Finished reading input. ++ echo CB6871/./s_1_1_sequence_read1.fastq ++ tr , ' ' + fastq_file_set1=CB6871/./s_1_1_sequence_read1.fastq ++ cd /data/maqgene/reads ++ wc -l ++ cat CB6871/./s_1_1_sequence_read1.fastq ++ cut -f 1 -d ' ' + TOTAL_LINES=129781660 ++ echo '(129781660 / 5000000) + (129781660 % 5000000 != 0)' ++ bc + num_chunks=26 + set +x make -j 14 -l 14 --always-make -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=1642653393 map_cksum=942445934 pileup_cksum=157464176 cns_cksum=3434501214 umdd=50000 dmdd=1000 umid=1000 dmid=1000 max_gene_radius=50000 full_results_dir=/data/maqgene/out/example_user/CB6871_redo outfile_basename=CB6871_redo 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=26 Will process 129781660 lines of input in 26 chunks make: Entering directory `/data/maqgene/work' # Thu Mar 31 22:54:30 BST 2011: Removing frontend files in case this is a duplicate run ... rm -f /data/maqgene/out/example_user/CB6871_redo/CB6871_redo_{grouped.txt,flat.txt} rm -f /data/maqgene/out/example_user/CB6871_redo/CB6871_redo_uncovered.txt /data/maqgene/out/example_user/CB6871_redo/CB6871_redo_coverage.txt /data/maqgene/out/example_user/CB6871_redo/CB6871_redo_pileup.txt /data/maqgene/out/example_user/CB6871_redo/CB6871_redo_log.txt /data/maqgene/out/example_user/CB6871_redo/CB6871_redo_check.txt /data/maqgene/out/example_user/CB6871_redo/CB6871_redo_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/CB6871/./s_1_1_sequence_read1.fastq) 942445934.1.fastq. # : Regrouping fastq reads into chunks of size 5000000. split -l 5000000 -a 5 -d <(cat /data/maqgene/reads/CB6871/./s_1_2_sequence_read2.fastq) 942445934.2.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 00024 00025; do mv 942445934.1.fastq.$stem 942445934.$stem.1.fastq; done touch 1642653393_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 00024 00025; do mv 942445934.2.fastq.$stem 942445934.$stem.2.fastq; done touch 1642653393_split2 # Thu Mar 31 22:55:19 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 942445934.00000.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 942445934.00000.1.bfq # Thu Mar 31 22:55:19 BST 2011: Converting fastq files to bfq ... # Thu Mar 31 22:55:19 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 942445934.00001.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 942445934.00001.1.bfq /data/maqgene/bin/maq sol2sanger 942445934.00002.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 942445934.00002.1.bfq # Thu Mar 31 22:55:19 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 942445934.00003.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 942445934.00003.1.bfq # Thu Mar 31 22:55:19 BST 2011: Converting fastq files to bfq ... # Thu Mar 31 22:55:19 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 942445934.00004.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 942445934.00004.1.bfq /data/maqgene/bin/maq sol2sanger 942445934.00005.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 942445934.00005.1.bfq # Thu Mar 31 22:55:19 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 942445934.00006.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 942445934.00006.1.bfq # Thu Mar 31 22:55:19 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 942445934.00007.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 942445934.00007.1.bfq # Thu Mar 31 22:55:19 BST 2011: Converting fastq files to bfq ... # Thu Mar 31 22:55:19 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 942445934.00008.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 942445934.00008.1.bfq /data/maqgene/bin/maq sol2sanger 942445934.00009.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 942445934.00009.1.bfq /data/maqgene/bin/maq sol2sanger 942445934.00010.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 942445934.00010.1.bfq # Thu Mar 31 22:55:19 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 942445934.00011.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 942445934.00011.1.bfq # Thu Mar 31 22:55:19 BST 2011: Converting fastq files to bfq ... # Thu Mar 31 22:55:19 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 942445934.00012.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 942445934.00012.1.bfq /data/maqgene/bin/maq sol2sanger 942445934.00013.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 942445934.00013.1.bfq -- finish writing file '942445934.00000.1.bfq' -- 1250000 sequences were loaded. # Thu Mar 31 22:55:41 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 942445934.00014.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 942445934.00014.1.bfq -- finish writing file '942445934.00008.1.bfq' -- 1250000 sequences were loaded. # Thu Mar 31 22:55:43 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 942445934.00015.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 942445934.00015.1.bfq -- finish writing file '942445934.00003.1.bfq' -- 1250000 sequences were loaded. # Thu Mar 31 22:55:44 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 942445934.00016.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 942445934.00016.1.bfq -- finish writing file '942445934.00010.1.bfq' -- 1250000 sequences were loaded. # Thu Mar 31 22:55:45 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 942445934.00017.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 942445934.00017.1.bfq -- finish writing file '942445934.00011.1.bfq' -- 1250000 sequences were loaded. # Thu Mar 31 22:55:45 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 942445934.00018.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 942445934.00018.1.bfq -- finish writing file '942445934.00005.1.bfq' -- 1250000 sequences were loaded. # Thu Mar 31 22:55:47 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 942445934.00019.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 942445934.00019.1.bfq -- finish writing file '942445934.00009.1.bfq' -- 1250000 sequences were loaded. # Thu Mar 31 22:55:47 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 942445934.00020.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 942445934.00020.1.bfq -- finish writing file '942445934.00001.1.bfq' -- 1250000 sequences were loaded. # Thu Mar 31 22:55:47 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 942445934.00021.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 942445934.00021.1.bfq -- finish writing file '942445934.00007.1.bfq' -- 1250000 sequences were loaded. # Thu Mar 31 22:55:47 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 942445934.00022.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 942445934.00022.1.bfq -- finish writing file '942445934.00006.1.bfq' -- 1250000 sequences were loaded. # Thu Mar 31 22:55:47 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 942445934.00023.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 942445934.00023.1.bfq -- finish writing file '942445934.00012.1.bfq' -- 1250000 sequences were loaded. # Thu Mar 31 22:55:48 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 942445934.00024.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 942445934.00024.1.bfq -- finish writing file '942445934.00013.1.bfq' -- 1250000 sequences were loaded. # Thu Mar 31 22:55:48 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 942445934.00025.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 942445934.00025.1.bfq -- finish writing file '942445934.00004.1.bfq' -- 1250000 sequences were loaded. # Thu Mar 31 22:55:49 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 942445934.00000.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 942445934.00000.2.bfq -- finish writing file '942445934.00002.1.bfq' -- 1250000 sequences were loaded. # Thu Mar 31 22:55:49 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 942445934.00001.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 942445934.00001.2.bfq -- finish writing file '942445934.00014.1.bfq' -- 1250000 sequences were loaded. # Thu Mar 31 22:56:03 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 942445934.00002.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 942445934.00002.2.bfq -- finish writing file '942445934.00023.1.bfq' -- 1250000 sequences were loaded. # Thu Mar 31 22:56:09 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 942445934.00003.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 942445934.00003.2.bfq -- finish writing file '942445934.00016.1.bfq' -- 1250000 sequences were loaded. # Thu Mar 31 22:56:11 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 942445934.00004.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 942445934.00004.2.bfq -- finish writing file '942445934.00015.1.bfq' -- 1250000 sequences were loaded. # Thu Mar 31 22:56:13 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 942445934.00005.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 942445934.00005.2.bfq -- finish writing file '942445934.00018.1.bfq' -- 1250000 sequences were loaded. # Thu Mar 31 22:56:14 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 942445934.00006.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 942445934.00006.2.bfq -- finish writing file '942445934.00017.1.bfq' -- 1250000 sequences were loaded. # Thu Mar 31 22:56:15 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 942445934.00007.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 942445934.00007.2.bfq -- finish writing file '942445934.00022.1.bfq' -- 1250000 sequences were loaded. # Thu Mar 31 22:56:15 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 942445934.00008.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 942445934.00008.2.bfq -- finish writing file '942445934.00025.1.bfq' -- 1195415 sequences were loaded. # Thu Mar 31 22:56:16 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 942445934.00009.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 942445934.00009.2.bfq -- finish writing file '942445934.00019.1.bfq' -- 1250000 sequences were loaded. # Thu Mar 31 22:56:17 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 942445934.00010.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 942445934.00010.2.bfq -- finish writing file '942445934.00021.1.bfq' -- 1250000 sequences were loaded. # Thu Mar 31 22:56:17 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 942445934.00011.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 942445934.00011.2.bfq -- finish writing file '942445934.00001.2.bfq' -- 1250000 sequences were loaded. # Thu Mar 31 22:56:17 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 942445934.00012.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 942445934.00012.2.bfq -- finish writing file '942445934.00000.2.bfq' -- 1250000 sequences were loaded. # Thu Mar 31 22:56:18 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 942445934.00013.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 942445934.00013.2.bfq -- finish writing file '942445934.00024.1.bfq' -- 1250000 sequences were loaded. # Thu Mar 31 22:56:18 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 942445934.00014.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 942445934.00014.2.bfq -- finish writing file '942445934.00020.1.bfq' -- 1250000 sequences were loaded. # Thu Mar 31 22:56:18 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 942445934.00015.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 942445934.00015.2.bfq -- finish writing file '942445934.00002.2.bfq' -- 1250000 sequences were loaded. # Thu Mar 31 22:56:25 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 942445934.00016.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 942445934.00016.2.bfq -- finish writing file '942445934.00011.2.bfq' -- 1250000 sequences were loaded. # Thu Mar 31 22:56:35 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 942445934.00017.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 942445934.00017.2.bfq -- finish writing file '942445934.00005.2.bfq' -- 1250000 sequences were loaded. # Thu Mar 31 22:56:36 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 942445934.00018.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 942445934.00018.2.bfq -- finish writing file '942445934.00003.2.bfq' -- 1250000 sequences were loaded. # Thu Mar 31 22:56:39 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 942445934.00019.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 942445934.00019.2.bfq -- finish writing file '942445934.00009.2.bfq' -- 1250000 sequences were loaded. # Thu Mar 31 22:56:41 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 942445934.00020.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 942445934.00020.2.bfq -- finish writing file '942445934.00004.2.bfq' -- 1250000 sequences were loaded. # Thu Mar 31 22:56:43 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 942445934.00021.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 942445934.00021.2.bfq -- finish writing file '942445934.00010.2.bfq' -- 1250000 sequences were loaded. # Thu Mar 31 22:56:43 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 942445934.00022.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 942445934.00022.2.bfq -- finish writing file '942445934.00006.2.bfq' -- 1250000 sequences were loaded. # Thu Mar 31 22:56:44 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 942445934.00023.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 942445934.00023.2.bfq -- finish writing file '942445934.00008.2.bfq' -- 1250000 sequences were loaded. # Thu Mar 31 22:56:45 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 942445934.00024.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 942445934.00024.2.bfq -- finish writing file '942445934.00007.2.bfq' -- 1250000 sequences were loaded. # Thu Mar 31 22:56:46 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 942445934.00025.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 942445934.00025.2.bfq -- finish writing file '942445934.00012.2.bfq' -- 1250000 sequences were loaded. # Thu Mar 31 22:56:46 BST 2011: Mapping file(s) 942445934.00000.1.bfq 942445934.00000.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 942445934.00000.unmapped -H 942445934.00000.mismatch \ 942445934.00000.map /data/maqgene/genomes/elegans.bfa 942445934.00000.1.bfq 942445934.00000.2.bfq 2> /dev/null -- finish writing file '942445934.00013.2.bfq' -- 1250000 sequences were loaded. # Thu Mar 31 22:56:48 BST 2011: Mapping file(s) 942445934.00001.1.bfq 942445934.00001.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 942445934.00001.unmapped -H 942445934.00001.mismatch \ 942445934.00001.map /data/maqgene/genomes/elegans.bfa 942445934.00001.1.bfq 942445934.00001.2.bfq 2> /dev/null -- finish writing file '942445934.00015.2.bfq' -- 1250000 sequences were loaded. # Thu Mar 31 22:56:48 BST 2011: Mapping file(s) 942445934.00002.1.bfq 942445934.00002.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 942445934.00002.unmapped -H 942445934.00002.mismatch \ 942445934.00002.map /data/maqgene/genomes/elegans.bfa 942445934.00002.1.bfq 942445934.00002.2.bfq 2> /dev/null -- finish writing file '942445934.00014.2.bfq' -- 1250000 sequences were loaded. # Thu Mar 31 22:56:49 BST 2011: Mapping file(s) 942445934.00003.1.bfq 942445934.00003.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 942445934.00003.unmapped -H 942445934.00003.mismatch \ 942445934.00003.map /data/maqgene/genomes/elegans.bfa 942445934.00003.1.bfq 942445934.00003.2.bfq 2> /dev/null -- finish writing file '942445934.00016.2.bfq' -- 1250000 sequences were loaded. # Thu Mar 31 22:56:56 BST 2011: Mapping file(s) 942445934.00004.1.bfq 942445934.00004.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 942445934.00004.unmapped -H 942445934.00004.mismatch \ 942445934.00004.map /data/maqgene/genomes/elegans.bfa 942445934.00004.1.bfq 942445934.00004.2.bfq 2> /dev/null -- finish writing file '942445934.00017.2.bfq' -- 1250000 sequences were loaded. # Thu Mar 31 22:56:56 BST 2011: Mapping file(s) 942445934.00005.1.bfq 942445934.00005.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 942445934.00005.unmapped -H 942445934.00005.mismatch \ 942445934.00005.map /data/maqgene/genomes/elegans.bfa 942445934.00005.1.bfq 942445934.00005.2.bfq 2> /dev/null -- finish writing file '942445934.00018.2.bfq' -- 1250000 sequences were loaded. # Thu Mar 31 22:57:01 BST 2011: Mapping file(s) 942445934.00006.1.bfq 942445934.00006.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 942445934.00006.unmapped -H 942445934.00006.mismatch \ 942445934.00006.map /data/maqgene/genomes/elegans.bfa 942445934.00006.1.bfq 942445934.00006.2.bfq 2> /dev/null -- finish writing file '942445934.00019.2.bfq' -- 1250000 sequences were loaded. # Thu Mar 31 22:57:03 BST 2011: Mapping file(s) 942445934.00007.1.bfq 942445934.00007.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 942445934.00007.unmapped -H 942445934.00007.mismatch \ 942445934.00007.map /data/maqgene/genomes/elegans.bfa 942445934.00007.1.bfq 942445934.00007.2.bfq 2> /dev/null -- finish writing file '942445934.00021.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '942445934.00020.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '942445934.00025.2.bfq' -- 1195415 sequences were loaded. -- finish writing file '942445934.00023.2.bfq' -- 1250000 sequences were loaded. # Thu Mar 31 22:57:10 BST 2011: Mapping file(s) 942445934.00010.1.bfq 942445934.00010.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 942445934.00010.unmapped -H 942445934.00010.mismatch \ 942445934.00010.map /data/maqgene/genomes/elegans.bfa 942445934.00010.1.bfq 942445934.00010.2.bfq 2> /dev/null -- finish writing file '942445934.00024.2.bfq' -- 1250000 sequences were loaded. # Thu Mar 31 22:57:11 BST 2011: Mapping file(s) 942445934.00011.1.bfq 942445934.00011.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 942445934.00011.unmapped -H 942445934.00011.mismatch \ 942445934.00011.map /data/maqgene/genomes/elegans.bfa 942445934.00011.1.bfq 942445934.00011.2.bfq 2> /dev/null # Thu Mar 31 22:57:12 BST 2011: Mapping file(s) 942445934.00012.1.bfq 942445934.00012.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 942445934.00012.unmapped -H 942445934.00012.mismatch \ 942445934.00012.map /data/maqgene/genomes/elegans.bfa 942445934.00012.1.bfq 942445934.00012.2.bfq 2> /dev/null -- finish writing file '942445934.00022.2.bfq' -- 1250000 sequences were loaded. # Thu Mar 31 22:57:12 BST 2011: Mapping file(s) 942445934.00009.1.bfq 942445934.00009.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 942445934.00009.unmapped -H 942445934.00009.mismatch \ 942445934.00009.map /data/maqgene/genomes/elegans.bfa 942445934.00009.1.bfq 942445934.00009.2.bfq 2> /dev/null # Thu Mar 31 22:57:13 BST 2011: Mapping file(s) 942445934.00013.1.bfq 942445934.00013.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 942445934.00013.unmapped -H 942445934.00013.mismatch \ 942445934.00013.map /data/maqgene/genomes/elegans.bfa 942445934.00013.1.bfq 942445934.00013.2.bfq 2> /dev/null # Thu Mar 31 22:57:14 BST 2011: Mapping file(s) 942445934.00008.1.bfq 942445934.00008.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 942445934.00008.unmapped -H 942445934.00008.mismatch \ 942445934.00008.map /data/maqgene/genomes/elegans.bfa 942445934.00008.1.bfq 942445934.00008.2.bfq 2> /dev/null # Thu Mar 31 23:03:42 BST 2011: Mapping file(s) 942445934.00019.1.bfq 942445934.00019.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 942445934.00019.unmapped -H 942445934.00019.mismatch \ 942445934.00019.map /data/maqgene/genomes/elegans.bfa 942445934.00019.1.bfq 942445934.00019.2.bfq 2> /dev/null # Thu Mar 31 23:03:42 BST 2011: Mapping file(s) 942445934.00018.1.bfq 942445934.00018.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 942445934.00018.unmapped -H 942445934.00018.mismatch \ 942445934.00018.map /data/maqgene/genomes/elegans.bfa 942445934.00018.1.bfq 942445934.00018.2.bfq 2> /dev/null # Thu Mar 31 23:03:43 BST 2011: Mapping file(s) 942445934.00020.1.bfq 942445934.00020.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 942445934.00020.unmapped -H 942445934.00020.mismatch \ 942445934.00020.map /data/maqgene/genomes/elegans.bfa 942445934.00020.1.bfq 942445934.00020.2.bfq 2> /dev/null # Thu Mar 31 23:03:44 BST 2011: Mapping file(s) 942445934.00017.1.bfq 942445934.00017.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 942445934.00017.unmapped -H 942445934.00017.mismatch \ 942445934.00017.map /data/maqgene/genomes/elegans.bfa 942445934.00017.1.bfq 942445934.00017.2.bfq 2> /dev/null # Thu Mar 31 23:03:45 BST 2011: Mapping file(s) 942445934.00016.1.bfq 942445934.00016.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 942445934.00016.unmapped -H 942445934.00016.mismatch \ 942445934.00016.map /data/maqgene/genomes/elegans.bfa 942445934.00016.1.bfq 942445934.00016.2.bfq 2> /dev/null # Thu Mar 31 23:03:46 BST 2011: Mapping file(s) 942445934.00015.1.bfq 942445934.00015.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 942445934.00015.unmapped -H 942445934.00015.mismatch \ 942445934.00015.map /data/maqgene/genomes/elegans.bfa 942445934.00015.1.bfq 942445934.00015.2.bfq 2> /dev/null # Thu Mar 31 23:04:16 BST 2011: Mapping file(s) 942445934.00025.1.bfq 942445934.00025.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 942445934.00025.unmapped -H 942445934.00025.mismatch \ 942445934.00025.map /data/maqgene/genomes/elegans.bfa 942445934.00025.1.bfq 942445934.00025.2.bfq 2> /dev/null # Thu Mar 31 23:10:25 BST 2011: Mapping file(s) 942445934.00024.1.bfq 942445934.00024.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 942445934.00024.unmapped -H 942445934.00024.mismatch \ 942445934.00024.map /data/maqgene/genomes/elegans.bfa 942445934.00024.1.bfq 942445934.00024.2.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 942445934.00023.unmapped -H 942445934.00023.mismatch \ 942445934.00023.map /data/maqgene/genomes/elegans.bfa 942445934.00023.1.bfq 942445934.00023.2.bfq 2> /dev/null # Thu Mar 31 23:10:25 BST 2011: Mapping file(s) 942445934.00022.1.bfq 942445934.00022.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 942445934.00022.unmapped -H 942445934.00022.mismatch \ 942445934.00022.map /data/maqgene/genomes/elegans.bfa 942445934.00022.1.bfq 942445934.00022.2.bfq 2> /dev/null # Thu Mar 31 23:17:36 BST 2011: Mapping file(s) 942445934.00021.1.bfq 942445934.00021.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 942445934.00021.unmapped -H 942445934.00021.mismatch \ 942445934.00021.map /data/maqgene/genomes/elegans.bfa 942445934.00021.1.bfq 942445934.00021.2.bfq 2> /dev/null # Thu Mar 31 23:23:46 BST 2011: Mapping file(s) 942445934.00014.1.bfq 942445934.00014.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 942445934.00014.unmapped -H 942445934.00014.mismatch \ 942445934.00014.map /data/maqgene/genomes/elegans.bfa 942445934.00014.1.bfq 942445934.00014.2.bfq 2> /dev/null # Thu Mar 31 23:28:09 BST 2011: Merging all maps ... /data/maqgene/bin/maq mapmerge 942445934.map 942445934.00000.map 942445934.00001.map 942445934.00002.map 942445934.00003.map 942445934.00004.map 942445934.00005.map 942445934.00006.map 942445934.00007.map 942445934.00008.map 942445934.00009.map 942445934.00010.map 942445934.00011.map 942445934.00012.map 942445934.00013.map 942445934.00014.map 942445934.00015.map 942445934.00016.map 942445934.00017.map 942445934.00018.map 942445934.00019.map 942445934.00020.map 942445934.00021.map 942445934.00022.map 942445934.00023.map 942445934.00024.map 942445934.00025.map cat 942445934.00000.unmapped 942445934.00001.unmapped 942445934.00002.unmapped 942445934.00003.unmapped 942445934.00004.unmapped 942445934.00005.unmapped 942445934.00006.unmapped 942445934.00007.unmapped 942445934.00008.unmapped 942445934.00009.unmapped 942445934.00010.unmapped 942445934.00011.unmapped 942445934.00012.unmapped 942445934.00013.unmapped 942445934.00014.unmapped 942445934.00015.unmapped 942445934.00016.unmapped 942445934.00017.unmapped 942445934.00018.unmapped 942445934.00019.unmapped 942445934.00020.unmapped 942445934.00021.unmapped 942445934.00022.unmapped 942445934.00023.unmapped 942445934.00024.unmapped 942445934.00025.unmapped > 942445934_unmapped.txt # Thu Mar 31 23:28:11 BST 2011: Linking backend file 942445934_unmapped.txt to /data/maqgene/out/example_user/CB6871_redo/CB6871_redo_unmapped.txt ln -fs /data/maqgene/work/942445934_unmapped.txt /data/maqgene/out/example_user/CB6871_redo/CB6871_redo_unmapped.txt /data/maqgene/makefile:126: warning: undefined variable `mapcheck_parameters' # Thu Mar 31 23:39:39 BST 2011: Generating consensus ... /data/maqgene/bin/maq assemble -N 2 -q 0 -r 0.0 -m 7 -Q 100 -p 3434501214.cns \ /data/maqgene/genomes/elegans.bfa 942445934.map 2> 3434501214_log.txt /data/maqgene/bin/maq pileup -Q 100 -p -m 7 -q 0 /data/maqgene/genomes/elegans.bfa 942445934.map > 157464176_pileup.txt # Thu Mar 31 23:39:39 BST 2011: Running 'mapcheck' ... /data/maqgene/bin/maq mapcheck /data/maqgene/genomes/elegans.bfa 942445934.map > 942445934_check.txt \ 2>/dev/null # Thu Mar 31 23:42:31 BST 2011: Linking backend file 942445934_check.txt to /data/maqgene/out/example_user/CB6871_redo/CB6871_redo_check.txt ln -fs /data/maqgene/work/942445934_check.txt /data/maqgene/out/example_user/CB6871_redo/CB6871_redo_check.txt /data/maqgene/bin/filter_matching_lines 157464176_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 \ > 157464176_known_snps # Thu Mar 31 23:42:58 BST 2011: Getting uncovered regions ... # Thu Mar 31 23:42:58 BST 2011: Making coverage histogram ... cut -f 1,2,4 157464176_pileup.txt \ | /data/maqgene/bin/get_uncovered_regions 50 \ > 157464176_uncovered.txt (echo -en "sequencing_depth\tnumber_of_bases\n"; \ cut -f 4 157464176_pileup.txt \ | /data/maqgene/bin/pileup_histogram 100) > 157464176_coverage.txt # Thu Mar 31 23:42:58 BST 2011: Linking backend file 157464176_pileup.txt to /data/maqgene/out/example_user/CB6871_redo/CB6871_redo_pileup.txt ln -fs /data/maqgene/work/157464176_pileup.txt /data/maqgene/out/example_user/CB6871_redo/CB6871_redo_pileup.txt # Thu Mar 31 23:43:24 BST 2011: Linking backend file 157464176_coverage.txt to /data/maqgene/out/example_user/CB6871_redo/CB6871_redo_coverage.txt ln -fs /data/maqgene/work/157464176_coverage.txt /data/maqgene/out/example_user/CB6871_redo/CB6871_redo_coverage.txt # Thu Mar 31 23:43:25 BST 2011: Filtering and loading pileup for analysis ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 157464176_pileup; create table 157464176_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 157464176_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 157464176_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 157464176_pileup" # Thu Mar 31 23:43:29 BST 2011: Linking backend file 157464176_uncovered.txt to /data/maqgene/out/example_user/CB6871_redo/CB6871_redo_uncovered.txt ln -fs /data/maqgene/work/157464176_uncovered.txt /data/maqgene/out/example_user/CB6871_redo/CB6871_redo_uncovered.txt cat 157464176_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 157464176_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 157464176_pileup" touch 157464176_pileup # Thu Mar 31 23:44:17 BST 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 157464176_pileup p using (dna,start)" > /data/maqgene/out/example_user/CB6871_redo/CB6871_redo_snp_read_counts.txt 0 snp read count lines written. # Thu Mar 31 23:44:34 BST 2011: Extracting point mutants from consensus ... # Thu Mar 31 23:44:34 BST 2011: Linking backend file 3434501214_log.txt to /data/maqgene/out/example_user/CB6871_redo/CB6871_redo_log.txt /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 3434501214_snps; create table 3434501214_snps ( id int(10) NOT NULL auto_increment, dna char(40) NOT NULL, start int(10) NOT NULL, end int(10) NOT NULL, indel_size int(5) NOT NULL, variant_type enum('indel', 'point') NOT NULL, ref_base char NOT NULL, sample_base char NOT NULL, snp_score int(5) NOT NULL, read_depth int(5) NOT NULL, loci_multiplicity double(5,2) NOT NULL, mapping_quality int(5) NOT NULL, neighbor_quality int(5) NOT NULL, primary key (id), unique key (dna, start), key (indel_size) )" ln -fs /data/maqgene/work/3434501214_log.txt /data/maqgene/out/example_user/CB6871_redo/CB6871_redo_log.txt /data/maqgene/bin/maq cns2snp 3434501214.cns \ | cat -b | /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "load data local infile '/dev/stdin' into table 3434501214_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 3434501214_snps;" # Thu Mar 31 23:44:48 BST 2011: Extracting indels from consensus ... /data/maqgene/bin/maq indelsoa /data/maqgene/genomes/elegans.bfa 942445934.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 3434501214_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 3434501214_snps;" # Thu Mar 31 23:46:27 BST 2011: Adding placeholders for known SNPs. cat 157464176_known_snps \ | /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "load data local infile '/dev/stdin' ignore into table 3434501214_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 3434501214_snps;" Found 161429 variants. touch 3434501214_snps # Thu Mar 31 23:46:29 BST 2011: Loading uncovered regions into table ... # Thu Mar 31 23:46:29 BST 2011: Finding all genomic features overlapping variants... cat 157464176_uncovered.txt \ | /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 157464176_uncovered; create table 157464176_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 = 161430; load data local infile '/dev/stdin' into table 157464176_uncovered (dna, start, end)" /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 3434501214_rel_snps; CREATE TABLE 3434501214_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) )" # Thu Mar 31 23:46:29 BST 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 3434501214_masked_ids; create table 3434501214_masked_ids (query_region_id int(10) NOT NULL, primary key (query_region_id)); load data local infile '/dev/stdin' ignore into table 3434501214_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 3434501214_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 3434501214_rel_snps; flush table 3434501214_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 3434501214_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 1429 II 17 2546 III 17 13476 IV 18 2843 V 15 1747 X 16 5967 touch 157464176_uncovered # Thu Mar 31 23:46:29 BST 2011: Finding mRNA features overlapping uncovered regions ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 157464176_uncovered_rel; CREATE TABLE 157464176_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 157464176_uncovered_rel; flush table 157464176_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 157464176_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 3434501214_masked_ids touch 157464176_uncovered_rel # Thu Mar 31 23:46:31 BST 2011: Calculating translation start offsets for uncovered regions... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 157464176_offsets_uncovered; create table 157464176_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 157464176_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 157464176_uncovered reg join 157464176_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 157464176_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 157464176_uncovered reg join 157464176_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 157464176_offsets_uncovered touch 3434501214_rel_snps # Thu Mar 31 23:46:32 BST 2011: Calculating translation start offsets... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 3434501214_offsets_snps; create table 3434501214_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 Mar 31 23:46:32 BST 2011: Getting intergenic regions /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 3434501214_rel_intergenic; create table 3434501214_rel_intergenic like 3434501214_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 3434501214_rel_intergenic; flush table 3434501214_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 3434501214_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 3434501214_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 3434501214_snps reg join 3434501214_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 Mar 31 23:46:35 BST 2011: Filtering masked intergenic regions /usr/bin/mysql -Dmaqgenedb -umaqgene --skip-column-names --batch --raw --local-infile -e "delete i.* from 3434501214_rel_intergenic i join 3434501214_masked_ids m using (query_region_id)" touch 3434501214_rel_intergenic # Thu Mar 31 23:46:40 BST 2011: Classifying intergenic relations /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 3434501214_intergenic_assoc; create table 3434501214_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 3434501214_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 3434501214_snps snp join 3434501214_rel_intergenic rel on (snp.id = rel.query_region_id) join elegans_features feature on (rel.target_region_id = feature.id)" touch 3434501214_intergenic_assoc touch 3434501214_offsets_snps # Thu Mar 31 23:46:50 BST 2011: Getting codons affected by point mutations... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 3434501214_codons; create table 3434501214_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 3434501214_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 3434501214_offsets_snps off join 3434501214_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 3434501214_codons /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 3434501214_marked; create table 3434501214_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 Mar 31 23:46:57 BST 2011: Finding exonic indels ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 3434501214_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 3434501214_snps snp join 3434501214_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 Mar 31 23:46:57 BST 2011: Finding coding variants ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 3434501214_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 3434501214_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 Mar 31 23:46:57 BST 2011: Finding noncoding variants ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 3434501214_marked select snp.id, feature.feature class, 'none' description, feature.attribute parent_feature from 3434501214_snps snp join 3434501214_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 Mar 31 23:46:57 BST 2011: Finding splice site variants ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 3434501214_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 3434501214_snps snp join 3434501214_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 Mar 31 23:46:58 BST 2011: Finding intergenic and intronic variants ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 3434501214_marked select id, 'nongenic' class, concat(if (relation in ('upstream','into'), - distance, distance),' ',relation) description, attribute from 3434501214_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 Mar 31 23:47:00 BST 2011: Finding uncovered regions in genes ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 3434501214_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 157464176_uncovered unc join 157464176_offsets_uncovered b using (id) join 157464176_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 157464176_uncovered unc join 157464176_offsets_uncovered b using (id) join 157464176_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 Mar 31 23:47:00 BST 2011: Variants found: +-----------------+-----------------+ | class | number_variants | +-----------------+-----------------+ | five_prime_UTR | 1291 | | frameshift | 59 | | inframe | 10 | | missense | 6169 | | ncRNA | 866 | | nongenic | 124897 | | non_start | 9 | | premature_stop | 689 | | readthrough | 19 | | silent | 7417 | | SNP | 1018 | | splice_acceptor | 45 | | splice_donor | 48 | | three_prime_UTR | 3541 | | uncovered | 34 | +-----------------+-----------------+ touch 3434501214_marked # Thu Mar 31 23:47:02 BST 2011: Combining results ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 3434501214_combined; create table 3434501214_combined (primary key (id, class, description), key (dna, start)) as select snp.id, 'CB6871_redo' 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 3434501214_snps snp join 157464176_pileup pile using (dna,start) join 3434501214_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, 'CB6871_redo' 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 157464176_uncovered unc join 3434501214_marked class on (unc.id = class.id) left join elegans_per_locus using (dna,start) group by id, class, description; alter table 3434501214_combined order by dna, start, length" touch 3434501214_combined # Thu Mar 31 23:47:03 BST 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 3434501214_combined group by id order by dna, start;" > /data/maqgene/out/example_user/CB6871_redo/CB6871_redo_grouped.txt # Thu Mar 31 23:47:03 BST 2011: Writing results to flat file ... /usr/bin/mysql -Dmaqgenedb -umaqgene --skip-column-names --batch --raw --local-infile --column-names -e "select * from 3434501214_combined" > /data/maqgene/out/example_user/CB6871_redo/CB6871_redo_flat.txt 3397 lines written. 2011 lines written. rm 942445934.00004.unmapped 942445934.00003.map 942445934.00006.2.bfq 942445934.00001.1.bfq 942445934.00010.1.bfq 942445934.00007.map 942445934.00004.1.fastq 942445934.00021.1.fastq 942445934.00016.1.bfq 942445934.00008.1.fastq 942445934.00000.2.bfq 942445934.00014.unmapped 942445934.00013.map 942445934.00025.2.fastq 942445934.00000.mismatch 942445934.00017.1.bfq 942445934.00001.2.bfq 942445934.00010.2.bfq 942445934.00020.1.bfq 942445934.00004.2.fastq 942445934.00001.mismatch 942445934.00010.mismatch 942445934.00016.2.bfq 942445934.00021.map 942445934.00008.map 942445934.00005.map 942445934.00009.1.fastq 942445934.00011.2.bfq 942445934.00012.1.bfq 942445934.00007.2.fastq 942445934.00023.map 942445934.00011.mismatch 942445934.00024.unmapped 942445934.00019.map 942445934.00024.1.fastq 942445934.00002.2.bfq 942445934.00020.2.bfq 942445934.00015.map 942445934.00020.mismatch 942445934.00007.1.bfq 942445934.00009.map 942445934.00006.unmapped 942445934.00012.2.bfq 942445934.00022.1.bfq 942445934.00011.1.bfq 942445934.00012.mismatch 942445934.00017.1.fastq 942445934.00019.mismatch 942445934.00006.1.fastq 942445934.00008.2.fastq 942445934.00002.1.bfq 942445934.00024.2.fastq 942445934.00000.unmapped 942445934.00003.1.bfq 942445934.00009.unmapped 942445934.00000.1.fastq 942445934.00018.mismatch 942445934.00008.1.bfq 942445934.00004.map 942445934.00005.2.bfq 942445934.00025.map 942445934.00001.unmapped 942445934.00010.unmapped 942445934.00022.2.bfq 942445934.00013.1.bfq 942445934.00016.unmapped 942445934.00014.1.fastq 942445934.00006.2.fastq 942445934.00017.map 942445934.00001.1.fastq 942445934.00010.1.fastq 942445934.00016.1.fastq 942445934.00009.2.fastq 942445934.00003.2.bfq 942445934.00011.unmapped 942445934.00003.mismatch 942445934.00000.2.fastq 942445934.00011.1.fastq 942445934.00005.1.bfq 1642653393_split1 942445934.00002.unmapped 942445934.00020.unmapped 942445934.00013.2.bfq 942445934.00014.map 942445934.00007.mismatch 942445934.00013.mismatch 942445934.00001.2.fastq 942445934.00010.2.fastq 942445934.00002.1.fastq 942445934.00007.2.bfq 942445934.00020.1.fastq 942445934.00019.1.bfq 942445934.00016.2.fastq 942445934.00018.map 942445934.00021.1.bfq 942445934.00015.mismatch 942445934.00012.unmapped 942445934.00015.1.bfq 942445934.00011.2.fastq 942445934.00012.1.fastq 942445934.00002.mismatch 942445934.00005.mismatch 942445934.00004.1.bfq 942445934.00017.2.fastq 942445934.00023.2.bfq 942445934.00018.unmapped 942445934.00002.2.fastq 942445934.00020.2.fastq 942445934.00023.mismatch 942445934.00024.map 942445934.00019.2.bfq 942445934.00007.unmapped 942445934.00016.mismatch 942445934.00008.mismatch 942445934.00021.2.bfq 942445934.00018.1.fastq 942445934.00022.unmapped 942445934.00015.2.bfq 942445934.00012.2.fastq 942445934.00014.2.fastq 942445934.00022.1.fastq 942445934.00023.1.bfq 942445934.00003.unmapped 942445934.00025.1.bfq 942445934.00006.map 942445934.00003.1.fastq 1642653393_split2 942445934.00018.2.fastq 942445934.00008.unmapped 942445934.00009.mismatch 942445934.00018.1.bfq 942445934.00013.unmapped 942445934.00009.2.bfq 942445934.00000.map 942445934.00008.2.bfq 942445934.00022.2.fastq 942445934.00013.1.fastq 942445934.00025.2.bfq 942445934.00025.mismatch 942445934.00001.map 942445934.00014.1.bfq 942445934.00019.1.fastq 942445934.00003.2.fastq 942445934.00016.map 942445934.00005.unmapped 942445934.00006.mismatch 942445934.00004.2.bfq 942445934.00005.1.fastq 942445934.00004.mismatch 942445934.00011.map 942445934.00023.unmapped 942445934.00013.2.fastq 942445934.00019.unmapped 942445934.00017.mismatch 942445934.00023.1.fastq 942445934.00017.2.bfq 942445934.00022.mismatch 942445934.00010.map 942445934.00002.map 942445934.00015.unmapped 942445934.00021.unmapped 942445934.00021.mismatch 942445934.00015.1.fastq 942445934.00005.2.fastq 942445934.00012.map 942445934.00024.1.bfq 942445934.00014.mismatch 942445934.00023.2.fastq 942445934.00014.2.bfq 942445934.00017.unmapped 942445934.00019.2.fastq 942445934.00018.2.bfq 942445934.00006.1.bfq 942445934.00007.1.fastq 942445934.00021.2.fastq 942445934.00024.2.bfq 942445934.00015.2.fastq 942445934.00024.mismatch 942445934.00025.unmapped 942445934.00009.1.bfq 942445934.00020.map 942445934.00000.1.bfq 942445934.00022.map 942445934.00025.1.fastq make: Leaving directory `/data/maqgene/work' make: Entering directory `/data/maqgene/work' # Thu Mar 31 23:47:04 BST 2011: Cleaning intermediate data ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 3434501214_snps,3434501214_rel,3434501214_masked_ids,3434501214_rel_intergenic,3434501214_intergenic_assoc,3434501214_offsets,3434501214_codons,3434501214_marked,3434501214_combined,157464176_pileup" rm -f 3434501214_snps 3434501214_rel 3434501214_masked_ids 3434501214_rel_intergenic 3434501214_intergenic_assoc 3434501214_offsets 3434501214_codons 3434501214_marked 3434501214_combined 157464176_pileup make: Leaving directory `/data/maqgene/work'