table=metaDb_tdreszer -vars="grant=Crawford dataType=ChipSeq cell=HepG2 antibody=Pol2 setType=exp view=RawData replicate=1 " -setVars="dateSubmitted=2009-09-29 dateUnrestricted=2010-06-29 " -test mdbUpdate hg19 table=metaDb_tdreszer -vars="grant=Crawford dataType=ChipSeq cell=MCF-7 antibody=c-Myc setType=exp view=RawData replicate=1 " -setVars="dateSubmitted=2009-12-28 dateUnrestricted=2010-09-28 " -test mdbUpdate hg19 table=metaDb_tdreszer -vars="grant=Crawford dataType=ChipSeq cell=HeLa-S3 antibody=Pol2 setType=exp view=RawData replicate=2 " -setVars="dateSubmitted=2009-12-28 dateUnrestricted=2010-09-28 " -test mdbUpdate hg19 table=metaDb_tdreszer -vars="grant=Crawford dataType=ChipSeq cell=MCF-7 antibody=c-Myc setType=exp view=RawData replicate=2 " -setVars="dateSubmitted=2009-12-28 dateUnrestricted=2010-09-28 " -test mdbUpdate hg19 table=metaDb_tdreszer -vars="grant=Crawford dataType=FaireSeq cell=PanIslets treatment=None view=RawData replicate=1" -setVars="dateSubmitted=2009-10-14 dateUnrestricted=2010-07-14" mdbUpdate hg19 table=metaDb_tdreszer -vars="grant=Crawford dataType=FaireSeq cell=GM12878 treatment=None view=RawData replicate=1" -setVars="dateSubmitted=2009-04-20 dateUnrestricted=2010-01-20" mdbUpdate hg19 table=metaDb_tdreszer -vars="grant=Crawford dataType=FaireSeq cell=GM18507 treatment=None view=RawData replicate=1 " -setVars="dateSubmitted=2009-12-20 dateUnrestricted=2010-09-19 " -test mdbUpdate hg19 table=metaDb_tdreszer -vars="grant=Crawford dataType=FaireSeq cell=GM19239 treatment=None view=RawData replicate=1 " -setVars="dateSubmitted=2009-12-18 dateUnrestricted=2010-09-18 " -test mdbUpdate hg19 table=metaDb_tdreszer -vars="grant=Crawford dataType=FaireSeq cell=H1-hESC treatment=None view=RawData replicate=1 " -setVars="dateSubmitted=2009-09-30 dateUnrestricted=2010-06-30 " -test mdbUpdate hg19 table=metaDb_tdreszer -vars="grant=Crawford dataType=FaireSeq cell=HeLa-S3 treatment=IFNa4h view=RawData replicate=1 " -setVars="dateSubmitted=2009-12-20 dateUnrestricted=2010-09-20 " -test mdbUpdate hg19 table=metaDb_tdreszer -vars="grant=Crawford dataType=FaireSeq cell=HeLa-S3 treatment=IFNg4h view=RawData replicate=1 " -setVars="dateSubmitted=2009-12-20 dateUnrestricted=2010-09-20 " -test mdbUpdate hg19 table=metaDb_tdreszer -vars="grant=Crawford dataType=FaireSeq cell=HeLa-S3 treatment=None view=RawData replicate=1 " -setVars="dateSubmitted=2009-03-22 dateUnrestricted=2009-12-22 " mdbUpdate hg19 table=metaDb_tdreszer -vars="grant=Crawford dataType=FaireSeq cell=HepG2 treatment=None view=RawData replicate=1 " -setVars="dateSubmitted=2009-04-17 dateUnrestricted=2010-01-17 " mdbUpdate hg19 table=metaDb_tdreszer -vars="grant=Crawford dataType=FaireSeq cell=HUVEC treatment=None view=RawData replicate=1 " -setVars="dateSubmitted=2009-09-24 dateUnrestricted=2010-06-24 " -test mdbUpdate hg19 table=metaDb_tdreszer -vars="grant=Crawford dataType=FaireSeq cell=K562 treatment=None view=RawData replicate=1 " -setVars="dateSubmitted=2008-12-09 dateUnrestricted=2009-08-09 " mdbUpdate hg19 table=metaDb_tdreszer -vars="grant=Crawford dataType=FaireSeq cell=LHSR treatment=androgen view=RawData replicate=1 " -setVars="dateSubmitted=2009-12-23 dateUnrestricted=2010-09-23 " mdbUpdate hg19 table=metaDb_tdreszer -vars="grant=Crawford dataType=FaireSeq cell=LHSR treatment=None view=RawData replicate=1 " -setVars="dateSubmitted=2009-12-23 dateUnrestricted=2010-09-23 " mdbUpdate hg19 table=metaDb_tdreszer -vars="grant=Crawford dataType=FaireSeq cell=NHBE treatment=None view=RawData replicate=1 " -setVars="dateSubmitted=2010-01-09 dateUnrestricted=2010-10-09 " -test mdbUpdate hg19 table=metaDb_tdreszer -vars="grant=Crawford dataType=FaireSeq cell=NHEK treatment=None view=RawData replicate=1 " -setVars="dateSubmitted=2009-09-30 dateUnrestricted=2010-06-30 " -test mdbUpdate hg19 table=metaDb_tdreszer -vars="grant=Crawford dataType=FaireSeq cell=GM12878 treatment=None view=RawData replicate=2 " -setVars="dateSubmitted=2009-04-20 dateUnrestricted=2010-01-20 " mdbUpdate hg19 table=metaDb_tdreszer -vars="grant=Crawford dataType=FaireSeq cell=GM18507 treatment=None view=RawData replicate=2 " -setVars="dateSubmitted=2009-12-20 dateUnrestricted=2010-09-19 " -test mdbUpdate hg19 table=metaDb_tdreszer -vars="grant=Crawford dataType=FaireSeq cell=GM19239 treatment=None view=RawData replicate=2 " -setVars="dateSubmitted=2009-12-18 dateUnrestricted=2010-09-18 " -test mdbUpdate hg19 table=metaDb_tdreszer -vars="grant=Crawford dataType=FaireSeq cell=H1-hESC treatment=None view=RawData replicate=2 " -setVars="dateSubmitted=2009-09-30 dateUnrestricted=2010-06-30 " -test mdbUpdate hg19 table=metaDb_tdreszer -vars="grant=Crawford dataType=FaireSeq cell=HeLa-S3 treatment=IFNa4h view=RawData replicate=2 " -setVars="dateSubmitted=2009-12-20 dateUnrestricted=2010-09-20 " -test mdbUpdate hg19 table=metaDb_tdreszer -vars="grant=Crawford dataType=FaireSeq cell=HeLa-S3 treatment=IFNg4h view=RawData replicate=2 " -setVars="dateSubmitted=2009-12-20 dateUnrestricted=2010-09-20 " -test mdbUpdate hg19 table=metaDb_tdreszer -vars="grant=Crawford dataType=FaireSeq cell=HeLa-S3 treatment=None view=RawData replicate=2 " -setVars="dateSubmitted=2009-03-22 dateUnrestricted=2009-12-22 " mdbUpdate hg19 table=metaDb_tdreszer -vars="grant=Crawford dataType=FaireSeq cell=HepG2 treatment=None view=RawData replicate=2 " -setVars="dateSubmitted=2009-04-17 dateUnrestricted=2010-01-17 " mdbUpdate hg19 table=metaDb_tdreszer -vars="grant=Crawford dataType=FaireSeq cell=HUVEC treatment=None view=RawData replicate=2 " -setVars="dateSubmitted=2009-09-24 dateUnrestricted=2010-06-24 " -test mdbUpdate hg19 table=metaDb_tdreszer -vars="grant=Crawford dataType=FaireSeq cell=K562 treatment=None view=RawData replicate=2 " -setVars="dateSubmitted=2008-12-09 dateUnrestricted=2009-08-09 " mdbUpdate hg19 table=metaDb_tdreszer -vars="grant=Crawford dataType=FaireSeq cell=LHSR treatment=androgen view=RawData replicate=2 " -setVars="dateSubmitted=2009-12-23 dateUnrestricted=2010-09-23 " mdbUpdate hg19 table=metaDb_tdreszer -vars="grant=Crawford dataType=FaireSeq cell=LHSR treatment=None view=RawData replicate=2 " -setVars="dateSubmitted=2009-12-23 dateUnrestricted=2010-09-23 " mdbUpdate hg19 table=metaDb_tdreszer -vars="grant=Crawford dataType=FaireSeq cell=NHBE treatment=None view=RawData replicate=2 " -setVars="dateSubmitted=2010-01-09 dateUnrestricted=2010-10-09 " -test mdbUpdate hg19 table=metaDb_tdreszer -vars="grant=Crawford dataType=FaireSeq cell=NHEK treatment=None view=RawData replicate=2 " -setVars="dateSubmitted=2009-09-30 dateUnrestricted=2010-06-30 " -test mdbUpdate hg19 table=metaDb_tdreszer -vars="grant=Crawford dataType=FaireSeq cell=HeLa-S3 treatment=None view=RawData replicate=3 " -setVars="dateSubmitted=2009-03-22 dateUnrestricted=2009-12-22 " mdbUpdate hg19 table=metaDb_tdreszer -vars="grant=Crawford dataType=FaireSeq cell=HepG2 treatment=None view=RawData replicate=3 " -setVars="dateSubmitted=2009-04-17 dateUnrestricted=2010-01-17 " mdbUpdate hg19 table=metaDb_tdreszer -vars="grant=Crawford dataType=FaireSeq cell=K562 treatment=None view=RawData replicate=3 " -setVars="dateSubmitted=2009-04-20 dateUnrestricted=2010-01-20 " # Check in changes: cd .. {mdb/alpha} mdbPrint hg19 -vars="composite=wgEncodeOpenChromChip" > wgEncodeOpenChromChip.ra e wgEncodeOpenChromChip.ra # standardize lab to UT-A mdbPrint hg19 -vars="composite=wgEncodeOpenChromFaire" > wgEncodeOpenChromFaire.ra e wgEncodeOpenChromFaire.ra # standardize lab to UNC mdbPrint hg19 -vars="composite=wgEncodeOpenChromDnase" > wgEncodeOpenChromDnase.ra grep "lab Duke" wgEncodeOpenChromDnase.ra | sort | uniq -c # Nothing actually changes git: up, add, ci, up, push cd ../../../../ (trackDb) make DBS=hg19; make alpha DBS=hg19 cd {hg19 downloads} cd wgEncodeOpenChromFaire/ encodeDownloadsPage.pl -db=hg19 index.html cd ../wgEncodeOpenChromChip/ encodeDownloadsPage.pl -db=hg19 index.html cd ../wgEncodeOpenChromDnase/ encodeDownloadsPage.pl -db=hg19 index.html ### TODO mdb5sum, check file counts, release1, pushQ ### File counts cd ../wgEncodeOpenChromChip/ # Experiments ls -1 *BaseOverlapSignal.bigWig | wl 34 ls -1 *Sig.bigWig | wl 43 - ls -1 *InputSig.bigWig | wl 9 ls -1 *.narrowPeak.gz | wl 34 # Peaks and Sigs as expected. 34 experiments # Replicated things: ls -1 *.bam | wl 78 ls -1 *.bam.bai | wl 78 ls -1 *.fastq.gz | wl 72 ### Where are 6? ls -1 | grep -v \.bai | grep -v \.bigWig | grep -v \.narrowPeak | wl ls -1 wgEncodeOpenChromChipGm12878Ctcf*Rep1*.fastq* ls -1 wgEncodeOpenChromChipGm12878Ctcf*Rep2*.fastq* ls -1 wgEncodeOpenChromChipGm12878Ctcf*Rep3*.fastq* # All are with V2! ls -1 wgEncodeOpenChromChipGm12878Ctcf*Rep?V2.fastq* # Should rename!!! update mdb ls -1 wgEncodeOpenChromChipHelas3Cmyc*Rep1.fastq* ls -1 wgEncodeOpenChromChipHelas3Cmyc*Rep2.fastq* ls -1 wgEncodeOpenChromChipHelas3Ctcf*Rep1.fastq* ls -1 wgEncodeOpenChromChipHelas3Ctcf*Rep2.fastq* # V2s # Should rename!!! update mdb mdbPrint hg19 -vars="composite=wgEncodeOpenChromChip cell=GM12878 antibody=CTCF view=RawData" -count mdbPrint hg19 -vars="composite=wgEncodeOpenChromChip cell=HeLa-S3 antibody=c-Myc view=RawData" -count mdbPrint hg19 -vars="composite=wgEncodeOpenChromChip cell=HeLa-S3 antibody=CTCF view=RawData" -count ls -1 wgEncodeOpenChromChipHepg2Cmyc*Rep1.fastq* ls -1 wgEncodeOpenChromChipHepg2Cmyc*Rep2.fastq* ls -1 wgEncodeOpenChromChipHepg2Cmyc*Rep3.fastq* ls -1 wgEncodeOpenChromChipHepg2Ctcf*Rep1.fastq* ls -1 wgEncodeOpenChromChipHepg2Ctcf*Rep2.fastq* # V2s # Should rename!!! update mdb ls -1 wgEncodeOpenChromChipK562Cmyc*Rep1.fastq* ls -1 wgEncodeOpenChromChipK562Cmyc*Rep2.fastq* ls -1 wgEncodeOpenChromChipK562Cmyc*Rep3.fastq* ls -1 wgEncodeOpenChromChipK562Ctcf*Rep1.fastq* ls -1 wgEncodeOpenChromChipK562Ctcf*Rep2.fastq* ls -1 wgEncodeOpenChromChipK562Ctcf*Rep3.fastq* # V2s # Should rename!!! update mdb mdbPrint hg19 -vars="composite=wgEncodeOpenChromChip cell=GM12878 antibody=CTCF view=RawData" >> tmp.mdb mdbPrint hg19 -vars="composite=wgEncodeOpenChromChip cell=HeLa-S3 antibody=c-Myc view=RawData" >> tmp.mdb mdbPrint hg19 -vars="composite=wgEncodeOpenChromChip cell=HeLa-S3 antibody=CTCF view=RawData" >> tmp.mdb mdbPrint hg19 -vars="composite=wgEncodeOpenChromChip cell=HepG2 antibody=c-Myc view=RawData" >> tmp.mdb mdbPrint hg19 -vars="composite=wgEncodeOpenChromChip cell=HepG2 antibody=CTCF view=RawData" >> tmp.mdb mdbPrint hg19 -vars="composite=wgEncodeOpenChromChip cell=K562 antibody=c-Myc view=RawData" >> tmp.mdb mdbPrint hg19 -vars="composite=wgEncodeOpenChromChip cell=K562 antibody=CTCF view=RawData" >> tmp.mdb mv wgEncodeOpenChromChipGm12878CtcfRawDataRep1V2.fastq.gz wgEncodeOpenChromChipGm12878CtcfRawDataRep1.fastq.gz mv wgEncodeOpenChromChipGm12878CtcfRawDataRep2V2.fastq.gz wgEncodeOpenChromChipGm12878CtcfRawDataRep2.fastq.gz mv wgEncodeOpenChromChipGm12878CtcfRawDataRep3V2.fastq.gz wgEncodeOpenChromChipGm12878CtcfRawDataRep3.fastq.gz mv wgEncodeOpenChromChipHelas3CmycRawDataRep1V2.fastq.gz wgEncodeOpenChromChipHelas3CmycRawDataRep1.fastq.gz mv wgEncodeOpenChromChipHelas3CmycRawDataRep2V2.fastq.gz wgEncodeOpenChromChipHelas3CmycRawDataRep2.fastq.gz mv wgEncodeOpenChromChipHelas3CtcfRawDataRep1V2.fastq.gz wgEncodeOpenChromChipHelas3CtcfRawDataRep1.fastq.gz mv wgEncodeOpenChromChipHelas3CtcfRawDataRep2V2.fastq.gz wgEncodeOpenChromChipHelas3CtcfRawDataRep2.fastq.gz mv wgEncodeOpenChromChipHepg2CmycRawDataRep1V2.fastq.gz wgEncodeOpenChromChipHepg2CmycRawDataRep1.fastq.gz mv wgEncodeOpenChromChipHepg2CmycRawDataRep2V2.fastq.gz wgEncodeOpenChromChipHepg2CmycRawDataRep2.fastq.gz mv wgEncodeOpenChromChipHepg2CmycRawDataRep3V2.fastq.gz wgEncodeOpenChromChipHepg2CmycRawDataRep3.fastq.gz mv wgEncodeOpenChromChipHepg2CtcfRawDataRep1V2.fastq.gz wgEncodeOpenChromChipHepg2CtcfRawDataRep1.fastq.gz mv wgEncodeOpenChromChipHepg2CtcfRawDataRep2V2.fastq.gz wgEncodeOpenChromChipHepg2CtcfRawDataRep2.fastq.gz mv wgEncodeOpenChromChipK562CmycRawDataRep1V2.fastq.gz wgEncodeOpenChromChipK562CmycRawDataRep1.fastq.gz mv wgEncodeOpenChromChipK562CmycRawDataRep2V2.fastq.gz wgEncodeOpenChromChipK562CmycRawDataRep2.fastq.gz mv wgEncodeOpenChromChipK562CmycRawDataRep3V2.fastq.gz wgEncodeOpenChromChipK562CmycRawDataRep3.fastq.gz mv wgEncodeOpenChromChipK562CtcfRawDataRep1V2.fastq.gz wgEncodeOpenChromChipK562CtcfRawDataRep1.fastq.gz mv wgEncodeOpenChromChipK562CtcfRawDataRep2V2.fastq.gz wgEncodeOpenChromChipK562CtcfRawDataRep2.fastq.gz mv wgEncodeOpenChromChipK562CtcfRawDataRep3V2.fastq.gz wgEncodeOpenChromChipK562CtcfRawDataRep3.fastq.gz rm tmp.mdb mdbPrint hg19 -vars="composite=wgEncodeOpenChromChip cell=GM12878 antibody=CTCF view=RawData" >> tmp.mdb mdbPrint hg19 -vars="composite=wgEncodeOpenChromChip cell=HeLa-S3 antibody=c-Myc view=RawData" >> tmp.mdb mdbPrint hg19 -vars="composite=wgEncodeOpenChromChip cell=HeLa-S3 antibody=CTCF view=RawData" >> tmp.mdb ls -1 wgEncodeOpenChromChipHuvecCmyc*Rep1.fastq* # No "Rep" wgEncodeOpenChromChipHuvecCmycRawData.fastq.gz # Should rename, update mdb mdbPrint hg19 -vars="composite=wgEncodeOpenChromChip cell=HUVEC antibody=c-Myc view=RawData" > tmp.mdb mv wgEncodeOpenChromChipHuvecCmycRawData.fastq.gz wgEncodeOpenChromChipHuvecCmycRawDataRep1.fastq.gz ######## Missing! ls -1 wgEncodeOpenChromChipFibroblCtcf*Rep1*.fastq* ls -1 wgEncodeOpenChromChipFibroblCtcf*Rep2*.fastq* ls -1 wgEncodeOpenChromChipFibroblInput*.fastq* ls -1 wgEncodeOpenChromChipProgfibCtcf*Rep1.fastq* ls -1 wgEncodeOpenChromChipProgfibCtcf*Rep2.fastq* ls -1 wgEncodeOpenChromChipProgfibInput*.fastq* ls -1 wgEncodeOpenChromChipProgfibPol2*Rep1.fastq* ls -1 wgEncodeOpenChromChipProgfibPol2*Rep2.fastq* ######## Missing! ### More file counts cd ../wgEncodeOpenChromDnase/ # Experiments ls -1 *BaseOverlapSignal.bigWig | wl 45 ls -1 *Sig.bigWig | wl 45 ls -1 *.narrowPeak.gz | wl 45 # Peaks and Sigs as expected. 45 experiments # Replicated things: ls -1 *.bam | wl 105 ls -1 *.bam.bai | wl 105 ls -1 *.fastq.gz | wl 70 ### Where are 35? rm tmp.mdb mdbPrint hg19 obj=wgEncodeOpenChromDnaseGm12878RawDataRep1V2 >> tmp.mdb mdbPrint hg19 obj=wgEncodeOpenChromDnaseGm12878RawDataRep2V2 >> tmp.mdb mdbPrint hg19 obj=wgEncodeOpenChromDnaseGm12878RawDataRep3V2 >> tmp.mdb mdbPrint hg19 obj=wgEncodeOpenChromDnaseHelas3RawDataRep1V2 >> tmp.mdb mdbPrint hg19 obj=wgEncodeOpenChromDnaseHelas3RawDataRep2V2 >> tmp.mdb mdbPrint hg19 obj=wgEncodeOpenChromDnaseHelas3RawDataRep3V2 >> tmp.mdb mdbPrint hg19 obj=wgEncodeOpenChromDnaseHepg2RawDataRep1V2 >> tmp.mdb mdbPrint hg19 obj=wgEncodeOpenChromDnaseHepg2RawDataRep2V2 >> tmp.mdb mdbPrint hg19 obj=wgEncodeOpenChromDnaseHepg2RawDataRep3V2 >> tmp.mdb mdbPrint hg19 obj=wgEncodeOpenChromDnaseK562RawDataRep1V2 >> tmp.mdb mdbPrint hg19 obj=wgEncodeOpenChromDnaseK562RawDataRep2V2 >> tmp.mdb e tmp.mdb mdbUpdate hg19 obj=wgEncodeOpenChromDnaseGm12878RawDataRep1 -delete mdbUpdate hg19 obj=wgEncodeOpenChromDnaseGm12878RawDataRep2 -delete mdbUpdate hg19 obj=wgEncodeOpenChromDnaseGm12878RawDataRep3 -delete mdbUpdate hg19 obj=wgEncodeOpenChromDnaseHelas3RawDataRep1 -delete mdbUpdate hg19 obj=wgEncodeOpenChromDnaseHelas3RawDataRep2 -delete mdbUpdate hg19 obj=wgEncodeOpenChromDnaseHelas3RawDataRep3 -delete mdbUpdate hg19 obj=wgEncodeOpenChromDnaseHepg2RawDataRep1 -delete mdbUpdate hg19 obj=wgEncodeOpenChromDnaseHepg2RawDataRep2 -delete mdbUpdate hg19 obj=wgEncodeOpenChromDnaseHepg2RawDataRep3 -delete mdbUpdate hg19 obj=wgEncodeOpenChromDnaseK562RawDataRep1 -delete mdbUpdate hg19 obj=wgEncodeOpenChromDnaseK562RawDataRep2 -delete mdbUpdate hg19 tmp.mdb mdbUpdate hg19 obj=wgEncodeOpenChromDnaseGm12878RawDataRep1V2 -delete mdbUpdate hg19 obj=wgEncodeOpenChromDnaseGm12878RawDataRep2V2 -delete mdbUpdate hg19 obj=wgEncodeOpenChromDnaseGm12878RawDataRep3V2 -delete mdbUpdate hg19 obj=wgEncodeOpenChromDnaseHelas3RawDataRep1V2 -delete mdbUpdate hg19 obj=wgEncodeOpenChromDnaseHelas3RawDataRep2V2 -delete mdbUpdate hg19 obj=wgEncodeOpenChromDnaseHelas3RawDataRep3V2 -delete mdbUpdate hg19 obj=wgEncodeOpenChromDnaseHepg2RawDataRep1V2 -delete mdbUpdate hg19 obj=wgEncodeOpenChromDnaseHepg2RawDataRep2V2 -delete mdbUpdate hg19 obj=wgEncodeOpenChromDnaseHepg2RawDataRep3V2 -delete mdbUpdate hg19 obj=wgEncodeOpenChromDnaseK562RawDataRep1V2 -delete mdbUpdate hg19 obj=wgEncodeOpenChromDnaseK562RawDataRep2V2 -delete ######## Missing! ls -1 wgEncodeOpenChromDnaseAosmcSerumfree*Rep1.fastq.* ls -1 wgEncodeOpenChromDnaseAosmcSerumfree*Rep2.fastq.* ls -1 wgEncodeOpenChromDnaseCll*Rep1.fastq.* ls -1 wgEncodeOpenChromDnaseCll*Rep2.fastq.* ls -1 wgEncodeOpenChromDnaseCll*Rep3.fastq.* ls -1 wgEncodeOpenChromDnaseFibrobl*Rep1.fastq.* ls -1 wgEncodeOpenChromDnaseFibrobl*Rep2.fastq.* ls -1 wgEncodeOpenChromDnaseFibrop*Rep1.fastq.* ls -1 wgEncodeOpenChromDnaseFibrop*Rep2.fastq.* ls -1 wgEncodeOpenChromDnaseFibrop*Rep3.fastq.* ls -1 wgEncodeOpenChromDnaseGm12878*Rep4.fastq.* ls -1 wgEncodeOpenChromDnaseGm12878*Rep5.fastq.* ls -1 wgEncodeOpenChromDnaseHmec*Rep1.fastq.* ls -1 wgEncodeOpenChromDnaseHmec*Rep2.fastq.* ls -1 wgEncodeOpenChromDnaseHsmm*Rep1.fastq.* ls -1 wgEncodeOpenChromDnaseHsmm*Rep2.fastq.* ls -1 wgEncodeOpenChromDnaseHsmm*Rep3.fastq.* ls -1 wgEncodeOpenChromDnaseHsmmt*Rep1.fastq.* ls -1 wgEncodeOpenChromDnaseHsmmt*Rep2.fastq.* ls -1 wgEncodeOpenChromDnaseHsmmt*Rep3.fastq.* ls -1 wgEncodeOpenChromDnaseIps*Rep1.fastq.* ls -1 wgEncodeOpenChromDnaseIps*Rep2.fastq.* ls -1 wgEncodeOpenChromDnaseIps*Rep3.fastq.* ls -1 wgEncodeOpenChromDnaseMyometr*Rep1.fastq.* ls -1 wgEncodeOpenChromDnaseMyometr*Rep2.fastq.* ls -1 wgEncodeOpenChromDnasePanisd*Rep1.fastq.* ls -1 wgEncodeOpenChromDnasePanisd*Rep2.fastq.* ls -1 wgEncodeOpenChromDnasePanisd*Rep3.fastq.* ls -1 wgEncodeOpenChromDnasePanislets*Rep1.fastq.* ls -1 wgEncodeOpenChromDnasePanislets*Rep2.fastq.* ls -1 wgEncodeOpenChromDnasePanislets*Rep3.fastq.* ls -1 wgEncodeOpenChromDnasePhte*Rep1.fastq.* ls -1 wgEncodeOpenChromDnasePhte*Rep2.fastq.* ls -1 wgEncodeOpenChromDnaseProgfib*Rep1.fastq.* ls -1 wgEncodeOpenChromDnaseProgfib*Rep2.fastq.* ######## Missing! ### More file counts cd ../wgEncodeOpenChromFaire/ # Experiments ls -1 *BaseOverlapSignal.bigWig | wl 20 ls -1 *Sig.bigWig | wl 20 ls -1 *.narrowPeak.gz | wl 20 # Peaks and Sigs as expected. 20 experiments # Replicated things: ls -1 *.bam | wl 42 ls -1 *.bam.bai | wl 42 ls -1 *.fastq.gz | wl 48 ### Extra 6 ? ls -1 *V2* wgEncodeOpenChromFaireGm12878RawDataRep1V2.fastq.gz wgEncodeOpenChromFaireGm12878RawDataRep2V2.fastq.gz wgEncodeOpenChromFaireGm12878RawDataRep3V2.fastq.gz wgEncodeOpenChromFaireHelas3RawDataRep1V2.fastq.gz wgEncodeOpenChromFaireHelas3RawDataRep2V2.fastq.gz wgEncodeOpenChromFaireHepg2RawDataRep1V2.fastq.gz wgEncodeOpenChromFaireHepg2RawDataRep2V2.fastq.gz wgEncodeOpenChromFaireHepg2RawDataRep3V2.fastq.gz wgEncodeOpenChromFaireK562RawDataRep1V2.fastq.gz wgEncodeOpenChromFaireK562RawDataRep2V2.fastq.gz mkdir ../obsolete/wgEncodeOpenChromatinFaire mv wgEncodeOpenChromFaireGm12878RawDataRep1.fastq.gz ../obsolete/wgEncodeOpenChromatinFaire mv wgEncodeOpenChromFaireGm12878RawDataRep2.fastq.gz ../obsolete/wgEncodeOpenChromatinFaire mv wgEncodeOpenChromFaireGm12878RawDataRep3.fastq.gz ../obsolete/wgEncodeOpenChromatinFaire mv wgEncodeOpenChromFaireHelas3RawDataRep1.fastq.gz ../obsolete/wgEncodeOpenChromatinFaire mv wgEncodeOpenChromFaireHelas3RawDataRep2.fastq.gz ../obsolete/wgEncodeOpenChromatinFaire mv wgEncodeOpenChromFaireHepg2RawDataRep1.fastq.gz ../obsolete/wgEncodeOpenChromatinFaire mv wgEncodeOpenChromFaireHepg2RawDataRep2.fastq.gz ../obsolete/wgEncodeOpenChromatinFaire mv wgEncodeOpenChromFaireHepg2RawDataRep3.fastq.gz ../obsolete/wgEncodeOpenChromatinFaire mv wgEncodeOpenChromFaireK562RawDataRep1.fastq.gz ../obsolete/wgEncodeOpenChromatinFaire mv wgEncodeOpenChromFaireK562RawDataRep2.fastq.gz ../obsolete/wgEncodeOpenChromatinFaire mv wgEncodeOpenChromFaireGm12878RawDataRep1V2.fastq.gz wgEncodeOpenChromFaireGm12878RawDataRep1.fastq.gz mv wgEncodeOpenChromFaireGm12878RawDataRep2V2.fastq.gz wgEncodeOpenChromFaireGm12878RawDataRep2.fastq.gz mv wgEncodeOpenChromFaireGm12878RawDataRep3V2.fastq.gz wgEncodeOpenChromFaireGm12878RawDataRep3.fastq.gz mv wgEncodeOpenChromFaireHelas3RawDataRep1V2.fastq.gz wgEncodeOpenChromFaireHelas3RawDataRep1.fastq.gz mv wgEncodeOpenChromFaireHelas3RawDataRep2V2.fastq.gz wgEncodeOpenChromFaireHelas3RawDataRep2.fastq.gz mv wgEncodeOpenChromFaireHepg2RawDataRep1V2.fastq.gz wgEncodeOpenChromFaireHepg2RawDataRep1.fastq.gz mv wgEncodeOpenChromFaireHepg2RawDataRep2V2.fastq.gz wgEncodeOpenChromFaireHepg2RawDataRep2.fastq.gz mv wgEncodeOpenChromFaireHepg2RawDataRep3V2.fastq.gz wgEncodeOpenChromFaireHepg2RawDataRep3.fastq.gz mv wgEncodeOpenChromFaireK562RawDataRep1V2.fastq.gz wgEncodeOpenChromFaireK562RawDataRep1.fastq.gz mv wgEncodeOpenChromFaireK562RawDataRep2V2.fastq.gz wgEncodeOpenChromFaireK562RawDataRep2.fastq.gz rm tmp.mdb mdbPrint hg19 obj=wgEncodeOpenChromFaireGm12878RawDataRep1V2 >> tmp.mdb mdbPrint hg19 obj=wgEncodeOpenChromFaireGm12878RawDataRep2V2 >> tmp.mdb mdbPrint hg19 obj=wgEncodeOpenChromFaireGm12878RawDataRep3V2 >> tmp.mdb mdbPrint hg19 obj=wgEncodeOpenChromFaireHelas3RawDataRep1V2 >> tmp.mdb mdbPrint hg19 obj=wgEncodeOpenChromFaireHelas3RawDataRep2V2 >> tmp.mdb mdbPrint hg19 obj=wgEncodeOpenChromFaireHepg2RawDataRep1V2 >> tmp.mdb mdbPrint hg19 obj=wgEncodeOpenChromFaireHepg2RawDataRep2V2 >> tmp.mdb mdbPrint hg19 obj=wgEncodeOpenChromFaireHepg2RawDataRep3V2 >> tmp.mdb mdbPrint hg19 obj=wgEncodeOpenChromFaireK562RawDataRep1V2 >> tmp.mdb mdbPrint hg19 obj=wgEncodeOpenChromFaireK562RawDataRep2V2 >> tmp.mdb e tmp.mdb mdbUpdate hg19 obj=wgEncodeOpenChromFaireGm12878RawDataRep1 -delete mdbUpdate hg19 obj=wgEncodeOpenChromFaireGm12878RawDataRep2 -delete mdbUpdate hg19 obj=wgEncodeOpenChromFaireGm12878RawDataRep3 -delete mdbUpdate hg19 obj=wgEncodeOpenChromFaireHelas3RawDataRep1 -delete mdbUpdate hg19 obj=wgEncodeOpenChromFaireHelas3RawDataRep2 -delete mdbUpdate hg19 obj=wgEncodeOpenChromFaireHepg2RawDataRep1 -delete mdbUpdate hg19 obj=wgEncodeOpenChromFaireHepg2RawDataRep2 -delete mdbUpdate hg19 obj=wgEncodeOpenChromFaireHepg2RawDataRep3 -delete mdbUpdate hg19 obj=wgEncodeOpenChromFaireK562RawDataRep1 -delete mdbUpdate hg19 obj=wgEncodeOpenChromFaireK562RawDataRep2 -delete mdbUpdate hg19 tmp.mdb mdbUpdate hg19 obj=wgEncodeOpenChromFaireGm12878RawDataRep1V2 -delete mdbUpdate hg19 obj=wgEncodeOpenChromFaireGm12878RawDataRep2V2 -delete mdbUpdate hg19 obj=wgEncodeOpenChromFaireGm12878RawDataRep3V2 -delete mdbUpdate hg19 obj=wgEncodeOpenChromFaireHelas3RawDataRep1V2 -delete mdbUpdate hg19 obj=wgEncodeOpenChromFaireHelas3RawDataRep2V2 -delete mdbUpdate hg19 obj=wgEncodeOpenChromFaireHepg2RawDataRep1V2 -delete mdbUpdate hg19 obj=wgEncodeOpenChromFaireHepg2RawDataRep2V2 -delete mdbUpdate hg19 obj=wgEncodeOpenChromFaireHepg2RawDataRep3V2 -delete mdbUpdate hg19 obj=wgEncodeOpenChromFaireK562RawDataRep1V2 -delete mdbUpdate hg19 obj=wgEncodeOpenChromFaireK562RawDataRep2V2 -delete ######## Extras ls -1 wgEncodeOpenChromFaireHelas3*Rep3.bam ls -1 wgEncodeOpenChromFaireK562*Rep3.bam ls -1 wgEncodeOpenChromFaireLhsrAndro*Rep1.bam ls -1 wgEncodeOpenChromFaireLhsrAndro*Rep2.bam ls -1 wgEncodeOpenChromFaireLhsr*Rep1.bam ls -1 wgEncodeOpenChromFaireLhsr*Rep2.bam ######## Extras # Check in changes: cd .. {hg19/metaDb.alpha} mdbPrint hg19 -vars="composite=wgEncodeOpenChromChip" > wgEncodeOpenChromChip.ra e wgEncodeOpenChromChip.ra # standardize lab to UT-A mdbPrint hg19 -vars="composite=wgEncodeOpenChromFaire" > wgEncodeOpenChromFaire.ra e wgEncodeOpenChromFaire.ra # standardize lab to UNC mdbPrint hg19 -vars="composite=wgEncodeOpenChromDnase" > wgEncodeOpenChromDnase.ra grep "lab Duke" wgEncodeOpenChromDnase.ra | sort | uniq -c # Nothing actually changes git: up, add, ci, up, push cd ../../../../ (trackDb) make DBS=hg19; make alpha DBS=hg19 cd {hg19 downloads} cd ../wgEncodeOpenChromChip/ encodeDownloadsPage.pl -db=hg19 index.html # 339 file. No Missing metadata cd ../wgEncodeOpenChromDnase/ encodeDownloadsPage.pl -db=hg19 index.html # 415 files. No Missing metadata cd ../wgEncodeOpenChromFaire/ encodeDownloadsPage.pl -db=hg19 index.html # 192 files. No Missing metadata ## TODO: mdb5sum, Contact Terry about missing fastqs ## Fastqs missing: DNase/AoSMC/SerumFree Rep1,Rep2 DNase/CLL Rep1,Rep2,Rep3 DNase/Fibrobl Rep1,Rep2 DNase/FibroP Rep1,Rep2,Rep3 DNase/GM12878 Rep4,Rep5 DNase/HMEC Rep1,Rep2 DNase/HSMM Rep1,Rep2,Rep3 DNase/HSMMtube Rep1,Rep2,Rep3 DNase/iPS Rep1,Rep2,Rep3 DNase/Myometr Rep1,Rep2 DNase/PanIsletD Rep1,Rep2,Rep3 DNase/PanIslets Rep1,Rep2,Rep3 DNase/pHTE Rep1,Rep2 DNase/ProgFib Rep1,Rep2 ChIPseq/Fibrobl/CTCF Rep1,Rep2 ChIPseq/Fibrobl/Input Rep1 ChIPseq/ProgFib/CTCF Rep1,Rep2 ChIPseq/ProgFib/Input Rep1 ChIPseq/ProgFib/Pol2 Rep1,Rep2 ### Extras FAIRE/HeLa-S3 Rep3 FAIRE/K562 Rep3 FAIRE/LHSR Rep1,Rep2 FAIRE/LHSR/androgen Rep1,Rep2 ### Extras FAIRE/HeLa-S3 Rep3 FAIRE/K562 Rep3 FAIRE/LHSR Rep1,Rep2 FAIRE/LHSR/androgen Rep1,Rep2 /cluster/data/encode/pipeline/bin/encodeStatus.pl 3141 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 3153 displayed # Extras are abandoned/revoked data and should be moved: mdbUpdate hg19 -vars="composite=wgEncodeOpenChromFaire cell=HeLa-S3 replicate=3" -delete Using table named 'hg19.metaDb_tdreszer'. Affected 35 row(s) in hg19.metaDb_tdreszer mv wgEncodeOpenChromFaireHelas3*Rep3.* ../obsolete/wgEncodeOpenChromFaire/ mdbUpdate hg19 -vars="composite=wgEncodeOpenChromFaire cell=K562 replicate=3" -delete Using table named 'hg19.metaDb_tdreszer'. Affected 35 row(s) in hg19.metaDb_tdreszer mv wgEncodeOpenChromFaireK562*Rep3.* ../obsolete/wgEncodeOpenChromFaire/ mdbUpdate hg19 -vars="composite=wgEncodeOpenChromFaire cell=LHSR" -delete Using table named 'hg19.metaDb_tdreszer'. Affected 68 row(s) in hg19.metaDb_tdreszer mv wgEncodeOpenChromFaireLhsr* ../obsolete/wgEncodeOpenChromFaire/ # Check in changes: cd .. {hg19/metaDb.alpha} mdbPrint hg19 -vars="composite=wgEncodeOpenChromFaire" > wgEncodeOpenChromFaire.ra gold wgEncodeOpenChromFaire.ra # standardize lab to UNC git: up, add, ci, up, push cd ../../../../ (trackDb) make DBS=hg19; make alpha DBS=hg19 cd ../wgEncodeOpenChromFaire/ encodeDownloadsPage.pl -db=hg19 index.html # 186 files. No Missing metadata ### 171 in hgFileUi (Where are missing 15?) # Private data should be marked in mdb: mdbUpdate hg19 -vars="composite=wgEncodeOpenChromDnase cell=AoSMC" -setVars="privacy=noSequence" Affected 5 row(s) in hg19.metaDb_tdreszer mdbUpdate hg19 -vars="composite=wgEncodeOpenChromDnase cell=CLL" -setVars="privacy=noSequence" Affected 6 row(s) in hg19.metaDb_tdreszer mdbUpdate hg19 -vars="composite=wgEncodeOpenChromDnase cell=Fibrobl" -setVars="privacy=noSequence" Affected 5 row(s) in hg19.metaDb_tdreszer mdbUpdate hg19 -vars="composite=wgEncodeOpenChromDnase cell=FibroP" -setVars="privacy=noSequence" Affected 6 row(s) in hg19.metaDb_tdreszer mdbUpdate hg19 -vars="composite=wgEncodeOpenChromDnase cell=HMEC" -setVars="privacy=noSequence" Affected 5 row(s) in hg19.metaDb_tdreszer mdbUpdate hg19 -vars="composite=wgEncodeOpenChromDnase cell=HSMM" -setVars="privacy=noSequence" Affected 6 row(s) in hg19.metaDb_tdreszer mdbUpdate hg19 -vars="composite=wgEncodeOpenChromDnase cell=HSMMtube" -setVars="privacy=noSequence" Affected 6 row(s) in hg19.metaDb_tdreszer mdbUpdate hg19 -vars="composite=wgEncodeOpenChromDnase cell=iPS" -setVars="privacy=noSequence" Affected 6 row(s) in hg19.metaDb_tdreszer mdbUpdate hg19 -vars="composite=wgEncodeOpenChromDnase cell=Myometr" -setVars="privacy=noSequence" Affected 5 row(s) in hg19.metaDb_tdreszer mdbUpdate hg19 -vars="composite=wgEncodeOpenChromDnase cell=PanIsletD" -setVars="privacy=noSequence" Affected 6 row(s) in hg19.metaDb_tdreszer mdbUpdate hg19 -vars="composite=wgEncodeOpenChromDnase cell=PanIslets" -setVars="privacy=noSequence" Affected 6 row(s) in hg19.metaDb_tdreszer mdbUpdate hg19 -vars="composite=wgEncodeOpenChromDnase cell=pHTE" -setVars="privacy=noSequence" Affected 5 row(s) in hg19.metaDb_tdreszer mdbUpdate hg19 -vars="composite=wgEncodeOpenChromDnase cell=ProgFib" -setVars="privacy=noSequence" Affected 5 row(s) in hg19.metaDb_tdreszer mdbUpdate hg19 -vars="composite=wgEncodeOpenChromChip cell=Fibrobl antibody=CTCF" -setVars="privacy=noSequence" Affected 5 row(s) in hg19.metaDb_tdreszer mdbUpdate hg19 -vars="composite=wgEncodeOpenChromChip cell=Fibrobl antibody=Input" -setVars="privacy=noSequence" Affected 2 row(s) in hg19.metaDb_tdreszer mdbUpdate hg19 -vars="composite=wgEncodeOpenChromChip cell=ProgFib antibody=CTCF" -setVars="privacy=noSequence" Affected 5 row(s) in hg19.metaDb_tdreszer mdbUpdate hg19 -vars="composite=wgEncodeOpenChromChip cell=ProgFib antibody=Input" -setVars="privacy=noSequence" Affected 2 row(s) in hg19.metaDb_tdreszer mdbUpdate hg19 -vars="composite=wgEncodeOpenChromChip cell=ProgFib antibody=Pol2" -setVars="privacy=noSequence" Affected 5 row(s) in hg19.metaDb_tdreszer # Check in changes: cd .. {hg19/metaDb.alpha} mdbPrint hg19 -vars="composite=wgEncodeOpenChromDnase" > wgEncodeOpenChromDnase.ra gold wgEncodeOpenChromDnase.ra mdbPrint hg19 -vars="composite=wgEncodeOpenChromChip" > wgEncodeOpenChromChip.ra gold wgEncodeOpenChromChip.ra git: up, add, ci, up, push cd ../../../../ (trackDb) make DBS=hg19; make alpha DBS=hg19 cd ../wgEncodeOpenChromDnase/ encodeDownloadsPage.pl -db=hg19 index.html # 415 files. No Missing metadata ### 372 found in hgFileUi ?? (where are missing 43??) cd ../wgEncodeOpenChromChip/ encodeDownloadsPage.pl -db=hg19 index.html # 339 files. No Missing metadata ### 320 found in hgFileUi ?? (where are missing 19??) ### Probably bai mdbPrint hg19 -count -vars="composite=wgEncodeOpenChromChip fileIndex=?"Using table named 'hg19.metaDb_tdreszer'. 59 objects mdbPrint hg19 -count -vars="composite=wgEncodeOpenChromChip fileName=%bam" Using table named 'hg19.metaDb_tdreszer'. 78 objects # diff 19 ! mdbPrint hg19 -count -vars="composite=wgEncodeOpenChromDnase fileName=%bam" 105 objects mdbPrint hg19 -count -vars="composite=wgEncodeOpenChromDnase fileIndex=?" 62 objects # diff 43 ! mdbPrint hg19 -count -vars="composite=wgEncodeOpenChromFaire fileName=%bam" 42 objects mdbPrint hg19 -count -vars="composite=wgEncodeOpenChromFaire fileIndex=?" 27 objects # diff 15 ! ## Need to update bai for a lot of objects rm tmp.mdb mdbPrint hg19 -vars="composite=wgEncodeOpenChromDnase fileName=%bam fileIndex!=" -updDb=hg19 -updMdb=metaDb_tdreszer -updSelect="composite,fileName,fileIndex" -updVars="fileName" >> tmp.mdb mdbPrint hg19 -vars="composite=wgEncodeOpenChromFaire fileName=%bam fileIndex!=" -updDb=hg19 -updMdb=metaDb_tdreszer -updSelect="composite,fileName,fileIndex" -updVars="fileName" >> tmp.mdb mdbPrint hg19 -vars="composite=wgEncodeOpenChromChip fileName=%bam fileIndex!=" -updDb=hg19 -updMdb=metaDb_tdreszer -updSelect="composite,fileName,fileIndex" -updVars="fileName" >> tmp.mdb e tmp.mdb # edit to add fileIndex chmod tmp.mdb ./tmp.mdb Affected 1 row(s) in hg19.metaDb_tdreszer ... rm tmp.mdb # Check in changes: cd .. {hg19/metaDb.alpha} mdbPrint hg19 -vars="composite=wgEncodeOpenChromDnase" > wgEncodeOpenChromDnase.ra gold wgEncodeOpenChromDnase.ra mdbPrint hg19 -vars="composite=wgEncodeOpenChromFaire" > wgEncodeOpenChromFaire.ra gold wgEncodeOpenChromFaire.ra mdbPrint hg19 -vars="composite=wgEncodeOpenChromChip" > wgEncodeOpenChromChip.ra gold wgEncodeOpenChromChip.ra git: up, add, ci, up, push cd ../../../../ (trackDb) make DBS=hg19; make alpha DBS=hg19 cd ../wgEncodeOpenChromDnase/ encodeDownloadsPage.pl -db=hg19 index.html # 415 files. No Missing metadata # 415 found in hgFileUi cd ../wgEncodeOpenChromChip/ encodeDownloadsPage.pl -db=hg19 index.html # 339 files. No Missing metadata # 339 found in hgFileUi ### Probably bai cd ../wgEncodeOpenChromFaire/ encodeDownloadsPage.pl -db=hg19 index.html # 186 files. No Missing metadata ### 186 found in hgFileUi # Missing DNase/GM12878 rep4 and rep5 fastqs found cd {pip}/1494 e *.DDF # were marked as reps 1 and 2 e out.load.ra mdb.txt cd .. doEncodeLoad.pl x 1494 # fastqs now in place mdbUpdate hg19 mdb.txt Read 2 metadata objects from hg19 Affected 30 row(s) in hg19.metaDb_tdreszer # Check in changes: cd .. {hg19/metaDb.alpha} mdbPrint hg19 -vars="composite=wgEncodeOpenChromDnase" > wgEncodeOpenChromDnase.ra gold wgEncodeOpenChromDnase.ra git: up, add, ci, up, push cd ../../../../ (trackDb) make DBS=hg19; make alpha DBS=hg19 cd ../wgEncodeOpenChromDnase/ encodeDownloadsPage.pl -db=hg19 index.html # 416 files. No Missing metadata # 416 found in hgFileUi ### Expected 417 ### Oops. Running deEncodeLoad.pl by hand caused problems. From pipeline pages 1494 => unload e 1494/*.DDF # not rep1 and rep2 but rep 4 and rep5 e 1494/*.DAF # DnaseSeq and allowReloads;skiupValidation From pipeline pages 1494 => validate (load) # mdb should already be up-to-date cd ../wgEncodeOpenChromDnase/ encodeDownloadsPage.pl -db=hg19 index.html # 417 files. No Missing metadata # 417 found in hgFileUi # All good /cluster/data/encode/pipeline/bin/encodeStatus.pl 1494 displayed 2011-01-12 Work on openChrom combo tracks ========================================= # Terry says the fields for the combo bed will be: chrom 2 - chromStart 3 - chromEnd 4 - unique name 5 - score (set to "1000" always) 6 - strand (set to ".." to indicate no strand) 7 - thickStart (set to chromStart) 8 - thickEnd (set to chromEnd) 9 - color: validated, peaks in both DNase and FAIRE: set to "0,0,0" (black) open chromatin, fisher combined p-value < 0.01, not validated: set to "0,0,255" (blue) dnase-only, peak in Dnase but combined > 0.01: set to "0,255,0" (green) faire-only, peak in FAIRE but combined > 0.01: set to "255,0,0" (red) chip-only, peak in one of the ChIP assays, not in DNase or FAIRE: set to "255,0,255" (pinkish) 10 - Open chromatin combined -log10(p-value) based on Fisher's method 11 - DNase-seq max parzen score 12 - DNase-seq -log10(p-value) 13 - FAIRE-seq max parzen score 14 - FAIRE-seq -log10(p-value) 15 - Pol II ChIP-seq max parzen score 16 - Pol II ChIP-seq -log10(p-value) 17 - CTCF ChIP-seq max parzen score 18 - CTCF ChIP-seq -log10(p-value) 19 - c-Myc ChIP-seq max parzen score 20 - c-Myc ChIP-seq -log10(p-value) 21 - validated (boolean) 22 - open chromatin code: set to 1 if peak in DNase and FAIRE set to 2 if peak in DNase-only set to 3 if peak in FAIRE-only set to 4 if peak in neither cd {pip}../ftp/prod/tsfurey mv mv K562_OC.bed.tgz ~/kent/src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/testing/ cd {m19}/testing tar -xzf K562_OC.bed.tgz K562_OC.bed openChromatin.sql #Locations of regions of open chromatin as determined by DNaseI HS and FAIRE experiments CREATE TABLE K562_OpenChromatin ( chrom varchar(255) not null, # Human chromosome number chromStart int unsigned not null, # Start position in genoSeq chromEnd int unsigned not null, # End position in genoSeq name varchar(255) not null, # Name of cytogenetic band score int(10) unsigned not null, # Always 1000 strand char(1) not null, # Always . thickStart int(10) unsigned not null, # Same as chromStart thickEnd int(10) unsigned not null, # Same as chromEnd color int(10) unsigned not null, # Encodes validated, open chromatin, DNase-only, FAIRE-only, ChIP- only pvalue float unsigned not null, # Combined DNase-seq and FAIRE-seq -log10(p-value) dnaseSignal float unsigned not null, # Max signal value for DNase-seq dnasePvalue float unsigned not null, # DNase-seq -log10(p-value) faireSignal float unsigned not null, # Max signal value for FAIRE-seq fairePvalue float unsigned not null, # FAIRE-seq -log10(p-value) polIISignal float unsigned, # Max signal value for PolII ChIP-seq polIIPvalue float unsigned, # PolII ChIP-seq -log10(p-value) ctcfSignal float unsigned, # Max signal value for CTCF ChIP-seq ctcfPvalue float unsigned, # CTCF ChIP-seq -log10(p-value) cmycSignal float unsigned, # Max signal value for c-Myc ChIP-seq cmycPvalue float unsigned, # c-Myc ChIP-seq -log10(p-value) ocCode int(10) unsigned not null, # Open Chromatin code for validated (=1), DNase-only (=2), FAIRE- only (=3), ChIP-only (=4) #Indices PRIMARY KEY(chrom(12),chromStart), UNIQUE(chrom(12),chromStart) ); cp openChromatin.sql ~/kent/src/hg/lib/encode/openChromCombinedPeaks.sql cd ~/kent/src/hg/lib/encode/ e openChromCombinedPeaks.sql cp openChromCombinedPeaks.sql /cluster/bin/sqlCreate/ # test load: /cluster/bin/x86_64/hgLoadBed -noNameIx $assembly $tableName stdin -tmpDir=$tempDir -sqlTable=$Encode::sqlCreate/${sqlTable}.sql -renameSqlTable $fillInArg"); $fillInArg = "-fillInScore=signalValue -minScore=500 " if $tableName =~ /^wgEncodeUwDnaseSeq/; /cluster/bin/x86_64/hgLoadBed -noNameIx hg19 tempK562Oc K562_OC.bed -tmpDir=/data/tmp -sqlTable=/cluster/bin/sqlCreate/openChromCombinedPeaks.sql -renameSqlTable -fillInScore=pValue -minScore=500 & /cluster/bin/x86_64/hgLoadBed -noNameIx hg19 tempK562Oc K562_OC.bed -tmpDir=/data/tmp -sqlTable=/cluster/bin/sqlCreate/openChromCombinedPeaks.sql -renameSqlTable & # Works #Now try pipeline # mkdir zipper and load DAF/DDF and bed tar -czf testIt.tgz K562_OC.bed openChromCombo.daf openChromCombo.ddf tar -tzf testIt.tgz K562_OC.bed openChromCombo.daf openChromCombo.ddf cd /hive/groups/encode/dcc/pipeline/ftp/prod/tdreszer mv ~/kent/src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/testing/zipper/testIt.tgz . ll # 4 submissions needing to be displayed: select id,name,status from projects where user_id = 17 and status = "loaded"; +------+-----------------------------------------------+--------+ | id | name | status | +------+-----------------------------------------------+--------+ | 3217 | DNCT Duke DNaseHS Urothelia 20110110 | loaded | | 3218 | DNCT Duke DNaseHS Urothelia UT189 20110110 | loaded | | 3241 | DNCT UTA CTCF K562 Signal and Peaks 20110112 | loaded | | 3242 | DNCT UTA PolII K562 Signal and Peaks 20110112 | loaded | # First 3241 and 3242 which are reloads # Wrong name for peaks! rename table wgEncodeOpenChromChipK562CtcfPk to wgEncodeOpenChromChipK562CtcfPk_old; rename table wgEncodeOpenChromChipK562CtcfPkRep1 to wgEncodeOpenChromChipK562CtcfPk; drop table wgEncodeOpenChromChipK562CtcfPk_old; rename table wgEncodeOpenChromChipK562Pol2Pk to wgEncodeOpenChromChipK562Pol2Pk_old; rename table wgEncodeOpenChromChipK562Pol2PkRep1 to wgEncodeOpenChromChipK562Pol2Pk; drop table wgEncodeOpenChromChipK562Pol2Pk_old; mdbUpdate hg19 -obj=wgEncodeOpenChromChipK562CtcfPk -setVars="dateResubmitted=2011-01-12" mdbUpdate hg19 -obj=wgEncodeOpenChromChipK562CtcfSig -setVars="dateResubmitted=2011-01-12" mdbUpdate hg19 -obj=wgEncodeOpenChromChipK562Pol2Pk -setVars="dateResubmitted=2011-01-12" mdbUpdate hg19 -obj=wgEncodeOpenChromChipK562Pol2Sig -setVars="dateResubmitted=2011-01-12" cd {downloadsDir} mkdir ../obsolete/wgEncodeOpenChromChip mv wgEncodeOpenChromChipK562CtcfPk.* ../obsolete/wgEncodeOpenChromChip/ mv wgEncodeOpenChromChipK562Pol2Pk.* ../obsolete/wgEncodeOpenChromChip/ mv wgEncodeOpenChromChipK562CtcfPkRep1.narrowPeak.gz wgEncodeOpenChromChipK562CtcfPk.narrowPeak.gz mv wgEncodeOpenChromChipK562Pol2PkRep1.narrowPeak.gz wgEncodeOpenChromChipK562Pol2Pk.narrowPeak.gz # Check in changes: cd .. {hg19/metaDb.alpha} mdbPrint hg19 -vars="composite=wgEncodeOpenChromChip" > wgEncodeOpenChromChip.ra gold wgEncodeOpenChromChip.ra git: up, add, ci, up, push cd ../../../../ (trackDb) make DBS=hg19; make alpha DBS=hg19 cd ../wgEncodeOpenChromChip/ encodeDownloadsPage.pl -db=hg19 index.html # 339 files. No Missing metadata # 339 found in hgFileUi # Now 3217, 3218 cd pip/3217/out e trackDb.ra ../../3218/out/trackDb.ra # edit for trackDb subGroups, composite name cd {tdb}/hg19 encodePatchTdb /hive/groups/encode/dcc/pipeline/encpipeline_prod/3217/out/trackDb.ra wgEncodeOpenChromDnase.ra encodePatchTdb /hive/groups/encode/dcc/pipeline/encpipeline_prod/3217/out/trackDb.ra wgEncodeOpenChromDnase.ra gold wgEncodeOpenChromDnase.ra git: up, add, ci, up, push cd pip/3217/out e mdb.txt ../../3218/out/mdb.txt # Look fine, no editing mdbUpdate hg19 mdb.txt Read 7 metadata objects from hg19 Affected 103 row(s) in hg19.metaDb_tdreszer mdbUpdate hg19 ../../3218/out/mdb.txt Using table named 'hg19.metaDb_tdreszer'. Read 7 metadata objects from hg19 Affected 110 row(s) in hg19.metaDb_tdreszer # Check in changes: cd .. {hg19/metaDb.alpha} mdbPrint hg19 -vars="composite=wgEncodeOpenChromDnase" > wgEncodeOpenChromDnase.ra gold wgEncodeOpenChromDnase.ra ### Ouch, missing bai's. Must fix pipeline! e wgEncodeOpenChromDnase.ra # add bai's mdbUpdate hg19 wgEncodeOpenChromDnase.ra git: up, add, ci, up, push cd ../../../../ (trackDb) make DBS=hg19; make alpha DBS=hg19 cd ../wgEncodeOpenChromDnase/ encodeDownloadsPage.pl -db=hg19 index.html # 435 files. No Missing metadata # 435 found in hgFileUi /cluster/data/encode/pipeline/bin/encodeStatus.pl 3217 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 3218 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 3241 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 3242 displayed 2011-01-18 First try of "Combo" wgEncodeOpenChromSynth load =========================================================== Using config path /hive/groups/encode/dcc/pipeline/encpipeline_prod/3273/../config Loading project in directory /hive/groups/encode/dcc/pipeline/encpipeline_prod/3273 set1/HepG2_OC.bed loaded into wgEncodeOpenChromSynthHepg2Pk ERROR: File(s) 'set1/GM12878_OC.bed' failed bed load: Reading stdin Loaded 231413 elements of size 21 Sorted Creating table definition for wgEncodeOpenChromSynthGm12878Pk Saving /data/tmp/loadBed_hgwdev_2c60_4955b0.tab Loading hg19 load of wgEncodeOpenChromSynthGm12878Pk did not go as planned: 231413 record(s), 11 row(s) skipped, 0 warning(s) load ing /data/tmp/loadBed_hgwdev_2c60_4955b0.tab ### Load error on second bed. Try hand load with verbose? cd {pip}/3273 wl /data/tmp/loadBed_hgwdev_2c60_4955b0.tab 231413 wl set1/GM12878_OC.bed 231413 select count(*) from select count(*) from wgEncodeOpenChromSynthGm12878Pk; | 231402 | # "11 row(s) skipped" ll /data/tmp/loadBed_hgwdev_2c60_4955b0.tab -rw-rw-r-- 1 encodeteam protein 33988533 Jan 17 11:15 /data/tmp/loadBed_hgwdev_2c60_4955b0.tab ll set1/GM12878_OC.bed -rw-rw-r-- 2 encodeteam protein 33317166 Jan 17 11:03 set1/GM12878_OC.bed # Files are different sort < set1/GM12878_OC.bed > tmp.bed uniq < tmp.bed > tmp2.bed [hgwdev:tdreszer 3273> ll tmp* -rw-rw-r-- 1 tdreszer protein 33317166 Jan 18 09:03 tmp.bed -rw-rw-r-- 1 tdreszer protein 33317166 Jan 18 09:04 tmp2.bed # No dups head -2 set1/GM12878_OC.bed chr1 10166 10376 FAIREOnly_1 1000 . 10166 10376 153,0,0 0.99 0.00160 0.00 0.01580 1.680.02650 1.51 0.00840 0.00 0.03360 0.00 3 chr1 91363 91505 ChIPOnly_1 1000 . 91363 91505 255,0,255 0.24 0.01320 0.62 0.00320 0.00 0.00000 0.00 0.22470 3.79 0.01890 0.00 4 head -2 /data/tmp/loadBed_hgwdev_2c60_4955b0.tab 585 chr1 10166 10376 FAIREOnly_1 1000 . 10166 10376 10027008 0.99 0.00160 0.000.01580 1.68 0.02650 1.51 0.00840 0.00 0.03360 0.00 3 585 chr1 91363 91505 ChIPOnly_1 1000 . 91363 91505 16711935 0.24 0.01320 0.620.00320 0.00 0.00000 0.00 0.22470 3.79 0.01890 0.00 4 # Bins added in tab /cluster/bin/x86_64/hgLoadBed -noNameIx $assembly $tableName stdin -tmpDir=$tempDir -sqlTable=$Encode::sqlCreate/${sqlTable}.sql -renameSqlTable $fillInArg" /cluster/bin/x86_64/hgLoadBed -noNameIx hg19 wgEncodeOpenChromSynthGm12878Pk_tmp set1/GM12878_OC.bed -tmpDir=/data/tmp/ -sqlTable=/cluster/bin/sqlCreate/openChromCombinedPeaks.sql -renameSqlTable -verbose=1 > tryLoad.txt 2>&1 & LOAD DATA INFILE '/data/tmp/loadBed_hgwdev_2c60_4955b0.tab' REPLACE INTO TABLE wgEncodeOpenChromSynthGm12878Pk_tmp; Deletes all and seems to accept all. However, table still has 11 missing. delete from wgEncodeOpenChromSynthGm12878Pk_tmp; LOAD DATA INFILE '/data/tmp/loadBed_hgwdev_2c60_4955b0.tab' INTO TABLE wgEncodeOpenChromSynthGm12878Pk_tmp; ERROR 1062 (23000): Duplicate entry 'chr21-48022706' for key 1 grep chr21 set1/GM12878_OC.bed | grep 48022706 chr21 48022706 48022858 FAIREOnly_71110 1000 . 48022706 48022858 153,0,0 1.110.01280 0.59 0.01310 1.24 0.00170 0.00 0.01750 0.00 0.03410 0.00 3 chr21 48022706 48022858 FAIREOnly_71113 1000 . 48022706 48022858 153,0,0 1.110.01280 0.59 0.01310 1.24 0.00170 0.00 0.01750 0.00 0.03410 0.00 3 delete from wgEncodeOpenChromSynthGm12878Pk_tmp; LOAD DATA INFILE '/data/tmp/loadBed_hgwdev_2c60_4955b0.tab' REPLACE INTO TABLE wgEncodeOpenChromSynthGm12878Pk_tmp; Query OK, 231424 rows affected (8.61 sec) Records: 231413 Deleted: 11 Skipped: 0 Warnings: 0 ## Now we know, it is duplicates!! Cleverness would awk print $1 $2 $3 and then uniq to find the culprits ### Terry fixed his data, but now there are errors when -1 is put into the unsigned float /cluster/bin/x86_64/hgLoadBed -noNameIx hg19 wgEncodeOpenChromSynthNhekPk_tmp set1/NHEK_OC.bed -tmpDir=/data/tmp/ -sqlTable=/cluster/bin/sqlCreate/openChromCombinedPeaks.sql -renameSqlTable -verbose=1 > tryLoad.txt 2>&1 & # Fixed .sql and reloaded. Awaiting creation of trackDb.ra # Updated three existing hg19 composites for long and short label standards 2011-01-19 Catch up with UTA TFBS and UNC FAIRE =============================================== select id,name,status from projects where user_id = 17 and status = "loaded"; | 3271 | DNCT UTA Input Monocytes-CD14+ 20110116 | loaded | | 3272 | DNCT UTA PolII Gliobla 20110117 | loaded | | 3273 | DNCT OpenChromCombo Set1 20110117 | loaded | | 3277 | DNCT UNC FAIRE-Seq Urothelia 20110117 | loaded | | 3278 | DNCT UNC FAIRE-Seq Urothelia UT189 20110117 | loaded | | 3378 | DNCT UNC FAIRE-Seq MCF-7 Hypoxia_LacAcid 20110119 | loaded | | 3379 | DNCT UNC FAIRE-Seq HTR8svn 20110119 | loaded | cd {pip}/3271 e out/trackDb.ra ../3272/out/trackDb.ra # edit for labels, subgroups etc. cd {tdb19} encodePatchTdb /hive/groups/encode/dcc/pipeline/encpipeline_prod/3272/out/trackDb.ra wgEncodeOpenChromChip.ra cd {pip}/3277 e out/trackDb.ra ../3278/out/trackDb.ra ../3378/out/trackDb.ra ../3379/out/trackDb.ra # edit for labels, subgroups etc. encodePatchTdb /hive/groups/encode/dcc/pipeline/encpipeline_prod/3379/out/trackDb.ra wgEncodeOpenChromFaire.ra # now metadata cd {pip}/3272 e out/mdb.txt # remove rep1 from peaks cd .. mdbUpdate hg19 3271/out/mdb.txt mdbUpdate hg19 3272/out/mdb.txt mdbUpdate hg19 3277/out/mdb.txt mdbUpdate hg19 3278/out/mdb.txt mdbUpdate hg19 3378/out/mdb.txt mdbUpdate hg19 3379/out/mdb.txt # Check in changes: cd .. {hg19/metaDb/alpha} mdbPrint hg19 -vars="composite=wgEncodeOpenChromChip" > wgEncodeOpenChromChip.ra gold wgEncodeOpenChromChip.ra mdbPrint hg19 -vars="composite=wgEncodeOpenChromFaire" > wgEncodeOpenChromFaire.ra gold wgEncodeOpenChromFaire.ra mdbPrint hg19 -vars="composite=wgEncodeOpenChromFaire" | grep -w lab | sort | uniq Using table named 'hg19.metaDb_tdreszer'. objects:173 vars:2862 lab UNC lab UNC(Lieb) [hgwdev:tdreszer alpha> mdbPrint hg19 -vars="composite=wgEncodeOpenChromChip" | grep -w lab | sort | uniq Using table named 'hg19.metaDb_tdreszer'. objects:275 vars:4996 lab UT-A lab UT-A(Iyer) mdbUpdate hg19 -vars="composite=wgEncodeOpenChromFaire lab=UNC(Lieb)" -setVars="lab=UNC" mdbUpdate hg19 -vars="composite=wgEncodeOpenChromChip lab=UT-A(Iyer)" -setVars="lab=UT-A" mdbPrint hg19 -vars="composite=wgEncodeOpenChromChip" > wgEncodeOpenChromChip.ra gold wgEncodeOpenChromChip.ra mdbPrint hg19 -vars="composite=wgEncodeOpenChromFaire" > wgEncodeOpenChromFaire.ra gold wgEncodeOpenChromFaire.ra git: up, add, ci, up, push cd ../../../../ (trackDb) make DBS=hg19; make alpha DBS=hg19 cd ../wgEncodeOpenChromChip/ encodeDownloadsPage.pl -db=hg19 index.html # 352 files. No Missing metadata # 352 found in hgFileUi cd ../wgEncodeOpenChromFaire/ encodeDownloadsPage.pl -db=hg19 index.html # 222 files. Missing metadata for 18!!! # 204 found in hgFileUi ### Brian! submissions 3378 and 3378 have doc id file and table names, but mdb obj names are old style. ### Brian! /cluster/data/encode/pipeline/bin/encodeStatus.pl 3271 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 3272 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 3277 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 3278 displayed wgEncodeOpenChromFaire000004008 wgEncodeOpenChromFaireMcf7HypoxlacRawDataRep1 wgEncodeOpenChromFaire000004009 wgEncodeOpenChromFaireMcf7HypoxlacRawDataRep2 wgEncodeOpenChromFaire000004010 wgEncodeOpenChromFaireMcf7HypoxlacAlnRep1 wgEncodeOpenChromFaire000004011 wgEncodeOpenChromFaireMcf7HypoxlacAlnRep2 wgEncodeOpenChromFaire000004012 wgEncodeOpenChromFaireMcf7HypoxlacBaseOverlapSignal wgEncodeOpenChromFaire000004013 wgEncodeOpenChromFaireMcf7HypoxlacPk wgEncodeOpenChromFaire000004014 wgEncodeOpenChromFaireMcf7HypoxlacSig wgEncodeOpenChromFaire000003992 wgEncodeOpenChromFaireHtr8RawDataRep1 wgEncodeOpenChromFaire000003993 wgEncodeOpenChromFaireHtr8RawDataRep2 wgEncodeOpenChromFaire000003994 wgEncodeOpenChromFaireHtr8AlnRep1 wgEncodeOpenChromFaire000003995 wgEncodeOpenChromFaireHtr8AlnRep2 wgEncodeOpenChromFaire000003996 wgEncodeOpenChromFaireHtr8BaseOverlapSignal wgEncodeOpenChromFaire000003997 wgEncodeOpenChromFaireHtr8Pk wgEncodeOpenChromFaire000003998 wgEncodeOpenChromFaireHtr8Sig rename table wgEncodeOpenChromFaire000004012 to wgEncodeOpenChromFaireMcf7HypoxlacBaseOverlapSignal; rename table wgEncodeOpenChromFaire000004013 to wgEncodeOpenChromFaireMcf7HypoxlacPk; rename table wgEncodeOpenChromFaire000004014 to wgEncodeOpenChromFaireMcf7HypoxlacSig; rename table wgEncodeOpenChromFaire000003996 to wgEncodeOpenChromFaireHtr8BaseOverlapSignal; rename table wgEncodeOpenChromFaire000003997 to wgEncodeOpenChromFaireHtr8Pk; rename table wgEncodeOpenChromFaire000003998 to wgEncodeOpenChromFaireHtr8Sig; update wgEncodeOpenChromFaireHtr8BaseOverlapSignal set fileName = "/gbdb/hg19/bbi/wgEncodeOpenChromFaireHtr8BaseOverlapSignal.bigWig" ; update wgEncodeOpenChromFaireHtr8Sig set fileName = "/gbdb/hg19/bbi/wgEncodeOpenChromFaireHtr8Sig.bigWig" ; update wgEncodeOpenChromFaireMcf7HypoxlacBaseOverlapSignal set fileName = "/gbdb/hg19/bbi/wgEncodeOpenChromFaireMcf7HypoxlacBaseOverlapSignal.bigWig"; update wgEncodeOpenChromFaireMcf7HypoxlacSig set fileName = "/gbdb/hg19/bbi/wgEncodeOpenChromFaireMcf7HypoxlacSig.bigWig"; mv wgEncodeOpenChromFaire000004008.fastq.gz wgEncodeOpenChromFaireMcf7HypoxlacRawDataRep1.fastq.gz mv wgEncodeOpenChromFaire000004009.fastq.gz wgEncodeOpenChromFaireMcf7HypoxlacRawDataRep2.fastq.gz mv wgEncodeOpenChromFaire000004010.bam wgEncodeOpenChromFaireMcf7HypoxlacAlnRep1.bam mv wgEncodeOpenChromFaire000004011.bam wgEncodeOpenChromFaireMcf7HypoxlacAlnRep2.bam mv wgEncodeOpenChromFaire000004010.bam.bai wgEncodeOpenChromFaireMcf7HypoxlacAlnRep1.bam.bai mv wgEncodeOpenChromFaire000004011.bam.bai wgEncodeOpenChromFaireMcf7HypoxlacAlnRep2.bam.bai mv wgEncodeOpenChromFaire000004012.bigWig wgEncodeOpenChromFaireMcf7HypoxlacBaseOverlapSignal.bigWig mv wgEncodeOpenChromFaire000004013.narrowPeak.gz wgEncodeOpenChromFaireMcf7HypoxlacPk.narrowPeak.gz mv wgEncodeOpenChromFaire000004014.bigWig wgEncodeOpenChromFaireMcf7HypoxlacSig.bigWig mv wgEncodeOpenChromFaire000003992.fastq.gz wgEncodeOpenChromFaireHtr8RawDataRep1.fastq.gz mv wgEncodeOpenChromFaire000003993.fastq.gz wgEncodeOpenChromFaireHtr8RawDataRep2.fastq.gz mv wgEncodeOpenChromFaire000003994.bam wgEncodeOpenChromFaireHtr8AlnRep1.bam mv wgEncodeOpenChromFaire000003995.bam wgEncodeOpenChromFaireHtr8AlnRep2.bam mv wgEncodeOpenChromFaire000003994.bam.bai wgEncodeOpenChromFaireHtr8AlnRep1.bam.bai mv wgEncodeOpenChromFaire000003995.bam.bai wgEncodeOpenChromFaireHtr8AlnRep2.bam.bai mv wgEncodeOpenChromFaire000003996.bigWig wgEncodeOpenChromFaireHtr8BaseOverlapSignal.bigWig mv wgEncodeOpenChromFaire000003997.narrowPeak.gz wgEncodeOpenChromFaireHtr8Pk.narrowPeak.gz mv wgEncodeOpenChromFaire000003998.bigWig wgEncodeOpenChromFaireHtr8Sig.bigWig mv /gbdb/hg19/bbi/wgEncodeOpenChromFaire000003996.bigWig /gbdb/hg19/bbi/wgEncodeOpenChromFaireHtr8BaseOverlapSignal.bigWig mv /gbdb/hg19/bbi/wgEncodeOpenChromFaire000003998.bigWig /gbdb/hg19/bbi/wgEncodeOpenChromFaireHtr8Sig.bigWig mv /gbdb/hg19/bbi/wgEncodeOpenChromFaire000004012.bigWig /gbdb/hg19/bbi/wgEncodeOpenChromFaireMcf7HypoxlacBaseOverlapSignal.bigWig mv /gbdb/hg19/bbi/wgEncodeOpenChromFaire000004014.bigWig /gbdb/hg19/bbi/wgEncodeOpenChromFaireMcf7HypoxlacSig.bigWig mv /gbdb/hg19/bbi/wgEncodeOpenChromFaire000003996.bigWig /gbdb/hg19/bbi/wgEncodeOpenChromFaireHtr8BaseOverlapSignal.bigWig mv /gbdb/hg19/bbi/wgEncodeOpenChromFaire000003998.bigWig /gbdb/hg19/bbi/wgEncodeOpenChromFaireHtr8Sig.bigWig mv /gbdb/hg19/bbi/wgEncodeOpenChromFaire000004012.bigWig /gbdb/hg19/bbi/wgEncodeOpenChromFaireMcf7HypoxlacBaseOverlapSignal.bigWig mv /gbdb/hg19/bbi/wgEncodeOpenChromFaire000004014.bigWig /gbdb/hg19/bbi/wgEncodeOpenChromFaireMcf7HypoxlacSig.bigWig # Oops rm /gbdb/hg19/bbi/wgEncodeOpenChromFaireHtr8BaseOverlapSignal.bigWig rm /gbdb/hg19/bbi/wgEncodeOpenChromFaireHtr8Sig.bigWig rm /gbdb/hg19/bbi/wgEncodeOpenChromFaireMcf7HypoxlacBaseOverlapSignal.bigWig rm /gbdb/hg19/bbi/wgEncodeOpenChromFaireMcf7HypoxlacSig.bigWig cd /gbdb/hg19/bbi ln -sf /usr/local/apache/htdocs-hgdownload/goldenPath/hg19/encodeDCC/wgEncodeOpenChromFaire/wgEncodeOpenChromFaireHtr8BaseOverlapSignal.bigWig wgEncodeOpenChromFaireHtr8BaseOverlapSignal.bigWig ln -sf /usr/local/apache/htdocs-hgdownload/goldenPath/hg19/encodeDCC/wgEncodeOpenChromFaire/wgEncodeOpenChromFaireHtr8Sig.bigWig wgEncodeOpenChromFaireHtr8Sig.bigWig ln -sf /usr/local/apache/htdocs-hgdownload/goldenPath/hg19/encodeDCC/wgEncodeOpenChromFaire/wgEncodeOpenChromFaireMcf7HypoxlacBaseOverlapSignal.bigWig wgEncodeOpenChromFaireMcf7HypoxlacBaseOverlapSignal.bigWig ln -sf /usr/local/apache/htdocs-hgdownload/goldenPath/hg19/encodeDCC/wgEncodeOpenChromFaire/wgEncodeOpenChromFaireMcf7HypoxlacSig.bigWig wgEncodeOpenChromFaireMcf7HypoxlacSig.bigWig cd ../wgEncodeOpenChromFaire/ encodeDownloadsPage.pl -db=hg19 index.html # 222 files. No missing metadata # 222 found in hgFileUi /cluster/data/encode/pipeline/bin/encodeStatus.pl 3378 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 3379 displayed # synth is okay so work on that cd {tdb}/hg19 cat /hive/groups/encode/dcc/pipeline/encpipeline_prod/3273/out/trackDb.ra >> wgEncodeOpenChromSynth.ra e wgEncodeOpenChromSynth.ra make DBS=hg19 # Looks fine # Actually, remove color settings and add itemRgb on, play with filters select max(pvalue), max(dnaseSignal), max(dnasePvalue), max(faireSignal), max(fairePvalue), max(polIISignal), max(polIIPvalue), max(ctcfSignal), max(ctcfPvalue), max(cmycSignal), max(cmycPvalue) from wgEncodeOpenChromSynthK562Pk; select min(pvalue), min(dnaseSignal), min(dnasePvalue), min(faireSignal), min(fairePvalue), min(polIISignal), min(polIIPvalue), min(ctcfSignal), min(ctcfPvalue), min(cmycSignal), min(cmycPvalue) from wgEncodeOpenChromSynthK562Pk; select min(score), max(score) from wgEncodeOpenChromSynthK562Pk; ### None of my filters are working. Will need to investigate later. Also hgc shows nothing useful, but I already knew that. # now metadata cd {pip}/3273 mdbUpdate hg19 out/mdb.txt # Check in changes: cd .. {hg19/metaDb/alpha} mdbPrint hg19 -vars="composite=wgEncodeOpenChromSynth" > wgEncodeOpenChromSynth.ra gold wgEncodeOpenChromChip.ra git: up, add, ci, up, push cd ../../../../ (trackDb) make DBS=hg19; make alpha DBS=hg19 cd ../wgEncodeOpenChromSynth/ encodeDownloadsPage.pl -db=hg19 index.html # 7 files. Little metadata # 7 found in hgFileUi ## Looks like mdb alpha was updated under my nose. encodeDownloadsPage.pl -db=hg19 index.html # 7 files. No missing metadata # 7 found in hgFileUi /cluster/data/encode/pipeline/bin/encodeStatus.pl 3273 displayed ### controlId problems: mdbPrint hg19 -vars="composite=wgEncodeOpenChromChip" -count 275 objects mdbPrint hg19 -vars="composite=wgEncodeOpenChromChip controlId=" -count 90 objects mdbPrint hg19 -vars="composite=wgEncodeOpenChromChip controlId!=" -count 185 objects mdbPrint hg19 -vars="composite=wgEncodeOpenChromChip controlId=modelled" -count 15 objects mdbPrint hg19 -vars="composite=wgEncodeOpenChromChip controlId!=modelled" -count 75 objects mdbPrint hg19 -vars="composite=wgEncodeOpenChromDnase" -count 326 objects mdbPrint hg19 -vars="composite=wgEncodeOpenChromDnase controlId=" -count 42 objects mdbPrint hg19 -vars="composite=wgEncodeOpenChromDnase controlId!=" -count 284 objects mdbPrint hg19 -vars="composite=wgEncodeOpenChromDnase controlId=modelled" -count 27 objects mdbPrint hg19 -vars="composite=wgEncodeOpenChromDnase controlId!=modelled" -count 15 objects mdbPrint hg19 -vars="composite=wgEncodeOpenChromFaire" -count 173 objects mdbPrint hg19 -vars="composite=wgEncodeOpenChromFaire controlId=" -count 27 objects mdbPrint hg19 -vars="composite=wgEncodeOpenChromFaire controlId!=" -count 146 objects mdbPrint hg19 -vars="composite=wgEncodeOpenChromFaire controlId=modelled" -count 11 objects mdbPrint hg19 -vars="composite=wgEncodeOpenChromFaire controlId!=modelled" -count 16 objects 2011-01-21 Update controlId in OpenChrom datasets ================================================= # Questions from me, ansers from Terry: >> - all of the ChIP data should have submitted Input data except NHEK and H1-hESC > I don't see input for any GM line except for GM12878. > QUESTION: Do these also use the "modelled" input? Yes. These are fairly "normal" cell lines. And just one minor clarification, we have different modeled input for males and females. In our submission files (DDF), you should see things like "iff_GM12878" or "iff_generic_male" or "iff_generic_female". These indicate the input file used for processing. >> - when available, DNase and FAIRE use models based on the input data generated. > See controlId explanation below. > QUESTION: So I should set the "controlId" to point to the available cell line's input in all Dnase and FAIRE cases? Yes. >> When not available, we have a composite input track from ~7 cell types (I think) that we use. > QUESTION: So I should set the "controlId" to point to "modelled" in all cases that do not have a cell specific input? To stay consistent with our nomenclature, can you call these "generic_male" or "generic_female"? Cell lines where the sex could not be determined used the generic_male model. mdbPrint hg19 -vars="composite=wgEncodeOpenChromChip view=Peaks cell= controlId!=" | grep cell | sort | uniq cell Fibrobl cell GM12878 cell GM12891 cell GM12892 cell GM19238 cell GM19239 cell GM19240 cell Gliobla cell H1-hESC cell HUVEC cell HeLa-S3 cell HepG2 cell K562 cell MCF-7 cell NHEK cell ProgFib mdbPrint hg19 -vars="composite=wgEncodeOpenChromChip controlId!=" -count 185 objects mdbUpdate hg19 -vars="composite=wgEncodeOpenChrom% composite!=wgEncodeOpenChromSynth cell=Fibrobl" -setVars="controlId=Fibrobl/Input" mdbUpdate hg19 -vars="composite=wgEncodeOpenChrom% composite!=wgEncodeOpenChromSynth cell=GM12878" -setVars="controlId=GM12878/Input" mdbUpdate hg19 -vars="composite=wgEncodeOpenChrom% composite!=wgEncodeOpenChromSynth cell=K562" -setVars="controlId=K562/Input" mdbUpdate hg19 -vars="composite=wgEncodeOpenChrom% composite!=wgEncodeOpenChromSynth cell=HeLa-S3" -setVars="controlId=HeLa-S3/Input" mdbUpdate hg19 -vars="composite=wgEncodeOpenChrom% composite!=wgEncodeOpenChromSynth cell=HepG2" -setVars="controlId=HepG2/Input" mdbUpdate hg19 -vars="composite=wgEncodeOpenChrom% composite!=wgEncodeOpenChromSynth cell=HUVEC" -setVars="controlId=HUVEC/Input" mdbUpdate hg19 -vars="composite=wgEncodeOpenChrom% composite!=wgEncodeOpenChromSynth cell=Gliobla" -setVars="controlId=Gliobla/Input" mdbUpdate hg19 -vars="composite=wgEncodeOpenChrom% composite!=wgEncodeOpenChromSynth cell=MCF-7" -setVars="controlId=MCF-7/Input" mdbUpdate hg19 -vars="composite=wgEncodeOpenChrom% composite!=wgEncodeOpenChromSynth cell=Monocytes-CD14+" -setVars="controlId=Monocytes-CD14+/Input" mdbUpdate hg19 -vars="composite=wgEncodeOpenChrom% composite!=wgEncodeOpenChromSynth cell=ProgFib" -setVars="controlId=ProgFib/Input" mdbPrint hg19 -vars="composite=wgEncodeOpenChromChip controlId!=" -count 42 objects mdbPrint hg19 -vars="composite=wgEncodeOpenChromChip controlId!=" | grep cell | sort | uniq objects:42 vars:771 cell GM12891 male iff_generic_male cell GM12892 f iff_generic_female cell GM19238 f iff_generic_female cell GM19239 m iff_generic_male cell GM19240 f iff_generic_female cell H1-hESC m iff_generic_male cell NHEK f iff_generic_female mdbUpdate hg19 -vars="composite=wgEncodeOpenChrom% composite!=wgEncodeOpenChromSynth cell=GM12891" -setVars="controlId=generic_male" mdbUpdate hg19 -vars="composite=wgEncodeOpenChrom% composite!=wgEncodeOpenChromSynth cell=GM12892" -setVars="controlId=generic_female" mdbUpdate hg19 -vars="composite=wgEncodeOpenChrom% composite!=wgEncodeOpenChromSynth cell=GM19238" -setVars="controlId=generic_female" mdbUpdate hg19 -vars="composite=wgEncodeOpenChrom% composite!=wgEncodeOpenChromSynth cell=GM19239" -setVars="controlId=generic_male" mdbUpdate hg19 -vars="composite=wgEncodeOpenChrom% composite!=wgEncodeOpenChromSynth cell=GM19240" -setVars="controlId=generic_female" mdbUpdate hg19 -vars="composite=wgEncodeOpenChrom% composite!=wgEncodeOpenChromSynth cell=H1-hESC" -setVars="controlId=generic_male" mdbUpdate hg19 -vars="composite=wgEncodeOpenChrom% composite!=wgEncodeOpenChromSynth cell=NHEK" -setVars="controlId=generic_female" mdbPrint hg19 -vars="composite=wgEncodeOpenChromChip controlId!=" -count 0 objects mdbPrint hg19 -vars="composite=wgEncodeOpenChromChip" | grep controlId | sort | uniq controlId Fibrobl/Input controlId GM12878/Input controlId Gliobla/Input controlId HUVEC/Input controlId HeLa-S3/Input controlId HepG2/Input controlId K562/Input controlId MCF-7/Input controlId Monocytes-CD14+/Input controlId ProgFib/Input controlId generic_female controlId generic_male # Chip all done. Pick up the pieces for FAIRE and DNase mdbPrint hg19 -vars="composite=wgEncodeOpenChromDnase controlId!=" -count 190 # was 284 mdbPrint hg19 -vars="composite=wgEncodeOpenChromDnase controlId!=" | grep cell | sort | uniq cell 8988T cell A549 cell AoSMC cell CLL cell Chorion cell FibroP cell GM18507 cell H9ES cell HMEC cell HPDE6-E6E7 cell HSMM cell HSMMtube cell HTR8svn cell Hepatocytes cell Huh-7 cell Huh-7.5 cell LNCaP cell Medullo cell Melano cell Myometr cell Osteobl cell PanIsletD cell PanIslets cell Stellate cell T-47D cell Urothelia cell iPS cell pHTE mdbPrint hg19 -vars="composite=wgEncodeOpenChromFaire controlId!=" -count 50 # was 146 mdbPrint hg19 -vars="composite=wgEncodeOpenChromFaire controlId!=" | grep cell | sort | uniq cell Astrocy cell GM18507 cell HTR8svn cell Medullo cell NHBE cell PanIslets cell Urothelia mdbPrint hg19 -byVar -var=labVersion -val=%generic_male | grep -v Chip metaVariable labVersion fseq v 1.84, iff_generic_male metaObject wgEncodeOpenChromDnaseA549Sig metaObject wgEncodeOpenChromDnaseAosmcSerumfreeSig metaObject wgEncodeOpenChromDnaseGm12891Sig metaObject wgEncodeOpenChromDnaseGm18507Sig metaObject wgEncodeOpenChromDnaseGm19239Sig metaObject wgEncodeOpenChromDnaseH1hescSig metaObject wgEncodeOpenChromDnaseHuh75Sig metaObject wgEncodeOpenChromDnaseHuh7Sig metaObject wgEncodeOpenChromDnaseIpsSig metaObject wgEncodeOpenChromDnaseLncapAndroSig metaObject wgEncodeOpenChromDnaseLncapSig metaObject wgEncodeOpenChromDnaseMyometrSig metaObject wgEncodeOpenChromDnasePanisdSig metaObject wgEncodeOpenChromDnasePanisletsSig metaObject wgEncodeOpenChromDnasePhteSig metaObject wgEncodeOpenChromFaireAstrocySig metaObject wgEncodeOpenChromFaireGm12891Sig metaObject wgEncodeOpenChromFaireGm18507Sig metaObject wgEncodeOpenChromFaireGm19239Sig metaObject wgEncodeOpenChromFaireH1hescSig metaObject wgEncodeOpenChromFaireNhbeSig metaObject wgEncodeOpenChromFairePanisletsSig mdbPrint hg19 -byVar -var=labVersion -val=%generic_female | grep -v Chip metaVariable labVersion fseq v 1.84, iff_generic_female metaObject wgEncodeOpenChromDnase8988tSig metaObject wgEncodeOpenChromDnaseChorionSig metaObject wgEncodeOpenChromDnaseCllSig metaObject wgEncodeOpenChromDnaseFibropSig metaObject wgEncodeOpenChromDnaseGm12892Sig metaObject wgEncodeOpenChromDnaseGm19238Sig metaObject wgEncodeOpenChromDnaseGm19240Sig metaObject wgEncodeOpenChromDnaseH9esSig metaObject wgEncodeOpenChromDnaseHepatocytesSig metaObject wgEncodeOpenChromDnaseHmecSig metaObject wgEncodeOpenChromDnaseHpde6e6e7Sig metaObject wgEncodeOpenChromDnaseHsmmSig metaObject wgEncodeOpenChromDnaseHsmmtSig metaObject wgEncodeOpenChromDnaseHtr8Sig metaObject wgEncodeOpenChromDnaseMedulloSig metaObject wgEncodeOpenChromDnaseMelanoSig metaObject wgEncodeOpenChromDnaseNhekSig metaObject wgEncodeOpenChromDnaseOsteoblSig metaObject wgEncodeOpenChromDnaseStellateSig metaObject wgEncodeOpenChromDnaseT47dSig metaObject wgEncodeOpenChromDnaseUrotsaSig metaObject wgEncodeOpenChromDnaseUrotsaUt189Sig metaObject wgEncodeOpenChromFaireGm12892Sig metaObject wgEncodeOpenChromFaireHtr8Sig metaObject wgEncodeOpenChromFaireMedulloSig metaObject wgEncodeOpenChromFaireNhekSig metaObject wgEncodeOpenChromFaireUrotsaSig metaObject wgEncodeOpenChromFaireUrotsaUt189Sig ### Some discrepancies between cell gender in cv and labVersion reported by Terry 8988T generic_female Dnase A549 generic_male Dnase AoSMC U* generic_male Dnase Astrocy U* generic_male Faire Chorion U generic_female Dnase CLL U generic_female Dnase FibroP generic_female Dnase GM12891 generic_male Dnase Faire GM12892 generic_female Dnase Faire GM18507 generic_male Dnase Faire GM19238 generic_female Dnase GM19239 generic_male Dnase Faire GM19240 generic_female Dnase H1-hESC generic_male Dnase Faire H9ES generic_female Dnase Hepatocytes U generic_female Dnase HMEC U generic_female Dnase HPDE6-E6E7 generic_female Dnase HSMM U generic_female Dnase HSMMtube U generic_female Dnase HTR8svn U generic_female Dnase Faire Huh-7.5 generic_male Dnase Huh-7 generic_male Dnase iPS U* generic_male Dnase LNCaP generic_male Dnase Medullo U generic_female Dnase Faire Melano U generic_female Dnase Myometr F generic_male Dnase NHBE U* generic_male Faire NHEK generic_female Dnase Faire Osteobl U generic_female Dnase PanIsletD U* generic_male Dnase PanIslets generic_male Dnase Faire pHTE U* generic_male Dnase Stellate generic_female Dnase T-47D generic_female Dnase Urothelia generic_female Dnase Faire ## Will update according to labVersion until Terry reports back. mdbUpdate hg19 -vars="composite=wgEncodeOpenChromDnase cell=8988T" -setVars="controlId=generic_female" mdbUpdate hg19 -vars="composite=wgEncodeOpenChromDnase cell=A549" -setVars="controlId=generic_male" mdbUpdate hg19 -vars="composite=wgEncodeOpenChromDnase cell=AoSMC" -setVars="controlId=generic_male" mdbUpdate hg19 -vars="composite=wgEncodeOpenChromDnase cell=CLL" -setVars="controlId=generic_female" mdbUpdate hg19 -vars="composite=wgEncodeOpenChromDnase cell=Chorion" -setVars="controlId=generic_female" mdbUpdate hg19 -vars="composite=wgEncodeOpenChromDnase cell=FibroP" -setVars="controlId=generic_female" mdbUpdate hg19 -vars="composite=wgEncodeOpenChromDnase cell=GM18507" -setVars="controlId=generic_male" mdbUpdate hg19 -vars="composite=wgEncodeOpenChromDnase cell=H9ES" -setVars="controlId=generic_female" mdbUpdate hg19 -vars="composite=wgEncodeOpenChromDnase cell=HMEC" -setVars="controlId=generic_female" mdbUpdate hg19 -vars="composite=wgEncodeOpenChromDnase cell=HPDE6-E6E7 " -setVars="controlId=generic_female" mdbUpdate hg19 -vars="composite=wgEncodeOpenChromDnase cell=HSMM" -setVars="controlId=generic_female" mdbUpdate hg19 -vars="composite=wgEncodeOpenChromDnase cell=HSMMtube" -setVars="controlId=generic_female" mdbUpdate hg19 -vars="composite=wgEncodeOpenChromDnase cell=HTR8svn" -setVars="controlId=generic_female" mdbUpdate hg19 -vars="composite=wgEncodeOpenChromDnase cell=Hepatocytes" -setVars="controlId=generic_female" mdbUpdate hg19 -vars="composite=wgEncodeOpenChromDnase cell=Huh-7" -setVars="controlId=generic_male" mdbUpdate hg19 -vars="composite=wgEncodeOpenChromDnase cell=Huh-7.5" -setVars="controlId=generic_male" mdbUpdate hg19 -vars="composite=wgEncodeOpenChromDnase cell=LNCaP" -setVars="controlId=generic_male" mdbUpdate hg19 -vars="composite=wgEncodeOpenChromDnase cell=Medullo" -setVars="controlId=generic_female" mdbUpdate hg19 -vars="composite=wgEncodeOpenChromDnase cell=Melano" -setVars="controlId=generic_female" mdbUpdate hg19 -vars="composite=wgEncodeOpenChromDnase cell=Myometr" -setVars="controlId=generic_male" mdbUpdate hg19 -vars="composite=wgEncodeOpenChromDnase cell=Osteobl" -setVars="controlId=generic_female" mdbUpdate hg19 -vars="composite=wgEncodeOpenChromDnase cell=PanIsletD" -setVars="controlId=generic_male" mdbUpdate hg19 -vars="composite=wgEncodeOpenChromDnase cell=PanIslets" -setVars="controlId=generic_male" mdbUpdate hg19 -vars="composite=wgEncodeOpenChromDnase cell=Stellate" -setVars="controlId=generic_female" mdbUpdate hg19 -vars="composite=wgEncodeOpenChromDnase cell=T-47D" -setVars="controlId=generic_female" mdbUpdate hg19 -vars="composite=wgEncodeOpenChromDnase cell=Urothelia" -setVars="controlId=generic_female" mdbUpdate hg19 -vars="composite=wgEncodeOpenChromDnase cell=iPS" -setVars="controlId=generic_male" mdbUpdate hg19 -vars="composite=wgEncodeOpenChromDnase cell=pHTE" -setVars="controlId=generic_male" mdbUpdate hg19 -vars="composite=wgEncodeOpenChromFaire cell=Astrocy" -setVars="controlId=generic_male" mdbUpdate hg19 -vars="composite=wgEncodeOpenChromFaire cell=GM18507" -setVars="controlId=generic_male" mdbUpdate hg19 -vars="composite=wgEncodeOpenChromFaire cell=HTR8svn" -setVars="controlId=generic_female" mdbUpdate hg19 -vars="composite=wgEncodeOpenChromFaire cell=Medullo" -setVars="controlId=generic_female" mdbUpdate hg19 -vars="composite=wgEncodeOpenChromFaire cell=NHBE" -setVars="controlId=generic_male" mdbUpdate hg19 -vars="composite=wgEncodeOpenChromFaire cell=PanIslets" -setVars="controlId=generic_male" mdbUpdate hg19 -vars="composite=wgEncodeOpenChromFaire cell=Urothelia" -setVars="controlId=generic_female" mdbPrint hg19 -vars="composite=wgEncodeOpenChromFDnase controlId!=" -count 0 objects mdbPrint hg19 -vars="composite=wgEncodeOpenChromFaire controlId!=" -count 0 objects # Check in changes: cd .. {hg19/metaDb/alpha} mdbPrint hg19 -vars="composite=wgEncodeOpenChromChip" > wgEncodeOpenChromChip.ra gold wgEncodeOpenChromChip.ra #missing setType mdbPrint hg19 -vars="composite=wgEncodeOpenChromChip setType=" -count 90 objects mdbPrint hg19 -vars="composite=wgEncodeOpenChromChip setType!=" -count 185 objects mdbPrint hg19 -vars="composite=wgEncodeOpenChromChip setType!= antibody=Input" -count 2 objects mdbPrint hg19 -vars="composite=wgEncodeOpenChromChip setType!= antibody!=Input" -count 183 objects mdbPrint hg19 -vars="composite=wgEncodeOpenChromChip setType!= antibody!=Input" | grep antibody | sort | uniq antibody CTCF antibody Pol2 antibody c-Myc mdbUpdate hg19 -vars="composite=wgEncodeOpenChromChip setType!= antibody=Input" -setVars="setType=input" mdbUpdate hg19 -vars="composite=wgEncodeOpenChromChip setType!= antibody!=Input" -setVars="setType=exp" # Complete list of Open Chrom controlIds: mdbPrint hg19 -vars="composite=wgEncodeOpenChrom%" | grep controlId | sort | uniq controlId Fibrobl/Input controlId GM12878/Input controlId Gliobla/Input controlId HUVEC/Input controlId HeLa-S3/Input controlId HepG2/Input controlId K562/Input controlId MCF-7/Input controlId Monocytes-CD14+/Input controlId ProgFib/Input controlId generic_female controlId generic_male # Again check in changes: mdbPrint hg19 -vars="composite=wgEncodeOpenChromChip" > wgEncodeOpenChromChip.ra gold wgEncodeOpenChromChip.ra mdbPrint hg19 -vars="composite=wgEncodeOpenChromDnase" > wgEncodeOpenChromDnase.ra gold wgEncodeOpenChromDnase.ra mdbPrint hg19 -vars="composite=wgEncodeOpenChromFaire" > wgEncodeOpenChromFaire.ra gold wgEncodeOpenChromFaire.ra git: up, add, ci, up, push cd ../../../../ (trackDb) make DBS=hg19; make alpha DBS=hg19 cd {downloadsHg19}/wgEncodeOpenChromChip/ encodeDownloadsPage.pl -db=hg19 index.html cd {downloadsHg19}/wgEncodeOpenChromDnase/ encodeDownloadsPage.pl -db=hg19 index.html cd {downloadsHg19}/wgEncodeOpenChromFaire/ encodeDownloadsPage.pl -db=hg19 index.html 2011-01-24 Last submission for freeze ===================================== cd {pip}/3496 e out/trackDb.ra cd {tdb19} encodePatchTdb /hive/groups/encode/dcc/pipeline/encpipeline_prod/3496/out/trackDb.ra wgEncodeOpenChromFaire.ra # now metadata cd {pip}/3496 e out/mdb.txt # no change needed cd .. mdbUpdate hg19 out/mdb.txt Read 7 metadata objects from hg19 Affected 103 row(s) in hg19.metaDb_tdreszer # Check in changes: cd .. {hg19/metaDb/alpha} mdbPrint hg19 -vars="composite=wgEncodeOpenChromFaire" > wgEncodeOpenChromFaire.ra gold wgEncodeOpenChromFaire.ra git: up, add, ci, up, push cd ../../../../ (trackDb) make DBS=hg19; make alpha DBS=hg19 mdbPrint hg19 -vars="composite=wgEncodeOpenChromFaire cell=A459" | grep labVersion | sort | uniq labVersion fseq v 1.84, iff_generic_male mdbUpdate hg19 -vars="composite=wgEncodeOpenChromFaire cell=A549" -setVars="controlId=generic_male" cd {downloadsHg19}/wgEncodeOpenChromFaire/ encodeDownloadsPage.pl -db=hg19 index.html # 352 files. All have metadata # 352 found in hgFileUi /cluster/data/encode/pipeline/bin/encodeStatus.pl 3496 displayed ### Currently unresolved with Terry: 1) controlId v. labVersion discrepencies 2) Description of compo tracks 3) hgc (and hgTrackUi filtering) of combo tracks 4) Validation docs by cell The following we seem to be in agreement on and were all submitted using the generic_male as they should have been: AoSMC - Undetermined Astrocy - Undetermined iPS - Male (combined two males and one female) PanIsletD - Male (combined two males and one female) pHTE - Undetermined (combined one male and one undetermined) The last one of this group, NHBE, was submitted as a "male" which I believe meant it was undetermined at the time of submission. But, I now see that Greg has this listed as "female" in our internal documents. Greg - can you confirm? NHBE - Female (submitted as male for FAIRE - screw up) The following cell lines have different/incorrect sex assignments from what we have. I'm not sure if these were incompletely described when blessed as a tier 3 line or what happened, but according to our documents, they should all be female: CLL - Female Chorion - Female HMEC - Female HTR8svn - Female Hepatocytes - Female Osteobl - Female The Melano cell line is of undetermined sex and was processed with the generic_male. We have this incorrectly listed as generic_female in the DDF. Melano - undetermined The next two originally consisted of only female replicates, but then later a male replicate was added making this a "male". So, they were processed with the generic_male, but we forgot to update the DDF for this: HSMM - Male (combined two females and one male) HSMMtube - Male (combined two females and one male) So, for the above three, it is an error in the DDF, but the data were submitted as they should have been. For the last one, Medullo, when we submitted the DNase, we were under the impression it was a female. Later, we were told it was a male, and FAIRE was then correctly submitted as a male. We had intended to go back and re-process the DNase data, but obviously we forgot. So, FAIRE is correct, but DNase is not. Medullo - Male (submitted as female for DNaseHS - screw up) In summary, I believe all but two of these can be fairly easily remedied, though I do profusely apologize the confusion on these. It has been a bit of a nightmare getting this information. The problem kid are FAIRE NHBE (female submitted as male) and DNase Medullo (male submitted as female). We should re-submit data for both of these transvestites, as it were, so I am guessing the easiest thing to do is to pull them back from further processing on your end, and we'll update these when the submission pipeline re-opens. How does this all work for you? Greg - please chime in if I have any of the above wrong. I am going off of information in the official cell lines doc. Terry Agree: mdbUpdate hg19 -vars="composite=wgEncodeOpenChromDnase cell=AoSMC" -setVars="controlId=generic_male" mdbUpdate hg19 -vars="composite=wgEncodeOpenChromFaire cell=Astrocy" -setVars="controlId=generic_male" mdbUpdate hg19 -vars="composite=wgEncodeOpenChromDnase cell=iPS" -setVars="controlId=generic_male" mdbUpdate hg19 -vars="composite=wgEncodeOpenChromDnase cell=PanIsletD" -setVars="controlId=generic_male" mdbUpdate hg19 -vars="composite=wgEncodeOpenChromDnase cell=pHTE" -setVars="controlId=generic_male" Affected 0 row(s) in hg19.metaDb_tdreszer # as expected! Should be Female not U Change cv.ra mdbUpdate hg19 -vars="composite=wgEncodeOpenChromDnase cell=CLL" -setVars="controlId=generic_female" mdbUpdate hg19 -vars="composite=wgEncodeOpenChromDnase cell=Chorion" -setVars="controlId=generic_female" mdbUpdate hg19 -vars="composite=wgEncodeOpenChromDnase cell=HMEC" -setVars="controlId=generic_female" mdbUpdate hg19 -vars="composite=wgEncodeOpenChromDnase cell=HTR8svn" -setVars="controlId=generic_female" mdbUpdate hg19 -vars="composite=wgEncodeOpenChromFaire cell=HTR8svn" -setVars="controlId=generic_female" mdbUpdate hg19 -vars="composite=wgEncodeOpenChromDnase cell=Hepatocytes" -setVars="controlId=generic_female" mdbUpdate hg19 -vars="composite=wgEncodeOpenChromDnase cell=Osteobl" -setVars="controlId=generic_female" Affected 0 row(s) in hg19.metaDb_tdreszer # as expected! # Change labVersion and controlId from female to male Still U in cv mdbPrint hg19 -vars="composite=wgEncodeOpenChromDnase cell=Melano labVersion=%generic_female" | grep labVersion | sort | uniq objects:1 vars:18 labVersion fseq v 1.84, iff_generic_female mdbUpdate hg19 -vars="composite=wgEncodeOpenChromDnase cell=Melano labVersion=%generic_female" -var=labVersion -val="fseq v 1.84, iff_generic_male" Affected 1 row(s) in hg19.metaDb_tdreszer mdbUpdate hg19 -vars="composite=wgEncodeOpenChromDnase cell=Melano" -setVars="controlId=generic_male" Affected 7 row(s) in hg19.metaDb_tdreszer # should be male though replicates were mixed! Change labVerion, controlId and cv.ra mdbPrint hg19 -vars="composite=wgEncodeOpenChromDnase cell=HSMM% labVersion=%generic_female" | grep labVersion labVersion fseq v 1.84, iff_generic_female labVersion fseq v 1.84, iff_generic_female mdbUpdate hg19 -vars="composite=wgEncodeOpenChromDnase cell=HSMM% labVersion=%generic_female" -var=labVersion -val="fseq v 1.84, iff_generic_male" Affected 2 row(s) in hg19.metaDb_tdreszer mdbUpdate hg19 -vars="composite=wgEncodeOpenChromDnase cell=HSMM" -setVars="controlId=generic_male" Affected 6 row(s) in hg19.metaDb_tdreszer mdbUpdate hg19 -vars="composite=wgEncodeOpenChromDnase cell=HSMMtube" -setVars="controlId=generic_male" Affected 6 row(s) in hg19.metaDb_tdreszer Should be F in cv and needs resubmission?? mdbPrint hg19 -vars="composite=wgEncodeOpenChromFaire cell=NHBE labVersion=%generic_male" | grep labVersion labVersion fseq v 1.84, iff_generic_male mdbUpdate hg19 -vars="composite=wgEncodeOpenChromFaire cell=NHBE labVersion=%generic_male" -var=labVersion -val="fseq v 1.84, iff_generic_female" Affected 1 row(s) in hg19.metaDb_tdreszer mdbUpdate hg19 -vars="composite=wgEncodeOpenChromFaire cell=NHBE" -setVars="controlId=generic_female" Affected 7 row(s) in hg19.metaDb_tdreszer # Oops: mdbUpdate hg19 -vars="composite=wgEncodeOpenChromFaire cell=NHBE labVersion=%generic_female" -var=labVersion -val="fseq v 1.84, iff_generic_male, should have been female" Affected 1 row(s) in hg19.metaDb_tdreszer mdbUpdate hg19 -vars="composite=wgEncodeOpenChromFaire cell=NHBE" -setVars="controlId=generic_male" Affected 7 row(s) in hg19.metaDb_tdreszer # FAIRE correct need to change labVersion and controlId to male NOTE: DNase was incorrectly submitted Need resubmission?? mdbPrint hg19 -vars="composite=wgEncodeOpenChromFaire cell=Medullo labVersion=%generic_female" | grep labVersion labVersion fseq v 1.84, iff_generic_female mdbUpdate hg19 -vars="composite=wgEncodeOpenChromFaire cell=Medullo labVersion=%generic_female" -var=labVersion -val="fseq v 1.84, iff_generic_male" Affected 1 row(s) in hg19.metaDb_tdreszer mdbUpdate hg19 -vars="composite=wgEncodeOpenChromFaire cell=Medullo" -setVars="controlId=generic_male" Affected 7 row(s) in hg19.metaDb_tdreszer mdbPrint hg19 -vars="composite=wgEncodeOpenChromDnase cell=Medullo labVersion=%generic_female" | grep labVersion labVersion fseq v 1.84, iff_generic_female mdbUpdate hg19 -vars="composite=wgEncodeOpenChromDnase cell=Medullo labVersion=%generic_female" -var=labVersion -val="fseq v 1.84, iff_generic_female, should have been male" Affected 1 row(s) in hg19.metaDb_tdreszer And one cell line we have marked as female your labVersion reports using generic_male Myometr # Check in changes: cd .. {hg19/metaDb/alpha} mdbPrint hg19 -vars="composite=wgEncodeOpenChromChip" > wgEncodeOpenChromChip.ra gold wgEncodeOpenChromChip.ra # identical mdbPrint hg19 -vars="composite=wgEncodeOpenChromDnase" > wgEncodeOpenChromDnase.ra gold wgEncodeOpenChromDnase.ra mdbPrint hg19 -vars="composite=wgEncodeOpenChromFaire" > wgEncodeOpenChromFaire.ra gold wgEncodeOpenChromFaire.ra git: up, add, ci, up, push cd ../../../../ (trackDb) make DBS=hg19; make alpha DBS=hg19 ## Will update according to labVersion until Terry reports back. ## mdbUpdate hg19 -vars="composite=wgEncodeOpenChromDnase cell=Myometr" -setVars="controlId=generic_male" ### Currently unresolved with Terry: 1) controlId v. labVersion discrepencies - Revoke DNase/Medulo ? - Revoke FAIRE/NHBE ? - What up Myometr - Verify that cv.ra is updated 2) Description of compo tracks 3) hgc (and hgTrackUi filtering) of combo tracks 4) Validation docs by cell 2011-01-26 More gender ambiguities ================================== - Myometr Terry: This is female and we processed as female, but incorrectly reported generic_male. # should be female: Change labVerion, controlId and cv.ra mdbPrint hg19 -vars="composite=wgEncodeOpenChromDnase cell=Myometr labVersion=%generic_male" | grep labVersion labVersion fseq v 1.84, iff_generic_male mdbUpdate hg19 -vars="composite=wgEncodeOpenChromDnase cell=Myometr labVersion=%generic_male" -var=labVersion -val="fseq v 1.84, iff_generic_female" mdbUpdate hg19 -vars="composite=wgEncodeOpenChromDnase cell=Myometr" -setVars="controlId=generic_female" Affected 5 row(s) in hg19.metaDb_tdreszer ## Myometr done. ### HSMM, HSMMtube, Hepatocytes, iPS, PanIsletD are not M or F but mixed! Resolution: cv change to 'B' for both. ### AoSMC is male (according to Greg). No changes in mdb. Need to change cv.ra ### NHBE - drop chrY Resolution: female in cv, labVersion should say male. Sigs and Peak should say male. fastqs/bams female, No changes to data. ### Medullo - DNase missing chrY Resolution: male in cv, labVersion should say female. Sigs and Peak should say female. fastqs/bams male, No changes to data. ### Hepatocytes - DNase missing chrY Resolution: male in cv, labVersion should say female. Sigs and Peak should say female. fastqs/bams male, No chaanges to data. ### Release note?? # In cv: AoSMC - M CLL - F Chorion - F HMEC - F HTR8svn - F Osteobl - F NHBE - F Melano - U Astrocy - U Ambiguous: Hepatocytes - Mixed iPS - Male (combined two males and one female) PanIsletD - Male (combined two males and one female) pHTE - Male (combined one male and one undetermined) ### To be changed in cv: AoSMC - M Hepatocytes - M/B Mixed iPS - M/B Mixed (combined two males and one female) PanIsletD - M/B Mixed (combined two males and one female) pHTE - M/B Mixed (combined one male and one undetermined) 2011-01-27 Fix dataTypes ======================== mdbPrint hg19 -vars="composite=wgEncodeOpenChromChip" | grep dataType | sort | uniq dataType ChIP-seq dataType ChipSeq mdbPrint hg19 -vars="composite=wgEncodeOpenChromDnase" | grep dataType | sort | uniq dataType DNase-seq dataType DnaseSeq mdbPrint hg19 -vars="composite=wgEncodeOpenChromFaire" | grep dataType | sort | uniq dataType FAIRE-seq dataType FaireSeq mdbUpdate hg19 -vars="composite=wgEncodeOpenChromChip dataType!=ChipSeq" -setVars="dataType=ChipSeq" Affected 7 row(s) in hg19.metaDb_tdreszer mdbUpdate hg19 -vars="composite=wgEncodeOpenChromDnase dataType!=DnaseSeq" -setVars="dataType=DnaseSeq" Affected 40 row(s) in hg19.metaDb_tdreszer mdbUpdate hg19 -vars="composite=wgEncodeOpenChromFaire dataType!=FaireSeq" -setVars="dataType=FaireSeq" Affected 14 row(s) in hg19.metaDb_tdreszer mdbPrint hg19 -vars="composite=wgEncodeOpenChromChip" | grep dataType | sort | uniq objects:275 vars:5366 dataType ChipSeq mdbPrint hg19 -vars="composite=wgEncodeOpenChromDnase" | grep dataType | sort | uniq objects:326 vars:5855 dataType DnaseSeq mdbPrint hg19 -vars="composite=wgEncodeOpenChromFaire" | grep dataType | sort | uniq objects:180 vars:3120 dataType FaireSeq ## Update bams lab version for two cross-gender experiments: mdbPrint hg19 -vars="composite=wgEncodeOpenChromDnase labVersion=%should%" | grep cell | sort | uniq Using table named 'hg19.metaDb_tdreszer'. cell Hepatocytes cell Medullo mdbPrint hg19 -vars="composite=wgEncodeOpenChromDnase labVersion=%should% view=RawData" | grep labVersion objects:4 vars:66 labVersion input was generic_female (should have been male) labVersion input was generic_female (should have been male) labVersion input was generic_female (should have been male) labVersion input was generic_female (should have been male) mdbUpdate hg19 -vars="composite=wgEncodeOpenChromDnase labVersion=%should% view=RawData" -var=labVersion -val="aligned to female and input was generic_female (should have been male)" -test Affected 4 row(s) in hg19.metaDb_tdreszer ## Revoke FAIRE/NHBE mdbPrint hg19 -vars="composite=wgEncodeOpenChromFaire labVersion=%should%" | grep cell | sort | uniq cell NHBE mdbPrint hg19 -vars="composite=wgEncodeOpenChromFaire labVersion=%should%" | grep subId | sort | uniq subId 1574, Alignments, Base_Overlap_Signal, Peaks, Signal subId 3153, RawData Can revoke 1574 and leave fastqs! Do this by hand, since 1574 may have had fastqs which were resubmitted. hgsql hg19 show tables like "wgEncodeOpenChromFaireNhbe%"; | wgEncodeOpenChromFaireNhbeBaseOverlapSignal | | wgEncodeOpenChromFaireNhbePk | | wgEncodeOpenChromFaireNhbeSig | drop table wgEncodeOpenChromFaireNhbeBaseOverlapSignal; drop table wgEncodeOpenChromFaireNhbePk; drop table wgEncodeOpenChromFaireNhbeSig; exit cd {downloads19}/wgEncodeOpenChromFaire ll wgEncodeOpenChromFaireNhbe* -rw-rw-r-- 1 braney protein 2019197467 Jul 24 2010 wgEncodeOpenChromFaireNhbeAlnRep1.bam -rw-rw-r-- 1 braney protein 6768496 Jul 24 2010 wgEncodeOpenChromFaireNhbeAlnRep1.bam.bai -rw-rw-r-- 1 braney protein 102 Aug 2 16:56 wgEncodeOpenChromFaireNhbeAlnRep1.bam.bai.md5sum -rw-rw-r-- 1 braney protein 98 Aug 2 17:14 wgEncodeOpenChromFaireNhbeAlnRep1.bam.md5sum -rw-rw-r-- 1 braney protein 2115333089 Jul 24 2010 wgEncodeOpenChromFaireNhbeAlnRep2.bam -rw-rw-r-- 1 braney protein 6803696 Jul 24 2010 wgEncodeOpenChromFaireNhbeAlnRep2.bam.bai -rw-rw-r-- 1 braney protein 102 Aug 2 16:56 wgEncodeOpenChromFaireNhbeAlnRep2.bam.bai.md5sum -rw-rw-r-- 1 braney protein 98 Aug 2 17:15 wgEncodeOpenChromFaireNhbeAlnRep2.bam.md5sum -rw-rw-r-- 1 braney protein 726811915 Jul 24 2010 wgEncodeOpenChromFaireNhbeBaseOverlapSignal.bigWig -rw-rw-r-- 1 braney protein 111 Aug 2 17:02 wgEncodeOpenChromFaireNhbeBaseOverlapSignal.bigWig.md5sum -rw-rw-r-- 3 qateam protein 4191370 Jun 17 2010 wgEncodeOpenChromFaireNhbePk.narrowPeak.gz -rw-rw-r-- 1 braney protein 103 Aug 2 16:56 wgEncodeOpenChromFaireNhbePk.narrowPeak.gz.md5sum -rw-rw-r-- 1 encodeteam protein 1799213535 Jan 7 19:09 wgEncodeOpenChromFaireNhbeRawDataRep1.fastq.gz -rw-rw-r-- 1 encodeteam protein 1874957836 Jan 7 17:53 wgEncodeOpenChromFaireNhbeRawDataRep2.fastq.gz -rw-rw-r-- 1 braney protein 1493269395 Jul 24 2010 wgEncodeOpenChromFaireNhbeSig.bigWig -rw-rw-r-- 1 braney protein 97 Aug 2 17:10 wgEncodeOpenChromFaireNhbeSig.bigWig.md5sum mv wgEncodeOpenChromFaireNhbeAln* ../obsolete/wgEncodeOpenChromFaire mv wgEncodeOpenChromFaireNhbeBase* ../obsolete/wgEncodeOpenChromFaire mv wgEncodeOpenChromFaireNhbePk* ../obsolete/wgEncodeOpenChromFaire mv wgEncodeOpenChromFaireNhbeSig* ../obsolete/wgEncodeOpenChromFaire ll wgEncodeOpenChromFaireNhbe* -rw-rw-r-- 1 encodeteam protein 1799213535 Jan 7 19:09 wgEncodeOpenChromFaireNhbeRawDataRep1.fastq.gz -rw-rw-r-- 1 encodeteam protein 1874957836 Jan 7 17:53 wgEncodeOpenChromFaireNhbeRawDataRep2.fastq.gz cd /gbdb/hg19/bbi ll wgEncodeOpenChromFaireNhbe* lrwxrwxrwx 1 braney protein 121 Aug 4 20:32 wgEncodeOpenChromFaireNhbeBaseOverlapSignal.bigWig -> /hive/groups/encode/dcc/pipeline/downloads/hg19/wgEncodeOpenChromFaire/wgEncodeOpenChromFaireNhbeBaseOverlapSignal.bigWig lrwxrwxrwx 1 braney protein 107 Aug 4 20:32 wgEncodeOpenChromFaireNhbeSig.bigWig -> /hive/groups/encode/dcc/pipeline/downloads/hg19/wgEncodeOpenChromFaire/wgEncodeOpenChromFaireNhbeSig.bigWig # both broken as expected rm wgEncodeOpenChromFaireNhbeBaseOverlapSignal.bigWig rm wgEncodeOpenChromFaireNhbeSig.bigWig ll wgEncodeOpenChromFaireNhbe* ls: wgEncodeOpenChromFaireNhbe*: No such file or directory mdbPrint hg19 -vars="composite=wgEncodeOpenChromFaire cell=NHBE" -count 7 objects mdbPrint hg19 -vars="composite=wgEncodeOpenChromFaire cell=NHBE view=Alignments" -count 2 objects 38 variables mdbPrint hg19 -vars="composite=wgEncodeOpenChromFaire cell=NHBE view=Base_Overlap_Signal" -count 1 object 18 variables mdbPrint hg19 -vars="composite=wgEncodeOpenChromFaire cell=NHBE view=Peaks" -count 1 object 18 variables mdbPrint hg19 -vars="composite=wgEncodeOpenChromFaire cell=NHBE view=Signal" -count 1 object 18 variables mdbUpdate hg19 -vars="composite=wgEncodeOpenChromFaire cell=NHBE view=Alignments" -delete Affected 38 row(s) in hg19.metaDb_tdreszer mdbUpdate hg19 -vars="composite=wgEncodeOpenChromFaire cell=NHBE view=Base_Overlap_Signal" -delete Affected 18 row(s) in hg19.metaDb_tdreszer mdbUpdate hg19 -vars="composite=wgEncodeOpenChromFaire cell=NHBE view=Peaks" -delete Affected 18 row(s) in hg19.metaDb_tdreszer mdbUpdate hg19 -vars="composite=wgEncodeOpenChromFaire cell=NHBE view=Signal" -delete Affected 18 row(s) in hg19.metaDb_tdreszer mdbPrint hg19 -vars="composite=wgEncodeOpenChromFaire cell=NHBE" | grep view 2 objects view RawData view RawData cd {tdb}/hg19 e wgEncodeOpenChromFaire.ra # remove NHBE stanzas gold wgEncodeOpenChromFaire.ra # Check in changes: gold wgEncodeOpenChromFaire.ra gadd wgEncodeOpenChromFaire.ra cd .. {hg19/metaDb/alpha} mdbPrint hg19 -vars="composite=wgEncodeOpenChromChip" > wgEncodeOpenChromChip.ra gold wgEncodeOpenChromChip.ra mdbPrint hg19 -vars="composite=wgEncodeOpenChromDnase" > wgEncodeOpenChromDnase.ra gold wgEncodeOpenChromDnase.ra mdbPrint hg19 -vars="composite=wgEncodeOpenChromFaire" > wgEncodeOpenChromFaire.ra gold wgEncodeOpenChromFaire.ra git: up, add, ci, up, push cd ../../../../ (trackDb) make DBS=hg19; make alpha DBS=hg19 hgsql encpipeline_prod select id,name,status from projects where id = 1574; | 1574 | DNCT UNC FAIRE-Seq NHBE 20100616 | displayed | update projects set status = "revoked" where id = 1574; Rows matched: 1 Changed: 1 Warnings: 0 exit cd {downloads19}/wgEncodeOpenChromChip encodeDownloadsPage.pl -db=hg19 index.html # 352 files. All have metadata # 352 found in hgFileUi cd {downloads19}/wgEncodeOpenChromDnase encodeDownloadsPage.pl -db=hg19 index.html # 435 files. All have metadata # 435 found in hgFileUi cd {downloads19}/wgEncodeOpenChromFaire encodeDownloadsPage.pl -db=hg19 index.html # 224 files. All have metadata # 224 found in hgFileUi ### Next step: prepare Chip,Dnase and Faire for release cd {downloads19}/wgEncodeOpenChromChip encodeDownloadsPage.pl -db=hg19 -checksum index.html & cd {downloads19}/wgEncodeOpenChromDnase encodeDownloadsPage.pl -db=hg19 -checksum index.html & cd {downloads19}/wgEncodeOpenChromFaire encodeDownloadsPage.pl -db=hg19 -checksum index.html & 2011-02-02 Open Chrom Synth should see extraFields in hgc. ========================================================== Added extraFields setting to trackDb, tagTypes and hgc.c code. wgEncodeOpenChromSynthGm12878Pk change column pvalue pValue float unsigned; Query OK, 231402 rows affected (9.18 sec) alter table wgEncodeOpenChromSynthH1hescPk change column pvalue pValue float unsigned; Query OK, 254605 rows affected (9.18 sec) alter table wgEncodeOpenChromSynthHelas3Pk change column pvalue pValue float unsigned; Query OK, 258525 rows affected (9.18 sec) alter table wgEncodeOpenChromSynthHepg2Pk change column pvalue pValue float unsigned NOT NULL; Query OK, 193323 rows affected (6.48 sec) alter table wgEncodeOpenChromSynthHuvecPk change column pvalue pValue float unsigned NOT NULL; Query OK, 280454 rows affected (9.93 sec) alter table wgEncodeOpenChromSynthK562Pk change column pvalue pValue float unsigned NOT NULL; Query OK, 277149 rows affected (9.72 sec) alter table wgEncodeOpenChromSynthNhekPk change column pvalue pValue float unsigned NOT NULL; Query OK, 276778 rows affected (9.89 sec) 2011-02-09 Package up 4 composites for QA ========================================= cd (downloadsHg19)/wgEncodeOpenChromSynth mkdir release1 cd release1/ cp ../index.html . cp ../files.txt . cp ../md5sum.txt . ln ../*.gz . ll ../ | grep -v \.gz$ | grep -v \.html | grep -v \.txt lrwxrwxrwx 1 tdreszer protein 38 Jan 19 14:58 supplemental -> ../wgEncodeOpenChromDnase/supplemental # Need suplemental ! ln -sf ../../wgEncodeOpenChromDnase/supplemental supplemental ls -1 | wl 11 # expect 7 + 3 + 1 = 11 cd .. ~/bin/scripts/encodeMkChangeNotes hg19 release1 - > release1/wgEncodeOpenChromSynth.release1.notes cp release1/wgEncodeOpenChromSynth.release1.notes ~/kent/src/hg/makeDb/doc/encodeDccHg19/ cd ../wgEncodeOpenChromChip/ mkdir release1 cd release1/ cp ../index.html . cp ../files.txt . cp ../md5sum.txt . ln -sf ../../wgEncodeOpenChromDnase/supplemental supplemental ln ../*.gz . ln ../*.bam . ln ../*.bam.bai . ln ../*.bigWig . # Don't link bigWig.md5sum's ll ../ | grep -v \.gz$ | grep -v \.bam* | grep -v \.bigWig | grep -v \.md5sum | grep -v \.html | grep -v \.txt # Nothing missing ls -1 | wl 356 # expect 352 + 3 + 1 = 356 cd .. ~/bin/scripts/encodeMkChangeNotes hg19 release1 - > release1/wgEncodeOpenChromChip.release1.notes could not find gbdb path in table hg19.wgEncodeOpenChromChipMcf7CmycVehAlnRep1 table wgEncodeOpenChromChipMcf7CmycVehAlnRep1 does not exist, from filetype bam ... # Okay, no bam tables for this composite! e release1/wgEncodeOpenChrom*.release1.notes # remove BAM warnings that are not relevant cp release1/wgEncodeOpenChrom*.release1.notes ~/kent/src/hg/makeDb/doc/encodeDccHg19/ cd ../wgEncodeOpenChromDnase/ mkdir release1 cd release1/ cp ../index.html . cp ../files.txt . cp ../md5sum.txt . ln -sf ../supplemental supplemental ln ../*.gz . ln ../*.bam . ln ../*.bam.bai . ln ../*.bigWig . ll ../ | grep -v \.gz$ | grep -v \.bam* | grep -v \.bigWig | grep -v \.md5sum | grep -v \.html | grep -v \.txt # Nothing missing ls -1 | wl 439 # expect 435 + 3 + 1 = 439 cd .. ~/bin/scripts/encodeMkChangeNotes hg19 release1 - > release1/wgEncodeOpenChromDnase.release1.notes e release1/wgEncodeOpenChrom*.release1.notes # remove BAM warnings that are not relevant cp release1/wgEncodeOpenChrom*.release1.notes ~/kent/src/hg/makeDb/doc/encodeDccHg19/ cd ../wgEncodeOpenChromFaire/ mkdir release1 cd release1/ cp ../index.html . cp ../files.txt . cp ../md5sum.txt . ln -sf ../../wgEncodeOpenChromDnase/supplemental supplemental ln ../*.gz . ln ../*.bam . ln ../*.bam.bai . ln ../*.bigWig . ll ../ | grep -v \.gz$ | grep -v \.bam* | grep -v \.bigWig | grep -v \.md5sum | grep -v \.html | grep -v \.txt # Nothing missing ls -1 | wl 228 # expect 224 + 3 + 1 = 228 cd .. ~/bin/scripts/encodeMkChangeNotes hg19 release1 - > release1/wgEncodeOpenChromFaire.release1.notes e release1/wgEncodeOpenChrom*.release1.notes # remove BAM warnings that are not relevant cp release1/wgEncodeOpenChrom*.release1.notes ~/kent/src/hg/makeDb/doc/encodeDccHg19/ cd ~/kent/src/hg/makeDb/doc/encodeDccHg19/ gadd wgEncodeOpenChrom*.release1.notes gci -m "Readying Open Chrom composites for QA" git up, push y=hg18 n=hg19 Dnase FAIRE CTCF c-Myc Pol2 Inp GM12878 Tier1 y y y y y y H1-hESC Tier1 y y y y y K562 Tier1 y y y y y y K562 NaBu n K562 urea n HeLa-S3 Tier2 y y y y y y HeLa-S3 IFNα y y HeLa-S3 IFNγ y HepG2 Tier2 y y y y y y HUVEC Tier2 y y y y y y A549 n n Astrocy n AoSMC Serum Free y AoSMC none n Chorion y Cll n Fibrobl y n n FibroP y Gliobla n n n n n GM12891 y n y GM12892 y n y GM18507 y y GM19238 y y GM19239 y y y GM19240 y y H9-hESC y Hepatocytes n HMEC n HPDE6-E6E7 n HSMM y HSMMtube y HTR8svn n n Huh-7 n Huh-7.5 n iPS n LNCaP n LNCaP androgen n LHSR y? y LHSR androgen y? y MCF-7 y y y n y MCF-7 Hypox n MCF-7 estrogen n n MCF-7 vehiclen n n Medullo y n Melano y Monocytes-CD14+ n Myometr y NHBE y NHEK y y y Osteobl n PA-TU-8988T n PanIslets y y PanIsletD n pHTE n ProgFib y y y y Stellate n T-47D n Urothelia n n Urothelia UT189 n n /cluster/data/encode/pipeline/bin/encodeStatus.pl 1517 approved /cluster/data/encode/pipeline/bin/encodeStatus.pl 1518 approved /cluster/data/encode/pipeline/bin/encodeStatus.pl 1515 approved /cluster/data/encode/pipeline/bin/encodeStatus.pl 1516 approved /cluster/data/encode/pipeline/bin/encodeStatus.pl 1606 approved /cluster/data/encode/pipeline/bin/encodeStatus.pl 1607 approved /cluster/data/encode/pipeline/bin/encodeStatus.pl 1608 approved /cluster/data/encode/pipeline/bin/encodeStatus.pl 1609 approved 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Notice origAssembly ion all of these cd {tdb}/hg19 grep -v origAssembly wgEncodeOpenChromChip.ra > wgEncodeOpenChromChip.ra2 grep -v origAssembly wgEncodeOpenChromDnase.ra > wgEncodeOpenChromDnase.ra2 grep -v origAssembly wgEncodeOpenChromFaire.ra > wgEncodeOpenChromFaire.ra2 cp wgEncodeOpenChromChip.ra wgEncodeOpenChromChip.ra.bak cp wgEncodeOpenChromDnase.ra wgEncodeOpenChromDnase.ra.bak cp wgEncodeOpenChromFaire.ra wgEncodeOpenChromFaire.ra.bak mv wgEncodeOpenChromChip.ra2 wgEncodeOpenChromChip.ra mv wgEncodeOpenChromDnase.ra2 wgEncodeOpenChromDnase.ra mv wgEncodeOpenChromFaire.ra2 wgEncodeOpenChromFaire.ra gdiff wgEncodeOpenChromChip.ra | grep -v origAssembly | grep -v \@\@ gdiff wgEncodeOpenChromDnase.ra | grep -v origAssembly | grep -v \@\@ gdiff wgEncodeOpenChromFaire.ra | grep -v origAssembly | grep -v \@\@ git up, add, ci, up, push cp wgEncodeOpenChromSynth.ra wgEncodeOpenChromSynth.ra.bak grep -v origAssembly wgEncodeOpenChromSynth.ra.bak > wgEncodeOpenChromSynth.ra gdiff wgEncodeOpenChromSynth.ra | grep -v origAssembly | grep -v \@\@ encodePatchTdb /hive/groups/encode/dcc/pipeline/encpipeline_prod/3507/out/trackDb.ra wgEncodeOpenChromFaire.ra # now metadata cd {pip}/3507 e out/mdb.txt # no change needed mdbUpdate hg19 out/mdb.txt Read 5 metadata objects from hg19 Affected 80 row(s) in hg19.metaDb_tdreszer # Check in changes: cd .. {hg19/metaDb/alpha} mdbPrint hg19 -vars="composite=wgEncodeOpenChromFaire" > wgEncodeOpenChromFaire.ra gold wgEncodeOpenChromFaire.ra git: up, add, ci, up, push # for mdb cd ../../../../ (trackDb) make DBS=hg19; # examine in browser git: up, add, ci, up, push # for trackDb make alpha DBS=hg19 mdbPrint hg19 -vars="composite=wgEncodeOpenChromFaire cell=A459" | grep labVersion | sort | uniq labVersion fseq v 1.84, iff_generic_male mdbUpdate hg19 -vars="composite=wgEncodeOpenChromFaire cell=A549" -setVars="controlId=generic_male" cd {downloadsHg19}/wgEncodeOpenChromFaire/ ll wgEncodeOpenChromFaireNhbe* Full set encodeDownloadsPage.pl -db=hg19 index.html # 231 files. All have metadata # 231 found in hgFileUi # dateSubmitted is wrong. Should be original date submitted cd {tdb}/hg19/metaDb/alpha e wgEncodeOpenChromFaire.ra mdbUpdate hg19 wgEncodeOpenChromFaire.ra Using table named 'hg19.metaDb_tdreszer'. Read 179 metadata objects from hg19 Affected 17 row(s) in hg19.metaDb_tdreszer git: up, add, ci, up, push # for mdb cd {downloadsHg19}/wgEncodeOpenChromFaire/ ll wgEncodeOpenChromFaireNhbe* Full set encodeDownloadsPage.pl -db=hg19 index.html # 231 files. All have CORRECT metadata # 231 found in hgFileUi /cluster/data/encode/pipeline/bin/encodeStatus.pl 3507 displayed cd release1/ ln ../wgEncodeOpenChromFaireNhbe* . # two errors on fastq's already there ls -1 wgEncodeOpenChromFaireNhbe* . # all are there cp ../index.html . cp ../files.txt . # need to update md5sum.txt but don't want to redo all md5sums cd .. ls -1 wgEncodeOpenChromFaireNhbe* . | grep -v fastq md5sum wgEncodeOpenChromFaireNhbeAlnRep1.bam > tmp.txt md5sum wgEncodeOpenChromFaireNhbeAlnRep1.bam.bai >> tmp.txt md5sum wgEncodeOpenChromFaireNhbeAlnRep2.bam >> tmp.txt md5sum wgEncodeOpenChromFaireNhbeAlnRep2.bam.bai >> tmp.txt md5sum wgEncodeOpenChromFaireNhbeBaseOverlapSignal.bigWig >> tmp.txt md5sum wgEncodeOpenChromFaireNhbePk.narrowPeak.gz >> tmp.txt md5sum wgEncodeOpenChromFaireNhbeSig.bigWig >> tmp.txt e tmp.txt md5sum.txt # add these md5sums to the md5sum file cp md5sum.txt release1/ rm tmp.txt /cluster/data/encode/pipeline/bin/encodeStatus.pl 3507 approved cd {docsHg19} e wgEncodeOpenChromFaire.release1.notes # add in the tables and files manually # Update pushQ /cluster/data/encode/pipeline/bin/encodeStatus.pl 3507 reviewing 2011-02-16 Update missing origAsembly as per Katrina's request ============================================================== mdbUpdate hg19 table=metaDb_tdreszer -vars="composite=wgEncodeOpenChromChip origAssembly!=" -setVars="origAssembly=hg19" Affected 62 row(s) in hg19.metaDb_tdreszer mdbUpdate hg19 table=metaDb_tdreszer -vars="composite=wgEncodeOpenChromDnase origAssembly!=" -setVars="origAssembly=hg19" Affected 131 row(s) in hg19.metaDb_tdreszer mdbUpdate hg19 table=metaDb_tdreszer -vars="composite=wgEncodeOpenChromFaire origAssembly!=" -setVars="origAssembly=hg19" Affected 86 row(s) in hg19.metaDb_tdreszer mdbUpdate hg19 table=metaDb_tdreszer -vars="composite=wgEncodeOpenChromSynth origAssembly!=" -setVars="origAssembly=hg19" -test Command would affected 0 row(s) in hg19.metaDb_tdreszer # check in mdbPrint hg19 -composite=wgEncodeOpenChromChip > wgEncodeOpenChromChip.ra objects:271 vars:5354 mdbPrint hg19 -composite=wgEncodeOpenChromDnase > wgEncodeOpenChromDnase.ra objects:326 vars:5986 mdbPrint hg19 -composite=wgEncodeOpenChromFaire > wgEncodeOpenChromFaire.ra objects:179 vars:3184 gold wgEncodeOpenChromChip.ra gold wgEncodeOpenChromDnase.ra gold wgEncodeOpenChromFaire.ra git up, add, ci, up, push make DBS=hg19; alpha cd {downloadsHg19}/wgEncodeOpenChromChip encodeDownloadsPage.pl -db=hg19 index.html cp index.html release1/ cp files.txt release1/ cd {downloadsHg19}/wgEncodeOpenChromDnase encodeDownloadsPage.pl -db=hg19 index.html cd {downloadsHg19}/wgEncodeOpenChromFaire encodeDownloadsPage.pl -db=hg19 index.html 2011-02-25 Accounting for Kate ============================== mdbUpdate hg19 -obj=wgEncodeOpenChromDnase -setVars="objType=composite composite=wgEncodeOpenChromDnase expVars=lab,dataType,cell,treatment" ~/bin/x86_64/mdbPrint hg19 -composite=wgEncodeOpenChromDnase -encodeExp Composite 'wgEncodeOpenChromDnase' has 47 recognizable experiments with 47 missing an expId. ~/bin/x86_64/mdbPrint hg19 -vars="composite=wgEncodeOpenChromDnase view=Signal" -var=dataVersion -val="ENCODE Jan 2011%" -encodeExp Composite 'wgEncodeOpenChromDnase' has 21 recognizable experiments with 21 missing an expId. mdbPrint hg19 -composite=wgEncodeOpenChromDnase | grep subId | sort | uniq | wl 66 mdbPrint hg19 -composite=wgEncodeOpenChromDnase -var=dataVersion -val="ENCODE Jan 2011%" | grep subId | sort | uniq | wl 21 mdbUpdate hg19 -obj=wgEncodeOpenChromFaire -setVars="objType=composite composite=wgEncodeOpenChromFaire expVars=lab,dataType,cell,treatment" ~/bin/x86_64/mdbPrint hg19 -composite=wgEncodeOpenChromFaire -encodeExp Composite 'wgEncodeOpenChromFaire' has 26 recognizable experiments with 26 missing an expId. ~/bin/x86_64/mdbPrint hg19 -vars="composite=wgEncodeOpenChromFaire view=Signal" -var=dataVersion -val="ENCODE Jan 2011%" -encodeExp Composite 'wgEncodeOpenChromFaire' has 12 recognizable experiments with 12 missing an expId. ~/bin/x86_64/mdbPrint hg19 -vars="composite=wgEncodeOpenChromFaire view=Signal" -var=dataVersion -val="post ENCODE Jan 2011%" -encodeExp Composite 'wgEncodeOpenChromFaire' has 1 recognizable experiment with 1 missing an expId. mdbPrint hg19 -composite=wgEncodeOpenChromFaire | grep subId | sort | uniq | wl 30 mdbPrint hg19 -composite=wgEncodeOpenChromFaire -var=dataVersion -val="ENCODE Jan 2011%" | grep subId | sort | uniq | wl 13 mdbPrint hg19 -composite=wgEncodeOpenChromFaire -var=dataVersion -val="post ENCODE Jan 2011%" | grep subId | sort | uniq | wl 1 mdbUpdate hg19 -obj=wgEncodeOpenChromChip -setVars="objType=composite composite=wgEncodeOpenChromChip expVars=lab,dataType,cell,treatment,antibody" ~/bin/x86_64/mdbPrint hg19 -composite=wgEncodeOpenChromChip -encodeExp Composite 'wgEncodeOpenChromChip' has 46 recognizable experiments with 46 missing an expId. ~/bin/x86_64/mdbPrint hg19 -vars="composite=wgEncodeOpenChromChip view=Signal" -var=dataVersion -val="ENCODE Jan 2011%" -encodeExp ~/bin/x86_64/mdbPrint hg19 -composite=wgEncodeOpenChromChip -var=dataVersion -val="ENCODE Jan 2011%" -encodeExp Composite 'wgEncodeOpenChromChip' has 11 recognizable experiments with 11 missing an expId. mdbPrint hg19 -composite=wgEncodeOpenChromChip | grep subId | sort | uniq | wl 77 mdbPrint hg19 -composite=wgEncodeOpenChromChip -var=dataVersion -val="ENCODE Jan 2011%" | grep subId | sort | uniq | wl 12 2011-02-25 Brian converted bigWigs ================================== cd {downloadsHg19}/wgEncodeOpenChromChip ll wgEncodeOpenChromChipFibroblCtcfBaseOverlapSignal.bigWig -rw-rw-r-- 3 encodeteam protein 435027785 Oct 11 13:51 wgEncodeOpenChromChipFibroblCtcfBaseOverlapSignal.bigWig ## There are three locations: # {downloadsHg19}/wgEncodeOpenChromChip # {downloadsHg19}/wgEncodeOpenChromChip/release1 # submission dir. Leave that one alone! ll /gbdb/hg19/bbi/wgEncodeOpenChromChipFibroblCtcfBaseOverlapSignal.bigWig /gbdb/hg19/bbi/wgEncodeOpenChromChipFibroblCtcfBaseOverlapSignal.bigWig -> /usr/local/apache/htdocs-hgdownload/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipFibroblCtcfBaseOverlapSignal.bigWig ## Don't forget to make sure this is still intact # Lonk them to obsolete so nothing gets lost cd ../obsolete/wgEncodeOpenChromChip ln ../../wgEncodeOpenChromChip/*.bigWig . ll *.bigWig | wl 80 # Why 80 and not 75? ls -1 *.bigWig | sort > tmp.txt # same thing for new bigWigs kompare -c wgEncodeOpenChromChipGlioblaPol2BaseOverlapSignal.bigWig wgEncodeOpenChromChipGlioblaPol2Sig.bigWig wgEncodeOpenChromChipK562CtcfSig.bigWig wgEncodeOpenChromChipK562Pol2Sig.bigWig wgEncodeOpenChromChipMonocd14InputSig.bigWig cd ../../wgEncodeOpenChromChip/ mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromChip/wgEncodeOpenChromChipFibroblCtcfBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromChipFibroblCtcfBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromChip/wgEncodeOpenChromChipFibroblCtcfSig.bigWig.new.bigWig wgEncodeOpenChromChipFibroblCtcfSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromChip/wgEncodeOpenChromChipFibroblInputSig.bigWig.new.bigWig wgEncodeOpenChromChipFibroblInputSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromChip/wgEncodeOpenChromChipGlioblaCtcfBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromChipGlioblaCtcfBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromChip/wgEncodeOpenChromChipGlioblaCtcfSig.bigWig.new.bigWig wgEncodeOpenChromChipGlioblaCtcfSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromChip/wgEncodeOpenChromChipGlioblaInputSig.bigWig.new.bigWig wgEncodeOpenChromChipGlioblaInputSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromChip/wgEncodeOpenChromChipGm12878CmycBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromChipGm12878CmycBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromChip/wgEncodeOpenChromChipGm12878CmycSig.bigWig.new.bigWig wgEncodeOpenChromChipGm12878CmycSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromChip/wgEncodeOpenChromChipGm12878CtcfBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromChipGm12878CtcfBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromChip/wgEncodeOpenChromChipGm12878CtcfSig.bigWig.new.bigWig wgEncodeOpenChromChipGm12878CtcfSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromChip/wgEncodeOpenChromChipGm12878InputSig.bigWig.new.bigWig wgEncodeOpenChromChipGm12878InputSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromChip/wgEncodeOpenChromChipGm12878Pol2BaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromChipGm12878Pol2BaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromChip/wgEncodeOpenChromChipGm12878Pol2Sig.bigWig.new.bigWig wgEncodeOpenChromChipGm12878Pol2Sig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromChip/wgEncodeOpenChromChipGm12891CtcfBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromChipGm12891CtcfBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromChip/wgEncodeOpenChromChipGm12891CtcfSig.bigWig.new.bigWig wgEncodeOpenChromChipGm12891CtcfSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromChip/wgEncodeOpenChromChipGm12892CtcfBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromChipGm12892CtcfBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromChip/wgEncodeOpenChromChipGm12892CtcfSig.bigWig.new.bigWig wgEncodeOpenChromChipGm12892CtcfSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromChip/wgEncodeOpenChromChipGm19238CtcfBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromChipGm19238CtcfBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromChip/wgEncodeOpenChromChipGm19238CtcfSig.bigWig.new.bigWig wgEncodeOpenChromChipGm19238CtcfSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromChip/wgEncodeOpenChromChipGm19239CtcfBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromChipGm19239CtcfBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromChip/wgEncodeOpenChromChipGm19239CtcfSig.bigWig.new.bigWig wgEncodeOpenChromChipGm19239CtcfSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromChip/wgEncodeOpenChromChipGm19240CtcfBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromChipGm19240CtcfBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromChip/wgEncodeOpenChromChipGm19240CtcfSig.bigWig.new.bigWig wgEncodeOpenChromChipGm19240CtcfSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromChip/wgEncodeOpenChromChipH1hescCmycBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromChipH1hescCmycBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromChip/wgEncodeOpenChromChipH1hescCmycSig.bigWig.new.bigWig wgEncodeOpenChromChipH1hescCmycSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromChip/wgEncodeOpenChromChipH1hescCtcfBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromChipH1hescCtcfBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromChip/wgEncodeOpenChromChipH1hescCtcfSig.bigWig.new.bigWig wgEncodeOpenChromChipH1hescCtcfSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromChip/wgEncodeOpenChromChipH1hescPol2BaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromChipH1hescPol2BaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromChip/wgEncodeOpenChromChipH1hescPol2Sig.bigWig.new.bigWig wgEncodeOpenChromChipH1hescPol2Sig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromChip/wgEncodeOpenChromChipHelas3CmycBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromChipHelas3CmycBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromChip/wgEncodeOpenChromChipHelas3CmycSig.bigWig.new.bigWig wgEncodeOpenChromChipHelas3CmycSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromChip/wgEncodeOpenChromChipHelas3CtcfBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromChipHelas3CtcfBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromChip/wgEncodeOpenChromChipHelas3CtcfSig.bigWig.new.bigWig wgEncodeOpenChromChipHelas3CtcfSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromChip/wgEncodeOpenChromChipHelas3InputSig.bigWig.new.bigWig wgEncodeOpenChromChipHelas3InputSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromChip/wgEncodeOpenChromChipHelas3Pol2BaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromChipHelas3Pol2BaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromChip/wgEncodeOpenChromChipHelas3Pol2Sig.bigWig.new.bigWig wgEncodeOpenChromChipHelas3Pol2Sig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromChip/wgEncodeOpenChromChipHepg2CmycBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromChipHepg2CmycBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromChip/wgEncodeOpenChromChipHepg2CmycSig.bigWig.new.bigWig wgEncodeOpenChromChipHepg2CmycSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromChip/wgEncodeOpenChromChipHepg2CtcfBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromChipHepg2CtcfBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromChip/wgEncodeOpenChromChipHepg2CtcfSig.bigWig.new.bigWig wgEncodeOpenChromChipHepg2CtcfSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromChip/wgEncodeOpenChromChipHepg2InputSig.bigWig.new.bigWig wgEncodeOpenChromChipHepg2InputSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromChip/wgEncodeOpenChromChipHepg2Pol2BaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromChipHepg2Pol2BaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromChip/wgEncodeOpenChromChipHepg2Pol2Sig.bigWig.new.bigWig wgEncodeOpenChromChipHepg2Pol2Sig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromChip/wgEncodeOpenChromChipHuvecCmycBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromChipHuvecCmycBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromChip/wgEncodeOpenChromChipHuvecCmycSig.bigWig.new.bigWig wgEncodeOpenChromChipHuvecCmycSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromChip/wgEncodeOpenChromChipHuvecCtcfBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromChipHuvecCtcfBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromChip/wgEncodeOpenChromChipHuvecCtcfSig.bigWig.new.bigWig wgEncodeOpenChromChipHuvecCtcfSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromChip/wgEncodeOpenChromChipHuvecInputSig.bigWig.new.bigWig wgEncodeOpenChromChipHuvecInputSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromChip/wgEncodeOpenChromChipHuvecPol2BaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromChipHuvecPol2BaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromChip/wgEncodeOpenChromChipHuvecPol2Sig.bigWig.new.bigWig wgEncodeOpenChromChipHuvecPol2Sig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromChip/wgEncodeOpenChromChipK562CmycBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromChipK562CmycBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromChip/wgEncodeOpenChromChipK562CmycSig.bigWig.new.bigWig wgEncodeOpenChromChipK562CmycSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromChip/wgEncodeOpenChromChipK562CtcfBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromChipK562CtcfBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromChip/wgEncodeOpenChromChipK562InputSig.bigWig.new.bigWig wgEncodeOpenChromChipK562InputSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromChip/wgEncodeOpenChromChipK562Pol2BaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromChipK562Pol2BaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromChip/wgEncodeOpenChromChipMcf7CmycEstroBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromChipMcf7CmycEstroBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromChip/wgEncodeOpenChromChipMcf7CmycEstroSig.bigWig.new.bigWig wgEncodeOpenChromChipMcf7CmycEstroSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromChip/wgEncodeOpenChromChipMcf7CmycVehBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromChipMcf7CmycVehBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromChip/wgEncodeOpenChromChipMcf7CmycVehSig.bigWig.new.bigWig wgEncodeOpenChromChipMcf7CmycVehSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromChip/wgEncodeOpenChromChipMcf7CtcfBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromChipMcf7CtcfBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromChip/wgEncodeOpenChromChipMcf7CtcfEstroBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromChipMcf7CtcfEstroBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromChip/wgEncodeOpenChromChipMcf7CtcfEstroSig.bigWig.new.bigWig wgEncodeOpenChromChipMcf7CtcfEstroSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromChip/wgEncodeOpenChromChipMcf7CtcfSig.bigWig.new.bigWig wgEncodeOpenChromChipMcf7CtcfSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromChip/wgEncodeOpenChromChipMcf7CtcfVehBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromChipMcf7CtcfVehBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromChip/wgEncodeOpenChromChipMcf7CtcfVehSig.bigWig.new.bigWig wgEncodeOpenChromChipMcf7CtcfVehSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromChip/wgEncodeOpenChromChipMcf7InputSig.bigWig.new.bigWig wgEncodeOpenChromChipMcf7InputSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromChip/wgEncodeOpenChromChipMcf7Pol2BaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromChipMcf7Pol2BaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromChip/wgEncodeOpenChromChipMcf7Pol2Sig.bigWig.new.bigWig wgEncodeOpenChromChipMcf7Pol2Sig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromChip/wgEncodeOpenChromChipNhekCtcfBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromChipNhekCtcfBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromChip/wgEncodeOpenChromChipNhekCtcfSig.bigWig.new.bigWig wgEncodeOpenChromChipNhekCtcfSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromChip/wgEncodeOpenChromChipProgfibCtcfBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromChipProgfibCtcfBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromChip/wgEncodeOpenChromChipProgfibCtcfSig.bigWig.new.bigWig wgEncodeOpenChromChipProgfibCtcfSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromChip/wgEncodeOpenChromChipProgfibInputSig.bigWig.new.bigWig wgEncodeOpenChromChipProgfibInputSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromChip/wgEncodeOpenChromChipProgfibPol2BaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromChipProgfibPol2BaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromChip/wgEncodeOpenChromChipProgfibPol2Sig.bigWig.new.bigWig wgEncodeOpenChromChipProgfibPol2Sig.bigWig cd release1/ ln ../*.bigWig . ln: creating hard link `./wgEncodeOpenChromChipProgfibPol2Sig.bigWig' to `../wgEncodeOpenChromChipProgfibPol2Sig.bigWig': File exists ## Have to remove and then ln rm *.bigWig ln ../*.bigWig . ls -1 *.bigWig | wl 80 # Soft links okay? ll /gbdb/hg19/bbi/wgEncodeOpenChromChipFibroblCtcfBaseOverlapSignal.bigWig lrwxrwxrwx 1 encodeteam protein 140 Oct 13 06:06 /gbdb/hg19/bbi/wgEncodeOpenChromChipFibroblCtcfBaseOverlapSignal.bigWig -> /usr/local/apache/htdocs-hgdownload/goldenPath/hg19/encodeDCC/wgEncodeOpenChromChip/wgEncodeOpenChromChipFibroblCtcfBaseOverlapSignal.bigWig ## Seen in browser ### Question: 80 in dir, 75 converted, 85 displayed. What is up with 5 under & 5 over counts? # 85 displayed is actually bad 'selecting' by hui.js when filterComp is involved (peaks being selected even though they are hidden) # Brian confirm sthat the 5 he didn't convert were already v4. All is well. # update the md5sums cd .. encodeDownloadsPage.pl -db=hg19 -checksum index.html & cp md5sum.txt release1/ 2011-03-04 Brian converted more bigWigs ======================================= cd {downloadsHg19}/wgEncodeOpenChromDnase ll wgEncodeOpenChromDnaseHepatocytesSig.bigWig -rw-rw-r-- 4 encodeteam protein 2041493918 Dec 5 10:37 wgEncodeOpenChromDnaseHepatocytesSig.bigWig ## There are 4 locations: # {downloadsHg19}/wgEncodeOpenChromDnase # {downloadsHg19}/wgEncodeOpenChromDnase/release1 # submission dir. Leave that one alone! # And fourth ?? Brian probably ll /gbdb/hg19/bbi/wgEncodeOpenChromDnaseHepatocytesSig.bigWig lrwxrwxrwx 1 encodeteam protein 128 Dec 7 13:40 /gbdb/hg19/bbi/wgEncodeOpenChromDnaseHepatocytesSig.bigWig -> /usr/local/apache/htdocs-hgdownload/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseHepatocytesSig.bigWig ## Don't forget to make sure this is still intact # Link them to obsolete so nothing gets lost cd ../obsolete/wgEncodeOpenChromDnase ln ../../wgEncodeOpenChromDnase/*.bigWig . ll *.bigWig | wl 94 ls -1 *.bigWig | sort > tmp.txt cd ../../obsolete/wgEncodeOpenChromFaire ln ../../wgEncodeOpenChromFaire/*.bigWig . ll *.bigWig | wl 50 ls -1 *.bigWig | sort > tmp.txt cd /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/ ll *.bigWig | wl 90 # 4 are missing and should be accounted for ls -1 *.bigWig | sort > /usr/local/apache/htdocs-hgdownload/goldenPath/hg19/encodeDCC/obsolete/wgEncodeOpenChromDnase/tmpV4.txt cd /usr/local/apache/htdocs-hgdownload/goldenPath/hg19/encodeDCC/obsolete/wgEncodeOpenChromDnase/ e tmpV4.txt # remove the .new.bigWigs kompare -c tmp.txt tmpV4.txt wgEncodeOpenChromDnaseUrotsaBaseOverlapSignal.bigWig wgEncodeOpenChromDnaseUrotsaSig.bigWig wgEncodeOpenChromDnaseUrotsaUt189BaseOverlapSignal.bigWig wgEncodeOpenChromDnaseUrotsaUt189Sig.bigWig # Should confirm that these are already v4 cd /hive/users/braney/bigWigConvert.wgEncodeOpenChromFaire/ ll *.bigWig | wl 38 # 12 are missing and should be accounted for ls -1 *.bigWig | sort > /usr/local/apache/htdocs-hgdownload/goldenPath/hg19/encodeDCC/obsolete/wgEncodeOpenChromFaire/tmpV4.txt cd /usr/local/apache/htdocs-hgdownload/goldenPath/hg19/encodeDCC/obsolete/wgEncodeOpenChromFaire/ e tmpV4.txt # remove the .new.bigWigs kompare -c tmp.txt tmpV4.txt & wgEncodeOpenChromFaireA549BaseOverlapSignal.bigWig wgEncodeOpenChromFaireA549Sig.bigWig wgEncodeOpenChromFaireHtr8BaseOverlapSignal.bigWig wgEncodeOpenChromFaireHtr8Sig.bigWig wgEncodeOpenChromFaireMcf7HypoxlacBaseOverlapSignal.bigWig wgEncodeOpenChromFaireMcf7HypoxlacSig.bigWig wgEncodeOpenChromFaireNhbeBaseOverlapSignal.bigWig wgEncodeOpenChromFaireNhbeSig.bigWig wgEncodeOpenChromFaireUrotsaBaseOverlapSignal.bigWig wgEncodeOpenChromFaireUrotsaSig.bigWig wgEncodeOpenChromFaireUrotsaUt189BaseOverlapSignal.bigWig wgEncodeOpenChromFaireUrotsaUt189Sig.bigWig # Should confirm that these are already v4 cd ../../wgEncodeOpenChromDnase/ mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnase8988tBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromDnase8988tBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnase8988tSig.bigWig.new.bigWig wgEncodeOpenChromDnase8988tSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseA549BaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromDnaseA549BaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseA549Sig.bigWig.new.bigWig wgEncodeOpenChromDnaseA549Sig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseAosmcSerumfreeBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromDnaseAosmcSerumfreeBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseAosmcSerumfreeSig.bigWig.new.bigWig wgEncodeOpenChromDnaseAosmcSerumfreeSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseChorionBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromDnaseChorionBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseChorionSig.bigWig.new.bigWig wgEncodeOpenChromDnaseChorionSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseCllBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromDnaseCllBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseCllSig.bigWig.new.bigWig wgEncodeOpenChromDnaseCllSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseFibroblBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromDnaseFibroblBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseFibroblSig.bigWig.new.bigWig wgEncodeOpenChromDnaseFibroblSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseFibropBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromDnaseFibropBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseFibropSig.bigWig.new.bigWig wgEncodeOpenChromDnaseFibropSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseGlioblaBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromDnaseGlioblaBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseGlioblaSig.bigWig.new.bigWig wgEncodeOpenChromDnaseGlioblaSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseGm12878BaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromDnaseGm12878BaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseGm12878Sig.bigWig.new.bigWig wgEncodeOpenChromDnaseGm12878Sig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseGm12891BaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromDnaseGm12891BaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseGm12891Sig.bigWig.new.bigWig wgEncodeOpenChromDnaseGm12891Sig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseGm12892BaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromDnaseGm12892BaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseGm12892Sig.bigWig.new.bigWig wgEncodeOpenChromDnaseGm12892Sig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseGm18507BaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromDnaseGm18507BaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseGm18507Sig.bigWig.new.bigWig wgEncodeOpenChromDnaseGm18507Sig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseGm19238BaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromDnaseGm19238BaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseGm19238Sig.bigWig.new.bigWig wgEncodeOpenChromDnaseGm19238Sig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseGm19239BaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromDnaseGm19239BaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseGm19239Sig.bigWig.new.bigWig wgEncodeOpenChromDnaseGm19239Sig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseGm19240BaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromDnaseGm19240BaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseGm19240Sig.bigWig.new.bigWig wgEncodeOpenChromDnaseGm19240Sig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseH1hescBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromDnaseH1hescBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseH1hescSig.bigWig.new.bigWig wgEncodeOpenChromDnaseH1hescSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseH9esBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromDnaseH9esBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseH9esSig.bigWig.new.bigWig wgEncodeOpenChromDnaseH9esSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseHelas3BaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromDnaseHelas3BaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseHelas3Ifna4hBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromDnaseHelas3Ifna4hBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseHelas3Ifna4hSig.bigWig.new.bigWig wgEncodeOpenChromDnaseHelas3Ifna4hSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseHelas3Sig.bigWig.new.bigWig wgEncodeOpenChromDnaseHelas3Sig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseHepatocytesBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromDnaseHepatocytesBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseHepatocytesSig.bigWig.new.bigWig wgEncodeOpenChromDnaseHepatocytesSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseHepg2BaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromDnaseHepg2BaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseHepg2Sig.bigWig.new.bigWig wgEncodeOpenChromDnaseHepg2Sig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseHmecBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromDnaseHmecBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseHmecSig.bigWig.new.bigWig wgEncodeOpenChromDnaseHmecSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseHpde6e6e7BaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromDnaseHpde6e6e7BaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseHpde6e6e7Sig.bigWig.new.bigWig wgEncodeOpenChromDnaseHpde6e6e7Sig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseHsmmBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromDnaseHsmmBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseHsmmSig.bigWig.new.bigWig wgEncodeOpenChromDnaseHsmmSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseHsmmtBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromDnaseHsmmtBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseHsmmtSig.bigWig.new.bigWig wgEncodeOpenChromDnaseHsmmtSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseHtr8BaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromDnaseHtr8BaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseHtr8Sig.bigWig.new.bigWig wgEncodeOpenChromDnaseHtr8Sig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseHuh75BaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromDnaseHuh75BaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseHuh75Sig.bigWig.new.bigWig wgEncodeOpenChromDnaseHuh75Sig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseHuh7BaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromDnaseHuh7BaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseHuh7Sig.bigWig.new.bigWig wgEncodeOpenChromDnaseHuh7Sig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseHuvecBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromDnaseHuvecBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseHuvecSig.bigWig.new.bigWig wgEncodeOpenChromDnaseHuvecSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseIpsBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromDnaseIpsBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseIpsSig.bigWig.new.bigWig wgEncodeOpenChromDnaseIpsSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseK562BaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromDnaseK562BaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseK562Sig.bigWig.new.bigWig wgEncodeOpenChromDnaseK562Sig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseLncapAndroBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromDnaseLncapAndroBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseLncapAndroSig.bigWig.new.bigWig wgEncodeOpenChromDnaseLncapAndroSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseLncapBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromDnaseLncapBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseLncapSig.bigWig.new.bigWig wgEncodeOpenChromDnaseLncapSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseMcf7BaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromDnaseMcf7BaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseMcf7Sig.bigWig.new.bigWig wgEncodeOpenChromDnaseMcf7Sig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseMedulloBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromDnaseMedulloBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseMedulloSig.bigWig.new.bigWig wgEncodeOpenChromDnaseMedulloSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseMelanoBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromDnaseMelanoBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseMelanoSig.bigWig.new.bigWig wgEncodeOpenChromDnaseMelanoSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseMyometrBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromDnaseMyometrBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseMyometrSig.bigWig.new.bigWig wgEncodeOpenChromDnaseMyometrSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseNhekBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromDnaseNhekBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseNhekSig.bigWig.new.bigWig wgEncodeOpenChromDnaseNhekSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseOsteoblBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromDnaseOsteoblBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseOsteoblSig.bigWig.new.bigWig wgEncodeOpenChromDnaseOsteoblSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnasePanisdBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromDnasePanisdBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnasePanisdSig.bigWig.new.bigWig wgEncodeOpenChromDnasePanisdSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnasePanisletsBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromDnasePanisletsBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnasePanisletsSig.bigWig.new.bigWig wgEncodeOpenChromDnasePanisletsSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnasePhteBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromDnasePhteBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnasePhteSig.bigWig.new.bigWig wgEncodeOpenChromDnasePhteSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseProgfibBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromDnaseProgfibBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseProgfibSig.bigWig.new.bigWig wgEncodeOpenChromDnaseProgfibSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseStellateBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromDnaseStellateBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseStellateSig.bigWig.new.bigWig wgEncodeOpenChromDnaseStellateSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseT47dBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromDnaseT47dBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseT47dSig.bigWig.new.bigWig wgEncodeOpenChromDnaseT47dSig.bigWig cd release1/ rm *.bigWig ln ../*.bigWig . ls -1 *.bigWig | wl ################################ Ouch!! I did rm *.bigWig not in the release dir!!! ln release1/*.bigWig . ls -1 *.bigWig | wl 94 #### Atleast the old files are not lost. Hopefully Brian can regen one more time. Or perhaps there is a backup cd ../../wgEncodeOpenChromFaire/ mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromFaire/wgEncodeOpenChromFaireAstrocyBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromFaireAstrocyBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromFaire/wgEncodeOpenChromFaireAstrocySig.bigWig.new.bigWig wgEncodeOpenChromFaireAstrocySig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromFaire/wgEncodeOpenChromFaireGlioblaBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromFaireGlioblaBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromFaire/wgEncodeOpenChromFaireGlioblaSig.bigWig.new.bigWig wgEncodeOpenChromFaireGlioblaSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromFaire/wgEncodeOpenChromFaireGm12878BaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromFaireGm12878BaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromFaire/wgEncodeOpenChromFaireGm12878Sig.bigWig.new.bigWig wgEncodeOpenChromFaireGm12878Sig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromFaire/wgEncodeOpenChromFaireGm12891BaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromFaireGm12891BaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromFaire/wgEncodeOpenChromFaireGm12891Sig.bigWig.new.bigWig wgEncodeOpenChromFaireGm12891Sig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromFaire/wgEncodeOpenChromFaireGm12892BaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromFaireGm12892BaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromFaire/wgEncodeOpenChromFaireGm12892Sig.bigWig.new.bigWig wgEncodeOpenChromFaireGm12892Sig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromFaire/wgEncodeOpenChromFaireGm18507BaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromFaireGm18507BaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromFaire/wgEncodeOpenChromFaireGm18507Sig.bigWig.new.bigWig wgEncodeOpenChromFaireGm18507Sig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromFaire/wgEncodeOpenChromFaireGm19239BaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromFaireGm19239BaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromFaire/wgEncodeOpenChromFaireGm19239Sig.bigWig.new.bigWig wgEncodeOpenChromFaireGm19239Sig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromFaire/wgEncodeOpenChromFaireH1hescBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromFaireH1hescBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromFaire/wgEncodeOpenChromFaireH1hescSig.bigWig.new.bigWig wgEncodeOpenChromFaireH1hescSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromFaire/wgEncodeOpenChromFaireHelas3BaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromFaireHelas3BaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromFaire/wgEncodeOpenChromFaireHelas3Ifna4hBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromFaireHelas3Ifna4hBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromFaire/wgEncodeOpenChromFaireHelas3Ifna4hSig.bigWig.new.bigWig wgEncodeOpenChromFaireHelas3Ifna4hSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromFaire/wgEncodeOpenChromFaireHelas3Ifng4hBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromFaireHelas3Ifng4hBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromFaire/wgEncodeOpenChromFaireHelas3Ifng4hSig.bigWig.new.bigWig wgEncodeOpenChromFaireHelas3Ifng4hSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromFaire/wgEncodeOpenChromFaireHelas3Sig.bigWig.new.bigWig wgEncodeOpenChromFaireHelas3Sig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromFaire/wgEncodeOpenChromFaireHepg2BaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromFaireHepg2BaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromFaire/wgEncodeOpenChromFaireHepg2Sig.bigWig.new.bigWig wgEncodeOpenChromFaireHepg2Sig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromFaire/wgEncodeOpenChromFaireHuvecBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromFaireHuvecBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromFaire/wgEncodeOpenChromFaireHuvecSig.bigWig.new.bigWig wgEncodeOpenChromFaireHuvecSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromFaire/wgEncodeOpenChromFaireK562BaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromFaireK562BaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromFaire/wgEncodeOpenChromFaireK562NabutBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromFaireK562NabutBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromFaire/wgEncodeOpenChromFaireK562NabutSig.bigWig.new.bigWig wgEncodeOpenChromFaireK562NabutSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromFaire/wgEncodeOpenChromFaireK562OhureaBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromFaireK562OhureaBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromFaire/wgEncodeOpenChromFaireK562OhureaSig.bigWig.new.bigWig wgEncodeOpenChromFaireK562OhureaSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromFaire/wgEncodeOpenChromFaireK562Sig.bigWig.new.bigWig wgEncodeOpenChromFaireK562Sig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromFaire/wgEncodeOpenChromFaireMedulloBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromFaireMedulloBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromFaire/wgEncodeOpenChromFaireMedulloSig.bigWig.new.bigWig wgEncodeOpenChromFaireMedulloSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromFaire/wgEncodeOpenChromFaireNhekBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromFaireNhekBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromFaire/wgEncodeOpenChromFaireNhekSig.bigWig.new.bigWig wgEncodeOpenChromFaireNhekSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromFaire/wgEncodeOpenChromFairePanisletsBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromFairePanisletsBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromFaire/wgEncodeOpenChromFairePanisletsSig.bigWig.new.bigWig wgEncodeOpenChromFairePanisletsSig.bigWig cd release1/ rm *.bigWig ln ../*.bigWig . ls -1 *.bigWig | wl 50 # Soft links okay? ll /gbdb/hg19/bbi/wgEncodeOpenChromDnaseGm12878Sig.bigWig lrwxrwxrwx 1 encodeteam protein 124 Jan 11 16:24 /gbdb/hg19/bbi/wgEncodeOpenChromDnaseGm12878Sig.bigWig -> /usr/local/apache/htdocs-hgdownload/goldenPath/hg19/encodeDCC/wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseGm12878Sig.bigWig ll /gbdb/hg19/bbi/wgEncodeOpenChromFaireGm12878Sig.bigWig lrwxrwxrwx 1 braney protein 110 Aug 4 2010 /gbdb/hg19/bbi/wgEncodeOpenChromFaireGm12878Sig.bigWig -> /hive/groups/encode/dcc/pipeline/downloads/hg19/wgEncodeOpenChromFaire/wgEncodeOpenChromFaireGm12878Sig.bigWig ## Seen in browser # update the md5sums cd {down19}/wgEncodeOpenChromFaire/ encodeDownloadsPage.pl -db=hg19 -checksum index.html & cp md5sum.txt release1/ ## Now redo DNase that I screwed up. cd /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/ ll *.bigWig | wl 90 cd {downhg19}/obsolete/wgEncodeOpenChromDnase # Yikes. Someone removed the obsolete dir. cd {downhg19} mkdir obsolete cd obsolete mkdir wgEncodeOpenChromDnase cd wgEncodeOpenChromDnase/ ln ../../wgEncodeOpenChromDnase/*.bigWig . ll *.bigWig | wl 94 cd ../../wgEncodeOpenChromDnase/ mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnase8988tBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromDnase8988tBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnase8988tSig.bigWig.new.bigWig wgEncodeOpenChromDnase8988tSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseA549BaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromDnaseA549BaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseA549Sig.bigWig.new.bigWig wgEncodeOpenChromDnaseA549Sig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseAosmcSerumfreeBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromDnaseAosmcSerumfreeBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseAosmcSerumfreeSig.bigWig.new.bigWig wgEncodeOpenChromDnaseAosmcSerumfreeSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseChorionBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromDnaseChorionBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseChorionSig.bigWig.new.bigWig wgEncodeOpenChromDnaseChorionSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseCllBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromDnaseCllBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseCllSig.bigWig.new.bigWig wgEncodeOpenChromDnaseCllSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseFibroblBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromDnaseFibroblBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseFibroblSig.bigWig.new.bigWig wgEncodeOpenChromDnaseFibroblSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseFibropBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromDnaseFibropBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseFibropSig.bigWig.new.bigWig wgEncodeOpenChromDnaseFibropSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseGlioblaBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromDnaseGlioblaBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseGlioblaSig.bigWig.new.bigWig wgEncodeOpenChromDnaseGlioblaSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseGm12878BaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromDnaseGm12878BaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseGm12878Sig.bigWig.new.bigWig wgEncodeOpenChromDnaseGm12878Sig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseGm12891BaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromDnaseGm12891BaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseGm12891Sig.bigWig.new.bigWig wgEncodeOpenChromDnaseGm12891Sig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseGm12892BaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromDnaseGm12892BaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseGm12892Sig.bigWig.new.bigWig wgEncodeOpenChromDnaseGm12892Sig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseGm18507BaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromDnaseGm18507BaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseGm18507Sig.bigWig.new.bigWig wgEncodeOpenChromDnaseGm18507Sig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseGm19238BaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromDnaseGm19238BaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseGm19238Sig.bigWig.new.bigWig wgEncodeOpenChromDnaseGm19238Sig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseGm19239BaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromDnaseGm19239BaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseGm19239Sig.bigWig.new.bigWig wgEncodeOpenChromDnaseGm19239Sig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseGm19240BaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromDnaseGm19240BaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseGm19240Sig.bigWig.new.bigWig wgEncodeOpenChromDnaseGm19240Sig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseH1hescBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromDnaseH1hescBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseH1hescSig.bigWig.new.bigWig wgEncodeOpenChromDnaseH1hescSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseH9esBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromDnaseH9esBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseH9esSig.bigWig.new.bigWig wgEncodeOpenChromDnaseH9esSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseHelas3BaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromDnaseHelas3BaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseHelas3Ifna4hBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromDnaseHelas3Ifna4hBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseHelas3Ifna4hSig.bigWig.new.bigWig wgEncodeOpenChromDnaseHelas3Ifna4hSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseHelas3Sig.bigWig.new.bigWig wgEncodeOpenChromDnaseHelas3Sig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseHepatocytesBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromDnaseHepatocytesBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseHepatocytesSig.bigWig.new.bigWig wgEncodeOpenChromDnaseHepatocytesSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseHepg2BaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromDnaseHepg2BaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseHepg2Sig.bigWig.new.bigWig wgEncodeOpenChromDnaseHepg2Sig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseHmecBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromDnaseHmecBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseHmecSig.bigWig.new.bigWig wgEncodeOpenChromDnaseHmecSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseHpde6e6e7BaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromDnaseHpde6e6e7BaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseHpde6e6e7Sig.bigWig.new.bigWig wgEncodeOpenChromDnaseHpde6e6e7Sig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseHsmmBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromDnaseHsmmBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseHsmmSig.bigWig.new.bigWig wgEncodeOpenChromDnaseHsmmSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseHsmmtBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromDnaseHsmmtBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseHsmmtSig.bigWig.new.bigWig wgEncodeOpenChromDnaseHsmmtSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseHtr8BaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromDnaseHtr8BaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseHtr8Sig.bigWig.new.bigWig wgEncodeOpenChromDnaseHtr8Sig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseHuh75BaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromDnaseHuh75BaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseHuh75Sig.bigWig.new.bigWig wgEncodeOpenChromDnaseHuh75Sig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseHuh7BaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromDnaseHuh7BaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseHuh7Sig.bigWig.new.bigWig wgEncodeOpenChromDnaseHuh7Sig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseHuvecBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromDnaseHuvecBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseHuvecSig.bigWig.new.bigWig wgEncodeOpenChromDnaseHuvecSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseIpsBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromDnaseIpsBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseIpsSig.bigWig.new.bigWig wgEncodeOpenChromDnaseIpsSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseK562BaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromDnaseK562BaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseK562Sig.bigWig.new.bigWig wgEncodeOpenChromDnaseK562Sig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseLncapAndroBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromDnaseLncapAndroBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseLncapAndroSig.bigWig.new.bigWig wgEncodeOpenChromDnaseLncapAndroSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseLncapBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromDnaseLncapBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseLncapSig.bigWig.new.bigWig wgEncodeOpenChromDnaseLncapSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseMcf7BaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromDnaseMcf7BaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseMcf7Sig.bigWig.new.bigWig wgEncodeOpenChromDnaseMcf7Sig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseMedulloBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromDnaseMedulloBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseMedulloSig.bigWig.new.bigWig wgEncodeOpenChromDnaseMedulloSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseMelanoBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromDnaseMelanoBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseMelanoSig.bigWig.new.bigWig wgEncodeOpenChromDnaseMelanoSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseMyometrBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromDnaseMyometrBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseMyometrSig.bigWig.new.bigWig wgEncodeOpenChromDnaseMyometrSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseNhekBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromDnaseNhekBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseNhekSig.bigWig.new.bigWig wgEncodeOpenChromDnaseNhekSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseOsteoblBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromDnaseOsteoblBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseOsteoblSig.bigWig.new.bigWig wgEncodeOpenChromDnaseOsteoblSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnasePanisdBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromDnasePanisdBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnasePanisdSig.bigWig.new.bigWig wgEncodeOpenChromDnasePanisdSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnasePanisletsBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromDnasePanisletsBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnasePanisletsSig.bigWig.new.bigWig wgEncodeOpenChromDnasePanisletsSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnasePhteBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromDnasePhteBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnasePhteSig.bigWig.new.bigWig wgEncodeOpenChromDnasePhteSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseProgfibBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromDnaseProgfibBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseProgfibSig.bigWig.new.bigWig wgEncodeOpenChromDnaseProgfibSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseStellateBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromDnaseStellateBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseStellateSig.bigWig.new.bigWig wgEncodeOpenChromDnaseStellateSig.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseT47dBaseOverlapSignal.bigWig.new.bigWig wgEncodeOpenChromDnaseT47dBaseOverlapSignal.bigWig mv /hive/users/braney/bigWigConvert.wgEncodeOpenChromDnase/wgEncodeOpenChromDnaseT47dSig.bigWig.new.bigWig wgEncodeOpenChromDnaseT47dSig.bigWig cd release1/ rm *.bigWig ln ../*.bigWig . ls -1 *.bigWig | wl 94 # update the md5sums cd .. encodeDownloadsPage.pl -db=hg19 -checksum index.html & cp md5sum.txt release1/ 2011-03-15 Making bigWig for Terry's uniqueness tracks ====================================================== cd {pip} cd ../ftp/prod/tsfurey cp 2 to {downloads}/wgEncodeOpenChromDnase/supplemental tar -xzf duke_uniqueness_20.tgz cd align_20/ cat chr1_20_freq.wig chr2_20_freq.wig chr3_20_freq.wig chr4_20_freq.wig chr5_20_freq.wig chr6_20_freq.wig chr7_20_freq.wig chr8_20_freq.wig chr9_20_freq.wig chr10_20_freq.wig chr11_20_freq.wig chr12_20_freq.wig chr13_20_freq.wig chr14_20_freq.wig chr15_20_freq.wig chr16_20_freq.wig chr17_20_freq.wig chr18_20_freq.wig chr19_20_freq.wig chr20_20_freq.wig chr21_20_freq.wig chr22_20_freq.wig chrX_20_freq.wig chrY_20_freq.wig chrM_20_freq.wig > allChrs_20_freq.wig wigToBigWig allChrs_20_freq.wig /hive/data/genomes/hg19/chrom.sizes wgEncodeDukeUniqueness20.bw & tar -xzf duke_uniqueness_35.tgz cd align_35/ cat chr1_35_freq.wig chr2_35_freq.wig chr3_35_freq.wig chr4_35_freq.wig chr5_35_freq.wig chr6_35_freq.wig chr7_35_freq.wig chr8_35_freq.wig chr9_35_freq.wig chr10_35_freq.wig chr11_35_freq.wig chr12_35_freq.wig chr13_35_freq.wig chr14_35_freq.wig chr15_35_freq.wig chr16_35_freq.wig chr17_35_freq.wig chr18_35_freq.wig chr19_35_freq.wig chr20_35_freq.wig chr21_35_freq.wig chr22_35_freq.wig chrX_35_freq.wig chrY_35_freq.wig chrM_35_freq.wig > allChrs_35_freq.wig wigToBigWig allChrs_35_freq.wig /hive/data/genomes/hg19/chrom.sizes wgEncodeDukeUniqueness35.bw & hashMustFindVal: 'chrMT' not found e chrM_35_freq.wig cat chr1_35_freq.wig chr2_35_freq.wig chr3_35_freq.wig chr4_35_freq.wig chr5_35_freq.wig chr6_35_freq.wig chr7_35_freq.wig chr8_35_freq.wig chr9_35_freq.wig chr10_35_freq.wig chr11_35_freq.wig chr12_35_freq.wig chr13_35_freq.wig chr14_35_freq.wig chr15_35_freq.wig chr16_35_freq.wig chr17_35_freq.wig chr18_35_freq.wig chr19_35_freq.wig chr20_35_freq.wig chr21_35_freq.wig chr22_35_freq.wig chrX_35_freq.wig chrY_35_freq.wig chrM_35_freq.wig > allChrs_35_freq.wig wigToBigWig allChrs_35_freq.wig /hive/data/genomes/hg19/chrom.sizes wgEncodeDukeUniqueness35.bw & 2011-03-18 Late changing statuses ================================= /cluster/data/encode/pipeline/bin/encodeStatus.pl 1229 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 1478 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 1490 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 1491 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 1499 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 1500 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 1501 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 1504 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 1505 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 1516 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 1517 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 1518 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 1525 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 1526 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 1527 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 1536 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 1537 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 1538 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 1539 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 1540 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 1541 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 1542 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 1543 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 1580 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 1606 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 1607 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 1608 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 1609 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 1652 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 1657 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 1832 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 1833 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 1834 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 2449 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 2480 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 2487 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 2495 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 2499 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 2502 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 2503 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 2504 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 2505 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 2516 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 3141 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 3241 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 3242 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 3271 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 3272 released 2011-03-18 Resume attempting to load Mapability =============================================== # In Terry's ftp dir, made bigwigs # No move everything there to make an archive # Mock up a DAF/DDF. Of course I expect submission to fail so errors don't matter much tar -czf dukeExtras.tgz dukeExtraTracks.daf dukeExtraTracks.ddf ucsc/dukeUnique20.bw ucsc/dukeUnique35.bw dukeExcludeRegions.bed 2011-03-28 Document what went down for validation by experiment docs ==================================================================== Terry submitted one tar and then we agreed upon a format: tar of tars submibmitted as downloadOnly view to sort with exp in downloads dir. Terry resubmitted: 3829, 3831, 3832 ### Problem: all the *.tgz's were converted to *.doc.gz by pipeline # Would be good to fix pipline before Terry submits more. Manually 1) renamed all to *.tgz/gz 2) gunzipped to *.tgz 3) edited mdb.txt # loaded mdb, rebuilt index.html: tgzs show up as they ought! /cluster/data/encode/pipeline/bin/encodeStatus.pl 3829 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 3829 approved /cluster/data/encode/pipeline/bin/encodeStatus.pl 3831 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 3831 approved /cluster/data/encode/pipeline/bin/encodeStatus.pl 3832 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 3832 approved 2011-03-29 Resume attempting to load Mapability (again) ======================================================= # submitted 3840 # took a few rounds to get the daf/ddf right cd out mdbUpdate hg19 mdb.txt e trackDb.ra # make a wgEncodeMapability.new.ra and wgEncodeMapability.new.html # standardize this as if a normal Terry submission: select id,name,status,user_id from projects where id = 3840; | 3840 | uniqTest | loaded | 9 | update projects set name = "DNCT Uniqueness and Excluded 2011-03-28" where id = 3840; update projects set user_id = 17 where id = 3840; select id,name,status,user_id from projects where id = 3840; +------+-----------------------------------------+--------+---------+ | id | name | status | user_id | +------+-----------------------------------------+--------+---------+ | 3840 | DNCT Uniqueness and Excluded 2011-03-28 | loaded | 17 | /cluster/data/encode/pipeline/bin/encodeStatus.pl 3840 displayed 2011-04-20 Experimentify ======================== cd trackDb/human/hg19/metaDb/alpha mdbPrint hg19 -composite=%OpenChromCh% -experimentify > tmp.txt Using hgFixed.encodeExp Using table named 'hg19.metaDb_tdreszer'. objects:278 vars:5459 Experiment 1128 has 2 objects based upon 4 EDVs: [lab=UT-A dataType=ChipSeq cell=Fibrobl treatment=None antibody=Input]. 1128 wgEncodeOpenChromChipFibroblInputAln needs updating to mdb. 1128 wgEncodeOpenChromChipFibroblInputSig needs updating to mdb. 1128 all 2 objects are missing an expId. No fastq ### Modeled? Experiment 593 has 2 objects based upon 4 EDVs: [lab=UT-A dataType=ChipSeq cell=ProgFib treatment=None antibody=Input]. 593 wgEncodeOpenChromChipProgfibInputAln needs updating to mdb. 593 wgEncodeOpenChromChipProgfibInputSig needs updating to mdb. 593 all 2 objects are missing an expId. No fastq ### Modeled? Experiment 599 has 2 objects based upon 4 EDVs: [lab=UT-A dataType=ChipSeq cell=MCF-7 treatment=None antibody=c-Myc]. 599 wgEncodeOpenChromChipMcf7CmycRawDataRep1 needs updating to mdb. 599 wgEncodeOpenChromChipMcf7CmycRawDataRep2 needs updating to mdb. 599 all 2 objects are missing an expId. 2 fastq's and also Estro and Veh exps. ### Extras, but no related mdbUpdate hg19 -composite=%OpenChromCh% -encodeExp=std -test Composite 'wgEncodeOpenChromChip' has 46 recognizable experiments with 46 missing an expId. objects/experiment: min:2 max:10 mean:6.021739. Found 277 of 278 object(s) would have their experiment ID updated. Command would affected 492 row(s) in hg19.metaDb_tdreszer mdbUpdate hg19 -composite=%OpenChromCh% -encodeExp=std Using hgFixed.encodeExp Using table named 'hg19.metaDb_tdreszer'. Composite 'wgEncodeOpenChromChip' has 46 recognizable experiments with 46 missing an expId. objects/experiment: min:2 max:10 mean:6.021739. Affected 492 row(s) in hg19.metaDb_tdreszer mdbUpdate hg19 -composite=%OpenChromCh% -encodeExp=std -accession -test Using hgFixed.encodeExp Using table named 'hg19.metaDb_tdreszer'. Composite 'wgEncodeOpenChromChip' has 46 recognizable experiments with 0 missing an expId. objects/experiment: min:2 max:10 mean:6.021739. Found 62 of 278 object(s) would have their experiment ID updated. Command would affected 62 row(s) in hg19.metaDb_tdreszer mdbUpdate hg19 -composite=%OpenChromCh% -encodeExp=std -accession Using hgFixed.encodeExp Using table named 'hg19.metaDb_tdreszer'. Composite 'wgEncodeOpenChromChip' has 46 recognizable experiments with 0 missing an expId. objects/experiment: min:2 max:10 mean:6.021739. Affected 62 row(s) in hg19.metaDb_tdreszer mdbPrint hg19 -composite=wgEncodeOpenChromChip > wgEncodeOpenChromChip.ra gold wgEncodeOpenChromChip.ra mdbPrint hg19 -composite=%OpenChromDnase -experimentify > tmp.txt Using hgFixed.encodeExp Using table named 'hg19.metaDb_tdreszer'. objects:329 vars:5997 mdbUpdate hg19 -composite=%OpenChromDnase -encodeExp=std -test Composite 'wgEncodeOpenChromDnase' has 47 recognizable experiments with 47 missing an expId. objects/experiment: min:5 max:14 mean:6.978723. Found 328 of 329 object(s) would have their experiment ID updated. Command would affected 519 row(s) in hg19.metaDb_tdreszer mdbUpdate hg19 -composite=%OpenChromDnase -encodeExp=std Using hgFixed.encodeExp Using table named 'hg19.metaDb_tdreszer'. Composite 'wgEncodeOpenChromDnase' has 47 recognizable experiments with 47 missing an expId. objects/experiment: min:5 max:14 mean:6.978723. Affected 519 row(s) in hg19.metaDb_tdreszer mdbUpdate hg19 -composite=%OpenChromDnase -encodeExp=std -accession -test Using hgFixed.encodeExp Using table named 'hg19.metaDb_tdreszer'. Composite 'wgEncodeOpenChromDnase' has 47 recognizable experiments with 0 missing an expId. objects/experiment: min:5 max:14 mean:6.978723. Found 137 of 329 object(s) would have their experiment ID updated. Command would affected 137 row(s) in hg19.metaDb_tdreszer mdbUpdate hg19 -composite=%OpenChromDnase -encodeExp=std -accession Using hgFixed.encodeExp Using table named 'hg19.metaDb_tdreszer'. Composite 'wgEncodeOpenChromDnase' has 47 recognizable experiments with 0 missing an expId. objects/experiment: min:5 max:14 mean:6.978723. Affected 137 row(s) in hg19.metaDb_tdreszer mdbPrint hg19 -composite=wgEncodeOpenChromDnase > wgEncodeOpenChromDnase.ra gold wgEncodeOpenChromDnase.ra mdbPrint hg19 -composite=%OpenChromFaire -experimentify > tmp.txt Using hgFixed.encodeExp Using table named 'hg19.metaDb_tdreszer'. objects:182 vars:3215 mdbUpdate hg19 -composite=%OpenChromFaire -encodeExp=std -test Using hgFixed.encodeExp Using table named 'hg19.metaDb_tdreszer'. Composite 'wgEncodeOpenChromFaire' has 25 recognizable experiments with 25 missing an expId. objects/experiment: min:5 max:10 mean:7.240000. Found 181 of 182 object(s) would have their experiment ID updated. Command would affected 276 row(s) in hg19.metaDb_tdreszer mdbUpdate hg19 -composite=%OpenChromFaire -encodeExp=std Using hgFixed.encodeExp Using table named 'hg19.metaDb_tdreszer'. Composite 'wgEncodeOpenChromFaire' has 25 recognizable experiments with 25 missing an expId. objects/experiment: min:5 max:10 mean:7.240000. Affected 276 row(s) in hg19.metaDb_tdreszer mdbUpdate hg19 -composite=%OpenChromFaire -encodeExp=std -accession -test Using hgFixed.encodeExp Using table named 'hg19.metaDb_tdreszer'. Composite 'wgEncodeOpenChromFaire' has 25 recognizable experiments with 0 missing an expId. objects/experiment: min:5 max:10 mean:7.240000. Found 86 of 182 object(s) would have their experiment ID updated. Command would affected 86 row(s) in hg19.metaDb_tdreszer mdbUpdate hg19 -composite=%OpenChromFaire -encodeExp=std -accession Using hgFixed.encodeExp Using table named 'hg19.metaDb_tdreszer'. Composite 'wgEncodeOpenChromFaire' has 25 recognizable experiments with 0 missing an expId. objects/experiment: min:5 max:10 mean:7.240000. Affected 86 row(s) in hg19.metaDb_tdreszer mdbPrint hg19 -composite=wgEncodeOpenChromFaire > wgEncodeOpenChromFaire.ra Using table named 'hg19.metaDb_tdreszer'. objects:182 vars:3577 gold wgEncodeOpenChromFaire.ra gold, gadd, gci, gup,gpush cd {downloads}/wgEncodeOpenChromChip encodeDownloadsPage.pl -db=hg19 index.html cd {downloads}/wgEncodeOpenChromDnase encodeDownloadsPage.pl -db=hg19 index.html cd {downloads}/wgEncodeOpenChromFaire encodeDownloadsPage.pl -db=hg19 index.html 2011-05-02 Resumbitted Open Chrom Synth to fix erroneous blues ============================================================== /cluster/data/encode/pipeline/bin/encodeStatus.pl 3273 displayed /cluster/data/encode/pipeline/bin/encodeStatus.pl 3273 approved /cluster/data/encode/pipeline/bin/encodeStatus.pl 3273 reviewing /cluster/data/encode/pipeline/bin/encodeStatus.pl 3507 reviewing /cluster/data/encode/pipeline/bin/encodeStatus.pl 3507 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 3840 approved 2011-05-04 Anshul's Black list regions ====================================== ### Should move to a separate doc but keeping here now for convenience # location: ftp://encodeftp.cse.ucsc.edu/users/akundaje/rawdata/blacklists/hg19/ # contents: Anshul_Hg19UltraHighSignalArtifactRegions.bed.gz ### bed 5 needs to be altered. # Duke_Hg19SignalRepeatArtifactRegions.bed.gz # Same as Duke Excluded regions already added # wgEncodeHg19ConsensusSignalArtifactRegions.bed.gz ### bed 6 but last column is 0, not '.' ### How to distinguish the three "Excluded Regions" tracks? # lab only distinguishes 1. # size? But what size? # A new term? No, use "uniqueness" which is currently only used by mababilty. # Terry's: uniqueness=excludedRegions # Anshul's: uniqueness=ultraHighSignalBlacklist # consensus: uniqueness=consensusBlacklist ### Requires cleaning up uniqueness in both hg18 and hg19 to use as expVar ### Needed to conform bed files for sith field '.'. Hand edited. tar -czf anshulBlacklist.tgz *.d?f anshulsUltraHighSignalBlacklist.bed consensusBlacklist.bed # Sticking point on grant Birney. For some reason doEncodeValidate.pl is not responding to the cv.ra ERROR: line 137:'chr11 122874443 122874443 Low_mappability_island 1000 .' chromStart == chromEnd (122874443) (zero-length item) # Neat awk command to list any problems awk '{printf "%d\t%s:%d-%d\n",$3 - $2,$1,$2,$3}' < consensusBlacklist.bed | sort -n 0 chr11:122874443-122874443 ### Anshul wants to just have the consensus track, but there is still a 0 length region # Ansul gave proper coordinates for 0 region and another small one. rename table wgEncodeMapabilityDacRegionsExcluded to wgEncodeMapabilityDacConsensusBlacklist; mv ../wgEncodeMapabilityDac/wgEncodeMapabilityDacRegionsExcluded.bed.gz wgEncodeMapabilityDacConsensusBlacklist.bed.gz 2011-05-13 More Validation Docs. Matt doing most of the work ============================================================= ### problem: files marked as *.tgz.tgz in downloads dir: -rw-rw-r-- 2 encodeteam genecats 50556959 May 11 13:07 wgEncodeOpenChromDnaseHepg2Validation.tgz.tgz -rw-rw-r-- 2 encodeteam genecats 50519897 May 11 13:07 wgEncodeOpenChromDnaseHelas3Validation.tgz.tgz -rw-rw-r-- 2 encodeteam genecats 36246228 May 11 13:15 wgEncodeOpenChromDnaseHuvecValidation.tgz.tgz -rw-rw-r-- 2 encodeteam genecats 36062115 May 11 13:28 wgEncodeOpenChromDnaseNhekValidation.tgz.tgz -rw-rw-r-- 2 encodeteam genecats 12129291 May 11 13:37 wgEncodeOpenChromDnaseProgfibValidation.tgz.tgz -rw-rw-r-- 2 encodeteam genecats 12303817 May 11 18:07 wgEncodeOpenChromDnaseFibroblValidation.tgz.tgz -rw-rw-r-- 2 encodeteam genecats 50485890 May 11 18:18 wgEncodeOpenChromDnaseGm18507Validation.tgz.tgz -rw-rw-r-- 2 encodeteam genecats 24115935 May 11 18:35 wgEncodeOpenChromDnaseLncapValidation.tgz.tgz -rw-rw-r-- 2 encodeteam genecats 36267278 May 11 18:49 wgEncodeOpenChromDnaseHmecValidation.tgz.tgz -rw-rw-r-- 2 encodeteam genecats 12161387 May 12 05:42 wgEncodeOpenChromDnaseLncapAndroValidation.tgz.tgz -rw-rw-r-- 2 encodeteam genecats 12290470 May 12 05:58 wgEncodeOpenChromDnaseMcf7Validation.tgz.tgz # Where they double tarred? NO! They were linked. But we must fix pipeline naming and rename these -rw-rw-r-- 2 encodeteam genecats 50556959 May 11 13:07 DNCT_Duke_DNaseHS_HepG2_ENCArray.tgz -rw-rw-r-- 2 encodeteam genecats 50519897 May 11 13:07 DNCT_Duke_DNaseHS_HeLa-S3_ENCArray.tgz -rw-rw-r-- 2 encodeteam genecats 36246228 May 11 13:15 DNCT_Duke_DNaseHS_HUVEC_ENCArray.tgz -rw-rw-r-- 2 encodeteam genecats 36062115 May 11 13:28 DNCT_Duke_DNaseHS_NHEK_ENCArray.tgz -rw-rw-r-- 2 encodeteam genecats 12129291 May 11 13:37 DNCT_Duke_DNaseHS_ProgFib_ENCArray.tgz -rw-rw-r-- 2 encodeteam genecats 12303817 May 11 18:07 DNCT_Duke_DNaseHS_Fibrobl_ENCArray.tgz -rw-rw-r-- 2 encodeteam genecats 50485890 May 11 18:18 DNCT_Duke_DNaseHS_GM18507_ENCArray.tgz -rw-rw-r-- 2 encodeteam genecats 24115935 May 11 18:35 DNCT_Duke_DNaseHS_LNCaP_ENCArray.tgz -rw-rw-r-- 2 encodeteam genecats 36267278 May 11 18:49 DNCT_Duke_DNaseHS_HMEC_ENCArray.tgz -rw-rw-r-- 2 encodeteam genecats 12161387 May 12 05:42 DNCT_Duke_DNaseHS_LNCaP_androgen_ENCArray.tgz -rw-rw-r-- 2 encodeteam genecats 12290470 May 12 05:58 DNCT_Duke_DNaseHS_MCF-7_ENCArray.tgz 2011-06-14 Open Chrom Synth has been released. ============================================== /cluster/data/encode/pipeline/bin/encodeStatus.pl 3273 released # These shouuld be approved: /cluster/data/encode/pipeline/bin/encodeStatus.pl 4107 approved /cluster/data/encode/pipeline/bin/encodeStatus.pl 4154 approved /cluster/data/encode/pipeline/bin/encodeStatus.pl 4155 approved /cluster/data/encode/pipeline/bin/encodeStatus.pl 4161 approved