Finished reading input. ++ echo CB6890/./s_3_1_sequence_read1.fastq ++ tr , ' ' + fastq_file_set1=CB6890/./s_3_1_sequence_read1.fastq ++ cd /data/maqgene/reads ++ wc -l ++ cat CB6890/./s_3_1_sequence_read1.fastq ++ cut -f 1 -d ' ' + TOTAL_LINES=132786656 ++ echo '(132786656 / 5000000) + (132786656 % 5000000 != 0)' ++ bc + num_chunks=27 + 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=2823899437 map_cksum=3539375150 pileup_cksum=3525956229 cns_cksum=3681587663 umdd=50000 dmdd=1000 umid=1000 dmid=1000 max_gene_radius=50000 full_results_dir=/data/maqgene/out/example_user/CB6890_redo outfile_basename=CB6890_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=27 Will process 132786656 lines of input in 27 chunks make: Entering directory `/data/maqgene/work' # Fri Apr 1 06:53:54 BST 2011: Removing frontend files in case this is a duplicate run ... rm -f /data/maqgene/out/example_user/CB6890_redo/CB6890_redo_{grouped.txt,flat.txt} rm -f /data/maqgene/out/example_user/CB6890_redo/CB6890_redo_uncovered.txt /data/maqgene/out/example_user/CB6890_redo/CB6890_redo_coverage.txt /data/maqgene/out/example_user/CB6890_redo/CB6890_redo_pileup.txt /data/maqgene/out/example_user/CB6890_redo/CB6890_redo_log.txt /data/maqgene/out/example_user/CB6890_redo/CB6890_redo_check.txt /data/maqgene/out/example_user/CB6890_redo/CB6890_redo_unmapped.txt make: Leaving directory `/data/maqgene/work' make: Entering directory `/data/maqgene/work' /data/maqgene/makefile:76: warning: undefined variable `date' /data/maqgene/makefile:78: warning: undefined variable `date' # : Regrouping fastq reads into chunks of size 5000000. split -l 5000000 -a 5 -d <(cat /data/maqgene/reads/CB6890/./s_3_1_sequence_read1.fastq) 3539375150.1.fastq. # : Regrouping fastq reads into chunks of size 5000000. split -l 5000000 -a 5 -d <(cat /data/maqgene/reads/CB6890/./s_3_2_sequence_read2.fastq) 3539375150.2.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 3539375150.1.fastq.$stem 3539375150.$stem.1.fastq; done touch 2823899437_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 3539375150.2.fastq.$stem 3539375150.$stem.2.fastq; done touch 2823899437_split2 # Fri Apr 1 06:54:59 BST 2011: Converting fastq files to bfq ... # Fri Apr 1 06:54:59 BST 2011: Converting fastq files to bfq ... # Fri Apr 1 06:54:59 BST 2011: Converting fastq files to bfq ... # Fri Apr 1 06:54:59 BST 2011: Converting fastq files to bfq ... # Fri Apr 1 06:54:59 BST 2011: Converting fastq files to bfq ... out | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3539375150.00002.1.bfq # Fri Apr 1 06:54:59 BST 2011: Converting fastq files to bfq ... # Fri Apr 1 06:54:59 BST 2011: Converting fastq files to bfq ... # Fri Apr 1 06:54:59 BST 2011: Converting fastq files to bfq ... # Fri Apr 1 06:54:59 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3539375150.00001.1.fastq /dev/stdout | \ # Fri Apr 1 06:54:59 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3539375150.00003.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3539375150.00003.1.bfq # Fri Apr 1 06:54:59 BST 2011: Converting fastq files to bfq ... # Fri Apr 1 06:54:59 BST 2011: Converting fastq files to bfq ... # Fri Apr 1 06:54:59 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3539375150.00000.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3539375150.00000.1.bfq # Fri Apr 1 06:54:59 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3539375150.00004.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3539375150.00004.1.bfq /data/maqgene/bin/maq sol2sanger 3539375150.00005.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3539375150.00005.1.bfq /data/maqgene/bin/maq sol2sanger 3539375150.00006.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3539375150.00006.1.bfq /data/maqgene/bin/maq sol2sanger 3539375150.00007.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3539375150.00007.1.bfq /data/maqgene/bin/maq sol2sanger 3539375150.00008.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3539375150.00008.1.bfq /data/maqgene/bin/maq sol2sanger 3539375150.00009.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3539375150.00009.1.bfq /data/maqgene/bin/maq sol2sanger 3539375150.00010.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3539375150.00010.1.bfq /data/maqgene/bin/maq sol2sanger 3539375150.00011.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3539375150.00011.1.bfq /data/maqgene/bin/maq sol2sanger 3539375150.00012.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3539375150.00012.1.bfq /data/maqgene/bin/maq sol2sanger 3539375150.00013.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3539375150.00013.1.bfq -- finish writing file '3539375150.00000.1.bfq' -- 1250000 sequences were loaded. # Fri Apr 1 06:55:15 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3539375150.00014.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3539375150.00014.1.bfq -- finish writing file '3539375150.00010.1.bfq' -- 1250000 sequences were loaded. # Fri Apr 1 06:55:15 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3539375150.00015.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3539375150.00015.1.bfq -- finish writing file '3539375150.00002.1.bfq' -- 1250000 sequences were loaded. # Fri Apr 1 06:55:23 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3539375150.00016.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3539375150.00016.1.bfq -- finish writing file '3539375150.00012.1.bfq' -- 1250000 sequences were loaded. # Fri Apr 1 06:55:25 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3539375150.00017.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3539375150.00017.1.bfq -- finish writing file '3539375150.00001.1.bfq' -- 1250000 sequences were loaded. # Fri Apr 1 06:55:27 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3539375150.00018.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3539375150.00018.1.bfq -- finish writing file '3539375150.00011.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3539375150.00004.1.bfq' -- 1250000 sequences were loaded. # Fri Apr 1 06:55:27 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3539375150.00019.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3539375150.00019.1.bfq # Fri Apr 1 06:55:27 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3539375150.00020.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3539375150.00020.1.bfq -- finish writing file '3539375150.00008.1.bfq' -- 1250000 sequences were loaded. # Fri Apr 1 06:55:27 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3539375150.00021.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3539375150.00021.1.bfq -- finish writing file '3539375150.00009.1.bfq' -- 1250000 sequences were loaded. # Fri Apr 1 06:55:27 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3539375150.00022.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3539375150.00022.1.bfq -- finish writing file '3539375150.00005.1.bfq' -- 1250000 sequences were loaded. # Fri Apr 1 06:55:27 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3539375150.00023.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3539375150.00023.1.bfq -- finish writing file '3539375150.00006.1.bfq' -- 1250000 sequences were loaded. # Fri Apr 1 06:55:27 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3539375150.00024.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3539375150.00024.1.bfq -- finish writing file '3539375150.00007.1.bfq' -- 1250000 sequences were loaded. # Fri Apr 1 06:55:28 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3539375150.00025.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3539375150.00025.1.bfq -- finish writing file '3539375150.00013.1.bfq' -- 1250000 sequences were loaded. # Fri Apr 1 06:55:28 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3539375150.00026.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3539375150.00026.1.bfq -- finish writing file '3539375150.00003.1.bfq' -- 1250000 sequences were loaded. # Fri Apr 1 06:55:28 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3539375150.00000.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3539375150.00000.2.bfq -- finish writing file '3539375150.00014.1.bfq' -- 1250000 sequences were loaded. # Fri Apr 1 06:55:38 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3539375150.00001.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3539375150.00001.2.bfq -- finish writing file '3539375150.00015.1.bfq' -- 1250000 sequences were loaded. # Fri Apr 1 06:55:44 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3539375150.00002.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3539375150.00002.2.bfq -- finish writing file '3539375150.00026.1.bfq' -- 696664 sequences were loaded. # Fri Apr 1 06:55:46 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3539375150.00003.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3539375150.00003.2.bfq -- finish writing file '3539375150.00018.1.bfq' -- 1250000 sequences were loaded. # Fri Apr 1 06:55:50 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3539375150.00004.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3539375150.00004.2.bfq -- finish writing file '3539375150.00016.1.bfq' -- 1250000 sequences were loaded. # Fri Apr 1 06:55:52 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3539375150.00005.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3539375150.00005.2.bfq -- finish writing file '3539375150.00017.1.bfq' -- 1250000 sequences were loaded. # Fri Apr 1 06:55:54 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3539375150.00006.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3539375150.00006.2.bfq -- finish writing file '3539375150.00022.1.bfq' -- 1250000 sequences were loaded. # Fri Apr 1 06:55:55 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3539375150.00007.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3539375150.00007.2.bfq -- finish writing file '3539375150.00023.1.bfq' -- 1250000 sequences were loaded. # Fri Apr 1 06:55:57 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3539375150.00008.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3539375150.00008.2.bfq -- finish writing file '3539375150.00025.1.bfq' -- 1250000 sequences were loaded. # Fri Apr 1 06:55:58 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3539375150.00009.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3539375150.00009.2.bfq -- finish writing file '3539375150.00019.1.bfq' -- 1250000 sequences were loaded. # Fri Apr 1 06:55:58 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3539375150.00010.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3539375150.00010.2.bfq -- finish writing file '3539375150.00020.1.bfq' -- 1250000 sequences were loaded. # Fri Apr 1 06:55:58 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3539375150.00011.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3539375150.00011.2.bfq -- finish writing file '3539375150.00021.1.bfq' -- 1250000 sequences were loaded. # Fri Apr 1 06:55:59 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3539375150.00012.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3539375150.00012.2.bfq -- finish writing file '3539375150.00024.1.bfq' -- 1250000 sequences were loaded. # Fri Apr 1 06:55:59 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3539375150.00013.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3539375150.00013.2.bfq -- finish writing file '3539375150.00000.2.bfq' -- 1250000 sequences were loaded. # Fri Apr 1 06:56:02 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3539375150.00014.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3539375150.00014.2.bfq -- finish writing file '3539375150.00001.2.bfq' -- 1250000 sequences were loaded. # Fri Apr 1 06:56:09 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3539375150.00015.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3539375150.00015.2.bfq -- finish writing file '3539375150.00002.2.bfq' -- 1250000 sequences were loaded. # Fri Apr 1 06:56:15 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3539375150.00016.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3539375150.00016.2.bfq -- finish writing file '3539375150.00003.2.bfq' -- 1250000 sequences were loaded. # Fri Apr 1 06:56:16 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3539375150.00017.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3539375150.00017.2.bfq -- finish writing file '3539375150.00005.2.bfq' -- 1250000 sequences were loaded. # Fri Apr 1 06:56:20 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3539375150.00018.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3539375150.00018.2.bfq -- finish writing file '3539375150.00004.2.bfq' -- 1250000 sequences were loaded. # Fri Apr 1 06:56:22 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3539375150.00019.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3539375150.00019.2.bfq -- finish writing file '3539375150.00008.2.bfq' -- 1250000 sequences were loaded. # Fri Apr 1 06:56:22 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3539375150.00020.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3539375150.00020.2.bfq -- finish writing file '3539375150.00007.2.bfq' -- 1250000 sequences were loaded. # Fri Apr 1 06:56:22 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3539375150.00021.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3539375150.00021.2.bfq -- finish writing file '3539375150.00006.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '3539375150.00012.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '3539375150.00011.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '3539375150.00010.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '3539375150.00013.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '3539375150.00014.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '3539375150.00009.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '3539375150.00015.2.bfq' -- 1250000 sequences were loaded. # Fri Apr 1 06:56:38 BST 2011: Mapping file(s) 3539375150.00001.1.bfq 3539375150.00001.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3539375150.00001.unmapped -H 3539375150.00001.mismatch \ 3539375150.00001.map /data/maqgene/genomes/elegans.bfa 3539375150.00001.1.bfq 3539375150.00001.2.bfq 2> /dev/null # Fri Apr 1 06:56:38 BST 2011: Mapping file(s) 3539375150.00002.1.bfq 3539375150.00002.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3539375150.00002.unmapped -H 3539375150.00002.mismatch \ 3539375150.00002.map /data/maqgene/genomes/elegans.bfa 3539375150.00002.1.bfq 3539375150.00002.2.bfq 2> /dev/null -- finish writing file '3539375150.00016.2.bfq' -- 1250000 sequences were loaded. # Fri Apr 1 06:56:39 BST 2011: Converting fastq files to bfq ... # Fri Apr 1 06:56:39 BST 2011: Mapping file(s) 3539375150.00000.1.bfq 3539375150.00000.2.bfq /data/maqgene/bin/maq sol2sanger 3539375150.00026.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3539375150.00026.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3539375150.00000.unmapped -H 3539375150.00000.mismatch \ 3539375150.00000.map /data/maqgene/genomes/elegans.bfa 3539375150.00000.1.bfq 3539375150.00000.2.bfq 2> /dev/null # Fri Apr 1 06:56:40 BST 2011: Mapping file(s) 3539375150.00003.1.bfq 3539375150.00003.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3539375150.00003.unmapped -H 3539375150.00003.mismatch \ 3539375150.00003.map /data/maqgene/genomes/elegans.bfa 3539375150.00003.1.bfq 3539375150.00003.2.bfq 2> /dev/null -- finish writing file '3539375150.00017.2.bfq' -- 1250000 sequences were loaded. # Fri Apr 1 06:56:40 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3539375150.00025.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3539375150.00025.2.bfq -- finish writing file '3539375150.00018.2.bfq' -- 1250000 sequences were loaded. # Fri Apr 1 06:56:41 BST 2011: Mapping file(s) 3539375150.00004.1.bfq 3539375150.00004.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3539375150.00004.unmapped -H 3539375150.00004.mismatch \ 3539375150.00004.map /data/maqgene/genomes/elegans.bfa 3539375150.00004.1.bfq 3539375150.00004.2.bfq 2> /dev/null # Fri Apr 1 06:56:41 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3539375150.00024.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3539375150.00024.2.bfq # Fri Apr 1 06:56:42 BST 2011: Mapping file(s) 3539375150.00005.1.bfq 3539375150.00005.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3539375150.00005.unmapped -H 3539375150.00005.mismatch \ 3539375150.00005.map /data/maqgene/genomes/elegans.bfa 3539375150.00005.1.bfq 3539375150.00005.2.bfq 2> /dev/null -- finish writing file '3539375150.00020.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '3539375150.00019.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '3539375150.00021.2.bfq' -- 1250000 sequences were loaded. # Fri Apr 1 06:56:48 BST 2011: Mapping file(s) 3539375150.00008.1.bfq 3539375150.00008.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3539375150.00008.unmapped -H 3539375150.00008.mismatch \ 3539375150.00008.map /data/maqgene/genomes/elegans.bfa 3539375150.00008.1.bfq 3539375150.00008.2.bfq 2> /dev/null # Fri Apr 1 06:56:49 BST 2011: Mapping file(s) 3539375150.00007.1.bfq 3539375150.00007.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3539375150.00007.unmapped -H 3539375150.00007.mismatch \ 3539375150.00007.map /data/maqgene/genomes/elegans.bfa 3539375150.00007.1.bfq 3539375150.00007.2.bfq 2> /dev/null # Fri Apr 1 06:56:50 BST 2011: Mapping file(s) 3539375150.00006.1.bfq 3539375150.00006.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3539375150.00006.unmapped -H 3539375150.00006.mismatch \ 3539375150.00006.map /data/maqgene/genomes/elegans.bfa 3539375150.00006.1.bfq 3539375150.00006.2.bfq 2> /dev/null -- finish writing file '3539375150.00026.2.bfq' -- 696664 sequences were loaded. # Fri Apr 1 06:56:50 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3539375150.00023.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3539375150.00023.2.bfq # Fri Apr 1 06:56:51 BST 2011: Mapping file(s) 3539375150.00009.1.bfq 3539375150.00009.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3539375150.00009.unmapped -H 3539375150.00009.mismatch \ 3539375150.00009.map /data/maqgene/genomes/elegans.bfa 3539375150.00009.1.bfq 3539375150.00009.2.bfq 2> /dev/null # Fri Apr 1 06:56:52 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3539375150.00022.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3539375150.00022.2.bfq -- finish writing file '3539375150.00025.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '3539375150.00024.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '3539375150.00022.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '3539375150.00023.2.bfq' -- 1250000 sequences were loaded. # Fri Apr 1 06:57:19 BST 2011: Mapping file(s) 3539375150.00013.1.bfq 3539375150.00013.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3539375150.00013.unmapped -H 3539375150.00013.mismatch \ 3539375150.00013.map /data/maqgene/genomes/elegans.bfa 3539375150.00013.1.bfq 3539375150.00013.2.bfq 2> /dev/null # Fri Apr 1 06:57:21 BST 2011: Mapping file(s) 3539375150.00012.1.bfq 3539375150.00012.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3539375150.00012.unmapped -H 3539375150.00012.mismatch \ 3539375150.00012.map /data/maqgene/genomes/elegans.bfa 3539375150.00012.1.bfq 3539375150.00012.2.bfq 2> /dev/null # Fri Apr 1 06:57:23 BST 2011: Mapping file(s) 3539375150.00011.1.bfq 3539375150.00011.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3539375150.00011.unmapped -H 3539375150.00011.mismatch \ 3539375150.00011.map /data/maqgene/genomes/elegans.bfa 3539375150.00011.1.bfq 3539375150.00011.2.bfq 2> /dev/null # Fri Apr 1 07:03:09 BST 2011: Mapping file(s) 3539375150.00016.1.bfq 3539375150.00016.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3539375150.00016.unmapped -H 3539375150.00016.mismatch \ 3539375150.00016.map /data/maqgene/genomes/elegans.bfa 3539375150.00016.1.bfq 3539375150.00016.2.bfq 2> /dev/null # Fri Apr 1 07:03:11 BST 2011: Mapping file(s) 3539375150.00015.1.bfq 3539375150.00015.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3539375150.00015.unmapped -H 3539375150.00015.mismatch \ 3539375150.00015.map /data/maqgene/genomes/elegans.bfa 3539375150.00015.1.bfq 3539375150.00015.2.bfq 2> /dev/null # Fri Apr 1 07:03:13 BST 2011: Mapping file(s) 3539375150.00014.1.bfq 3539375150.00014.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3539375150.00014.unmapped -H 3539375150.00014.mismatch \ 3539375150.00014.map /data/maqgene/genomes/elegans.bfa 3539375150.00014.1.bfq 3539375150.00014.2.bfq 2> /dev/null # Fri Apr 1 07:03:49 BST 2011: Mapping file(s) 3539375150.00021.1.bfq 3539375150.00021.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3539375150.00021.unmapped -H 3539375150.00021.mismatch \ 3539375150.00021.map /data/maqgene/genomes/elegans.bfa 3539375150.00021.1.bfq 3539375150.00021.2.bfq 2> /dev/null # Fri Apr 1 07:03:50 BST 2011: Mapping file(s) 3539375150.00020.1.bfq 3539375150.00020.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3539375150.00020.unmapped -H 3539375150.00020.mismatch \ 3539375150.00020.map /data/maqgene/genomes/elegans.bfa 3539375150.00020.1.bfq 3539375150.00020.2.bfq 2> /dev/null # Fri Apr 1 07:03:51 BST 2011: Mapping file(s) 3539375150.00019.1.bfq 3539375150.00019.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3539375150.00019.unmapped -H 3539375150.00019.mismatch \ 3539375150.00019.map /data/maqgene/genomes/elegans.bfa 3539375150.00019.1.bfq 3539375150.00019.2.bfq 2> /dev/null # Fri Apr 1 07:03:52 BST 2011: Mapping file(s) 3539375150.00018.1.bfq 3539375150.00018.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3539375150.00018.unmapped -H 3539375150.00018.mismatch \ 3539375150.00018.map /data/maqgene/genomes/elegans.bfa 3539375150.00018.1.bfq 3539375150.00018.2.bfq 2> /dev/null # Fri Apr 1 07:03:53 BST 2011: Mapping file(s) 3539375150.00017.1.bfq 3539375150.00017.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3539375150.00017.unmapped -H 3539375150.00017.mismatch \ 3539375150.00017.map /data/maqgene/genomes/elegans.bfa 3539375150.00017.1.bfq 3539375150.00017.2.bfq 2> /dev/null # Fri Apr 1 07:04:34 BST 2011: Mapping file(s) 3539375150.00025.1.bfq 3539375150.00025.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3539375150.00025.unmapped -H 3539375150.00025.mismatch \ 3539375150.00025.map /data/maqgene/genomes/elegans.bfa 3539375150.00025.1.bfq 3539375150.00025.2.bfq 2> /dev/null # Fri Apr 1 07:04:35 BST 2011: Mapping file(s) 3539375150.00024.1.bfq 3539375150.00024.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3539375150.00024.unmapped -H 3539375150.00024.mismatch \ 3539375150.00024.map /data/maqgene/genomes/elegans.bfa 3539375150.00024.1.bfq 3539375150.00024.2.bfq 2> /dev/null # Fri Apr 1 07:04:36 BST 2011: Mapping file(s) 3539375150.00023.1.bfq 3539375150.00023.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3539375150.00023.unmapped -H 3539375150.00023.mismatch \ 3539375150.00023.map /data/maqgene/genomes/elegans.bfa 3539375150.00023.1.bfq 3539375150.00023.2.bfq 2> /dev/null # Fri Apr 1 07:04:37 BST 2011: Mapping file(s) 3539375150.00022.1.bfq 3539375150.00022.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3539375150.00022.unmapped -H 3539375150.00022.mismatch \ 3539375150.00022.map /data/maqgene/genomes/elegans.bfa 3539375150.00022.1.bfq 3539375150.00022.2.bfq 2> /dev/null # Fri Apr 1 07:04:38 BST 2011: Mapping file(s) 3539375150.00010.1.bfq 3539375150.00010.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3539375150.00010.unmapped -H 3539375150.00010.mismatch \ 3539375150.00010.map /data/maqgene/genomes/elegans.bfa 3539375150.00010.1.bfq 3539375150.00010.2.bfq 2> /dev/null # Fri Apr 1 07:10:12 BST 2011: Mapping file(s) 3539375150.00026.1.bfq 3539375150.00026.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3539375150.00026.unmapped -H 3539375150.00026.mismatch \ 3539375150.00026.map /data/maqgene/genomes/elegans.bfa 3539375150.00026.1.bfq 3539375150.00026.2.bfq 2> /dev/null # Fri Apr 1 07:14:28 BST 2011: Merging all maps ... /data/maqgene/bin/maq mapmerge 3539375150.map 3539375150.00000.map 3539375150.00001.map 3539375150.00002.map 3539375150.00003.map 3539375150.00004.map 3539375150.00005.map 3539375150.00006.map 3539375150.00007.map 3539375150.00008.map 3539375150.00009.map 3539375150.00010.map 3539375150.00011.map 3539375150.00012.map 3539375150.00013.map 3539375150.00014.map 3539375150.00015.map 3539375150.00016.map 3539375150.00017.map 3539375150.00018.map 3539375150.00019.map 3539375150.00020.map 3539375150.00021.map 3539375150.00022.map 3539375150.00023.map 3539375150.00024.map 3539375150.00025.map 3539375150.00026.map /data/maqgene/makefile:126: warning: undefined variable `mapcheck_parameters' # Fri Apr 1 07:27:15 BST 2011: Merging all *.unmapped files ... cat 3539375150.00000.unmapped 3539375150.00001.unmapped 3539375150.00002.unmapped 3539375150.00003.unmapped 3539375150.00004.unmapped 3539375150.00005.unmapped 3539375150.00006.unmapped 3539375150.00007.unmapped 3539375150.00008.unmapped 3539375150.00009.unmapped 3539375150.00010.unmapped 3539375150.00011.unmapped 3539375150.00012.unmapped 3539375150.00013.unmapped 3539375150.00014.unmapped 3539375150.00015.unmapped 3539375150.00016.unmapped 3539375150.00017.unmapped 3539375150.00018.unmapped 3539375150.00019.unmapped 3539375150.00020.unmapped 3539375150.00021.unmapped 3539375150.00022.unmapped 3539375150.00023.unmapped 3539375150.00024.unmapped 3539375150.00025.unmapped 3539375150.00026.unmapped > 3539375150_unmapped.txt # Fri Apr 1 07:27:15 BST 2011: Generating consensus ... # Fri Apr 1 07:27:15 BST 2011: Creating pileup ... /data/maqgene/bin/maq assemble -N 2 -q 0 -r 0.0 -m 7 -Q 100 -p 3681587663.cns \ /data/maqgene/genomes/elegans.bfa 3539375150.map 2> 3681587663_log.txt # Fri Apr 1 07:27:15 BST 2011: Running 'mapcheck' ... /data/maqgene/bin/maq pileup -Q 100 -p -m 7 -q 0 /data/maqgene/genomes/elegans.bfa 3539375150.map > 3525956229_pileup.txt /data/maqgene/bin/maq mapcheck /data/maqgene/genomes/elegans.bfa 3539375150.map > 3539375150_check.txt \ 2>/dev/null # Fri Apr 1 07:27:16 BST 2011: Linking backend file 3539375150_unmapped.txt to /data/maqgene/out/example_user/CB6890_redo/CB6890_redo_unmapped.txt ln -fs /data/maqgene/work/3539375150_unmapped.txt /data/maqgene/out/example_user/CB6890_redo/CB6890_redo_unmapped.txt # Fri Apr 1 07:30:10 BST 2011: Linking backend file 3539375150_check.txt to /data/maqgene/out/example_user/CB6890_redo/CB6890_redo_check.txt ln -fs /data/maqgene/work/3539375150_check.txt /data/maqgene/out/example_user/CB6890_redo/CB6890_redo_check.txt /data/maqgene/bin/filter_matching_lines 3525956229_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 \ > 3525956229_known_snps # Fri Apr 1 07:30:37 BST 2011: Getting uncovered regions ... # Fri Apr 1 07:30:37 BST 2011: Making coverage histogram ... cut -f 1,2,4 3525956229_pileup.txt \ | /data/maqgene/bin/get_uncovered_regions 50 \ > 3525956229_uncovered.txt (echo -en "sequencing_depth\tnumber_of_bases\n"; \ cut -f 4 3525956229_pileup.txt \ | /data/maqgene/bin/pileup_histogram 100) > 3525956229_coverage.txt # Fri Apr 1 07:30:37 BST 2011: Linking backend file 3525956229_pileup.txt to /data/maqgene/out/example_user/CB6890_redo/CB6890_redo_pileup.txt ln -fs /data/maqgene/work/3525956229_pileup.txt /data/maqgene/out/example_user/CB6890_redo/CB6890_redo_pileup.txt # Fri Apr 1 07:30:56 BST 2011: Linking backend file 3525956229_coverage.txt to /data/maqgene/out/example_user/CB6890_redo/CB6890_redo_coverage.txt ln -fs /data/maqgene/work/3525956229_coverage.txt /data/maqgene/out/example_user/CB6890_redo/CB6890_redo_coverage.txt # Fri Apr 1 07:31:04 BST 2011: Filtering and loading pileup for analysis ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 3525956229_pileup; create table 3525956229_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 3525956229_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 3525956229_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 3525956229_pileup" # Fri Apr 1 07:31:06 BST 2011: Linking backend file 3525956229_uncovered.txt to /data/maqgene/out/example_user/CB6890_redo/CB6890_redo_uncovered.txt ln -fs /data/maqgene/work/3525956229_uncovered.txt /data/maqgene/out/example_user/CB6890_redo/CB6890_redo_uncovered.txt cat 3525956229_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 3525956229_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 3525956229_pileup" touch 3525956229_pileup # Fri Apr 1 07:31:55 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 3525956229_pileup p using (dna,start)" > /data/maqgene/out/example_user/CB6890_redo/CB6890_redo_snp_read_counts.txt 0 snp read count lines written. # Fri Apr 1 07:32:11 BST 2011: Linking backend file 3681587663_log.txt to /data/maqgene/out/example_user/CB6890_redo/CB6890_redo_log.txt # Fri Apr 1 07:32:11 BST 2011: Extracting point mutants from consensus ... ln -fs /data/maqgene/work/3681587663_log.txt /data/maqgene/out/example_user/CB6890_redo/CB6890_redo_log.txt /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 3681587663_snps; create table 3681587663_snps ( id int(10) NOT NULL auto_increment, dna char(40) NOT NULL, start int(10) NOT NULL, end int(10) NOT NULL, indel_size int(5) NOT NULL, variant_type enum('indel', 'point') NOT NULL, ref_base char NOT NULL, sample_base char NOT NULL, snp_score int(5) NOT NULL, read_depth int(5) NOT NULL, loci_multiplicity double(5,2) NOT NULL, mapping_quality int(5) NOT NULL, neighbor_quality int(5) NOT NULL, primary key (id), unique key (dna, start), key (indel_size) )" /data/maqgene/bin/maq cns2snp 3681587663.cns \ | cat -b | /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "load data local infile '/dev/stdin' into table 3681587663_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 3681587663_snps;" # Fri Apr 1 07:32:24 BST 2011: Extracting indels from consensus ... /data/maqgene/bin/maq indelsoa /data/maqgene/genomes/elegans.bfa 3539375150.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 3681587663_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 3681587663_snps;" # Fri Apr 1 07:34:05 BST 2011: Adding placeholders for known SNPs. cat 3525956229_known_snps \ | /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "load data local infile '/dev/stdin' ignore into table 3681587663_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 3681587663_snps;" Found 162972 variants. touch 3681587663_snps # Fri Apr 1 07:34:07 BST 2011: Loading uncovered regions into table ... # Fri Apr 1 07:34:07 BST 2011: Finding all genomic features overlapping variants... cat 3525956229_uncovered.txt \ | /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 3525956229_uncovered; create table 3525956229_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 = 162973; load data local infile '/dev/stdin' into table 3525956229_uncovered (dna, start, end)" /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 3681587663_rel_snps; CREATE TABLE 3681587663_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 07:34:07 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 3681587663_masked_ids; create table 3681587663_masked_ids (query_region_id int(10) NOT NULL, primary key (query_region_id)); load data local infile '/dev/stdin' ignore into table 3681587663_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 3681587663_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; 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 3681587663_rel_snps; flush table 3681587663_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 3681587663_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 18 2794 II 28 6319 III 18 1691 IV 20 9547 V 21 2077 X 14 5886 touch 3525956229_uncovered # Fri Apr 1 07:34:09 BST 2011: Finding mRNA features overlapping uncovered regions ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 3525956229_uncovered_rel; CREATE TABLE 3525956229_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 3525956229_uncovered_rel; flush table 3525956229_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 3525956229_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 3681587663_masked_ids touch 3525956229_uncovered_rel # Fri Apr 1 07:34:11 BST 2011: Calculating translation start offsets for uncovered regions... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 3525956229_offsets_uncovered; create table 3525956229_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 3525956229_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 3525956229_uncovered reg join 3525956229_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 3525956229_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 3525956229_uncovered reg join 3525956229_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 3525956229_offsets_uncovered touch 3681587663_rel_snps # Fri Apr 1 07:34:12 BST 2011: Calculating translation start offsets... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 3681587663_offsets_snps; create table 3681587663_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 07:34:12 BST 2011: Getting intergenic regions /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 3681587663_rel_intergenic; create table 3681587663_rel_intergenic like 3681587663_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 3681587663_rel_intergenic; flush table 3681587663_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 3681587663_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 3681587663_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 3681587663_snps reg join 3681587663_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 07:34:15 BST 2011: Filtering masked intergenic regions /usr/bin/mysql -Dmaqgenedb -umaqgene --skip-column-names --batch --raw --local-infile -e "delete i.* from 3681587663_rel_intergenic i join 3681587663_masked_ids m using (query_region_id)" touch 3681587663_rel_intergenic # Fri Apr 1 07:34:20 BST 2011: Classifying intergenic relations /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 3681587663_intergenic_assoc; create table 3681587663_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 3681587663_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 3681587663_snps snp join 3681587663_rel_intergenic rel on (snp.id = rel.query_region_id) join elegans_features feature on (rel.target_region_id = feature.id)" touch 3681587663_intergenic_assoc touch 3681587663_offsets_snps # Fri Apr 1 07:34:30 BST 2011: Getting codons affected by point mutations... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 3681587663_codons; create table 3681587663_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 3681587663_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 3681587663_offsets_snps off join 3681587663_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 3681587663_codons /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 3681587663_marked; create table 3681587663_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 07:34:40 BST 2011: Finding exonic indels ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 3681587663_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 3681587663_snps snp join 3681587663_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 07:34:40 BST 2011: Finding coding variants ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 3681587663_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 3681587663_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 07:34:40 BST 2011: Finding noncoding variants ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 3681587663_marked select snp.id, feature.feature class, 'none' description, feature.attribute parent_feature from 3681587663_snps snp join 3681587663_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 07:34:41 BST 2011: Finding splice site variants ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 3681587663_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 3681587663_snps snp join 3681587663_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 07:34:41 BST 2011: Finding intergenic and intronic variants ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 3681587663_marked select id, 'nongenic' class, concat(if (relation in ('upstream','into'), - distance, distance),' ',relation) description, attribute from 3681587663_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 07:34:43 BST 2011: Finding uncovered regions in genes ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 3681587663_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 3525956229_uncovered unc join 3525956229_offsets_uncovered b using (id) join 3525956229_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 3525956229_uncovered unc join 3525956229_offsets_uncovered b using (id) join 3525956229_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 07:34:43 BST 2011: Variants found: +-----------------+-----------------+ | class | number_variants | +-----------------+-----------------+ | five_prime_UTR | 1293 | | frameshift | 48 | | inframe | 13 | | missense | 6203 | | ncRNA | 878 | | nongenic | 126282 | | non_start | 9 | | premature_stop | 688 | | readthrough | 20 | | silent | 7426 | | SNP | 1018 | | splice_acceptor | 46 | | splice_donor | 45 | | three_prime_UTR | 3574 | | uncovered | 45 | +-----------------+-----------------+ touch 3681587663_marked # Fri Apr 1 07:34:44 BST 2011: Combining results ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 3681587663_combined; create table 3681587663_combined (primary key (id, class, description), key (dna, start)) as select snp.id, 'CB6890_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 3681587663_snps snp join 3525956229_pileup pile using (dna,start) join 3681587663_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, 'CB6890_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 3525956229_uncovered unc join 3681587663_marked class on (unc.id = class.id) left join elegans_per_locus using (dna,start) group by id, class, description; alter table 3681587663_combined order by dna, start, length" touch 3681587663_combined # Fri Apr 1 07:34:45 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 3681587663_combined group by id order by dna, start;" > /data/maqgene/out/example_user/CB6890_redo/CB6890_redo_grouped.txt # Fri Apr 1 07:34:45 BST 2011: Writing results to flat file ... /usr/bin/mysql -Dmaqgenedb -umaqgene --skip-column-names --batch --raw --local-infile --column-names -e "select * from 3681587663_combined" > /data/maqgene/out/example_user/CB6890_redo/CB6890_redo_flat.txt 3932 lines written. 2313 lines written. rm 3539375150.00018.2.bfq 3539375150.00000.1.fastq 3539375150.00018.mismatch 3539375150.00014.2.bfq 2823899437_split2 3539375150.00021.1.bfq 3539375150.00025.map 3539375150.00010.2.fastq 3539375150.00010.unmapped 3539375150.00022.2.bfq 3539375150.00007.1.fastq 3539375150.00013.1.bfq 3539375150.00022.mismatch 3539375150.00006.2.fastq 3539375150.00001.1.fastq 3539375150.00010.1.fastq 3539375150.00016.1.fastq 3539375150.00004.map 3539375150.00003.2.bfq 3539375150.00003.mismatch 3539375150.00001.2.fastq 3539375150.00000.2.fastq 3539375150.00011.1.fastq 3539375150.00017.unmapped 3539375150.00005.1.bfq 3539375150.00002.unmapped 3539375150.00020.unmapped 3539375150.00013.2.bfq 3539375150.00017.1.fastq 3539375150.00007.map 3539375150.00014.map 3539375150.00021.1.fastq 3539375150.00013.mismatch 3539375150.00008.1.fastq 3539375150.00002.1.fastq 3539375150.00020.1.fastq 3539375150.00005.2.fastq 3539375150.00023.1.bfq 3539375150.00019.1.bfq 3539375150.00016.2.fastq 3539375150.00012.unmapped 3539375150.00015.1.bfq 3539375150.00011.2.fastq 3539375150.00012.1.fastq 3539375150.00026.unmapped 3539375150.00005.mismatch 3539375150.00017.2.fastq 3539375150.00026.1.fastq 3539375150.00023.2.bfq 3539375150.00018.unmapped 3539375150.00021.map 3539375150.00002.2.fastq 3539375150.00020.2.fastq 3539375150.00008.map 3539375150.00024.map 3539375150.00019.2.bfq 3539375150.00009.1.fastq 3539375150.00018.1.fastq 3539375150.00019.mismatch 3539375150.00022.unmapped 3539375150.00008.1.bfq 3539375150.00007.2.fastq 3539375150.00012.2.fastq 3539375150.00015.mismatch 3539375150.00022.1.fastq 3539375150.00012.map 3539375150.00003.unmapped 3539375150.00025.1.bfq 3539375150.00026.2.fastq 3539375150.00006.map 3539375150.00010.2.bfq 3539375150.00007.1.bfq 3539375150.00003.1.fastq 3539375150.00018.2.fastq 3539375150.00009.map 3539375150.00004.1.bfq 3539375150.00013.unmapped 3539375150.00000.map 3539375150.00023.mismatch 3539375150.00021.2.fastq 3539375150.00022.2.fastq 3539375150.00008.2.fastq 3539375150.00013.1.fastq 3539375150.00025.2.bfq 3539375150.00025.mismatch 3539375150.00001.map 3539375150.00010.map 3539375150.00014.1.bfq 3539375150.00003.2.fastq 3539375150.00016.map 3539375150.00004.2.bfq 3539375150.00005.2.bfq 3539375150.00005.1.fastq 3539375150.00004.mismatch 3539375150.00011.map 3539375150.00023.unmapped 3539375150.00008.unmapped 3539375150.00011.mismatch 3539375150.00013.2.fastq 3539375150.00019.unmapped 3539375150.00001.unmapped 3539375150.00023.1.fastq 3539375150.00017.map 3539375150.00009.2.fastq 3539375150.00019.1.fastq 3539375150.00002.map 3539375150.00020.map 3539375150.00015.unmapped 3539375150.00014.mismatch 3539375150.00024.1.bfq 3539375150.00015.1.fastq 3539375150.00005.unmapped 3539375150.00009.1.bfq 3539375150.00007.mismatch 3539375150.00007.2.bfq 3539375150.00023.2.fastq 3539375150.00011.unmapped 3539375150.00019.2.fastq 3539375150.00026.map 3539375150.00015.2.bfq 3539375150.00006.1.bfq 3539375150.00016.unmapped 3539375150.00018.map 3539375150.00024.2.bfq 3539375150.00015.2.fastq 3539375150.00003.map 3539375150.00025.unmapped 3539375150.00000.1.bfq 3539375150.00022.map 3539375150.00025.1.fastq 3539375150.00021.mismatch 3539375150.00007.unmapped 3539375150.00008.mismatch 3539375150.00021.2.bfq 3539375150.00008.2.bfq 3539375150.00004.unmapped 3539375150.00022.1.bfq 3539375150.00006.2.bfq 3539375150.00001.1.bfq 3539375150.00010.1.bfq 3539375150.00004.1.fastq 3539375150.00006.mismatch 3539375150.00016.1.bfq 3539375150.00011.1.bfq 3539375150.00000.2.bfq 3539375150.00014.unmapped 3539375150.00013.map 3539375150.00025.2.fastq 3539375150.00000.mismatch 3539375150.00014.1.fastq 3539375150.00021.unmapped 3539375150.00017.1.bfq 3539375150.00009.mismatch 2823899437_split1 3539375150.00001.2.bfq 3539375150.00009.2.bfq 3539375150.00002.1.bfq 3539375150.00020.1.bfq 3539375150.00004.2.fastq 3539375150.00001.mismatch 3539375150.00010.mismatch 3539375150.00016.2.bfq 3539375150.00024.mismatch 3539375150.00016.mismatch 3539375150.00005.map 3539375150.00011.2.bfq 3539375150.00012.1.bfq 3539375150.00023.map 3539375150.00024.unmapped 3539375150.00014.2.fastq 3539375150.00019.map 3539375150.00017.2.bfq 3539375150.00026.1.bfq 3539375150.00024.1.fastq 3539375150.00017.mismatch 3539375150.00002.2.bfq 3539375150.00020.2.bfq 3539375150.00009.unmapped 3539375150.00002.mismatch 3539375150.00015.map 3539375150.00020.mismatch 3539375150.00018.1.bfq 3539375150.00006.unmapped 3539375150.00012.2.bfq 3539375150.00012.mismatch 3539375150.00026.2.bfq 3539375150.00024.2.fastq 3539375150.00006.1.fastq 3539375150.00026.mismatch 3539375150.00000.unmapped 3539375150.00003.1.bfq make: Leaving directory `/data/maqgene/work' make: Entering directory `/data/maqgene/work' # Fri Apr 1 07:34:46 BST 2011: Cleaning intermediate data ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 3681587663_snps,3681587663_rel,3681587663_masked_ids,3681587663_rel_intergenic,3681587663_intergenic_assoc,3681587663_offsets,3681587663_codons,3681587663_marked,3681587663_combined,3525956229_pileup" rm -f 3681587663_snps 3681587663_rel 3681587663_masked_ids 3681587663_rel_intergenic 3681587663_intergenic_assoc 3681587663_offsets 3681587663_codons 3681587663_marked 3681587663_combined 3525956229_pileup make: Leaving directory `/data/maqgene/work'