Finished reading input. ++ tr , ' ' ++ echo CB6880/./s_8_1_sequence_read1.fastq + fastq_file_set1=CB6880/./s_8_1_sequence_read1.fastq ++ cd /data/maqgene/reads ++ wc -l ++ cat CB6880/./s_8_1_sequence_read1.fastq ++ cut -f 1 -d ' ' + TOTAL_LINES=128908084 ++ echo '(128908084 / 5000000) + (128908084 % 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=1078206964 map_cksum=1953515093 pileup_cksum=3304907316 cns_cksum=3356714135 umdd=50000 dmdd=1000 umid=1000 dmid=1000 max_gene_radius=50000 full_results_dir=/data/maqgene/out/example_user/CB6880_redo outfile_basename=CB6880_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 128908084 lines of input in 26 chunks make: Entering directory `/data/maqgene/work' # Fri Apr 1 06:55:32 BST 2011: Removing frontend files in case this is a duplicate run ... rm -f /data/maqgene/out/example_user/CB6880_redo/CB6880_redo_{grouped.txt,flat.txt} rm -f /data/maqgene/out/example_user/CB6880_redo/CB6880_redo_uncovered.txt /data/maqgene/out/example_user/CB6880_redo/CB6880_redo_coverage.txt /data/maqgene/out/example_user/CB6880_redo/CB6880_redo_pileup.txt /data/maqgene/out/example_user/CB6880_redo/CB6880_redo_log.txt /data/maqgene/out/example_user/CB6880_redo/CB6880_redo_check.txt /data/maqgene/out/example_user/CB6880_redo/CB6880_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. # : Regrouping fastq reads into chunks of size 5000000. split -l 5000000 -a 5 -d <(cat /data/maqgene/reads/CB6880/./s_8_1_sequence_read1.fastq) 1953515093.1.fastq. split -l 5000000 -a 5 -d <(cat /data/maqgene/reads/CB6880/./s_8_2_sequence_read2.fastq) 1953515093.2.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 1953515093.1.fastq.$stem 1953515093.$stem.1.fastq; done touch 1078206964_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 1953515093.2.fastq.$stem 1953515093.$stem.2.fastq; done touch 1078206964_split2 # Fri Apr 1 06:57:04 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1953515093.00000.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1953515093.00000.1.bfq # Fri Apr 1 06:57:18 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1953515093.00013.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1953515093.00013.1.bfq # Fri Apr 1 06:57:20 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1953515093.00012.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1953515093.00012.1.bfq -- finish writing file '1953515093.00000.1.bfq' -- 1250000 sequences were loaded. # Fri Apr 1 06:57:22 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1953515093.00011.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1953515093.00011.1.bfq -- finish writing file '1953515093.00012.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1953515093.00013.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1953515093.00011.1.bfq' -- 1250000 sequences were loaded. # Fri Apr 1 06:57:46 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1953515093.00016.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1953515093.00016.1.bfq -- finish writing file '1953515093.00016.1.bfq' -- 1250000 sequences were loaded. # Fri Apr 1 06:58:08 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1953515093.00017.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1953515093.00017.1.bfq -- finish writing file '1953515093.00017.1.bfq' -- 1250000 sequences were loaded. # Fri Apr 1 06:58:28 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1953515093.00018.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1953515093.00018.1.bfq -- finish writing file '1953515093.00018.1.bfq' -- 1250000 sequences were loaded. # Fri Apr 1 06:58:54 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1953515093.00019.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1953515093.00019.1.bfq -- finish writing file '1953515093.00019.1.bfq' -- 1250000 sequences were loaded. # Fri Apr 1 06:59:15 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1953515093.00020.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1953515093.00020.1.bfq -- finish writing file '1953515093.00020.1.bfq' -- 1250000 sequences were loaded. # Fri Apr 1 06:59:36 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1953515093.00021.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1953515093.00021.1.bfq -- finish writing file '1953515093.00021.1.bfq' -- 1250000 sequences were loaded. # Fri Apr 1 06:59:56 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1953515093.00022.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1953515093.00022.1.bfq -- finish writing file '1953515093.00022.1.bfq' -- 1250000 sequences were loaded. # Fri Apr 1 07:00:16 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1953515093.00023.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1953515093.00023.1.bfq -- finish writing file '1953515093.00023.1.bfq' -- 1250000 sequences were loaded. # Fri Apr 1 07:00:38 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1953515093.00024.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1953515093.00024.1.bfq -- finish writing file '1953515093.00024.1.bfq' -- 1250000 sequences were loaded. # Fri Apr 1 07:00:58 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1953515093.00025.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1953515093.00025.1.bfq -- finish writing file '1953515093.00025.1.bfq' -- 977021 sequences were loaded. # Fri Apr 1 07:01:14 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1953515093.00000.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1953515093.00000.2.bfq -- finish writing file '1953515093.00000.2.bfq' -- 1250000 sequences were loaded. # Fri Apr 1 07:01:35 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1953515093.00001.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1953515093.00001.2.bfq -- finish writing file '1953515093.00001.2.bfq' -- 1250000 sequences were loaded. # Fri Apr 1 07:01:51 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1953515093.00002.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1953515093.00002.2.bfq -- finish writing file '1953515093.00002.2.bfq' -- 1250000 sequences were loaded. # Fri Apr 1 07:02:08 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1953515093.00003.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1953515093.00003.2.bfq -- finish writing file '1953515093.00003.2.bfq' -- 1250000 sequences were loaded. # Fri Apr 1 07:02:25 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1953515093.00004.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1953515093.00004.2.bfq -- finish writing file '1953515093.00004.2.bfq' -- 1250000 sequences were loaded. # Fri Apr 1 07:02:41 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1953515093.00005.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1953515093.00005.2.bfq -- finish writing file '1953515093.00005.2.bfq' -- 1250000 sequences were loaded. # Fri Apr 1 07:03:00 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1953515093.00006.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1953515093.00006.2.bfq # Fri Apr 1 07:03:09 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1953515093.00007.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1953515093.00007.2.bfq # Fri Apr 1 07:03:11 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1953515093.00015.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1953515093.00015.1.bfq # Fri Apr 1 07:03:13 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1953515093.00014.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1953515093.00014.1.bfq -- finish writing file '1953515093.00006.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1953515093.00007.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1953515093.00015.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1953515093.00014.1.bfq' -- 1250000 sequences were loaded. # Fri Apr 1 07:03:36 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1953515093.00010.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1953515093.00010.2.bfq # Fri Apr 1 07:03:49 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1953515093.00011.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1953515093.00011.2.bfq # Fri Apr 1 07:03:50 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1953515093.00009.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1953515093.00009.2.bfq # Fri Apr 1 07:03:51 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1953515093.00008.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1953515093.00008.2.bfq # Fri Apr 1 07:03:52 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1953515093.00010.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1953515093.00010.1.bfq # Fri Apr 1 07:03:53 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1953515093.00009.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1953515093.00009.1.bfq -- finish writing file '1953515093.00010.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1953515093.00011.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1953515093.00009.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1953515093.00010.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1953515093.00009.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1953515093.00008.2.bfq' -- 1250000 sequences were loaded. # Fri Apr 1 07:04:19 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1953515093.00016.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1953515093.00016.2.bfq # Fri Apr 1 07:04:34 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1953515093.00017.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1953515093.00017.2.bfq # Fri Apr 1 07:04:35 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1953515093.00015.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1953515093.00015.2.bfq # Fri Apr 1 07:04:36 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1953515093.00014.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1953515093.00014.2.bfq # Fri Apr 1 07:04:37 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1953515093.00013.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1953515093.00013.2.bfq # Fri Apr 1 07:04:38 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1953515093.00012.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1953515093.00012.2.bfq -- finish writing file '1953515093.00016.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1953515093.00017.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1953515093.00014.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1953515093.00013.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1953515093.00012.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1953515093.00015.2.bfq' -- 1250000 sequences were loaded. # Fri Apr 1 07:05:10 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1953515093.00022.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1953515093.00022.2.bfq -- finish writing file '1953515093.00022.2.bfq' -- 1250000 sequences were loaded. # Fri Apr 1 07:05:34 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1953515093.00023.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1953515093.00023.2.bfq -- finish writing file '1953515093.00023.2.bfq' -- 1250000 sequences were loaded. # Fri Apr 1 07:05:54 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1953515093.00024.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1953515093.00024.2.bfq -- finish writing file '1953515093.00024.2.bfq' -- 1250000 sequences were loaded. # Fri Apr 1 07:06:14 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1953515093.00025.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1953515093.00025.2.bfq -- finish writing file '1953515093.00025.2.bfq' -- 977021 sequences were loaded. # Fri Apr 1 07:06:30 BST 2011: Mapping file(s) 1953515093.00000.1.bfq 1953515093.00000.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1953515093.00000.unmapped -H 1953515093.00000.mismatch \ 1953515093.00000.map /data/maqgene/genomes/elegans.bfa 1953515093.00000.1.bfq 1953515093.00000.2.bfq 2> /dev/null # Fri Apr 1 07:09:29 BST 2011: Mapping file(s) 1953515093.00009.1.bfq 1953515093.00009.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1953515093.00009.unmapped -H 1953515093.00009.mismatch \ 1953515093.00009.map /data/maqgene/genomes/elegans.bfa 1953515093.00009.1.bfq 1953515093.00009.2.bfq 2> /dev/null # Fri Apr 1 07:09:31 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1953515093.00021.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1953515093.00021.2.bfq # Fri Apr 1 07:09:33 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1953515093.00020.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1953515093.00020.2.bfq -- finish writing file '1953515093.00021.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1953515093.00020.2.bfq' -- 1250000 sequences were loaded. # Fri Apr 1 07:10:10 BST 2011: Mapping file(s) 1953515093.00011.1.bfq 1953515093.00011.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1953515093.00011.unmapped -H 1953515093.00011.mismatch \ 1953515093.00011.map /data/maqgene/genomes/elegans.bfa 1953515093.00011.1.bfq 1953515093.00011.2.bfq 2> /dev/null # Fri Apr 1 07:10:12 BST 2011: Mapping file(s) 1953515093.00010.1.bfq 1953515093.00010.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1953515093.00010.unmapped -H 1953515093.00010.mismatch \ 1953515093.00010.map /data/maqgene/genomes/elegans.bfa 1953515093.00010.1.bfq 1953515093.00010.2.bfq 2> /dev/null # Fri Apr 1 07:10:14 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1953515093.00019.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1953515093.00019.2.bfq # Fri Apr 1 07:10:16 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1953515093.00018.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1953515093.00018.2.bfq # Fri Apr 1 07:10:18 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1953515093.00008.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1953515093.00008.1.bfq -- finish writing file '1953515093.00019.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1953515093.00018.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1953515093.00008.1.bfq' -- 1250000 sequences were loaded. # Fri Apr 1 07:10:40 BST 2011: Mapping file(s) 1953515093.00014.1.bfq 1953515093.00014.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1953515093.00014.unmapped -H 1953515093.00014.mismatch \ 1953515093.00014.map /data/maqgene/genomes/elegans.bfa 1953515093.00014.1.bfq 1953515093.00014.2.bfq 2> /dev/null # Fri Apr 1 07:10:41 BST 2011: Mapping file(s) 1953515093.00013.1.bfq 1953515093.00013.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1953515093.00013.unmapped -H 1953515093.00013.mismatch \ 1953515093.00013.map /data/maqgene/genomes/elegans.bfa 1953515093.00013.1.bfq 1953515093.00013.2.bfq 2> /dev/null # Fri Apr 1 07:10:42 BST 2011: Mapping file(s) 1953515093.00012.1.bfq 1953515093.00012.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1953515093.00012.unmapped -H 1953515093.00012.mismatch \ 1953515093.00012.map /data/maqgene/genomes/elegans.bfa 1953515093.00012.1.bfq 1953515093.00012.2.bfq 2> /dev/null # Fri Apr 1 07:10:43 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1953515093.00007.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1953515093.00007.1.bfq # Fri Apr 1 07:10:44 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1953515093.00006.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1953515093.00006.1.bfq -- finish writing file '1953515093.00007.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1953515093.00006.1.bfq' -- 1250000 sequences were loaded. # Fri Apr 1 07:11:20 BST 2011: Mapping file(s) 1953515093.00016.1.bfq 1953515093.00016.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1953515093.00016.unmapped -H 1953515093.00016.mismatch \ 1953515093.00016.map /data/maqgene/genomes/elegans.bfa 1953515093.00016.1.bfq 1953515093.00016.2.bfq 2> /dev/null # Fri Apr 1 07:11:21 BST 2011: Mapping file(s) 1953515093.00015.1.bfq 1953515093.00015.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1953515093.00015.unmapped -H 1953515093.00015.mismatch \ 1953515093.00015.map /data/maqgene/genomes/elegans.bfa 1953515093.00015.1.bfq 1953515093.00015.2.bfq 2> /dev/null # Fri Apr 1 07:11:22 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1953515093.00005.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1953515093.00005.1.bfq # Fri Apr 1 07:11:23 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1953515093.00004.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1953515093.00004.1.bfq # Fri Apr 1 07:11:24 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1953515093.00003.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1953515093.00003.1.bfq # Fri Apr 1 07:11:25 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1953515093.00002.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1953515093.00002.1.bfq # Fri Apr 1 07:11:26 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1953515093.00001.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1953515093.00001.1.bfq -- finish writing file '1953515093.00005.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1953515093.00004.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1953515093.00003.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1953515093.00002.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1953515093.00001.1.bfq' -- 1250000 sequences were loaded. # Fri Apr 1 07:11:55 BST 2011: Mapping file(s) 1953515093.00021.1.bfq 1953515093.00021.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1953515093.00021.unmapped -H 1953515093.00021.mismatch \ 1953515093.00021.map /data/maqgene/genomes/elegans.bfa 1953515093.00021.1.bfq 1953515093.00021.2.bfq 2> /dev/null # Fri Apr 1 07:11:56 BST 2011: Mapping file(s) 1953515093.00020.1.bfq 1953515093.00020.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1953515093.00020.unmapped -H 1953515093.00020.mismatch \ 1953515093.00020.map /data/maqgene/genomes/elegans.bfa 1953515093.00020.1.bfq 1953515093.00020.2.bfq 2> /dev/null # Fri Apr 1 07:11:57 BST 2011: Mapping file(s) 1953515093.00019.1.bfq 1953515093.00019.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1953515093.00019.unmapped -H 1953515093.00019.mismatch \ 1953515093.00019.map /data/maqgene/genomes/elegans.bfa 1953515093.00019.1.bfq 1953515093.00019.2.bfq 2> /dev/null # Fri Apr 1 07:11:58 BST 2011: Mapping file(s) 1953515093.00018.1.bfq 1953515093.00018.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1953515093.00018.unmapped -H 1953515093.00018.mismatch \ 1953515093.00018.map /data/maqgene/genomes/elegans.bfa 1953515093.00018.1.bfq 1953515093.00018.2.bfq 2> /dev/null # Fri Apr 1 07:11:59 BST 2011: Mapping file(s) 1953515093.00017.1.bfq 1953515093.00017.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1953515093.00017.unmapped -H 1953515093.00017.mismatch \ 1953515093.00017.map /data/maqgene/genomes/elegans.bfa 1953515093.00017.1.bfq 1953515093.00017.2.bfq 2> /dev/null # Fri Apr 1 07:14:50 BST 2011: Mapping file(s) 1953515093.00022.1.bfq 1953515093.00022.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1953515093.00022.unmapped -H 1953515093.00022.mismatch \ 1953515093.00022.map /data/maqgene/genomes/elegans.bfa 1953515093.00022.1.bfq 1953515093.00022.2.bfq 2> /dev/null # Fri Apr 1 07:16:52 BST 2011: Mapping file(s) 1953515093.00024.1.bfq 1953515093.00024.2.bfq # Fri Apr 1 07:16:52 BST 2011: Mapping file(s) 1953515093.00025.1.bfq 1953515093.00025.2.bfq # Fri Apr 1 07:16:52 BST 2011: Mapping file(s) 1953515093.00023.1.bfq 1953515093.00023.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1953515093.00024.unmapped -H 1953515093.00024.mismatch \ 1953515093.00024.map /data/maqgene/genomes/elegans.bfa 1953515093.00024.1.bfq 1953515093.00024.2.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 1953515093.00025.unmapped -H 1953515093.00025.mismatch \ 1953515093.00025.map /data/maqgene/genomes/elegans.bfa 1953515093.00025.1.bfq 1953515093.00025.2.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 1953515093.00023.unmapped -H 1953515093.00023.mismatch \ 1953515093.00023.map /data/maqgene/genomes/elegans.bfa 1953515093.00023.1.bfq 1953515093.00023.2.bfq 2> /dev/null # Fri Apr 1 07:16:53 BST 2011: Mapping file(s) 1953515093.00001.1.bfq 1953515093.00001.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1953515093.00001.unmapped -H 1953515093.00001.mismatch \ 1953515093.00001.map /data/maqgene/genomes/elegans.bfa 1953515093.00001.1.bfq 1953515093.00001.2.bfq 2> /dev/null # Fri Apr 1 07:16:54 BST 2011: Mapping file(s) 1953515093.00002.1.bfq 1953515093.00002.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1953515093.00002.unmapped -H 1953515093.00002.mismatch \ 1953515093.00002.map /data/maqgene/genomes/elegans.bfa 1953515093.00002.1.bfq 1953515093.00002.2.bfq 2> /dev/null # Fri Apr 1 07:17:09 BST 2011: Mapping file(s) 1953515093.00003.1.bfq 1953515093.00003.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1953515093.00003.unmapped -H 1953515093.00003.mismatch \ 1953515093.00003.map /data/maqgene/genomes/elegans.bfa 1953515093.00003.1.bfq 1953515093.00003.2.bfq 2> /dev/null # Fri Apr 1 07:17:45 BST 2011: Mapping file(s) 1953515093.00005.1.bfq 1953515093.00005.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1953515093.00005.unmapped -H 1953515093.00005.mismatch \ 1953515093.00005.map /data/maqgene/genomes/elegans.bfa 1953515093.00005.1.bfq 1953515093.00005.2.bfq 2> /dev/null # Fri Apr 1 07:17:46 BST 2011: Mapping file(s) 1953515093.00004.1.bfq 1953515093.00004.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1953515093.00004.unmapped -H 1953515093.00004.mismatch \ 1953515093.00004.map /data/maqgene/genomes/elegans.bfa 1953515093.00004.1.bfq 1953515093.00004.2.bfq 2> /dev/null # Fri Apr 1 07:18:24 BST 2011: Mapping file(s) 1953515093.00008.1.bfq 1953515093.00008.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1953515093.00008.unmapped -H 1953515093.00008.mismatch \ 1953515093.00008.map /data/maqgene/genomes/elegans.bfa 1953515093.00008.1.bfq 1953515093.00008.2.bfq 2> /dev/null # Fri Apr 1 07:19:13 BST 2011: Mapping file(s) 1953515093.00007.1.bfq 1953515093.00007.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1953515093.00007.unmapped -H 1953515093.00007.mismatch \ 1953515093.00007.map /data/maqgene/genomes/elegans.bfa 1953515093.00007.1.bfq 1953515093.00007.2.bfq 2> /dev/null # Fri Apr 1 07:19:13 BST 2011: Mapping file(s) 1953515093.00006.1.bfq 1953515093.00006.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1953515093.00006.unmapped -H 1953515093.00006.mismatch \ 1953515093.00006.map /data/maqgene/genomes/elegans.bfa 1953515093.00006.1.bfq 1953515093.00006.2.bfq 2> /dev/null # Fri Apr 1 07:24:41 BST 2011: Merging all maps ... # Fri Apr 1 07:24:41 BST 2011: Merging all *.unmapped files ... /data/maqgene/bin/maq mapmerge 1953515093.map 1953515093.00000.map 1953515093.00001.map 1953515093.00002.map 1953515093.00003.map 1953515093.00004.map 1953515093.00005.map 1953515093.00006.map 1953515093.00007.map 1953515093.00008.map 1953515093.00009.map 1953515093.00010.map 1953515093.00011.map 1953515093.00012.map 1953515093.00013.map 1953515093.00014.map 1953515093.00015.map 1953515093.00016.map 1953515093.00017.map 1953515093.00018.map 1953515093.00019.map 1953515093.00020.map 1953515093.00021.map 1953515093.00022.map 1953515093.00023.map 1953515093.00024.map 1953515093.00025.map cat 1953515093.00000.unmapped 1953515093.00001.unmapped 1953515093.00002.unmapped 1953515093.00003.unmapped 1953515093.00004.unmapped 1953515093.00005.unmapped 1953515093.00006.unmapped 1953515093.00007.unmapped 1953515093.00008.unmapped 1953515093.00009.unmapped 1953515093.00010.unmapped 1953515093.00011.unmapped 1953515093.00012.unmapped 1953515093.00013.unmapped 1953515093.00014.unmapped 1953515093.00015.unmapped 1953515093.00016.unmapped 1953515093.00017.unmapped 1953515093.00018.unmapped 1953515093.00019.unmapped 1953515093.00020.unmapped 1953515093.00021.unmapped 1953515093.00022.unmapped 1953515093.00023.unmapped 1953515093.00024.unmapped 1953515093.00025.unmapped > 1953515093_unmapped.txt # Fri Apr 1 07:24:41 BST 2011: Linking backend file 1953515093_unmapped.txt to /data/maqgene/out/example_user/CB6880_redo/CB6880_redo_unmapped.txt ln -fs /data/maqgene/work/1953515093_unmapped.txt /data/maqgene/out/example_user/CB6880_redo/CB6880_redo_unmapped.txt /data/maqgene/makefile:126: warning: undefined variable `mapcheck_parameters' # Fri Apr 1 07:33:25 BST 2011: Generating consensus ... # Fri Apr 1 07:33:25 BST 2011: Creating pileup ... /data/maqgene/bin/maq assemble -N 2 -q 0 -r 0.0 -m 7 -Q 100 -p 3356714135.cns \ /data/maqgene/genomes/elegans.bfa 1953515093.map 2> 3356714135_log.txt /data/maqgene/bin/maq pileup -Q 100 -p -m 7 -q 0 /data/maqgene/genomes/elegans.bfa 1953515093.map > 3304907316_pileup.txt # Fri Apr 1 07:33:25 BST 2011: Running 'mapcheck' ... /data/maqgene/bin/maq mapcheck /data/maqgene/genomes/elegans.bfa 1953515093.map > 1953515093_check.txt \ 2>/dev/null # Fri Apr 1 07:36:01 BST 2011: Linking backend file 1953515093_check.txt to /data/maqgene/out/example_user/CB6880_redo/CB6880_redo_check.txt ln -fs /data/maqgene/work/1953515093_check.txt /data/maqgene/out/example_user/CB6880_redo/CB6880_redo_check.txt /data/maqgene/bin/filter_matching_lines 3304907316_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 \ > 3304907316_known_snps # Fri Apr 1 07:36:27 BST 2011: Getting uncovered regions ... cut -f 1,2,4 3304907316_pileup.txt \ | /data/maqgene/bin/get_uncovered_regions 50 \ > 3304907316_uncovered.txt # Fri Apr 1 07:36:27 BST 2011: Making coverage histogram ... # Fri Apr 1 07:36:27 BST 2011: Linking backend file 3304907316_pileup.txt to /data/maqgene/out/example_user/CB6880_redo/CB6880_redo_pileup.txt (echo -en "sequencing_depth\tnumber_of_bases\n"; \ cut -f 4 3304907316_pileup.txt \ | /data/maqgene/bin/pileup_histogram 100) > 3304907316_coverage.txt ln -fs /data/maqgene/work/3304907316_pileup.txt /data/maqgene/out/example_user/CB6880_redo/CB6880_redo_pileup.txt # Fri Apr 1 07:36:46 BST 2011: Linking backend file 3304907316_coverage.txt to /data/maqgene/out/example_user/CB6880_redo/CB6880_redo_coverage.txt ln -fs /data/maqgene/work/3304907316_coverage.txt /data/maqgene/out/example_user/CB6880_redo/CB6880_redo_coverage.txt # Fri Apr 1 07:36:53 BST 2011: Filtering and loading pileup for analysis ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 3304907316_pileup; create table 3304907316_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 3304907316_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 3304907316_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 3304907316_pileup" # Fri Apr 1 07:36:54 BST 2011: Linking backend file 3304907316_uncovered.txt to /data/maqgene/out/example_user/CB6880_redo/CB6880_redo_uncovered.txt ln -fs /data/maqgene/work/3304907316_uncovered.txt /data/maqgene/out/example_user/CB6880_redo/CB6880_redo_uncovered.txt cat 3304907316_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 3304907316_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 3304907316_pileup" touch 3304907316_pileup # Fri Apr 1 07:37:43 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 3304907316_pileup p using (dna,start)" > /data/maqgene/out/example_user/CB6880_redo/CB6880_redo_snp_read_counts.txt 0 snp read count lines written. # Fri Apr 1 07:37:47 BST 2011: Extracting point mutants from consensus ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 3356714135_snps; create table 3356714135_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) )" # Fri Apr 1 07:37:47 BST 2011: Linking backend file 3356714135_log.txt to /data/maqgene/out/example_user/CB6880_redo/CB6880_redo_log.txt ln -fs /data/maqgene/work/3356714135_log.txt /data/maqgene/out/example_user/CB6880_redo/CB6880_redo_log.txt /data/maqgene/bin/maq cns2snp 3356714135.cns \ | cat -b | /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "load data local infile '/dev/stdin' into table 3356714135_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 3356714135_snps;" # Fri Apr 1 07:38:00 BST 2011: Extracting indels from consensus ... /data/maqgene/bin/maq indelsoa /data/maqgene/genomes/elegans.bfa 1953515093.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 3356714135_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 3356714135_snps;" # Fri Apr 1 07:39:24 BST 2011: Adding placeholders for known SNPs. cat 3304907316_known_snps \ | /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "load data local infile '/dev/stdin' ignore into table 3356714135_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 3356714135_snps;" Found 163691 variants. touch 3356714135_snps # Fri Apr 1 07:39:25 BST 2011: Loading uncovered regions into table ... cat 3304907316_uncovered.txt \ | /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 3304907316_uncovered; create table 3304907316_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 = 163692; load data local infile '/dev/stdin' into table 3304907316_uncovered (dna, start, end)" # Fri Apr 1 07:39:25 BST 2011: Finding all genomic features overlapping variants... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 3356714135_rel_snps; CREATE TABLE 3356714135_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) )" # Fri Apr 1 07:39:25 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 3356714135_masked_ids; create table 3356714135_masked_ids (query_region_id int(10) NOT NULL, primary key (query_region_id)); load data local infile '/dev/stdin' ignore into table 3356714135_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 3356714135_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 3356714135_rel_snps; flush table 3356714135_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 3356714135_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 28 2384 II 23 3048 III 17 1572 IV 20 1634 V 23 2677 X 21 6505 touch 3304907316_uncovered # Fri Apr 1 07:39:25 BST 2011: Finding mRNA features overlapping uncovered regions ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 3304907316_uncovered_rel; CREATE TABLE 3304907316_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 3304907316_uncovered_rel; flush table 3304907316_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 3304907316_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 3356714135_masked_ids touch 3304907316_uncovered_rel # Fri Apr 1 07:39:28 BST 2011: Calculating translation start offsets for uncovered regions... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 3304907316_offsets_uncovered; create table 3304907316_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 3304907316_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 3304907316_uncovered reg join 3304907316_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 3304907316_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 3304907316_uncovered reg join 3304907316_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 3304907316_offsets_uncovered touch 3356714135_rel_snps # Fri Apr 1 07:39:28 BST 2011: Calculating translation start offsets... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 3356714135_offsets_snps; create table 3356714135_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) );" # Fri Apr 1 07:39:28 BST 2011: Getting intergenic regions /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 3356714135_rel_intergenic; create table 3356714135_rel_intergenic like 3356714135_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 3356714135_rel_intergenic; flush table 3356714135_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 3356714135_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 3356714135_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 3356714135_snps reg join 3356714135_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" # Fri Apr 1 07:39:32 BST 2011: Filtering masked intergenic regions /usr/bin/mysql -Dmaqgenedb -umaqgene --skip-column-names --batch --raw --local-infile -e "delete i.* from 3356714135_rel_intergenic i join 3356714135_masked_ids m using (query_region_id)" touch 3356714135_rel_intergenic # Fri Apr 1 07:39:37 BST 2011: Classifying intergenic relations /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 3356714135_intergenic_assoc; create table 3356714135_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 3356714135_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 3356714135_snps snp join 3356714135_rel_intergenic rel on (snp.id = rel.query_region_id) join elegans_features feature on (rel.target_region_id = feature.id)" touch 3356714135_intergenic_assoc touch 3356714135_offsets_snps # Fri Apr 1 07:39:49 BST 2011: Getting codons affected by point mutations... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 3356714135_codons; create table 3356714135_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 3356714135_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 3356714135_offsets_snps off join 3356714135_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 3356714135_codons /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 3356714135_marked; create table 3356714135_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) );" # Fri Apr 1 07:39:55 BST 2011: Finding exonic indels ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 3356714135_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 3356714135_snps snp join 3356714135_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';" # Fri Apr 1 07:39:55 BST 2011: Finding coding variants ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 3356714135_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 3356714135_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);" # Fri Apr 1 07:39:56 BST 2011: Finding noncoding variants ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 3356714135_marked select snp.id, feature.feature class, 'none' description, feature.attribute parent_feature from 3356714135_snps snp join 3356714135_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');" # Fri Apr 1 07:39:56 BST 2011: Finding splice site variants ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 3356714135_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 3356714135_snps snp join 3356714135_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;" # Fri Apr 1 07:39:56 BST 2011: Finding intergenic and intronic variants ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 3356714135_marked select id, 'nongenic' class, concat(if (relation in ('upstream','into'), - distance, distance),' ',relation) description, attribute from 3356714135_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' );" # Fri Apr 1 07:39:59 BST 2011: Finding uncovered regions in genes ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 3356714135_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 3304907316_uncovered unc join 3304907316_offsets_uncovered b using (id) join 3304907316_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 3304907316_uncovered unc join 3304907316_offsets_uncovered b using (id) join 3304907316_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'" # Fri Apr 1 07:39:59 BST 2011: Variants found: +-----------------+-----------------+ | class | number_variants | +-----------------+-----------------+ | five_prime_UTR | 1302 | | frameshift | 69 | | inframe | 25 | | missense | 6197 | | ncRNA | 876 | | nongenic | 126839 | | non_start | 10 | | premature_stop | 693 | | readthrough | 19 | | silent | 7447 | | SNP | 1029 | | splice_acceptor | 50 | | splice_donor | 48 | | three_prime_UTR | 3576 | | uncovered | 43 | +-----------------+-----------------+ touch 3356714135_marked # Fri Apr 1 07:40:00 BST 2011: Combining results ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 3356714135_combined; create table 3356714135_combined (primary key (id, class, description), key (dna, start)) as select snp.id, 'CB6880_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 3356714135_snps snp join 3304907316_pileup pile using (dna,start) join 3356714135_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, 'CB6880_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 3304907316_uncovered unc join 3356714135_marked class on (unc.id = class.id) left join elegans_per_locus using (dna,start) group by id, class, description; alter table 3356714135_combined order by dna, start, length" touch 3356714135_combined # Fri Apr 1 07:40:01 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 3356714135_combined group by id order by dna, start;" > /data/maqgene/out/example_user/CB6880_redo/CB6880_redo_grouped.txt # Fri Apr 1 07:40:01 BST 2011: Writing results to flat file ... /usr/bin/mysql -Dmaqgenedb -umaqgene --skip-column-names --batch --raw --local-infile --column-names -e "select * from 3356714135_combined" > /data/maqgene/out/example_user/CB6880_redo/CB6880_redo_flat.txt 3871 lines written. 2301 lines written. rm 1953515093.00021.unmapped 1953515093.00003.unmapped 1953515093.00025.1.bfq 1953515093.00009.map 1953515093.00006.map 1953515093.00003.1.fastq 1953515093.00007.unmapped 1953515093.00023.mismatch 1953515093.00021.2.fastq 1953515093.00018.2.fastq 1953515093.00008.2.fastq 1953515093.00015.map 1953515093.00002.1.bfq 1953515093.00013.unmapped 1953515093.00000.map 1953515093.00007.2.bfq 1953515093.00022.2.fastq 1953515093.00010.unmapped 1953515093.00021.1.bfq 1953515093.00025.2.bfq 1953515093.00025.mismatch 1953515093.00001.map 1953515093.00014.1.bfq 1953515093.00003.2.fastq 1953515093.00016.map 1953515093.00005.unmapped 1953515093.00004.2.bfq 1953515093.00011.2.bfq 1953515093.00005.1.fastq 1953515093.00009.2.fastq 1953515093.00011.map 1953515093.00023.unmapped 1953515093.00023.2.bfq 1953515093.00013.2.fastq 1953515093.00019.unmapped 1953515093.00023.1.fastq 1953515093.00017.map 1953515093.00019.1.fastq 1953515093.00020.map 1953515093.00015.unmapped 1953515093.00009.1.bfq 1953515093.00014.mismatch 1953515093.00007.mismatch 1953515093.00015.1.fastq 1953515093.00011.unmapped 1953515093.00005.2.fastq 1953515093.00008.unmapped 1953515093.00012.map 1953515093.00023.2.fastq 1953515093.00002.mismatch 1953515093.00019.2.fastq 1953515093.00002.2.bfq 1953515093.00006.1.bfq 1953515093.00013.1.fastq 1953515093.00018.map 1953515093.00024.2.bfq 1953515093.00015.2.fastq 1953515093.00005.2.bfq 1953515093.00021.mismatch 1953515093.00024.mismatch 1953515093.00025.unmapped 1953515093.00008.mismatch 1953515093.00021.2.bfq 1953515093.00008.2.bfq 1078206964_split1 1953515093.00000.1.bfq 1953515093.00022.map 1953515093.00025.1.fastq 1953515093.00014.2.fastq 1953515093.00004.unmapped 1953515093.00003.map 1953515093.00006.2.bfq 1953515093.00001.1.bfq 1953515093.00010.1.bfq 1953515093.00004.1.fastq 1953515093.00006.mismatch 1953515093.00010.map 1953515093.00016.1.bfq 1953515093.00000.2.bfq 1953515093.00014.unmapped 1953515093.00009.mismatch 1953515093.00013.map 1953515093.00025.2.fastq 1953515093.00000.mismatch 1078206964_split2 1953515093.00014.1.fastq 1953515093.00009.unmapped 1953515093.00017.1.bfq 1953515093.00001.2.bfq 1953515093.00010.2.bfq 1953515093.00020.1.bfq 1953515093.00004.2.fastq 1953515093.00001.mismatch 1953515093.00010.mismatch 1953515093.00016.2.bfq 1953515093.00009.2.bfq 1953515093.00016.mismatch 1953515093.00005.map 1953515093.00004.mismatch 1953515093.00012.1.bfq 1953515093.00023.map 1953515093.00011.mismatch 1953515093.00024.unmapped 1953515093.00004.1.bfq 1953515093.00019.map 1953515093.00017.2.bfq 1953515093.00024.1.fastq 1953515093.00017.mismatch 1953515093.00020.2.bfq 1953515093.00024.2.fastq 1953515093.00020.mismatch 1953515093.00018.1.bfq 1953515093.00006.unmapped 1953515093.00012.2.bfq 1953515093.00022.1.bfq 1953515093.00012.mismatch 1953515093.00024.1.bfq 1953515093.00006.1.fastq 1953515093.00014.2.bfq 1953515093.00003.1.bfq 1953515093.00018.2.bfq 1953515093.00007.1.fastq 1953515093.00000.1.fastq 1953515093.00018.mismatch 1953515093.00025.map 1953515093.00001.unmapped 1953515093.00022.2.bfq 1953515093.00013.1.bfq 1953515093.00016.unmapped 1953515093.00022.mismatch 1953515093.00006.2.fastq 1953515093.00001.1.fastq 1953515093.00010.1.fastq 1953515093.00002.1.fastq 1953515093.00016.1.fastq 1953515093.00004.map 1953515093.00003.2.bfq 1953515093.00023.1.bfq 1953515093.00003.mismatch 1953515093.00000.2.fastq 1953515093.00007.map 1953515093.00021.1.fastq 1953515093.00011.1.fastq 1953515093.00017.unmapped 1953515093.00005.1.bfq 1953515093.00008.1.fastq 1953515093.00011.1.bfq 1953515093.00002.unmapped 1953515093.00020.unmapped 1953515093.00013.2.bfq 1953515093.00017.1.fastq 1953515093.00014.map 1953515093.00013.mismatch 1953515093.00001.2.fastq 1953515093.00010.2.fastq 1953515093.00020.1.fastq 1953515093.00019.1.bfq 1953515093.00016.2.fastq 1953515093.00002.map 1953515093.00012.unmapped 1953515093.00015.1.bfq 1953515093.00011.2.fastq 1953515093.00012.1.fastq 1953515093.00021.map 1953515093.00008.1.bfq 1953515093.00008.map 1953515093.00005.mismatch 1953515093.00009.1.fastq 1953515093.00017.2.fastq 1953515093.00018.unmapped 1953515093.00002.2.fastq 1953515093.00020.2.fastq 1953515093.00007.2.fastq 1953515093.00024.map 1953515093.00019.2.bfq 1953515093.00018.1.fastq 1953515093.00019.mismatch 1953515093.00022.unmapped 1953515093.00015.2.bfq 1953515093.00012.2.fastq 1953515093.00015.mismatch 1953515093.00000.unmapped 1953515093.00022.1.fastq 1953515093.00007.1.bfq make: Leaving directory `/data/maqgene/work' make: Entering directory `/data/maqgene/work' # Fri Apr 1 07:40:02 BST 2011: Cleaning intermediate data ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 3356714135_snps,3356714135_rel,3356714135_masked_ids,3356714135_rel_intergenic,3356714135_intergenic_assoc,3356714135_offsets,3356714135_codons,3356714135_marked,3356714135_combined,3304907316_pileup" rm -f 3356714135_snps 3356714135_rel 3356714135_masked_ids 3356714135_rel_intergenic 3356714135_intergenic_assoc 3356714135_offsets 3356714135_codons 3356714135_marked 3356714135_combined 3304907316_pileup make: Leaving directory `/data/maqgene/work'