Finished reading input. ++ echo CB7103c/./s_6_1_sequence_read1.fastq ++ tr , ' ' + fastq_file_set1=CB7103c/./s_6_1_sequence_read1.fastq ++ cd /data/maqgene/reads ++ cat CB7103c/./s_6_1_sequence_read1.fastq ++ wc -l ++ cut -f 1 -d ' ' + TOTAL_LINES=85316276 ++ echo '(85316276 / 5000000) + (85316276 % 5000000 != 0)' ++ bc + num_chunks=18 + set +x make -j 14 -l 14 -C /data/maqgene/work --warn-undefined-variables -I /data/maqgene -f /data/maqgene/makefile BFA_FILE=elegans.bfa MAQGENE_GENOME_DIR=/data/maqgene/genomes reads_cksum=1641004721 map_cksum=3060321379 pileup_cksum=1851439560 cns_cksum=3649018006 umdd=50000 dmdd=1000 umid=1000 dmid=1000 max_gene_radius=50000 full_results_dir=/data/maqgene/out/example_user/CB7103c outfile_basename=CB7103c map_parameters=" -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0" assemble_parameters=" -N 2 -q 0 -r 0.0 -m 7 -Q 100 -p " pileup_parameters=" -Q 100 -p -m 7 -q 0" CHUNK_SIZE=5000000 NUM_CHUNKS=18 Will process 85316276 lines of input in 18 chunks make: Entering directory `/data/maqgene/work' # Wed Nov 7 19:08:19 GMT 2012: Removing frontend files in case this is a duplicate run ... rm -f /data/maqgene/out/example_user/CB7103c/CB7103c_{grouped.txt,flat.txt} rm -f /data/maqgene/out/example_user/CB7103c/CB7103c_uncovered.txt /data/maqgene/out/example_user/CB7103c/CB7103c_coverage.txt /data/maqgene/out/example_user/CB7103c/CB7103c_pileup.txt /data/maqgene/out/example_user/CB7103c/CB7103c_log.txt /data/maqgene/out/example_user/CB7103c/CB7103c_check.txt /data/maqgene/out/example_user/CB7103c/CB7103c_unmapped.txt make: Leaving directory `/data/maqgene/work' make: Entering directory `/data/maqgene/work' /data/maqgene/makefile:76: warning: undefined variable `date' /data/maqgene/makefile:78: warning: undefined variable `date' # : Regrouping fastq reads into chunks of size 5000000. split -l 5000000 -a 5 -d <(cat /data/maqgene/reads/CB7103c/./s_6_2_sequence_read2.fastq) 3060321379.2.fastq. # : Regrouping fastq reads into chunks of size 5000000. split -l 5000000 -a 5 -d <(cat /data/maqgene/reads/CB7103c/./s_6_1_sequence_read1.fastq) 3060321379.1.fastq. for stem in 00000 00001 00002 00003 00004 00005 00006 00007 00008 00009 00010 00011 00012 00013 00014 00015 00016 00017; do mv 3060321379.1.fastq.$stem 3060321379.$stem.1.fastq; done touch 1641004721_split1 for stem in 00000 00001 00002 00003 00004 00005 00006 00007 00008 00009 00010 00011 00012 00013 00014 00015 00016 00017; do mv 3060321379.2.fastq.$stem 3060321379.$stem.2.fastq; done touch 1641004721_split2 # Wed Nov 7 19:08:57 GMT 2012: Converting fastq files to bfq ... # Wed Nov 7 19:08:57 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3060321379.00001.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3060321379.00001.1.bfq # Wed Nov 7 19:08:57 GMT 2012: Converting fastq files to bfq ... # Wed Nov 7 19:08:57 GMT 2012: Converting fastq files to bfq ... # Wed Nov 7 19:08:57 GMT 2012: Converting fastq files to bfq ... # Wed Nov 7 19:08:57 GMT 2012: Converting fastq files to bfq ... # Wed Nov 7 19:08:57 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3060321379.00000.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3060321379.00000.1.bfq /data/maqgene/bin/maq sol2sanger 3060321379.00003.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3060321379.00003.1.bfq # Wed Nov 7 19:08:57 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3060321379.00005.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3060321379.00005.1.bfq /data/maqgene/bin/maq sol2sanger 3060321379.00006.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3060321379.00006.1.bfq # Wed Nov 7 19:08:57 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3060321379.00004.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3060321379.00004.1.bfq # Wed Nov 7 19:08:57 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3060321379.00007.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3060321379.00007.1.bfq # Wed Nov 7 19:08:57 GMT 2012: Converting fastq files to bfq ... # Wed Nov 7 19:08:57 GMT 2012: Converting fastq files to bfq ... # Wed Nov 7 19:08:57 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3060321379.00002.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3060321379.00002.1.bfq /data/maqgene/bin/maq sol2sanger 3060321379.00008.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3060321379.00008.1.bfq /data/maqgene/bin/maq sol2sanger 3060321379.00009.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3060321379.00009.1.bfq /data/maqgene/bin/maq sol2sanger 3060321379.00010.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3060321379.00010.1.bfq # Wed Nov 7 19:08:57 GMT 2012: Converting fastq files to bfq ... out | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3060321379.00011.1.bfq /data/maqgene/bin/maq sol2sanger 3060321379.00012.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3060321379.00012.1.bfq /data/maqgene/bin/maq sol2sanger 3060321379.00013.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3060321379.00013.1.bfq -- finish writing file '3060321379.00013.1.bfq' -- 1250000 sequences were loaded. # Wed Nov 7 19:09:25 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3060321379.00014.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3060321379.00014.1.bfq -- finish writing file '3060321379.00002.1.bfq' -- 1250000 sequences were loaded. # Wed Nov 7 19:09:27 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3060321379.00015.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3060321379.00015.1.bfq -- finish writing file '3060321379.00012.1.bfq' -- 1250000 sequences were loaded. # Wed Nov 7 19:09:27 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3060321379.00016.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3060321379.00016.1.bfq -- finish writing file '3060321379.00001.1.bfq' -- 1250000 sequences were loaded. # Wed Nov 7 19:09:28 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3060321379.00017.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3060321379.00017.1.bfq -- finish writing file '3060321379.00009.1.bfq' -- 1250000 sequences were loaded. # Wed Nov 7 19:09:28 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3060321379.00000.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3060321379.00000.2.bfq -- finish writing file '3060321379.00005.1.bfq' -- 1250000 sequences were loaded. # Wed Nov 7 19:09:28 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3060321379.00001.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3060321379.00001.2.bfq -- finish writing file '3060321379.00008.1.bfq' -- 1250000 sequences were loaded. # Wed Nov 7 19:09:29 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3060321379.00002.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3060321379.00002.2.bfq -- finish writing file '3060321379.00004.1.bfq' -- 1250000 sequences were loaded. # Wed Nov 7 19:09:29 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3060321379.00003.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3060321379.00003.2.bfq -- finish writing file '3060321379.00006.1.bfq' -- 1250000 sequences were loaded. # Wed Nov 7 19:09:29 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3060321379.00004.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3060321379.00004.2.bfq -- finish writing file '3060321379.00010.1.bfq' -- 1250000 sequences were loaded. # Wed Nov 7 19:09:29 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3060321379.00005.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3060321379.00005.2.bfq -- finish writing file '3060321379.00007.1.bfq' -- 1250000 sequences were loaded. # Wed Nov 7 19:09:29 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3060321379.00006.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3060321379.00006.2.bfq -- finish writing file '3060321379.00000.1.bfq' -- 1250000 sequences were loaded. # Wed Nov 7 19:09:29 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3060321379.00007.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3060321379.00007.2.bfq -- finish writing file '3060321379.00003.1.bfq' -- 1250000 sequences were loaded. # Wed Nov 7 19:09:29 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3060321379.00008.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3060321379.00008.2.bfq -- finish writing file '3060321379.00011.1.bfq' -- 1250000 sequences were loaded. # Wed Nov 7 19:09:30 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3060321379.00009.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3060321379.00009.2.bfq -- finish writing file '3060321379.00017.1.bfq' -- 79069 sequences were loaded. # Wed Nov 7 19:09:30 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3060321379.00010.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3060321379.00010.2.bfq -- finish writing file '3060321379.00014.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3060321379.00002.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '3060321379.00015.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3060321379.00005.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '3060321379.00004.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '3060321379.00008.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '3060321379.00016.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3060321379.00001.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '3060321379.00009.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '3060321379.00007.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '3060321379.00000.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '3060321379.00003.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '3060321379.00006.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '3060321379.00010.2.bfq' -- 1250000 sequences were loaded. # Wed Nov 7 19:10:00 GMT 2012: Mapping file(s) 3060321379.00009.1.bfq 3060321379.00009.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3060321379.00009.unmapped -H 3060321379.00009.mismatch \ 3060321379.00009.map /data/maqgene/genomes/elegans.bfa 3060321379.00009.1.bfq 3060321379.00009.2.bfq 2> /dev/null # Wed Nov 7 19:10:11 GMT 2012: Mapping file(s) 3060321379.00008.1.bfq 3060321379.00008.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3060321379.00000.unmapped -H 3060321379.00000.mismatch \ 3060321379.00000.map /data/maqgene/genomes/elegans.bfa 3060321379.00000.1.bfq 3060321379.00000.2.bfq 2> /dev/null /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3060321379.00008.unmapped -H 3060321379.00008.mismatch \ 3060321379.00008.map /data/maqgene/genomes/elegans.bfa 3060321379.00008.1.bfq 3060321379.00008.2.bfq 2> /dev/null # Wed Nov 7 19:10:12 GMT 2012: Mapping file(s) 3060321379.00007.1.bfq 3060321379.00007.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3060321379.00007.unmapped -H 3060321379.00007.mismatch \ 3060321379.00007.map /data/maqgene/genomes/elegans.bfa 3060321379.00007.1.bfq 3060321379.00007.2.bfq 2> /dev/null # Wed Nov 7 19:10:13 GMT 2012: Mapping file(s) 3060321379.00005.1.bfq 3060321379.00005.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3060321379.00005.unmapped -H 3060321379.00005.mismatch \ 3060321379.00005.map /data/maqgene/genomes/elegans.bfa 3060321379.00005.1.bfq 3060321379.00005.2.bfq 2> /dev/null # Wed Nov 7 19:10:14 GMT 2012: Mapping file(s) 3060321379.00004.1.bfq 3060321379.00004.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3060321379.00004.unmapped -H 3060321379.00004.mismatch \ 3060321379.00004.map /data/maqgene/genomes/elegans.bfa 3060321379.00004.1.bfq 3060321379.00004.2.bfq 2> /dev/null # Wed Nov 7 19:10:15 GMT 2012: Mapping file(s) 3060321379.00002.1.bfq 3060321379.00002.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3060321379.00002.unmapped -H 3060321379.00002.mismatch \ 3060321379.00002.map /data/maqgene/genomes/elegans.bfa 3060321379.00002.1.bfq 3060321379.00002.2.bfq 2> /dev/null # Wed Nov 7 19:10:16 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3060321379.00016.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3060321379.00016.2.bfq # Wed Nov 7 19:10:16 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3060321379.00017.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3060321379.00017.2.bfq # Wed Nov 7 19:10:17 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3060321379.00015.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3060321379.00015.2.bfq /data/maqgene/bin/maq sol2sanger 3060321379.00014.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3060321379.00014.2.bfq -- finish writing file '3060321379.00017.2.bfq' -- 79069 sequences were loaded. # Wed Nov 7 19:10:18 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3060321379.00013.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3060321379.00013.2.bfq # Wed Nov 7 19:10:18 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3060321379.00012.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3060321379.00012.2.bfq # Wed Nov 7 19:10:19 GMT 2012: Mapping file(s) 3060321379.00001.1.bfq 3060321379.00001.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3060321379.00001.unmapped -H 3060321379.00001.mismatch \ 3060321379.00001.map /data/maqgene/genomes/elegans.bfa 3060321379.00001.1.bfq 3060321379.00001.2.bfq 2> /dev/null # Wed Nov 7 19:10:19 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3060321379.00011.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3060321379.00011.2.bfq -- finish writing file '3060321379.00016.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '3060321379.00013.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '3060321379.00015.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '3060321379.00012.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '3060321379.00014.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '3060321379.00011.2.bfq' -- 1250000 sequences were loaded. # Wed Nov 7 19:11:32 GMT 2012: Mapping file(s) 3060321379.00016.1.bfq 3060321379.00016.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3060321379.00016.unmapped -H 3060321379.00016.mismatch \ 3060321379.00016.map /data/maqgene/genomes/elegans.bfa 3060321379.00016.1.bfq 3060321379.00016.2.bfq 2> /dev/null # Wed Nov 7 19:11:33 GMT 2012: Mapping file(s) 3060321379.00015.1.bfq 3060321379.00015.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3060321379.00015.unmapped -H 3060321379.00015.mismatch \ 3060321379.00015.map /data/maqgene/genomes/elegans.bfa 3060321379.00015.1.bfq 3060321379.00015.2.bfq 2> /dev/null # Wed Nov 7 19:11:34 GMT 2012: Mapping file(s) 3060321379.00013.1.bfq 3060321379.00013.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3060321379.00013.unmapped -H 3060321379.00013.mismatch \ 3060321379.00013.map /data/maqgene/genomes/elegans.bfa 3060321379.00013.1.bfq 3060321379.00013.2.bfq 2> /dev/null # Wed Nov 7 19:11:35 GMT 2012: Mapping file(s) 3060321379.00010.1.bfq 3060321379.00010.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3060321379.00010.unmapped -H 3060321379.00010.mismatch \ 3060321379.00010.map /data/maqgene/genomes/elegans.bfa 3060321379.00010.1.bfq 3060321379.00010.2.bfq 2> /dev/null # Wed Nov 7 19:11:36 GMT 2012: Mapping file(s) 3060321379.00006.1.bfq 3060321379.00006.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3060321379.00006.unmapped -H 3060321379.00006.mismatch \ 3060321379.00006.map /data/maqgene/genomes/elegans.bfa 3060321379.00006.1.bfq 3060321379.00006.2.bfq 2> /dev/null # Wed Nov 7 19:11:37 GMT 2012: Mapping file(s) 3060321379.00003.1.bfq 3060321379.00003.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3060321379.00003.unmapped -H 3060321379.00003.mismatch \ 3060321379.00003.map /data/maqgene/genomes/elegans.bfa 3060321379.00003.1.bfq 3060321379.00003.2.bfq 2> /dev/null # Wed Nov 7 19:18:22 GMT 2012: Mapping file(s) 3060321379.00012.1.bfq 3060321379.00012.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3060321379.00012.unmapped -H 3060321379.00012.mismatch \ 3060321379.00012.map /data/maqgene/genomes/elegans.bfa 3060321379.00012.1.bfq 3060321379.00012.2.bfq 2> /dev/null # Wed Nov 7 19:18:22 GMT 2012: Mapping file(s) 3060321379.00014.1.bfq 3060321379.00014.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3060321379.00014.unmapped -H 3060321379.00014.mismatch \ 3060321379.00014.map /data/maqgene/genomes/elegans.bfa 3060321379.00014.1.bfq 3060321379.00014.2.bfq 2> /dev/null # Wed Nov 7 19:18:25 GMT 2012: Mapping file(s) 3060321379.00017.1.bfq 3060321379.00017.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3060321379.00017.unmapped -H 3060321379.00017.mismatch \ 3060321379.00017.map /data/maqgene/genomes/elegans.bfa 3060321379.00017.1.bfq 3060321379.00017.2.bfq 2> /dev/null # Wed Nov 7 19:18:25 GMT 2012: Mapping file(s) 3060321379.00011.1.bfq 3060321379.00011.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3060321379.00011.unmapped -H 3060321379.00011.mismatch \ 3060321379.00011.map /data/maqgene/genomes/elegans.bfa 3060321379.00011.1.bfq 3060321379.00011.2.bfq 2> /dev/null # Wed Nov 7 19:24:31 GMT 2012: Merging all maps ... # Wed Nov 7 19:24:31 GMT 2012: Merging all *.unmapped files ... /data/maqgene/bin/maq mapmerge 3060321379.map 3060321379.00000.map 3060321379.00001.map 3060321379.00002.map 3060321379.00003.map 3060321379.00004.map 3060321379.00005.map 3060321379.00006.map 3060321379.00007.map 3060321379.00008.map 3060321379.00009.map 3060321379.00010.map 3060321379.00011.map 3060321379.00012.map 3060321379.00013.map 3060321379.00014.map 3060321379.00015.map 3060321379.00016.map 3060321379.00017.map cat 3060321379.00000.unmapped 3060321379.00001.unmapped 3060321379.00002.unmapped 3060321379.00003.unmapped 3060321379.00004.unmapped 3060321379.00005.unmapped 3060321379.00006.unmapped 3060321379.00007.unmapped 3060321379.00008.unmapped 3060321379.00009.unmapped 3060321379.00010.unmapped 3060321379.00011.unmapped 3060321379.00012.unmapped 3060321379.00013.unmapped 3060321379.00014.unmapped 3060321379.00015.unmapped 3060321379.00016.unmapped 3060321379.00017.unmapped > 3060321379_unmapped.txt # Wed Nov 7 19:24:31 GMT 2012: Linking backend file 3060321379_unmapped.txt to /data/maqgene/out/example_user/CB7103c/CB7103c_unmapped.txt ln -fs /data/maqgene/work/3060321379_unmapped.txt /data/maqgene/out/example_user/CB7103c/CB7103c_unmapped.txt /data/maqgene/makefile:126: warning: undefined variable `mapcheck_parameters' # Wed Nov 7 19:31:06 GMT 2012: Creating pileup ... # Wed Nov 7 19:31:06 GMT 2012: Generating consensus ... /data/maqgene/bin/maq pileup -Q 100 -p -m 7 -q 0 /data/maqgene/genomes/elegans.bfa 3060321379.map > 1851439560_pileup.txt /data/maqgene/bin/maq assemble -N 2 -q 0 -r 0.0 -m 7 -Q 100 -p 3649018006.cns \ /data/maqgene/genomes/elegans.bfa 3060321379.map 2> 3649018006_log.txt # Wed Nov 7 19:31:06 GMT 2012: Running 'mapcheck' ... /data/maqgene/bin/maq mapcheck /data/maqgene/genomes/elegans.bfa 3060321379.map > 3060321379_check.txt \ 2>/dev/null # Wed Nov 7 19:32:38 GMT 2012: Linking backend file 3060321379_check.txt to /data/maqgene/out/example_user/CB7103c/CB7103c_check.txt ln -fs /data/maqgene/work/3060321379_check.txt /data/maqgene/out/example_user/CB7103c/CB7103c_check.txt /data/maqgene/bin/filter_matching_lines 1851439560_pileup.txt "%s\t%i\t" \ <(/usr/bin/mysql -Dmaqgenedb -umaqgene --skip-column-names --batch --raw --local-infile -e "select distinct dna, start + 1 from elegans_features where feature = 'SNP' order by dna, start") "%s\t%i\n" si \ | /data/maqgene/bin/filter_maq_pileup 'AaCcGgTt,.' 0 \ > 1851439560_known_snps # Wed Nov 7 19:33:11 GMT 2012: Getting uncovered regions ... cut -f 1,2,4 1851439560_pileup.txt \ | /data/maqgene/bin/get_uncovered_regions 50 \ > 1851439560_uncovered.txt # Wed Nov 7 19:33:11 GMT 2012: Making coverage histogram ... (echo -en "sequencing_depth\tnumber_of_bases\n"; \ cut -f 4 1851439560_pileup.txt \ | /data/maqgene/bin/pileup_histogram 100) > 1851439560_coverage.txt # Wed Nov 7 19:33:11 GMT 2012: Linking backend file 1851439560_pileup.txt to /data/maqgene/out/example_user/CB7103c/CB7103c_pileup.txt ln -fs /data/maqgene/work/1851439560_pileup.txt /data/maqgene/out/example_user/CB7103c/CB7103c_pileup.txt # Wed Nov 7 19:33:29 GMT 2012: Linking backend file 1851439560_coverage.txt to /data/maqgene/out/example_user/CB7103c/CB7103c_coverage.txt ln -fs /data/maqgene/work/1851439560_coverage.txt /data/maqgene/out/example_user/CB7103c/CB7103c_coverage.txt # Wed Nov 7 19:33:37 GMT 2012: Filtering and loading pileup for analysis ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 1851439560_pileup; create table 1851439560_pileup ( dna enum('I','II','III','IV','MtDNA','V','X') NOT NULL, start int(10) NOT NULL, ref_base char(1) NOT NULL, read_depth int(5) NOT NULL, sample_reads varchar(100) NOT NULL, A_fwd int(5) NOT NULL, A_rev int(5) NOT NULL, C_fwd int(5) NOT NULL, C_rev int(5) NOT NULL, G_fwd int(5) NOT NULL, G_rev int(5) NOT NULL, T_fwd int(5) NOT NULL, T_rev int(5) NOT NULL, wt_fwd int(5) NOT NULL, wt_rev int(5) NOT NULL, primary key (dna, start) );" cat 1851439560_pileup.txt \ | /data/maqgene/bin/filter_maq_pileup 'AaCcGgTt,.' 2 \ | awk 'BEGIN { OFS="\t" } { $5=substr($5,1,100); print $0 }' \ | /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "load data local infile '/dev/stdin' into table 1851439560_pileup (dna, @start, ref_base, read_depth, sample_reads, A_fwd, A_rev, C_fwd, C_rev, G_fwd, G_rev, T_fwd, T_rev, wt_fwd, wt_rev) set start = @start - 1; flush table 1851439560_pileup" # Wed Nov 7 19:33:41 GMT 2012: Linking backend file 1851439560_uncovered.txt to /data/maqgene/out/example_user/CB7103c/CB7103c_uncovered.txt ln -fs /data/maqgene/work/1851439560_uncovered.txt /data/maqgene/out/example_user/CB7103c/CB7103c_uncovered.txt cat 1851439560_known_snps \ | awk 'BEGIN { OFS="\t" } { $5=substr($5,1,100); print $0 }' \ | /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "load data local infile '/dev/stdin' into table 1851439560_pileup (dna, @start, ref_base, read_depth, sample_reads, A_fwd, A_rev, C_fwd, C_rev, G_fwd, G_rev, T_fwd, T_rev, wt_fwd, wt_rev) set start = @start - 1; flush table 1851439560_pileup" touch 1851439560_pileup # Wed Nov 7 19:34:21 GMT 2012: Writing snp read counts ... /usr/bin/mysql -Dmaqgenedb -umaqgene --skip-column-names --batch --raw --local-infile --column-names -e "select f.id, f.dna, f.start + 1 start, e.snp_name, e.snp_base, if(e.snp_base = 'a', p.A_fwd + p.A_rev, if (e.snp_base = 'c', p.C_fwd + p.C_rev, if (e.snp_base = 'g', p.G_fwd + p.G_rev, if (e.snp_base = 't', p.T_fwd + p.T_rev, -1)))) snp_reads, p.ref_base, p.wt_fwd + p.wt_rev wt_reads, p.read_depth, p.sample_reads from elegans_features f join elegans_snp_changes e on (f.attribute = e.snp_name) join 1851439560_pileup p using (dna,start)" > /data/maqgene/out/example_user/CB7103c/CB7103c_snp_read_counts.txt 0 snp read count lines written. # Wed Nov 7 19:34:25 GMT 2012: Linking backend file 3649018006_log.txt to /data/maqgene/out/example_user/CB7103c/CB7103c_log.txt ln -fs /data/maqgene/work/3649018006_log.txt /data/maqgene/out/example_user/CB7103c/CB7103c_log.txt # Wed Nov 7 19:34:25 GMT 2012: Extracting point mutants from consensus ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 3649018006_snps; create table 3649018006_snps ( id int(10) NOT NULL auto_increment, dna char(40) NOT NULL, start int(10) NOT NULL, end int(10) NOT NULL, indel_size int(5) NOT NULL, variant_type enum('indel', 'point') NOT NULL, ref_base char NOT NULL, sample_base char NOT NULL, snp_score int(5) NOT NULL, read_depth int(5) NOT NULL, loci_multiplicity double(5,2) NOT NULL, mapping_quality int(5) NOT NULL, neighbor_quality int(5) NOT NULL, primary key (id), unique key (dna, start), key (indel_size) )" /data/maqgene/bin/maq cns2snp 3649018006.cns \ | cat -b | /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "load data local infile '/dev/stdin' into table 3649018006_snps (id, dna, @start, ref_base, sample_base, snp_score, read_depth, loci_multiplicity, mapping_quality, neighbor_quality) set start = @start - 1, end = @start, indel_size = 0, variant_type = 'point'; flush table 3649018006_snps;" # Wed Nov 7 19:34:31 GMT 2012: Extracting indels from consensus ... /data/maqgene/bin/maq indelsoa /data/maqgene/genomes/elegans.bfa 3060321379.map \ | awk '{ if ($5+$6-$4 >= 5 && $4 <= 1) { print $0 } }' \ | /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "load data local infile '/dev/stdin' into table 3649018006_snps (dna, @start, indel_size, @num_spanning_reads, @num_left_reads, @num_right_reads, @junk) set id = NULL, start = @start - 1, end = @start - 1 + if (indel_size > 0, 0, -indel_size), ref_base = 'X', sample_base = 'X', variant_type = 'indel', snp_score = -1000, read_depth = if (@num_left_reads < @num_right_reads, @num_left_reads, @num_right_reads), loci_multiplicity = -1000, mapping_quality = -1000, neighbor_quality = -1000; flush table 3649018006_snps;" # Wed Nov 7 19:35:16 GMT 2012: Adding placeholders for known SNPs. cat 1851439560_known_snps \ | /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "load data local infile '/dev/stdin' ignore into table 3649018006_snps (dna, @start, ref_base, read_depth, @junk) set id = NULL, start = @start - 1, end = @start - 1, variant_type = 'point', snp_score = -1000, loci_multiplicity = -1000, mapping_quality = -1000, neighbor_quality = -1000; flush table 3649018006_snps;" Found 160674 variants. touch 3649018006_snps # Wed Nov 7 19:35:17 GMT 2012: Loading uncovered regions into table ... # Wed Nov 7 19:35:17 GMT 2012: Finding all genomic features overlapping variants... cat 1851439560_uncovered.txt \ | /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 1851439560_uncovered; create table 1851439560_uncovered ( id int(10) NOT NULL auto_increment, dna char(40) NOT NULL, start int(10) NOT NULL, end int(10) NOT NULL, primary key (id) ) auto_increment = 160675; load data local infile '/dev/stdin' into table 1851439560_uncovered (dna, start, end)" /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 3649018006_rel_snps; CREATE TABLE 3649018006_rel_snps ( association_id INT(10) NOT NULL, query_region_id INT(10) unsigned NOT NULL, target_region_id INT(10) NOT NULL, distance INT(10) NOT NULL, overlap INT(10) NOT NULL, same_strand enum('SAME', 'OPP') NOT NULL, num_regions_between INT(3) NOT NULL, PRIMARY KEY (association_id), KEY (query_region_id), KEY (target_region_id) )" # Wed Nov 7 19:35:17 GMT 2012: Getting masking regions /data/maqgene/bin/associate_regions -b -1 -c -1000000 -m 2 -o >(/usr/bin/mysql -Dmaqgenedb -umaqgene --skip-column-names --batch --raw --local-infile -e "drop table if exists 3649018006_masked_ids; create table 3649018006_masked_ids (query_region_id int(10) NOT NULL, primary key (query_region_id)); load data local infile '/dev/stdin' ignore into table 3649018006_masked_ids (@j1, query_region_id, @j3, @j4, @j5, @j6, @j7)") -d /data/maqgene/genomes/elegans.dnas -p /data/maqgene/genomes -q <(/usr/bin/mysql -Dmaqgenedb -umaqgene --skip-column-names --batch --raw --local-infile -e "select id, 'elegans', dna, start, end, '+' from 3649018006_snps") -t <(/usr/bin/mysql -Dmaqgenedb -umaqgene --skip-column-names --batch --raw --local-infile -e "select id,'elegans',dna,start,end,strand from elegans_features feature where feature.feature not in ('mRNA', 'intron')") 1>/dev/null; /data/maqgene/bin/associate_regions -b -1 -c -1000000 -m 0 -o >(/usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "load data local infile '/dev/stdin' into table 3649018006_rel_snps; flush table 3649018006_rel_snps") -d /data/maqgene/genomes/elegans.dnas -p /data/maqgene/genomes -q <(/usr/bin/mysql -Dmaqgenedb -umaqgene --skip-column-names --batch --raw --local-infile -e "select id, 'elegans', dna, start, end, '+' from 3649018006_snps") -t <(/usr/bin/mysql -Dmaqgenedb -umaqgene --skip-column-names --batch --raw --local-infile -e "select id, 'elegans', dna,start,end,strand from elegans_features where feature in ('SNP','exon','five_prime_UTR','intron','mRNA','three_prime_UTR','ncRNA')") 1>/dev/null Uncovered region statistics: chromosome number_uncovered_regions total_uncovered_length I 8 926 II 20 2328 III 16 1349 IV 24 3590 V 19 3942 X 21 6568 touch 1851439560_uncovered # Wed Nov 7 19:35:18 GMT 2012: Finding mRNA features overlapping uncovered regions ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 1851439560_uncovered_rel; CREATE TABLE 1851439560_uncovered_rel ( association_id INT(10) NOT NULL, query_region_id INT(10) unsigned NOT NULL, target_region_id INT(10) NOT NULL, distance INT(10) NOT NULL, overlap INT(10) NOT NULL, same_strand enum('SAME', 'OPP') NOT NULL, num_regions_between INT(3) NOT NULL, PRIMARY KEY (association_id), KEY (query_region_id), KEY (target_region_id) )" /data/maqgene/bin/associate_regions -b -1 -c -1000000 -m 0 -o >(/usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "load data local infile '/dev/stdin' into table 1851439560_uncovered_rel; flush table 1851439560_uncovered_rel") -d /data/maqgene/genomes/elegans.dnas -p /data/maqgene/genomes -q <(/usr/bin/mysql -Dmaqgenedb -umaqgene --skip-column-names --batch --raw --local-infile -e "select id, 'elegans', dna, start, end, '+' from 1851439560_uncovered") -t <(/usr/bin/mysql -Dmaqgenedb -umaqgene --skip-column-names --batch --raw --local-infile -e "select id, 'elegans', dna,start,end,strand from elegans_features where feature in ('SNP','exon','five_prime_UTR','intron','mRNA','three_prime_UTR','ncRNA')") 1>/dev/null touch 1851439560_uncovered_rel # Wed Nov 7 19:35:20 GMT 2012: Calculating translation start offsets for uncovered regions... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 1851439560_offsets_uncovered; create table 1851439560_offsets_uncovered ( id int(10) NOT NULL, gene varchar(50) NOT NULL, 5prime_offset int(10) NOT NULL, 3prime_offset int(10) NOT NULL, total_length int(10) NOT NULL, boundary_type char(20) NOT NULL, primary key (id, gene, boundary_type) );" /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 1851439560_offsets_uncovered select reg.id, gene.attribute gene, if(exon.strand = '+', if(reg.start < min(exon.start), reg.start - min(exon.start), sum(if(reg.start < exon.end, reg.start, exon.end) - if(reg.start < exon.start, reg.start, exon.start))), if(max(exon.end) < reg.start, max(exon.end) - reg.start, sum(if(exon.end < reg.start, reg.start, exon.end) - if(exon.start < reg.start, reg.start, exon.start))) ), if(exon.strand = '+', if(max(exon.end) < reg.start, max(exon.end) - reg.start, sum(if(exon.end < reg.start, reg.start, exon.end) - if(exon.start < reg.start, reg.start, exon.start))), if(reg.start < min(exon.start), reg.start - min(exon.start), sum(if(reg.start < exon.end, reg.start, exon.end) - if(reg.start < exon.start, reg.start, exon.start)))), sum(exon.end - exon.start) total_length, 'start' boundary_type from 1851439560_uncovered reg join 1851439560_uncovered_rel rel on (reg.id = rel.query_region_id) join elegans_features gene on (rel.target_region_id = gene.id) join elegans_features exon on (exon.attribute = gene.attribute) where exon.feature = 'exon' and gene.feature = 'mRNA' group by reg.id, gene.attribute" touch 3649018006_masked_ids /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 1851439560_offsets_uncovered select reg.id, gene.attribute gene, if(exon.strand = '+', if(reg.end < min(exon.start), reg.end - min(exon.start), sum(if(reg.end < exon.end, reg.end, exon.end) - if(reg.end < exon.start, reg.end, exon.start))), if(max(exon.end) < reg.end, max(exon.end) - reg.end, sum(if(exon.end < reg.end, reg.end, exon.end) - if(exon.start < reg.end, reg.end, exon.start))) ), if(exon.strand = '+', if(max(exon.end) < reg.end, max(exon.end) - reg.end, sum(if(exon.end < reg.end, reg.end, exon.end) - if(exon.start < reg.end, reg.end, exon.start))), if(reg.end < min(exon.start), reg.end - min(exon.start), sum(if(reg.end < exon.end, reg.end, exon.end) - if(reg.end < exon.start, reg.end, exon.start)))), sum(exon.end - exon.start) total_length, 'end' boundary_type from 1851439560_uncovered reg join 1851439560_uncovered_rel rel on (reg.id = rel.query_region_id) join elegans_features gene on (rel.target_region_id = gene.id) join elegans_features exon on (exon.attribute = gene.attribute) where exon.feature = 'exon' and gene.feature = 'mRNA' group by reg.id, gene.attribute" touch 1851439560_offsets_uncovered touch 3649018006_rel_snps # Wed Nov 7 19:35:21 GMT 2012: Calculating translation start offsets... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 3649018006_offsets_snps; create table 3649018006_offsets_snps ( id int(10) NOT NULL, gene varchar(50) NOT NULL, 5prime_offset int(10) NOT NULL, 3prime_offset int(10) NOT NULL, total_length int(10) NOT NULL, boundary_type char(20) NOT NULL, primary key (id, gene, boundary_type) );" # Wed Nov 7 19:35:21 GMT 2012: Getting intergenic regions /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 3649018006_rel_intergenic; create table 3649018006_rel_intergenic like 3649018006_rel_snps"; /data/maqgene/bin/associate_regions -b 50000 -c -1000000 -m 2 -o >(/usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "load data local infile '/dev/stdin' into table 3649018006_rel_intergenic; flush table 3649018006_rel_intergenic") -d /data/maqgene/genomes/elegans.dnas -p /data/maqgene/genomes -q <(/usr/bin/mysql -Dmaqgenedb -umaqgene --skip-column-names --batch --raw --local-infile -e "select id, 'elegans', dna, start, end, '+' from 3649018006_snps") -t <(/usr/bin/mysql -Dmaqgenedb -umaqgene --skip-column-names --batch --raw --local-infile -e "select id, 'elegans',dna,start,end,strand from elegans_features feature where feature.feature = 'mRNA'") 1>/dev/null; /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 3649018006_offsets_snps select reg.id, gene.attribute gene, if(exon.strand = '+', if(reg.start < min(exon.start), reg.start - min(exon.start), sum(if(reg.start < exon.end, reg.start, exon.end) - if(reg.start < exon.start, reg.start, exon.start))), if(max(exon.end) < reg.start, max(exon.end) - reg.start, sum(if(exon.end < reg.start, reg.start, exon.end) - if(exon.start < reg.start, reg.start, exon.start))) ), if(exon.strand = '+', if(max(exon.end) < reg.start, max(exon.end) - reg.start, sum(if(exon.end < reg.start, reg.start, exon.end) - if(exon.start < reg.start, reg.start, exon.start))), if(reg.start < min(exon.start), reg.start - min(exon.start), sum(if(reg.start < exon.end, reg.start, exon.end) - if(reg.start < exon.start, reg.start, exon.start)))), sum(exon.end - exon.start) total_length, 'start' boundary_type from 3649018006_snps reg join 3649018006_rel_snps rel on (reg.id = rel.query_region_id) join elegans_features gene on (rel.target_region_id = gene.id) join elegans_features exon on (exon.attribute = gene.attribute) where exon.feature = 'exon' and gene.feature = 'mRNA' group by reg.id, gene.attribute" # Wed Nov 7 19:35:24 GMT 2012: Filtering masked intergenic regions /usr/bin/mysql -Dmaqgenedb -umaqgene --skip-column-names --batch --raw --local-infile -e "delete i.* from 3649018006_rel_intergenic i join 3649018006_masked_ids m using (query_region_id)" touch 3649018006_rel_intergenic # Wed Nov 7 19:35:29 GMT 2012: Classifying intergenic relations /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 3649018006_intergenic_assoc; create table 3649018006_intergenic_assoc ( id INT(10) NOT NULL, target_region_id INT(10) NOT NULL, relation enum ('upstream', 'downstream', 'into') NOT NULL, distance INT(10) NOT NULL, num_regions_between INT(3) NOT NULL, attribute varchar(50) NOT NULL, primary key (id, target_region_id), key (id, attribute) ); insert into 3649018006_intergenic_assoc select snp.id, rel.target_region_id, if (rel.overlap > 0, 'into', if (feature.strand = '+', if (snp.end < feature.start, 'upstream', 'downstream'), if (feature.end < snp.start, 'upstream', 'downstream') ) ) relation, rel.distance, rel.num_regions_between, feature.attribute from 3649018006_snps snp join 3649018006_rel_intergenic rel on (snp.id = rel.query_region_id) join elegans_features feature on (rel.target_region_id = feature.id)" touch 3649018006_intergenic_assoc touch 3649018006_offsets_snps # Wed Nov 7 19:35:43 GMT 2012: Getting codons affected by point mutations... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 3649018006_codons; create table 3649018006_codons ( id int(10) NOT NULL, gene varchar(50) NOT NULL, ref_codon char(4) NOT NULL, sam_codon char(4) NOT NULL, start char(1) NOT NULL, primary key (id, gene) ); insert into 3649018006_codons select snp.id, off.gene, @ref_codon := substr(gene_dna.sequence, (floor(if(feature.strand = '+', off.5prime_offset, off.5prime_offset - 1 ) / 3 ) * 3 ) + 1, 3 ) ref_codon, insert(@ref_codon, (if(feature.strand = '+', off.5prime_offset, off.5prime_offset - 1) % 3) + 1, 1, if(feature.strand = '+', snp.sample_base, substr('ACGTTGCA', instr('ACGTTGCA', snp.sample_base)+4, 1) ) ) sam_codon, if((feature.strand = '+' && off.5prime_offset < 3) || (feature.strand = '-' && off.5prime_offset - 1 < 3), 'Y', 'N') start from 3649018006_offsets_snps off join 3649018006_snps snp on (off.id = snp.id) join elegans_coding_dna gene_dna using (gene) join elegans_features feature on (gene_dna.gene = feature.attribute and feature.start <= snp.start and feature.end >= snp.end) where snp.variant_type = 'point' and feature.feature = 'exon' and off.boundary_type = 'start' and off.5prime_offset >= 0 and off.3prime_offset >= 0;" touch 3649018006_codons /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 3649018006_marked; create table 3649018006_marked ( id int(10) NOT NULL, class varchar(100) NOT NULL, description varchar(100) NOT NULL, parent_feature varchar(100) NOT NULL, primary key (id, class, parent_feature) );" # Wed Nov 7 19:35:50 GMT 2012: Finding exonic indels ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 3649018006_marked select snp.id, if (snp.indel_size < 0, if (rel.overlap % 3 = 0, 'inframe', 'frameshift'), if (snp.indel_size % 3 = 0, 'inframe', 'frameshift')) class, if (rel.overlap != snp.end - snp.start, 'exon_boundary', 'none') description, feature.attribute parent_feature from 3649018006_snps snp join 3649018006_rel_snps rel on (snp.id = rel.query_region_id) join elegans_features feature on (rel.target_region_id = feature.id) where feature.feature = 'exon' and snp.variant_type = 'indel';" # Wed Nov 7 19:35:51 GMT 2012: Finding coding variants ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 3649018006_marked select trans.id, if (reference_codons.amino = sample_codons.amino, 'silent', if (reference_codons.amino3 = 'stop', 'readthrough', if (sample_codons.amino3 = 'stop', 'premature_stop', if (trans.start = 'Y' and sample_codons.is_start != 'Y', 'non_start', 'missense') ) ) ) class, concat(ref_codon,'->',sam_codon,'[', reference_codons.amino3,'->',sample_codons.amino3,']') description, trans.gene from 3649018006_codons trans join elegans_genetic_code reference_codons on (trans.ref_codon = reference_codons.codon) join elegans_genetic_code sample_codons on (trans.sam_codon = sample_codons.codon);" # Wed Nov 7 19:35:51 GMT 2012: Finding noncoding variants ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 3649018006_marked select snp.id, feature.feature class, 'none' description, feature.attribute parent_feature from 3649018006_snps snp join 3649018006_rel_snps rel on (snp.id = rel.query_region_id) join elegans_features feature on (rel.target_region_id = feature.id) where feature.feature not in ('exon', 'intron', 'mRNA');" # Wed Nov 7 19:35:51 GMT 2012: Finding splice site variants ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 3649018006_marked select snp.id, if (feature.strand = '+', if (snp.start - feature.start < 2, 'splice_donor', 'splice_acceptor'), if (snp.start - feature.start < 2, 'splice_acceptor', 'splice_donor')) class, 'none' description, feature.attribute parent_feature from 3649018006_snps snp join 3649018006_rel_snps rel on (snp.id = rel.query_region_id) join elegans_features feature on (rel.target_region_id = feature.id) where feature.feature = 'intron' and rel.distance > -2;" # Wed Nov 7 19:35:52 GMT 2012: Finding intergenic and intronic variants ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 3649018006_marked select id, 'nongenic' class, concat(if (relation in ('upstream','into'), - distance, distance),' ',relation) description, attribute from 3649018006_intergenic_assoc where ((relation = 'upstream' and num_regions_between = 0 and distance < 50000) or (relation = 'upstream' and num_regions_between < 2 and distance < 1000) or (relation = 'downstream' and num_regions_between = 0 and distance < 1000) or (relation = 'downstream' and num_regions_between < 2 and distance < 1000) or relation = 'into' );" # Wed Nov 7 19:35:54 GMT 2012: Finding uncovered regions in genes ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 3649018006_marked select b.id, 'uncovered', if(b.5prime_offset = e.5prime_offset, concat('non-exonic, ',unc.start - gene.start,' to ',unc.end - gene.start,' bp into'), concat( if(b.5prime_offset < 0, concat(-b.5prime_offset, ' bp upstream'), if(b.3prime_offset < 0, concat(-b.3prime_offset, ' bp downstream'), concat('codon ',floor(b.5prime_offset / 3) + 1) ) ), ' to ', if(e.3prime_offset < 0, concat(-e.3prime_offset, ' bp downstream'), if(e.5prime_offset < 0, concat(-e.5prime_offset, ' bp upstream'), concat('codon ',ceiling(e.5prime_offset / 3) + 1) ) ), ' (', format(100 * (if(e.5prime_offset < 0,0,e.5prime_offset) - (if(b.5prime_offset < 0,0,b.5prime_offset)) ) / b.total_length,0 ), ' % of ', floor(b.total_length/3), ' codons)' ) ) description, b.gene from 1851439560_uncovered unc join 1851439560_offsets_uncovered b using (id) join 1851439560_offsets_uncovered e using (id, gene) join elegans_features gene on (e.gene = gene.attribute) where b.boundary_type = 'start' and e.boundary_type = 'end' and gene.strand = '+' and gene.feature = 'mRNA' union select b.id, 'uncovered', if(b.5prime_offset = e.5prime_offset, concat('non-exonic, ',gene.end - unc.end,' to ',gene.end - unc.start,' bp into'), concat( if(e.5prime_offset < 0, concat(-e.5prime_offset, ' bp upstream'), if(e.3prime_offset < 0, concat(-e.3prime_offset, ' bp downstream'), concat('codon ',floor(e.5prime_offset / 3) + 1) ) ), ' to ', if(b.3prime_offset < 0, concat(-b.3prime_offset, ' bp downstream'), if(b.5prime_offset < 0, concat(-b.5prime_offset, ' bp upstream'), concat('codon ',ceiling(b.5prime_offset / 3) + 1) ) ), ' (', format(100 * (if(b.5prime_offset < 0,0,b.5prime_offset) - (if(e.5prime_offset < 0,0,e.5prime_offset)) ) / b.total_length,0 ), ' % of ', floor(b.total_length/3), ' codons)' ) ) description, b.gene from 1851439560_uncovered unc join 1851439560_offsets_uncovered b using (id) join 1851439560_offsets_uncovered e using (id, gene) join elegans_features gene on (e.gene = gene.attribute) where b.boundary_type = 'start' and e.boundary_type = 'end' and gene.strand = '-' and gene.feature = 'mRNA'" # Wed Nov 7 19:35:54 GMT 2012: Variants found: +-----------------+-----------------+ | class | number_variants | +-----------------+-----------------+ | five_prime_UTR | 1281 | | frameshift | 17 | | inframe | 1 | | missense | 6210 | | ncRNA | 867 | | nongenic | 124227 | | non_start | 9 | | premature_stop | 687 | | readthrough | 20 | | silent | 7428 | | SNP | 1008 | | splice_acceptor | 46 | | splice_donor | 48 | | three_prime_UTR | 3562 | | uncovered | 27 | +-----------------+-----------------+ touch 3649018006_marked # Wed Nov 7 19:35:55 GMT 2012: Combining results ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 3649018006_combined; create table 3649018006_combined (primary key (id, class, description), key (dna, start)) as select snp.id, 'CB7103c' mutant_strain, snp.dna, snp.start + 1 start, snp.end - snp.start length, snp.ref_base reference_base, snp.sample_base sample_base, snp.snp_score consensus_score, snp.loci_multiplicity, snp.mapping_quality, snp.neighbor_quality, (pile.wt_fwd + pile.wt_rev) number_wildtype_reads, (snp.read_depth - (pile.wt_fwd + pile.wt_rev)) number_variant_reads, snp.read_depth sequencing_depth, pile.sample_reads, snp.variant_type, snp.indel_size, class.class, class.description, group_concat(class.parent_feature order by class.parent_feature) parent_features from 3649018006_snps snp join 1851439560_pileup pile using (dna,start) join 3649018006_marked class on (snp.id = class.id) left join elegans_per_locus using (dna,start) where (snp.variant_type = 'point' and (snp.snp_score >= 3 and snp.loci_multiplicity <= 10 and snp.neighbor_quality >= 0 and pile.read_depth >= 4 and ((pile.read_depth - pile.wt_fwd - pile.wt_rev) / pile.read_depth) >= 0.5) or snp.variant_type = 'indel' ) group by id, class, description union select unc.id id, 'CB7103c' mutant_strain, unc.dna, unc.start + 1 start, unc.end - unc.start length, '-' reference_base, '-' sample_base, 0 consensus_score, 0, 0, 0, 0 number_wildtype_reads, 0 number_variant_reads, 0 sequencing_depth, '' sample_reads, 'uncovered', 0, class.class, class.description, group_concat(class.parent_feature order by class.parent_feature) parent_features from 1851439560_uncovered unc join 3649018006_marked class on (unc.id = class.id) left join elegans_per_locus using (dna,start) group by id, class, description; alter table 3649018006_combined order by dna, start, length" touch 3649018006_combined # Wed Nov 7 19:35:56 GMT 2012: Writing results to grouped file ... /usr/bin/mysql -Dmaqgenedb -umaqgene --skip-column-names --batch --raw --local-infile --column-names -e "select id, mutant_strain, dna, start, length, reference_base, sample_base, consensus_score, loci_multiplicity, mapping_quality, neighbor_quality, number_wildtype_reads, number_variant_reads, sequencing_depth, sample_reads, variant_type, indel_size, group_concat(class) classes, group_concat(description) descriptions, group_concat(concat('{',parent_features,'}')) parent_features from 3649018006_combined group by id order by dna, start;" > /data/maqgene/out/example_user/CB7103c/CB7103c_grouped.txt # Wed Nov 7 19:35:56 GMT 2012: Writing results to flat file ... /usr/bin/mysql -Dmaqgenedb -umaqgene --skip-column-names --batch --raw --local-infile --column-names -e "select * from 3649018006_combined" > /data/maqgene/out/example_user/CB7103c/CB7103c_flat.txt 3032 lines written. 1837 lines written. rm 3060321379.00003.map 3060321379.00006.2.bfq 3060321379.00001.1.bfq 3060321379.00010.1.bfq 3060321379.00004.1.fastq 3060321379.00006.mismatch 3060321379.00016.1.bfq 3060321379.00001.2.bfq 3060321379.00000.2.bfq 3060321379.00014.unmapped 3060321379.00009.unmapped 3060321379.00014.1.fastq 3060321379.00017.1.bfq 3060321379.00010.2.bfq 3060321379.00002.1.bfq 3060321379.00004.2.fastq 3060321379.00010.mismatch 3060321379.00016.2.bfq 3060321379.00016.mismatch 3060321379.00005.map 3060321379.00012.1.bfq 3060321379.00011.mismatch 3060321379.00014.2.fastq 3060321379.00017.2.bfq 3060321379.00017.mismatch 3060321379.00002.mismatch 3060321379.00015.map 3060321379.00008.map 3060321379.00007.1.fastq 3060321379.00006.unmapped 3060321379.00012.2.bfq 3060321379.00012.mismatch 3060321379.00006.1.fastq 3060321379.00002.1.fastq 3060321379.00000.unmapped 3060321379.00003.1.bfq 3060321379.00007.map 3060321379.00000.1.fastq 3060321379.00008.1.bfq 3060321379.00008.1.fastq 3060321379.00001.unmapped 3060321379.00010.unmapped 3060321379.00013.1.bfq 3060321379.00016.unmapped 3060321379.00006.2.fastq 3060321379.00001.1.fastq 3060321379.00010.1.fastq 3060321379.00016.1.fastq 3060321379.00004.map 3060321379.00003.2.bfq 3060321379.00011.unmapped 3060321379.00003.mismatch 3060321379.00000.mismatch 3060321379.00000.2.fastq 3060321379.00011.1.fastq 3060321379.00017.unmapped 3060321379.00005.1.bfq 3060321379.00002.unmapped 3060321379.00009.1.fastq 3060321379.00013.2.bfq 3060321379.00017.1.fastq 3060321379.00014.map 3060321379.00013.mismatch 3060321379.00001.2.fastq 3060321379.00010.2.fastq 3060321379.00007.2.fastq 3060321379.00016.2.fastq 3060321379.00012.map 3060321379.00012.unmapped 3060321379.00015.1.bfq 3060321379.00011.2.fastq 3060321379.00012.1.fastq 3060321379.00007.1.bfq 3060321379.00009.map 3060321379.00017.2.fastq 3060321379.00002.2.fastq 3060321379.00001.mismatch 3060321379.00008.2.fastq 3060321379.00015.2.bfq 3060321379.00012.2.fastq 3060321379.00015.mismatch 3060321379.00003.unmapped 3060321379.00005.2.bfq 3060321379.00006.map 3060321379.00003.1.fastq 1641004721_split2 3060321379.00011.2.bfq 3060321379.00004.1.bfq 3060321379.00013.unmapped 3060321379.00009.2.fastq 3060321379.00000.map 3060321379.00013.1.fastq 3060321379.00008.2.bfq 3060321379.00005.mismatch 3060321379.00001.map 3060321379.00010.map 3060321379.00009.1.bfq 3060321379.00014.1.bfq 3060321379.00003.2.fastq 3060321379.00016.map 3060321379.00005.unmapped 3060321379.00007.2.bfq 3060321379.00004.2.bfq 3060321379.00005.1.fastq 3060321379.00004.mismatch 3060321379.00011.map 3060321379.00011.1.bfq 3060321379.00013.2.fastq 3060321379.00017.map 3060321379.00002.2.bfq 3060321379.00002.map 3060321379.00014.2.bfq 3060321379.00015.unmapped 3060321379.00014.mismatch 3060321379.00015.1.fastq 3060321379.00007.unmapped 3060321379.00008.mismatch 3060321379.00005.2.fastq 3060321379.00007.mismatch 3060321379.00006.1.bfq 3060321379.00013.map 3060321379.00015.2.fastq 1641004721_split1 3060321379.00008.unmapped 3060321379.00009.mismatch 3060321379.00000.1.bfq 3060321379.00009.2.bfq 3060321379.00004.unmapped make: Leaving directory `/data/maqgene/work' make: Entering directory `/data/maqgene/work' # Wed Nov 7 19:35:58 GMT 2012: Cleaning intermediate data ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 3649018006_snps,3649018006_rel,3649018006_masked_ids,3649018006_rel_intergenic,3649018006_intergenic_assoc,3649018006_offsets,3649018006_codons,3649018006_marked,3649018006_combined,1851439560_pileup" rm -f 3649018006_snps 3649018006_rel 3649018006_masked_ids 3649018006_rel_intergenic 3649018006_intergenic_assoc 3649018006_offsets 3649018006_codons 3649018006_marked 3649018006_combined 1851439560_pileup make: Leaving directory `/data/maqgene/work'