Finished reading input. ++ echo hyp-3/./s_s_1_sequence_read1.fastq ++ tr , ' ' + fastq_file_set1=hyp-3/./s_s_1_sequence_read1.fastq ++ cd /data/maqgene/reads ++ cat hyp-3/./s_s_1_sequence_read1.fastq ++ wc -l ++ cut -f 1 -d ' ' + TOTAL_LINES=238789852 ++ echo '(238789852 / 5000000) + (238789852 % 5000000 != 0)' ++ bc + num_chunks=48 + 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=2310056006 map_cksum=1801671628 pileup_cksum=2162726738 cns_cksum=619536435 umdd=50000 dmdd=1000 umid=1000 dmid=1000 max_gene_radius=50000 full_results_dir=/data/maqgene/out/example_user/hyp_3 outfile_basename=hyp_3 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=48 Will process 238789852 lines of input in 48 chunks make: Entering directory `/data/maqgene/work' # Wed Mar 28 13:32:26 BST 2012: Removing frontend files in case this is a duplicate run ... rm -f /data/maqgene/out/example_user/hyp_3/hyp_3_{grouped.txt,flat.txt} rm -f /data/maqgene/out/example_user/hyp_3/hyp_3_uncovered.txt /data/maqgene/out/example_user/hyp_3/hyp_3_coverage.txt /data/maqgene/out/example_user/hyp_3/hyp_3_pileup.txt /data/maqgene/out/example_user/hyp_3/hyp_3_log.txt /data/maqgene/out/example_user/hyp_3/hyp_3_check.txt /data/maqgene/out/example_user/hyp_3/hyp_3_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/hyp-3/./s_s_1_sequence_read1.fastq) 1801671628.1.fastq. # : Regrouping fastq reads into chunks of size 5000000. split -l 5000000 -a 5 -d <(cat /data/maqgene/reads/hyp-3/./s_s_2_sequence_read2.fastq) 1801671628.2.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 00030 00031 00032 00033 00034 00035 00036 00037 00038 00039 00040 00041 00042 00043 00044 00045 00046 00047; do mv 1801671628.1.fastq.$stem 1801671628.$stem.1.fastq; done touch 2310056006_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 00030 00031 00032 00033 00034 00035 00036 00037 00038 00039 00040 00041 00042 00043 00044 00045 00046 00047; do mv 1801671628.2.fastq.$stem 1801671628.$stem.2.fastq; done touch 2310056006_split2 # Wed Mar 28 13:34:52 BST 2012: Converting fastq files to bfq ... # Wed Mar 28 13:34:52 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1801671628.00000.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00000.1.bfq # Wed Mar 28 13:34:52 BST 2012: Converting fastq files to bfq ... # Wed Mar 28 13:34:52 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1801671628.00001.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00001.1.bfq /data/maqgene/bin/maq sol2sanger 1801671628.00002.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00002.1.bfq /data/maqgene/bin/maq sol2sanger 1801671628.00003.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00003.1.bfq /data/maqgene/bin/maq sol2sanger 1801671628.00004.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00004.1.bfq # Wed Mar 28 13:34:53 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1801671628.00011.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00011.1.bfq # Wed Mar 28 13:34:53 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1801671628.00012.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00012.1.bfq # Wed Mar 28 13:34:53 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1801671628.00013.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00013.1.bfq # Wed Mar 28 13:34:54 BST 2012: Converting fastq files to bfq ... # Wed Mar 28 13:34:54 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1801671628.00008.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00008.1.bfq /data/maqgene/bin/maq sol2sanger 1801671628.00010.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00010.1.bfq /data/maqgene/bin/maq sol2sanger 1801671628.00009.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00009.1.bfq # Wed Mar 28 13:34:55 BST 2012: Converting fastq files to bfq ... # Wed Mar 28 13:34:55 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1801671628.00007.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00007.1.bfq /data/maqgene/bin/maq sol2sanger 1801671628.00005.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00005.1.bfq # Wed Mar 28 13:34:55 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1801671628.00006.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00006.1.bfq -- finish writing file '1801671628.00013.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1801671628.00007.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1801671628.00001.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1801671628.00004.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1801671628.00012.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1801671628.00000.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1801671628.00010.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1801671628.00008.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1801671628.00002.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1801671628.00003.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1801671628.00011.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1801671628.00009.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1801671628.00005.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1801671628.00006.1.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 13:35:21 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1801671628.00026.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00026.1.bfq -- finish writing file '1801671628.00026.1.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 13:35:34 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1801671628.00027.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00027.1.bfq -- finish writing file '1801671628.00027.1.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 13:35:46 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1801671628.00028.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00028.1.bfq -- finish writing file '1801671628.00028.1.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 13:35:57 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1801671628.00029.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00029.1.bfq -- finish writing file '1801671628.00029.1.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 13:36:09 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1801671628.00030.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00030.1.bfq -- finish writing file '1801671628.00030.1.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 13:36:19 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1801671628.00031.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00031.1.bfq -- finish writing file '1801671628.00031.1.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 13:36:30 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1801671628.00032.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00032.1.bfq # Wed Mar 28 13:36:41 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1801671628.00033.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00033.1.bfq -- finish writing file '1801671628.00032.1.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 13:36:42 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1801671628.00025.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00025.1.bfq # Wed Mar 28 13:36:44 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1801671628.00034.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00034.1.bfq # Wed Mar 28 13:36:46 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1801671628.00024.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00024.1.bfq # Wed Mar 28 13:36:48 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1801671628.00023.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00023.1.bfq # Wed Mar 28 13:36:50 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1801671628.00022.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00022.1.bfq -- finish writing file '1801671628.00033.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1801671628.00025.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1801671628.00034.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1801671628.00024.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1801671628.00023.1.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 13:37:01 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1801671628.00038.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00038.1.bfq -- finish writing file '1801671628.00022.1.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 13:37:02 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1801671628.00039.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00039.1.bfq # Wed Mar 28 13:37:03 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1801671628.00040.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00040.1.bfq # Wed Mar 28 13:37:04 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1801671628.00037.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00037.1.bfq # Wed Mar 28 13:37:05 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1801671628.00036.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00036.1.bfq # Wed Mar 28 13:37:06 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1801671628.00035.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00035.1.bfq -- finish writing file '1801671628.00039.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1801671628.00038.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1801671628.00040.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1801671628.00037.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1801671628.00036.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1801671628.00035.1.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 13:37:20 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1801671628.00045.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00045.1.bfq # Wed Mar 28 13:37:22 BST 2012: Converting fastq files to bfq ... # Wed Mar 28 13:37:22 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1801671628.00046.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00046.1.bfq /data/maqgene/bin/maq sol2sanger 1801671628.00044.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00044.1.bfq # Wed Mar 28 13:37:23 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1801671628.00043.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00043.1.bfq # Wed Mar 28 13:37:24 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1801671628.00041.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00041.1.bfq # Wed Mar 28 13:37:24 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1801671628.00042.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00042.1.bfq # Wed Mar 28 13:37:25 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1801671628.00021.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00021.1.bfq # Wed Mar 28 13:37:26 BST 2012: Converting fastq files to bfq ... # Wed Mar 28 13:37:26 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1801671628.00019.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00019.1.bfq /data/maqgene/bin/maq sol2sanger 1801671628.00020.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00020.1.bfq -- finish writing file '1801671628.00045.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1801671628.00044.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1801671628.00043.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1801671628.00046.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1801671628.00042.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1801671628.00041.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1801671628.00021.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1801671628.00019.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1801671628.00020.1.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 13:37:44 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1801671628.00006.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00006.2.bfq # Wed Mar 28 13:37:52 BST 2012: Converting fastq files to bfq ... # Wed Mar 28 13:37:52 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1801671628.00005.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00005.2.bfq /data/maqgene/bin/maq sol2sanger 1801671628.00007.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00007.2.bfq # Wed Mar 28 13:37:53 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1801671628.00004.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00004.2.bfq # Wed Mar 28 13:37:54 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1801671628.00003.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00003.2.bfq # Wed Mar 28 13:37:55 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1801671628.00002.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00002.2.bfq # Wed Mar 28 13:37:56 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1801671628.00001.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00001.2.bfq -- finish writing file '1801671628.00006.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1801671628.00007.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1801671628.00005.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1801671628.00004.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1801671628.00003.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1801671628.00002.2.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 13:38:12 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1801671628.00013.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00013.2.bfq -- finish writing file '1801671628.00001.2.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 13:38:12 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1801671628.00012.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00012.2.bfq # Wed Mar 28 13:38:13 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1801671628.00014.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00014.2.bfq # Wed Mar 28 13:38:14 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1801671628.00011.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00011.2.bfq # Wed Mar 28 13:38:15 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1801671628.00010.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00010.2.bfq # Wed Mar 28 13:38:16 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1801671628.00009.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00009.2.bfq # Wed Mar 28 13:38:17 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1801671628.00008.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00008.2.bfq # Wed Mar 28 13:38:18 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1801671628.00000.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00000.2.bfq # Wed Mar 28 13:38:19 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1801671628.00047.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00047.1.bfq # Wed Mar 28 13:38:20 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1801671628.00018.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00018.1.bfq -- finish writing file '1801671628.00013.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1801671628.00012.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1801671628.00014.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1801671628.00010.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1801671628.00011.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1801671628.00047.1.bfq' -- 947463 sequences were loaded. -- finish writing file '1801671628.00008.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1801671628.00009.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1801671628.00018.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1801671628.00000.2.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 13:38:38 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1801671628.00023.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00023.2.bfq # Wed Mar 28 13:38:42 BST 2012: Converting fastq files to bfq ... # Wed Mar 28 13:38:42 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1801671628.00024.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00024.2.bfq /data/maqgene/bin/maq sol2sanger 1801671628.00022.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00022.2.bfq # Wed Mar 28 13:38:43 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1801671628.00021.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00021.2.bfq # Wed Mar 28 13:38:44 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1801671628.00020.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00020.2.bfq # Wed Mar 28 13:38:44 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1801671628.00019.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00019.2.bfq # Wed Mar 28 13:38:45 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1801671628.00018.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00018.2.bfq # Wed Mar 28 13:38:46 BST 2012: Converting fastq files to bfq ... # Wed Mar 28 13:38:46 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1801671628.00017.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00017.2.bfq /data/maqgene/bin/maq sol2sanger 1801671628.00016.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00016.2.bfq # Wed Mar 28 13:38:47 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1801671628.00015.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00015.2.bfq # Wed Mar 28 13:38:48 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1801671628.00017.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00017.1.bfq # Wed Mar 28 13:38:49 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1801671628.00016.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00016.1.bfq # Wed Mar 28 13:38:50 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1801671628.00015.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00015.1.bfq -- finish writing file '1801671628.00023.2.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 13:38:50 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1801671628.00014.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00014.1.bfq # Wed Mar 28 13:38:51 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1801671628.00025.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00025.2.bfq -- finish writing file '1801671628.00024.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1801671628.00020.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1801671628.00022.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1801671628.00021.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1801671628.00015.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1801671628.00018.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1801671628.00019.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1801671628.00017.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1801671628.00016.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1801671628.00025.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1801671628.00017.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1801671628.00016.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1801671628.00014.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1801671628.00015.1.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 13:39:12 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1801671628.00038.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00038.2.bfq -- finish writing file '1801671628.00038.2.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 13:39:24 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1801671628.00039.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00039.2.bfq -- finish writing file '1801671628.00039.2.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 13:39:35 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1801671628.00040.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00040.2.bfq -- finish writing file '1801671628.00040.2.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 13:39:47 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1801671628.00041.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00041.2.bfq # Wed Mar 28 13:39:52 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1801671628.00042.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00042.2.bfq # Wed Mar 28 13:39:54 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1801671628.00037.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00037.2.bfq # Wed Mar 28 13:39:56 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1801671628.00036.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00036.2.bfq # Wed Mar 28 13:39:57 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1801671628.00035.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00035.2.bfq # Wed Mar 28 13:39:58 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1801671628.00034.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00034.2.bfq -- finish writing file '1801671628.00041.2.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 13:39:59 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1801671628.00033.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00033.2.bfq # Wed Mar 28 13:40:00 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1801671628.00043.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00043.2.bfq # Wed Mar 28 13:40:01 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1801671628.00032.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00032.2.bfq -- finish writing file '1801671628.00042.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1801671628.00037.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1801671628.00036.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1801671628.00035.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1801671628.00034.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1801671628.00033.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1801671628.00043.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1801671628.00032.2.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 13:40:15 BST 2012: Mapping file(s) 1801671628.00002.1.bfq 1801671628.00002.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1801671628.00002.unmapped -H 1801671628.00002.mismatch \ 1801671628.00002.map /data/maqgene/genomes/elegans.bfa 1801671628.00002.1.bfq 1801671628.00002.2.bfq 2> /dev/null # Wed Mar 28 13:40:36 BST 2012: Mapping file(s) 1801671628.00003.1.bfq 1801671628.00003.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1801671628.00003.unmapped -H 1801671628.00003.mismatch \ 1801671628.00003.map /data/maqgene/genomes/elegans.bfa 1801671628.00003.1.bfq 1801671628.00003.2.bfq 2> /dev/null # Wed Mar 28 13:40:37 BST 2012: Mapping file(s) 1801671628.00001.1.bfq 1801671628.00001.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1801671628.00001.unmapped -H 1801671628.00001.mismatch \ 1801671628.00001.map /data/maqgene/genomes/elegans.bfa 1801671628.00001.1.bfq 1801671628.00001.2.bfq 2> /dev/null # Wed Mar 28 13:40:38 BST 2012: Mapping file(s) 1801671628.00000.1.bfq 1801671628.00000.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1801671628.00000.unmapped -H 1801671628.00000.mismatch \ 1801671628.00000.map /data/maqgene/genomes/elegans.bfa 1801671628.00000.1.bfq 1801671628.00000.2.bfq 2> /dev/null # Wed Mar 28 13:40:39 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1801671628.00047.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00047.2.bfq # Wed Mar 28 13:40:40 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1801671628.00046.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00046.2.bfq -- finish writing file '1801671628.00047.2.bfq' -- 947463 sequences were loaded. -- finish writing file '1801671628.00046.2.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 13:45:15 BST 2012: Mapping file(s) 1801671628.00008.1.bfq 1801671628.00008.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1801671628.00008.unmapped -H 1801671628.00008.mismatch \ 1801671628.00008.map /data/maqgene/genomes/elegans.bfa 1801671628.00008.1.bfq 1801671628.00008.2.bfq 2> /dev/null # Wed Mar 28 13:47:12 BST 2012: Mapping file(s) 1801671628.00009.1.bfq 1801671628.00009.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1801671628.00009.unmapped -H 1801671628.00009.mismatch \ 1801671628.00009.map /data/maqgene/genomes/elegans.bfa 1801671628.00009.1.bfq 1801671628.00009.2.bfq 2> /dev/null # Wed Mar 28 13:47:13 BST 2012: Mapping file(s) 1801671628.00007.1.bfq 1801671628.00007.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1801671628.00007.unmapped -H 1801671628.00007.mismatch \ 1801671628.00007.map /data/maqgene/genomes/elegans.bfa 1801671628.00007.1.bfq 1801671628.00007.2.bfq 2> /dev/null # Wed Mar 28 13:47:14 BST 2012: Mapping file(s) 1801671628.00006.1.bfq 1801671628.00006.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1801671628.00006.unmapped -H 1801671628.00006.mismatch \ 1801671628.00006.map /data/maqgene/genomes/elegans.bfa 1801671628.00006.1.bfq 1801671628.00006.2.bfq 2> /dev/null # Wed Mar 28 13:47:15 BST 2012: Mapping file(s) 1801671628.00005.1.bfq 1801671628.00005.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1801671628.00005.unmapped -H 1801671628.00005.mismatch \ 1801671628.00005.map /data/maqgene/genomes/elegans.bfa 1801671628.00005.1.bfq 1801671628.00005.2.bfq 2> /dev/null # Wed Mar 28 13:47:16 BST 2012: Mapping file(s) 1801671628.00004.1.bfq 1801671628.00004.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1801671628.00004.unmapped -H 1801671628.00004.mismatch \ 1801671628.00004.map /data/maqgene/genomes/elegans.bfa 1801671628.00004.1.bfq 1801671628.00004.2.bfq 2> /dev/null # Wed Mar 28 13:52:19 BST 2012: Mapping file(s) 1801671628.00014.1.bfq 1801671628.00014.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1801671628.00014.unmapped -H 1801671628.00014.mismatch \ 1801671628.00014.map /data/maqgene/genomes/elegans.bfa 1801671628.00014.1.bfq 1801671628.00014.2.bfq 2> /dev/null # Wed Mar 28 13:53:39 BST 2012: Mapping file(s) 1801671628.00015.1.bfq 1801671628.00015.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1801671628.00015.unmapped -H 1801671628.00015.mismatch \ 1801671628.00015.map /data/maqgene/genomes/elegans.bfa 1801671628.00015.1.bfq 1801671628.00015.2.bfq 2> /dev/null # Wed Mar 28 13:53:41 BST 2012: Mapping file(s) 1801671628.00013.1.bfq 1801671628.00013.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1801671628.00013.unmapped -H 1801671628.00013.mismatch \ 1801671628.00013.map /data/maqgene/genomes/elegans.bfa 1801671628.00013.1.bfq 1801671628.00013.2.bfq 2> /dev/null # Wed Mar 28 13:53:43 BST 2012: Mapping file(s) 1801671628.00012.1.bfq 1801671628.00012.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1801671628.00012.unmapped -H 1801671628.00012.mismatch \ 1801671628.00012.map /data/maqgene/genomes/elegans.bfa 1801671628.00012.1.bfq 1801671628.00012.2.bfq 2> /dev/null # Wed Mar 28 13:58:48 BST 2012: Mapping file(s) 1801671628.00018.1.bfq 1801671628.00018.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1801671628.00018.unmapped -H 1801671628.00018.mismatch \ 1801671628.00018.map /data/maqgene/genomes/elegans.bfa 1801671628.00018.1.bfq 1801671628.00018.2.bfq 2> /dev/null # Wed Mar 28 13:59:10 BST 2012: Mapping file(s) 1801671628.00019.1.bfq 1801671628.00019.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1801671628.00019.unmapped -H 1801671628.00019.mismatch \ 1801671628.00019.map /data/maqgene/genomes/elegans.bfa 1801671628.00019.1.bfq 1801671628.00019.2.bfq 2> /dev/null # Wed Mar 28 13:59:12 BST 2012: Mapping file(s) 1801671628.00017.1.bfq 1801671628.00017.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1801671628.00017.unmapped -H 1801671628.00017.mismatch \ 1801671628.00017.map /data/maqgene/genomes/elegans.bfa 1801671628.00017.1.bfq 1801671628.00017.2.bfq 2> /dev/null # Wed Mar 28 13:59:14 BST 2012: Mapping file(s) 1801671628.00016.1.bfq 1801671628.00016.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1801671628.00016.unmapped -H 1801671628.00016.mismatch \ 1801671628.00016.map /data/maqgene/genomes/elegans.bfa 1801671628.00016.1.bfq 1801671628.00016.2.bfq 2> /dev/null # Wed Mar 28 14:04:40 BST 2012: Mapping file(s) 1801671628.00022.1.bfq 1801671628.00022.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1801671628.00022.unmapped -H 1801671628.00022.mismatch \ 1801671628.00022.map /data/maqgene/genomes/elegans.bfa 1801671628.00022.1.bfq 1801671628.00022.2.bfq 2> /dev/null # Wed Mar 28 14:05:45 BST 2012: Mapping file(s) 1801671628.00023.1.bfq 1801671628.00023.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1801671628.00023.unmapped -H 1801671628.00023.mismatch \ 1801671628.00023.map /data/maqgene/genomes/elegans.bfa 1801671628.00023.1.bfq 1801671628.00023.2.bfq 2> /dev/null # Wed Mar 28 14:05:47 BST 2012: Mapping file(s) 1801671628.00021.1.bfq 1801671628.00021.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1801671628.00021.unmapped -H 1801671628.00021.mismatch \ 1801671628.00021.map /data/maqgene/genomes/elegans.bfa 1801671628.00021.1.bfq 1801671628.00021.2.bfq 2> /dev/null # Wed Mar 28 14:05:49 BST 2012: Mapping file(s) 1801671628.00020.1.bfq 1801671628.00020.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1801671628.00020.unmapped -H 1801671628.00020.mismatch \ 1801671628.00020.map /data/maqgene/genomes/elegans.bfa 1801671628.00020.1.bfq 1801671628.00020.2.bfq 2> /dev/null # Wed Mar 28 14:10:49 BST 2012: Mapping file(s) 1801671628.00032.1.bfq 1801671628.00032.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1801671628.00032.unmapped -H 1801671628.00032.mismatch \ 1801671628.00032.map /data/maqgene/genomes/elegans.bfa 1801671628.00032.1.bfq 1801671628.00032.2.bfq 2> /dev/null # Wed Mar 28 14:15:38 BST 2012: Mapping file(s) 1801671628.00033.1.bfq 1801671628.00033.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1801671628.00033.unmapped -H 1801671628.00033.mismatch \ 1801671628.00033.map /data/maqgene/genomes/elegans.bfa 1801671628.00033.1.bfq 1801671628.00033.2.bfq 2> /dev/null # Wed Mar 28 14:17:27 BST 2012: Mapping file(s) 1801671628.00034.1.bfq 1801671628.00034.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1801671628.00034.unmapped -H 1801671628.00034.mismatch \ 1801671628.00034.map /data/maqgene/genomes/elegans.bfa 1801671628.00034.1.bfq 1801671628.00034.2.bfq 2> /dev/null # Wed Mar 28 14:17:29 BST 2012: Mapping file(s) 1801671628.00025.1.bfq 1801671628.00025.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1801671628.00025.unmapped -H 1801671628.00025.mismatch \ 1801671628.00025.map /data/maqgene/genomes/elegans.bfa 1801671628.00025.1.bfq 1801671628.00025.2.bfq 2> /dev/null # Wed Mar 28 14:17:31 BST 2012: Mapping file(s) 1801671628.00024.1.bfq 1801671628.00024.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1801671628.00024.unmapped -H 1801671628.00024.mismatch \ 1801671628.00024.map /data/maqgene/genomes/elegans.bfa 1801671628.00024.1.bfq 1801671628.00024.2.bfq 2> /dev/null # Wed Mar 28 14:22:25 BST 2012: Mapping file(s) 1801671628.00037.1.bfq 1801671628.00037.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1801671628.00037.unmapped -H 1801671628.00037.mismatch \ 1801671628.00037.map /data/maqgene/genomes/elegans.bfa 1801671628.00037.1.bfq 1801671628.00037.2.bfq 2> /dev/null # Wed Mar 28 14:23:07 BST 2012: Mapping file(s) 1801671628.00038.1.bfq 1801671628.00038.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1801671628.00038.unmapped -H 1801671628.00038.mismatch \ 1801671628.00038.map /data/maqgene/genomes/elegans.bfa 1801671628.00038.1.bfq 1801671628.00038.2.bfq 2> /dev/null # Wed Mar 28 14:23:08 BST 2012: Mapping file(s) 1801671628.00036.1.bfq 1801671628.00036.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1801671628.00036.unmapped -H 1801671628.00036.mismatch \ 1801671628.00036.map /data/maqgene/genomes/elegans.bfa 1801671628.00036.1.bfq 1801671628.00036.2.bfq 2> /dev/null # Wed Mar 28 14:23:09 BST 2012: Mapping file(s) 1801671628.00035.1.bfq 1801671628.00035.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1801671628.00035.unmapped -H 1801671628.00035.mismatch \ 1801671628.00035.map /data/maqgene/genomes/elegans.bfa 1801671628.00035.1.bfq 1801671628.00035.2.bfq 2> /dev/null # Wed Mar 28 14:23:10 BST 2012: Mapping file(s) 1801671628.00011.1.bfq 1801671628.00011.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1801671628.00011.unmapped -H 1801671628.00011.mismatch \ 1801671628.00011.map /data/maqgene/genomes/elegans.bfa 1801671628.00011.1.bfq 1801671628.00011.2.bfq 2> /dev/null # Wed Mar 28 14:23:11 BST 2012: Mapping file(s) 1801671628.00010.1.bfq 1801671628.00010.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1801671628.00010.unmapped -H 1801671628.00010.mismatch \ 1801671628.00010.map /data/maqgene/genomes/elegans.bfa 1801671628.00010.1.bfq 1801671628.00010.2.bfq 2> /dev/null # Wed Mar 28 14:28:40 BST 2012: Mapping file(s) 1801671628.00043.1.bfq 1801671628.00043.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1801671628.00043.unmapped -H 1801671628.00043.mismatch \ 1801671628.00043.map /data/maqgene/genomes/elegans.bfa 1801671628.00043.1.bfq 1801671628.00043.2.bfq 2> /dev/null # Wed Mar 28 14:29:13 BST 2012: Mapping file(s) 1801671628.00046.1.bfq 1801671628.00046.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1801671628.00046.unmapped -H 1801671628.00046.mismatch \ 1801671628.00046.map /data/maqgene/genomes/elegans.bfa 1801671628.00046.1.bfq 1801671628.00046.2.bfq 2> /dev/null # Wed Mar 28 14:29:14 BST 2012: Mapping file(s) 1801671628.00042.1.bfq 1801671628.00042.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1801671628.00042.unmapped -H 1801671628.00042.mismatch \ 1801671628.00042.map /data/maqgene/genomes/elegans.bfa 1801671628.00042.1.bfq 1801671628.00042.2.bfq 2> /dev/null # Wed Mar 28 14:29:15 BST 2012: Mapping file(s) 1801671628.00041.1.bfq 1801671628.00041.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1801671628.00041.unmapped -H 1801671628.00041.mismatch \ 1801671628.00041.map /data/maqgene/genomes/elegans.bfa 1801671628.00041.1.bfq 1801671628.00041.2.bfq 2> /dev/null # Wed Mar 28 14:29:16 BST 2012: Mapping file(s) 1801671628.00040.1.bfq 1801671628.00040.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1801671628.00040.unmapped -H 1801671628.00040.mismatch \ 1801671628.00040.map /data/maqgene/genomes/elegans.bfa 1801671628.00040.1.bfq 1801671628.00040.2.bfq 2> /dev/null # Wed Mar 28 14:29:17 BST 2012: Mapping file(s) 1801671628.00039.1.bfq 1801671628.00039.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1801671628.00039.unmapped -H 1801671628.00039.mismatch \ 1801671628.00039.map /data/maqgene/genomes/elegans.bfa 1801671628.00039.1.bfq 1801671628.00039.2.bfq 2> /dev/null # Wed Mar 28 14:29:19 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1801671628.00045.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00045.2.bfq # Wed Mar 28 14:29:21 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1801671628.00044.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00044.2.bfq -- finish writing file '1801671628.00045.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1801671628.00044.2.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 14:34:25 BST 2012: Mapping file(s) 1801671628.00045.1.bfq 1801671628.00045.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1801671628.00045.unmapped -H 1801671628.00045.mismatch \ 1801671628.00045.map /data/maqgene/genomes/elegans.bfa 1801671628.00045.1.bfq 1801671628.00045.2.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 1801671628.00044.unmapped -H 1801671628.00044.mismatch \ 1801671628.00044.map /data/maqgene/genomes/elegans.bfa 1801671628.00044.1.bfq 1801671628.00044.2.bfq 2> /dev/null # Wed Mar 28 14:34:25 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1801671628.00031.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00031.2.bfq # Wed Mar 28 14:34:25 BST 2012: Mapping file(s) 1801671628.00047.1.bfq 1801671628.00047.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1801671628.00047.unmapped -H 1801671628.00047.mismatch \ 1801671628.00047.map /data/maqgene/genomes/elegans.bfa 1801671628.00047.1.bfq 1801671628.00047.2.bfq 2> /dev/null # Wed Mar 28 14:34:25 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1801671628.00028.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00028.2.bfq # Wed Mar 28 14:34:25 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1801671628.00027.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00027.2.bfq # Wed Mar 28 14:34:25 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1801671628.00030.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00030.2.bfq /data/maqgene/bin/maq sol2sanger 1801671628.00026.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00026.2.bfq # Wed Mar 28 14:34:25 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1801671628.00029.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1801671628.00029.2.bfq -- finish writing file '1801671628.00030.2.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 14:34:42 BST 2012: Mapping file(s) 1801671628.00030.1.bfq 1801671628.00030.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1801671628.00030.unmapped -H 1801671628.00030.mismatch \ 1801671628.00030.map /data/maqgene/genomes/elegans.bfa 1801671628.00030.1.bfq 1801671628.00030.2.bfq 2> /dev/null -- finish writing file '1801671628.00029.2.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 14:34:43 BST 2012: Mapping file(s) 1801671628.00029.1.bfq 1801671628.00029.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1801671628.00029.unmapped -H 1801671628.00029.mismatch \ 1801671628.00029.map /data/maqgene/genomes/elegans.bfa 1801671628.00029.1.bfq 1801671628.00029.2.bfq 2> /dev/null -- finish writing file '1801671628.00027.2.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 14:34:44 BST 2012: Mapping file(s) 1801671628.00027.1.bfq 1801671628.00027.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1801671628.00027.unmapped -H 1801671628.00027.mismatch \ 1801671628.00027.map /data/maqgene/genomes/elegans.bfa 1801671628.00027.1.bfq 1801671628.00027.2.bfq 2> /dev/null -- finish writing file '1801671628.00026.2.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 14:34:44 BST 2012: Mapping file(s) 1801671628.00026.1.bfq 1801671628.00026.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1801671628.00026.unmapped -H 1801671628.00026.mismatch \ 1801671628.00026.map /data/maqgene/genomes/elegans.bfa 1801671628.00026.1.bfq 1801671628.00026.2.bfq 2> /dev/null -- finish writing file '1801671628.00028.2.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 14:34:44 BST 2012: Mapping file(s) 1801671628.00028.1.bfq 1801671628.00028.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1801671628.00028.unmapped -H 1801671628.00028.mismatch \ 1801671628.00028.map /data/maqgene/genomes/elegans.bfa 1801671628.00028.1.bfq 1801671628.00028.2.bfq 2> /dev/null -- finish writing file '1801671628.00031.2.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 14:34:45 BST 2012: Mapping file(s) 1801671628.00031.1.bfq 1801671628.00031.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1801671628.00031.unmapped -H 1801671628.00031.mismatch \ 1801671628.00031.map /data/maqgene/genomes/elegans.bfa 1801671628.00031.1.bfq 1801671628.00031.2.bfq 2> /dev/null # Wed Mar 28 14:40:10 BST 2012: Merging all *.unmapped files ... # Wed Mar 28 14:40:10 BST 2012: Merging all maps ... cat 1801671628.00000.unmapped 1801671628.00001.unmapped 1801671628.00002.unmapped 1801671628.00003.unmapped 1801671628.00004.unmapped 1801671628.00005.unmapped 1801671628.00006.unmapped 1801671628.00007.unmapped 1801671628.00008.unmapped 1801671628.00009.unmapped 1801671628.00010.unmapped 1801671628.00011.unmapped 1801671628.00012.unmapped 1801671628.00013.unmapped 1801671628.00014.unmapped 1801671628.00015.unmapped 1801671628.00016.unmapped 1801671628.00017.unmapped 1801671628.00018.unmapped 1801671628.00019.unmapped 1801671628.00020.unmapped 1801671628.00021.unmapped 1801671628.00022.unmapped 1801671628.00023.unmapped 1801671628.00024.unmapped 1801671628.00025.unmapped 1801671628.00026.unmapped 1801671628.00027.unmapped 1801671628.00028.unmapped 1801671628.00029.unmapped 1801671628.00030.unmapped 1801671628.00031.unmapped 1801671628.00032.unmapped 1801671628.00033.unmapped 1801671628.00034.unmapped 1801671628.00035.unmapped 1801671628.00036.unmapped 1801671628.00037.unmapped 1801671628.00038.unmapped 1801671628.00039.unmapped 1801671628.00040.unmapped 1801671628.00041.unmapped 1801671628.00042.unmapped 1801671628.00043.unmapped 1801671628.00044.unmapped 1801671628.00045.unmapped 1801671628.00046.unmapped 1801671628.00047.unmapped > 1801671628_unmapped.txt /data/maqgene/bin/maq mapmerge 1801671628.map 1801671628.00000.map 1801671628.00001.map 1801671628.00002.map 1801671628.00003.map 1801671628.00004.map 1801671628.00005.map 1801671628.00006.map 1801671628.00007.map 1801671628.00008.map 1801671628.00009.map 1801671628.00010.map 1801671628.00011.map 1801671628.00012.map 1801671628.00013.map 1801671628.00014.map 1801671628.00015.map 1801671628.00016.map 1801671628.00017.map 1801671628.00018.map 1801671628.00019.map 1801671628.00020.map 1801671628.00021.map 1801671628.00022.map 1801671628.00023.map 1801671628.00024.map 1801671628.00025.map 1801671628.00026.map 1801671628.00027.map 1801671628.00028.map 1801671628.00029.map 1801671628.00030.map 1801671628.00031.map 1801671628.00032.map 1801671628.00033.map 1801671628.00034.map 1801671628.00035.map 1801671628.00036.map 1801671628.00037.map 1801671628.00038.map 1801671628.00039.map 1801671628.00040.map 1801671628.00041.map 1801671628.00042.map 1801671628.00043.map 1801671628.00044.map 1801671628.00045.map 1801671628.00046.map 1801671628.00047.map # Wed Mar 28 14:40:16 BST 2012: Linking backend file 1801671628_unmapped.txt to /data/maqgene/out/example_user/hyp_3/hyp_3_unmapped.txt ln -fs /data/maqgene/work/1801671628_unmapped.txt /data/maqgene/out/example_user/hyp_3/hyp_3_unmapped.txt /data/maqgene/makefile:126: warning: undefined variable `mapcheck_parameters' # Wed Mar 28 15:00:46 BST 2012: Generating consensus ... /data/maqgene/bin/maq assemble -N 2 -q 0 -r 0.0 -m 7 -Q 100 -p 619536435.cns \ /data/maqgene/genomes/elegans.bfa 1801671628.map 2> 619536435_log.txt # Wed Mar 28 15:00:46 BST 2012: Creating pileup ... # Wed Mar 28 15:00:46 BST 2012: Running 'mapcheck' ... /data/maqgene/bin/maq pileup -Q 100 -p -m 7 -q 0 /data/maqgene/genomes/elegans.bfa 1801671628.map > 2162726738_pileup.txt /data/maqgene/bin/maq mapcheck /data/maqgene/genomes/elegans.bfa 1801671628.map > 1801671628_check.txt \ 2>/dev/null # Wed Mar 28 15:09:47 BST 2012: Linking backend file 2162726738_pileup.txt to /data/maqgene/out/example_user/hyp_3/hyp_3_pileup.txt ln -fs /data/maqgene/work/2162726738_pileup.txt /data/maqgene/out/example_user/hyp_3/hyp_3_pileup.txt # Wed Mar 28 15:09:47 BST 2012: Linking backend file 619536435_log.txt to /data/maqgene/out/example_user/hyp_3/hyp_3_log.txt ln -fs /data/maqgene/work/619536435_log.txt /data/maqgene/out/example_user/hyp_3/hyp_3_log.txt # Wed Mar 28 15:09:47 BST 2012: Making coverage histogram ... (echo -en "sequencing_depth\tnumber_of_bases\n"; \ cut -f 4 2162726738_pileup.txt \ | /data/maqgene/bin/pileup_histogram 100) > 2162726738_coverage.txt /data/maqgene/bin/filter_matching_lines 2162726738_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 \ > 2162726738_known_snps # Wed Mar 28 15:10:29 BST 2012: Getting uncovered regions ... # Wed Mar 28 15:10:29 BST 2012: Linking backend file 1801671628_check.txt to /data/maqgene/out/example_user/hyp_3/hyp_3_check.txt cut -f 1,2,4 2162726738_pileup.txt \ | /data/maqgene/bin/get_uncovered_regions 50 \ > 2162726738_uncovered.txt ln -fs /data/maqgene/work/1801671628_check.txt /data/maqgene/out/example_user/hyp_3/hyp_3_check.txt # Wed Mar 28 15:10:29 BST 2012: Linking backend file 2162726738_coverage.txt to /data/maqgene/out/example_user/hyp_3/hyp_3_coverage.txt ln -fs /data/maqgene/work/2162726738_coverage.txt /data/maqgene/out/example_user/hyp_3/hyp_3_coverage.txt # Wed Mar 28 15:11:00 BST 2012: Extracting point mutants from consensus ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 619536435_snps; create table 619536435_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) )" # Wed Mar 28 15:11:00 BST 2012: Filtering and loading pileup for analysis ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 2162726738_pileup; create table 2162726738_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) );" /data/maqgene/bin/maq cns2snp 619536435.cns \ | cat -b | /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "load data local infile '/dev/stdin' into table 619536435_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 619536435_snps;" cat 2162726738_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 2162726738_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 2162726738_pileup" # Wed Mar 28 15:11:15 BST 2012: Extracting indels from consensus ... /data/maqgene/bin/maq indelsoa /data/maqgene/genomes/elegans.bfa 1801671628.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 619536435_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 619536435_snps;" cat 2162726738_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 2162726738_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 2162726738_pileup" touch 2162726738_pileup # Wed Mar 28 15:14:36 BST 2012: Adding placeholders for known SNPs. cat 2162726738_known_snps \ | /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "load data local infile '/dev/stdin' ignore into table 619536435_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 619536435_snps;" Found 162310 variants. touch 619536435_snps # Wed Mar 28 15:14:37 BST 2012: Writing snp read counts ... # Wed Mar 28 15:14:37 BST 2012: Linking backend file 2162726738_uncovered.txt to /data/maqgene/out/example_user/hyp_3/hyp_3_uncovered.txt /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 2162726738_pileup p using (dna,start)" > /data/maqgene/out/example_user/hyp_3/hyp_3_snp_read_counts.txt ln -fs /data/maqgene/work/2162726738_uncovered.txt /data/maqgene/out/example_user/hyp_3/hyp_3_uncovered.txt # Wed Mar 28 15:14:37 BST 2012: Loading uncovered regions into table ... cat 2162726738_uncovered.txt \ | /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 2162726738_uncovered; create table 2162726738_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 = 162311; load data local infile '/dev/stdin' into table 2162726738_uncovered (dna, start, end)" # Wed Mar 28 15:14:37 BST 2012: Getting masking regions # Wed Mar 28 15:14:37 BST 2012: Finding all genomic features overlapping variants... /data/maqgene/bin/associate_regions -b -1 -c -1000000 -m 2 -o >(/usr/bin/mysql -Dmaqgenedb -umaqgene --skip-column-names --batch --raw --local-infile -e "drop table if exists 619536435_masked_ids; create table 619536435_masked_ids (query_region_id int(10) NOT NULL, primary key (query_region_id)); load data local infile '/dev/stdin' ignore into table 619536435_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 619536435_snps") -t <(/usr/bin/mysql -Dmaqgenedb -umaqgene --skip-column-names --batch --raw --local-infile -e "select id,'elegans',dna,start,end,strand from elegans_features feature where feature.feature not in ('mRNA', 'intron')") 1>/dev/null; /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 619536435_rel_snps; CREATE TABLE 619536435_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) )" 0 snp read count lines written. Uncovered region statistics: /data/maqgene/bin/associate_regions -b -1 -c -1000000 -m 0 -o >(/usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "load data local infile '/dev/stdin' into table 619536435_rel_snps; flush table 619536435_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 619536435_snps") -t <(/usr/bin/mysql -Dmaqgenedb -umaqgene --skip-column-names --batch --raw --local-infile -e "select id, 'elegans', dna,start,end,strand from elegans_features where feature in ('SNP','exon','five_prime_UTR','intron','mRNA','three_prime_UTR','ncRNA')") 1>/dev/null chromosome number_uncovered_regions total_uncovered_length I 6 729 II 14 2209 III 6 780 IV 13 1139 V 9 1148 X 11 5632 touch 2162726738_uncovered # Wed Mar 28 15:14:38 BST 2012: Finding mRNA features overlapping uncovered regions ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 2162726738_uncovered_rel; CREATE TABLE 2162726738_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 2162726738_uncovered_rel; flush table 2162726738_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 2162726738_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 2162726738_uncovered_rel # Wed Mar 28 15:14:40 BST 2012: Calculating translation start offsets for uncovered regions... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 2162726738_offsets_uncovered; create table 2162726738_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 2162726738_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 2162726738_uncovered reg join 2162726738_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 619536435_masked_ids /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 2162726738_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 2162726738_uncovered reg join 2162726738_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 2162726738_offsets_uncovered touch 619536435_rel_snps # Wed Mar 28 15:14:41 BST 2012: Calculating translation start offsets... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 619536435_offsets_snps; create table 619536435_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) );" # Wed Mar 28 15:14:41 BST 2012: Getting intergenic regions /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 619536435_rel_intergenic; create table 619536435_rel_intergenic like 619536435_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 619536435_rel_intergenic; flush table 619536435_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 619536435_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 619536435_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 619536435_snps reg join 619536435_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" # Wed Mar 28 15:14:44 BST 2012: Filtering masked intergenic regions /usr/bin/mysql -Dmaqgenedb -umaqgene --skip-column-names --batch --raw --local-infile -e "delete i.* from 619536435_rel_intergenic i join 619536435_masked_ids m using (query_region_id)" touch 619536435_rel_intergenic # Wed Mar 28 15:14:49 BST 2012: Classifying intergenic relations /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 619536435_intergenic_assoc; create table 619536435_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 619536435_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 619536435_snps snp join 619536435_rel_intergenic rel on (snp.id = rel.query_region_id) join elegans_features feature on (rel.target_region_id = feature.id)" touch 619536435_intergenic_assoc touch 619536435_offsets_snps # Wed Mar 28 15:15:01 BST 2012: Getting codons affected by point mutations... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 619536435_codons; create table 619536435_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 619536435_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 619536435_offsets_snps off join 619536435_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 619536435_codons /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 619536435_marked; create table 619536435_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) );" # Wed Mar 28 15:15:07 BST 2012: Finding exonic indels ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 619536435_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 619536435_snps snp join 619536435_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';" # Wed Mar 28 15:15:07 BST 2012: Finding coding variants ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 619536435_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 619536435_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);" # Wed Mar 28 15:15:07 BST 2012: Finding noncoding variants ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 619536435_marked select snp.id, feature.feature class, 'none' description, feature.attribute parent_feature from 619536435_snps snp join 619536435_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');" # Wed Mar 28 15:15:08 BST 2012: Finding splice site variants ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 619536435_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 619536435_snps snp join 619536435_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;" # Wed Mar 28 15:15:08 BST 2012: Finding intergenic and intronic variants ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 619536435_marked select id, 'nongenic' class, concat(if (relation in ('upstream','into'), - distance, distance),' ',relation) description, attribute from 619536435_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' );" # Wed Mar 28 15:15:11 BST 2012: Finding uncovered regions in genes ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 619536435_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 2162726738_uncovered unc join 2162726738_offsets_uncovered b using (id) join 2162726738_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 2162726738_uncovered unc join 2162726738_offsets_uncovered b using (id) join 2162726738_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'" # Wed Mar 28 15:15:11 BST 2012: Variants found: +-----------------+-----------------+ | class | number_variants | +-----------------+-----------------+ | five_prime_UTR | 1310 | | frameshift | 87 | | inframe | 27 | | missense | 6477 | | ncRNA | 876 | | nongenic | 123641 | | non_start | 9 | | premature_stop | 680 | | readthrough | 19 | | silent | 7573 | | SNP | 3296 | | splice_acceptor | 47 | | splice_donor | 46 | | three_prime_UTR | 3563 | | uncovered | 15 | +-----------------+-----------------+ touch 619536435_marked # Wed Mar 28 15:15:11 BST 2012: Combining results ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 619536435_combined; create table 619536435_combined (primary key (id, class, description), key (dna, start)) as select snp.id, 'hyp_3' 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 619536435_snps snp join 2162726738_pileup pile using (dna,start) join 619536435_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, 'hyp_3' 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 2162726738_uncovered unc join 619536435_marked class on (unc.id = class.id) left join elegans_per_locus using (dna,start) group by id, class, description; alter table 619536435_combined order by dna, start, length" touch 619536435_combined # Wed Mar 28 15:15:13 BST 2012: 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 619536435_combined group by id order by dna, start;" > /data/maqgene/out/example_user/hyp_3/hyp_3_grouped.txt # Wed Mar 28 15:15:13 BST 2012: Writing results to flat file ... /usr/bin/mysql -Dmaqgenedb -umaqgene --skip-column-names --batch --raw --local-infile --column-names -e "select * from 619536435_combined" > /data/maqgene/out/example_user/hyp_3/hyp_3_flat.txt 7293 lines written. 4813 lines written. rm 1801671628.00015.2.fastq 1801671628.00024.mismatch 1801671628.00025.unmapped 1801671628.00007.1.fastq 1801671628.00045.map 1801671628.00046.2.bfq 1801671628.00000.1.bfq 1801671628.00035.1.bfq 1801671628.00022.map 1801671628.00031.2.bfq 1801671628.00033.unmapped 1801671628.00025.1.fastq 1801671628.00046.mismatch 1801671628.00029.mismatch 1801671628.00032.1.bfq 1801671628.00037.unmapped 1801671628.00004.unmapped 1801671628.00033.1.fastq 1801671628.00040.unmapped 1801671628.00028.2.fastq 1801671628.00003.map 1801671628.00038.2.bfq 1801671628.00030.map 1801671628.00001.1.bfq 1801671628.00010.1.bfq 1801671628.00043.map 1801671628.00004.1.fastq 1801671628.00006.mismatch 1801671628.00027.map 1801671628.00040.1.fastq 1801671628.00016.1.bfq 1801671628.00014.2.bfq 1801671628.00044.2.fastq 1801671628.00018.unmapped 1801671628.00034.1.bfq 1801671628.00007.map 1801671628.00041.unmapped 1801671628.00021.1.fastq 1801671628.00014.unmapped 1801671628.00008.1.fastq 1801671628.00025.2.fastq 1801671628.00023.2.bfq 1801671628.00000.mismatch 1801671628.00039.unmapped 1801671628.00041.1.fastq 1801671628.00037.2.bfq 1801671628.00014.1.fastq 1801671628.00033.2.fastq 1801671628.00043.mismatch 1801671628.00039.1.fastq 1801671628.00038.mismatch 1801671628.00010.2.bfq 1801671628.00002.1.bfq 1801671628.00020.1.bfq 1801671628.00004.2.fastq 1801671628.00040.2.fastq 1801671628.00001.mismatch 1801671628.00012.2.fastq 1801671628.00016.2.bfq 1801671628.00040.map 1801671628.00016.mismatch 1801671628.00005.map 1801671628.00034.2.bfq 1801671628.00034.mismatch 1801671628.00036.map 1801671628.00029.2.bfq 1801671628.00021.map 1801671628.00042.unmapped 1801671628.00040.2.bfq 1801671628.00012.1.bfq 1801671628.00008.map 1801671628.00032.map 1801671628.00043.2.fastq 1801671628.00023.map 1801671628.00011.mismatch 1801671628.00041.2.fastq 1801671628.00009.1.fastq 1801671628.00014.2.fastq 1801671628.00009.map 1801671628.00042.1.fastq 1801671628.00017.2.bfq 1801671628.00026.1.bfq 1801671628.00047.1.bfq 1801671628.00039.2.fastq 1801671628.00008.2.bfq 1801671628.00024.1.fastq 1801671628.00007.2.fastq 1801671628.00002.2.bfq 1801671628.00003.1.bfq 2310056006_split1 1801671628.00002.mismatch 1801671628.00015.map 1801671628.00020.mismatch 1801671628.00047.2.bfq 1801671628.00037.mismatch 1801671628.00036.1.bfq 1801671628.00005.2.bfq 1801671628.00046.1.fastq 1801671628.00047.mismatch 1801671628.00019.map 1801671628.00000.2.bfq 1801671628.00024.unmapped 1801671628.00006.unmapped 1801671628.00012.2.bfq 1801671628.00007.1.bfq 1801671628.00011.1.bfq 1801671628.00033.1.bfq 1801671628.00012.mismatch 1801671628.00027.mismatch 1801671628.00042.2.fastq 1801671628.00006.1.fastq 1801671628.00027.2.bfq 1801671628.00028.map 1801671628.00026.2.bfq 1801671628.00024.2.fastq 1801671628.00026.mismatch 1801671628.00000.unmapped 1801671628.00023.mismatch 1801671628.00021.2.fastq 1801671628.00030.1.bfq 1801671628.00008.2.fastq 1801671628.00018.2.bfq 1801671628.00027.1.bfq 1801671628.00046.2.fastq 1801671628.00000.1.fastq 1801671628.00038.unmapped 1801671628.00044.mismatch 1801671628.00044.2.bfq 1801671628.00025.map 1801671628.00045.2.bfq 1801671628.00001.unmapped 1801671628.00010.unmapped 1801671628.00025.1.bfq 1801671628.00022.2.bfq 1801671628.00031.1.bfq 1801671628.00038.1.fastq 1801671628.00045.mismatch 1801671628.00016.unmapped 1801671628.00037.1.fastq 1801671628.00033.map 1801671628.00006.2.fastq 1801671628.00001.1.fastq 1801671628.00010.1.fastq 1801671628.00034.unmapped 1801671628.00009.mismatch 1801671628.00016.1.fastq 1801671628.00004.map 1801671628.00003.2.bfq 1801671628.00030.2.bfq 1801671628.00011.unmapped 1801671628.00017.map 1801671628.00034.1.fastq 1801671628.00003.mismatch 1801671628.00030.mismatch 1801671628.00011.2.bfq 1801671628.00000.2.fastq 1801671628.00029.1.fastq 1801671628.00009.2.fastq 1801671628.00011.1.fastq 1801671628.00017.unmapped 1801671628.00005.1.bfq 1801671628.00013.2.bfq 1801671628.00006.2.bfq 1801671628.00039.map 2310056006_split2 1801671628.00002.unmapped 1801671628.00020.unmapped 1801671628.00041.map 1801671628.00038.2.fastq 1801671628.00017.1.fastq 1801671628.00014.map 1801671628.00047.unmapped 1801671628.00031.mismatch 1801671628.00013.mismatch 1801671628.00001.2.fastq 1801671628.00010.2.fastq 1801671628.00035.mismatch 1801671628.00002.1.fastq 1801671628.00043.2.bfq 1801671628.00020.1.fastq 1801671628.00010.mismatch 1801671628.00019.1.bfq 1801671628.00009.1.bfq 1801671628.00016.2.fastq 1801671628.00047.1.fastq 1801671628.00007.mismatch 1801671628.00012.unmapped 1801671628.00034.2.fastq 1801671628.00035.2.bfq 1801671628.00007.2.bfq 1801671628.00015.1.bfq 1801671628.00029.2.fastq 1801671628.00011.2.fastq 1801671628.00029.unmapped 1801671628.00012.1.fastq 1801671628.00026.unmapped 1801671628.00015.mismatch 1801671628.00005.mismatch 1801671628.00036.2.bfq 1801671628.00031.map 1801671628.00017.2.fastq 1801671628.00026.1.fastq 1801671628.00036.mismatch 1801671628.00042.map 1801671628.00035.2.fastq 1801671628.00002.2.fastq 1801671628.00032.mismatch 1801671628.00020.2.fastq 1801671628.00029.map 1801671628.00024.map 1801671628.00019.2.bfq 1801671628.00043.unmapped 1801671628.00028.1.bfq 1801671628.00004.1.bfq 1801671628.00047.2.fastq 1801671628.00018.1.fastq 1801671628.00019.mismatch 1801671628.00045.unmapped 1801671628.00037.map 1801671628.00022.unmapped 1801671628.00021.mismatch 1801671628.00046.map 1801671628.00035.unmapped 1801671628.00015.2.bfq 1801671628.00007.unmapped 1801671628.00008.mismatch 1801671628.00017.1.bfq 1801671628.00042.1.bfq 1801671628.00045.1.fastq 1801671628.00037.2.fastq 1801671628.00022.1.fastq 1801671628.00022.1.bfq 1801671628.00040.1.bfq 1801671628.00003.unmapped 1801671628.00030.unmapped 1801671628.00032.2.bfq 1801671628.00026.2.fastq 1801671628.00006.map 1801671628.00027.unmapped 1801671628.00003.1.fastq 1801671628.00030.1.fastq 1801671628.00028.2.bfq 1801671628.00037.1.bfq 1801671628.00018.2.fastq 1801671628.00013.map 1801671628.00027.1.fastq 1801671628.00028.mismatch 1801671628.00046.unmapped 1801671628.00035.1.fastq 1801671628.00023.1.bfq 1801671628.00031.unmapped 1801671628.00013.unmapped 1801671628.00000.map 1801671628.00045.2.fastq 1801671628.00021.unmapped 1801671628.00033.2.bfq 1801671628.00022.2.fastq 1801671628.00008.unmapped 1801671628.00031.1.fastq 1801671628.00013.1.fastq 1801671628.00018.1.bfq 1801671628.00001.2.bfq 1801671628.00009.2.bfq 1801671628.00038.map 1801671628.00025.2.bfq 1801671628.00041.1.bfq 1801671628.00025.mismatch 1801671628.00001.map 1801671628.00010.map 1801671628.00014.1.bfq 1801671628.00021.1.bfq 1801671628.00003.2.fastq 1801671628.00030.2.fastq 1801671628.00016.map 1801671628.00005.unmapped 1801671628.00039.1.bfq 1801671628.00033.mismatch 1801671628.00044.1.bfq 1801671628.00027.2.fastq 1801671628.00029.1.bfq 1801671628.00034.map 1801671628.00004.2.bfq 1801671628.00036.unmapped 1801671628.00038.1.bfq 1801671628.00035.map 1801671628.00005.1.fastq 1801671628.00004.mismatch 1801671628.00032.unmapped 1801671628.00044.unmapped 1801671628.00011.map 1801671628.00040.mismatch 1801671628.00023.unmapped 1801671628.00045.1.bfq 1801671628.00043.1.bfq 1801671628.00036.1.fastq 1801671628.00031.2.fastq 1801671628.00013.2.fastq 1801671628.00019.unmapped 1801671628.00044.1.fastq 1801671628.00008.1.bfq 1801671628.00032.1.fastq 1801671628.00023.1.fastq 1801671628.00009.unmapped 1801671628.00041.2.bfq 1801671628.00019.1.fastq 1801671628.00002.map 1801671628.00020.map 1801671628.00015.unmapped 1801671628.00017.mismatch 1801671628.00041.mismatch 1801671628.00014.mismatch 1801671628.00047.map 1801671628.00039.2.bfq 1801671628.00022.mismatch 1801671628.00015.1.fastq 1801671628.00039.mismatch 1801671628.00013.1.bfq 1801671628.00005.2.fastq 1801671628.00012.map 1801671628.00046.1.bfq 1801671628.00036.2.fastq 1801671628.00028.unmapped 1801671628.00032.2.fastq 1801671628.00023.2.fastq 1801671628.00044.map 1801671628.00026.map 1801671628.00020.2.bfq 1801671628.00024.1.bfq 1801671628.00019.2.fastq 1801671628.00028.1.fastq 1801671628.00042.2.bfq 1801671628.00006.1.bfq 1801671628.00043.1.fastq 1801671628.00042.mismatch 1801671628.00018.map 1801671628.00024.2.bfq 1801671628.00018.mismatch 1801671628.00021.2.bfq make: Leaving directory `/data/maqgene/work' make: Entering directory `/data/maqgene/work' # Wed Mar 28 15:15:15 BST 2012: Cleaning intermediate data ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 619536435_snps,619536435_rel,619536435_masked_ids,619536435_rel_intergenic,619536435_intergenic_assoc,619536435_offsets,619536435_codons,619536435_marked,619536435_combined,2162726738_pileup" rm -f 619536435_snps 619536435_rel 619536435_masked_ids 619536435_rel_intergenic 619536435_intergenic_assoc 619536435_offsets 619536435_codons 619536435_marked 619536435_combined 2162726738_pileup make: Leaving directory `/data/maqgene/work'