/data/maqgene/bin/run_maq.sh: line 44: export: `single_CB7045/./WTCHG_52866_06_2.fastq=on': not a valid identifier /data/maqgene/bin/run_maq.sh: line 44: export: `single_CB7045/./WTCHG_52866_06_1.fastq=on': not a valid identifier Finished reading input. ++ echo CB7045/./WTCHG_52866_06_2.fastq,CB7045/./WTCHG_52866_06_1.fastq ++ tr , ' ' + fastq_file_set1='CB7045/./WTCHG_52866_06_2.fastq CB7045/./WTCHG_52866_06_1.fastq' ++ cd /data/maqgene/reads ++ wc -l ++ cat CB7045/./WTCHG_52866_06_2.fastq CB7045/./WTCHG_52866_06_1.fastq ++ cut -f 1 -d ' ' + TOTAL_LINES=119020496 ++ echo '(119020496 / 5000000) + (119020496 % 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=2865057837 map_cksum=1190394099 pileup_cksum=2776322182 cns_cksum=2879202080 umdd=50000 dmdd=1000 umid=1000 dmid=1000 max_gene_radius=50000 full_results_dir=/data/maqgene/out/example_user/CB7045 outfile_basename=CB7045 map_parameters=" -m 0.00001 -C 250 -n 2 -e 100 -1 0" assemble_parameters=" -N 2 -q 0 -r 0.0 -m 7 -Q 100 -p " pileup_parameters=" -Q 100 -m 7 -q 0" CHUNK_SIZE=5000000 NUM_CHUNKS=24 Will process 119020496 lines of input in 24 chunks make: Entering directory `/data/maqgene/work' # Thu Apr 11 07:48:59 BST 2013: Removing frontend files in case this is a duplicate run ... rm -f /data/maqgene/out/example_user/CB7045/CB7045_{grouped.txt,flat.txt} rm -f /data/maqgene/out/example_user/CB7045/CB7045_uncovered.txt /data/maqgene/out/example_user/CB7045/CB7045_coverage.txt /data/maqgene/out/example_user/CB7045/CB7045_pileup.txt /data/maqgene/out/example_user/CB7045/CB7045_log.txt /data/maqgene/out/example_user/CB7045/CB7045_check.txt /data/maqgene/out/example_user/CB7045/CB7045_unmapped.txt make: Leaving directory `/data/maqgene/work' make: Entering directory `/data/maqgene/work' /data/maqgene/makefile:73: warning: undefined variable `date' # : Regrouping fastq reads into chunks of size 5000000. split -l 5000000 -a 5 -d <(cat /data/maqgene/reads/CB7045/./WTCHG_52866_06_2.fastq /data/maqgene/reads/CB7045/./WTCHG_52866_06_1.fastq) 1190394099.1.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 1190394099.1.fastq.$stem 1190394099.$stem.1.fastq; done touch 2865057837_split1 # Thu Apr 11 07:49:06 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1190394099.00000.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1190394099.00000.1.bfq # Thu Apr 11 07:49:06 BST 2013: Converting fastq files to bfq ... # Thu Apr 11 07:49:06 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1190394099.00001.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1190394099.00001.1.bfq # Thu Apr 11 07:49:06 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1190394099.00002.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1190394099.00002.1.bfq /data/maqgene/bin/maq sol2sanger 1190394099.00003.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1190394099.00003.1.bfq # Thu Apr 11 07:49:06 BST 2013: Converting fastq files to bfq ... # Thu Apr 11 07:49:06 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1190394099.00004.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1190394099.00004.1.bfq /data/maqgene/bin/maq sol2sanger 1190394099.00006.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1190394099.00006.1.bfq # Thu Apr 11 07:49:06 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1190394099.00007.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1190394099.00007.1.bfq # Thu Apr 11 07:49:06 BST 2013: Converting fastq files to bfq ... # Thu Apr 11 07:49:06 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1190394099.00008.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1190394099.00008.1.bfq /data/maqgene/bin/maq sol2sanger 1190394099.00005.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1190394099.00005.1.bfq /data/maqgene/bin/maq sol2sanger 1190394099.00009.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1190394099.00009.1.bfq # Thu Apr 11 07:49:06 BST 2013: Converting fastq files to bfq ... # Thu Apr 11 07:49:06 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1190394099.00010.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1190394099.00010.1.bfq /data/maqgene/bin/maq sol2sanger 1190394099.00011.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1190394099.00011.1.bfq # Thu Apr 11 07:49:06 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1190394099.00012.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1190394099.00012.1.bfq # Thu Apr 11 07:49:06 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1190394099.00013.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1190394099.00013.1.bfq -- finish writing file '1190394099.00007.1.bfq' -- 1250000 sequences were loaded. # Thu Apr 11 07:49:32 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1190394099.00014.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1190394099.00014.1.bfq -- finish writing file '1190394099.00005.1.bfq' -- 1250000 sequences were loaded. # Thu Apr 11 07:49:34 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1190394099.00015.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1190394099.00015.1.bfq -- finish writing file '1190394099.00001.1.bfq' -- 1250000 sequences were loaded. # Thu Apr 11 07:49:34 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1190394099.00016.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1190394099.00016.1.bfq -- finish writing file '1190394099.00003.1.bfq' -- 1250000 sequences were loaded. # Thu Apr 11 07:49:35 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1190394099.00017.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1190394099.00017.1.bfq -- finish writing file '1190394099.00010.1.bfq' -- 1250000 sequences were loaded. # Thu Apr 11 07:49:38 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1190394099.00018.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1190394099.00018.1.bfq -- finish writing file '1190394099.00012.1.bfq' -- 1250000 sequences were loaded. # Thu Apr 11 07:49:39 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1190394099.00019.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1190394099.00019.1.bfq -- finish writing file '1190394099.00006.1.bfq' -- 1250000 sequences were loaded. # Thu Apr 11 07:49:39 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1190394099.00020.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1190394099.00020.1.bfq -- finish writing file '1190394099.00008.1.bfq' -- 1250000 sequences were loaded. # Thu Apr 11 07:49:39 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1190394099.00021.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1190394099.00021.1.bfq -- finish writing file '1190394099.00013.1.bfq' -- 1250000 sequences were loaded. # Thu Apr 11 07:49:39 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1190394099.00022.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1190394099.00022.1.bfq -- finish writing file '1190394099.00000.1.bfq' -- 1250000 sequences were loaded. # Thu Apr 11 07:49:40 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1190394099.00023.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1190394099.00023.1.bfq -- finish writing file '1190394099.00002.1.bfq' -- 1250000 sequences were loaded. # Thu Apr 11 07:49:40 BST 2013: Mapping file(s) 1190394099.00000.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 1190394099.00000.unmapped -H 1190394099.00000.mismatch \ 1190394099.00000.map /data/maqgene/genomes/elegans.bfa 1190394099.00000.1.bfq 2> /dev/null -- finish writing file '1190394099.00004.1.bfq' -- 1250000 sequences were loaded. # Thu Apr 11 07:49:40 BST 2013: Mapping file(s) 1190394099.00001.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 1190394099.00001.unmapped -H 1190394099.00001.mismatch \ 1190394099.00001.map /data/maqgene/genomes/elegans.bfa 1190394099.00001.1.bfq 2> /dev/null -- finish writing file '1190394099.00009.1.bfq' -- 1250000 sequences were loaded. # Thu Apr 11 07:49:41 BST 2013: Mapping file(s) 1190394099.00002.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 1190394099.00002.unmapped -H 1190394099.00002.mismatch \ 1190394099.00002.map /data/maqgene/genomes/elegans.bfa 1190394099.00002.1.bfq 2> /dev/null -- finish writing file '1190394099.00011.1.bfq' -- 1250000 sequences were loaded. # Thu Apr 11 07:49:41 BST 2013: Mapping file(s) 1190394099.00003.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 1190394099.00003.unmapped -H 1190394099.00003.mismatch \ 1190394099.00003.map /data/maqgene/genomes/elegans.bfa 1190394099.00003.1.bfq 2> /dev/null -- finish writing file '1190394099.00014.1.bfq' -- 1250000 sequences were loaded. # Thu Apr 11 07:50:01 BST 2013: Mapping file(s) 1190394099.00004.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 1190394099.00004.unmapped -H 1190394099.00004.mismatch \ 1190394099.00004.map /data/maqgene/genomes/elegans.bfa 1190394099.00004.1.bfq 2> /dev/null -- finish writing file '1190394099.00021.1.bfq' -- 1250000 sequences were loaded. # Thu Apr 11 07:50:03 BST 2013: Mapping file(s) 1190394099.00005.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 1190394099.00005.unmapped -H 1190394099.00005.mismatch \ 1190394099.00005.map /data/maqgene/genomes/elegans.bfa 1190394099.00005.1.bfq 2> /dev/null -- finish writing file '1190394099.00015.1.bfq' -- 1250000 sequences were loaded. # Thu Apr 11 07:50:04 BST 2013: Mapping file(s) 1190394099.00006.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 1190394099.00006.unmapped -H 1190394099.00006.mismatch \ 1190394099.00006.map /data/maqgene/genomes/elegans.bfa 1190394099.00006.1.bfq 2> /dev/null -- finish writing file '1190394099.00023.1.bfq' -- 1005124 sequences were loaded. # Thu Apr 11 07:50:05 BST 2013: Mapping file(s) 1190394099.00007.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 1190394099.00007.unmapped -H 1190394099.00007.mismatch \ 1190394099.00007.map /data/maqgene/genomes/elegans.bfa 1190394099.00007.1.bfq 2> /dev/null -- finish writing file '1190394099.00016.1.bfq' -- 1250000 sequences were loaded. # Thu Apr 11 07:50:07 BST 2013: Mapping file(s) 1190394099.00008.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 1190394099.00008.unmapped -H 1190394099.00008.mismatch \ 1190394099.00008.map /data/maqgene/genomes/elegans.bfa 1190394099.00008.1.bfq 2> /dev/null -- finish writing file '1190394099.00017.1.bfq' -- 1250000 sequences were loaded. # Thu Apr 11 07:50:08 BST 2013: Mapping file(s) 1190394099.00009.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 1190394099.00009.unmapped -H 1190394099.00009.mismatch \ 1190394099.00009.map /data/maqgene/genomes/elegans.bfa 1190394099.00009.1.bfq 2> /dev/null -- finish writing file '1190394099.00019.1.bfq' -- 1250000 sequences were loaded. # Thu Apr 11 07:50:08 BST 2013: Mapping file(s) 1190394099.00010.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 1190394099.00010.unmapped -H 1190394099.00010.mismatch \ 1190394099.00010.map /data/maqgene/genomes/elegans.bfa 1190394099.00010.1.bfq 2> /dev/null -- finish writing file '1190394099.00022.1.bfq' -- 1250000 sequences were loaded. # Thu Apr 11 07:50:09 BST 2013: Mapping file(s) 1190394099.00011.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 1190394099.00011.unmapped -H 1190394099.00011.mismatch \ 1190394099.00011.map /data/maqgene/genomes/elegans.bfa 1190394099.00011.1.bfq 2> /dev/null -- finish writing file '1190394099.00020.1.bfq' -- 1250000 sequences were loaded. # Thu Apr 11 07:50:10 BST 2013: Mapping file(s) 1190394099.00012.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 1190394099.00012.unmapped -H 1190394099.00012.mismatch \ 1190394099.00012.map /data/maqgene/genomes/elegans.bfa 1190394099.00012.1.bfq 2> /dev/null -- finish writing file '1190394099.00018.1.bfq' -- 1250000 sequences were loaded. # Thu Apr 11 07:50:11 BST 2013: Mapping file(s) 1190394099.00013.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 1190394099.00013.unmapped -H 1190394099.00013.mismatch \ 1190394099.00013.map /data/maqgene/genomes/elegans.bfa 1190394099.00013.1.bfq 2> /dev/null # Thu Apr 11 07:53:28 BST 2013: Mapping file(s) 1190394099.00016.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 1190394099.00016.unmapped -H 1190394099.00016.mismatch \ 1190394099.00016.map /data/maqgene/genomes/elegans.bfa 1190394099.00016.1.bfq 2> /dev/null # Thu Apr 11 07:53:29 BST 2013: Mapping file(s) 1190394099.00015.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 1190394099.00015.unmapped -H 1190394099.00015.mismatch \ 1190394099.00015.map /data/maqgene/genomes/elegans.bfa 1190394099.00015.1.bfq 2> /dev/null # Thu Apr 11 07:53:30 BST 2013: Mapping file(s) 1190394099.00014.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 1190394099.00014.unmapped -H 1190394099.00014.mismatch \ 1190394099.00014.map /data/maqgene/genomes/elegans.bfa 1190394099.00014.1.bfq 2> /dev/null # Thu Apr 11 07:53:32 BST 2013: Mapping file(s) 1190394099.00017.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 1190394099.00017.unmapped -H 1190394099.00017.mismatch \ 1190394099.00017.map /data/maqgene/genomes/elegans.bfa 1190394099.00017.1.bfq 2> /dev/null # Thu Apr 11 07:53:43 BST 2013: Mapping file(s) 1190394099.00019.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 1190394099.00019.unmapped -H 1190394099.00019.mismatch \ 1190394099.00019.map /data/maqgene/genomes/elegans.bfa 1190394099.00019.1.bfq 2> /dev/null # Thu Apr 11 07:53:44 BST 2013: Mapping file(s) 1190394099.00018.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 1190394099.00018.unmapped -H 1190394099.00018.mismatch \ 1190394099.00018.map /data/maqgene/genomes/elegans.bfa 1190394099.00018.1.bfq 2> /dev/null # Thu Apr 11 07:53:44 BST 2013: Mapping file(s) 1190394099.00020.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 1190394099.00020.unmapped -H 1190394099.00020.mismatch \ 1190394099.00020.map /data/maqgene/genomes/elegans.bfa 1190394099.00020.1.bfq 2> /dev/null # Thu Apr 11 07:54:00 BST 2013: Mapping file(s) 1190394099.00023.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 1190394099.00023.unmapped -H 1190394099.00023.mismatch \ 1190394099.00023.map /data/maqgene/genomes/elegans.bfa 1190394099.00023.1.bfq 2> /dev/null # Thu Apr 11 07:54:20 BST 2013: Mapping file(s) 1190394099.00022.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 1190394099.00022.unmapped -H 1190394099.00022.mismatch \ 1190394099.00022.map /data/maqgene/genomes/elegans.bfa 1190394099.00022.1.bfq 2> /dev/null # Thu Apr 11 07:54:20 BST 2013: Mapping file(s) 1190394099.00021.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 1190394099.00021.unmapped -H 1190394099.00021.mismatch \ 1190394099.00021.map /data/maqgene/genomes/elegans.bfa 1190394099.00021.1.bfq 2> /dev/null # Thu Apr 11 07:57:37 BST 2013: Merging all maps ... /data/maqgene/bin/maq mapmerge 1190394099.map 1190394099.00000.map 1190394099.00001.map 1190394099.00002.map 1190394099.00003.map 1190394099.00004.map 1190394099.00005.map 1190394099.00006.map 1190394099.00007.map 1190394099.00008.map 1190394099.00009.map 1190394099.00010.map 1190394099.00011.map 1190394099.00012.map 1190394099.00013.map 1190394099.00014.map 1190394099.00015.map 1190394099.00016.map 1190394099.00017.map 1190394099.00018.map 1190394099.00019.map 1190394099.00020.map 1190394099.00021.map 1190394099.00022.map 1190394099.00023.map # Thu Apr 11 07:57:37 BST 2013: Merging all *.unmapped files ... cat 1190394099.00000.unmapped 1190394099.00001.unmapped 1190394099.00002.unmapped 1190394099.00003.unmapped 1190394099.00004.unmapped 1190394099.00005.unmapped 1190394099.00006.unmapped 1190394099.00007.unmapped 1190394099.00008.unmapped 1190394099.00009.unmapped 1190394099.00010.unmapped 1190394099.00011.unmapped 1190394099.00012.unmapped 1190394099.00013.unmapped 1190394099.00014.unmapped 1190394099.00015.unmapped 1190394099.00016.unmapped 1190394099.00017.unmapped 1190394099.00018.unmapped 1190394099.00019.unmapped 1190394099.00020.unmapped 1190394099.00021.unmapped 1190394099.00022.unmapped 1190394099.00023.unmapped > 1190394099_unmapped.txt # Thu Apr 11 07:57:38 BST 2013: Linking backend file 1190394099_unmapped.txt to /data/maqgene/out/example_user/CB7045/CB7045_unmapped.txt ln -fs /data/maqgene/work/1190394099_unmapped.txt /data/maqgene/out/example_user/CB7045/CB7045_unmapped.txt /data/maqgene/makefile:126: warning: undefined variable `mapcheck_parameters' # Thu Apr 11 08:01:05 BST 2013: Generating consensus ... # Thu Apr 11 08:01:05 BST 2013: Creating pileup ... /data/maqgene/bin/maq assemble -N 2 -q 0 -r 0.0 -m 7 -Q 100 -p 2879202080.cns \ /data/maqgene/genomes/elegans.bfa 1190394099.map 2> 2879202080_log.txt # Thu Apr 11 08:01:05 BST 2013: Running 'mapcheck' ... /data/maqgene/bin/maq pileup -Q 100 -m 7 -q 0 /data/maqgene/genomes/elegans.bfa 1190394099.map > 2776322182_pileup.txt /data/maqgene/bin/maq mapcheck /data/maqgene/genomes/elegans.bfa 1190394099.map > 1190394099_check.txt \ 2>/dev/null # Thu Apr 11 08:01:44 BST 2013: Linking backend file 1190394099_check.txt to /data/maqgene/out/example_user/CB7045/CB7045_check.txt ln -fs /data/maqgene/work/1190394099_check.txt /data/maqgene/out/example_user/CB7045/CB7045_check.txt /data/maqgene/bin/filter_matching_lines 2776322182_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 \ > 2776322182_known_snps # Thu Apr 11 08:02:20 BST 2013: Getting uncovered regions ... # Thu Apr 11 08:02:20 BST 2013: Making coverage histogram ... cut -f 1,2,4 2776322182_pileup.txt \ | /data/maqgene/bin/get_uncovered_regions 50 \ > 2776322182_uncovered.txt # Thu Apr 11 08:02:20 BST 2013: Linking backend file 2776322182_pileup.txt to /data/maqgene/out/example_user/CB7045/CB7045_pileup.txt (echo -en "sequencing_depth\tnumber_of_bases\n"; \ cut -f 4 2776322182_pileup.txt \ | /data/maqgene/bin/pileup_histogram 100) > 2776322182_coverage.txt ln -fs /data/maqgene/work/2776322182_pileup.txt /data/maqgene/out/example_user/CB7045/CB7045_pileup.txt # Thu Apr 11 08:02:33 BST 2013: Linking backend file 2776322182_coverage.txt to /data/maqgene/out/example_user/CB7045/CB7045_coverage.txt ln -fs /data/maqgene/work/2776322182_coverage.txt /data/maqgene/out/example_user/CB7045/CB7045_coverage.txt # Thu Apr 11 08:02:44 BST 2013: Linking backend file 2776322182_uncovered.txt to /data/maqgene/out/example_user/CB7045/CB7045_uncovered.txt ln -fs /data/maqgene/work/2776322182_uncovered.txt /data/maqgene/out/example_user/CB7045/CB7045_uncovered.txt # Thu Apr 11 08:02:44 BST 2013: Filtering and loading pileup for analysis ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 2776322182_pileup; create table 2776322182_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 2776322182_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 2776322182_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 2776322182_pileup" cat 2776322182_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 2776322182_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 2776322182_pileup" touch 2776322182_pileup # Thu Apr 11 08:03:24 BST 2013: 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 2776322182_pileup p using (dna,start)" > /data/maqgene/out/example_user/CB7045/CB7045_snp_read_counts.txt 0 snp read count lines written. # Thu Apr 11 08:03:37 BST 2013: Extracting point mutants from consensus ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 2879202080_snps; create table 2879202080_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) )" # Thu Apr 11 08:03:37 BST 2013: Linking backend file 2879202080_log.txt to /data/maqgene/out/example_user/CB7045/CB7045_log.txt ln -fs /data/maqgene/work/2879202080_log.txt /data/maqgene/out/example_user/CB7045/CB7045_log.txt /data/maqgene/bin/maq cns2snp 2879202080.cns \ | cat -b | /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "load data local infile '/dev/stdin' into table 2879202080_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 2879202080_snps;" # Thu Apr 11 08:03:45 BST 2013: Extracting indels from consensus ... /data/maqgene/bin/maq indelsoa /data/maqgene/genomes/elegans.bfa 1190394099.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 2879202080_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 2879202080_snps;" # Thu Apr 11 08:04:07 BST 2013: Adding placeholders for known SNPs. cat 2776322182_known_snps \ | /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "load data local infile '/dev/stdin' ignore into table 2879202080_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 2879202080_snps;" Found 166465 variants. touch 2879202080_snps # Thu Apr 11 08:04:08 BST 2013: Loading uncovered regions into table ... cat 2776322182_uncovered.txt \ | /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 2776322182_uncovered; create table 2776322182_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 = 166466; load data local infile '/dev/stdin' into table 2776322182_uncovered (dna, start, end)" # Thu Apr 11 08:04:08 BST 2013: Finding all genomic features overlapping variants... # Thu Apr 11 08:04:08 BST 2013: Getting masking regions /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 2879202080_rel_snps; CREATE TABLE 2879202080_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 2 -o >(/usr/bin/mysql -Dmaqgenedb -umaqgene --skip-column-names --batch --raw --local-infile -e "drop table if exists 2879202080_masked_ids; create table 2879202080_masked_ids (query_region_id int(10) NOT NULL, primary key (query_region_id)); load data local infile '/dev/stdin' ignore into table 2879202080_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 2879202080_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 2879202080_rel_snps; flush table 2879202080_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 2879202080_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 14 2313 II 13 2679 III 14 1130 IV 15 1574 V 28 8320 X 14 5529 touch 2776322182_uncovered # Thu Apr 11 08:04:08 BST 2013: Finding mRNA features overlapping uncovered regions ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 2776322182_uncovered_rel; CREATE TABLE 2776322182_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 2776322182_uncovered_rel; flush table 2776322182_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 2776322182_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 2879202080_masked_ids touch 2776322182_uncovered_rel # Thu Apr 11 08:04:10 BST 2013: Calculating translation start offsets for uncovered regions... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 2776322182_offsets_uncovered; create table 2776322182_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 2776322182_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 2776322182_uncovered reg join 2776322182_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 2776322182_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 2776322182_uncovered reg join 2776322182_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 2776322182_offsets_uncovered touch 2879202080_rel_snps # Thu Apr 11 08:04:11 BST 2013: Calculating translation start offsets... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 2879202080_offsets_snps; create table 2879202080_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 Apr 11 08:04:11 BST 2013: Getting intergenic regions /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 2879202080_rel_intergenic; create table 2879202080_rel_intergenic like 2879202080_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 2879202080_rel_intergenic; flush table 2879202080_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 2879202080_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 2879202080_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 2879202080_snps reg join 2879202080_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 Apr 11 08:04:15 BST 2013: Filtering masked intergenic regions /usr/bin/mysql -Dmaqgenedb -umaqgene --skip-column-names --batch --raw --local-infile -e "delete i.* from 2879202080_rel_intergenic i join 2879202080_masked_ids m using (query_region_id)" touch 2879202080_rel_intergenic # Thu Apr 11 08:04:19 BST 2013: Classifying intergenic relations /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 2879202080_intergenic_assoc; create table 2879202080_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 2879202080_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 2879202080_snps snp join 2879202080_rel_intergenic rel on (snp.id = rel.query_region_id) join elegans_features feature on (rel.target_region_id = feature.id)" touch 2879202080_intergenic_assoc touch 2879202080_offsets_snps # Thu Apr 11 08:04:32 BST 2013: Getting codons affected by point mutations... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 2879202080_codons; create table 2879202080_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 2879202080_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 2879202080_offsets_snps off join 2879202080_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 2879202080_codons /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 2879202080_marked; create table 2879202080_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 Apr 11 08:04:38 BST 2013: Finding exonic indels ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 2879202080_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 2879202080_snps snp join 2879202080_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 Apr 11 08:04:39 BST 2013: Finding coding variants ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 2879202080_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 2879202080_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 Apr 11 08:04:39 BST 2013: Finding noncoding variants ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 2879202080_marked select snp.id, feature.feature class, 'none' description, feature.attribute parent_feature from 2879202080_snps snp join 2879202080_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 Apr 11 08:04:39 BST 2013: Finding splice site variants ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 2879202080_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 2879202080_snps snp join 2879202080_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 Apr 11 08:04:40 BST 2013: Finding intergenic and intronic variants ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 2879202080_marked select id, 'nongenic' class, concat(if (relation in ('upstream','into'), - distance, distance),' ',relation) description, attribute from 2879202080_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 Apr 11 08:04:42 BST 2013: Finding uncovered regions in genes ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 2879202080_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 2776322182_uncovered unc join 2776322182_offsets_uncovered b using (id) join 2776322182_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 2776322182_uncovered unc join 2776322182_offsets_uncovered b using (id) join 2776322182_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 Apr 11 08:04:42 BST 2013: Variants found: +-----------------+-----------------+ | class | number_variants | +-----------------+-----------------+ | five_prime_UTR | 1338 | | frameshift | 17 | | inframe | 5 | | missense | 6621 | | ncRNA | 900 | | nongenic | 128972 | | non_start | 10 | | premature_stop | 717 | | readthrough | 21 | | silent | 7582 | | SNP | 1066 | | splice_acceptor | 46 | | splice_donor | 53 | | three_prime_UTR | 3642 | | uncovered | 45 | +-----------------+-----------------+ touch 2879202080_marked # Thu Apr 11 08:04:43 BST 2013: Combining results ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 2879202080_combined; create table 2879202080_combined (primary key (id, class, description), key (dna, start)) as select snp.id, 'CB7045' 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 2879202080_snps snp join 2776322182_pileup pile using (dna,start) join 2879202080_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, 'CB7045' 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 2776322182_uncovered unc join 2879202080_marked class on (unc.id = class.id) left join elegans_per_locus using (dna,start) group by id, class, description; alter table 2879202080_combined order by dna, start, length" touch 2879202080_combined # Thu Apr 11 08:04:44 BST 2013: Writing results to flat file ... /usr/bin/mysql -Dmaqgenedb -umaqgene --skip-column-names --batch --raw --local-infile --column-names -e "select * from 2879202080_combined" > /data/maqgene/out/example_user/CB7045/CB7045_flat.txt # Thu Apr 11 08:04:44 BST 2013: 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 2879202080_combined group by id order by dna, start;" > /data/maqgene/out/example_user/CB7045/CB7045_grouped.txt 4712 lines written. 2786 lines written. rm 1190394099.00013.map 1190394099.00000.mismatch 1190394099.00021.mismatch 1190394099.00007.unmapped 1190394099.00014.1.fastq 1190394099.00017.1.bfq 1190394099.00002.1.bfq 1190394099.00020.1.bfq 1190394099.00001.mismatch 1190394099.00010.mismatch 1190394099.00016.mismatch 1190394099.00005.map 1190394099.00012.mismatch 1190394099.00008.mismatch 1190394099.00012.1.bfq 1190394099.00023.map 1190394099.00011.mismatch 1190394099.00005.unmapped 1190394099.00018.1.bfq 1190394099.00019.map 1190394099.00008.unmapped 1190394099.00009.mismatch 1190394099.00002.mismatch 1190394099.00015.map 1190394099.00020.mismatch 1190394099.00011.1.bfq 1190394099.00006.unmapped 1190394099.00022.1.bfq 2865057837_split1 1190394099.00006.1.fastq 1190394099.00000.unmapped 1190394099.00003.1.bfq 1190394099.00009.unmapped 1190394099.00000.1.fastq 1190394099.00018.mismatch 1190394099.00001.unmapped 1190394099.00013.1.bfq 1190394099.00016.unmapped 1190394099.00022.mismatch 1190394099.00001.1.fastq 1190394099.00010.1.fastq 1190394099.00016.1.fastq 1190394099.00004.map 1190394099.00011.unmapped 1190394099.00003.mismatch 1190394099.00011.1.fastq 1190394099.00017.unmapped 1190394099.00005.1.bfq 1190394099.00002.unmapped 1190394099.00020.unmapped 1190394099.00017.mismatch 1190394099.00007.1.fastq 1190394099.00014.map 1190394099.00023.1.bfq 1190394099.00013.mismatch 1190394099.00002.1.fastq 1190394099.00020.1.fastq 1190394099.00019.1.bfq 1190394099.00012.unmapped 1190394099.00015.1.bfq 1190394099.00012.1.fastq 1190394099.00005.mismatch 1190394099.00007.map 1190394099.00018.unmapped 1190394099.00021.1.fastq 1190394099.00008.1.fastq 1190394099.00018.1.fastq 1190394099.00019.mismatch 1190394099.00022.unmapped 1190394099.00015.mismatch 1190394099.00022.1.fastq 1190394099.00003.unmapped 1190394099.00006.map 1190394099.00021.map 1190394099.00003.1.fastq 1190394099.00008.map 1190394099.00009.1.fastq 1190394099.00004.1.bfq 1190394099.00013.unmapped 1190394099.00000.map 1190394099.00016.map 1190394099.00013.1.fastq 1190394099.00001.map 1190394099.00014.1.bfq 1190394099.00007.1.bfq 1190394099.00009.map 1190394099.00005.1.fastq 1190394099.00004.mismatch 1190394099.00011.map 1190394099.00023.unmapped 1190394099.00023.mismatch 1190394099.00017.1.fastq 1190394099.00019.unmapped 1190394099.00023.1.fastq 1190394099.00017.map 1190394099.00019.1.fastq 1190394099.00002.map 1190394099.00020.map 1190394099.00015.unmapped 1190394099.00010.unmapped 1190394099.00014.mismatch 1190394099.00021.1.bfq 1190394099.00015.1.fastq 1190394099.00008.1.bfq 1190394099.00010.map 1190394099.00012.map 1190394099.00021.unmapped 1190394099.00006.1.bfq 1190394099.00018.map 1190394099.00009.1.bfq 1190394099.00000.1.bfq 1190394099.00022.map 1190394099.00007.mismatch 1190394099.00004.unmapped 1190394099.00003.map 1190394099.00001.1.bfq 1190394099.00010.1.bfq 1190394099.00004.1.fastq 1190394099.00006.mismatch 1190394099.00016.1.bfq 1190394099.00014.unmapped make: Leaving directory `/data/maqgene/work' make: Entering directory `/data/maqgene/work' # Thu Apr 11 08:04:45 BST 2013: Cleaning intermediate data ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 2879202080_snps,2879202080_rel,2879202080_masked_ids,2879202080_rel_intergenic,2879202080_intergenic_assoc,2879202080_offsets,2879202080_codons,2879202080_marked,2879202080_combined,2776322182_pileup" rm -f 2879202080_snps 2879202080_rel 2879202080_masked_ids 2879202080_rel_intergenic 2879202080_intergenic_assoc 2879202080_offsets 2879202080_codons 2879202080_marked 2879202080_combined 2776322182_pileup make: Leaving directory `/data/maqgene/work'