Finished reading input. ++ echo DC9b/./s_4_1_sequence_read1.fastq ++ tr , ' ' + fastq_file_set1=DC9b/./s_4_1_sequence_read1.fastq ++ cd /data/maqgene/reads ++ cat DC9b/./s_4_1_sequence_read1.fastq ++ wc -l ++ cut -f 1 -d ' ' + TOTAL_LINES=92239540 ++ echo '(92239540 / 5000000) + (92239540 % 5000000 != 0)' ++ bc + num_chunks=19 + 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=1348410179 map_cksum=1865274982 pileup_cksum=2993879594 cns_cksum=704221325 umdd=50000 dmdd=1000 umid=1000 dmid=1000 max_gene_radius=50000 full_results_dir=/data/maqgene/out/example_user/DC9b outfile_basename=DC9b 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=19 Will process 92239540 lines of input in 19 chunks make: Entering directory `/data/maqgene/work' # Wed Nov 7 19:38:01 GMT 2012: Removing frontend files in case this is a duplicate run ... rm -f /data/maqgene/out/example_user/DC9b/DC9b_{grouped.txt,flat.txt} rm -f /data/maqgene/out/example_user/DC9b/DC9b_uncovered.txt /data/maqgene/out/example_user/DC9b/DC9b_coverage.txt /data/maqgene/out/example_user/DC9b/DC9b_pileup.txt /data/maqgene/out/example_user/DC9b/DC9b_log.txt /data/maqgene/out/example_user/DC9b/DC9b_check.txt /data/maqgene/out/example_user/DC9b/DC9b_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. # : Regrouping fastq reads into chunks of size 5000000. split -l 5000000 -a 5 -d <(cat /data/maqgene/reads/DC9b/./s_4_1_sequence_read1.fastq) 1865274982.1.fastq. split -l 5000000 -a 5 -d <(cat /data/maqgene/reads/DC9b/./s_4_2_sequence_read2.fastq) 1865274982.2.fastq. for stem in 00000 00001 00002 00003 00004 00005 00006 00007 00008 00009 00010 00011 00012 00013 00014 00015 00016 00017 00018; do mv 1865274982.1.fastq.$stem 1865274982.$stem.1.fastq; done touch 1348410179_split1 for stem in 00000 00001 00002 00003 00004 00005 00006 00007 00008 00009 00010 00011 00012 00013 00014 00015 00016 00017 00018; do mv 1865274982.2.fastq.$stem 1865274982.$stem.2.fastq; done touch 1348410179_split2 # Wed Nov 7 19:38:39 GMT 2012: Converting fastq files to bfq ... # Wed Nov 7 19:38:39 GMT 2012: Converting fastq files to bfq ... # Wed Nov 7 19:38:39 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1865274982.00001.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1865274982.00001.1.bfq # Wed Nov 7 19:38:39 GMT 2012: Converting fastq files to bfq ... # Wed Nov 7 19:38:39 GMT 2012: Converting fastq files to bfq ... # Wed Nov 7 19:38:39 GMT 2012: Converting fastq files to bfq ... # Wed Nov 7 19:38:39 GMT 2012: Converting fastq files to bfq ... # Wed Nov 7 19:38:39 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1865274982.00005.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1865274982.00005.1.bfq # Wed Nov 7 19:38:39 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1865274982.00002.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1865274982.00002.1.bfq /data/maqgene/bin/maq sol2sanger 1865274982.00000.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1865274982.00000.1.bfq # Wed Nov 7 19:38:39 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1865274982.00004.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1865274982.00004.1.bfq /data/maqgene/bin/maq sol2sanger 1865274982.00007.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1865274982.00007.1.bfq # Wed Nov 7 19:38:39 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1865274982.00009.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1865274982.00009.1.bfq /data/maqgene/bin/maq sol2sanger 1865274982.00010.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1865274982.00010.1.bfq /data/maqgene/bin/maq sol2sanger 1865274982.00003.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1865274982.00003.1.bfq # Wed Nov 7 19:38:39 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1865274982.00008.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1865274982.00008.1.bfq /data/maqgene/bin/maq sol2sanger 1865274982.00006.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1865274982.00006.1.bfq /data/maqgene/bin/maq sol2sanger 1865274982.00011.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1865274982.00011.1.bfq /data/maqgene/bin/maq sol2sanger 1865274982.00012.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1865274982.00012.1.bfq /data/maqgene/bin/maq sol2sanger 1865274982.00013.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1865274982.00013.1.bfq -- finish writing file '1865274982.00002.1.bfq' -- 1250000 sequences were loaded. # Wed Nov 7 19:39:08 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1865274982.00014.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1865274982.00014.1.bfq -- finish writing file '1865274982.00012.1.bfq' -- 1250000 sequences were loaded. # Wed Nov 7 19:39:09 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1865274982.00015.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1865274982.00015.1.bfq -- finish writing file '1865274982.00003.1.bfq' -- 1250000 sequences were loaded. # Wed Nov 7 19:39:09 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1865274982.00016.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1865274982.00016.1.bfq -- finish writing file '1865274982.00008.1.bfq' -- 1250000 sequences were loaded. # Wed Nov 7 19:39:10 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1865274982.00017.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1865274982.00017.1.bfq -- finish writing file '1865274982.00007.1.bfq' -- 1250000 sequences were loaded. # Wed Nov 7 19:39:10 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1865274982.00018.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1865274982.00018.1.bfq -- finish writing file '1865274982.00005.1.bfq' -- 1250000 sequences were loaded. # Wed Nov 7 19:39:10 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1865274982.00000.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1865274982.00000.2.bfq -- finish writing file '1865274982.00001.1.bfq' -- 1250000 sequences were loaded. # Wed Nov 7 19:39:10 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1865274982.00001.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1865274982.00001.2.bfq -- finish writing file '1865274982.00006.1.bfq' -- 1250000 sequences were loaded. # Wed Nov 7 19:39:10 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1865274982.00002.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1865274982.00002.2.bfq -- finish writing file '1865274982.00010.1.bfq' -- 1250000 sequences were loaded. # Wed Nov 7 19:39:11 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1865274982.00003.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1865274982.00003.2.bfq -- finish writing file '1865274982.00004.1.bfq' -- 1250000 sequences were loaded. # Wed Nov 7 19:39:11 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1865274982.00004.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1865274982.00004.2.bfq -- finish writing file '1865274982.00000.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1865274982.00013.1.bfq' -- 1250000 sequences were loaded. # Wed Nov 7 19:39:11 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1865274982.00006.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1865274982.00006.2.bfq # Wed Nov 7 19:39:11 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1865274982.00005.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1865274982.00005.2.bfq -- finish writing file '1865274982.00009.1.bfq' -- 1250000 sequences were loaded. # Wed Nov 7 19:39:12 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1865274982.00007.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1865274982.00007.2.bfq -- finish writing file '1865274982.00011.1.bfq' -- 1250000 sequences were loaded. # Wed Nov 7 19:39:12 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1865274982.00008.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1865274982.00008.2.bfq -- finish writing file '1865274982.00018.1.bfq' -- 559885 sequences were loaded. -- finish writing file '1865274982.00014.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1865274982.00001.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1865274982.00016.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1865274982.00005.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1865274982.00017.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1865274982.00004.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1865274982.00015.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1865274982.00002.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1865274982.00008.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1865274982.00006.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1865274982.00000.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1865274982.00003.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1865274982.00007.2.bfq' -- 1250000 sequences were loaded. # Wed Nov 7 19:39:41 GMT 2012: Mapping file(s) 1865274982.00004.1.bfq 1865274982.00004.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1865274982.00004.unmapped -H 1865274982.00004.mismatch \ 1865274982.00004.map /data/maqgene/genomes/elegans.bfa 1865274982.00004.1.bfq 1865274982.00004.2.bfq 2> /dev/null # Wed Nov 7 19:39:49 GMT 2012: Mapping file(s) 1865274982.00005.1.bfq 1865274982.00005.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1865274982.00005.unmapped -H 1865274982.00005.mismatch \ 1865274982.00005.map /data/maqgene/genomes/elegans.bfa 1865274982.00005.1.bfq 1865274982.00005.2.bfq 2> /dev/null # Wed Nov 7 19:39:51 GMT 2012: Mapping file(s) 1865274982.00002.1.bfq 1865274982.00002.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1865274982.00002.unmapped -H 1865274982.00002.mismatch \ 1865274982.00002.map /data/maqgene/genomes/elegans.bfa 1865274982.00002.1.bfq 1865274982.00002.2.bfq 2> /dev/null # Wed Nov 7 19:39:53 GMT 2012: Mapping file(s) 1865274982.00001.1.bfq 1865274982.00001.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1865274982.00001.unmapped -H 1865274982.00001.mismatch \ 1865274982.00001.map /data/maqgene/genomes/elegans.bfa 1865274982.00001.1.bfq 1865274982.00001.2.bfq 2> /dev/null # Wed Nov 7 19:39:54 GMT 2012: Converting fastq files to bfq ... # Wed Nov 7 19:39:54 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1865274982.00018.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1865274982.00018.2.bfq /data/maqgene/bin/maq sol2sanger 1865274982.00017.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1865274982.00017.2.bfq # Wed Nov 7 19:39:55 GMT 2012: Converting fastq files to bfq ... # Wed Nov 7 19:39:55 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1865274982.00016.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1865274982.00016.2.bfq /data/maqgene/bin/maq sol2sanger 1865274982.00015.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1865274982.00015.2.bfq # Wed Nov 7 19:39:56 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1865274982.00014.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1865274982.00014.2.bfq # Wed Nov 7 19:39:56 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1865274982.00013.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1865274982.00013.2.bfq # Wed Nov 7 19:39:57 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1865274982.00011.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1865274982.00011.2.bfq # Wed Nov 7 19:39:57 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1865274982.00012.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1865274982.00012.2.bfq # Wed Nov 7 19:39:59 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1865274982.00010.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1865274982.00010.2.bfq # Wed Nov 7 19:39:59 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1865274982.00009.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1865274982.00009.2.bfq -- finish writing file '1865274982.00018.2.bfq' -- 559885 sequences were loaded. -- finish writing file '1865274982.00015.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1865274982.00017.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1865274982.00016.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1865274982.00013.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1865274982.00014.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1865274982.00009.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1865274982.00010.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1865274982.00011.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1865274982.00012.2.bfq' -- 1250000 sequences were loaded. # Wed Nov 7 19:40:40 GMT 2012: Mapping file(s) 1865274982.00009.1.bfq 1865274982.00009.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1865274982.00009.unmapped -H 1865274982.00009.mismatch \ 1865274982.00009.map /data/maqgene/genomes/elegans.bfa 1865274982.00009.1.bfq 1865274982.00009.2.bfq 2> /dev/null # Wed Nov 7 19:40:41 GMT 2012: Mapping file(s) 1865274982.00003.1.bfq 1865274982.00003.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1865274982.00003.unmapped -H 1865274982.00003.mismatch \ 1865274982.00003.map /data/maqgene/genomes/elegans.bfa 1865274982.00003.1.bfq 1865274982.00003.2.bfq 2> /dev/null # Wed Nov 7 19:40:42 GMT 2012: Mapping file(s) 1865274982.00000.1.bfq 1865274982.00000.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1865274982.00000.unmapped -H 1865274982.00000.mismatch \ 1865274982.00000.map /data/maqgene/genomes/elegans.bfa 1865274982.00000.1.bfq 1865274982.00000.2.bfq 2> /dev/null # Wed Nov 7 19:40:43 GMT 2012: Mapping file(s) 1865274982.00018.1.bfq 1865274982.00018.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1865274982.00018.unmapped -H 1865274982.00018.mismatch \ 1865274982.00018.map /data/maqgene/genomes/elegans.bfa 1865274982.00018.1.bfq 1865274982.00018.2.bfq 2> /dev/null # Wed Nov 7 19:40:44 GMT 2012: Mapping file(s) 1865274982.00017.1.bfq 1865274982.00017.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1865274982.00017.unmapped -H 1865274982.00017.mismatch \ 1865274982.00017.map /data/maqgene/genomes/elegans.bfa 1865274982.00017.1.bfq 1865274982.00017.2.bfq 2> /dev/null # Wed Nov 7 19:40:45 GMT 2012: Mapping file(s) 1865274982.00016.1.bfq 1865274982.00016.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1865274982.00016.unmapped -H 1865274982.00016.mismatch \ 1865274982.00016.map /data/maqgene/genomes/elegans.bfa 1865274982.00016.1.bfq 1865274982.00016.2.bfq 2> /dev/null # Wed Nov 7 19:40:46 GMT 2012: Mapping file(s) 1865274982.00015.1.bfq 1865274982.00015.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1865274982.00015.unmapped -H 1865274982.00015.mismatch \ 1865274982.00015.map /data/maqgene/genomes/elegans.bfa 1865274982.00015.1.bfq 1865274982.00015.2.bfq 2> /dev/null # Wed Nov 7 19:40:47 GMT 2012: Mapping file(s) 1865274982.00008.1.bfq 1865274982.00008.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1865274982.00008.unmapped -H 1865274982.00008.mismatch \ 1865274982.00008.map /data/maqgene/genomes/elegans.bfa 1865274982.00008.1.bfq 1865274982.00008.2.bfq 2> /dev/null # Wed Nov 7 19:40:48 GMT 2012: Mapping file(s) 1865274982.00007.1.bfq 1865274982.00007.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1865274982.00007.unmapped -H 1865274982.00007.mismatch \ 1865274982.00007.map /data/maqgene/genomes/elegans.bfa 1865274982.00007.1.bfq 1865274982.00007.2.bfq 2> /dev/null # Wed Nov 7 19:40:49 GMT 2012: Mapping file(s) 1865274982.00006.1.bfq 1865274982.00006.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1865274982.00006.unmapped -H 1865274982.00006.mismatch \ 1865274982.00006.map /data/maqgene/genomes/elegans.bfa 1865274982.00006.1.bfq 1865274982.00006.2.bfq 2> /dev/null # Wed Nov 7 19:48:22 GMT 2012: Mapping file(s) 1865274982.00014.1.bfq 1865274982.00014.2.bfq # Wed Nov 7 19:48:22 GMT 2012: Mapping file(s) 1865274982.00012.1.bfq 1865274982.00012.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1865274982.00014.unmapped -H 1865274982.00014.mismatch \ 1865274982.00014.map /data/maqgene/genomes/elegans.bfa 1865274982.00014.1.bfq 1865274982.00014.2.bfq 2> /dev/null # Wed Nov 7 19:48:22 GMT 2012: Mapping file(s) 1865274982.00013.1.bfq 1865274982.00013.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1865274982.00012.unmapped -H 1865274982.00012.mismatch \ 1865274982.00012.map /data/maqgene/genomes/elegans.bfa 1865274982.00012.1.bfq 1865274982.00012.2.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 1865274982.00013.unmapped -H 1865274982.00013.mismatch \ 1865274982.00013.map /data/maqgene/genomes/elegans.bfa 1865274982.00013.1.bfq 1865274982.00013.2.bfq 2> /dev/null # Wed Nov 7 19:48:47 GMT 2012: Mapping file(s) 1865274982.00010.1.bfq 1865274982.00010.2.bfq # Wed Nov 7 19:48:47 GMT 2012: Mapping file(s) 1865274982.00011.1.bfq 1865274982.00011.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1865274982.00010.unmapped -H 1865274982.00010.mismatch \ 1865274982.00010.map /data/maqgene/genomes/elegans.bfa 1865274982.00010.1.bfq 1865274982.00010.2.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 1865274982.00011.unmapped -H 1865274982.00011.mismatch \ 1865274982.00011.map /data/maqgene/genomes/elegans.bfa 1865274982.00011.1.bfq 1865274982.00011.2.bfq 2> /dev/null # Wed Nov 7 19:54:43 GMT 2012: Merging all *.unmapped files ... cat 1865274982.00000.unmapped 1865274982.00001.unmapped 1865274982.00002.unmapped 1865274982.00003.unmapped 1865274982.00004.unmapped 1865274982.00005.unmapped 1865274982.00006.unmapped 1865274982.00007.unmapped 1865274982.00008.unmapped 1865274982.00009.unmapped 1865274982.00010.unmapped 1865274982.00011.unmapped 1865274982.00012.unmapped 1865274982.00013.unmapped 1865274982.00014.unmapped 1865274982.00015.unmapped 1865274982.00016.unmapped 1865274982.00017.unmapped 1865274982.00018.unmapped > 1865274982_unmapped.txt # Wed Nov 7 19:54:43 GMT 2012: Merging all maps ... /data/maqgene/bin/maq mapmerge 1865274982.map 1865274982.00000.map 1865274982.00001.map 1865274982.00002.map 1865274982.00003.map 1865274982.00004.map 1865274982.00005.map 1865274982.00006.map 1865274982.00007.map 1865274982.00008.map 1865274982.00009.map 1865274982.00010.map 1865274982.00011.map 1865274982.00012.map 1865274982.00013.map 1865274982.00014.map 1865274982.00015.map 1865274982.00016.map 1865274982.00017.map 1865274982.00018.map # Wed Nov 7 19:54:43 GMT 2012: Linking backend file 1865274982_unmapped.txt to /data/maqgene/out/example_user/DC9b/DC9b_unmapped.txt ln -fs /data/maqgene/work/1865274982_unmapped.txt /data/maqgene/out/example_user/DC9b/DC9b_unmapped.txt /data/maqgene/makefile:126: warning: undefined variable `mapcheck_parameters' # Wed Nov 7 20:01:51 GMT 2012: Generating consensus ... /data/maqgene/bin/maq assemble -N 2 -q 0 -r 0.0 -m 7 -Q 100 -p 704221325.cns \ /data/maqgene/genomes/elegans.bfa 1865274982.map 2> 704221325_log.txt # Wed Nov 7 20:01:51 GMT 2012: Creating pileup ... /data/maqgene/bin/maq pileup -Q 100 -p -m 7 -q 0 /data/maqgene/genomes/elegans.bfa 1865274982.map > 2993879594_pileup.txt # Wed Nov 7 20:01:51 GMT 2012: Running 'mapcheck' ... /data/maqgene/bin/maq mapcheck /data/maqgene/genomes/elegans.bfa 1865274982.map > 1865274982_check.txt \ 2>/dev/null # Wed Nov 7 20:03:33 GMT 2012: Linking backend file 1865274982_check.txt to /data/maqgene/out/example_user/DC9b/DC9b_check.txt ln -fs /data/maqgene/work/1865274982_check.txt /data/maqgene/out/example_user/DC9b/DC9b_check.txt /data/maqgene/bin/filter_matching_lines 2993879594_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 \ > 2993879594_known_snps # Wed Nov 7 20:04:05 GMT 2012: Getting uncovered regions ... cut -f 1,2,4 2993879594_pileup.txt \ | /data/maqgene/bin/get_uncovered_regions 50 \ > 2993879594_uncovered.txt (echo -en "sequencing_depth\tnumber_of_bases\n"; \ cut -f 4 2993879594_pileup.txt \ | /data/maqgene/bin/pileup_histogram 100) > 2993879594_coverage.txt # Wed Nov 7 20:04:05 GMT 2012: Linking backend file 2993879594_pileup.txt to /data/maqgene/out/example_user/DC9b/DC9b_pileup.txt ln -fs /data/maqgene/work/2993879594_pileup.txt /data/maqgene/out/example_user/DC9b/DC9b_pileup.txt # Wed Nov 7 20:04:22 GMT 2012: Linking backend file 2993879594_coverage.txt to /data/maqgene/out/example_user/DC9b/DC9b_coverage.txt ln -fs /data/maqgene/work/2993879594_coverage.txt /data/maqgene/out/example_user/DC9b/DC9b_coverage.txt # Wed Nov 7 20:04:31 GMT 2012: Linking backend file 2993879594_uncovered.txt to /data/maqgene/out/example_user/DC9b/DC9b_uncovered.txt ln -fs /data/maqgene/work/2993879594_uncovered.txt /data/maqgene/out/example_user/DC9b/DC9b_uncovered.txt # Wed Nov 7 20:04:32 GMT 2012: Filtering and loading pileup for analysis ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 2993879594_pileup; create table 2993879594_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 2993879594_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 2993879594_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 2993879594_pileup" # Wed Nov 7 20:05:14 GMT 2012: Linking backend file 704221325_log.txt to /data/maqgene/out/example_user/DC9b/DC9b_log.txt /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 704221325_snps; create table 704221325_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) )" ln -fs /data/maqgene/work/704221325_log.txt /data/maqgene/out/example_user/DC9b/DC9b_log.txt /data/maqgene/bin/maq cns2snp 704221325.cns \ | cat -b | /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "load data local infile '/dev/stdin' into table 704221325_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 704221325_snps;" cat 2993879594_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 2993879594_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 2993879594_pileup" touch 2993879594_pileup # Wed Nov 7 20:05:20 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 2993879594_pileup p using (dna,start)" > /data/maqgene/out/example_user/DC9b/DC9b_snp_read_counts.txt 0 snp read count lines written. # Wed Nov 7 20:05:20 GMT 2012: Extracting indels from consensus ... /data/maqgene/bin/maq indelsoa /data/maqgene/genomes/elegans.bfa 1865274982.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 704221325_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 704221325_snps;" # Wed Nov 7 20:06:09 GMT 2012: Adding placeholders for known SNPs. cat 2993879594_known_snps \ | /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "load data local infile '/dev/stdin' ignore into table 704221325_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 704221325_snps;" Found 160313 variants. touch 704221325_snps # Wed Nov 7 20:06:10 GMT 2012: Loading uncovered regions into table ... cat 2993879594_uncovered.txt \ | /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 2993879594_uncovered; create table 2993879594_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 = 160314; load data local infile '/dev/stdin' into table 2993879594_uncovered (dna, start, end)" /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 704221325_rel_snps; CREATE TABLE 704221325_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 20:06:10 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 704221325_masked_ids; create table 704221325_masked_ids (query_region_id int(10) NOT NULL, primary key (query_region_id)); load data local infile '/dev/stdin' ignore into table 704221325_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 704221325_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 704221325_rel_snps; flush table 704221325_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 704221325_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 12 1442 II 18 2061 III 15 1503 IV 21 1695 V 17 1913 X 15 6499 touch 2993879594_uncovered # Wed Nov 7 20:06:11 GMT 2012: Finding mRNA features overlapping uncovered regions ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 2993879594_uncovered_rel; CREATE TABLE 2993879594_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 2993879594_uncovered_rel; flush table 2993879594_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 2993879594_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 704221325_masked_ids touch 2993879594_uncovered_rel # Wed Nov 7 20:06:13 GMT 2012: Calculating translation start offsets for uncovered regions... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 2993879594_offsets_uncovered; create table 2993879594_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 2993879594_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 2993879594_uncovered reg join 2993879594_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" /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 2993879594_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 2993879594_uncovered reg join 2993879594_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 704221325_rel_snps # Wed Nov 7 20:06:14 GMT 2012: Calculating translation start offsets... # Wed Nov 7 20:06:14 GMT 2012: Getting intergenic regions /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 704221325_offsets_snps; create table 704221325_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) );" /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 704221325_rel_intergenic; create table 704221325_rel_intergenic like 704221325_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 704221325_rel_intergenic; flush table 704221325_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 704221325_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 704221325_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 704221325_snps reg join 704221325_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" touch 2993879594_offsets_uncovered # Wed Nov 7 20:06:17 GMT 2012: Filtering masked intergenic regions /usr/bin/mysql -Dmaqgenedb -umaqgene --skip-column-names --batch --raw --local-infile -e "delete i.* from 704221325_rel_intergenic i join 704221325_masked_ids m using (query_region_id)" touch 704221325_rel_intergenic # Wed Nov 7 20:06:24 GMT 2012: Classifying intergenic relations /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 704221325_intergenic_assoc; create table 704221325_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 704221325_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 704221325_snps snp join 704221325_rel_intergenic rel on (snp.id = rel.query_region_id) join elegans_features feature on (rel.target_region_id = feature.id)" touch 704221325_offsets_snps # Wed Nov 7 20:06:37 GMT 2012: Getting codons affected by point mutations... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 704221325_codons; create table 704221325_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 704221325_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 704221325_offsets_snps off join 704221325_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 704221325_intergenic_assoc touch 704221325_codons /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 704221325_marked; create table 704221325_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 20:06:44 GMT 2012: Finding exonic indels ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 704221325_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 704221325_snps snp join 704221325_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 20:06:44 GMT 2012: Finding coding variants ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 704221325_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 704221325_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 20:06:45 GMT 2012: Finding noncoding variants ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 704221325_marked select snp.id, feature.feature class, 'none' description, feature.attribute parent_feature from 704221325_snps snp join 704221325_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 20:06:45 GMT 2012: Finding splice site variants ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 704221325_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 704221325_snps snp join 704221325_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 20:06:45 GMT 2012: Finding intergenic and intronic variants ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 704221325_marked select id, 'nongenic' class, concat(if (relation in ('upstream','into'), - distance, distance),' ',relation) description, attribute from 704221325_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 20:06:48 GMT 2012: Finding uncovered regions in genes ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 704221325_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 2993879594_uncovered unc join 2993879594_offsets_uncovered b using (id) join 2993879594_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 2993879594_uncovered unc join 2993879594_offsets_uncovered b using (id) join 2993879594_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 20:06:48 GMT 2012: Variants found: +-----------------+-----------------+ | class | number_variants | +-----------------+-----------------+ | five_prime_UTR | 1279 | | frameshift | 27 | | inframe | 4 | | missense | 6137 | | ncRNA | 860 | | nongenic | 123975 | | non_start | 9 | | premature_stop | 687 | | readthrough | 20 | | silent | 7397 | | SNP | 1015 | | splice_acceptor | 44 | | splice_donor | 45 | | three_prime_UTR | 3541 | | uncovered | 31 | +-----------------+-----------------+ touch 704221325_marked # Wed Nov 7 20:06:49 GMT 2012: Combining results ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 704221325_combined; create table 704221325_combined (primary key (id, class, description), key (dna, start)) as select snp.id, 'DC9b' 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 704221325_snps snp join 2993879594_pileup pile using (dna,start) join 704221325_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, 'DC9b' 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 2993879594_uncovered unc join 704221325_marked class on (unc.id = class.id) left join elegans_per_locus using (dna,start) group by id, class, description; alter table 704221325_combined order by dna, start, length" touch 704221325_combined # Wed Nov 7 20:06:50 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 704221325_combined group by id order by dna, start;" > /data/maqgene/out/example_user/DC9b/DC9b_grouped.txt # Wed Nov 7 20:06:50 GMT 2012: Writing results to flat file ... /usr/bin/mysql -Dmaqgenedb -umaqgene --skip-column-names --batch --raw --local-infile --column-names -e "select * from 704221325_combined" > /data/maqgene/out/example_user/DC9b/DC9b_flat.txt 2672 lines written. 1616 lines written. rm 1865274982.00008.unmapped 1865274982.00009.mismatch 1865274982.00002.map 1865274982.00009.2.bfq 1865274982.00014.mismatch 1865274982.00015.1.fastq 1865274982.00005.2.fastq 1865274982.00012.map 1865274982.00013.2.fastq 1865274982.00006.1.bfq 1865274982.00009.unmapped 1865274982.00000.1.bfq 1865274982.00004.unmapped 1865274982.00003.map 1865274982.00006.2.bfq 1865274982.00004.1.fastq 1865274982.00016.1.bfq 1865274982.00014.2.bfq 1865274982.00006.mismatch 1865274982.00000.2.bfq 1865274982.00014.unmapped 1865274982.00013.map 1865274982.00007.1.fastq 1865274982.00000.mismatch 1865274982.00004.2.bfq 1865274982.00014.1.fastq 1865274982.00017.1.bfq 1865274982.00001.2.bfq 1865274982.00010.map 1865274982.00002.mismatch 1865274982.00002.1.bfq 1865274982.00004.2.fastq 1865274982.00010.1.bfq 1865274982.00001.mismatch 1865274982.00010.mismatch 1865274982.00016.2.bfq 1865274982.00009.map 1865274982.00016.mismatch 1865274982.00005.map 1865274982.00011.2.bfq 1865274982.00012.1.bfq 1865274982.00007.map 1865274982.00011.mismatch 1865274982.00014.2.fastq 1865274982.00008.1.fastq 1865274982.00017.2.bfq 1865274982.00017.mismatch 1865274982.00002.2.bfq 1865274982.00015.map 1865274982.00018.1.bfq 1865274982.00006.unmapped 1865274982.00006.1.fastq 1865274982.00008.map 1865274982.00009.1.fastq 1865274982.00000.unmapped 1865274982.00003.1.bfq 1865274982.00018.2.bfq 1865274982.00007.2.fastq 1865274982.00000.1.fastq 1865274982.00018.mismatch 1865274982.00001.1.bfq 1865274982.00015.2.fastq 1865274982.00001.unmapped 1865274982.00010.unmapped 1865274982.00013.1.bfq 1865274982.00016.unmapped 1865274982.00010.2.bfq 1865274982.00006.2.fastq 1865274982.00007.1.bfq 1865274982.00001.1.fastq 1865274982.00010.1.fastq 1865274982.00016.1.fastq 1865274982.00004.map 1865274982.00003.mismatch 1865274982.00000.2.fastq 1865274982.00011.1.fastq 1865274982.00008.2.fastq 1865274982.00017.unmapped 1865274982.00005.1.bfq 1865274982.00002.unmapped 1865274982.00013.2.bfq 1865274982.00017.1.fastq 1865274982.00014.map 1865274982.00013.mismatch 1865274982.00001.2.fastq 1865274982.00010.2.fastq 1865274982.00002.1.fastq 1865274982.00016.2.fastq 1865274982.00008.1.bfq 1865274982.00005.2.bfq 1865274982.00012.unmapped 1865274982.00015.1.bfq 1348410179_split1 1865274982.00011.2.fastq 1865274982.00012.1.fastq 1865274982.00005.mismatch 1865274982.00009.2.fastq 1865274982.00017.2.fastq 1865274982.00018.unmapped 1865274982.00003.2.bfq 1865274982.00002.2.fastq 1865274982.00018.1.fastq 1865274982.00005.unmapped 1865274982.00009.1.bfq 1865274982.00015.2.bfq 1865274982.00007.mismatch 1865274982.00012.2.fastq 1865274982.00015.mismatch 1865274982.00007.2.bfq 1865274982.00011.unmapped 1865274982.00018.map 1865274982.00003.unmapped 1865274982.00006.map 1865274982.00003.1.fastq 1865274982.00018.2.fastq 1865274982.00004.1.bfq 1865274982.00013.unmapped 1865274982.00000.map 1865274982.00011.1.bfq 1865274982.00013.1.fastq 1865274982.00007.unmapped 1865274982.00008.mismatch 1865274982.00008.2.bfq 1865274982.00001.map 1348410179_split2 1865274982.00014.1.bfq 1865274982.00015.unmapped 1865274982.00003.2.fastq 1865274982.00016.map 1865274982.00012.mismatch 1865274982.00012.2.bfq 1865274982.00005.1.fastq 1865274982.00004.mismatch 1865274982.00011.map 1865274982.00017.map make: Leaving directory `/data/maqgene/work' make: Entering directory `/data/maqgene/work' # Wed Nov 7 20:06:51 GMT 2012: Cleaning intermediate data ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 704221325_snps,704221325_rel,704221325_masked_ids,704221325_rel_intergenic,704221325_intergenic_assoc,704221325_offsets,704221325_codons,704221325_marked,704221325_combined,2993879594_pileup" rm -f 704221325_snps 704221325_rel 704221325_masked_ids 704221325_rel_intergenic 704221325_intergenic_assoc 704221325_offsets 704221325_codons 704221325_marked 704221325_combined 2993879594_pileup make: Leaving directory `/data/maqgene/work'