Finished reading input. ++ echo CB6871/./s_1_1_sequence_read1.fastq,ot340/./ot340_chrI_11m_12m_read1.fastq ++ tr , ' ' + fastq_file_set1='CB6871/./s_1_1_sequence_read1.fastq ot340/./ot340_chrI_11m_12m_read1.fastq' ++ cd /data/maqgene/reads ++ wc -l ++ cat CB6871/./s_1_1_sequence_read1.fastq ot340/./ot340_chrI_11m_12m_read1.fastq ++ cut -f 1 -d ' ' + TOTAL_LINES=130260252 ++ echo '(130260252 / 5000000) + (130260252 % 5000000 != 0)' ++ bc + num_chunks=27 + 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=3477649743 map_cksum=36058762 pileup_cksum=2759793305 cns_cksum=371791328 umdd=50000 dmdd=1000 umid=1000 dmid=1000 max_gene_radius=50000 full_results_dir=/data/maqgene/out/example_user/CB6871 outfile_basename=CB6871 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=27 Will process 130260252 lines of input in 27 chunks make: Entering directory `/data/maqgene/work' # Thu Feb 3 17:20:26 GMT 2011: Removing frontend files in case this is a duplicate run ... rm -f /data/maqgene/out/example_user/CB6871/CB6871_{grouped.txt,flat.txt} rm -f /data/maqgene/out/example_user/CB6871/CB6871_uncovered.txt /data/maqgene/out/example_user/CB6871/CB6871_coverage.txt /data/maqgene/out/example_user/CB6871/CB6871_pileup.txt /data/maqgene/out/example_user/CB6871/CB6871_log.txt /data/maqgene/out/example_user/CB6871/CB6871_check.txt /data/maqgene/out/example_user/CB6871/CB6871_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 /data/maqgene/reads/ot340/./ot340_chrI_11m_12m_read1.fastq) 36058762.1.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 /data/maqgene/reads/ot340/./ot340_chrI_11m_12m_read2.fastq) 36058762.2.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 00026; do mv 36058762.1.fastq.$stem 36058762.$stem.1.fastq; done touch 3477649743_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 00026; do mv 36058762.2.fastq.$stem 36058762.$stem.2.fastq; done touch 3477649743_split2 # Thu Feb 3 17:21:02 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 36058762.00000.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 36058762.00000.1.bfq # Thu Feb 3 17:21:02 GMT 2011: Converting fastq files to bfq ... # Thu Feb 3 17:21:02 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 36058762.00001.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 36058762.00001.1.bfq /data/maqgene/bin/maq sol2sanger 36058762.00002.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 36058762.00002.1.bfq # Thu Feb 3 17:21:02 GMT 2011: Converting fastq files to bfq ... # Thu Feb 3 17:21:02 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 36058762.00003.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 36058762.00003.1.bfq /data/maqgene/bin/maq sol2sanger 36058762.00004.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 36058762.00004.1.bfq # Thu Feb 3 17:21:02 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 36058762.00005.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 36058762.00005.1.bfq # Thu Feb 3 17:21:02 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 36058762.00006.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 36058762.00006.1.bfq # Thu Feb 3 17:21:02 GMT 2011: Converting fastq files to bfq ... # Thu Feb 3 17:21:02 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 36058762.00008.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 36058762.00008.1.bfq /data/maqgene/bin/maq sol2sanger 36058762.00007.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 36058762.00007.1.bfq # Thu Feb 3 17:21:02 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 36058762.00009.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 36058762.00009.1.bfq # Thu Feb 3 17:21:02 GMT 2011: Converting fastq files to bfq ... # Thu Feb 3 17:21:02 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 36058762.00011.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 36058762.00011.1.bfq /data/maqgene/bin/maq sol2sanger 36058762.00010.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 36058762.00010.1.bfq # Thu Feb 3 17:21:02 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 36058762.00012.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 36058762.00012.1.bfq # Thu Feb 3 17:21:02 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 36058762.00013.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 36058762.00013.1.bfq -- finish writing file '36058762.00000.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 17:21:22 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 36058762.00014.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 36058762.00014.1.bfq -- finish writing file '36058762.00010.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 17:21:26 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 36058762.00015.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 36058762.00015.1.bfq -- finish writing file '36058762.00003.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 17:21:26 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 36058762.00016.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 36058762.00016.1.bfq -- finish writing file '36058762.00005.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 17:21:28 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 36058762.00017.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 36058762.00017.1.bfq -- finish writing file '36058762.00006.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 17:21:29 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 36058762.00018.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 36058762.00018.1.bfq -- finish writing file '36058762.00012.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 17:21:30 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 36058762.00019.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 36058762.00019.1.bfq -- finish writing file '36058762.00008.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 17:21:30 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 36058762.00020.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 36058762.00020.1.bfq -- finish writing file '36058762.00011.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 17:21:31 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 36058762.00021.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 36058762.00021.1.bfq -- finish writing file '36058762.00007.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 17:21:32 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 36058762.00022.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 36058762.00022.1.bfq -- finish writing file '36058762.00004.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 17:21:32 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 36058762.00023.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 36058762.00023.1.bfq -- finish writing file '36058762.00009.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 17:21:33 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 36058762.00024.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 36058762.00024.1.bfq -- finish writing file '36058762.00013.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 17:21:33 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 36058762.00025.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 36058762.00025.1.bfq -- finish writing file '36058762.00001.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 17:21:33 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 36058762.00026.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 36058762.00026.1.bfq -- finish writing file '36058762.00026.1.bfq' -- 65063 sequences were loaded. # Thu Feb 3 17:21:34 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 36058762.00000.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 36058762.00000.2.bfq -- finish writing file '36058762.00002.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 17:21:35 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 36058762.00001.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 36058762.00001.2.bfq -- finish writing file '36058762.00014.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 17:21:50 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 36058762.00002.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 36058762.00002.2.bfq -- finish writing file '36058762.00017.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 17:21:54 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 36058762.00003.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 36058762.00003.2.bfq -- finish writing file '36058762.00018.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 17:21:55 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 36058762.00004.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 36058762.00004.2.bfq -- finish writing file '36058762.00016.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 17:21:55 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 36058762.00005.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 36058762.00005.2.bfq -- finish writing file '36058762.00015.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 17:21:56 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 36058762.00006.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 36058762.00006.2.bfq -- finish writing file '36058762.00020.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 17:21:58 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 36058762.00007.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 36058762.00007.2.bfq -- finish writing file '36058762.00019.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 17:21:58 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 36058762.00008.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 36058762.00008.2.bfq -- finish writing file '36058762.00000.2.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 17:22:00 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 36058762.00009.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 36058762.00009.2.bfq -- finish writing file '36058762.00022.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 17:22:00 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 36058762.00010.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 36058762.00010.2.bfq -- finish writing file '36058762.00021.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 17:22:01 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 36058762.00011.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 36058762.00011.2.bfq -- finish writing file '36058762.00024.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 17:22:01 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 36058762.00012.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 36058762.00012.2.bfq -- finish writing file '36058762.00001.2.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 17:22:02 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 36058762.00013.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 36058762.00013.2.bfq -- finish writing file '36058762.00025.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 17:22:02 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 36058762.00014.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 36058762.00014.2.bfq -- finish writing file '36058762.00023.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 17:22:06 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 36058762.00015.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 36058762.00015.2.bfq -- finish writing file '36058762.00002.2.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 17:22:16 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 36058762.00016.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 36058762.00016.2.bfq -- finish writing file '36058762.00003.2.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 17:22:18 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 36058762.00017.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 36058762.00017.2.bfq -- finish writing file '36058762.00004.2.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 17:22:21 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 36058762.00018.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 36058762.00018.2.bfq -- finish writing file '36058762.00005.2.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 17:22:25 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 36058762.00019.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 36058762.00019.2.bfq -- finish writing file '36058762.00008.2.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 17:22:25 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 36058762.00020.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 36058762.00020.2.bfq -- finish writing file '36058762.00007.2.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 17:22:26 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 36058762.00021.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 36058762.00021.2.bfq -- finish writing file '36058762.00006.2.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 17:22:26 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 36058762.00022.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 36058762.00022.2.bfq -- finish writing file '36058762.00013.2.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 17:22:27 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 36058762.00023.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 36058762.00023.2.bfq -- finish writing file '36058762.00010.2.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 17:22:27 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 36058762.00024.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 36058762.00024.2.bfq -- finish writing file '36058762.00009.2.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 17:22:28 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 36058762.00025.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 36058762.00025.2.bfq -- finish writing file '36058762.00014.2.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 17:22:29 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 36058762.00026.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 36058762.00026.2.bfq -- finish writing file '36058762.00011.2.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 17:22:30 GMT 2011: Mapping file(s) 36058762.00000.1.bfq 36058762.00000.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 36058762.00000.unmapped -H 36058762.00000.mismatch \ 36058762.00000.map /data/maqgene/genomes/elegans.bfa 36058762.00000.1.bfq 36058762.00000.2.bfq 2> /dev/null -- finish writing file '36058762.00012.2.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 17:22:30 GMT 2011: Mapping file(s) 36058762.00001.1.bfq 36058762.00001.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 36058762.00001.unmapped -H 36058762.00001.mismatch \ 36058762.00001.map /data/maqgene/genomes/elegans.bfa 36058762.00001.1.bfq 36058762.00001.2.bfq 2> /dev/null -- finish writing file '36058762.00026.2.bfq' -- 65063 sequences were loaded. # Thu Feb 3 17:22:31 GMT 2011: Mapping file(s) 36058762.00002.1.bfq 36058762.00002.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 36058762.00002.unmapped -H 36058762.00002.mismatch \ 36058762.00002.map /data/maqgene/genomes/elegans.bfa 36058762.00002.1.bfq 36058762.00002.2.bfq 2> /dev/null -- finish writing file '36058762.00015.2.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 17:22:36 GMT 2011: Mapping file(s) 36058762.00003.1.bfq 36058762.00003.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 36058762.00003.unmapped -H 36058762.00003.mismatch \ 36058762.00003.map /data/maqgene/genomes/elegans.bfa 36058762.00003.1.bfq 36058762.00003.2.bfq 2> /dev/null -- finish writing file '36058762.00016.2.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 17:22:43 GMT 2011: Mapping file(s) 36058762.00004.1.bfq 36058762.00004.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 36058762.00004.unmapped -H 36058762.00004.mismatch \ 36058762.00004.map /data/maqgene/genomes/elegans.bfa 36058762.00004.1.bfq 36058762.00004.2.bfq 2> /dev/null -- finish writing file '36058762.00017.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '36058762.00018.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '36058762.00019.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '36058762.00021.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '36058762.00020.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '36058762.00025.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '36058762.00022.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '36058762.00023.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '36058762.00024.2.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 17:22:54 GMT 2011: Mapping file(s) 36058762.00012.1.bfq 36058762.00012.2.bfq # Thu Feb 3 17:22:54 GMT 2011: Mapping file(s) 36058762.00011.1.bfq 36058762.00011.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 36058762.00012.unmapped -H 36058762.00012.mismatch \ 36058762.00012.map /data/maqgene/genomes/elegans.bfa 36058762.00012.1.bfq 36058762.00012.2.bfq 2> /dev/null # Thu Feb 3 17:22:54 GMT 2011: Mapping file(s) 36058762.00013.1.bfq 36058762.00013.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 36058762.00013.unmapped -H 36058762.00013.mismatch \ 36058762.00013.map /data/maqgene/genomes/elegans.bfa 36058762.00013.1.bfq 36058762.00013.2.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 36058762.00011.unmapped -H 36058762.00011.mismatch \ 36058762.00011.map /data/maqgene/genomes/elegans.bfa 36058762.00011.1.bfq 36058762.00011.2.bfq 2> /dev/null # Thu Feb 3 17:22:55 GMT 2011: Mapping file(s) 36058762.00010.1.bfq 36058762.00010.2.bfq # Thu Feb 3 17:22:55 GMT 2011: Mapping file(s) 36058762.00009.1.bfq 36058762.00009.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 36058762.00010.unmapped -H 36058762.00010.mismatch \ 36058762.00010.map /data/maqgene/genomes/elegans.bfa 36058762.00010.1.bfq 36058762.00010.2.bfq 2> /dev/null /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 36058762.00009.unmapped -H 36058762.00009.mismatch \ 36058762.00009.map /data/maqgene/genomes/elegans.bfa 36058762.00009.1.bfq 36058762.00009.2.bfq 2> /dev/null # Thu Feb 3 17:22:56 GMT 2011: Mapping file(s) 36058762.00006.1.bfq 36058762.00006.2.bfq # Thu Feb 3 17:22:56 GMT 2011: Mapping file(s) 36058762.00007.1.bfq 36058762.00007.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 36058762.00006.unmapped -H 36058762.00006.mismatch \ 36058762.00006.map /data/maqgene/genomes/elegans.bfa 36058762.00006.1.bfq 36058762.00006.2.bfq 2> /dev/null /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 36058762.00007.unmapped -H 36058762.00007.mismatch \ 36058762.00007.map /data/maqgene/genomes/elegans.bfa 36058762.00007.1.bfq 36058762.00007.2.bfq 2> /dev/null # Thu Feb 3 17:22:56 GMT 2011: Mapping file(s) 36058762.00008.1.bfq 36058762.00008.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 36058762.00008.unmapped -H 36058762.00008.mismatch \ 36058762.00008.map /data/maqgene/genomes/elegans.bfa 36058762.00008.1.bfq 36058762.00008.2.bfq 2> /dev/null # Thu Feb 3 17:22:57 GMT 2011: Mapping file(s) 36058762.00005.1.bfq 36058762.00005.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 36058762.00005.unmapped -H 36058762.00005.mismatch \ 36058762.00005.map /data/maqgene/genomes/elegans.bfa 36058762.00005.1.bfq 36058762.00005.2.bfq 2> /dev/null # Thu Feb 3 17:28:50 GMT 2011: Mapping file(s) 36058762.00015.1.bfq 36058762.00015.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 36058762.00015.unmapped -H 36058762.00015.mismatch \ 36058762.00015.map /data/maqgene/genomes/elegans.bfa 36058762.00015.1.bfq 36058762.00015.2.bfq 2> /dev/null # Thu Feb 3 17:28:51 GMT 2011: Mapping file(s) 36058762.00014.1.bfq 36058762.00014.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 36058762.00014.unmapped -H 36058762.00014.mismatch \ 36058762.00014.map /data/maqgene/genomes/elegans.bfa 36058762.00014.1.bfq 36058762.00014.2.bfq 2> /dev/null # Thu Feb 3 17:28:58 GMT 2011: Mapping file(s) 36058762.00016.1.bfq 36058762.00016.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 36058762.00016.unmapped -H 36058762.00016.mismatch \ 36058762.00016.map /data/maqgene/genomes/elegans.bfa 36058762.00016.1.bfq 36058762.00016.2.bfq 2> /dev/null # Thu Feb 3 17:29:01 GMT 2011: Mapping file(s) 36058762.00017.1.bfq 36058762.00017.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 36058762.00017.unmapped -H 36058762.00017.mismatch \ 36058762.00017.map /data/maqgene/genomes/elegans.bfa 36058762.00017.1.bfq 36058762.00017.2.bfq 2> /dev/null # Thu Feb 3 17:29:16 GMT 2011: Mapping file(s) 36058762.00018.1.bfq 36058762.00018.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 36058762.00018.unmapped -H 36058762.00018.mismatch \ 36058762.00018.map /data/maqgene/genomes/elegans.bfa 36058762.00018.1.bfq 36058762.00018.2.bfq 2> /dev/null # Thu Feb 3 17:29:16 GMT 2011: Mapping file(s) 36058762.00019.1.bfq 36058762.00019.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 36058762.00019.unmapped -H 36058762.00019.mismatch \ 36058762.00019.map /data/maqgene/genomes/elegans.bfa 36058762.00019.1.bfq 36058762.00019.2.bfq 2> /dev/null # Thu Feb 3 17:29:23 GMT 2011: Mapping file(s) 36058762.00020.1.bfq 36058762.00020.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 36058762.00020.unmapped -H 36058762.00020.mismatch \ 36058762.00020.map /data/maqgene/genomes/elegans.bfa 36058762.00020.1.bfq 36058762.00020.2.bfq 2> /dev/null # Thu Feb 3 17:29:27 GMT 2011: Mapping file(s) 36058762.00021.1.bfq 36058762.00021.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 36058762.00021.unmapped -H 36058762.00021.mismatch \ 36058762.00021.map /data/maqgene/genomes/elegans.bfa 36058762.00021.1.bfq 36058762.00021.2.bfq 2> /dev/null # Thu Feb 3 17:29:28 GMT 2011: Mapping file(s) 36058762.00022.1.bfq 36058762.00022.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 36058762.00022.unmapped -H 36058762.00022.mismatch \ 36058762.00022.map /data/maqgene/genomes/elegans.bfa 36058762.00022.1.bfq 36058762.00022.2.bfq 2> /dev/null # Thu Feb 3 17:29:30 GMT 2011: Mapping file(s) 36058762.00023.1.bfq 36058762.00023.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 36058762.00023.unmapped -H 36058762.00023.mismatch \ 36058762.00023.map /data/maqgene/genomes/elegans.bfa 36058762.00023.1.bfq 36058762.00023.2.bfq 2> /dev/null # Thu Feb 3 17:29:33 GMT 2011: Mapping file(s) 36058762.00024.1.bfq 36058762.00024.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 36058762.00024.unmapped -H 36058762.00024.mismatch \ 36058762.00024.map /data/maqgene/genomes/elegans.bfa 36058762.00024.1.bfq 36058762.00024.2.bfq 2> /dev/null # Thu Feb 3 17:30:06 GMT 2011: Mapping file(s) 36058762.00025.1.bfq 36058762.00025.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 36058762.00025.unmapped -H 36058762.00025.mismatch \ 36058762.00025.map /data/maqgene/genomes/elegans.bfa 36058762.00025.1.bfq 36058762.00025.2.bfq 2> /dev/null # Thu Feb 3 17:30:08 GMT 2011: Mapping file(s) 36058762.00026.1.bfq 36058762.00026.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 36058762.00026.unmapped -H 36058762.00026.mismatch \ 36058762.00026.map /data/maqgene/genomes/elegans.bfa 36058762.00026.1.bfq 36058762.00026.2.bfq 2> /dev/null # Thu Feb 3 17:36:10 GMT 2011: Merging all maps ... /data/maqgene/bin/maq mapmerge 36058762.map 36058762.00000.map 36058762.00001.map 36058762.00002.map 36058762.00003.map 36058762.00004.map 36058762.00005.map 36058762.00006.map 36058762.00007.map 36058762.00008.map 36058762.00009.map 36058762.00010.map 36058762.00011.map 36058762.00012.map 36058762.00013.map 36058762.00014.map 36058762.00015.map 36058762.00016.map 36058762.00017.map 36058762.00018.map 36058762.00019.map 36058762.00020.map 36058762.00021.map 36058762.00022.map 36058762.00023.map 36058762.00024.map 36058762.00025.map 36058762.00026.map # Thu Feb 3 17:36:10 GMT 2011: Merging all *.unmapped files ... cat 36058762.00000.unmapped 36058762.00001.unmapped 36058762.00002.unmapped 36058762.00003.unmapped 36058762.00004.unmapped 36058762.00005.unmapped 36058762.00006.unmapped 36058762.00007.unmapped 36058762.00008.unmapped 36058762.00009.unmapped 36058762.00010.unmapped 36058762.00011.unmapped 36058762.00012.unmapped 36058762.00013.unmapped 36058762.00014.unmapped 36058762.00015.unmapped 36058762.00016.unmapped 36058762.00017.unmapped 36058762.00018.unmapped 36058762.00019.unmapped 36058762.00020.unmapped 36058762.00021.unmapped 36058762.00022.unmapped 36058762.00023.unmapped 36058762.00024.unmapped 36058762.00025.unmapped 36058762.00026.unmapped > 36058762_unmapped.txt # Thu Feb 3 17:36:10 GMT 2011: Linking backend file 36058762_unmapped.txt to /data/maqgene/out/example_user/CB6871/CB6871_unmapped.txt ln -fs /data/maqgene/work/36058762_unmapped.txt /data/maqgene/out/example_user/CB6871/CB6871_unmapped.txt /data/maqgene/makefile:126: warning: undefined variable `mapcheck_parameters' # Thu Feb 3 17:47:25 GMT 2011: Creating pileup ... # Thu Feb 3 17:47:25 GMT 2011: Generating consensus ... /data/maqgene/bin/maq pileup -Q 100 -p -m 7 -q 0 /data/maqgene/genomes/elegans.bfa 36058762.map > 2759793305_pileup.txt # Thu Feb 3 17:47:25 GMT 2011: Running 'mapcheck' ... /data/maqgene/bin/maq assemble -N 2 -q 0 -r 0.0 -m 7 -Q 100 -p 371791328.cns \ /data/maqgene/genomes/elegans.bfa 36058762.map 2> 371791328_log.txt /data/maqgene/bin/maq mapcheck /data/maqgene/genomes/elegans.bfa 36058762.map > 36058762_check.txt \ 2>/dev/null # Thu Feb 3 17:50:15 GMT 2011: Linking backend file 36058762_check.txt to /data/maqgene/out/example_user/CB6871/CB6871_check.txt ln -fs /data/maqgene/work/36058762_check.txt /data/maqgene/out/example_user/CB6871/CB6871_check.txt /data/maqgene/bin/filter_matching_lines 2759793305_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 \ > 2759793305_known_snps # Thu Feb 3 17:50:41 GMT 2011: Making coverage histogram ... # Thu Feb 3 17:50:41 GMT 2011: Getting uncovered regions ... (echo -en "sequencing_depth\tnumber_of_bases\n"; \ cut -f 4 2759793305_pileup.txt \ | /data/maqgene/bin/pileup_histogram 100) > 2759793305_coverage.txt # Thu Feb 3 17:50:41 GMT 2011: Linking backend file 2759793305_pileup.txt to /data/maqgene/out/example_user/CB6871/CB6871_pileup.txt cut -f 1,2,4 2759793305_pileup.txt \ | /data/maqgene/bin/get_uncovered_regions 50 \ > 2759793305_uncovered.txt ln -fs /data/maqgene/work/2759793305_pileup.txt /data/maqgene/out/example_user/CB6871/CB6871_pileup.txt # Thu Feb 3 17:51:03 GMT 2011: Linking backend file 2759793305_coverage.txt to /data/maqgene/out/example_user/CB6871/CB6871_coverage.txt ln -fs /data/maqgene/work/2759793305_coverage.txt /data/maqgene/out/example_user/CB6871/CB6871_coverage.txt # Thu Feb 3 17:51:07 GMT 2011: Filtering and loading pileup for analysis ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 2759793305_pileup; create table 2759793305_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 2759793305_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 2759793305_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 2759793305_pileup" # Thu Feb 3 17:51:09 GMT 2011: Linking backend file 2759793305_uncovered.txt to /data/maqgene/out/example_user/CB6871/CB6871_uncovered.txt ln -fs /data/maqgene/work/2759793305_uncovered.txt /data/maqgene/out/example_user/CB6871/CB6871_uncovered.txt cat 2759793305_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 2759793305_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 2759793305_pileup" touch 2759793305_pileup # Thu Feb 3 17:51:58 GMT 2011: Writing snp read counts ... /usr/bin/mysql -Dmaqgenedb -umaqgene --skip-column-names --batch --raw --local-infile --column-names -e "select f.id, f.dna, f.start + 1 start, e.snp_name, e.snp_base, if(e.snp_base = 'a', p.A_fwd + p.A_rev, if (e.snp_base = 'c', p.C_fwd + p.C_rev, if (e.snp_base = 'g', p.G_fwd + p.G_rev, if (e.snp_base = 't', p.T_fwd + p.T_rev, -1)))) snp_reads, p.ref_base, p.wt_fwd + p.wt_rev wt_reads, p.read_depth, p.sample_reads from elegans_features f join elegans_snp_changes e on (f.attribute = e.snp_name) join 2759793305_pileup p using (dna,start)" > /data/maqgene/out/example_user/CB6871/CB6871_snp_read_counts.txt 0 snp read count lines written. # Thu Feb 3 17:52:12 GMT 2011: Extracting point mutants from consensus ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 371791328_snps; create table 371791328_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 Feb 3 17:52:12 GMT 2011: Linking backend file 371791328_log.txt to /data/maqgene/out/example_user/CB6871/CB6871_log.txt ln -fs /data/maqgene/work/371791328_log.txt /data/maqgene/out/example_user/CB6871/CB6871_log.txt /data/maqgene/bin/maq cns2snp 371791328.cns \ | cat -b | /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "load data local infile '/dev/stdin' into table 371791328_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 371791328_snps;" # Thu Feb 3 17:52:25 GMT 2011: Extracting indels from consensus ... /data/maqgene/bin/maq indelsoa /data/maqgene/genomes/elegans.bfa 36058762.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 371791328_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 371791328_snps;" # Thu Feb 3 17:54:03 GMT 2011: Adding placeholders for known SNPs. cat 2759793305_known_snps \ | /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "load data local infile '/dev/stdin' ignore into table 371791328_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 371791328_snps;" Found 161411 variants. touch 371791328_snps # Thu Feb 3 17:54:04 GMT 2011: Loading uncovered regions into table ... cat 2759793305_uncovered.txt \ | /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 2759793305_uncovered; create table 2759793305_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 = 161412; load data local infile '/dev/stdin' into table 2759793305_uncovered (dna, start, end)" # Thu Feb 3 17:54:04 GMT 2011: Getting masking regions # Thu Feb 3 17:54:04 GMT 2011: Finding all genomic features overlapping variants... /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 371791328_masked_ids; create table 371791328_masked_ids (query_region_id int(10) NOT NULL, primary key (query_region_id)); load data local infile '/dev/stdin' ignore into table 371791328_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 371791328_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; /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 371791328_rel_snps; CREATE TABLE 371791328_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) )" Uncovered region statistics: /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 371791328_rel_snps; flush table 371791328_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 371791328_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 chromosome number_uncovered_regions total_uncovered_length I 13 1273 II 17 2670 III 14 13317 IV 18 2828 V 15 1584 X 15 5895 touch 2759793305_uncovered # Thu Feb 3 17:54:04 GMT 2011: Finding mRNA features overlapping uncovered regions ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 2759793305_uncovered_rel; CREATE TABLE 2759793305_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 2759793305_uncovered_rel; flush table 2759793305_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 2759793305_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 371791328_masked_ids touch 2759793305_uncovered_rel # Thu Feb 3 17:54:06 GMT 2011: Calculating translation start offsets for uncovered regions... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 2759793305_offsets_uncovered; create table 2759793305_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 2759793305_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 2759793305_uncovered reg join 2759793305_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 2759793305_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 2759793305_uncovered reg join 2759793305_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 2759793305_offsets_uncovered touch 371791328_rel_snps # Thu Feb 3 17:54:07 GMT 2011: Calculating translation start offsets... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 371791328_offsets_snps; create table 371791328_offsets_snps ( id int(10) NOT NULL, gene varchar(50) NOT NULL, 5prime_offset int(10) NOT NULL, 3prime_offset int(10) NOT NULL, total_length int(10) NOT NULL, boundary_type char(20) NOT NULL, primary key (id, gene, boundary_type) );" # Thu Feb 3 17:54:07 GMT 2011: Getting intergenic regions /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 371791328_rel_intergenic; create table 371791328_rel_intergenic like 371791328_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 371791328_rel_intergenic; flush table 371791328_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 371791328_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 371791328_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 371791328_snps reg join 371791328_rel_snps rel on (reg.id = rel.query_region_id) join elegans_features gene on (rel.target_region_id = gene.id) join elegans_features exon on (exon.attribute = gene.attribute) where exon.feature = 'exon' and gene.feature = 'mRNA' group by reg.id, gene.attribute" # Thu Feb 3 17:54:10 GMT 2011: Filtering masked intergenic regions /usr/bin/mysql -Dmaqgenedb -umaqgene --skip-column-names --batch --raw --local-infile -e "delete i.* from 371791328_rel_intergenic i join 371791328_masked_ids m using (query_region_id)" touch 371791328_rel_intergenic # Thu Feb 3 17:54:15 GMT 2011: Classifying intergenic relations /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 371791328_intergenic_assoc; create table 371791328_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 371791328_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 371791328_snps snp join 371791328_rel_intergenic rel on (snp.id = rel.query_region_id) join elegans_features feature on (rel.target_region_id = feature.id)" touch 371791328_intergenic_assoc touch 371791328_offsets_snps # Thu Feb 3 17:54:27 GMT 2011: Getting codons affected by point mutations... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 371791328_codons; create table 371791328_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 371791328_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 371791328_offsets_snps off join 371791328_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 371791328_codons /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 371791328_marked; create table 371791328_marked ( id int(10) NOT NULL, class varchar(100) NOT NULL, description varchar(100) NOT NULL, parent_feature varchar(100) NOT NULL, primary key (id, class, parent_feature) );" # Thu Feb 3 17:54:34 GMT 2011: Finding exonic indels ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 371791328_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 371791328_snps snp join 371791328_rel_snps rel on (snp.id = rel.query_region_id) join elegans_features feature on (rel.target_region_id = feature.id) where feature.feature = 'exon' and snp.variant_type = 'indel';" # Thu Feb 3 17:54:34 GMT 2011: Finding coding variants ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 371791328_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 371791328_codons trans join elegans_genetic_code reference_codons on (trans.ref_codon = reference_codons.codon) join elegans_genetic_code sample_codons on (trans.sam_codon = sample_codons.codon);" # Thu Feb 3 17:54:34 GMT 2011: Finding noncoding variants ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 371791328_marked select snp.id, feature.feature class, 'none' description, feature.attribute parent_feature from 371791328_snps snp join 371791328_rel_snps rel on (snp.id = rel.query_region_id) join elegans_features feature on (rel.target_region_id = feature.id) where feature.feature not in ('exon', 'intron', 'mRNA');" # Thu Feb 3 17:54:35 GMT 2011: Finding splice site variants ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 371791328_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 371791328_snps snp join 371791328_rel_snps rel on (snp.id = rel.query_region_id) join elegans_features feature on (rel.target_region_id = feature.id) where feature.feature = 'intron' and rel.distance > -2;" # Thu Feb 3 17:54:35 GMT 2011: Finding intergenic and intronic variants ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 371791328_marked select id, 'nongenic' class, concat(if (relation in ('upstream','into'), - distance, distance),' ',relation) description, attribute from 371791328_intergenic_assoc where ((relation = 'upstream' and num_regions_between = 0 and distance < 50000) or (relation = 'upstream' and num_regions_between < 2 and distance < 1000) or (relation = 'downstream' and num_regions_between = 0 and distance < 1000) or (relation = 'downstream' and num_regions_between < 2 and distance < 1000) or relation = 'into' );" # Thu Feb 3 17:54:37 GMT 2011: Finding uncovered regions in genes ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 371791328_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 2759793305_uncovered unc join 2759793305_offsets_uncovered b using (id) join 2759793305_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 2759793305_uncovered unc join 2759793305_offsets_uncovered b using (id) join 2759793305_offsets_uncovered e using (id, gene) join elegans_features gene on (e.gene = gene.attribute) where b.boundary_type = 'start' and e.boundary_type = 'end' and gene.strand = '-' and gene.feature = 'mRNA'" # Thu Feb 3 17:54:37 GMT 2011: Variants found: +-----------------+-----------------+ | class | number_variants | +-----------------+-----------------+ | five_prime_UTR | 1291 | | frameshift | 59 | | inframe | 10 | | missense | 6160 | | ncRNA | 866 | | nongenic | 124875 | | non_start | 9 | | premature_stop | 689 | | readthrough | 19 | | silent | 7416 | | SNP | 1022 | | splice_acceptor | 45 | | splice_donor | 48 | | three_prime_UTR | 3540 | | uncovered | 29 | +-----------------+-----------------+ touch 371791328_marked # Thu Feb 3 17:54:38 GMT 2011: Combining results ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 371791328_combined; create table 371791328_combined (primary key (id, class, description), key (dna, start)) as select snp.id, 'CB6871' 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 371791328_snps snp join 2759793305_pileup pile using (dna,start) join 371791328_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' 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 2759793305_uncovered unc join 371791328_marked class on (unc.id = class.id) left join elegans_per_locus using (dna,start) group by id, class, description; alter table 371791328_combined order by dna, start, length" touch 371791328_combined # Thu Feb 3 17:54:39 GMT 2011: Writing results to grouped file ... /usr/bin/mysql -Dmaqgenedb -umaqgene --skip-column-names --batch --raw --local-infile --column-names -e "select id, mutant_strain, dna, start, length, reference_base, sample_base, consensus_score, loci_multiplicity, mapping_quality, neighbor_quality, number_wildtype_reads, number_variant_reads, sequencing_depth, sample_reads, variant_type, indel_size, group_concat(class) classes, group_concat(description) descriptions, group_concat(concat('{',parent_features,'}')) parent_features from 371791328_combined group by id order by dna, start;" > /data/maqgene/out/example_user/CB6871/CB6871_grouped.txt # Thu Feb 3 17:54:39 GMT 2011: Writing results to flat file ... /usr/bin/mysql -Dmaqgenedb -umaqgene --skip-column-names --batch --raw --local-infile --column-names -e "select * from 371791328_combined" > /data/maqgene/out/example_user/CB6871/CB6871_flat.txt 3359 lines written. 1982 lines written. rm 36058762.00003.mismatch 36058762.00000.2.fastq 36058762.00011.1.fastq 36058762.00017.unmapped 36058762.00005.1.bfq 36058762.00004.mismatch 36058762.00002.unmapped 36058762.00009.unmapped 36058762.00020.unmapped 36058762.00013.2.bfq 36058762.00014.map 36058762.00023.1.bfq 36058762.00013.mismatch 36058762.00001.2.fastq 36058762.00010.2.fastq 36058762.00002.1.fastq 36058762.00020.1.fastq 36058762.00017.2.bfq 36058762.00019.1.bfq 36058762.00016.2.fastq 36058762.00005.2.bfq 36058762.00012.unmapped 36058762.00001.map 36058762.00015.1.bfq 36058762.00011.2.fastq 36058762.00012.1.fastq 36058762.00026.unmapped 36058762.00005.mismatch 36058762.00017.2.fastq 36058762.00026.1.fastq 36058762.00023.2.bfq 36058762.00018.unmapped 36058762.00002.2.fastq 36058762.00020.2.fastq 36058762.00023.mismatch 36058762.00024.map 36058762.00014.2.bfq 36058762.00019.2.bfq 36058762.00018.1.fastq 36058762.00019.mismatch 36058762.00007.1.fastq 36058762.00022.unmapped 36058762.00015.2.bfq 36058762.00012.2.fastq 36058762.00015.mismatch 36058762.00022.1.fastq 36058762.00006.map 36058762.00024.2.bfq 36058762.00025.1.bfq 36058762.00026.2.fastq 36058762.00003.1.fastq 36058762.00018.2.fastq 36058762.00013.unmapped 36058762.00007.map 36058762.00021.1.fastq 36058762.00008.1.fastq 36058762.00022.2.fastq 36058762.00013.1.fastq 36058762.00025.2.bfq 36058762.00003.unmapped 36058762.00025.mismatch 36058762.00010.map 36058762.00014.1.bfq 36058762.00003.2.fastq 36058762.00016.map 36058762.00005.unmapped 36058762.00004.2.bfq 36058762.00005.1.fastq 36058762.00000.2.bfq 36058762.00011.map 36058762.00023.unmapped 36058762.00021.map 36058762.00008.map 36058762.00013.2.fastq 36058762.00019.unmapped 36058762.00009.1.fastq 36058762.00023.1.fastq 36058762.00017.map 36058762.00020.1.bfq 36058762.00019.1.fastq 36058762.00002.map 36058762.00007.2.fastq 36058762.00020.map 36058762.00015.unmapped 36058762.00014.mismatch 36058762.00024.1.bfq 36058762.00015.1.fastq 36058762.00005.2.fastq 36058762.00012.map 36058762.00007.1.bfq 36058762.00023.2.fastq 36058762.00009.map 36058762.00026.map 36058762.00019.2.fastq 36058762.00006.1.bfq 36058762.00017.1.fastq 36058762.00018.map 36058762.00008.2.fastq 36058762.00015.2.fastq 36058762.00024.mismatch 36058762.00025.unmapped 36058762.00000.1.bfq 36058762.00025.1.fastq 36058762.00021.1.bfq 36058762.00004.unmapped 3477649743_split1 36058762.00003.map 36058762.00006.2.bfq 36058762.00001.1.bfq 36058762.00010.1.bfq 36058762.00004.1.fastq 36058762.00006.mismatch 36058762.00011.2.bfq 36058762.00016.1.bfq 36058762.00022.map 36058762.00009.2.fastq 36058762.00008.1.bfq 36058762.00014.unmapped 36058762.00013.map 36058762.00025.2.fastq 36058762.00000.mismatch 36058762.00014.1.fastq 36058762.00017.1.bfq 36058762.00009.1.bfq 36058762.00001.2.bfq 36058762.00010.2.bfq 36058762.00002.1.bfq 36058762.00007.mismatch 36058762.00004.2.fastq 36058762.00001.mismatch 36058762.00010.mismatch 36058762.00007.2.bfq 36058762.00016.2.bfq 36058762.00016.mismatch 36058762.00005.map 36058762.00006.unmapped 36058762.00012.1.bfq 36058762.00021.mismatch 36058762.00023.map 36058762.00011.mismatch 36058762.00024.unmapped 36058762.00014.2.fastq 36058762.00019.map 36058762.00026.1.bfq 36058762.00004.1.bfq 36058762.00024.1.fastq 36058762.00017.mismatch 36058762.00002.2.bfq 36058762.00020.2.bfq 36058762.00002.mismatch 36058762.00015.map 36058762.00020.mismatch 36058762.00007.unmapped 36058762.00018.1.bfq 36058762.00008.mismatch 36058762.00021.2.bfq 36058762.00008.2.bfq 3477649743_split2 36058762.00011.1.bfq 36058762.00021.2.fastq 36058762.00012.2.bfq 36058762.00022.1.bfq 36058762.00012.mismatch 36058762.00006.1.fastq 36058762.00026.2.bfq 36058762.00024.2.fastq 36058762.00026.mismatch 36058762.00000.unmapped 36058762.00003.1.bfq 36058762.00018.2.bfq 36058762.00021.unmapped 36058762.00000.1.fastq 36058762.00018.mismatch 36058762.00008.unmapped 36058762.00009.mismatch 36058762.00010.1.fastq 36058762.00000.map 36058762.00025.map 36058762.00009.2.bfq 36058762.00001.unmapped 36058762.00010.unmapped 36058762.00022.2.bfq 36058762.00013.1.bfq 36058762.00016.unmapped 36058762.00022.mismatch 36058762.00006.2.fastq 36058762.00001.1.fastq 36058762.00016.1.fastq 36058762.00004.map 36058762.00003.2.bfq 36058762.00011.unmapped make: Leaving directory `/data/maqgene/work' make: Entering directory `/data/maqgene/work' # Thu Feb 3 17:54:41 GMT 2011: Cleaning intermediate data ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 371791328_snps,371791328_rel,371791328_masked_ids,371791328_rel_intergenic,371791328_intergenic_assoc,371791328_offsets,371791328_codons,371791328_marked,371791328_combined,2759793305_pileup" rm -f 371791328_snps 371791328_rel 371791328_masked_ids 371791328_rel_intergenic 371791328_intergenic_assoc 371791328_offsets 371791328_codons 371791328_marked 371791328_combined 2759793305_pileup make: Leaving directory `/data/maqgene/work'