############ wgEncodeSydn... Histone, Tfbs composite's hg19 submissions ############### 2010-06-08 Mini-freeze ====================== There was only one submission! cd {t19}/metaDb/alpha mkdir testing cd testing ~/bin/x86_64/mdbPrint hg18 -table=metaDb -vars="composite=wgEncodeYaleChIPseq" -updDb=hg19 -updMdb=metaDb_tdreszer -updExp="grant,cell,treatment,antibody,control,replicate,view" -updVars="dateSubmitted,dateUnrestricted" > sydhTfbsHg18.txt objects:1075 vars:22450 1075 sydhTfbsHg18.txt Possible remaps? Yale Stanford ChIP-seq GM12878 None Jun-2010 2010-06-03 none loaded hg19 1246 Yale Stanford ChIP-seq HepG2/None/Input/IgG-rab Input Jun-2010 2010-04-27 none displayed hg19 1136 Yale Stanford ChIP-seq K562/None/Input/IgG-rab Input Jun-2010 2010-04-27 none displayed hg19 1132 Yale Stanford ChIP-seq NT2-D1/None/Input/std Input Jun-2010 2010-05-04 none displayed hg19 1123 Yale UCD ChIP-seq HUVEC/None/Input/UCDavis Input Jun-2010 2010-05-20 none displayed hg19 1207 Yale UCD ChIP-seq HeLa-S3/None/Input/UCDavis Jun-2010 2010-04-27 none displayed hg19 1140 mdbPrint hg19 -table=metaDb -vars="subId=1246" -countObjs 1 object # all the rest have three None of the others are new grep GM12878 sydhTfbsHg18.txt | grep Input | grep None | grep std | grep Alignments | wl grep GM12878 sydhTfbsHg18.txt | grep Input | grep None | grep std | grep Alignments > sydhTfbsGm12878.txt e sydhTfbsGm12878.txt # add dateResubmitted=2010-06-03 chmod 755 sydhTfbsGm12878.txt ./sydhTfbsGm12878.txt Command would affected 0 row(s) in hg19.metaDb_tdreszer mdbUpdate hg19 wgEncodeSydhTfbs.ra Using table named 'hg19.metaDb_tdreszer'. Read 151 metadata objects from hg19 Affected 3020 row(s) in hg19.metaDb_tdreszer ./sydhTfbsGm12878.txt Command would affected 3 row(s) in hg19.metaDb_tdreszer e sydhTfbsGm12878.txt # remove -test ./sydhTfbsGm12878.txt Affected 3 row(s) in hg19.metaDb_tdreszer mdbPrint hg19 -vars="composite=wgEncodeSydhTfbs" -countObjs Using table named 'hg19.metaDb_tdreszer'. 151 objects mdbPrint hg19 -vars="composite=wgEncodeSydhTfbs" > wgEncodeSydhTfbs.ra mdbUpdate hg19 -table=metaDb wgEncodeSydhTfbs.ra ### Kates pet peeve semicolons mdbPrint hg19 -table=metaDb -vars="labVersion=%;%" -countObjs ~/bin/x86_64/mdbPrint hg19 -table=metaDb -vars="labVersion=%;%" -updDb=hg19 -updMdb=metaDb_tdreszer -updExp="composite,cell,treatment,antibody,control,replicate,view" -updVars="labVersion" > tmp.txt # hand edit then force. Affected 1 row(s) in hg19.metaDb Affected 1 row(s) in hg19.metaDb Affected 1 row(s) in hg19.metaDb Affected 1 row(s) in hg19.metaDb Affected 1 row(s) in hg19.metaDb Affected 1 row(s) in hg19.metaDb Affected 1 row(s) in hg19.metaDb Affected 1 row(s) in hg19.metaDb Affected 1 row(s) in hg19.metaDb Affected 1 row(s) in hg19.metaDb Affected 1 row(s) in hg19.metaDb Affected 1 row(s) in hg19.metaDb Affected 1 row(s) in hg19.metaDb Affected 1 row(s) in hg19.metaDb Affected 1 row(s) in hg19.metaDb Affected 1 row(s) in hg19.metaDb Affected 1 row(s) in hg19.metaDb mdbPrint hg19 -table=metaDb -vars="composite=wgEncodeSydhTfbs" > wgEncodeSydhTfbs.ra mdbPrint hg19 -table=metaDb -vars="composite=wgEncodeSydhHistone" > wgEncodeSydhHistone.ra 2010-06-22 Change all those downloads to displayed ================================================== select id,name,status,user_id from projects where status = "downloads" and user_id = 39 order by id; +------+-------------------------+-----------+---------+ | id | name | status | user_id | +------+-------------------------+-----------+---------+ | 1282 | SYDH_Hg19_Remap1 | downloads | 39 | | 1340 | SYDH_Remap_Harvard_0 | downloads | 39 | | 1341 | SYDH_Remap_Harvard_1 | downloads | 39 | | 1342 | SYDH_Remap_Harvard_2 | downloads | 39 | | 1343 | SYDH_Remap_Harvard_3 | downloads | 39 | | 1344 | SYDH_Remap_Harvard_4 | downloads | 39 | | 1345 | SYDH_GM12878_TBP | downloads | 39 | | 1346 | SYDH_HeLa_STAT3 | downloads | 39 | | 1347 | SYDH_HepG2_JunD | downloads | 39 | | 1348 | SYDH_HepG2_Nrf1 | downloads | 39 | | 1349 | SYDH_HepG2_Rad21 | downloads | 39 | | 1355 | SYDH_U2OS_Control | downloads | 39 | | 1356 | SYDH_U2OS_SetDB1 | downloads | 39 | | 1357 | SYDH_HepG2_USF2 | downloads | 39 | | 1358 | SYDH_Remap_Davis_0 | downloads | 39 | | 1359 | SYDH_Remap_Davis_1 | downloads | 39 | | 1360 | SYDH_Remap_Davis_2 | downloads | 39 | | 1361 | SYDH_Remap_Davis_3 | downloads | 39 | | 1362 | SYDH_Remap_Davis_4 | downloads | 39 | | 1364 | SYDH_Remap_Davis_6 | downloads | 39 | | 1365 | SYDH_HepG2_IRF3_V2 | downloads | 39 | | 1366 | SYDH_Remap_Stanford_1 | downloads | 39 | | 1367 | SYDH_Remap_Stanford_2 | downloads | 39 | | 1368 | SYDH_Remap_Stanford_3 | downloads | 39 | | 1369 | SYDH_Remap_Stanford_4 | downloads | 39 | | 1370 | SYDH_Remap_Stanford_5 | downloads | 39 | | 1371 | SYDH_Remap_Stanford_6 | downloads | 39 | | 1372 | SYDH_Remap_Stanford_7 | downloads | 39 | | 1373 | SYDH_Remap_Stanford_8 | downloads | 39 | | 1374 | SYDH_Remap_Stanford_9 | downloads | 39 | | 1375 | SYDH_Remap_Stanford_10 | downloads | 39 | | 1376 | SYDH_Remap_Stanford_11 | downloads | 39 | | 1377 | SYDH_Remap_Stanford_12 | downloads | 39 | | 1378 | SYDH_Remap_Stanford_13 | downloads | 39 | | 1379 | SYDH_Remap_Stanford_14 | downloads | 39 | | 1380 | SYDH_Remap_Stanford_15 | downloads | 39 | | 1381 | SYDH_Remap_Stanford_16 | downloads | 39 | | 1382 | SYDH_Remap_Stanford_17 | downloads | 39 | | 1383 | SYDH_Remap_Stanford_18 | downloads | 39 | | 1384 | SYDH_Remap_Stanford_19 | downloads | 39 | | 1385 | SYDH_Remap_Stanford_20 | downloads | 39 | | 1386 | SYDH_Remap_Stanford_21 | downloads | 39 | | 1387 | SYDH_Remap_Stanford_22 | downloads | 39 | | 1388 | SYDH_Remap_Stanford_23 | downloads | 39 | | 1389 | SYDH_Remap_Stanford_24 | downloads | 39 | | 1390 | SYDH_Remap_Stanford_25 | downloads | 39 | | 1391 | SYDH_Remap_Stanford_26 | downloads | 39 | | 1392 | SYDH_Remap_Stanford_27 | downloads | 39 | | 1393 | SYDH_Remap_Stanford_28 | downloads | 39 | | 1394 | SYDH_Remap_Stanford_29 | downloads | 39 | | 1395 | SYDH_Remap_Stanford_7b | downloads | 39 | | 1396 | SYDH_Remap_Stanford_17b | downloads | 39 | | 1397 | SYDH_Remap_Stanford_18b | downloads | 39 | | 1398 | SYDH_Remap_Stanford_20b | downloads | 39 | +------+-------------------------+-----------+---------+ 54 rows in set (0.00 sec) /cluster/data/encode/pipeline/bin/encodeStatus.pl 1282 displayed -force /cluster/data/encode/pipeline/bin/encodeStatus.pl 1340 displayed -force /cluster/data/encode/pipeline/bin/encodeStatus.pl 1341 displayed -force /cluster/data/encode/pipeline/bin/encodeStatus.pl 1342 displayed -force /cluster/data/encode/pipeline/bin/encodeStatus.pl 1343 displayed -force /cluster/data/encode/pipeline/bin/encodeStatus.pl 1344 displayed -force /cluster/data/encode/pipeline/bin/encodeStatus.pl 1345 displayed -force /cluster/data/encode/pipeline/bin/encodeStatus.pl 1346 displayed -force /cluster/data/encode/pipeline/bin/encodeStatus.pl 1347 displayed -force /cluster/data/encode/pipeline/bin/encodeStatus.pl 1348 displayed -force /cluster/data/encode/pipeline/bin/encodeStatus.pl 1349 displayed -force /cluster/data/encode/pipeline/bin/encodeStatus.pl 1355 displayed -force /cluster/data/encode/pipeline/bin/encodeStatus.pl 1356 displayed -force /cluster/data/encode/pipeline/bin/encodeStatus.pl 1357 displayed -force /cluster/data/encode/pipeline/bin/encodeStatus.pl 1358 displayed -force /cluster/data/encode/pipeline/bin/encodeStatus.pl 1359 displayed -force /cluster/data/encode/pipeline/bin/encodeStatus.pl 1360 displayed -force /cluster/data/encode/pipeline/bin/encodeStatus.pl 1361 displayed -force /cluster/data/encode/pipeline/bin/encodeStatus.pl 1362 displayed -force /cluster/data/encode/pipeline/bin/encodeStatus.pl 1364 displayed -force /cluster/data/encode/pipeline/bin/encodeStatus.pl 1365 displayed -force /cluster/data/encode/pipeline/bin/encodeStatus.pl 1366 displayed -force /cluster/data/encode/pipeline/bin/encodeStatus.pl 1367 displayed -force /cluster/data/encode/pipeline/bin/encodeStatus.pl 1368 displayed -force /cluster/data/encode/pipeline/bin/encodeStatus.pl 1369 displayed -force /cluster/data/encode/pipeline/bin/encodeStatus.pl 1370 displayed -force /cluster/data/encode/pipeline/bin/encodeStatus.pl 1371 displayed -force /cluster/data/encode/pipeline/bin/encodeStatus.pl 1372 displayed -force /cluster/data/encode/pipeline/bin/encodeStatus.pl 1373 displayed -force /cluster/data/encode/pipeline/bin/encodeStatus.pl 1374 displayed -force /cluster/data/encode/pipeline/bin/encodeStatus.pl 1375 displayed -force /cluster/data/encode/pipeline/bin/encodeStatus.pl 1376 displayed -force /cluster/data/encode/pipeline/bin/encodeStatus.pl 1377 displayed -force /cluster/data/encode/pipeline/bin/encodeStatus.pl 1378 displayed -force /cluster/data/encode/pipeline/bin/encodeStatus.pl 1379 displayed -force /cluster/data/encode/pipeline/bin/encodeStatus.pl 1380 displayed -force /cluster/data/encode/pipeline/bin/encodeStatus.pl 1381 displayed -force /cluster/data/encode/pipeline/bin/encodeStatus.pl 1382 displayed -force /cluster/data/encode/pipeline/bin/encodeStatus.pl 1383 displayed -force /cluster/data/encode/pipeline/bin/encodeStatus.pl 1384 displayed -force /cluster/data/encode/pipeline/bin/encodeStatus.pl 1385 displayed -force /cluster/data/encode/pipeline/bin/encodeStatus.pl 1386 displayed -force /cluster/data/encode/pipeline/bin/encodeStatus.pl 1387 displayed -force /cluster/data/encode/pipeline/bin/encodeStatus.pl 1388 displayed -force /cluster/data/encode/pipeline/bin/encodeStatus.pl 1389 displayed -force /cluster/data/encode/pipeline/bin/encodeStatus.pl 1390 displayed -force /cluster/data/encode/pipeline/bin/encodeStatus.pl 1391 displayed -force /cluster/data/encode/pipeline/bin/encodeStatus.pl 1392 displayed -force /cluster/data/encode/pipeline/bin/encodeStatus.pl 1393 displayed -force /cluster/data/encode/pipeline/bin/encodeStatus.pl 1394 displayed -force /cluster/data/encode/pipeline/bin/encodeStatus.pl 1395 displayed -force /cluster/data/encode/pipeline/bin/encodeStatus.pl 1396 displayed -force /cluster/data/encode/pipeline/bin/encodeStatus.pl 1397 displayed -force /cluster/data/encode/pipeline/bin/encodeStatus.pl 1398 displayed -force select id,name,status,user_id from projects where status = "downloads" and user_id = 39 order by id; Empty set (0.01 sec) 2010-06-22 Mark hg18 loads as on hold ===================================== select id,name,status,user_id from projects where id in (1182,1183,1183,1184,1185,1186); +------+--------------------+-----------------+---------+ | id | name | status | user_id | +------+--------------------+-----------------+---------+ | 1182 | SYDH_GM12878_Max | validate failed | 39 | | 1183 | SYDH_GM12878_Pol2 | validate failed | 39 | | 1184 | SYDH_GM12878_c_Fos | validate failed | 39 | | 1185 | SYDH_GM12878_c_Jun | validate failed | 39 | | 1186 | SYDH_GM12878_c_Myc | validate failed | 39 | +------+--------------------+-----------------+---------+ 5 rows in set (0.00 sec) update projects set status = "hold hg18" where id in (1182,1183,1183,1184,1185,1186); Rows matched: 5 Changed: 5 Warnings: 0 select id,name,status,user_id from projects where id in (1182,1183,1183,1184,1185,1186); +------+--------------------+-----------+---------+ | id | name | status | user_id | +------+--------------------+-----------+---------+ | 1182 | SYDH_GM12878_Max | hold hg18 | 39 | | 1183 | SYDH_GM12878_Pol2 | hold hg18 | 39 | | 1184 | SYDH_GM12878_c_Fos | hold hg18 | 39 | | 1185 | SYDH_GM12878_c_Jun | hold hg18 | 39 | | 1186 | SYDH_GM12878_c_Myc | hold hg18 | 39 | +------+--------------------+-----------+---------+ 5 rows in set (0.00 sec)