Finished reading input. ++ echo CB6889/./s_2_1_sequence_read1.fastq ++ tr , ' ' + fastq_file_set1=CB6889/./s_2_1_sequence_read1.fastq ++ cd /data/maqgene/reads ++ cat CB6889/./s_2_1_sequence_read1.fastq ++ wc -l ++ cut -f 1 -d ' ' + TOTAL_LINES=115767168 ++ echo '(115767168 / 5000000) + (115767168 % 5000000 != 0)' ++ bc + num_chunks=24 + 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=2180719828 map_cksum=506066491 pileup_cksum=719105296 cns_cksum=2684181821 umdd=50000 dmdd=1000 umid=1000 dmid=1000 max_gene_radius=50000 full_results_dir=/data/maqgene/out/example_user/CB6889 outfile_basename=CB6889 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=24 Will process 115767168 lines of input in 24 chunks make: Entering directory `/data/maqgene/work' # Thu Feb 3 21:13:55 GMT 2011: Removing frontend files in case this is a duplicate run ... rm -f /data/maqgene/out/example_user/CB6889/CB6889_{grouped.txt,flat.txt} rm -f /data/maqgene/out/example_user/CB6889/CB6889_uncovered.txt /data/maqgene/out/example_user/CB6889/CB6889_coverage.txt /data/maqgene/out/example_user/CB6889/CB6889_pileup.txt /data/maqgene/out/example_user/CB6889/CB6889_log.txt /data/maqgene/out/example_user/CB6889/CB6889_check.txt /data/maqgene/out/example_user/CB6889/CB6889_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/CB6889/./s_2_1_sequence_read1.fastq) 506066491.1.fastq. # : Regrouping fastq reads into chunks of size 5000000. split -l 5000000 -a 5 -d <(cat /data/maqgene/reads/CB6889/./s_2_2_sequence_read2.fastq) 506066491.2.fastq. for stem in 00000 00001 00002 00003 00004 00005 00006 00007 00008 00009 00010 00011 00012 00013 00014 00015 00016 00017 00018 00019 00020 00021 00022 00023; do mv 506066491.1.fastq.$stem 506066491.$stem.1.fastq; done touch 2180719828_split1 for stem in 00000 00001 00002 00003 00004 00005 00006 00007 00008 00009 00010 00011 00012 00013 00014 00015 00016 00017 00018 00019 00020 00021 00022 00023; do mv 506066491.2.fastq.$stem 506066491.$stem.2.fastq; done touch 2180719828_split2 # Thu Feb 3 21:14:48 GMT 2011: Converting fastq files to bfq ... # Thu Feb 3 21:14:48 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 506066491.00000.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 506066491.00000.1.bfq # Thu Feb 3 21:14:48 GMT 2011: Converting fastq files to bfq ... # Thu Feb 3 21:14:48 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 506066491.00003.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 506066491.00003.1.bfq # Thu Feb 3 21:14:48 GMT 2011: Converting fastq files to bfq ... # Thu Feb 3 21:14:48 GMT 2011: Converting fastq files to bfq ... # Thu Feb 3 21:14:48 GMT 2011: Converting fastq files to bfq ... # Thu Feb 3 21:14:48 GMT 2011: Converting fastq files to bfq ... # Thu Feb 3 21:14:48 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 506066491.00001.1.fastq /dev/stdout | \ # Thu Feb 3 21:14:48 GMT 2011: Converting fastq files to bfq ... # Thu Feb 3 21:14:48 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 506066491.00002.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 506066491.00002.1.bfq # Thu Feb 3 21:14:48 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 506066491.00004.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 506066491.00004.1.bfq /data/maqgene/bin/maq sol2sanger 506066491.00006.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 506066491.00006.1.bfq # Thu Feb 3 21:14:48 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 506066491.00007.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 506066491.00007.1.bfq /data/maqgene/bin/maq sol2sanger 506066491.00005.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 506066491.00005.1.bfq /data/maqgene/bin/maq sol2sanger 506066491.00008.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 506066491.00008.1.bfq /data/maqgene/bin/maq sol2sanger 506066491.00009.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 506066491.00009.1.bfq /data/maqgene/bin/maq sol2sanger 506066491.00010.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 506066491.00010.1.bfq /data/maqgene/bin/maq sol2sanger 506066491.00011.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 506066491.00011.1.bfq /data/maqgene/bin/maq sol2sanger 506066491.00012.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 506066491.00012.1.bfq /data/maqgene/bin/maq sol2sanger 506066491.00013.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 506066491.00013.1.bfq -- finish writing file '506066491.00009.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 21:15:08 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 506066491.00014.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 506066491.00014.1.bfq -- finish writing file '506066491.00003.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 21:15:14 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 506066491.00015.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 506066491.00015.1.bfq -- finish writing file '506066491.00013.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 21:15:17 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 506066491.00016.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 506066491.00016.1.bfq -- finish writing file '506066491.00005.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 21:15:17 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 506066491.00017.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 506066491.00017.1.bfq -- finish writing file '506066491.00002.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 21:15:17 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 506066491.00018.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 506066491.00018.1.bfq -- finish writing file '506066491.00000.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 21:15:17 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 506066491.00019.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 506066491.00019.1.bfq -- finish writing file '506066491.00010.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 21:15:17 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 506066491.00020.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 506066491.00020.1.bfq -- finish writing file '506066491.00008.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 21:15:18 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 506066491.00021.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 506066491.00021.1.bfq -- finish writing file '506066491.00006.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 21:15:18 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 506066491.00022.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 506066491.00022.1.bfq -- finish writing file '506066491.00007.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 21:15:18 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 506066491.00023.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 506066491.00023.1.bfq -- finish writing file '506066491.00012.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 21:15:19 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 506066491.00000.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 506066491.00000.2.bfq -- finish writing file '506066491.00004.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 21:15:19 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 506066491.00001.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 506066491.00001.2.bfq -- finish writing file '506066491.00001.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 21:15:19 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 506066491.00002.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 506066491.00002.2.bfq -- finish writing file '506066491.00011.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 21:15:20 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 506066491.00003.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 506066491.00003.2.bfq -- finish writing file '506066491.00023.1.bfq' -- 191792 sequences were loaded. # Thu Feb 3 21:15:23 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 506066491.00004.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 506066491.00004.2.bfq -- finish writing file '506066491.00014.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 21:15:39 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 506066491.00005.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 506066491.00005.2.bfq -- finish writing file '506066491.00015.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 21:15:43 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 506066491.00006.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 506066491.00006.2.bfq -- finish writing file '506066491.00021.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 21:15:44 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 506066491.00007.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 506066491.00007.2.bfq -- finish writing file '506066491.00004.2.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 21:15:44 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 506066491.00008.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 506066491.00008.2.bfq -- finish writing file '506066491.00017.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 21:15:45 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 506066491.00009.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 506066491.00009.2.bfq -- finish writing file '506066491.00019.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 21:15:46 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 506066491.00010.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 506066491.00010.2.bfq -- finish writing file '506066491.00022.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 21:15:47 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 506066491.00011.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 506066491.00011.2.bfq -- finish writing file '506066491.00016.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 21:15:47 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 506066491.00012.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 506066491.00012.2.bfq -- finish writing file '506066491.00000.2.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 21:15:47 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 506066491.00013.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 506066491.00013.2.bfq -- finish writing file '506066491.00018.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 21:15:47 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 506066491.00014.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 506066491.00014.2.bfq -- finish writing file '506066491.00020.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 21:15:47 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 506066491.00015.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 506066491.00015.2.bfq -- finish writing file '506066491.00001.2.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 21:15:48 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 506066491.00016.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 506066491.00016.2.bfq -- finish writing file '506066491.00002.2.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 21:15:49 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 506066491.00017.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 506066491.00017.2.bfq -- finish writing file '506066491.00003.2.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 21:15:49 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 506066491.00018.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 506066491.00018.2.bfq -- finish writing file '506066491.00008.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '506066491.00005.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '506066491.00011.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '506066491.00009.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '506066491.00006.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '506066491.00012.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '506066491.00014.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '506066491.00007.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '506066491.00010.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '506066491.00015.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '506066491.00016.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '506066491.00017.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '506066491.00013.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '506066491.00018.2.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 21:16:16 GMT 2011: Mapping file(s) 506066491.00007.1.bfq 506066491.00007.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 506066491.00007.unmapped -H 506066491.00007.mismatch \ 506066491.00007.map /data/maqgene/genomes/elegans.bfa 506066491.00007.1.bfq 506066491.00007.2.bfq 2> /dev/null # Thu Feb 3 21:16:18 GMT 2011: Mapping file(s) 506066491.00008.1.bfq 506066491.00008.2.bfq # Thu Feb 3 21:16:18 GMT 2011: Mapping file(s) 506066491.00006.1.bfq 506066491.00006.2.bfq # Thu Feb 3 21:16:18 GMT 2011: Mapping file(s) 506066491.00005.1.bfq 506066491.00005.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 506066491.00008.unmapped -H 506066491.00008.mismatch \ 506066491.00008.map /data/maqgene/genomes/elegans.bfa 506066491.00008.1.bfq 506066491.00008.2.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 506066491.00006.unmapped -H 506066491.00006.mismatch \ 506066491.00006.map /data/maqgene/genomes/elegans.bfa 506066491.00006.1.bfq 506066491.00006.2.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 506066491.00005.unmapped -H 506066491.00005.mismatch \ 506066491.00005.map /data/maqgene/genomes/elegans.bfa 506066491.00005.1.bfq 506066491.00005.2.bfq 2> /dev/null # Thu Feb 3 21:16:19 GMT 2011: Mapping file(s) 506066491.00004.1.bfq 506066491.00004.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 506066491.00004.unmapped -H 506066491.00004.mismatch \ 506066491.00004.map /data/maqgene/genomes/elegans.bfa 506066491.00004.1.bfq 506066491.00004.2.bfq 2> /dev/null # Thu Feb 3 21:16:19 GMT 2011: Mapping file(s) 506066491.00003.1.bfq 506066491.00003.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 506066491.00003.unmapped -H 506066491.00003.mismatch \ 506066491.00003.map /data/maqgene/genomes/elegans.bfa 506066491.00003.1.bfq 506066491.00003.2.bfq 2> /dev/null # Thu Feb 3 21:16:20 GMT 2011: Mapping file(s) 506066491.00002.1.bfq 506066491.00002.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 506066491.00002.unmapped -H 506066491.00002.mismatch \ 506066491.00002.map /data/maqgene/genomes/elegans.bfa 506066491.00002.1.bfq 506066491.00002.2.bfq 2> /dev/null # Thu Feb 3 21:16:20 GMT 2011: Mapping file(s) 506066491.00001.1.bfq 506066491.00001.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 506066491.00001.unmapped -H 506066491.00001.mismatch \ 506066491.00001.map /data/maqgene/genomes/elegans.bfa 506066491.00001.1.bfq 506066491.00001.2.bfq 2> /dev/null # Thu Feb 3 21:16:21 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 506066491.00023.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 506066491.00023.2.bfq # Thu Feb 3 21:16:21 GMT 2011: Mapping file(s) 506066491.00000.1.bfq 506066491.00000.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 506066491.00000.unmapped -H 506066491.00000.mismatch \ 506066491.00000.map /data/maqgene/genomes/elegans.bfa 506066491.00000.1.bfq 506066491.00000.2.bfq 2> /dev/null # Thu Feb 3 21:16:22 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 506066491.00021.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 506066491.00021.2.bfq # Thu Feb 3 21:16:22 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 506066491.00022.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 506066491.00022.2.bfq # Thu Feb 3 21:16:23 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 506066491.00019.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 506066491.00019.2.bfq # Thu Feb 3 21:16:23 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 506066491.00020.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 506066491.00020.2.bfq -- finish writing file '506066491.00023.2.bfq' -- 191792 sequences were loaded. # Thu Feb 3 21:16:24 GMT 2011: Mapping file(s) 506066491.00009.1.bfq 506066491.00009.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 506066491.00009.unmapped -H 506066491.00009.mismatch \ 506066491.00009.map /data/maqgene/genomes/elegans.bfa 506066491.00009.1.bfq 506066491.00009.2.bfq 2> /dev/null -- finish writing file '506066491.00019.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '506066491.00021.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '506066491.00022.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '506066491.00020.2.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 21:16:53 GMT 2011: Mapping file(s) 506066491.00013.1.bfq 506066491.00013.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 506066491.00013.unmapped -H 506066491.00013.mismatch \ 506066491.00013.map /data/maqgene/genomes/elegans.bfa 506066491.00013.1.bfq 506066491.00013.2.bfq 2> /dev/null # Thu Feb 3 21:16:55 GMT 2011: Mapping file(s) 506066491.00012.1.bfq 506066491.00012.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 506066491.00012.unmapped -H 506066491.00012.mismatch \ 506066491.00012.map /data/maqgene/genomes/elegans.bfa 506066491.00012.1.bfq 506066491.00012.2.bfq 2> /dev/null # Thu Feb 3 21:16:57 GMT 2011: Mapping file(s) 506066491.00011.1.bfq 506066491.00011.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 506066491.00011.unmapped -H 506066491.00011.mismatch \ 506066491.00011.map /data/maqgene/genomes/elegans.bfa 506066491.00011.1.bfq 506066491.00011.2.bfq 2> /dev/null # Thu Feb 3 21:16:59 GMT 2011: Mapping file(s) 506066491.00010.1.bfq 506066491.00010.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 506066491.00010.unmapped -H 506066491.00010.mismatch \ 506066491.00010.map /data/maqgene/genomes/elegans.bfa 506066491.00010.1.bfq 506066491.00010.2.bfq 2> /dev/null # Thu Feb 3 21:23:03 GMT 2011: Mapping file(s) 506066491.00018.1.bfq 506066491.00018.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 506066491.00018.unmapped -H 506066491.00018.mismatch \ 506066491.00018.map /data/maqgene/genomes/elegans.bfa 506066491.00018.1.bfq 506066491.00018.2.bfq 2> /dev/null # Thu Feb 3 21:23:04 GMT 2011: Mapping file(s) 506066491.00017.1.bfq 506066491.00017.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 506066491.00017.unmapped -H 506066491.00017.mismatch \ 506066491.00017.map /data/maqgene/genomes/elegans.bfa 506066491.00017.1.bfq 506066491.00017.2.bfq 2> /dev/null # Thu Feb 3 21:23:05 GMT 2011: Mapping file(s) 506066491.00019.1.bfq 506066491.00019.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 506066491.00019.unmapped -H 506066491.00019.mismatch \ 506066491.00019.map /data/maqgene/genomes/elegans.bfa 506066491.00019.1.bfq 506066491.00019.2.bfq 2> /dev/null # Thu Feb 3 21:23:05 GMT 2011: Mapping file(s) 506066491.00016.1.bfq 506066491.00016.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 506066491.00016.unmapped -H 506066491.00016.mismatch \ 506066491.00016.map /data/maqgene/genomes/elegans.bfa 506066491.00016.1.bfq 506066491.00016.2.bfq 2> /dev/null # Thu Feb 3 21:23:06 GMT 2011: Mapping file(s) 506066491.00020.1.bfq 506066491.00020.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 506066491.00020.unmapped -H 506066491.00020.mismatch \ 506066491.00020.map /data/maqgene/genomes/elegans.bfa 506066491.00020.1.bfq 506066491.00020.2.bfq 2> /dev/null # Thu Feb 3 21:23:07 GMT 2011: Mapping file(s) 506066491.00015.1.bfq 506066491.00015.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 506066491.00015.unmapped -H 506066491.00015.mismatch \ 506066491.00015.map /data/maqgene/genomes/elegans.bfa 506066491.00015.1.bfq 506066491.00015.2.bfq 2> /dev/null # Thu Feb 3 21:23:08 GMT 2011: Mapping file(s) 506066491.00014.1.bfq 506066491.00014.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 506066491.00014.unmapped -H 506066491.00014.mismatch \ 506066491.00014.map /data/maqgene/genomes/elegans.bfa 506066491.00014.1.bfq 506066491.00014.2.bfq 2> /dev/null # Thu Feb 3 21:23:19 GMT 2011: Mapping file(s) 506066491.00021.1.bfq 506066491.00021.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 506066491.00021.unmapped -H 506066491.00021.mismatch \ 506066491.00021.map /data/maqgene/genomes/elegans.bfa 506066491.00021.1.bfq 506066491.00021.2.bfq 2> /dev/null # Thu Feb 3 21:23:22 GMT 2011: Mapping file(s) 506066491.00022.1.bfq 506066491.00022.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 506066491.00022.unmapped -H 506066491.00022.mismatch \ 506066491.00022.map /data/maqgene/genomes/elegans.bfa 506066491.00022.1.bfq 506066491.00022.2.bfq 2> /dev/null # Thu Feb 3 21:24:08 GMT 2011: Mapping file(s) 506066491.00023.1.bfq 506066491.00023.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 506066491.00023.unmapped -H 506066491.00023.mismatch \ 506066491.00023.map /data/maqgene/genomes/elegans.bfa 506066491.00023.1.bfq 506066491.00023.2.bfq 2> /dev/null # Thu Feb 3 21:29:15 GMT 2011: Merging all maps ... /data/maqgene/bin/maq mapmerge 506066491.map 506066491.00000.map 506066491.00001.map 506066491.00002.map 506066491.00003.map 506066491.00004.map 506066491.00005.map 506066491.00006.map 506066491.00007.map 506066491.00008.map 506066491.00009.map 506066491.00010.map 506066491.00011.map 506066491.00012.map 506066491.00013.map 506066491.00014.map 506066491.00015.map 506066491.00016.map 506066491.00017.map 506066491.00018.map 506066491.00019.map 506066491.00020.map 506066491.00021.map 506066491.00022.map 506066491.00023.map # Thu Feb 3 21:29:15 GMT 2011: Merging all *.unmapped files ... cat 506066491.00000.unmapped 506066491.00001.unmapped 506066491.00002.unmapped 506066491.00003.unmapped 506066491.00004.unmapped 506066491.00005.unmapped 506066491.00006.unmapped 506066491.00007.unmapped 506066491.00008.unmapped 506066491.00009.unmapped 506066491.00010.unmapped 506066491.00011.unmapped 506066491.00012.unmapped 506066491.00013.unmapped 506066491.00014.unmapped 506066491.00015.unmapped 506066491.00016.unmapped 506066491.00017.unmapped 506066491.00018.unmapped 506066491.00019.unmapped 506066491.00020.unmapped 506066491.00021.unmapped 506066491.00022.unmapped 506066491.00023.unmapped > 506066491_unmapped.txt # Thu Feb 3 21:29:15 GMT 2011: Linking backend file 506066491_unmapped.txt to /data/maqgene/out/example_user/CB6889/CB6889_unmapped.txt ln -fs /data/maqgene/work/506066491_unmapped.txt /data/maqgene/out/example_user/CB6889/CB6889_unmapped.txt /data/maqgene/makefile:126: warning: undefined variable `mapcheck_parameters' # Thu Feb 3 21:38:07 GMT 2011: Creating pileup ... # Thu Feb 3 21:38:07 GMT 2011: Running 'mapcheck' ... /data/maqgene/bin/maq assemble -N 2 -q 0 -r 0.0 -m 7 -Q 100 -p 2684181821.cns \ /data/maqgene/genomes/elegans.bfa 506066491.map 2> 2684181821_log.txt /data/maqgene/bin/maq pileup -Q 100 -p -m 7 -q 0 /data/maqgene/genomes/elegans.bfa 506066491.map > 719105296_pileup.txt /data/maqgene/bin/maq mapcheck /data/maqgene/genomes/elegans.bfa 506066491.map > 506066491_check.txt \ 2>/dev/null # Thu Feb 3 21:40:35 GMT 2011: Linking backend file 506066491_check.txt to /data/maqgene/out/example_user/CB6889/CB6889_check.txt ln -fs /data/maqgene/work/506066491_check.txt /data/maqgene/out/example_user/CB6889/CB6889_check.txt /data/maqgene/bin/filter_matching_lines 719105296_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 \ > 719105296_known_snps # Thu Feb 3 21:41:03 GMT 2011: Getting uncovered regions ... # Thu Feb 3 21:41:03 GMT 2011: Making coverage histogram ... (echo -en "sequencing_depth\tnumber_of_bases\n"; \ cut -f 4 719105296_pileup.txt \ | /data/maqgene/bin/pileup_histogram 100) > 719105296_coverage.txt # Thu Feb 3 21:41:03 GMT 2011: Linking backend file 719105296_pileup.txt to /data/maqgene/out/example_user/CB6889/CB6889_pileup.txt cut -f 1,2,4 719105296_pileup.txt \ | /data/maqgene/bin/get_uncovered_regions 50 \ > 719105296_uncovered.txt ln -fs /data/maqgene/work/719105296_pileup.txt /data/maqgene/out/example_user/CB6889/CB6889_pileup.txt # Thu Feb 3 21:41:21 GMT 2011: Linking backend file 719105296_coverage.txt to /data/maqgene/out/example_user/CB6889/CB6889_coverage.txt ln -fs /data/maqgene/work/719105296_coverage.txt /data/maqgene/out/example_user/CB6889/CB6889_coverage.txt # Thu Feb 3 21:41:29 GMT 2011: Filtering and loading pileup for analysis ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 719105296_pileup; create table 719105296_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 719105296_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 719105296_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 719105296_pileup" # Thu Feb 3 21:41:31 GMT 2011: Linking backend file 719105296_uncovered.txt to /data/maqgene/out/example_user/CB6889/CB6889_uncovered.txt ln -fs /data/maqgene/work/719105296_uncovered.txt /data/maqgene/out/example_user/CB6889/CB6889_uncovered.txt cat 719105296_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 719105296_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 719105296_pileup" touch 719105296_pileup # Thu Feb 3 21:42:19 GMT 2011: 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 719105296_pileup p using (dna,start)" > /data/maqgene/out/example_user/CB6889/CB6889_snp_read_counts.txt 0 snp read count lines written. # Thu Feb 3 21:42:33 GMT 2011: Linking backend file 2684181821_log.txt to /data/maqgene/out/example_user/CB6889/CB6889_log.txt # Thu Feb 3 21:42:33 GMT 2011: Extracting point mutants from consensus ... ln -fs /data/maqgene/work/2684181821_log.txt /data/maqgene/out/example_user/CB6889/CB6889_log.txt /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 2684181821_snps; create table 2684181821_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 2684181821.cns \ | cat -b | /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "load data local infile '/dev/stdin' into table 2684181821_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 2684181821_snps;" # Thu Feb 3 21:42:46 GMT 2011: Extracting indels from consensus ... /data/maqgene/bin/maq indelsoa /data/maqgene/genomes/elegans.bfa 506066491.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 2684181821_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 2684181821_snps;" # Thu Feb 3 21:44:12 GMT 2011: Adding placeholders for known SNPs. cat 719105296_known_snps \ | /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "load data local infile '/dev/stdin' ignore into table 2684181821_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 2684181821_snps;" Found 162266 variants. touch 2684181821_snps # Thu Feb 3 21:44:13 GMT 2011: Loading uncovered regions into table ... cat 719105296_uncovered.txt \ | /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 719105296_uncovered; create table 719105296_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 = 162267; load data local infile '/dev/stdin' into table 719105296_uncovered (dna, start, end)" # Thu Feb 3 21:44:13 GMT 2011: 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 2684181821_masked_ids; create table 2684181821_masked_ids (query_region_id int(10) NOT NULL, primary key (query_region_id)); load data local infile '/dev/stdin' ignore into table 2684181821_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 2684181821_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; # Thu Feb 3 21:44:13 GMT 2011: Finding all genomic features overlapping variants... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 2684181821_rel_snps; CREATE TABLE 2684181821_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) )" /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 2684181821_rel_snps; flush table 2684181821_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 2684181821_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 13 1251 II 17 2328 III 19 1633 IV 20 2135 V 13 2479 X 14 5871 touch 719105296_uncovered # Thu Feb 3 21:44:13 GMT 2011: Finding mRNA features overlapping uncovered regions ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 719105296_uncovered_rel; CREATE TABLE 719105296_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 719105296_uncovered_rel; flush table 719105296_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 719105296_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 2684181821_masked_ids touch 719105296_uncovered_rel # Thu Feb 3 21:44:16 GMT 2011: Calculating translation start offsets for uncovered regions... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 719105296_offsets_uncovered; create table 719105296_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 719105296_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 719105296_uncovered reg join 719105296_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 719105296_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 719105296_uncovered reg join 719105296_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 719105296_offsets_uncovered touch 2684181821_rel_snps # Thu Feb 3 21:44:16 GMT 2011: Calculating translation start offsets... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 2684181821_offsets_snps; create table 2684181821_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) );" # Thu Feb 3 21:44:16 GMT 2011: Getting intergenic regions /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 2684181821_rel_intergenic; create table 2684181821_rel_intergenic like 2684181821_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 2684181821_rel_intergenic; flush table 2684181821_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 2684181821_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 2684181821_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 2684181821_snps reg join 2684181821_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" # Thu Feb 3 21:44:20 GMT 2011: Filtering masked intergenic regions /usr/bin/mysql -Dmaqgenedb -umaqgene --skip-column-names --batch --raw --local-infile -e "delete i.* from 2684181821_rel_intergenic i join 2684181821_masked_ids m using (query_region_id)" touch 2684181821_rel_intergenic # Thu Feb 3 21:44:24 GMT 2011: Classifying intergenic relations /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 2684181821_intergenic_assoc; create table 2684181821_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 2684181821_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 2684181821_snps snp join 2684181821_rel_intergenic rel on (snp.id = rel.query_region_id) join elegans_features feature on (rel.target_region_id = feature.id)" touch 2684181821_intergenic_assoc touch 2684181821_offsets_snps # Thu Feb 3 21:44:36 GMT 2011: Getting codons affected by point mutations... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 2684181821_codons; create table 2684181821_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 2684181821_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 2684181821_offsets_snps off join 2684181821_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 2684181821_codons /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 2684181821_marked; create table 2684181821_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) );" # Thu Feb 3 21:44:42 GMT 2011: Finding exonic indels ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 2684181821_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 2684181821_snps snp join 2684181821_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';" # Thu Feb 3 21:44:42 GMT 2011: Finding coding variants ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 2684181821_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 2684181821_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);" # Thu Feb 3 21:44:42 GMT 2011: Finding noncoding variants ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 2684181821_marked select snp.id, feature.feature class, 'none' description, feature.attribute parent_feature from 2684181821_snps snp join 2684181821_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');" # Thu Feb 3 21:44:43 GMT 2011: Finding splice site variants ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 2684181821_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 2684181821_snps snp join 2684181821_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;" # Thu Feb 3 21:44:43 GMT 2011: Finding intergenic and intronic variants ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 2684181821_marked select id, 'nongenic' class, concat(if (relation in ('upstream','into'), - distance, distance),' ',relation) description, attribute from 2684181821_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' );" # Thu Feb 3 21:44:46 GMT 2011: Finding uncovered regions in genes ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 2684181821_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 719105296_uncovered unc join 719105296_offsets_uncovered b using (id) join 719105296_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 719105296_uncovered unc join 719105296_offsets_uncovered b using (id) join 719105296_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'" # Thu Feb 3 21:44:46 GMT 2011: Variants found: +-----------------+-----------------+ | class | number_variants | +-----------------+-----------------+ | five_prime_UTR | 1277 | | frameshift | 37 | | inframe | 15 | | missense | 6187 | | ncRNA | 879 | | nongenic | 125672 | | non_start | 9 | | premature_stop | 686 | | readthrough | 20 | | silent | 7439 | | SNP | 1009 | | splice_acceptor | 45 | | splice_donor | 45 | | three_prime_UTR | 3546 | | uncovered | 32 | +-----------------+-----------------+ touch 2684181821_marked # Thu Feb 3 21:44:46 GMT 2011: Combining results ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 2684181821_combined; create table 2684181821_combined (primary key (id, class, description), key (dna, start)) as select snp.id, 'CB6889' 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 2684181821_snps snp join 719105296_pileup pile using (dna,start) join 2684181821_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, 'CB6889' 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 719105296_uncovered unc join 2684181821_marked class on (unc.id = class.id) left join elegans_per_locus using (dna,start) group by id, class, description; alter table 2684181821_combined order by dna, start, length" touch 2684181821_combined # Thu Feb 3 21:44:47 GMT 2011: 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 2684181821_combined group by id order by dna, start;" > /data/maqgene/out/example_user/CB6889/CB6889_grouped.txt # Thu Feb 3 21:44:47 GMT 2011: Writing results to flat file ... /usr/bin/mysql -Dmaqgenedb -umaqgene --skip-column-names --batch --raw --local-infile --column-names -e "select * from 2684181821_combined" > /data/maqgene/out/example_user/CB6889/CB6889_flat.txt 3397 lines written. 2037 lines written. rm 506066491.00018.mismatch 506066491.00012.2.fastq 506066491.00018.2.bfq 506066491.00022.1.fastq 506066491.00007.1.fastq 506066491.00003.unmapped 506066491.00003.1.fastq 506066491.00018.2.fastq 506066491.00006.map 506066491.00004.1.bfq 506066491.00013.unmapped 506066491.00000.map 506066491.00022.2.fastq 506066491.00009.mismatch 506066491.00007.map 506066491.00021.1.fastq 506066491.00008.1.fastq 506066491.00001.map 506066491.00003.2.fastq 506066491.00016.map 506066491.00005.unmapped 506066491.00015.mismatch 506066491.00004.2.bfq 506066491.00005.1.fastq 506066491.00004.mismatch 506066491.00011.map 506066491.00023.unmapped 506066491.00013.2.fastq 506066491.00019.unmapped 506066491.00000.mismatch 506066491.00017.map 506066491.00000.2.bfq 506066491.00021.map 506066491.00019.1.fastq 506066491.00008.map 506066491.00002.map 506066491.00020.map 506066491.00015.unmapped 506066491.00009.1.fastq 506066491.00014.mismatch 506066491.00015.1.fastq 506066491.00007.2.fastq 506066491.00005.2.fastq 506066491.00012.map 506066491.00023.2.fastq 506066491.00019.2.fastq 506066491.00007.1.bfq 506066491.00006.1.bfq 506066491.00009.map 506066491.00018.map 506066491.00015.2.fastq 506066491.00021.2.fastq 506066491.00008.2.fastq 506066491.00000.1.bfq 506066491.00004.unmapped 506066491.00003.map 506066491.00006.2.bfq 506066491.00021.1.bfq 506066491.00001.1.bfq 506066491.00010.1.bfq 506066491.00008.1.bfq 506066491.00004.1.fastq 506066491.00006.mismatch 506066491.00005.2.bfq 506066491.00016.1.bfq 506066491.00014.unmapped 506066491.00022.map 506066491.00009.2.fastq 506066491.00014.1.fastq 506066491.00017.1.bfq 506066491.00001.2.bfq 506066491.00010.2.bfq 506066491.00002.1.bfq 506066491.00020.1.bfq 506066491.00004.2.fastq 506066491.00001.mismatch 506066491.00010.mismatch 506066491.00016.2.bfq 506066491.00009.1.bfq 506066491.00016.mismatch 506066491.00005.map 506066491.00007.mismatch 506066491.00007.2.bfq 506066491.00011.2.bfq 506066491.00012.1.bfq 506066491.00023.map 506066491.00011.mismatch 506066491.00014.2.fastq 506066491.00019.map 506066491.00017.2.bfq 506066491.00010.map 506066491.00020.2.bfq 506066491.00002.mismatch 506066491.00015.map 506066491.00020.mismatch 506066491.00002.2.bfq 506066491.00021.unmapped 506066491.00013.1.fastq 506066491.00021.mismatch 506066491.00006.unmapped 506066491.00012.2.bfq 506066491.00007.unmapped 506066491.00008.mismatch 506066491.00021.2.bfq 506066491.00022.1.bfq 506066491.00006.1.fastq 506066491.00000.unmapped 506066491.00003.1.bfq 506066491.00000.1.fastq 506066491.00013.map 506066491.00001.unmapped 506066491.00010.unmapped 2180719828_split1 506066491.00022.2.bfq 506066491.00014.1.bfq 506066491.00013.1.bfq 506066491.00012.mismatch 506066491.00016.unmapped 506066491.00022.mismatch 506066491.00006.2.fastq 506066491.00018.1.bfq 506066491.00001.1.fastq 506066491.00010.1.fastq 506066491.00009.2.bfq 506066491.00016.1.fastq 506066491.00004.map 506066491.00003.2.bfq 506066491.00011.unmapped 506066491.00003.mismatch 506066491.00000.2.fastq 506066491.00011.1.fastq 506066491.00017.unmapped 506066491.00005.1.bfq 506066491.00023.1.fastq 506066491.00002.unmapped 506066491.00020.unmapped 506066491.00013.2.bfq 506066491.00017.1.fastq 506066491.00023.1.bfq 506066491.00013.mismatch 506066491.00001.2.fastq 506066491.00010.2.fastq 506066491.00002.1.fastq 506066491.00020.1.fastq 506066491.00019.1.bfq 506066491.00009.unmapped 506066491.00016.2.fastq 506066491.00012.unmapped 506066491.00017.mismatch 506066491.00015.1.bfq 506066491.00011.2.fastq 506066491.00012.1.fastq 506066491.00008.2.bfq 506066491.00005.mismatch 506066491.00017.2.fastq 506066491.00023.2.bfq 506066491.00018.unmapped 506066491.00002.2.fastq 506066491.00020.2.fastq 506066491.00014.map 506066491.00023.mismatch 506066491.00019.2.bfq 506066491.00018.1.fastq 506066491.00019.mismatch 2180719828_split2 506066491.00011.1.bfq 506066491.00022.unmapped 506066491.00008.unmapped 506066491.00015.2.bfq 506066491.00014.2.bfq make: Leaving directory `/data/maqgene/work' make: Entering directory `/data/maqgene/work' # Thu Feb 3 21:44:51 GMT 2011: Cleaning intermediate data ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 2684181821_snps,2684181821_rel,2684181821_masked_ids,2684181821_rel_intergenic,2684181821_intergenic_assoc,2684181821_offsets,2684181821_codons,2684181821_marked,2684181821_combined,719105296_pileup" rm -f 2684181821_snps 2684181821_rel 2684181821_masked_ids 2684181821_rel_intergenic 2684181821_intergenic_assoc 2684181821_offsets 2684181821_codons 2684181821_marked 2684181821_combined 719105296_pileup make: Leaving directory `/data/maqgene/work'