Finished reading input. ++ echo CB6903/./s_5_1_sequence_read1.fastq ++ tr , ' ' + fastq_file_set1=CB6903/./s_5_1_sequence_read1.fastq ++ cd /data/maqgene/reads ++ cat CB6903/./s_5_1_sequence_read1.fastq ++ wc -l ++ cut -f 1 -d ' ' + TOTAL_LINES=146623512 ++ echo '(146623512 / 5000000) + (146623512 % 5000000 != 0)' ++ bc + num_chunks=30 + set +x make -j 14 -l 14 -C /data/maqgene/work --warn-undefined-variables -I /data/maqgene -f /data/maqgene/makefile BFA_FILE=elegans.bfa MAQGENE_GENOME_DIR=/data/maqgene/genomes reads_cksum=1417774392 map_cksum=279513930 pileup_cksum=4186578056 cns_cksum=3239054323 umdd=50000 dmdd=1000 umid=1000 dmid=1000 max_gene_radius=50000 full_results_dir=/data/maqgene/out/example_user/CB6903 outfile_basename=CB6903 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=30 Will process 146623512 lines of input in 30 chunks make: Entering directory `/data/maqgene/work' # Thu Feb 3 22:21:04 GMT 2011: Removing frontend files in case this is a duplicate run ... rm -f /data/maqgene/out/example_user/CB6903/CB6903_{grouped.txt,flat.txt} rm -f /data/maqgene/out/example_user/CB6903/CB6903_uncovered.txt /data/maqgene/out/example_user/CB6903/CB6903_coverage.txt /data/maqgene/out/example_user/CB6903/CB6903_pileup.txt /data/maqgene/out/example_user/CB6903/CB6903_log.txt /data/maqgene/out/example_user/CB6903/CB6903_check.txt /data/maqgene/out/example_user/CB6903/CB6903_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/CB6903/./s_5_1_sequence_read1.fastq) 279513930.1.fastq. split -l 5000000 -a 5 -d <(cat /data/maqgene/reads/CB6903/./s_5_2_sequence_read2.fastq) 279513930.2.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 00027 00028 00029; do mv 279513930.1.fastq.$stem 279513930.$stem.1.fastq; done touch 1417774392_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 00027 00028 00029; do mv 279513930.2.fastq.$stem 279513930.$stem.2.fastq; done touch 1417774392_split2 # Thu Feb 3 22:22:20 GMT 2011: Converting fastq files to bfq ... # Thu Feb 3 22:22:20 GMT 2011: Converting fastq files to bfq ... # Thu Feb 3 22:22:20 GMT 2011: Converting fastq files to bfq ... # Thu Feb 3 22:22:20 GMT 2011: Converting fastq files to bfq ... # Thu Feb 3 22:22:20 GMT 2011: Converting fastq files to bfq ... # Thu Feb 3 22:22:20 GMT 2011: Converting fastq files to bfq ... # Thu Feb 3 22:22:20 GMT 2011: Converting fastq files to bfq ... # Thu Feb 3 22:22:20 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 279513930.00000.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 279513930.00000.1.bfq /data/maqgene/bin/maq sol2sanger 279513930.00001.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 279513930.00001.1.bfq # Thu Feb 3 22:22:20 GMT 2011: Converting fastq files to bfq ... # Thu Feb 3 22:22:20 GMT 2011: Converting fastq files to bfq ... # Thu Feb 3 22:22:20 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 279513930.00002.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 279513930.00002.1.bfq # Thu Feb 3 22:22:20 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 279513930.00003.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 279513930.00003.1.bfq # Thu Feb 3 22:22:20 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 279513930.00004.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 279513930.00004.1.bfq /data/maqgene/bin/maq sol2sanger 279513930.00005.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 279513930.00005.1.bfq /data/maqgene/bin/maq sol2sanger 279513930.00006.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 279513930.00006.1.bfq /data/maqgene/bin/maq sol2sanger 279513930.00007.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 279513930.00007.1.bfq /data/maqgene/bin/maq sol2sanger 279513930.00008.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 279513930.00008.1.bfq /data/maqgene/bin/maq sol2sanger 279513930.00009.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 279513930.00009.1.bfq /data/maqgene/bin/maq sol2sanger 279513930.00010.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 279513930.00010.1.bfq /data/maqgene/bin/maq sol2sanger 279513930.00011.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 279513930.00011.1.bfq /data/maqgene/bin/maq sol2sanger 279513930.00012.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 279513930.00012.1.bfq /data/maqgene/bin/maq sol2sanger 279513930.00013.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 279513930.00013.1.bfq -- finish writing file '279513930.00003.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 22:22:50 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 279513930.00014.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 279513930.00014.1.bfq -- finish writing file '279513930.00001.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 22:22:52 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 279513930.00015.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 279513930.00015.1.bfq -- finish writing file '279513930.00007.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 22:22:52 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 279513930.00016.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 279513930.00016.1.bfq -- finish writing file '279513930.00002.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 22:22:52 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 279513930.00017.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 279513930.00017.1.bfq -- finish writing file '279513930.00009.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 22:22:53 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 279513930.00018.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 279513930.00018.1.bfq -- finish writing file '279513930.00006.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 22:22:53 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 279513930.00019.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 279513930.00019.1.bfq -- finish writing file '279513930.00013.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 22:22:53 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 279513930.00020.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 279513930.00020.1.bfq -- finish writing file '279513930.00008.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 22:22:53 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 279513930.00021.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 279513930.00021.1.bfq -- finish writing file '279513930.00000.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 22:22:54 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 279513930.00022.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 279513930.00022.1.bfq -- finish writing file '279513930.00012.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 22:22:55 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 279513930.00023.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 279513930.00023.1.bfq -- finish writing file '279513930.00010.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 22:22:55 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 279513930.00024.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 279513930.00024.1.bfq -- finish writing file '279513930.00005.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 22:22:56 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 279513930.00025.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 279513930.00025.1.bfq -- finish writing file '279513930.00004.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 22:22:56 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 279513930.00026.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 279513930.00026.1.bfq -- finish writing file '279513930.00011.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 22:22:57 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 279513930.00027.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 279513930.00027.1.bfq -- finish writing file '279513930.00014.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '279513930.00020.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '279513930.00015.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '279513930.00018.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '279513930.00016.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '279513930.00024.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '279513930.00021.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '279513930.00019.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '279513930.00022.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '279513930.00017.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '279513930.00026.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '279513930.00023.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '279513930.00025.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '279513930.00027.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 22:23:29 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 279513930.00010.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 279513930.00010.2.bfq # Thu Feb 3 22:23:35 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 279513930.00011.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 279513930.00011.2.bfq # Thu Feb 3 22:23:35 GMT 2011: Converting fastq files to bfq ... # Thu Feb 3 22:23:35 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 279513930.00009.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 279513930.00009.2.bfq /data/maqgene/bin/maq sol2sanger 279513930.00008.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 279513930.00008.2.bfq # Thu Feb 3 22:23:36 GMT 2011: Converting fastq files to bfq ... # Thu Feb 3 22:23:36 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 279513930.00006.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 279513930.00006.2.bfq /data/maqgene/bin/maq sol2sanger 279513930.00007.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 279513930.00007.2.bfq # Thu Feb 3 22:23:37 GMT 2011: Converting fastq files to bfq ... # Thu Feb 3 22:23:37 GMT 2011: Converting fastq files to bfq ... # Thu Feb 3 22:23:37 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 279513930.00004.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 279513930.00004.2.bfq /data/maqgene/bin/maq sol2sanger 279513930.00005.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 279513930.00005.2.bfq /data/maqgene/bin/maq sol2sanger 279513930.00003.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 279513930.00003.2.bfq # Thu Feb 3 22:23:38 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 279513930.00002.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 279513930.00002.2.bfq # Thu Feb 3 22:23:38 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 279513930.00001.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 279513930.00001.2.bfq # Thu Feb 3 22:23:39 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 279513930.00000.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 279513930.00000.2.bfq # Thu Feb 3 22:23:39 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 279513930.00029.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 279513930.00029.1.bfq # Thu Feb 3 22:23:39 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 279513930.00028.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 279513930.00028.1.bfq -- finish writing file '279513930.00029.1.bfq' -- 405878 sequences were loaded. -- finish writing file '279513930.00010.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '279513930.00011.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '279513930.00006.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '279513930.00008.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '279513930.00009.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '279513930.00001.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '279513930.00007.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '279513930.00004.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '279513930.00002.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '279513930.00005.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '279513930.00028.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '279513930.00003.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '279513930.00000.2.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 22:24:08 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 279513930.00024.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 279513930.00024.2.bfq # Thu Feb 3 22:24:11 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 279513930.00025.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 279513930.00025.2.bfq # Thu Feb 3 22:24:11 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 279513930.00023.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 279513930.00023.2.bfq # Thu Feb 3 22:24:11 GMT 2011: Converting fastq files to bfq ... # Thu Feb 3 22:24:11 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 279513930.00022.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 279513930.00022.2.bfq /data/maqgene/bin/maq sol2sanger 279513930.00021.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 279513930.00021.2.bfq # Thu Feb 3 22:24:12 GMT 2011: Converting fastq files to bfq ... # Thu Feb 3 22:24:12 GMT 2011: Converting fastq files to bfq ... # Thu Feb 3 22:24:12 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 279513930.00020.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 279513930.00020.2.bfq /data/maqgene/bin/maq sol2sanger 279513930.00019.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 279513930.00019.2.bfq /data/maqgene/bin/maq sol2sanger 279513930.00018.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 279513930.00018.2.bfq # Thu Feb 3 22:24:13 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 279513930.00016.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 279513930.00016.2.bfq # Thu Feb 3 22:24:13 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 279513930.00015.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 279513930.00015.2.bfq # Thu Feb 3 22:24:13 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 279513930.00017.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 279513930.00017.2.bfq # Thu Feb 3 22:24:14 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 279513930.00014.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 279513930.00014.2.bfq # Thu Feb 3 22:24:14 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 279513930.00012.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 279513930.00012.2.bfq # Thu Feb 3 22:24:14 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 279513930.00013.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 279513930.00013.2.bfq -- finish writing file '279513930.00024.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '279513930.00021.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '279513930.00023.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '279513930.00022.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '279513930.00019.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '279513930.00025.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '279513930.00016.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '279513930.00017.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '279513930.00020.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '279513930.00018.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '279513930.00012.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '279513930.00013.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '279513930.00015.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '279513930.00014.2.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 22:24:46 GMT 2011: Mapping file(s) 279513930.00008.1.bfq 279513930.00008.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 279513930.00008.unmapped -H 279513930.00008.mismatch \ 279513930.00008.map /data/maqgene/genomes/elegans.bfa 279513930.00008.1.bfq 279513930.00008.2.bfq 2> /dev/null # Thu Feb 3 22:24:51 GMT 2011: Mapping file(s) 279513930.00009.1.bfq 279513930.00009.2.bfq # Thu Feb 3 22:24:51 GMT 2011: Mapping file(s) 279513930.00007.1.bfq 279513930.00007.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 279513930.00009.unmapped -H 279513930.00009.mismatch \ 279513930.00009.map /data/maqgene/genomes/elegans.bfa 279513930.00009.1.bfq 279513930.00009.2.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 279513930.00007.unmapped -H 279513930.00007.mismatch \ 279513930.00007.map /data/maqgene/genomes/elegans.bfa 279513930.00007.1.bfq 279513930.00007.2.bfq 2> /dev/null # Thu Feb 3 22:24:52 GMT 2011: Mapping file(s) 279513930.00006.1.bfq 279513930.00006.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 279513930.00006.unmapped -H 279513930.00006.mismatch \ 279513930.00006.map /data/maqgene/genomes/elegans.bfa 279513930.00006.1.bfq 279513930.00006.2.bfq 2> /dev/null # Thu Feb 3 22:24:53 GMT 2011: Mapping file(s) 279513930.00004.1.bfq 279513930.00004.2.bfq # Thu Feb 3 22:24:53 GMT 2011: Mapping file(s) 279513930.00005.1.bfq 279513930.00005.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 279513930.00004.unmapped -H 279513930.00004.mismatch \ 279513930.00004.map /data/maqgene/genomes/elegans.bfa 279513930.00004.1.bfq 279513930.00004.2.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 279513930.00005.unmapped -H 279513930.00005.mismatch \ 279513930.00005.map /data/maqgene/genomes/elegans.bfa 279513930.00005.1.bfq 279513930.00005.2.bfq 2> /dev/null # Thu Feb 3 22:24:54 GMT 2011: Mapping file(s) 279513930.00003.1.bfq 279513930.00003.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 279513930.00003.unmapped -H 279513930.00003.mismatch \ 279513930.00003.map /data/maqgene/genomes/elegans.bfa 279513930.00003.1.bfq 279513930.00003.2.bfq 2> /dev/null # Thu Feb 3 22:24:55 GMT 2011: Mapping file(s) 279513930.00002.1.bfq 279513930.00002.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 279513930.00002.unmapped -H 279513930.00002.mismatch \ 279513930.00002.map /data/maqgene/genomes/elegans.bfa 279513930.00002.1.bfq 279513930.00002.2.bfq 2> /dev/null # Thu Feb 3 22:24:55 GMT 2011: Mapping file(s) 279513930.00001.1.bfq 279513930.00001.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 279513930.00001.unmapped -H 279513930.00001.mismatch \ 279513930.00001.map /data/maqgene/genomes/elegans.bfa 279513930.00001.1.bfq 279513930.00001.2.bfq 2> /dev/null # Thu Feb 3 22:24:56 GMT 2011: Mapping file(s) 279513930.00000.1.bfq 279513930.00000.2.bfq # Thu Feb 3 22:24:56 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 279513930.00000.unmapped -H 279513930.00000.mismatch \ 279513930.00000.map /data/maqgene/genomes/elegans.bfa 279513930.00000.1.bfq 279513930.00000.2.bfq 2> /dev/null /data/maqgene/bin/maq sol2sanger 279513930.00029.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 279513930.00029.2.bfq # Thu Feb 3 22:24:57 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 279513930.00028.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 279513930.00028.2.bfq # Thu Feb 3 22:24:57 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 279513930.00027.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 279513930.00027.2.bfq # Thu Feb 3 22:24:58 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 279513930.00026.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 279513930.00026.2.bfq -- finish writing file '279513930.00029.2.bfq' -- 405878 sequences were loaded. # Thu Feb 3 22:25:05 GMT 2011: Mapping file(s) 279513930.00010.1.bfq 279513930.00010.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 279513930.00010.unmapped -H 279513930.00010.mismatch \ 279513930.00010.map /data/maqgene/genomes/elegans.bfa 279513930.00010.1.bfq 279513930.00010.2.bfq 2> /dev/null -- finish writing file '279513930.00026.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '279513930.00028.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '279513930.00027.2.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 22:25:56 GMT 2011: Mapping file(s) 279513930.00013.1.bfq 279513930.00013.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 279513930.00013.unmapped -H 279513930.00013.mismatch \ 279513930.00013.map /data/maqgene/genomes/elegans.bfa 279513930.00013.1.bfq 279513930.00013.2.bfq 2> /dev/null # Thu Feb 3 22:25:58 GMT 2011: Mapping file(s) 279513930.00012.1.bfq 279513930.00012.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 279513930.00012.unmapped -H 279513930.00012.mismatch \ 279513930.00012.map /data/maqgene/genomes/elegans.bfa 279513930.00012.1.bfq 279513930.00012.2.bfq 2> /dev/null # Thu Feb 3 22:26:00 GMT 2011: Mapping file(s) 279513930.00011.1.bfq 279513930.00011.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 279513930.00011.unmapped -H 279513930.00011.mismatch \ 279513930.00011.map /data/maqgene/genomes/elegans.bfa 279513930.00011.1.bfq 279513930.00011.2.bfq 2> /dev/null # Thu Feb 3 22:32:32 GMT 2011: Mapping file(s) 279513930.00023.1.bfq 279513930.00023.2.bfq # Thu Feb 3 22:32:32 GMT 2011: Mapping file(s) 279513930.00022.1.bfq 279513930.00022.2.bfq # Thu Feb 3 22:32:32 GMT 2011: Mapping file(s) 279513930.00024.1.bfq 279513930.00024.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 279513930.00023.unmapped -H 279513930.00023.mismatch \ 279513930.00023.map /data/maqgene/genomes/elegans.bfa 279513930.00023.1.bfq 279513930.00023.2.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 279513930.00024.unmapped -H 279513930.00024.mismatch \ 279513930.00024.map /data/maqgene/genomes/elegans.bfa 279513930.00024.1.bfq 279513930.00024.2.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 279513930.00022.unmapped -H 279513930.00022.mismatch \ 279513930.00022.map /data/maqgene/genomes/elegans.bfa 279513930.00022.1.bfq 279513930.00022.2.bfq 2> /dev/null # Thu Feb 3 22:32:33 GMT 2011: Mapping file(s) 279513930.00021.1.bfq 279513930.00021.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 279513930.00021.unmapped -H 279513930.00021.mismatch \ 279513930.00021.map /data/maqgene/genomes/elegans.bfa 279513930.00021.1.bfq 279513930.00021.2.bfq 2> /dev/null # Thu Feb 3 22:32:33 GMT 2011: Mapping file(s) 279513930.00020.1.bfq 279513930.00020.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 279513930.00020.unmapped -H 279513930.00020.mismatch \ 279513930.00020.map /data/maqgene/genomes/elegans.bfa 279513930.00020.1.bfq 279513930.00020.2.bfq 2> /dev/null # Thu Feb 3 22:32:34 GMT 2011: Mapping file(s) 279513930.00019.1.bfq 279513930.00019.2.bfq # Thu Feb 3 22:32:34 GMT 2011: Mapping file(s) 279513930.00018.1.bfq 279513930.00018.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 279513930.00019.unmapped -H 279513930.00019.mismatch \ 279513930.00019.map /data/maqgene/genomes/elegans.bfa 279513930.00019.1.bfq 279513930.00019.2.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 279513930.00018.unmapped -H 279513930.00018.mismatch \ 279513930.00018.map /data/maqgene/genomes/elegans.bfa 279513930.00018.1.bfq 279513930.00018.2.bfq 2> /dev/null # Thu Feb 3 22:32:35 GMT 2011: Mapping file(s) 279513930.00017.1.bfq 279513930.00017.2.bfq # Thu Feb 3 22:32:35 GMT 2011: Mapping file(s) 279513930.00016.1.bfq 279513930.00016.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 279513930.00017.unmapped -H 279513930.00017.mismatch \ 279513930.00017.map /data/maqgene/genomes/elegans.bfa 279513930.00017.1.bfq 279513930.00017.2.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 279513930.00016.unmapped -H 279513930.00016.mismatch \ 279513930.00016.map /data/maqgene/genomes/elegans.bfa 279513930.00016.1.bfq 279513930.00016.2.bfq 2> /dev/null # Thu Feb 3 22:32:36 GMT 2011: Mapping file(s) 279513930.00014.1.bfq 279513930.00014.2.bfq # Thu Feb 3 22:32:36 GMT 2011: Mapping file(s) 279513930.00015.1.bfq 279513930.00015.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 279513930.00014.unmapped -H 279513930.00014.mismatch \ 279513930.00014.map /data/maqgene/genomes/elegans.bfa 279513930.00014.1.bfq 279513930.00014.2.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 279513930.00015.unmapped -H 279513930.00015.mismatch \ 279513930.00015.map /data/maqgene/genomes/elegans.bfa 279513930.00015.1.bfq 279513930.00015.2.bfq 2> /dev/null # Thu Feb 3 22:32:49 GMT 2011: Mapping file(s) 279513930.00025.1.bfq 279513930.00025.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 279513930.00025.unmapped -H 279513930.00025.mismatch \ 279513930.00025.map /data/maqgene/genomes/elegans.bfa 279513930.00025.1.bfq 279513930.00025.2.bfq 2> /dev/null # Thu Feb 3 22:38:48 GMT 2011: Mapping file(s) 279513930.00028.1.bfq 279513930.00028.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 279513930.00028.unmapped -H 279513930.00028.mismatch \ 279513930.00028.map /data/maqgene/genomes/elegans.bfa 279513930.00028.1.bfq 279513930.00028.2.bfq 2> /dev/null # Thu Feb 3 22:38:48 GMT 2011: Mapping file(s) 279513930.00027.1.bfq 279513930.00027.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 279513930.00027.unmapped -H 279513930.00027.mismatch \ 279513930.00027.map /data/maqgene/genomes/elegans.bfa 279513930.00027.1.bfq 279513930.00027.2.bfq 2> /dev/null # Thu Feb 3 22:38:49 GMT 2011: Mapping file(s) 279513930.00026.1.bfq 279513930.00026.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 279513930.00026.unmapped -H 279513930.00026.mismatch \ 279513930.00026.map /data/maqgene/genomes/elegans.bfa 279513930.00026.1.bfq 279513930.00026.2.bfq 2> /dev/null # Thu Feb 3 22:38:50 GMT 2011: Mapping file(s) 279513930.00029.1.bfq 279513930.00029.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 279513930.00029.unmapped -H 279513930.00029.mismatch \ 279513930.00029.map /data/maqgene/genomes/elegans.bfa 279513930.00029.1.bfq 279513930.00029.2.bfq 2> /dev/null # Thu Feb 3 22:43:32 GMT 2011: Merging all maps ... /data/maqgene/bin/maq mapmerge 279513930.map 279513930.00000.map 279513930.00001.map 279513930.00002.map 279513930.00003.map 279513930.00004.map 279513930.00005.map 279513930.00006.map 279513930.00007.map 279513930.00008.map 279513930.00009.map 279513930.00010.map 279513930.00011.map 279513930.00012.map 279513930.00013.map 279513930.00014.map 279513930.00015.map 279513930.00016.map 279513930.00017.map 279513930.00018.map 279513930.00019.map 279513930.00020.map 279513930.00021.map 279513930.00022.map 279513930.00023.map 279513930.00024.map 279513930.00025.map 279513930.00026.map 279513930.00027.map 279513930.00028.map 279513930.00029.map # Thu Feb 3 22:43:32 GMT 2011: Merging all *.unmapped files ... cat 279513930.00000.unmapped 279513930.00001.unmapped 279513930.00002.unmapped 279513930.00003.unmapped 279513930.00004.unmapped 279513930.00005.unmapped 279513930.00006.unmapped 279513930.00007.unmapped 279513930.00008.unmapped 279513930.00009.unmapped 279513930.00010.unmapped 279513930.00011.unmapped 279513930.00012.unmapped 279513930.00013.unmapped 279513930.00014.unmapped 279513930.00015.unmapped 279513930.00016.unmapped 279513930.00017.unmapped 279513930.00018.unmapped 279513930.00019.unmapped 279513930.00020.unmapped 279513930.00021.unmapped 279513930.00022.unmapped 279513930.00023.unmapped 279513930.00024.unmapped 279513930.00025.unmapped 279513930.00026.unmapped 279513930.00027.unmapped 279513930.00028.unmapped 279513930.00029.unmapped > 279513930_unmapped.txt # Thu Feb 3 22:43:33 GMT 2011: Linking backend file 279513930_unmapped.txt to /data/maqgene/out/example_user/CB6903/CB6903_unmapped.txt ln -fs /data/maqgene/work/279513930_unmapped.txt /data/maqgene/out/example_user/CB6903/CB6903_unmapped.txt /data/maqgene/makefile:126: warning: undefined variable `mapcheck_parameters' # Thu Feb 3 22:55:46 GMT 2011: Creating pileup ... # Thu Feb 3 22:55:46 GMT 2011: Generating consensus ... # Thu Feb 3 22:55:46 GMT 2011: Running 'mapcheck' ... /data/maqgene/bin/maq pileup -Q 100 -p -m 7 -q 0 /data/maqgene/genomes/elegans.bfa 279513930.map > 4186578056_pileup.txt /data/maqgene/bin/maq assemble -N 2 -q 0 -r 0.0 -m 7 -Q 100 -p 3239054323.cns \ /data/maqgene/genomes/elegans.bfa 279513930.map 2> 3239054323_log.txt /data/maqgene/bin/maq mapcheck /data/maqgene/genomes/elegans.bfa 279513930.map > 279513930_check.txt \ 2>/dev/null # Thu Feb 3 23:03:08 GMT 2011: Linking backend file 4186578056_pileup.txt to /data/maqgene/out/example_user/CB6903/CB6903_pileup.txt ln -fs /data/maqgene/work/4186578056_pileup.txt /data/maqgene/out/example_user/CB6903/CB6903_pileup.txt # Thu Feb 3 23:03:08 GMT 2011: Linking backend file 3239054323_log.txt to /data/maqgene/out/example_user/CB6903/CB6903_log.txt ln -fs /data/maqgene/work/3239054323_log.txt /data/maqgene/out/example_user/CB6903/CB6903_log.txt # Thu Feb 3 23:03:08 GMT 2011: Making coverage histogram ... (echo -en "sequencing_depth\tnumber_of_bases\n"; \ cut -f 4 4186578056_pileup.txt \ | /data/maqgene/bin/pileup_histogram 100) > 4186578056_coverage.txt # Thu Feb 3 23:03:58 GMT 2011: Getting uncovered regions ... cut -f 1,2,4 4186578056_pileup.txt \ | /data/maqgene/bin/get_uncovered_regions 50 \ > 4186578056_uncovered.txt # Thu Feb 3 23:05:03 GMT 2011: Linking backend file 4186578056_coverage.txt to /data/maqgene/out/example_user/CB6903/CB6903_coverage.txt ln -fs /data/maqgene/work/4186578056_coverage.txt /data/maqgene/out/example_user/CB6903/CB6903_coverage.txt # Thu Feb 3 23:05:03 GMT 2011: Linking backend file 4186578056_uncovered.txt to /data/maqgene/out/example_user/CB6903/CB6903_uncovered.txt ln -fs /data/maqgene/work/4186578056_uncovered.txt /data/maqgene/out/example_user/CB6903/CB6903_uncovered.txt /data/maqgene/bin/filter_matching_lines 4186578056_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 \ > 4186578056_known_snps # Thu Feb 3 23:05:40 GMT 2011: Linking backend file 279513930_check.txt to /data/maqgene/out/example_user/CB6903/CB6903_check.txt ln -fs /data/maqgene/work/279513930_check.txt /data/maqgene/out/example_user/CB6903/CB6903_check.txt # Thu Feb 3 23:05:40 GMT 2011: Filtering and loading pileup for analysis ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 4186578056_pileup; create table 4186578056_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 4186578056_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 4186578056_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 4186578056_pileup" cat 4186578056_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 4186578056_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 4186578056_pileup" touch 4186578056_pileup # Thu Feb 3 23:07:02 GMT 2011: Extracting point mutants from consensus ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 3239054323_snps; create table 3239054323_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 3239054323.cns \ | cat -b | /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "load data local infile '/dev/stdin' into table 3239054323_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 3239054323_snps;" # Thu Feb 3 23:07:21 GMT 2011: Extracting indels from consensus ... /data/maqgene/bin/maq indelsoa /data/maqgene/genomes/elegans.bfa 279513930.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 3239054323_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 3239054323_snps;" # Thu Feb 3 23:10:10 GMT 2011: Adding placeholders for known SNPs. cat 4186578056_known_snps \ | /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "load data local infile '/dev/stdin' ignore into table 3239054323_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 3239054323_snps;" Found 161461 variants. touch 3239054323_snps # Thu Feb 3 23:10:13 GMT 2011: Writing snp read counts ... /usr/bin/mysql -Dmaqgenedb -umaqgene --skip-column-names --batch --raw --local-infile --column-names -e "select f.id, f.dna, f.start + 1 start, e.snp_name, e.snp_base, if(e.snp_base = 'a', p.A_fwd + p.A_rev, if (e.snp_base = 'c', p.C_fwd + p.C_rev, if (e.snp_base = 'g', p.G_fwd + p.G_rev, if (e.snp_base = 't', p.T_fwd + p.T_rev, -1)))) snp_reads, p.ref_base, p.wt_fwd + p.wt_rev wt_reads, p.read_depth, p.sample_reads from elegans_features f join elegans_snp_changes e on (f.attribute = e.snp_name) join 4186578056_pileup p using (dna,start)" > /data/maqgene/out/example_user/CB6903/CB6903_snp_read_counts.txt 0 snp read count lines written. # Thu Feb 3 23:10:13 GMT 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 3239054323_masked_ids; create table 3239054323_masked_ids (query_region_id int(10) NOT NULL, primary key (query_region_id)); load data local infile '/dev/stdin' ignore into table 3239054323_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 3239054323_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; touch 3239054323_masked_ids # Thu Feb 3 23:10:17 GMT 2011: Finding all genomic features overlapping variants... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 3239054323_rel_snps; CREATE TABLE 3239054323_rel_snps ( association_id INT(10) NOT NULL, query_region_id INT(10) unsigned NOT NULL, target_region_id INT(10) NOT NULL, distance INT(10) NOT NULL, overlap INT(10) NOT NULL, same_strand enum('SAME', 'OPP') NOT NULL, num_regions_between INT(3) NOT NULL, PRIMARY KEY (association_id), KEY (query_region_id), KEY (target_region_id) )" /data/maqgene/bin/associate_regions -b -1 -c -1000000 -m 0 -o >(/usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "load data local infile '/dev/stdin' into table 3239054323_rel_snps; flush table 3239054323_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 3239054323_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 # Thu Feb 3 23:10:17 GMT 2011: Loading uncovered regions into table ... cat 4186578056_uncovered.txt \ | /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 4186578056_uncovered; create table 4186578056_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 = 161462; load data local infile '/dev/stdin' into table 4186578056_uncovered (dna, start, end)" Uncovered region statistics: chromosome number_uncovered_regions total_uncovered_length I 15 2391 II 20 2696 III 18 1715 IV 17 1617 MtDNA 1 130 V 21 2140 X 19 6210 touch 4186578056_uncovered # Thu Feb 3 23:10:17 GMT 2011: Finding mRNA features overlapping uncovered regions ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 4186578056_uncovered_rel; CREATE TABLE 4186578056_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 4186578056_uncovered_rel; flush table 4186578056_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 4186578056_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 4186578056_uncovered_rel touch 3239054323_rel_snps # Thu Feb 3 23:10:23 GMT 2011: Calculating translation start offsets for uncovered regions... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 4186578056_offsets_uncovered; create table 4186578056_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 4186578056_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 4186578056_uncovered reg join 4186578056_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 4186578056_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 4186578056_uncovered reg join 4186578056_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 4186578056_offsets_uncovered # Thu Feb 3 23:10:23 GMT 2011: Getting intergenic regions /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 3239054323_rel_intergenic; create table 3239054323_rel_intergenic like 3239054323_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 3239054323_rel_intergenic; flush table 3239054323_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 3239054323_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; # Thu Feb 3 23:10:31 GMT 2011: Filtering masked intergenic regions /usr/bin/mysql -Dmaqgenedb -umaqgene --skip-column-names --batch --raw --local-infile -e "delete i.* from 3239054323_rel_intergenic i join 3239054323_masked_ids m using (query_region_id)" touch 3239054323_rel_intergenic # Thu Feb 3 23:10:37 GMT 2011: Calculating translation start offsets... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 3239054323_offsets_snps; create table 3239054323_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) );" /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 3239054323_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 3239054323_snps reg join 3239054323_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" touch 3239054323_offsets_snps # Thu Feb 3 23:11:00 GMT 2011: Classifying intergenic relations /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 3239054323_intergenic_assoc; create table 3239054323_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 3239054323_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 3239054323_snps snp join 3239054323_rel_intergenic rel on (snp.id = rel.query_region_id) join elegans_features feature on (rel.target_region_id = feature.id)" touch 3239054323_intergenic_assoc # Thu Feb 3 23:11:13 GMT 2011: Getting codons affected by point mutations... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 3239054323_codons; create table 3239054323_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 3239054323_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 3239054323_offsets_snps off join 3239054323_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 3239054323_codons /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 3239054323_marked; create table 3239054323_marked ( id int(10) NOT NULL, class varchar(100) NOT NULL, description varchar(100) NOT NULL, parent_feature varchar(100) NOT NULL, primary key (id, class, parent_feature) );" # Thu Feb 3 23:11:23 GMT 2011: Finding exonic indels ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 3239054323_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 3239054323_snps snp join 3239054323_rel_snps rel on (snp.id = rel.query_region_id) join elegans_features feature on (rel.target_region_id = feature.id) where feature.feature = 'exon' and snp.variant_type = 'indel';" # Thu Feb 3 23:11:24 GMT 2011: Finding coding variants ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 3239054323_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 3239054323_codons trans join elegans_genetic_code reference_codons on (trans.ref_codon = reference_codons.codon) join elegans_genetic_code sample_codons on (trans.sam_codon = sample_codons.codon);" # Thu Feb 3 23:11:24 GMT 2011: Finding noncoding variants ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 3239054323_marked select snp.id, feature.feature class, 'none' description, feature.attribute parent_feature from 3239054323_snps snp join 3239054323_rel_snps rel on (snp.id = rel.query_region_id) join elegans_features feature on (rel.target_region_id = feature.id) where feature.feature not in ('exon', 'intron', 'mRNA');" # Thu Feb 3 23:11:25 GMT 2011: Finding splice site variants ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 3239054323_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 3239054323_snps snp join 3239054323_rel_snps rel on (snp.id = rel.query_region_id) join elegans_features feature on (rel.target_region_id = feature.id) where feature.feature = 'intron' and rel.distance > -2;" # Thu Feb 3 23:11:25 GMT 2011: Finding intergenic and intronic variants ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 3239054323_marked select id, 'nongenic' class, concat(if (relation in ('upstream','into'), - distance, distance),' ',relation) description, attribute from 3239054323_intergenic_assoc where ((relation = 'upstream' and num_regions_between = 0 and distance < 50000) or (relation = 'upstream' and num_regions_between < 2 and distance < 1000) or (relation = 'downstream' and num_regions_between = 0 and distance < 1000) or (relation = 'downstream' and num_regions_between < 2 and distance < 1000) or relation = 'into' );" # Thu Feb 3 23:11:29 GMT 2011: Finding uncovered regions in genes ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 3239054323_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 4186578056_uncovered unc join 4186578056_offsets_uncovered b using (id) join 4186578056_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 4186578056_uncovered unc join 4186578056_offsets_uncovered b using (id) join 4186578056_offsets_uncovered e using (id, gene) join elegans_features gene on (e.gene = gene.attribute) where b.boundary_type = 'start' and e.boundary_type = 'end' and gene.strand = '-' and gene.feature = 'mRNA'" # Thu Feb 3 23:11:29 GMT 2011: Variants found: +-----------------+-----------------+ | class | number_variants | +-----------------+-----------------+ | five_prime_UTR | 1301 | | frameshift | 70 | | inframe | 16 | | missense | 6231 | | ncRNA | 860 | | nongenic | 124863 | | non_start | 10 | | premature_stop | 689 | | readthrough | 19 | | silent | 7438 | | SNP | 1033 | | splice_acceptor | 45 | | splice_donor | 47 | | three_prime_UTR | 3547 | | uncovered | 32 | +-----------------+-----------------+ touch 3239054323_marked # Thu Feb 3 23:11:31 GMT 2011: Combining results ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 3239054323_combined; create table 3239054323_combined (primary key (id, class, description), key (dna, start)) as select snp.id, 'CB6903' 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 3239054323_snps snp join 4186578056_pileup pile using (dna,start) join 3239054323_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, 'CB6903' 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 4186578056_uncovered unc join 3239054323_marked class on (unc.id = class.id) left join elegans_per_locus using (dna,start) group by id, class, description; alter table 3239054323_combined order by dna, start, length" touch 3239054323_combined # Thu Feb 3 23:11:36 GMT 2011: Writing results to grouped file ... /usr/bin/mysql -Dmaqgenedb -umaqgene --skip-column-names --batch --raw --local-infile --column-names -e "select id, mutant_strain, dna, start, length, reference_base, sample_base, consensus_score, loci_multiplicity, mapping_quality, neighbor_quality, number_wildtype_reads, number_variant_reads, sequencing_depth, sample_reads, variant_type, indel_size, group_concat(class) classes, group_concat(description) descriptions, group_concat(concat('{',parent_features,'}')) parent_features from 3239054323_combined group by id order by dna, start;" > /data/maqgene/out/example_user/CB6903/CB6903_grouped.txt 2283 lines written. # Thu Feb 3 23:11:36 GMT 2011: Writing results to flat file ... /usr/bin/mysql -Dmaqgenedb -umaqgene --skip-column-names --batch --raw --local-infile --column-names -e "select * from 3239054323_combined" > /data/maqgene/out/example_user/CB6903/CB6903_flat.txt 3781 lines written. rm 279513930.00004.1.fastq 279513930.00006.mismatch 279513930.00027.map 279513930.00016.1.bfq 279513930.00012.unmapped 279513930.00000.2.bfq 279513930.00014.unmapped 279513930.00029.1.bfq 279513930.00013.map 279513930.00025.2.fastq 279513930.00004.mismatch 279513930.00014.1.fastq 279513930.00017.1.bfq 279513930.00001.2.bfq 279513930.00010.2.bfq 279513930.00002.1.bfq 279513930.00004.2.fastq 279513930.00001.mismatch 279513930.00010.mismatch 279513930.00016.2.bfq 279513930.00028.map 279513930.00016.mismatch 279513930.00005.map 279513930.00029.2.bfq 279513930.00011.2.bfq 279513930.00012.1.bfq 279513930.00029.mismatch 279513930.00023.map 279513930.00011.mismatch 279513930.00024.unmapped 279513930.00014.2.fastq 279513930.00019.map 279513930.00017.2.bfq 279513930.00026.1.bfq 279513930.00024.1.fastq 279513930.00017.mismatch 279513930.00011.1.bfq 279513930.00002.2.bfq 279513930.00020.2.bfq 279513930.00002.mismatch 279513930.00015.map 279513930.00020.mismatch 279513930.00022.unmapped 279513930.00007.1.fastq 279513930.00006.unmapped 279513930.00012.2.bfq 279513930.00022.1.bfq 279513930.00012.mismatch 279513930.00015.1.fastq 279513930.00006.1.fastq 279513930.00026.2.bfq 279513930.00024.2.fastq 279513930.00026.mismatch 279513930.00000.unmapped 279513930.00003.1.bfq 279513930.00018.2.bfq 279513930.00027.1.bfq 279513930.00000.1.fastq 279513930.00018.mismatch 279513930.00007.map 279513930.00021.1.fastq 279513930.00025.map 279513930.00026.unmapped 279513930.00001.unmapped 279513930.00010.unmapped 279513930.00008.1.fastq 279513930.00022.2.bfq 279513930.00013.1.bfq 279513930.00016.unmapped 279513930.00022.mismatch 279513930.00006.2.fastq 279513930.00001.1.fastq 279513930.00010.1.fastq 279513930.00013.mismatch 279513930.00029.unmapped 279513930.00016.1.fastq 279513930.00004.map 279513930.00003.2.bfq 279513930.00011.unmapped 279513930.00002.map 279513930.00003.mismatch 279513930.00027.2.bfq 279513930.00005.1.bfq 279513930.00000.2.fastq 279513930.00029.1.fastq 279513930.00027.mismatch 279513930.00011.1.fastq 279513930.00017.unmapped 279513930.00000.mismatch 279513930.00028.1.bfq 279513930.00024.2.bfq 279513930.00021.map 279513930.00002.unmapped 279513930.00020.unmapped 279513930.00013.2.bfq 279513930.00008.map 279513930.00017.1.fastq 279513930.00014.map 279513930.00023.1.bfq 279513930.00001.2.fastq 279513930.00010.2.fastq 279513930.00002.1.fastq 279513930.00020.1.fastq 279513930.00019.1.bfq 279513930.00016.2.fastq 279513930.00020.1.bfq 279513930.00007.2.fastq 279513930.00015.1.bfq 279513930.00029.2.fastq 279513930.00011.2.fastq 279513930.00012.1.fastq 279513930.00018.1.bfq 1417774392_split1 279513930.00005.mismatch 279513930.00007.1.bfq 279513930.00017.2.fastq 279513930.00007.2.bfq 279513930.00026.1.fastq 279513930.00023.2.bfq 279513930.00018.unmapped 279513930.00002.2.fastq 279513930.00009.map 279513930.00020.2.fastq 279513930.00023.mismatch 279513930.00024.map 279513930.00019.2.bfq 279513930.00018.1.fastq 279513930.00019.mismatch 279513930.00021.2.fastq 279513930.00009.1.bfq 279513930.00008.2.fastq 279513930.00015.2.bfq 279513930.00014.2.bfq 279513930.00012.2.fastq 279513930.00015.mismatch 279513930.00022.1.fastq 279513930.00003.unmapped 279513930.00025.1.bfq 279513930.00026.2.fastq 279513930.00021.1.bfq 279513930.00009.1.fastq 279513930.00027.unmapped 279513930.00008.1.bfq 279513930.00003.1.fastq 279513930.00005.2.bfq 279513930.00028.2.bfq 279513930.00018.2.fastq 279513930.00027.1.fastq 279513930.00028.mismatch 279513930.00004.1.bfq 279513930.00013.unmapped 279513930.00000.map 279513930.00009.2.fastq 279513930.00022.2.fastq 279513930.00025.2.bfq 279513930.00025.mismatch 279513930.00001.map 279513930.00010.map 279513930.00014.1.bfq 279513930.00003.2.fastq 279513930.00016.map 1417774392_split2 279513930.00005.unmapped 279513930.00027.2.fastq 279513930.00004.2.bfq 279513930.00007.mismatch 279513930.00005.1.fastq 279513930.00029.map 279513930.00011.map 279513930.00023.unmapped 279513930.00013.2.fastq 279513930.00019.unmapped 279513930.00023.1.fastq 279513930.00017.map 279513930.00019.1.fastq 279513930.00020.map 279513930.00015.unmapped 279513930.00014.mismatch 279513930.00024.1.bfq 279513930.00013.1.fastq 279513930.00005.2.fastq 279513930.00021.mismatch 279513930.00007.unmapped 279513930.00012.map 279513930.00008.mismatch 279513930.00021.2.bfq 279513930.00008.2.bfq 279513930.00028.unmapped 279513930.00023.2.fastq 279513930.00026.map 279513930.00006.map 279513930.00019.2.fastq 279513930.00028.1.fastq 279513930.00006.1.bfq 279513930.00018.map 279513930.00009.unmapped 279513930.00015.2.fastq 279513930.00024.mismatch 279513930.00025.unmapped 279513930.00000.1.bfq 279513930.00022.map 279513930.00021.unmapped 279513930.00009.2.bfq 279513930.00025.1.fastq 279513930.00008.unmapped 279513930.00009.mismatch 279513930.00004.unmapped 279513930.00028.2.fastq 279513930.00003.map 279513930.00006.2.bfq 279513930.00001.1.bfq 279513930.00010.1.bfq make: Leaving directory `/data/maqgene/work' make: Entering directory `/data/maqgene/work' # Thu Feb 3 23:11:37 GMT 2011: Cleaning intermediate data ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 3239054323_snps,3239054323_rel,3239054323_masked_ids,3239054323_rel_intergenic,3239054323_intergenic_assoc,3239054323_offsets,3239054323_codons,3239054323_marked,3239054323_combined,4186578056_pileup" rm -f 3239054323_snps 3239054323_rel 3239054323_masked_ids 3239054323_rel_intergenic 3239054323_intergenic_assoc 3239054323_offsets 3239054323_codons 3239054323_marked 3239054323_combined 4186578056_pileup make: Leaving directory `/data/maqgene/work'