Finished reading input. ++ echo CB6633/./WTCHG_15226_read1.fastq ++ tr , ' ' + fastq_file_set1=CB6633/./WTCHG_15226_read1.fastq ++ cd /data/maqgene/reads ++ cat CB6633/./WTCHG_15226_read1.fastq ++ wc -l ++ cut -f 1 -d ' ' + TOTAL_LINES=148480900 ++ echo '(148480900 / 5000000) + (148480900 % 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=237322051 map_cksum=2492407019 pileup_cksum=1782228453 cns_cksum=1575301867 umdd=50000 dmdd=1000 umid=1000 dmid=1000 max_gene_radius=50000 full_results_dir=/data/maqgene/out/example_user/CB6633 outfile_basename=CB6633 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 148480900 lines of input in 30 chunks make: Entering directory `/data/maqgene/work' # Thu Apr 28 10:03:45 BST 2011: Removing frontend files in case this is a duplicate run ... rm -f /data/maqgene/out/example_user/CB6633/CB6633_{grouped.txt,flat.txt} rm -f /data/maqgene/out/example_user/CB6633/CB6633_uncovered.txt /data/maqgene/out/example_user/CB6633/CB6633_coverage.txt /data/maqgene/out/example_user/CB6633/CB6633_pileup.txt /data/maqgene/out/example_user/CB6633/CB6633_log.txt /data/maqgene/out/example_user/CB6633/CB6633_check.txt /data/maqgene/out/example_user/CB6633/CB6633_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/CB6633/./WTCHG_15226_read1.fastq) 2492407019.1.fastq. # : Regrouping fastq reads into chunks of size 5000000. split -l 5000000 -a 5 -d <(cat /data/maqgene/reads/CB6633/./WTCHG_15226_read2.fastq) 2492407019.2.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 2492407019.1.fastq.$stem 2492407019.$stem.1.fastq; done touch 237322051_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 2492407019.2.fastq.$stem 2492407019.$stem.2.fastq; done touch 237322051_split2 # Thu Apr 28 10:04:50 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2492407019.00000.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2492407019.00000.1.bfq # Thu Apr 28 10:04:50 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2492407019.00001.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2492407019.00001.1.bfq # Thu Apr 28 10:04:50 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2492407019.00002.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2492407019.00002.1.bfq # Thu Apr 28 10:04:50 BST 2011: Converting fastq files to bfq ... # Thu Apr 28 10:04:50 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2492407019.00003.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2492407019.00003.1.bfq /data/maqgene/bin/maq sol2sanger 2492407019.00004.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2492407019.00004.1.bfq # Thu Apr 28 10:04:50 BST 2011: Converting fastq files to bfq ... # Thu Apr 28 10:04:50 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2492407019.00005.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2492407019.00005.1.bfq /data/maqgene/bin/maq sol2sanger 2492407019.00006.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2492407019.00006.1.bfq # Thu Apr 28 10:04:50 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2492407019.00007.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2492407019.00007.1.bfq # Thu Apr 28 10:04:50 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2492407019.00010.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2492407019.00010.1.bfq # Thu Apr 28 10:04:50 BST 2011: Converting fastq files to bfq ... # Thu Apr 28 10:04:50 BST 2011: Converting fastq files to bfq ... # Thu Apr 28 10:04:50 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2492407019.00008.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2492407019.00008.1.bfq /data/maqgene/bin/maq sol2sanger 2492407019.00011.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2492407019.00011.1.bfq /data/maqgene/bin/maq sol2sanger 2492407019.00012.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2492407019.00012.1.bfq # Thu Apr 28 10:04:50 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2492407019.00013.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2492407019.00013.1.bfq # Thu Apr 28 10:04:50 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2492407019.00009.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2492407019.00009.1.bfq -- finish writing file '2492407019.00011.1.bfq' -- 1250000 sequences were loaded. # Thu Apr 28 10:05:11 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2492407019.00014.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2492407019.00014.1.bfq -- finish writing file '2492407019.00009.1.bfq' -- 1250000 sequences were loaded. # Thu Apr 28 10:05:13 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2492407019.00015.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2492407019.00015.1.bfq -- finish writing file '2492407019.00000.1.bfq' -- 1250000 sequences were loaded. # Thu Apr 28 10:05:16 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2492407019.00016.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2492407019.00016.1.bfq -- finish writing file '2492407019.00005.1.bfq' -- 1250000 sequences were loaded. # Thu Apr 28 10:05:17 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2492407019.00017.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2492407019.00017.1.bfq -- finish writing file '2492407019.00008.1.bfq' -- 1250000 sequences were loaded. # Thu Apr 28 10:05:17 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2492407019.00018.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2492407019.00018.1.bfq -- finish writing file '2492407019.00003.1.bfq' -- 1250000 sequences were loaded. # Thu Apr 28 10:05:18 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2492407019.00019.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2492407019.00019.1.bfq -- finish writing file '2492407019.00013.1.bfq' -- 1250000 sequences were loaded. # Thu Apr 28 10:05:18 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2492407019.00020.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2492407019.00020.1.bfq -- finish writing file '2492407019.00007.1.bfq' -- 1250000 sequences were loaded. # Thu Apr 28 10:05:19 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2492407019.00021.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2492407019.00021.1.bfq -- finish writing file '2492407019.00004.1.bfq' -- 1250000 sequences were loaded. # Thu Apr 28 10:05:19 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2492407019.00022.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2492407019.00022.1.bfq -- finish writing file '2492407019.00006.1.bfq' -- 1250000 sequences were loaded. # Thu Apr 28 10:05:19 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2492407019.00023.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2492407019.00023.1.bfq -- finish writing file '2492407019.00001.1.bfq' -- 1250000 sequences were loaded. # Thu Apr 28 10:05:20 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2492407019.00024.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2492407019.00024.1.bfq -- finish writing file '2492407019.00010.1.bfq' -- 1250000 sequences were loaded. # Thu Apr 28 10:05:20 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2492407019.00025.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2492407019.00025.1.bfq -- finish writing file '2492407019.00012.1.bfq' -- 1250000 sequences were loaded. # Thu Apr 28 10:05:21 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2492407019.00026.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2492407019.00026.1.bfq -- finish writing file '2492407019.00002.1.bfq' -- 1250000 sequences were loaded. # Thu Apr 28 10:05:21 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2492407019.00027.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2492407019.00027.1.bfq -- finish writing file '2492407019.00014.1.bfq' -- 1250000 sequences were loaded. # Thu Apr 28 10:05:40 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2492407019.00028.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2492407019.00028.1.bfq -- finish writing file '2492407019.00015.1.bfq' -- 1250000 sequences were loaded. # Thu Apr 28 10:05:41 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2492407019.00029.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2492407019.00029.1.bfq -- finish writing file '2492407019.00017.1.bfq' -- 1250000 sequences were loaded. # Thu Apr 28 10:05:44 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2492407019.00000.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2492407019.00000.2.bfq -- finish writing file '2492407019.00016.1.bfq' -- 1250000 sequences were loaded. # Thu Apr 28 10:05:46 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2492407019.00001.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2492407019.00001.2.bfq -- finish writing file '2492407019.00021.1.bfq' -- 1250000 sequences were loaded. # Thu Apr 28 10:05:47 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2492407019.00002.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2492407019.00002.2.bfq -- finish writing file '2492407019.00020.1.bfq' -- 1250000 sequences were loaded. # Thu Apr 28 10:05:47 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2492407019.00003.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2492407019.00003.2.bfq -- finish writing file '2492407019.00018.1.bfq' -- 1250000 sequences were loaded. # Thu Apr 28 10:05:47 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2492407019.00004.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2492407019.00004.2.bfq -- finish writing file '2492407019.00022.1.bfq' -- 1250000 sequences were loaded. # Thu Apr 28 10:05:48 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2492407019.00005.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2492407019.00005.2.bfq -- finish writing file '2492407019.00019.1.bfq' -- 1250000 sequences were loaded. # Thu Apr 28 10:05:48 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2492407019.00006.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2492407019.00006.2.bfq -- finish writing file '2492407019.00026.1.bfq' -- 1250000 sequences were loaded. # Thu Apr 28 10:05:49 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2492407019.00007.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2492407019.00007.2.bfq -- finish writing file '2492407019.00023.1.bfq' -- 1250000 sequences were loaded. # Thu Apr 28 10:05:49 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2492407019.00008.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2492407019.00008.2.bfq -- finish writing file '2492407019.00024.1.bfq' -- 1250000 sequences were loaded. # Thu Apr 28 10:05:50 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2492407019.00009.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2492407019.00009.2.bfq -- finish writing file '2492407019.00027.1.bfq' -- 1250000 sequences were loaded. # Thu Apr 28 10:05:50 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2492407019.00010.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2492407019.00010.2.bfq -- finish writing file '2492407019.00025.1.bfq' -- 1250000 sequences were loaded. # Thu Apr 28 10:05:51 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2492407019.00011.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2492407019.00011.2.bfq -- finish writing file '2492407019.00029.1.bfq' -- 870225 sequences were loaded. -- finish writing file '2492407019.00007.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '2492407019.00028.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2492407019.00003.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '2492407019.00000.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '2492407019.00004.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '2492407019.00002.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '2492407019.00001.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '2492407019.00010.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '2492407019.00008.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '2492407019.00009.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '2492407019.00011.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '2492407019.00006.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '2492407019.00005.2.bfq' -- 1250000 sequences were loaded. # Thu Apr 28 10:06:16 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2492407019.00024.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2492407019.00024.2.bfq # Thu Apr 28 10:06:17 BST 2011: Converting fastq files to bfq ... # Thu Apr 28 10:06:17 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2492407019.00023.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2492407019.00023.2.bfq /data/maqgene/bin/maq sol2sanger 2492407019.00025.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2492407019.00025.2.bfq # Thu Apr 28 10:06:18 BST 2011: Converting fastq files to bfq ... # Thu Apr 28 10:06:18 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2492407019.00021.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2492407019.00021.2.bfq /data/maqgene/bin/maq sol2sanger 2492407019.00022.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2492407019.00022.2.bfq # Thu Apr 28 10:06:19 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2492407019.00020.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2492407019.00020.2.bfq # Thu Apr 28 10:06:19 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2492407019.00019.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2492407019.00019.2.bfq # Thu Apr 28 10:06:20 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2492407019.00017.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2492407019.00017.2.bfq # Thu Apr 28 10:06:20 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2492407019.00018.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2492407019.00018.2.bfq # Thu Apr 28 10:06:21 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2492407019.00016.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2492407019.00016.2.bfq # Thu Apr 28 10:06:21 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2492407019.00015.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2492407019.00015.2.bfq # Thu Apr 28 10:06:22 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2492407019.00014.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2492407019.00014.2.bfq # Thu Apr 28 10:06:23 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2492407019.00013.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2492407019.00013.2.bfq # Thu Apr 28 10:06:24 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2492407019.00012.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2492407019.00012.2.bfq -- finish writing file '2492407019.00022.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '2492407019.00024.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '2492407019.00025.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '2492407019.00023.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '2492407019.00021.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '2492407019.00013.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '2492407019.00014.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '2492407019.00020.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '2492407019.00017.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '2492407019.00019.2.bfq' -- 1250000 sequences were loaded. # Thu Apr 28 10:06:47 BST 2011: Mapping file(s) 2492407019.00005.1.bfq 2492407019.00005.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 2492407019.00005.unmapped -H 2492407019.00005.mismatch \ 2492407019.00005.map /data/maqgene/genomes/elegans.bfa 2492407019.00005.1.bfq 2492407019.00005.2.bfq 2> /dev/null -- finish writing file '2492407019.00018.2.bfq' -- 1250000 sequences were loaded. # Thu Apr 28 10:06:47 BST 2011: Mapping file(s) 2492407019.00004.1.bfq 2492407019.00004.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 2492407019.00004.unmapped -H 2492407019.00004.mismatch \ 2492407019.00004.map /data/maqgene/genomes/elegans.bfa 2492407019.00004.1.bfq 2492407019.00004.2.bfq 2> /dev/null -- finish writing file '2492407019.00015.2.bfq' -- 1250000 sequences were loaded. # Thu Apr 28 10:06:47 BST 2011: Mapping file(s) 2492407019.00006.1.bfq 2492407019.00006.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 2492407019.00006.unmapped -H 2492407019.00006.mismatch \ 2492407019.00006.map /data/maqgene/genomes/elegans.bfa 2492407019.00006.1.bfq 2492407019.00006.2.bfq 2> /dev/null -- finish writing file '2492407019.00016.2.bfq' -- 1250000 sequences were loaded. # Thu Apr 28 10:06:48 BST 2011: Mapping file(s) 2492407019.00007.1.bfq 2492407019.00007.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 2492407019.00007.unmapped -H 2492407019.00007.mismatch \ 2492407019.00007.map /data/maqgene/genomes/elegans.bfa 2492407019.00007.1.bfq 2492407019.00007.2.bfq 2> /dev/null -- finish writing file '2492407019.00012.2.bfq' -- 1250000 sequences were loaded. # Thu Apr 28 10:06:48 BST 2011: Mapping file(s) 2492407019.00008.1.bfq 2492407019.00008.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 2492407019.00008.unmapped -H 2492407019.00008.mismatch \ 2492407019.00008.map /data/maqgene/genomes/elegans.bfa 2492407019.00008.1.bfq 2492407019.00008.2.bfq 2> /dev/null # Thu Apr 28 10:06:49 BST 2011: Mapping file(s) 2492407019.00009.1.bfq 2492407019.00009.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 2492407019.00009.unmapped -H 2492407019.00009.mismatch \ 2492407019.00009.map /data/maqgene/genomes/elegans.bfa 2492407019.00009.1.bfq 2492407019.00009.2.bfq 2> /dev/null # Thu Apr 28 10:06:50 BST 2011: Mapping file(s) 2492407019.00003.1.bfq 2492407019.00003.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 2492407019.00003.unmapped -H 2492407019.00003.mismatch \ 2492407019.00003.map /data/maqgene/genomes/elegans.bfa 2492407019.00003.1.bfq 2492407019.00003.2.bfq 2> /dev/null # Thu Apr 28 10:06:51 BST 2011: Mapping file(s) 2492407019.00002.1.bfq 2492407019.00002.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 2492407019.00002.unmapped -H 2492407019.00002.mismatch \ 2492407019.00002.map /data/maqgene/genomes/elegans.bfa 2492407019.00002.1.bfq 2492407019.00002.2.bfq 2> /dev/null # Thu Apr 28 10:06:53 BST 2011: Mapping file(s) 2492407019.00001.1.bfq 2492407019.00001.2.bfq # Thu Apr 28 10:06:53 BST 2011: Mapping file(s) 2492407019.00000.1.bfq 2492407019.00000.2.bfq 00001.unmapped -H 2492407019.00001.mismatch \ 2492407019.00001.map /data/maqgene/genomes/elegans.bfa 2492407019.00001.1.bfq 2492407019.00001.2.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 2492407019.00000.unmapped -H 2492407019.00000.mismatch \ 2492407019.00000.map /data/maqgene/genomes/elegans.bfa 2492407019.00000.1.bfq 2492407019.00000.2.bfq 2> /dev/null # Thu Apr 28 10:06:53 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2492407019.00029.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2492407019.00029.2.bfq # Thu Apr 28 10:06:53 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2492407019.00028.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2492407019.00028.2.bfq # Thu Apr 28 10:06:54 BST 2011: Converting fastq files to bfq ... # Thu Apr 28 10:06:54 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2492407019.00027.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2492407019.00027.2.bfq /data/maqgene/bin/maq sol2sanger 2492407019.00026.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2492407019.00026.2.bfq -- finish writing file '2492407019.00029.2.bfq' -- 870225 sequences were loaded. -- finish writing file '2492407019.00028.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '2492407019.00027.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '2492407019.00026.2.bfq' -- 1250000 sequences were loaded. # Thu Apr 28 10:07:28 BST 2011: Mapping file(s) 2492407019.00013.1.bfq 2492407019.00013.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 2492407019.00013.unmapped -H 2492407019.00013.mismatch \ 2492407019.00013.map /data/maqgene/genomes/elegans.bfa 2492407019.00013.1.bfq 2492407019.00013.2.bfq 2> /dev/null # Thu Apr 28 10:07:29 BST 2011: Mapping file(s) 2492407019.00012.1.bfq 2492407019.00012.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 2492407019.00012.unmapped -H 2492407019.00012.mismatch \ 2492407019.00012.map /data/maqgene/genomes/elegans.bfa 2492407019.00012.1.bfq 2492407019.00012.2.bfq 2> /dev/null # Thu Apr 28 10:07:30 BST 2011: Mapping file(s) 2492407019.00011.1.bfq 2492407019.00011.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 2492407019.00011.unmapped -H 2492407019.00011.mismatch \ 2492407019.00011.map /data/maqgene/genomes/elegans.bfa 2492407019.00011.1.bfq 2492407019.00011.2.bfq 2> /dev/null # Thu Apr 28 10:07:31 BST 2011: Mapping file(s) 2492407019.00010.1.bfq 2492407019.00010.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 2492407019.00010.unmapped -H 2492407019.00010.mismatch \ 2492407019.00010.map /data/maqgene/genomes/elegans.bfa 2492407019.00010.1.bfq 2492407019.00010.2.bfq 2> /dev/null # Thu Apr 28 10:13:34 BST 2011: Mapping file(s) 2492407019.00020.1.bfq 2492407019.00020.2.bfq # Thu Apr 28 10:13:34 BST 2011: Mapping file(s) 2492407019.00019.1.bfq 2492407019.00019.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 2492407019.00020.unmapped -H 2492407019.00020.mismatch \ 2492407019.00020.map /data/maqgene/genomes/elegans.bfa 2492407019.00020.1.bfq 2492407019.00020.2.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 2492407019.00019.unmapped -H 2492407019.00019.mismatch \ 2492407019.00019.map /data/maqgene/genomes/elegans.bfa 2492407019.00019.1.bfq 2492407019.00019.2.bfq 2> /dev/null # Thu Apr 28 10:13:35 BST 2011: Mapping file(s) 2492407019.00018.1.bfq 2492407019.00018.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 2492407019.00018.unmapped -H 2492407019.00018.mismatch \ 2492407019.00018.map /data/maqgene/genomes/elegans.bfa 2492407019.00018.1.bfq 2492407019.00018.2.bfq 2> /dev/null # Thu Apr 28 10:13:36 BST 2011: Mapping file(s) 2492407019.00017.1.bfq 2492407019.00017.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 2492407019.00017.unmapped -H 2492407019.00017.mismatch \ 2492407019.00017.map /data/maqgene/genomes/elegans.bfa 2492407019.00017.1.bfq 2492407019.00017.2.bfq 2> /dev/null # Thu Apr 28 10:13:36 BST 2011: Mapping file(s) 2492407019.00016.1.bfq 2492407019.00016.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 2492407019.00016.unmapped -H 2492407019.00016.mismatch \ 2492407019.00016.map /data/maqgene/genomes/elegans.bfa 2492407019.00016.1.bfq 2492407019.00016.2.bfq 2> /dev/null # Thu Apr 28 10:13:37 BST 2011: Mapping file(s) 2492407019.00021.1.bfq 2492407019.00021.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 2492407019.00021.unmapped -H 2492407019.00021.mismatch \ 2492407019.00021.map /data/maqgene/genomes/elegans.bfa 2492407019.00021.1.bfq 2492407019.00021.2.bfq 2> /dev/null # Thu Apr 28 10:13:38 BST 2011: Mapping file(s) 2492407019.00015.1.bfq 2492407019.00015.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 2492407019.00015.unmapped -H 2492407019.00015.mismatch \ 2492407019.00015.map /data/maqgene/genomes/elegans.bfa 2492407019.00015.1.bfq 2492407019.00015.2.bfq 2> /dev/null # Thu Apr 28 10:13:38 BST 2011: Mapping file(s) 2492407019.00014.1.bfq 2492407019.00014.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 2492407019.00014.unmapped -H 2492407019.00014.mismatch \ 2492407019.00014.map /data/maqgene/genomes/elegans.bfa 2492407019.00014.1.bfq 2492407019.00014.2.bfq 2> /dev/null # Thu Apr 28 10:13:38 BST 2011: Mapping file(s) 2492407019.00022.1.bfq 2492407019.00022.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 2492407019.00022.unmapped -H 2492407019.00022.mismatch \ 2492407019.00022.map /data/maqgene/genomes/elegans.bfa 2492407019.00022.1.bfq 2492407019.00022.2.bfq 2> /dev/null # Thu Apr 28 10:13:47 BST 2011: Mapping file(s) 2492407019.00023.1.bfq 2492407019.00023.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 2492407019.00023.unmapped -H 2492407019.00023.mismatch \ 2492407019.00023.map /data/maqgene/genomes/elegans.bfa 2492407019.00023.1.bfq 2492407019.00023.2.bfq 2> /dev/null # Thu Apr 28 10:14:28 BST 2011: Mapping file(s) 2492407019.00027.1.bfq 2492407019.00027.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 2492407019.00027.unmapped -H 2492407019.00027.mismatch \ 2492407019.00027.map /data/maqgene/genomes/elegans.bfa 2492407019.00027.1.bfq 2492407019.00027.2.bfq 2> /dev/null # Thu Apr 28 10:14:29 BST 2011: Mapping file(s) 2492407019.00026.1.bfq 2492407019.00026.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 2492407019.00026.unmapped -H 2492407019.00026.mismatch \ 2492407019.00026.map /data/maqgene/genomes/elegans.bfa 2492407019.00026.1.bfq 2492407019.00026.2.bfq 2> /dev/null # Thu Apr 28 10:14:30 BST 2011: Mapping file(s) 2492407019.00025.1.bfq 2492407019.00025.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 2492407019.00025.unmapped -H 2492407019.00025.mismatch \ 2492407019.00025.map /data/maqgene/genomes/elegans.bfa 2492407019.00025.1.bfq 2492407019.00025.2.bfq 2> /dev/null # Thu Apr 28 10:14:31 BST 2011: Mapping file(s) 2492407019.00024.1.bfq 2492407019.00024.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 2492407019.00024.unmapped -H 2492407019.00024.mismatch \ 2492407019.00024.map /data/maqgene/genomes/elegans.bfa 2492407019.00024.1.bfq 2492407019.00024.2.bfq 2> /dev/null # Thu Apr 28 10:20:17 BST 2011: Mapping file(s) 2492407019.00029.1.bfq 2492407019.00029.2.bfq # Thu Apr 28 10:20:17 BST 2011: Mapping file(s) 2492407019.00028.1.bfq 2492407019.00028.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 2492407019.00029.unmapped -H 2492407019.00029.mismatch \ 2492407019.00029.map /data/maqgene/genomes/elegans.bfa 2492407019.00029.1.bfq 2492407019.00029.2.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 2492407019.00028.unmapped -H 2492407019.00028.mismatch \ 2492407019.00028.map /data/maqgene/genomes/elegans.bfa 2492407019.00028.1.bfq 2492407019.00028.2.bfq 2> /dev/null # Thu Apr 28 10:24:55 BST 2011: Merging all maps ... # Thu Apr 28 10:24:55 BST 2011: Merging all *.unmapped files ... /data/maqgene/bin/maq mapmerge 2492407019.map 2492407019.00000.map 2492407019.00001.map 2492407019.00002.map 2492407019.00003.map 2492407019.00004.map 2492407019.00005.map 2492407019.00006.map 2492407019.00007.map 2492407019.00008.map 2492407019.00009.map 2492407019.00010.map 2492407019.00011.map 2492407019.00012.map 2492407019.00013.map 2492407019.00014.map 2492407019.00015.map 2492407019.00016.map 2492407019.00017.map 2492407019.00018.map 2492407019.00019.map 2492407019.00020.map 2492407019.00021.map 2492407019.00022.map 2492407019.00023.map 2492407019.00024.map 2492407019.00025.map 2492407019.00026.map 2492407019.00027.map 2492407019.00028.map 2492407019.00029.map cat 2492407019.00000.unmapped 2492407019.00001.unmapped 2492407019.00002.unmapped 2492407019.00003.unmapped 2492407019.00004.unmapped 2492407019.00005.unmapped 2492407019.00006.unmapped 2492407019.00007.unmapped 2492407019.00008.unmapped 2492407019.00009.unmapped 2492407019.00010.unmapped 2492407019.00011.unmapped 2492407019.00012.unmapped 2492407019.00013.unmapped 2492407019.00014.unmapped 2492407019.00015.unmapped 2492407019.00016.unmapped 2492407019.00017.unmapped 2492407019.00018.unmapped 2492407019.00019.unmapped 2492407019.00020.unmapped 2492407019.00021.unmapped 2492407019.00022.unmapped 2492407019.00023.unmapped 2492407019.00024.unmapped 2492407019.00025.unmapped 2492407019.00026.unmapped 2492407019.00027.unmapped 2492407019.00028.unmapped 2492407019.00029.unmapped > 2492407019_unmapped.txt # Thu Apr 28 10:24:56 BST 2011: Linking backend file 2492407019_unmapped.txt to /data/maqgene/out/example_user/CB6633/CB6633_unmapped.txt ln -fs /data/maqgene/work/2492407019_unmapped.txt /data/maqgene/out/example_user/CB6633/CB6633_unmapped.txt /data/maqgene/makefile:126: warning: undefined variable `mapcheck_parameters' # Thu Apr 28 10:36:11 BST 2011: Generating consensus ... # Thu Apr 28 10:36:11 BST 2011: Creating pileup ... /data/maqgene/bin/maq assemble -N 2 -q 0 -r 0.0 -m 7 -Q 100 -p 1575301867.cns \ /data/maqgene/genomes/elegans.bfa 2492407019.map 2> 1575301867_log.txt /data/maqgene/bin/maq pileup -Q 100 -p -m 7 -q 0 /data/maqgene/genomes/elegans.bfa 2492407019.map > 1782228453_pileup.txt /data/maqgene/bin/maq mapcheck /data/maqgene/genomes/elegans.bfa 2492407019.map > 2492407019_check.txt \ 2>/dev/null # Thu Apr 28 10:39:13 BST 2011: Linking backend file 2492407019_check.txt to /data/maqgene/out/example_user/CB6633/CB6633_check.txt ln -fs /data/maqgene/work/2492407019_check.txt /data/maqgene/out/example_user/CB6633/CB6633_check.txt /data/maqgene/bin/filter_matching_lines 1782228453_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 \ > 1782228453_known_snps # Thu Apr 28 10:39:39 BST 2011: Getting uncovered regions ... # Thu Apr 28 10:39:39 BST 2011: Making coverage histogram ... cut -f 1,2,4 1782228453_pileup.txt \ | /data/maqgene/bin/get_uncovered_regions 50 \ > 1782228453_uncovered.txt # Thu Apr 28 10:39:39 BST 2011: Linking backend file 1782228453_pileup.txt to /data/maqgene/out/example_user/CB6633/CB6633_pileup.txt (echo -en "sequencing_depth\tnumber_of_bases\n"; \ cut -f 4 1782228453_pileup.txt \ | /data/maqgene/bin/pileup_histogram 100) > 1782228453_coverage.txt ln -fs /data/maqgene/work/1782228453_pileup.txt /data/maqgene/out/example_user/CB6633/CB6633_pileup.txt # Thu Apr 28 10:39:58 BST 2011: Linking backend file 1782228453_coverage.txt to /data/maqgene/out/example_user/CB6633/CB6633_coverage.txt ln -fs /data/maqgene/work/1782228453_coverage.txt /data/maqgene/out/example_user/CB6633/CB6633_coverage.txt # Thu Apr 28 10:40:07 BST 2011: Filtering and loading pileup for analysis ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 1782228453_pileup; create table 1782228453_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 1782228453_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 1782228453_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 1782228453_pileup" # Thu Apr 28 10:40:08 BST 2011: Linking backend file 1782228453_uncovered.txt to /data/maqgene/out/example_user/CB6633/CB6633_uncovered.txt ln -fs /data/maqgene/work/1782228453_uncovered.txt /data/maqgene/out/example_user/CB6633/CB6633_uncovered.txt cat 1782228453_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 1782228453_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 1782228453_pileup" touch 1782228453_pileup # Thu Apr 28 10:40:57 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 1782228453_pileup p using (dna,start)" > /data/maqgene/out/example_user/CB6633/CB6633_snp_read_counts.txt 0 snp read count lines written. # Thu Apr 28 10:41:17 BST 2011: Extracting point mutants from consensus ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 1575301867_snps; create table 1575301867_snps ( id int(10) NOT NULL auto_increment, dna char(40) NOT NULL, start int(10) NOT NULL, end int(10) NOT NULL, indel_size int(5) NOT NULL, variant_type enum('indel', 'point') NOT NULL, ref_base char NOT NULL, sample_base char NOT NULL, snp_score int(5) NOT NULL, read_depth int(5) NOT NULL, loci_multiplicity double(5,2) NOT NULL, mapping_quality int(5) NOT NULL, neighbor_quality int(5) NOT NULL, primary key (id), unique key (dna, start), key (indel_size) )" ln -fs /data/maqgene/work/1575301867_log.txt /data/maqgene/out/example_user/CB6633/CB6633_log.txt /data/maqgene/bin/maq cns2snp 1575301867.cns \ | cat -b | /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "load data local infile '/dev/stdin' into table 1575301867_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 1575301867_snps;" # Thu Apr 28 10:41:31 BST 2011: Extracting indels from consensus ... /data/maqgene/bin/maq indelsoa /data/maqgene/genomes/elegans.bfa 2492407019.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 1575301867_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 1575301867_snps;" # Thu Apr 28 10:43:21 BST 2011: Adding placeholders for known SNPs. cat 1782228453_known_snps \ | /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "load data local infile '/dev/stdin' ignore into table 1575301867_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 1575301867_snps;" Found 163317 variants. touch 1575301867_snps # Thu Apr 28 10:43:22 BST 2011: Loading uncovered regions into table ... # Thu Apr 28 10:43:22 BST 2011: Finding all genomic features overlapping variants... cat 1782228453_uncovered.txt \ | /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 1782228453_uncovered; create table 1782228453_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 = 163318; load data local infile '/dev/stdin' into table 1782228453_uncovered (dna, start, end)" /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 1575301867_rel_snps; CREATE TABLE 1575301867_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 2 -o >(/usr/bin/mysql -Dmaqgenedb -umaqgene --skip-column-names --batch --raw --local-infile -e "drop table if exists 1575301867_masked_ids; create table 1575301867_masked_ids (query_region_id int(10) NOT NULL, primary key (query_region_id)); load data local infile '/dev/stdin' ignore into table 1575301867_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 1575301867_snps") -t <(/usr/bin/mysql -Dmaqgenedb -umaqgene --skip-column-names --batch --raw --local-infile -e "select id,'elegans',dna,start,end,strand from elegans_features feature where feature.feature not in ('mRNA', 'intron')") 1>/dev/null; /data/maqgene/bin/associate_regions -b -1 -c -1000000 -m 0 -o >(/usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "load data local infile '/dev/stdin' into table 1575301867_rel_snps; flush table 1575301867_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 1575301867_snps") -t <(/usr/bin/mysql -Dmaqgenedb -umaqgene --skip-column-names --batch --raw --local-infile -e "select id, 'elegans', dna,start,end,strand from elegans_features where feature in ('SNP','exon','five_prime_UTR','intron','mRNA','three_prime_UTR','ncRNA')") 1>/dev/null Uncovered region statistics: chromosome number_uncovered_regions total_uncovered_length I 1740 234545 II 1433 201341 III 1778 229591 IV 1628 189002 V 1586 196456 X 496 57349 touch 1782228453_uncovered # Thu Apr 28 10:43:23 BST 2011: Finding mRNA features overlapping uncovered regions ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 1782228453_uncovered_rel; CREATE TABLE 1782228453_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 1782228453_uncovered_rel; flush table 1782228453_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 1782228453_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 1575301867_masked_ids touch 1782228453_uncovered_rel # Thu Apr 28 10:43:25 BST 2011: Calculating translation start offsets for uncovered regions... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 1782228453_offsets_uncovered; create table 1782228453_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 1782228453_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 1782228453_uncovered reg join 1782228453_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 1575301867_rel_snps # Thu Apr 28 10:43:26 BST 2011: Calculating translation start offsets... # Thu Apr 28 10:43:26 BST 2011: Getting intergenic regions /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 1575301867_offsets_snps; create table 1575301867_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 "drop table if exists 1575301867_rel_intergenic; create table 1575301867_rel_intergenic like 1575301867_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 1575301867_rel_intergenic; flush table 1575301867_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 1575301867_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 1575301867_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 1575301867_snps reg join 1575301867_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" /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 1782228453_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 1782228453_uncovered reg join 1782228453_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 1782228453_offsets_uncovered # Thu Apr 28 10:43:29 BST 2011: Filtering masked intergenic regions /usr/bin/mysql -Dmaqgenedb -umaqgene --skip-column-names --batch --raw --local-infile -e "delete i.* from 1575301867_rel_intergenic i join 1575301867_masked_ids m using (query_region_id)" touch 1575301867_rel_intergenic # Thu Apr 28 10:43:33 BST 2011: Classifying intergenic relations /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 1575301867_intergenic_assoc; create table 1575301867_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 1575301867_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 1575301867_snps snp join 1575301867_rel_intergenic rel on (snp.id = rel.query_region_id) join elegans_features feature on (rel.target_region_id = feature.id)" touch 1575301867_intergenic_assoc touch 1575301867_offsets_snps # Thu Apr 28 10:43:43 BST 2011: Getting codons affected by point mutations... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 1575301867_codons; create table 1575301867_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 1575301867_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 1575301867_offsets_snps off join 1575301867_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 1575301867_codons /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 1575301867_marked; create table 1575301867_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 Apr 28 10:43:50 BST 2011: Finding exonic indels ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 1575301867_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 1575301867_snps snp join 1575301867_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 Apr 28 10:43:50 BST 2011: Finding coding variants ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 1575301867_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 1575301867_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 Apr 28 10:43:51 BST 2011: Finding noncoding variants ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 1575301867_marked select snp.id, feature.feature class, 'none' description, feature.attribute parent_feature from 1575301867_snps snp join 1575301867_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 Apr 28 10:43:51 BST 2011: Finding splice site variants ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 1575301867_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 1575301867_snps snp join 1575301867_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 Apr 28 10:43:51 BST 2011: Finding intergenic and intronic variants ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 1575301867_marked select id, 'nongenic' class, concat(if (relation in ('upstream','into'), - distance, distance),' ',relation) description, attribute from 1575301867_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 Apr 28 10:43:54 BST 2011: Finding uncovered regions in genes ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 1575301867_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 1782228453_uncovered unc join 1782228453_offsets_uncovered b using (id) join 1782228453_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 1782228453_uncovered unc join 1782228453_offsets_uncovered b using (id) join 1782228453_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 Apr 28 10:43:54 BST 2011: Variants found: +-----------------+-----------------+ | class | number_variants | +-----------------+-----------------+ | five_prime_UTR | 1293 | | frameshift | 75 | | inframe | 18 | | missense | 6178 | | ncRNA | 889 | | nongenic | 126589 | | non_start | 10 | | premature_stop | 690 | | readthrough | 19 | | silent | 7428 | | SNP | 1016 | | splice_acceptor | 47 | | splice_donor | 46 | | three_prime_UTR | 3584 | | uncovered | 5195 | +-----------------+-----------------+ touch 1575301867_marked # Thu Apr 28 10:43:55 BST 2011: Combining results ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 1575301867_combined; create table 1575301867_combined (primary key (id, class, description), key (dna, start)) as select snp.id, 'CB6633' 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 1575301867_snps snp join 1782228453_pileup pile using (dna,start) join 1575301867_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, 'CB6633' 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 1782228453_uncovered unc join 1575301867_marked class on (unc.id = class.id) left join elegans_per_locus using (dna,start) group by id, class, description; alter table 1575301867_combined order by dna, start, length" touch 1575301867_combined # Thu Apr 28 10:43:57 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 1575301867_combined group by id order by dna, start;" > /data/maqgene/out/example_user/CB6633/CB6633_grouped.txt # Thu Apr 28 10:43:57 BST 2011: Writing results to flat file ... /usr/bin/mysql -Dmaqgenedb -umaqgene --skip-column-names --batch --raw --local-infile --column-names -e "select * from 1575301867_combined" > /data/maqgene/out/example_user/CB6633/CB6633_flat.txt 9360 lines written. 6812 lines written. rm 2492407019.00021.2.bfq 2492407019.00002.2.fastq 2492407019.00020.2.fastq 2492407019.00023.mismatch 2492407019.00024.map 2492407019.00019.2.bfq 237322051_split1 2492407019.00028.1.bfq 2492407019.00018.1.fastq 2492407019.00019.mismatch 2492407019.00022.unmapped 2492407019.00015.2.bfq 2492407019.00010.1.bfq 2492407019.00012.2.fastq 2492407019.00015.mismatch 2492407019.00022.1.fastq 2492407019.00009.unmapped 2492407019.00003.unmapped 2492407019.00025.1.bfq 2492407019.00026.2.fastq 2492407019.00006.map 2492407019.00007.2.fastq 2492407019.00003.1.fastq 2492407019.00008.1.bfq 2492407019.00028.2.bfq 2492407019.00018.2.fastq 2492407019.00027.1.fastq 2492407019.00028.mismatch 2492407019.00004.1.bfq 2492407019.00013.unmapped 2492407019.00000.map 2492407019.00022.2.fastq 2492407019.00025.2.bfq 2492407019.00014.mismatch 2492407019.00025.mismatch 2492407019.00001.map 2492407019.00010.map 2492407019.00014.1.bfq 2492407019.00014.2.bfq 2492407019.00003.2.fastq 2492407019.00016.map 2492407019.00027.2.fastq 2492407019.00007.1.fastq 2492407019.00004.2.bfq 2492407019.00008.mismatch 2492407019.00005.1.fastq 2492407019.00004.mismatch 2492407019.00029.map 2492407019.00011.map 2492407019.00023.unmapped 237322051_split2 2492407019.00013.2.fastq 2492407019.00019.unmapped 2492407019.00023.1.fastq 2492407019.00017.map 2492407019.00000.unmapped 2492407019.00019.1.fastq 2492407019.00002.map 2492407019.00020.map 2492407019.00015.unmapped 2492407019.00024.1.bfq 2492407019.00015.1.fastq 2492407019.00007.map 2492407019.00021.1.fastq 2492407019.00005.2.fastq 2492407019.00011.1.bfq 2492407019.00008.1.fastq 2492407019.00012.map 2492407019.00028.unmapped 2492407019.00023.2.fastq 2492407019.00026.map 2492407019.00019.2.fastq 2492407019.00028.1.fastq 2492407019.00006.1.bfq 2492407019.00005.1.bfq 2492407019.00018.map 2492407019.00024.2.bfq 2492407019.00015.2.fastq 2492407019.00024.mismatch 2492407019.00025.unmapped 2492407019.00021.map 2492407019.00008.map 2492407019.00000.1.bfq 2492407019.00022.map 2492407019.00025.1.fastq 2492407019.00009.1.fastq 2492407019.00009.mismatch 2492407019.00004.unmapped 2492407019.00028.2.fastq 2492407019.00006.2.bfq 2492407019.00004.1.fastq 2492407019.00006.mismatch 2492407019.00027.map 2492407019.00016.1.bfq 2492407019.00013.1.fastq 2492407019.00007.1.bfq 2492407019.00000.2.bfq 2492407019.00014.unmapped 2492407019.00029.1.bfq 2492407019.00013.map 2492407019.00025.2.fastq 2492407019.00027.mismatch 2492407019.00000.mismatch 2492407019.00009.map 2492407019.00014.1.fastq 2492407019.00017.1.bfq 2492407019.00021.2.fastq 2492407019.00001.2.bfq 2492407019.00010.2.bfq 2492407019.00002.1.bfq 2492407019.00008.2.fastq 2492407019.00020.1.bfq 2492407019.00001.mismatch 2492407019.00010.mismatch 2492407019.00016.2.bfq 2492407019.00016.mismatch 2492407019.00005.map 2492407019.00029.2.bfq 2492407019.00011.2.bfq 2492407019.00021.1.bfq 2492407019.00012.1.bfq 2492407019.00029.mismatch 2492407019.00023.map 2492407019.00011.mismatch 2492407019.00024.unmapped 2492407019.00005.2.bfq 2492407019.00014.2.fastq 2492407019.00027.unmapped 2492407019.00019.map 2492407019.00017.2.bfq 2492407019.00026.1.bfq 2492407019.00024.1.fastq 2492407019.00017.mismatch 2492407019.00002.2.bfq 2492407019.00020.2.bfq 2492407019.00002.mismatch 2492407019.00015.map 2492407019.00018.1.bfq 2492407019.00009.2.fastq 2492407019.00020.mismatch 2492407019.00006.unmapped 2492407019.00012.2.bfq 2492407019.00022.1.bfq 2492407019.00012.mismatch 2492407019.00006.1.fastq 2492407019.00009.1.bfq 2492407019.00028.map 2492407019.00026.2.bfq 2492407019.00024.2.fastq 2492407019.00007.mismatch 2492407019.00026.mismatch 2492407019.00003.1.bfq 2492407019.00007.2.bfq 2492407019.00011.unmapped 2492407019.00018.2.bfq 2492407019.00027.1.bfq 2492407019.00004.2.fastq 2492407019.00005.unmapped 2492407019.00000.1.fastq 2492407019.00018.mismatch 2492407019.00025.map 2492407019.00001.unmapped 2492407019.00010.unmapped 2492407019.00022.2.bfq 2492407019.00013.1.bfq 2492407019.00003.map 2492407019.00016.unmapped 2492407019.00022.mismatch 2492407019.00006.2.fastq 2492407019.00001.1.fastq 2492407019.00010.1.fastq 2492407019.00016.1.fastq 2492407019.00004.map 2492407019.00003.2.bfq 2492407019.00029.unmapped 2492407019.00021.mismatch 2492407019.00007.unmapped 2492407019.00003.mismatch 2492407019.00027.2.bfq 2492407019.00008.2.bfq 2492407019.00000.2.fastq 2492407019.00029.1.fastq 2492407019.00011.1.fastq 2492407019.00017.unmapped 2492407019.00001.1.bfq 2492407019.00002.unmapped 2492407019.00020.unmapped 2492407019.00013.2.bfq 2492407019.00017.1.fastq 2492407019.00014.map 2492407019.00023.1.bfq 2492407019.00013.mismatch 2492407019.00001.2.fastq 2492407019.00010.2.fastq 2492407019.00002.1.fastq 2492407019.00020.1.fastq 2492407019.00019.1.bfq 2492407019.00016.2.fastq 2492407019.00012.unmapped 2492407019.00021.unmapped 2492407019.00015.1.bfq 2492407019.00029.2.fastq 2492407019.00008.unmapped 2492407019.00011.2.fastq 2492407019.00012.1.fastq 2492407019.00026.unmapped 2492407019.00009.2.bfq 2492407019.00005.mismatch 2492407019.00017.2.fastq 2492407019.00026.1.fastq 2492407019.00023.2.bfq 2492407019.00018.unmapped make: Leaving directory `/data/maqgene/work' make: Entering directory `/data/maqgene/work' # Thu Apr 28 10:44:00 BST 2011: Cleaning intermediate data ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 1575301867_snps,1575301867_rel,1575301867_masked_ids,1575301867_rel_intergenic,1575301867_intergenic_assoc,1575301867_offsets,1575301867_codons,1575301867_marked,1575301867_combined,1782228453_pileup" rm -f 1575301867_snps 1575301867_rel 1575301867_masked_ids 1575301867_rel_intergenic 1575301867_intergenic_assoc 1575301867_offsets 1575301867_codons 1575301867_marked 1575301867_combined 1782228453_pileup make: Leaving directory `/data/maqgene/work'