/data/maqgene/bin/run_maq.sh: line 44: export: `single_CB6972-2/./WTCHG_54189_05_1.fastq=on': not a valid identifier /data/maqgene/bin/run_maq.sh: line 44: export: `single_CB6930-2/./WTCHG_54189_04_1.fastq=on': not a valid identifier /data/maqgene/bin/run_maq.sh: line 44: export: `single_CB7045-2/./WTCHG_54189_06_2.fastq=on': not a valid identifier /data/maqgene/bin/run_maq.sh: line 44: export: `single_CB7045-2/./WTCHG_54189_06_1.fastq=on': not a valid identifier /data/maqgene/bin/run_maq.sh: line 44: export: `single_CB6930-2/./WTCHG_54189_04_2.fastq=on': not a valid identifier /data/maqgene/bin/run_maq.sh: line 44: export: `single_CB6972-2/./WTCHG_54189_05_2.fastq=on': not a valid identifier /data/maqgene/bin/run_maq.sh: line 44: export: `single_CB1122-2/./WTCHG_54189_02_1.fastq=on': not a valid identifier /data/maqgene/bin/run_maq.sh: line 44: export: `single_CB1122-2/./WTCHG_54189_02_2.fastq=on': not a valid identifier Finished reading input. ++ echo CB6972-2/./WTCHG_54189_05_1.fastq,CB6930-2/./WTCHG_54189_04_1.fastq,CB7045-2/./WTCHG_54189_06_2.fastq,CB7045-2/./WTCHG_54189_06_1.fastq,CB6930-2/./WTCHG_54189_04_2.fastq,CB6972-2/./WTCHG_54189_05_2.fastq,CB1122-2/./WTCHG_54189_02_1.fastq,CB1122-2/./WTCHG_54189_02_2.fastq ++ tr , ' ' + fastq_file_set1='CB6972-2/./WTCHG_54189_05_1.fastq CB6930-2/./WTCHG_54189_04_1.fastq CB7045-2/./WTCHG_54189_06_2.fastq CB7045-2/./WTCHG_54189_06_1.fastq CB6930-2/./WTCHG_54189_04_2.fastq CB6972-2/./WTCHG_54189_05_2.fastq CB1122-2/./WTCHG_54189_02_1.fastq CB1122-2/./WTCHG_54189_02_2.fastq' ++ cd /data/maqgene/reads ++ cat CB6972-2/./WTCHG_54189_05_1.fastq CB6930-2/./WTCHG_54189_04_1.fastq CB7045-2/./WTCHG_54189_06_2.fastq CB7045-2/./WTCHG_54189_06_1.fastq CB6930-2/./WTCHG_54189_04_2.fastq CB6972-2/./WTCHG_54189_05_2.fastq CB1122-2/./WTCHG_54189_02_1.fastq CB1122-2/./WTCHG_54189_02_2.fastq ++ wc -l ++ cut -f 1 -d ' ' + TOTAL_LINES=805465352 ++ echo '(805465352 / 5000000) + (805465352 % 5000000 != 0)' ++ bc + num_chunks=162 + 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=2769662419 map_cksum=3525698466 pileup_cksum=2929290487 cns_cksum=2734059306 umdd=50000 dmdd=1000 umid=1000 dmid=1000 max_gene_radius=50000 full_results_dir=/data/maqgene/out/example_user/CB7045_2 outfile_basename=CB7045_2 map_parameters=" -m 0.00001 -C 250 -n 2 -e 100 -1 0" assemble_parameters=" -N 2 -q 0 -r 0.0 -m 7 -Q 100 -p " pileup_parameters=" -Q 100 -m 7 -q 0" CHUNK_SIZE=5000000 NUM_CHUNKS=162 Will process 805465352 lines of input in 162 chunks make: Entering directory `/data/maqgene/work' # Mon Apr 22 13:33:43 BST 2013: Removing frontend files in case this is a duplicate run ... rm -f /data/maqgene/out/example_user/CB7045_2/CB7045_2_{grouped.txt,flat.txt} rm -f /data/maqgene/out/example_user/CB7045_2/CB7045_2_uncovered.txt /data/maqgene/out/example_user/CB7045_2/CB7045_2_coverage.txt /data/maqgene/out/example_user/CB7045_2/CB7045_2_pileup.txt /data/maqgene/out/example_user/CB7045_2/CB7045_2_log.txt /data/maqgene/out/example_user/CB7045_2/CB7045_2_check.txt /data/maqgene/out/example_user/CB7045_2/CB7045_2_unmapped.txt make: Leaving directory `/data/maqgene/work' make: Entering directory `/data/maqgene/work' /data/maqgene/makefile:73: warning: undefined variable `date' # : Regrouping fastq reads into chunks of size 5000000. split -l 5000000 -a 5 -d <(cat /data/maqgene/reads/CB6972-2/./WTCHG_54189_05_1.fastq /data/maqgene/reads/CB6930-2/./WTCHG_54189_04_1.fastq /data/maqgene/reads/CB7045-2/./WTCHG_54189_06_2.fastq /data/maqgene/reads/CB7045-2/./WTCHG_54189_06_1.fastq /data/maqgene/reads/CB6930-2/./WTCHG_54189_04_2.fastq /data/maqgene/reads/CB6972-2/./WTCHG_54189_05_2.fastq /data/maqgene/reads/CB1122-2/./WTCHG_54189_02_1.fastq /data/maqgene/reads/CB1122-2/./WTCHG_54189_02_2.fastq) 3525698466.1.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 00048 00049 00050 00051 00052 00053 00054 00055 00056 00057 00058 00059 00060 00061 00062 00063 00064 00065 00066 00067 00068 00069 00070 00071 00072 00073 00074 00075 00076 00077 00078 00079 00080 00081 00082 00083 00084 00085 00086 00087 00088 00089 00090 00091 00092 00093 00094 00095 00096 00097 00098 00099 00100 00101 00102 00103 00104 00105 00106 00107 00108 00109 00110 00111 00112 00113 00114 00115 00116 00117 00118 00119 00120 00121 00122 00123 00124 00125 00126 00127 00128 00129 00130 00131 00132 00133 00134 00135 00136 00137 00138 00139 00140 00141 00142 00143 00144 00145 00146 00147 00148 00149 00150 00151 00152 00153 00154 00155 00156 00157 00158 00159 00160 00161; do mv 3525698466.1.fastq.$stem 3525698466.$stem.1.fastq; done touch 2769662419_split1 # Mon Apr 22 13:39:02 BST 2013: Converting fastq files to bfq ... # Mon Apr 22 13:39:02 BST 2013: Converting fastq files to bfq ... # Mon Apr 22 13:39:02 BST 2013: Converting fastq files to bfq ... # Mon Apr 22 13:39:02 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00000.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00000.1.bfq /data/maqgene/bin/maq sol2sanger 3525698466.00001.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00001.1.bfq /data/maqgene/bin/maq sol2sanger 3525698466.00002.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00002.1.bfq # Mon Apr 22 13:39:02 BST 2013: Converting fastq files to bfq ... # Mon Apr 22 13:39:02 BST 2013: Converting fastq files to bfq ... # Mon Apr 22 13:39:02 BST 2013: Converting fastq files to bfq ... # Mon Apr 22 13:39:02 BST 2013: Converting fastq files to bfq ... # Mon Apr 22 13:39:02 BST 2013: Converting fastq files to bfq ... # Mon Apr 22 13:39:02 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00003.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00003.1.bfq /data/maqgene/bin/maq sol2sanger 3525698466.00004.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00004.1.bfq /data/maqgene/bin/maq sol2sanger 3525698466.00005.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00005.1.bfq # Mon Apr 22 13:39:02 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00006.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00006.1.bfq # Mon Apr 22 13:39:02 BST 2013: Converting fastq files to bfq ... # Mon Apr 22 13:39:02 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00007.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00007.1.bfq /data/maqgene/bin/maq sol2sanger 3525698466.00008.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00008.1.bfq /data/maqgene/bin/maq sol2sanger 3525698466.00009.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00009.1.bfq /data/maqgene/bin/maq sol2sanger 3525698466.00010.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00010.1.bfq /data/maqgene/bin/maq sol2sanger 3525698466.00011.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00011.1.bfq /data/maqgene/bin/maq sol2sanger 3525698466.00012.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00012.1.bfq # Mon Apr 22 13:39:02 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00013.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00013.1.bfq -- finish writing file '3525698466.00005.1.bfq' -- 1250000 sequences were loaded. # Mon Apr 22 13:39:25 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00014.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00014.1.bfq -- finish writing file '3525698466.00000.1.bfq' -- 1250000 sequences were loaded. # Mon Apr 22 13:39:35 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00015.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00015.1.bfq -- finish writing file '3525698466.00011.1.bfq' -- 1250000 sequences were loaded. # Mon Apr 22 13:39:35 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00016.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00016.1.bfq -- finish writing file '3525698466.00009.1.bfq' -- 1250000 sequences were loaded. # Mon Apr 22 13:39:36 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00017.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00017.1.bfq -- finish writing file '3525698466.00007.1.bfq' -- 1250000 sequences were loaded. # Mon Apr 22 13:39:36 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00018.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00018.1.bfq -- finish writing file '3525698466.00012.1.bfq' -- 1250000 sequences were loaded. # Mon Apr 22 13:39:36 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00019.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00019.1.bfq -- finish writing file '3525698466.00006.1.bfq' -- 1250000 sequences were loaded. # Mon Apr 22 13:39:36 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00020.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00020.1.bfq -- finish writing file '3525698466.00001.1.bfq' -- 1250000 sequences were loaded. # Mon Apr 22 13:39:36 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00021.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00021.1.bfq -- finish writing file '3525698466.00013.1.bfq' -- 1250000 sequences were loaded. # Mon Apr 22 13:39:36 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00022.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00022.1.bfq -- finish writing file '3525698466.00002.1.bfq' -- 1250000 sequences were loaded. # Mon Apr 22 13:39:36 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00023.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00023.1.bfq -- finish writing file '3525698466.00004.1.bfq' -- 1250000 sequences were loaded. # Mon Apr 22 13:39:37 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00024.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00024.1.bfq -- finish writing file '3525698466.00003.1.bfq' -- 1250000 sequences were loaded. # Mon Apr 22 13:39:37 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00025.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00025.1.bfq -- finish writing file '3525698466.00008.1.bfq' -- 1250000 sequences were loaded. # Mon Apr 22 13:39:38 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00026.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00026.1.bfq -- finish writing file '3525698466.00010.1.bfq' -- 1250000 sequences were loaded. # Mon Apr 22 13:39:38 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00027.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00027.1.bfq -- finish writing file '3525698466.00014.1.bfq' -- 1250000 sequences were loaded. # Mon Apr 22 13:39:58 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00028.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00028.1.bfq -- finish writing file '3525698466.00017.1.bfq' -- 1250000 sequences were loaded. # Mon Apr 22 13:39:59 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00029.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00029.1.bfq -- finish writing file '3525698466.00016.1.bfq' -- 1250000 sequences were loaded. # Mon Apr 22 13:40:08 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00030.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00030.1.bfq -- finish writing file '3525698466.00015.1.bfq' -- 1250000 sequences were loaded. # Mon Apr 22 13:40:10 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00031.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00031.1.bfq -- finish writing file '3525698466.00022.1.bfq' -- 1250000 sequences were loaded. # Mon Apr 22 13:40:11 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00032.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00032.1.bfq -- finish writing file '3525698466.00023.1.bfq' -- 1250000 sequences were loaded. # Mon Apr 22 13:40:11 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00033.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00033.1.bfq -- finish writing file '3525698466.00018.1.bfq' -- 1250000 sequences were loaded. # Mon Apr 22 13:40:11 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00034.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00034.1.bfq -- finish writing file '3525698466.00021.1.bfq' -- 1250000 sequences were loaded. # Mon Apr 22 13:40:12 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00035.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00035.1.bfq -- finish writing file '3525698466.00024.1.bfq' -- 1250000 sequences were loaded. # Mon Apr 22 13:40:13 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00036.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00036.1.bfq -- finish writing file '3525698466.00019.1.bfq' -- 1250000 sequences were loaded. # Mon Apr 22 13:40:13 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00037.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00037.1.bfq -- finish writing file '3525698466.00026.1.bfq' -- 1250000 sequences were loaded. # Mon Apr 22 13:40:13 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00038.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00038.1.bfq -- finish writing file '3525698466.00025.1.bfq' -- 1250000 sequences were loaded. # Mon Apr 22 13:40:13 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00039.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00039.1.bfq -- finish writing file '3525698466.00020.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00027.1.bfq' # Mon Apr 22 13:40:14 BST 2013: Converting fastq files to bfq ... -- 1250000 sequences were loaded. /data/maqgene/bin/maq sol2sanger 3525698466.00040.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00040.1.bfq # Mon Apr 22 13:40:14 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00041.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00041.1.bfq -- finish writing file '3525698466.00028.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00029.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00037.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00031.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00035.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00030.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00038.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00033.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00041.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00034.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00032.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00039.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00036.1.bfq' -- 1250000 sequences were loaded. # Mon Apr 22 13:40:46 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00052.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00052.1.bfq # Mon Apr 22 13:40:46 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00053.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00053.1.bfq -- finish writing file '3525698466.00040.1.bfq' -- 1250000 sequences were loaded. # Mon Apr 22 13:40:47 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00054.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00054.1.bfq # Mon Apr 22 13:40:48 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00055.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00055.1.bfq # Mon Apr 22 13:40:49 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00051.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00051.1.bfq # Mon Apr 22 13:40:50 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00050.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00050.1.bfq # Mon Apr 22 13:40:51 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00049.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00049.1.bfq # Mon Apr 22 13:40:52 BST 2013: Converting fastq files to bfq ... # Mon Apr 22 13:40:52 BST 2013: Converting fastq files to bfq ... # Mon Apr 22 13:40:52 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00046.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00046.1.bfq /data/maqgene/bin/maq sol2sanger 3525698466.00048.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00048.1.bfq /data/maqgene/bin/maq sol2sanger 3525698466.00047.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00047.1.bfq # Mon Apr 22 13:40:53 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00044.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00044.1.bfq # Mon Apr 22 13:40:53 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00045.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00045.1.bfq # Mon Apr 22 13:40:54 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00043.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00043.1.bfq # Mon Apr 22 13:40:54 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00042.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00042.1.bfq -- finish writing file '3525698466.00052.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00053.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00050.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00054.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00047.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00055.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00051.1.bfq' -- 1250000 sequences were loaded. # Mon Apr 22 13:41:22 BST 2013: Converting fastq files to bfq ... # Mon Apr 22 13:41:22 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00062.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00062.1.bfq /data/maqgene/bin/maq sol2sanger 3525698466.00061.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00061.1.bfq -- finish writing file '3525698466.00045.1.bfq' -- 1250000 sequences were loaded. # Mon Apr 22 13:41:22 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00060.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00060.1.bfq -- finish writing file '3525698466.00049.1.bfq' -- 1250000 sequences were loaded. # Mon Apr 22 13:41:22 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00063.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00063.1.bfq -- finish writing file '3525698466.00044.1.bfq' -- 1250000 sequences were loaded. # Mon Apr 22 13:41:23 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00064.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00064.1.bfq -- finish writing file '3525698466.00048.1.bfq' -- 1250000 sequences were loaded. # Mon Apr 22 13:41:23 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00065.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00065.1.bfq -- finish writing file '3525698466.00046.1.bfq' -- 1250000 sequences were loaded. # Mon Apr 22 13:41:23 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00066.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00066.1.bfq # Mon Apr 22 13:41:24 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00067.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00067.1.bfq -- finish writing file '3525698466.00043.1.bfq' -- 1250000 sequences were loaded. # Mon Apr 22 13:41:25 BST 2013: Converting fastq files to bfq ... # Mon Apr 22 13:41:25 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00058.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00058.1.bfq /data/maqgene/bin/maq sol2sanger 3525698466.00059.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00059.1.bfq -- finish writing file '3525698466.00042.1.bfq' -- 1250000 sequences were loaded. # Mon Apr 22 13:41:26 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00068.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00068.1.bfq # Mon Apr 22 13:41:27 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00057.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00057.1.bfq # Mon Apr 22 13:41:27 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00056.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00056.1.bfq # Mon Apr 22 13:41:27 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00069.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00069.1.bfq -- finish writing file '3525698466.00066.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00063.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00056.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00061.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00065.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00060.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00062.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00068.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00064.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00057.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00067.1.bfq' -- 1250000 sequences were loaded. # Mon Apr 22 13:41:57 BST 2013: Converting fastq files to bfq ... # Mon Apr 22 13:41:57 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00079.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00079.1.bfq /data/maqgene/bin/maq sol2sanger 3525698466.00078.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00078.1.bfq -- finish writing file '3525698466.00059.1.bfq' -- 1250000 sequences were loaded. # Mon Apr 22 13:41:58 BST 2013: Converting fastq files to bfq ... # Mon Apr 22 13:41:58 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00080.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00080.1.bfq /data/maqgene/bin/maq sol2sanger 3525698466.00077.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00077.1.bfq -- finish writing file '3525698466.00058.1.bfq' -- 1250000 sequences were loaded. # Mon Apr 22 13:41:58 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00081.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00081.1.bfq # Mon Apr 22 13:41:59 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00076.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00076.1.bfq # Mon Apr 22 13:41:59 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00082.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00082.1.bfq # Mon Apr 22 13:42:00 BST 2013: Converting fastq files to bfq ... # Mon Apr 22 13:42:00 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00075.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00075.1.bfq /data/maqgene/bin/maq sol2sanger 3525698466.00074.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00074.1.bfq -- finish writing file '3525698466.00069.1.bfq' -- 1250000 sequences were loaded. # Mon Apr 22 13:42:00 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00073.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00073.1.bfq # Mon Apr 22 13:42:01 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00083.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00083.1.bfq # Mon Apr 22 13:42:01 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00072.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00072.1.bfq # Mon Apr 22 13:42:02 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00071.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00071.1.bfq # Mon Apr 22 13:42:03 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00070.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00070.1.bfq -- finish writing file '3525698466.00079.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00074.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00078.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00080.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00077.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00071.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00081.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00082.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00076.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00075.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00083.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00072.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00073.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00070.1.bfq' -- 1250000 sequences were loaded. # Mon Apr 22 13:42:36 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00096.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00096.1.bfq # Mon Apr 22 13:42:37 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00097.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00097.1.bfq # Mon Apr 22 13:42:37 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00095.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00095.1.bfq /data/maqgene/bin/maq sol2sanger 3525698466.00094.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00094.1.bfq # Mon Apr 22 13:42:38 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00092.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00092.1.bfq # Mon Apr 22 13:42:38 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00093.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00093.1.bfq # Mon Apr 22 13:42:39 BST 2013: Converting fastq files to bfq ... # Mon Apr 22 13:42:39 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00091.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00091.1.bfq /data/maqgene/bin/maq sol2sanger 3525698466.00090.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00090.1.bfq # Mon Apr 22 13:42:40 BST 2013: Converting fastq files to bfq ... # Mon Apr 22 13:42:40 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00089.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00089.1.bfq /data/maqgene/bin/maq sol2sanger 3525698466.00088.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00088.1.bfq # Mon Apr 22 13:42:41 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00087.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00087.1.bfq # Mon Apr 22 13:42:41 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00086.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00086.1.bfq # Mon Apr 22 13:42:42 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00084.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00084.1.bfq # Mon Apr 22 13:42:42 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00085.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00085.1.bfq -- finish writing file '3525698466.00086.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00096.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00097.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00094.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00095.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00093.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00092.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00090.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00091.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00089.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00088.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00087.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00085.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00084.1.bfq' -- 1250000 sequences were loaded. # Mon Apr 22 13:43:13 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00110.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00110.1.bfq # Mon Apr 22 13:43:17 BST 2013: Converting fastq files to bfq ... # Mon Apr 22 13:43:17 BST 2013: Converting fastq files to bfq ... out | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00109.1.bfq /data/maqgene/bin/maq sol2sanger 3525698466.00111.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00111.1.bfq # Mon Apr 22 13:43:17 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00108.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00108.1.bfq # Mon Apr 22 13:43:18 BST 2013: Converting fastq files to bfq ... # Mon Apr 22 13:43:18 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00107.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00107.1.bfq # Mon Apr 22 13:43:18 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00105.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00105.1.bfq /data/maqgene/bin/maq sol2sanger 3525698466.00106.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00106.1.bfq # Mon Apr 22 13:43:19 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00104.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00104.1.bfq # Mon Apr 22 13:43:19 BST 2013: Converting fastq files to bfq ... # Mon Apr 22 13:43:19 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00102.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00102.1.bfq /data/maqgene/bin/maq sol2sanger 3525698466.00103.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00103.1.bfq # Mon Apr 22 13:43:20 BST 2013: Converting fastq files to bfq ... # Mon Apr 22 13:43:20 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00099.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00099.1.bfq /data/maqgene/bin/maq sol2sanger 3525698466.00100.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00100.1.bfq # Mon Apr 22 13:43:20 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00101.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00101.1.bfq # Mon Apr 22 13:43:21 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00098.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00098.1.bfq -- finish writing file '3525698466.00105.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00110.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00111.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00103.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00106.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00109.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00108.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00098.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00107.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00104.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00099.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00100.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00102.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00101.1.bfq' -- 1250000 sequences were loaded. # Mon Apr 22 13:43:54 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00124.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00124.1.bfq # Mon Apr 22 13:43:57 BST 2013: Converting fastq files to bfq ... # Mon Apr 22 13:43:57 BST 2013: Converting fastq files to bfq ... # Mon Apr 22 13:43:57 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00125.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00125.1.bfq /data/maqgene/bin/maq sol2sanger 3525698466.00123.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00123.1.bfq /data/maqgene/bin/maq sol2sanger 3525698466.00122.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00122.1.bfq # Mon Apr 22 13:43:58 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00121.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00121.1.bfq # Mon Apr 22 13:43:58 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00120.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00120.1.bfq # Mon Apr 22 13:43:59 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00119.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00119.1.bfq # Mon Apr 22 13:43:59 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00118.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00118.1.bfq # Mon Apr 22 13:44:00 BST 2013: Converting fastq files to bfq ... # Mon Apr 22 13:44:00 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00117.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00117.1.bfq /data/maqgene/bin/maq sol2sanger 3525698466.00116.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00116.1.bfq # Mon Apr 22 13:44:01 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00114.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00114.1.bfq # Mon Apr 22 13:44:01 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00115.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00115.1.bfq # Mon Apr 22 13:44:02 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00113.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00113.1.bfq # Mon Apr 22 13:44:03 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00112.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00112.1.bfq -- finish writing file '3525698466.00122.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00121.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00124.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00123.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00125.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00118.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00117.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00120.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00119.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00116.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00115.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00114.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00113.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00112.1.bfq' -- 1250000 sequences were loaded. # Mon Apr 22 13:44:34 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00138.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00138.1.bfq # Mon Apr 22 13:44:37 BST 2013: Converting fastq files to bfq ... # Mon Apr 22 13:44:37 BST 2013: Converting fastq files to bfq ... # Mon Apr 22 13:44:37 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00137.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00137.1.bfq /data/maqgene/bin/maq sol2sanger 3525698466.00139.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00139.1.bfq /data/maqgene/bin/maq sol2sanger 3525698466.00136.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00136.1.bfq /data/maqgene/bin/maq sol2sanger 3525698466.00135.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00135.1.bfq # Mon Apr 22 13:44:38 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00134.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00134.1.bfq # Mon Apr 22 13:44:38 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00133.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00133.1.bfq # Mon Apr 22 13:44:38 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00132.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00132.1.bfq # Mon Apr 22 13:44:39 BST 2013: Converting fastq files to bfq ... # Mon Apr 22 13:44:39 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00130.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00130.1.bfq # Mon Apr 22 13:44:39 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00131.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00131.1.bfq /data/maqgene/bin/maq sol2sanger 3525698466.00129.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00129.1.bfq # Mon Apr 22 13:44:40 BST 2013: Converting fastq files to bfq ... # Mon Apr 22 13:44:40 BST 2013: Converting fastq files to bfq ... out | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00127.1.bfq /data/maqgene/bin/maq sol2sanger 3525698466.00126.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00126.1.bfq # Mon Apr 22 13:44:40 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00128.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00128.1.bfq -- finish writing file '3525698466.00139.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00138.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00131.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00135.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00133.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00130.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00136.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00137.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00128.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00134.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00132.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00126.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00129.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00127.1.bfq' -- 1250000 sequences were loaded. # Mon Apr 22 13:45:13 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00152.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00152.1.bfq # Mon Apr 22 13:45:17 BST 2013: Converting fastq files to bfq ... # Mon Apr 22 13:45:17 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00151.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00151.1.bfq /data/maqgene/bin/maq sol2sanger 3525698466.00153.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00153.1.bfq # Mon Apr 22 13:45:18 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00150.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00150.1.bfq # Mon Apr 22 13:45:19 BST 2013: Converting fastq files to bfq ... # Mon Apr 22 13:45:19 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00149.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00149.1.bfq /data/maqgene/bin/maq sol2sanger 3525698466.00148.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00148.1.bfq # Mon Apr 22 13:45:20 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00147.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00147.1.bfq # Mon Apr 22 13:45:21 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00146.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00146.1.bfq # Mon Apr 22 13:45:21 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00145.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00145.1.bfq # Mon Apr 22 13:45:22 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00144.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00144.1.bfq # Mon Apr 22 13:45:22 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00143.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00143.1.bfq # Mon Apr 22 13:45:23 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00142.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00142.1.bfq # Mon Apr 22 13:45:23 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00141.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00141.1.bfq # Mon Apr 22 13:45:24 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00140.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00140.1.bfq -- finish writing file '3525698466.00152.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00151.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00150.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00153.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00148.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00142.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00147.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00146.1.bfq' -- 1250000 sequences were loaded. # Mon Apr 22 13:45:52 BST 2013: Converting fastq files to bfq ... # Mon Apr 22 13:45:52 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00160.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00160.1.bfq /data/maqgene/bin/maq sol2sanger 3525698466.00161.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00161.1.bfq -- finish writing file '3525698466.00149.1.bfq' -- 1250000 sequences were loaded. # Mon Apr 22 13:45:52 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00159.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00159.1.bfq # Mon Apr 22 13:45:53 BST 2013: Mapping file(s) 3525698466.00000.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00000.unmapped -H 3525698466.00000.mismatch \ 3525698466.00000.map /data/maqgene/genomes/elegans.bfa 3525698466.00000.1.bfq 2> /dev/null -- finish writing file '3525698466.00145.1.bfq' -- 1250000 sequences were loaded. # Mon Apr 22 13:45:54 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00158.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00158.1.bfq # Mon Apr 22 13:45:54 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00157.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00157.1.bfq -- finish writing file '3525698466.00141.1.bfq' -- 1250000 sequences were loaded. # Mon Apr 22 13:45:54 BST 2013: Mapping file(s) 3525698466.00001.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00001.unmapped -H 3525698466.00001.mismatch \ 3525698466.00001.map /data/maqgene/genomes/elegans.bfa 3525698466.00001.1.bfq 2> /dev/null -- finish writing file '3525698466.00143.1.bfq' -- 1250000 sequences were loaded. # Mon Apr 22 13:45:54 BST 2013: Mapping file(s) 3525698466.00002.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00002.unmapped -H 3525698466.00002.mismatch \ 3525698466.00002.map /data/maqgene/genomes/elegans.bfa 3525698466.00002.1.bfq 2> /dev/null -- finish writing file '3525698466.00144.1.bfq' -- 1250000 sequences were loaded. # Mon Apr 22 13:45:54 BST 2013: Mapping file(s) 3525698466.00003.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00003.unmapped -H 3525698466.00003.mismatch \ 3525698466.00003.map /data/maqgene/genomes/elegans.bfa 3525698466.00003.1.bfq 2> /dev/null -- finish writing file '3525698466.00161.1.bfq' -- 116338 sequences were loaded. # Mon Apr 22 13:45:54 BST 2013: Mapping file(s) 3525698466.00004.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00004.unmapped -H 3525698466.00004.mismatch \ 3525698466.00004.map /data/maqgene/genomes/elegans.bfa 3525698466.00004.1.bfq 2> /dev/null -- finish writing file '3525698466.00140.1.bfq' -- 1250000 sequences were loaded. # Mon Apr 22 13:45:55 BST 2013: Converting fastq files to bfq ... # Mon Apr 22 13:45:55 BST 2013: Mapping file(s) 3525698466.00005.1.bfq /data/maqgene/bin/maq sol2sanger 3525698466.00156.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00156.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00005.unmapped -H 3525698466.00005.mismatch \ 3525698466.00005.map /data/maqgene/genomes/elegans.bfa 3525698466.00005.1.bfq 2> /dev/null # Mon Apr 22 13:45:56 BST 2013: Mapping file(s) 3525698466.00006.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00006.unmapped -H 3525698466.00006.mismatch \ 3525698466.00006.map /data/maqgene/genomes/elegans.bfa 3525698466.00006.1.bfq 2> /dev/null # Mon Apr 22 13:45:57 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00155.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00155.1.bfq # Mon Apr 22 13:45:58 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3525698466.00154.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3525698466.00154.1.bfq -- finish writing file '3525698466.00158.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00159.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00160.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00156.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3525698466.00157.1.bfq' -- 1250000 sequences were loaded. # Mon Apr 22 13:46:28 BST 2013: Mapping file(s) 3525698466.00011.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00011.unmapped -H 3525698466.00011.mismatch \ 3525698466.00011.map /data/maqgene/genomes/elegans.bfa 3525698466.00011.1.bfq 2> /dev/null # Mon Apr 22 13:46:29 BST 2013: Mapping file(s) 3525698466.00010.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00010.unmapped -H 3525698466.00010.mismatch \ 3525698466.00010.map /data/maqgene/genomes/elegans.bfa 3525698466.00010.1.bfq 2> /dev/null -- finish writing file '3525698466.00155.1.bfq' -- 1250000 sequences were loaded. # Mon Apr 22 13:46:29 BST 2013: Mapping file(s) 3525698466.00009.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00009.unmapped -H 3525698466.00009.mismatch \ 3525698466.00009.map /data/maqgene/genomes/elegans.bfa 3525698466.00009.1.bfq 2> /dev/null # Mon Apr 22 13:46:30 BST 2013: Mapping file(s) 3525698466.00012.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00012.unmapped -H 3525698466.00012.mismatch \ 3525698466.00012.map /data/maqgene/genomes/elegans.bfa 3525698466.00012.1.bfq 2> /dev/null -- finish writing file '3525698466.00154.1.bfq' -- 1250000 sequences were loaded. # Mon Apr 22 13:46:31 BST 2013: Mapping file(s) 3525698466.00008.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00008.unmapped -H 3525698466.00008.mismatch \ 3525698466.00008.map /data/maqgene/genomes/elegans.bfa 3525698466.00008.1.bfq 2> /dev/null # Mon Apr 22 13:46:32 BST 2013: Mapping file(s) 3525698466.00013.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00013.unmapped -H 3525698466.00013.mismatch \ 3525698466.00013.map /data/maqgene/genomes/elegans.bfa 3525698466.00013.1.bfq 2> /dev/null # Mon Apr 22 13:46:33 BST 2013: Mapping file(s) 3525698466.00007.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00007.unmapped -H 3525698466.00007.mismatch \ 3525698466.00007.map /data/maqgene/genomes/elegans.bfa 3525698466.00007.1.bfq 2> /dev/null # Mon Apr 22 13:50:18 BST 2013: Mapping file(s) 3525698466.00020.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00020.unmapped -H 3525698466.00020.mismatch \ 3525698466.00020.map /data/maqgene/genomes/elegans.bfa 3525698466.00020.1.bfq 2> /dev/null # Mon Apr 22 13:50:19 BST 2013: Mapping file(s) 3525698466.00019.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00019.unmapped -H 3525698466.00019.mismatch \ 3525698466.00019.map /data/maqgene/genomes/elegans.bfa 3525698466.00019.1.bfq 2> /dev/null # Mon Apr 22 13:50:20 BST 2013: Mapping file(s) 3525698466.00018.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00018.unmapped -H 3525698466.00018.mismatch \ 3525698466.00018.map /data/maqgene/genomes/elegans.bfa 3525698466.00018.1.bfq 2> /dev/null # Mon Apr 22 13:50:21 BST 2013: Mapping file(s) 3525698466.00017.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00017.unmapped -H 3525698466.00017.mismatch \ 3525698466.00017.map /data/maqgene/genomes/elegans.bfa 3525698466.00017.1.bfq 2> /dev/null # Mon Apr 22 13:50:22 BST 2013: Mapping file(s) 3525698466.00016.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00016.unmapped -H 3525698466.00016.mismatch \ 3525698466.00016.map /data/maqgene/genomes/elegans.bfa 3525698466.00016.1.bfq 2> /dev/null # Mon Apr 22 13:50:23 BST 2013: Mapping file(s) 3525698466.00015.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00015.unmapped -H 3525698466.00015.mismatch \ 3525698466.00015.map /data/maqgene/genomes/elegans.bfa 3525698466.00015.1.bfq 2> /dev/null # Mon Apr 22 13:50:24 BST 2013: Mapping file(s) 3525698466.00014.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00014.unmapped -H 3525698466.00014.mismatch \ 3525698466.00014.map /data/maqgene/genomes/elegans.bfa 3525698466.00014.1.bfq 2> /dev/null # Mon Apr 22 13:50:25 BST 2013: Mapping file(s) 3525698466.00021.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00021.unmapped -H 3525698466.00021.mismatch \ 3525698466.00021.map /data/maqgene/genomes/elegans.bfa 3525698466.00021.1.bfq 2> /dev/null # Mon Apr 22 13:50:43 BST 2013: Mapping file(s) 3525698466.00026.1.bfq # Mon Apr 22 13:50:43 BST 2013: Mapping file(s) 3525698466.00025.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00026.unmapped -H 3525698466.00026.mismatch \ 3525698466.00026.map /data/maqgene/genomes/elegans.bfa 3525698466.00026.1.bfq 2> /dev/null /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00025.unmapped -H 3525698466.00025.mismatch \ 3525698466.00025.map /data/maqgene/genomes/elegans.bfa 3525698466.00025.1.bfq 2> /dev/null # Mon Apr 22 13:50:44 BST 2013: Mapping file(s) 3525698466.00024.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00024.unmapped -H 3525698466.00024.mismatch \ 3525698466.00024.map /data/maqgene/genomes/elegans.bfa 3525698466.00024.1.bfq 2> /dev/null # Mon Apr 22 13:50:45 BST 2013: Mapping file(s) 3525698466.00023.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00023.unmapped -H 3525698466.00023.mismatch \ 3525698466.00023.map /data/maqgene/genomes/elegans.bfa 3525698466.00023.1.bfq 2> /dev/null # Mon Apr 22 13:50:46 BST 2013: Mapping file(s) 3525698466.00022.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00022.unmapped -H 3525698466.00022.mismatch \ 3525698466.00022.map /data/maqgene/genomes/elegans.bfa 3525698466.00022.1.bfq 2> /dev/null # Mon Apr 22 13:50:46 BST 2013: Mapping file(s) 3525698466.00027.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00027.unmapped -H 3525698466.00027.mismatch \ 3525698466.00027.map /data/maqgene/genomes/elegans.bfa 3525698466.00027.1.bfq 2> /dev/null # Mon Apr 22 13:54:38 BST 2013: Mapping file(s) 3525698466.00033.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00033.unmapped -H 3525698466.00033.mismatch \ 3525698466.00033.map /data/maqgene/genomes/elegans.bfa 3525698466.00033.1.bfq 2> /dev/null # Mon Apr 22 13:54:40 BST 2013: Mapping file(s) 3525698466.00034.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00034.unmapped -H 3525698466.00034.mismatch \ 3525698466.00034.map /data/maqgene/genomes/elegans.bfa 3525698466.00034.1.bfq 2> /dev/null # Mon Apr 22 13:54:42 BST 2013: Mapping file(s) 3525698466.00035.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00035.unmapped -H 3525698466.00035.mismatch \ 3525698466.00035.map /data/maqgene/genomes/elegans.bfa 3525698466.00035.1.bfq 2> /dev/null # Mon Apr 22 13:54:43 BST 2013: Mapping file(s) 3525698466.00031.1.bfq # Mon Apr 22 13:54:43 BST 2013: Mapping file(s) 3525698466.00032.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00031.unmapped -H 3525698466.00031.mismatch \ 3525698466.00031.map /data/maqgene/genomes/elegans.bfa 3525698466.00031.1.bfq 2> /dev/null /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00032.unmapped -H 3525698466.00032.mismatch \ 3525698466.00032.map /data/maqgene/genomes/elegans.bfa 3525698466.00032.1.bfq 2> /dev/null # Mon Apr 22 13:54:44 BST 2013: Mapping file(s) 3525698466.00030.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00030.unmapped -H 3525698466.00030.mismatch \ 3525698466.00030.map /data/maqgene/genomes/elegans.bfa 3525698466.00030.1.bfq 2> /dev/null # Mon Apr 22 13:54:45 BST 2013: Mapping file(s) 3525698466.00028.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00028.unmapped -H 3525698466.00028.mismatch \ 3525698466.00028.map /data/maqgene/genomes/elegans.bfa 3525698466.00028.1.bfq 2> /dev/null # Mon Apr 22 13:54:45 BST 2013: Mapping file(s) 3525698466.00029.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00029.unmapped -H 3525698466.00029.mismatch \ 3525698466.00029.map /data/maqgene/genomes/elegans.bfa 3525698466.00029.1.bfq 2> /dev/null # Mon Apr 22 13:54:47 BST 2013: Mapping file(s) 3525698466.00036.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00036.unmapped -H 3525698466.00036.mismatch \ 3525698466.00036.map /data/maqgene/genomes/elegans.bfa 3525698466.00036.1.bfq 2> /dev/null # Mon Apr 22 13:54:51 BST 2013: Mapping file(s) 3525698466.00037.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00037.unmapped -H 3525698466.00037.mismatch \ 3525698466.00037.map /data/maqgene/genomes/elegans.bfa 3525698466.00037.1.bfq 2> /dev/null # Mon Apr 22 13:54:55 BST 2013: Mapping file(s) 3525698466.00038.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00038.unmapped -H 3525698466.00038.mismatch \ 3525698466.00038.map /data/maqgene/genomes/elegans.bfa 3525698466.00038.1.bfq 2> /dev/null # Mon Apr 22 13:55:01 BST 2013: Mapping file(s) 3525698466.00039.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00039.unmapped -H 3525698466.00039.mismatch \ 3525698466.00039.map /data/maqgene/genomes/elegans.bfa 3525698466.00039.1.bfq 2> /dev/null # Mon Apr 22 13:55:23 BST 2013: Mapping file(s) 3525698466.00041.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00041.unmapped -H 3525698466.00041.mismatch \ 3525698466.00041.map /data/maqgene/genomes/elegans.bfa 3525698466.00041.1.bfq 2> /dev/null # Mon Apr 22 13:55:24 BST 2013: Mapping file(s) 3525698466.00040.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00040.unmapped -H 3525698466.00040.mismatch \ 3525698466.00040.map /data/maqgene/genomes/elegans.bfa 3525698466.00040.1.bfq 2> /dev/null # Mon Apr 22 13:58:54 BST 2013: Mapping file(s) 3525698466.00046.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00046.unmapped -H 3525698466.00046.mismatch \ 3525698466.00046.map /data/maqgene/genomes/elegans.bfa 3525698466.00046.1.bfq 2> /dev/null # Mon Apr 22 13:58:55 BST 2013: Mapping file(s) 3525698466.00045.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00045.unmapped -H 3525698466.00045.mismatch \ 3525698466.00045.map /data/maqgene/genomes/elegans.bfa 3525698466.00045.1.bfq 2> /dev/null # Mon Apr 22 13:58:56 BST 2013: Mapping file(s) 3525698466.00047.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00047.unmapped -H 3525698466.00047.mismatch \ 3525698466.00047.map /data/maqgene/genomes/elegans.bfa 3525698466.00047.1.bfq 2> /dev/null # Mon Apr 22 13:58:57 BST 2013: Mapping file(s) 3525698466.00044.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00044.unmapped -H 3525698466.00044.mismatch \ 3525698466.00044.map /data/maqgene/genomes/elegans.bfa 3525698466.00044.1.bfq 2> /dev/null # Mon Apr 22 13:58:57 BST 2013: Mapping file(s) 3525698466.00043.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00043.unmapped -H 3525698466.00043.mismatch \ 3525698466.00043.map /data/maqgene/genomes/elegans.bfa 3525698466.00043.1.bfq 2> /dev/null # Mon Apr 22 13:58:58 BST 2013: Mapping file(s) 3525698466.00048.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00048.unmapped -H 3525698466.00048.mismatch \ 3525698466.00048.map /data/maqgene/genomes/elegans.bfa 3525698466.00048.1.bfq 2> /dev/null # Mon Apr 22 13:58:58 BST 2013: Mapping file(s) 3525698466.00042.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00042.unmapped -H 3525698466.00042.mismatch \ 3525698466.00042.map /data/maqgene/genomes/elegans.bfa 3525698466.00042.1.bfq 2> /dev/null # Mon Apr 22 13:58:59 BST 2013: Mapping file(s) 3525698466.00049.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00049.unmapped -H 3525698466.00049.mismatch \ 3525698466.00049.map /data/maqgene/genomes/elegans.bfa 3525698466.00049.1.bfq 2> /dev/null # Mon Apr 22 13:59:02 BST 2013: Mapping file(s) 3525698466.00050.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00050.unmapped -H 3525698466.00050.mismatch \ 3525698466.00050.map /data/maqgene/genomes/elegans.bfa 3525698466.00050.1.bfq 2> /dev/null # Mon Apr 22 13:59:19 BST 2013: Mapping file(s) 3525698466.00052.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00052.unmapped -H 3525698466.00052.mismatch \ 3525698466.00052.map /data/maqgene/genomes/elegans.bfa 3525698466.00052.1.bfq 2> /dev/null # Mon Apr 22 13:59:20 BST 2013: Mapping file(s) 3525698466.00051.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00051.unmapped -H 3525698466.00051.mismatch \ 3525698466.00051.map /data/maqgene/genomes/elegans.bfa 3525698466.00051.1.bfq 2> /dev/null # Mon Apr 22 14:00:04 BST 2013: Mapping file(s) 3525698466.00055.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00055.unmapped -H 3525698466.00055.mismatch \ 3525698466.00055.map /data/maqgene/genomes/elegans.bfa 3525698466.00055.1.bfq 2> /dev/null # Mon Apr 22 14:00:05 BST 2013: Mapping file(s) 3525698466.00054.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00054.unmapped -H 3525698466.00054.mismatch \ 3525698466.00054.map /data/maqgene/genomes/elegans.bfa 3525698466.00054.1.bfq 2> /dev/null # Mon Apr 22 14:00:06 BST 2013: Mapping file(s) 3525698466.00053.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00053.unmapped -H 3525698466.00053.mismatch \ 3525698466.00053.map /data/maqgene/genomes/elegans.bfa 3525698466.00053.1.bfq 2> /dev/null # Mon Apr 22 14:03:05 BST 2013: Mapping file(s) 3525698466.00062.1.bfq # Mon Apr 22 14:03:05 BST 2013: Mapping file(s) 3525698466.00061.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00062.unmapped -H 3525698466.00062.mismatch \ 3525698466.00062.map /data/maqgene/genomes/elegans.bfa 3525698466.00062.1.bfq 2> /dev/null /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00061.unmapped -H 3525698466.00061.mismatch \ 3525698466.00061.map /data/maqgene/genomes/elegans.bfa 3525698466.00061.1.bfq 2> /dev/null # Mon Apr 22 14:03:06 BST 2013: Mapping file(s) 3525698466.00060.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00060.unmapped -H 3525698466.00060.mismatch \ 3525698466.00060.map /data/maqgene/genomes/elegans.bfa 3525698466.00060.1.bfq 2> /dev/null # Mon Apr 22 14:03:07 BST 2013: Mapping file(s) 3525698466.00058.1.bfq # Mon Apr 22 14:03:07 BST 2013: Mapping file(s) 3525698466.00059.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00058.unmapped -H 3525698466.00058.mismatch \ 3525698466.00058.map /data/maqgene/genomes/elegans.bfa 3525698466.00058.1.bfq 2> /dev/null /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00059.unmapped -H 3525698466.00059.mismatch \ 3525698466.00059.map /data/maqgene/genomes/elegans.bfa 3525698466.00059.1.bfq 2> /dev/null # Mon Apr 22 14:03:07 BST 2013: Mapping file(s) 3525698466.00057.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00057.unmapped -H 3525698466.00057.mismatch \ 3525698466.00057.map /data/maqgene/genomes/elegans.bfa 3525698466.00057.1.bfq 2> /dev/null # Mon Apr 22 14:03:08 BST 2013: Mapping file(s) 3525698466.00063.1.bfq # Mon Apr 22 14:03:08 BST 2013: Mapping file(s) 3525698466.00056.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00063.unmapped -H 3525698466.00063.mismatch \ 3525698466.00063.map /data/maqgene/genomes/elegans.bfa 3525698466.00063.1.bfq 2> /dev/null /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00056.unmapped -H 3525698466.00056.mismatch \ 3525698466.00056.map /data/maqgene/genomes/elegans.bfa 3525698466.00056.1.bfq 2> /dev/null # Mon Apr 22 14:03:09 BST 2013: Mapping file(s) 3525698466.00064.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00064.unmapped -H 3525698466.00064.mismatch \ 3525698466.00064.map /data/maqgene/genomes/elegans.bfa 3525698466.00064.1.bfq 2> /dev/null # Mon Apr 22 14:03:16 BST 2013: Mapping file(s) 3525698466.00065.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00065.unmapped -H 3525698466.00065.mismatch \ 3525698466.00065.map /data/maqgene/genomes/elegans.bfa 3525698466.00065.1.bfq 2> /dev/null # Mon Apr 22 14:03:29 BST 2013: Mapping file(s) 3525698466.00066.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00066.unmapped -H 3525698466.00066.mismatch \ 3525698466.00066.map /data/maqgene/genomes/elegans.bfa 3525698466.00066.1.bfq 2> /dev/null # Mon Apr 22 14:04:30 BST 2013: Mapping file(s) 3525698466.00068.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00068.unmapped -H 3525698466.00068.mismatch \ 3525698466.00068.map /data/maqgene/genomes/elegans.bfa 3525698466.00068.1.bfq 2> /dev/null # Mon Apr 22 14:04:32 BST 2013: Mapping file(s) 3525698466.00067.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00067.unmapped -H 3525698466.00067.mismatch \ 3525698466.00067.map /data/maqgene/genomes/elegans.bfa 3525698466.00067.1.bfq 2> /dev/null # Mon Apr 22 14:05:50 BST 2013: Mapping file(s) 3525698466.00069.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00069.unmapped -H 3525698466.00069.mismatch \ 3525698466.00069.map /data/maqgene/genomes/elegans.bfa 3525698466.00069.1.bfq 2> /dev/null # Mon Apr 22 14:07:15 BST 2013: Mapping file(s) 3525698466.00076.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00076.unmapped -H 3525698466.00076.mismatch \ 3525698466.00076.map /data/maqgene/genomes/elegans.bfa 3525698466.00076.1.bfq 2> /dev/null # Mon Apr 22 14:07:15 BST 2013: Mapping file(s) 3525698466.00075.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00075.unmapped -H 3525698466.00075.mismatch \ 3525698466.00075.map /data/maqgene/genomes/elegans.bfa 3525698466.00075.1.bfq 2> /dev/null # Mon Apr 22 14:07:16 BST 2013: Mapping file(s) 3525698466.00077.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00077.unmapped -H 3525698466.00077.mismatch \ 3525698466.00077.map /data/maqgene/genomes/elegans.bfa 3525698466.00077.1.bfq 2> /dev/null # Mon Apr 22 14:07:17 BST 2013: Mapping file(s) 3525698466.00074.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00074.unmapped -H 3525698466.00074.mismatch \ 3525698466.00074.map /data/maqgene/genomes/elegans.bfa 3525698466.00074.1.bfq 2> /dev/null # Mon Apr 22 14:07:17 BST 2013: Mapping file(s) 3525698466.00073.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00073.unmapped -H 3525698466.00073.mismatch \ 3525698466.00073.map /data/maqgene/genomes/elegans.bfa 3525698466.00073.1.bfq 2> /dev/null # Mon Apr 22 14:07:18 BST 2013: Mapping file(s) 3525698466.00078.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00078.unmapped -H 3525698466.00078.mismatch \ 3525698466.00078.map /data/maqgene/genomes/elegans.bfa 3525698466.00078.1.bfq 2> /dev/null # Mon Apr 22 14:07:19 BST 2013: Mapping file(s) 3525698466.00072.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00072.unmapped -H 3525698466.00072.mismatch \ 3525698466.00072.map /data/maqgene/genomes/elegans.bfa 3525698466.00072.1.bfq 2> /dev/null # Mon Apr 22 14:07:19 BST 2013: Mapping file(s) 3525698466.00071.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00071.unmapped -H 3525698466.00071.mismatch \ 3525698466.00071.map /data/maqgene/genomes/elegans.bfa 3525698466.00071.1.bfq 2> /dev/null # Mon Apr 22 14:07:20 BST 2013: Mapping file(s) 3525698466.00070.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00070.unmapped -H 3525698466.00070.mismatch \ 3525698466.00070.map /data/maqgene/genomes/elegans.bfa 3525698466.00070.1.bfq 2> /dev/null # Mon Apr 22 14:07:20 BST 2013: Mapping file(s) 3525698466.00079.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00079.unmapped -H 3525698466.00079.mismatch \ 3525698466.00079.map /data/maqgene/genomes/elegans.bfa 3525698466.00079.1.bfq 2> /dev/null # Mon Apr 22 14:07:21 BST 2013: Mapping file(s) 3525698466.00080.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00080.unmapped -H 3525698466.00080.mismatch \ 3525698466.00080.map /data/maqgene/genomes/elegans.bfa 3525698466.00080.1.bfq 2> /dev/null # Mon Apr 22 14:10:10 BST 2013: Mapping file(s) 3525698466.00083.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00083.unmapped -H 3525698466.00083.mismatch \ 3525698466.00083.map /data/maqgene/genomes/elegans.bfa 3525698466.00083.1.bfq 2> /dev/null # Mon Apr 22 14:10:11 BST 2013: Mapping file(s) 3525698466.00082.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00082.unmapped -H 3525698466.00082.mismatch \ 3525698466.00082.map /data/maqgene/genomes/elegans.bfa 3525698466.00082.1.bfq 2> /dev/null # Mon Apr 22 14:10:12 BST 2013: Mapping file(s) 3525698466.00081.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00081.unmapped -H 3525698466.00081.mismatch \ 3525698466.00081.map /data/maqgene/genomes/elegans.bfa 3525698466.00081.1.bfq 2> /dev/null # Mon Apr 22 14:11:30 BST 2013: Mapping file(s) 3525698466.00093.1.bfq # Mon Apr 22 14:11:30 BST 2013: Mapping file(s) 3525698466.00092.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00093.unmapped -H 3525698466.00093.mismatch \ 3525698466.00093.map /data/maqgene/genomes/elegans.bfa 3525698466.00093.1.bfq 2> /dev/null /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00092.unmapped -H 3525698466.00092.mismatch \ 3525698466.00092.map /data/maqgene/genomes/elegans.bfa 3525698466.00092.1.bfq 2> /dev/null # Mon Apr 22 14:11:31 BST 2013: Mapping file(s) 3525698466.00091.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00091.unmapped -H 3525698466.00091.mismatch \ 3525698466.00091.map /data/maqgene/genomes/elegans.bfa 3525698466.00091.1.bfq 2> /dev/null # Mon Apr 22 14:11:32 BST 2013: Mapping file(s) 3525698466.00090.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00090.unmapped -H 3525698466.00090.mismatch \ 3525698466.00090.map /data/maqgene/genomes/elegans.bfa 3525698466.00090.1.bfq 2> /dev/null # Mon Apr 22 14:11:33 BST 2013: Mapping file(s) 3525698466.00088.1.bfq # Mon Apr 22 14:11:33 BST 2013: Mapping file(s) 3525698466.00089.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00088.unmapped -H 3525698466.00088.mismatch \ 3525698466.00088.map /data/maqgene/genomes/elegans.bfa 3525698466.00088.1.bfq 2> /dev/null /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00089.unmapped -H 3525698466.00089.mismatch \ 3525698466.00089.map /data/maqgene/genomes/elegans.bfa 3525698466.00089.1.bfq 2> /dev/null # Mon Apr 22 14:11:34 BST 2013: Mapping file(s) 3525698466.00094.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00094.unmapped -H 3525698466.00094.mismatch \ 3525698466.00094.map /data/maqgene/genomes/elegans.bfa 3525698466.00094.1.bfq 2> /dev/null # Mon Apr 22 14:11:35 BST 2013: Mapping file(s) 3525698466.00087.1.bfq # Mon Apr 22 14:11:35 BST 2013: Mapping file(s) 3525698466.00086.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00087.unmapped -H 3525698466.00087.mismatch \ 3525698466.00087.map /data/maqgene/genomes/elegans.bfa 3525698466.00087.1.bfq 2> /dev/null /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00086.unmapped -H 3525698466.00086.mismatch \ 3525698466.00086.map /data/maqgene/genomes/elegans.bfa 3525698466.00086.1.bfq 2> /dev/null # Mon Apr 22 14:11:36 BST 2013: Mapping file(s) 3525698466.00084.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00084.unmapped -H 3525698466.00084.mismatch \ 3525698466.00084.map /data/maqgene/genomes/elegans.bfa 3525698466.00084.1.bfq 2> /dev/null # Mon Apr 22 14:11:36 BST 2013: Mapping file(s) 3525698466.00085.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00085.unmapped -H 3525698466.00085.mismatch \ 3525698466.00085.map /data/maqgene/genomes/elegans.bfa 3525698466.00085.1.bfq 2> /dev/null # Mon Apr 22 14:16:16 BST 2013: Mapping file(s) 3525698466.00105.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00105.unmapped -H 3525698466.00105.mismatch \ 3525698466.00105.map /data/maqgene/genomes/elegans.bfa 3525698466.00105.1.bfq 2> /dev/null /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00104.unmapped -H 3525698466.00104.mismatch \ 3525698466.00104.map /data/maqgene/genomes/elegans.bfa 3525698466.00104.1.bfq 2> /dev/null # Mon Apr 22 14:16:16 BST 2013: Mapping file(s) 3525698466.00103.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00103.unmapped -H 3525698466.00103.mismatch \ 3525698466.00103.map /data/maqgene/genomes/elegans.bfa 3525698466.00103.1.bfq 2> /dev/null # Mon Apr 22 14:16:17 BST 2013: Mapping file(s) 3525698466.00102.1.bfq # Mon Apr 22 14:16:17 BST 2013: Mapping file(s) 3525698466.00106.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00102.unmapped -H 3525698466.00102.mismatch \ 3525698466.00102.map /data/maqgene/genomes/elegans.bfa 3525698466.00102.1.bfq 2> /dev/null /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00106.unmapped -H 3525698466.00106.mismatch \ 3525698466.00106.map /data/maqgene/genomes/elegans.bfa 3525698466.00106.1.bfq 2> /dev/null # Mon Apr 22 14:16:18 BST 2013: Mapping file(s) 3525698466.00100.1.bfq # Mon Apr 22 14:16:18 BST 2013: Mapping file(s) 3525698466.00101.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00101.unmapped -H 3525698466.00101.mismatch \ 3525698466.00101.map /data/maqgene/genomes/elegans.bfa 3525698466.00101.1.bfq 2> /dev/null /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00100.unmapped -H 3525698466.00100.mismatch \ 3525698466.00100.map /data/maqgene/genomes/elegans.bfa 3525698466.00100.1.bfq 2> /dev/null # Mon Apr 22 14:16:19 BST 2013: Mapping file(s) 3525698466.00099.1.bfq # Mon Apr 22 14:16:19 BST 2013: Mapping file(s) 3525698466.00098.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00099.unmapped -H 3525698466.00099.mismatch \ 3525698466.00099.map /data/maqgene/genomes/elegans.bfa 3525698466.00099.1.bfq 2> /dev/null /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00098.unmapped -H 3525698466.00098.mismatch \ 3525698466.00098.map /data/maqgene/genomes/elegans.bfa 3525698466.00098.1.bfq 2> /dev/null # Mon Apr 22 14:16:20 BST 2013: Mapping file(s) 3525698466.00097.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00097.unmapped -H 3525698466.00097.mismatch \ 3525698466.00097.map /data/maqgene/genomes/elegans.bfa 3525698466.00097.1.bfq 2> /dev/null # Mon Apr 22 14:16:20 BST 2013: Mapping file(s) 3525698466.00096.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00096.unmapped -H 3525698466.00096.mismatch \ 3525698466.00096.map /data/maqgene/genomes/elegans.bfa 3525698466.00096.1.bfq 2> /dev/null # Mon Apr 22 14:16:22 BST 2013: Mapping file(s) 3525698466.00095.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00095.unmapped -H 3525698466.00095.mismatch \ 3525698466.00095.map /data/maqgene/genomes/elegans.bfa 3525698466.00095.1.bfq 2> /dev/null # Mon Apr 22 14:20:36 BST 2013: Mapping file(s) 3525698466.00115.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00115.unmapped -H 3525698466.00115.mismatch \ 3525698466.00115.map /data/maqgene/genomes/elegans.bfa 3525698466.00115.1.bfq 2> /dev/null # Mon Apr 22 14:20:37 BST 2013: Mapping file(s) 3525698466.00114.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00114.unmapped -H 3525698466.00114.mismatch \ 3525698466.00114.map /data/maqgene/genomes/elegans.bfa 3525698466.00114.1.bfq 2> /dev/null # Mon Apr 22 14:20:38 BST 2013: Mapping file(s) 3525698466.00113.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00113.unmapped -H 3525698466.00113.mismatch \ 3525698466.00113.map /data/maqgene/genomes/elegans.bfa 3525698466.00113.1.bfq 2> /dev/null # Mon Apr 22 14:20:39 BST 2013: Mapping file(s) 3525698466.00112.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00112.unmapped -H 3525698466.00112.mismatch \ 3525698466.00112.map /data/maqgene/genomes/elegans.bfa 3525698466.00112.1.bfq 2> /dev/null # Mon Apr 22 14:20:40 BST 2013: Mapping file(s) 3525698466.00111.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00111.unmapped -H 3525698466.00111.mismatch \ 3525698466.00111.map /data/maqgene/genomes/elegans.bfa 3525698466.00111.1.bfq 2> /dev/null # Mon Apr 22 14:20:41 BST 2013: Mapping file(s) 3525698466.00116.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00116.unmapped -H 3525698466.00116.mismatch \ 3525698466.00116.map /data/maqgene/genomes/elegans.bfa 3525698466.00116.1.bfq 2> /dev/null # Mon Apr 22 14:20:42 BST 2013: Mapping file(s) 3525698466.00117.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00117.unmapped -H 3525698466.00117.mismatch \ 3525698466.00117.map /data/maqgene/genomes/elegans.bfa 3525698466.00117.1.bfq 2> /dev/null # Mon Apr 22 14:20:43 BST 2013: Mapping file(s) 3525698466.00110.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00110.unmapped -H 3525698466.00110.mismatch \ 3525698466.00110.map /data/maqgene/genomes/elegans.bfa 3525698466.00110.1.bfq 2> /dev/null # Mon Apr 22 14:20:44 BST 2013: Mapping file(s) 3525698466.00109.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00109.unmapped -H 3525698466.00109.mismatch \ 3525698466.00109.map /data/maqgene/genomes/elegans.bfa 3525698466.00109.1.bfq 2> /dev/null # Mon Apr 22 14:20:45 BST 2013: Mapping file(s) 3525698466.00108.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00108.unmapped -H 3525698466.00108.mismatch \ 3525698466.00108.map /data/maqgene/genomes/elegans.bfa 3525698466.00108.1.bfq 2> /dev/null # Mon Apr 22 14:20:46 BST 2013: Mapping file(s) 3525698466.00107.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00107.unmapped -H 3525698466.00107.mismatch \ 3525698466.00107.map /data/maqgene/genomes/elegans.bfa 3525698466.00107.1.bfq 2> /dev/null # Mon Apr 22 14:21:32 BST 2013: Mapping file(s) 3525698466.00120.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00120.unmapped -H 3525698466.00120.mismatch \ 3525698466.00120.map /data/maqgene/genomes/elegans.bfa 3525698466.00120.1.bfq 2> /dev/null # Mon Apr 22 14:21:34 BST 2013: Mapping file(s) 3525698466.00119.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00119.unmapped -H 3525698466.00119.mismatch \ 3525698466.00119.map /data/maqgene/genomes/elegans.bfa 3525698466.00119.1.bfq 2> /dev/null # Mon Apr 22 14:21:36 BST 2013: Mapping file(s) 3525698466.00118.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00118.unmapped -H 3525698466.00118.mismatch \ 3525698466.00118.map /data/maqgene/genomes/elegans.bfa 3525698466.00118.1.bfq 2> /dev/null # Mon Apr 22 14:24:57 BST 2013: Mapping file(s) 3525698466.00131.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00131.unmapped -H 3525698466.00131.mismatch \ 3525698466.00131.map /data/maqgene/genomes/elegans.bfa 3525698466.00131.1.bfq 2> /dev/null # Mon Apr 22 14:24:58 BST 2013: Mapping file(s) 3525698466.00130.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00130.unmapped -H 3525698466.00130.mismatch \ 3525698466.00130.map /data/maqgene/genomes/elegans.bfa 3525698466.00130.1.bfq 2> /dev/null # Mon Apr 22 14:24:59 BST 2013: Mapping file(s) 3525698466.00129.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00129.unmapped -H 3525698466.00129.mismatch \ 3525698466.00129.map /data/maqgene/genomes/elegans.bfa 3525698466.00129.1.bfq 2> /dev/null # Mon Apr 22 14:25:00 BST 2013: Mapping file(s) 3525698466.00128.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00128.unmapped -H 3525698466.00128.mismatch \ 3525698466.00128.map /data/maqgene/genomes/elegans.bfa 3525698466.00128.1.bfq 2> /dev/null # Mon Apr 22 14:25:01 BST 2013: Mapping file(s) 3525698466.00127.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00127.unmapped -H 3525698466.00127.mismatch \ 3525698466.00127.map /data/maqgene/genomes/elegans.bfa 3525698466.00127.1.bfq 2> /dev/null # Mon Apr 22 14:25:02 BST 2013: Mapping file(s) 3525698466.00126.1.bfq # Mon Apr 22 14:25:02 BST 2013: Mapping file(s) 3525698466.00125.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00126.unmapped -H 3525698466.00126.mismatch \ 3525698466.00126.map /data/maqgene/genomes/elegans.bfa 3525698466.00126.1.bfq 2> /dev/null /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00125.unmapped -H 3525698466.00125.mismatch \ 3525698466.00125.map /data/maqgene/genomes/elegans.bfa 3525698466.00125.1.bfq 2> /dev/null # Mon Apr 22 14:25:03 BST 2013: Mapping file(s) 3525698466.00123.1.bfq # Mon Apr 22 14:25:03 BST 2013: Mapping file(s) 3525698466.00124.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00124.unmapped -H 3525698466.00124.mismatch \ 3525698466.00124.map /data/maqgene/genomes/elegans.bfa 3525698466.00124.1.bfq 2> /dev/null /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00123.unmapped -H 3525698466.00123.mismatch \ 3525698466.00123.map /data/maqgene/genomes/elegans.bfa 3525698466.00123.1.bfq 2> /dev/null # Mon Apr 22 14:25:04 BST 2013: Mapping file(s) 3525698466.00122.1.bfq # Mon Apr 22 14:25:04 BST 2013: Mapping file(s) 3525698466.00121.1.bfq 466.00122.unmapped -H 3525698466.00122.mismatch \ 3525698466.00122.map /data/maqgene/genomes/elegans.bfa 3525698466.00122.1.bfq 2> /dev/null /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00121.unmapped -H 3525698466.00121.mismatch \ 3525698466.00121.map /data/maqgene/genomes/elegans.bfa 3525698466.00121.1.bfq 2> /dev/null # Mon Apr 22 14:26:48 BST 2013: Mapping file(s) 3525698466.00134.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00134.unmapped -H 3525698466.00134.mismatch \ 3525698466.00134.map /data/maqgene/genomes/elegans.bfa 3525698466.00134.1.bfq 2> /dev/null # Mon Apr 22 14:26:49 BST 2013: Mapping file(s) 3525698466.00133.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00133.unmapped -H 3525698466.00133.mismatch \ 3525698466.00133.map /data/maqgene/genomes/elegans.bfa 3525698466.00133.1.bfq 2> /dev/null # Mon Apr 22 14:26:50 BST 2013: Mapping file(s) 3525698466.00132.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00132.unmapped -H 3525698466.00132.mismatch \ 3525698466.00132.map /data/maqgene/genomes/elegans.bfa 3525698466.00132.1.bfq 2> /dev/null # Mon Apr 22 14:29:48 BST 2013: Mapping file(s) 3525698466.00143.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00143.unmapped -H 3525698466.00143.mismatch \ 3525698466.00143.map /data/maqgene/genomes/elegans.bfa 3525698466.00143.1.bfq 2> /dev/null # Mon Apr 22 14:29:50 BST 2013: Mapping file(s) 3525698466.00142.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00142.unmapped -H 3525698466.00142.mismatch \ 3525698466.00142.map /data/maqgene/genomes/elegans.bfa 3525698466.00142.1.bfq 2> /dev/null # Mon Apr 22 14:29:52 BST 2013: Mapping file(s) 3525698466.00141.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00141.unmapped -H 3525698466.00141.mismatch \ 3525698466.00141.map /data/maqgene/genomes/elegans.bfa 3525698466.00141.1.bfq 2> /dev/null # Mon Apr 22 14:29:53 BST 2013: Mapping file(s) 3525698466.00140.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00140.unmapped -H 3525698466.00140.mismatch \ 3525698466.00140.map /data/maqgene/genomes/elegans.bfa 3525698466.00140.1.bfq 2> /dev/null # Mon Apr 22 14:29:54 BST 2013: Mapping file(s) 3525698466.00139.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00139.unmapped -H 3525698466.00139.mismatch \ 3525698466.00139.map /data/maqgene/genomes/elegans.bfa 3525698466.00139.1.bfq 2> /dev/null # Mon Apr 22 14:29:55 BST 2013: Mapping file(s) 3525698466.00138.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00138.unmapped -H 3525698466.00138.mismatch \ 3525698466.00138.map /data/maqgene/genomes/elegans.bfa 3525698466.00138.1.bfq 2> /dev/null # Mon Apr 22 14:29:56 BST 2013: Mapping file(s) 3525698466.00137.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00137.unmapped -H 3525698466.00137.mismatch \ 3525698466.00137.map /data/maqgene/genomes/elegans.bfa 3525698466.00137.1.bfq 2> /dev/null # Mon Apr 22 14:29:57 BST 2013: Mapping file(s) 3525698466.00136.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00136.unmapped -H 3525698466.00136.mismatch \ 3525698466.00136.map /data/maqgene/genomes/elegans.bfa 3525698466.00136.1.bfq 2> /dev/null # Mon Apr 22 14:29:58 BST 2013: Mapping file(s) 3525698466.00135.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00135.unmapped -H 3525698466.00135.mismatch \ 3525698466.00135.map /data/maqgene/genomes/elegans.bfa 3525698466.00135.1.bfq 2> /dev/null # Mon Apr 22 14:32:08 BST 2013: Mapping file(s) 3525698466.00148.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00148.unmapped -H 3525698466.00148.mismatch \ 3525698466.00148.map /data/maqgene/genomes/elegans.bfa 3525698466.00148.1.bfq 2> /dev/null # Mon Apr 22 14:32:09 BST 2013: Mapping file(s) 3525698466.00147.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00147.unmapped -H 3525698466.00147.mismatch \ 3525698466.00147.map /data/maqgene/genomes/elegans.bfa 3525698466.00147.1.bfq 2> /dev/null # Mon Apr 22 14:32:10 BST 2013: Mapping file(s) 3525698466.00146.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00146.unmapped -H 3525698466.00146.mismatch \ 3525698466.00146.map /data/maqgene/genomes/elegans.bfa 3525698466.00146.1.bfq 2> /dev/null # Mon Apr 22 14:32:11 BST 2013: Mapping file(s) 3525698466.00145.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00145.unmapped -H 3525698466.00145.mismatch \ 3525698466.00145.map /data/maqgene/genomes/elegans.bfa 3525698466.00145.1.bfq 2> /dev/null # Mon Apr 22 14:32:12 BST 2013: Mapping file(s) 3525698466.00144.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00144.unmapped -H 3525698466.00144.mismatch \ 3525698466.00144.map /data/maqgene/genomes/elegans.bfa 3525698466.00144.1.bfq 2> /dev/null # Mon Apr 22 14:34:38 BST 2013: Mapping file(s) 3525698466.00155.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00155.unmapped -H 3525698466.00155.mismatch \ 3525698466.00155.map /data/maqgene/genomes/elegans.bfa 3525698466.00155.1.bfq 2> /dev/null # Mon Apr 22 14:34:40 BST 2013: Mapping file(s) 3525698466.00154.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00154.unmapped -H 3525698466.00154.mismatch \ 3525698466.00154.map /data/maqgene/genomes/elegans.bfa 3525698466.00154.1.bfq 2> /dev/null # Mon Apr 22 14:34:42 BST 2013: Mapping file(s) 3525698466.00153.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00153.unmapped -H 3525698466.00153.mismatch \ 3525698466.00153.map /data/maqgene/genomes/elegans.bfa 3525698466.00153.1.bfq 2> /dev/null # Mon Apr 22 14:34:43 BST 2013: Mapping file(s) 3525698466.00152.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00152.unmapped -H 3525698466.00152.mismatch \ 3525698466.00152.map /data/maqgene/genomes/elegans.bfa 3525698466.00152.1.bfq 2> /dev/null # Mon Apr 22 14:34:44 BST 2013: Mapping file(s) 3525698466.00151.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00151.unmapped -H 3525698466.00151.mismatch \ 3525698466.00151.map /data/maqgene/genomes/elegans.bfa 3525698466.00151.1.bfq 2> /dev/null # Mon Apr 22 14:34:45 BST 2013: Mapping file(s) 3525698466.00150.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00150.unmapped -H 3525698466.00150.mismatch \ 3525698466.00150.map /data/maqgene/genomes/elegans.bfa 3525698466.00150.1.bfq 2> /dev/null # Mon Apr 22 14:34:46 BST 2013: Mapping file(s) 3525698466.00149.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00149.unmapped -H 3525698466.00149.mismatch \ 3525698466.00149.map /data/maqgene/genomes/elegans.bfa 3525698466.00149.1.bfq 2> /dev/null # Mon Apr 22 14:37:16 BST 2013: Mapping file(s) 3525698466.00156.1.bfq # Mon Apr 22 14:37:16 BST 2013: Mapping file(s) 3525698466.00158.1.bfq # Mon Apr 22 14:37:16 BST 2013: Mapping file(s) 3525698466.00161.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00161.unmapped -H 3525698466.00161.mismatch \ 3525698466.00161.map /data/maqgene/genomes/elegans.bfa 3525698466.00161.1.bfq 2> /dev/null /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00160.unmapped -H 3525698466.00160.mismatch \ 3525698466.00160.map /data/maqgene/genomes/elegans.bfa 3525698466.00160.1.bfq 2> /dev/null /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00159.unmapped -H 3525698466.00159.mismatch \ 3525698466.00159.map /data/maqgene/genomes/elegans.bfa 3525698466.00159.1.bfq 2> /dev/null /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00158.unmapped -H 3525698466.00158.mismatch \ 3525698466.00158.map /data/maqgene/genomes/elegans.bfa 3525698466.00158.1.bfq 2> /dev/null /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00157.unmapped -H 3525698466.00157.mismatch \ 3525698466.00157.map /data/maqgene/genomes/elegans.bfa 3525698466.00157.1.bfq 2> /dev/null /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 3525698466.00156.unmapped -H 3525698466.00156.mismatch \ 3525698466.00156.map /data/maqgene/genomes/elegans.bfa 3525698466.00156.1.bfq 2> /dev/null # Mon Apr 22 14:41:31 BST 2013: Merging all maps ... # Mon Apr 22 14:41:31 BST 2013: Merging all *.unmapped files ... /data/maqgene/bin/maq mapmerge 3525698466.map 3525698466.00000.map 3525698466.00001.map 3525698466.00002.map 3525698466.00003.map 3525698466.00004.map 3525698466.00005.map 3525698466.00006.map 3525698466.00007.map 3525698466.00008.map 3525698466.00009.map 3525698466.00010.map 3525698466.00011.map 3525698466.00012.map 3525698466.00013.map 3525698466.00014.map 3525698466.00015.map 3525698466.00016.map 3525698466.00017.map 3525698466.00018.map 3525698466.00019.map 3525698466.00020.map 3525698466.00021.map 3525698466.00022.map 3525698466.00023.map 3525698466.00024.map 3525698466.00025.map 3525698466.00026.map 3525698466.00027.map 3525698466.00028.map 3525698466.00029.map 3525698466.00030.map 3525698466.00031.map 3525698466.00032.map 3525698466.00033.map 3525698466.00034.map 3525698466.00035.map 3525698466.00036.map 3525698466.00037.map 3525698466.00038.map 3525698466.00039.map 3525698466.00040.map 3525698466.00041.map 3525698466.00042.map 3525698466.00043.map 3525698466.00044.map 3525698466.00045.map 3525698466.00046.map 3525698466.00047.map 3525698466.00048.map 3525698466.00049.map 3525698466.00050.map 3525698466.00051.map 3525698466.00052.map 3525698466.00053.map 3525698466.00054.map 3525698466.00055.map 3525698466.00056.map 3525698466.00057.map 3525698466.00058.map 3525698466.00059.map 3525698466.00060.map 3525698466.00061.map 3525698466.00062.map 3525698466.00063.map 3525698466.00064.map 3525698466.00065.map 3525698466.00066.map 3525698466.00067.map 3525698466.00068.map 3525698466.00069.map 3525698466.00070.map 3525698466.00071.map 3525698466.00072.map 3525698466.00073.map 3525698466.00074.map 3525698466.00075.map 3525698466.00076.map 3525698466.00077.map 3525698466.00078.map 3525698466.00079.map 3525698466.00080.map 3525698466.00081.map 3525698466.00082.map 3525698466.00083.map 3525698466.00084.map 3525698466.00085.map 3525698466.00086.map 3525698466.00087.map 3525698466.00088.map 3525698466.00089.map 3525698466.00090.map 3525698466.00091.map 3525698466.00092.map 3525698466.00093.map 3525698466.00094.map 3525698466.00095.map 3525698466.00096.map 3525698466.00097.map 3525698466.00098.map 3525698466.00099.map 3525698466.00100.map 3525698466.00101.map 3525698466.00102.map 3525698466.00103.map 3525698466.00104.map 3525698466.00105.map 3525698466.00106.map 3525698466.00107.map 3525698466.00108.map 3525698466.00109.map 3525698466.00110.map 3525698466.00111.map 3525698466.00112.map 3525698466.00113.map 3525698466.00114.map 3525698466.00115.map 3525698466.00116.map 3525698466.00117.map 3525698466.00118.map 3525698466.00119.map 3525698466.00120.map 3525698466.00121.map 3525698466.00122.map 3525698466.00123.map 3525698466.00124.map 3525698466.00125.map 3525698466.00126.map 3525698466.00127.map 3525698466.00128.map 3525698466.00129.map 3525698466.00130.map 3525698466.00131.map 3525698466.00132.map 3525698466.00133.map 3525698466.00134.map 3525698466.00135.map 3525698466.00136.map 3525698466.00137.map 3525698466.00138.map 3525698466.00139.map 3525698466.00140.map 3525698466.00141.map 3525698466.00142.map 3525698466.00143.map 3525698466.00144.map 3525698466.00145.map 3525698466.00146.map 3525698466.00147.map 3525698466.00148.map 3525698466.00149.map 3525698466.00150.map 3525698466.00151.map 3525698466.00152.map 3525698466.00153.map 3525698466.00154.map 3525698466.00155.map 3525698466.00156.map 3525698466.00157.map 3525698466.00158.map 3525698466.00159.map 3525698466.00160.map 3525698466.00161.map cat 3525698466.00000.unmapped 3525698466.00001.unmapped 3525698466.00002.unmapped 3525698466.00003.unmapped 3525698466.00004.unmapped 3525698466.00005.unmapped 3525698466.00006.unmapped 3525698466.00007.unmapped 3525698466.00008.unmapped 3525698466.00009.unmapped 3525698466.00010.unmapped 3525698466.00011.unmapped 3525698466.00012.unmapped 3525698466.00013.unmapped 3525698466.00014.unmapped 3525698466.00015.unmapped 3525698466.00016.unmapped 3525698466.00017.unmapped 3525698466.00018.unmapped 3525698466.00019.unmapped 3525698466.00020.unmapped 3525698466.00021.unmapped 3525698466.00022.unmapped 3525698466.00023.unmapped 3525698466.00024.unmapped 3525698466.00025.unmapped 3525698466.00026.unmapped 3525698466.00027.unmapped 3525698466.00028.unmapped 3525698466.00029.unmapped 3525698466.00030.unmapped 3525698466.00031.unmapped 3525698466.00032.unmapped 3525698466.00033.unmapped 3525698466.00034.unmapped 3525698466.00035.unmapped 3525698466.00036.unmapped 3525698466.00037.unmapped 3525698466.00038.unmapped 3525698466.00039.unmapped 3525698466.00040.unmapped 3525698466.00041.unmapped 3525698466.00042.unmapped 3525698466.00043.unmapped 3525698466.00044.unmapped 3525698466.00045.unmapped 3525698466.00046.unmapped 3525698466.00047.unmapped 3525698466.00048.unmapped 3525698466.00049.unmapped 3525698466.00050.unmapped 3525698466.00051.unmapped 3525698466.00052.unmapped 3525698466.00053.unmapped 3525698466.00054.unmapped 3525698466.00055.unmapped 3525698466.00056.unmapped 3525698466.00057.unmapped 3525698466.00058.unmapped 3525698466.00059.unmapped 3525698466.00060.unmapped 3525698466.00061.unmapped 3525698466.00062.unmapped 3525698466.00063.unmapped 3525698466.00064.unmapped 3525698466.00065.unmapped 3525698466.00066.unmapped 3525698466.00067.unmapped 3525698466.00068.unmapped 3525698466.00069.unmapped 3525698466.00070.unmapped 3525698466.00071.unmapped 3525698466.00072.unmapped 3525698466.00073.unmapped 3525698466.00074.unmapped 3525698466.00075.unmapped 3525698466.00076.unmapped 3525698466.00077.unmapped 3525698466.00078.unmapped 3525698466.00079.unmapped 3525698466.00080.unmapped 3525698466.00081.unmapped 3525698466.00082.unmapped 3525698466.00083.unmapped 3525698466.00084.unmapped 3525698466.00085.unmapped 3525698466.00086.unmapped 3525698466.00087.unmapped 3525698466.00088.unmapped 3525698466.00089.unmapped 3525698466.00090.unmapped 3525698466.00091.unmapped 3525698466.00092.unmapped 3525698466.00093.unmapped 3525698466.00094.unmapped 3525698466.00095.unmapped 3525698466.00096.unmapped 3525698466.00097.unmapped 3525698466.00098.unmapped 3525698466.00099.unmapped 3525698466.00100.unmapped 3525698466.00101.unmapped 3525698466.00102.unmapped 3525698466.00103.unmapped 3525698466.00104.unmapped 3525698466.00105.unmapped 3525698466.00106.unmapped 3525698466.00107.unmapped 3525698466.00108.unmapped 3525698466.00109.unmapped 3525698466.00110.unmapped 3525698466.00111.unmapped 3525698466.00112.unmapped 3525698466.00113.unmapped 3525698466.00114.unmapped 3525698466.00115.unmapped 3525698466.00116.unmapped 3525698466.00117.unmapped 3525698466.00118.unmapped 3525698466.00119.unmapped 3525698466.00120.unmapped 3525698466.00121.unmapped 3525698466.00122.unmapped 3525698466.00123.unmapped 3525698466.00124.unmapped 3525698466.00125.unmapped 3525698466.00126.unmapped 3525698466.00127.unmapped 3525698466.00128.unmapped 3525698466.00129.unmapped 3525698466.00130.unmapped 3525698466.00131.unmapped 3525698466.00132.unmapped 3525698466.00133.unmapped 3525698466.00134.unmapped 3525698466.00135.unmapped 3525698466.00136.unmapped 3525698466.00137.unmapped 3525698466.00138.unmapped 3525698466.00139.unmapped 3525698466.00140.unmapped 3525698466.00141.unmapped 3525698466.00142.unmapped 3525698466.00143.unmapped 3525698466.00144.unmapped 3525698466.00145.unmapped 3525698466.00146.unmapped 3525698466.00147.unmapped 3525698466.00148.unmapped 3525698466.00149.unmapped 3525698466.00150.unmapped 3525698466.00151.unmapped 3525698466.00152.unmapped 3525698466.00153.unmapped 3525698466.00154.unmapped 3525698466.00155.unmapped 3525698466.00156.unmapped 3525698466.00157.unmapped 3525698466.00158.unmapped 3525698466.00159.unmapped 3525698466.00160.unmapped 3525698466.00161.unmapped > 3525698466_unmapped.txt # Mon Apr 22 14:42:04 BST 2013: Linking backend file 3525698466_unmapped.txt to /data/maqgene/out/example_user/CB7045_2/CB7045_2_unmapped.txt ln -fs /data/maqgene/work/3525698466_unmapped.txt /data/maqgene/out/example_user/CB7045_2/CB7045_2_unmapped.txt /data/maqgene/makefile:126: warning: undefined variable `mapcheck_parameters' # Mon Apr 22 15:07:02 BST 2013: Generating consensus ... /data/maqgene/bin/maq assemble -N 2 -q 0 -r 0.0 -m 7 -Q 100 -p 2734059306.cns \ /data/maqgene/genomes/elegans.bfa 3525698466.map 2> 2734059306_log.txt # Mon Apr 22 15:07:02 BST 2013: Creating pileup ... /data/maqgene/bin/maq pileup -Q 100 -m 7 -q 0 /data/maqgene/genomes/elegans.bfa 3525698466.map > 2929290487_pileup.txt /data/maqgene/bin/maq mapcheck /data/maqgene/genomes/elegans.bfa 3525698466.map > 3525698466_check.txt \ 2>/dev/null # Mon Apr 22 15:13:02 BST 2013: Linking backend file 3525698466_check.txt to /data/maqgene/out/example_user/CB7045_2/CB7045_2_check.txt ln -fs /data/maqgene/work/3525698466_check.txt /data/maqgene/out/example_user/CB7045_2/CB7045_2_check.txt /data/maqgene/bin/filter_matching_lines 2929290487_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 \ > 2929290487_known_snps # Mon Apr 22 15:14:40 BST 2013: Getting uncovered regions ... cut -f 1,2,4 2929290487_pileup.txt \ | /data/maqgene/bin/get_uncovered_regions 50 \ > 2929290487_uncovered.txt # Mon Apr 22 15:14:40 BST 2013: Making coverage histogram ... # Mon Apr 22 15:14:40 BST 2013: Linking backend file 2929290487_pileup.txt to /data/maqgene/out/example_user/CB7045_2/CB7045_2_pileup.txt (echo -en "sequencing_depth\tnumber_of_bases\n"; \ cut -f 4 2929290487_pileup.txt \ | /data/maqgene/bin/pileup_histogram 100) > 2929290487_coverage.txt ln -fs /data/maqgene/work/2929290487_pileup.txt /data/maqgene/out/example_user/CB7045_2/CB7045_2_pileup.txt # Mon Apr 22 15:16:16 BST 2013: Filtering and loading pileup for analysis ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 2929290487_pileup; create table 2929290487_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 2929290487_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 2929290487_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 2929290487_pileup" # Mon Apr 22 15:16:17 BST 2013: Linking backend file 2929290487_coverage.txt to /data/maqgene/out/example_user/CB7045_2/CB7045_2_coverage.txt ln -fs /data/maqgene/work/2929290487_coverage.txt /data/maqgene/out/example_user/CB7045_2/CB7045_2_coverage.txt # Mon Apr 22 15:16:17 BST 2013: Linking backend file 2929290487_uncovered.txt to /data/maqgene/out/example_user/CB7045_2/CB7045_2_uncovered.txt ln -fs /data/maqgene/work/2929290487_uncovered.txt /data/maqgene/out/example_user/CB7045_2/CB7045_2_uncovered.txt cat 2929290487_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 2929290487_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 2929290487_pileup" touch 2929290487_pileup # Mon Apr 22 15:17:51 BST 2013: 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 2929290487_pileup p using (dna,start)" > /data/maqgene/out/example_user/CB7045_2/CB7045_2_snp_read_counts.txt 0 snp read count lines written. # Mon Apr 22 15:18:29 BST 2013: Extracting point mutants from consensus ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 2734059306_snps; create table 2734059306_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/2734059306_log.txt /data/maqgene/out/example_user/CB7045_2/CB7045_2_log.txt /data/maqgene/bin/maq cns2snp 2734059306.cns \ | cat -b | /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "load data local infile '/dev/stdin' into table 2734059306_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 2734059306_snps;" # Mon Apr 22 15:18:38 BST 2013: Extracting indels from consensus ... /data/maqgene/bin/maq indelsoa /data/maqgene/genomes/elegans.bfa 3525698466.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 2734059306_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 2734059306_snps;" # Mon Apr 22 15:21:47 BST 2013: Adding placeholders for known SNPs. cat 2929290487_known_snps \ | /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "load data local infile '/dev/stdin' ignore into table 2734059306_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 2734059306_snps;" Found 162447 variants. touch 2734059306_snps # Mon Apr 22 15:21:49 BST 2013: Loading uncovered regions into table ... cat 2929290487_uncovered.txt \ | /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 2929290487_uncovered; create table 2929290487_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 = 162448; load data local infile '/dev/stdin' into table 2929290487_uncovered (dna, start, end)" # Mon Apr 22 15:21:49 BST 2013: Getting masking regions /data/maqgene/bin/associate_regions -b -1 -c -1000000 -m 2 -o >(/usr/bin/mysql -Dmaqgenedb -umaqgene --skip-column-names --batch --raw --local-infile -e "drop table if exists 2734059306_masked_ids; create table 2734059306_masked_ids (query_region_id int(10) NOT NULL, primary key (query_region_id)); load data local infile '/dev/stdin' ignore into table 2734059306_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 2734059306_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; # Mon Apr 22 15:21:49 BST 2013: Finding all genomic features overlapping variants... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 2734059306_rel_snps; CREATE TABLE 2734059306_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) )" 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 2734059306_rel_snps; flush table 2734059306_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 2734059306_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 2 174 II 6 968 III 2 133 IV 6 560 V 3 502 X 3 4775 touch 2929290487_uncovered # Mon Apr 22 15:21:49 BST 2013: Finding mRNA features overlapping uncovered regions ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 2929290487_uncovered_rel; CREATE TABLE 2929290487_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 2929290487_uncovered_rel; flush table 2929290487_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 2929290487_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 2929290487_uncovered_rel # Mon Apr 22 15:21:51 BST 2013: Calculating translation start offsets for uncovered regions... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 2929290487_offsets_uncovered; create table 2929290487_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 2929290487_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 2929290487_uncovered reg join 2929290487_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 2734059306_masked_ids /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 2929290487_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 2929290487_uncovered reg join 2929290487_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 2929290487_offsets_uncovered touch 2734059306_rel_snps # Mon Apr 22 15:21:52 BST 2013: Getting intergenic regions # Mon Apr 22 15:21:52 BST 2013: Calculating translation start offsets... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 2734059306_rel_intergenic; create table 2734059306_rel_intergenic like 2734059306_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 2734059306_rel_intergenic; flush table 2734059306_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 2734059306_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 "drop table if exists 2734059306_offsets_snps; create table 2734059306_offsets_snps ( id int(10) NOT NULL, gene varchar(50) NOT NULL, 5prime_offset int(10) NOT NULL, 3prime_offset int(10) NOT NULL, total_length int(10) NOT NULL, boundary_type char(20) NOT NULL, primary key (id, gene, boundary_type) );" /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 2734059306_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 2734059306_snps reg join 2734059306_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" # Mon Apr 22 15:21:56 BST 2013: Filtering masked intergenic regions /usr/bin/mysql -Dmaqgenedb -umaqgene --skip-column-names --batch --raw --local-infile -e "delete i.* from 2734059306_rel_intergenic i join 2734059306_masked_ids m using (query_region_id)" touch 2734059306_rel_intergenic # Mon Apr 22 15:22:02 BST 2013: Classifying intergenic relations /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 2734059306_intergenic_assoc; create table 2734059306_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 2734059306_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 2734059306_snps snp join 2734059306_rel_intergenic rel on (snp.id = rel.query_region_id) join elegans_features feature on (rel.target_region_id = feature.id)" touch 2734059306_intergenic_assoc touch 2734059306_offsets_snps # Mon Apr 22 15:22:14 BST 2013: Getting codons affected by point mutations... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 2734059306_codons; create table 2734059306_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 2734059306_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 2734059306_offsets_snps off join 2734059306_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 2734059306_codons /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 2734059306_marked; create table 2734059306_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) );" # Mon Apr 22 15:22:21 BST 2013: Finding exonic indels ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 2734059306_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 2734059306_snps snp join 2734059306_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';" # Mon Apr 22 15:22:22 BST 2013: Finding coding variants ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 2734059306_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 2734059306_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);" # Mon Apr 22 15:22:22 BST 2013: Finding noncoding variants ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 2734059306_marked select snp.id, feature.feature class, 'none' description, feature.attribute parent_feature from 2734059306_snps snp join 2734059306_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');" # Mon Apr 22 15:22:22 BST 2013: Finding splice site variants ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 2734059306_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 2734059306_snps snp join 2734059306_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;" # Mon Apr 22 15:22:23 BST 2013: Finding intergenic and intronic variants ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 2734059306_marked select id, 'nongenic' class, concat(if (relation in ('upstream','into'), - distance, distance),' ',relation) description, attribute from 2734059306_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' );" # Mon Apr 22 15:22:25 BST 2013: Finding uncovered regions in genes ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 2734059306_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 2929290487_uncovered unc join 2929290487_offsets_uncovered b using (id) join 2929290487_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 2929290487_uncovered unc join 2929290487_offsets_uncovered b using (id) join 2929290487_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'" # Mon Apr 22 15:22:25 BST 2013: Variants found: +-----------------+-----------------+ | class | number_variants | +-----------------+-----------------+ | five_prime_UTR | 1326 | | frameshift | 94 | | inframe | 19 | | missense | 6189 | | ncRNA | 883 | | nongenic | 125627 | | non_start | 9 | | premature_stop | 690 | | readthrough | 20 | | silent | 7421 | | SNP | 1069 | | splice_acceptor | 46 | | splice_donor | 48 | | three_prime_UTR | 3584 | | uncovered | 6 | +-----------------+-----------------+ touch 2734059306_marked # Mon Apr 22 15:22:26 BST 2013: Combining results ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 2734059306_combined; create table 2734059306_combined (primary key (id, class, description), key (dna, start)) as select snp.id, 'CB7045_2' 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 2734059306_snps snp join 2929290487_pileup pile using (dna,start) join 2734059306_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, 'CB7045_2' 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 2929290487_uncovered unc join 2734059306_marked class on (unc.id = class.id) left join elegans_per_locus using (dna,start) group by id, class, description; alter table 2734059306_combined order by dna, start, length" touch 2734059306_combined # Mon Apr 22 15:22:27 BST 2013: 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 2734059306_combined group by id order by dna, start;" > /data/maqgene/out/example_user/CB7045_2/CB7045_2_grouped.txt # Mon Apr 22 15:22:27 BST 2013: Writing results to flat file ... /usr/bin/mysql -Dmaqgenedb -umaqgene --skip-column-names --batch --raw --local-infile --column-names -e "select * from 2734059306_combined" > /data/maqgene/out/example_user/CB7045_2/CB7045_2_flat.txt 5474 lines written. 3109 lines written. rm 3525698466.00027.map 3525698466.00150.mismatch 3525698466.00148.map 3525698466.00022.1.fastq 3525698466.00135.map 3525698466.00132.mismatch 3525698466.00131.1.bfq 3525698466.00066.1.bfq 3525698466.00118.1.fastq 3525698466.00063.unmapped 3525698466.00025.1.bfq 3525698466.00154.1.fastq 3525698466.00013.1.bfq 3525698466.00007.map 3525698466.00011.1.fastq 3525698466.00076.unmapped 3525698466.00070.map 3525698466.00080.map 3525698466.00090.map 3525698466.00003.1.fastq 3525698466.00146.map 3525698466.00030.1.fastq 3525698466.00073.1.fastq 3525698466.00081.1.bfq 3525698466.00151.mismatch 3525698466.00122.1.fastq 3525698466.00027.1.fastq 3525698466.00104.mismatch 3525698466.00159.map 3525698466.00020.1.fastq 3525698466.00093.1.fastq 3525698466.00116.1.bfq 3525698466.00125.1.bfq 3525698466.00157.unmapped 3525698466.00145.1.bfq 3525698466.00000.map 3525698466.00107.map 3525698466.00052.mismatch 3525698466.00148.1.bfq 3525698466.00071.map 3525698466.00075.mismatch 3525698466.00081.map 3525698466.00091.map 3525698466.00031.1.fastq 3525698466.00013.1.fastq 3525698466.00130.1.fastq 3525698466.00127.map 3525698466.00057.map 3525698466.00127.1.fastq 3525698466.00086.map 3525698466.00028.map 3525698466.00064.1.bfq 3525698466.00068.1.fastq 3525698466.00048.mismatch 3525698466.00001.map 3525698466.00010.map 3525698466.00113.1.bfq 3525698466.00080.mismatch 3525698466.00123.map 3525698466.00005.unmapped 3525698466.00072.1.fastq 3525698466.00113.1.fastq 3525698466.00050.unmapped 3525698466.00131.1.fastq 3525698466.00095.mismatch 3525698466.00152.mismatch 3525698466.00044.unmapped 3525698466.00155.1.bfq 3525698466.00120.1.fastq 3525698466.00152.1.bfq 3525698466.00101.map 3525698466.00011.map 3525698466.00125.mismatch 3525698466.00068.mismatch 3525698466.00053.1.bfq 3525698466.00148.mismatch 3525698466.00036.map 3525698466.00105.unmapped 3525698466.00065.1.bfq 3525698466.00032.1.fastq 3525698466.00072.map 3525698466.00117.unmapped 3525698466.00017.map 3525698466.00092.map 3525698466.00136.unmapped 3525698466.00019.1.fastq 3525698466.00055.1.fastq 3525698466.00020.map 3525698466.00122.unmapped 3525698466.00111.map 3525698466.00150.unmapped 3525698466.00008.1.fastq 3525698466.00098.map 3525698466.00035.1.bfq 3525698466.00089.mismatch 3525698466.00039.mismatch 3525698466.00026.1.fastq 3525698466.00101.1.fastq 3525698466.00123.1.fastq 3525698466.00015.map 3525698466.00046.1.bfq 3525698466.00153.1.bfq 3525698466.00044.1.bfq 3525698466.00119.1.fastq 3525698466.00102.map 3525698466.00012.map 3525698466.00120.map 3525698466.00132.1.bfq 3525698466.00156.mismatch 3525698466.00048.unmapped 3525698466.00089.1.bfq 3525698466.00100.unmapped 3525698466.00053.mismatch 3525698466.00059.mismatch 3525698466.00045.unmapped 3525698466.00135.1.bfq 3525698466.00134.1.fastq 3525698466.00139.mismatch 3525698466.00052.unmapped 3525698466.00065.1.fastq 3525698466.00089.1.fastq 3525698466.00054.map 3525698466.00074.1.bfq 3525698466.00151.1.bfq 3525698466.00075.unmapped 3525698466.00007.1.bfq 3525698466.00071.1.bfq 3525698466.00121.map 3525698466.00070.1.bfq 3525698466.00080.1.bfq 3525698466.00090.mismatch 3525698466.00108.1.fastq 3525698466.00126.unmapped 3525698466.00119.1.bfq 3525698466.00146.1.bfq 3525698466.00123.1.bfq 3525698466.00083.unmapped 3525698466.00009.1.fastq 3525698466.00017.1.fastq 3525698466.00025.unmapped 3525698466.00114.map 3525698466.00069.map 3525698466.00045.map 3525698466.00128.1.fastq 3525698466.00078.1.bfq 3525698466.00000.1.bfq 3525698466.00153.mismatch 3525698466.00022.map 3525698466.00120.1.bfq 3525698466.00058.1.fastq 3525698466.00088.mismatch 3525698466.00141.1.bfq 3525698466.00118.map 3525698466.00095.unmapped 3525698466.00152.unmapped 3525698466.00144.1.bfq 3525698466.00154.map 3525698466.00150.1.bfq 3525698466.00033.1.fastq 3525698466.00135.mismatch 3525698466.00125.unmapped 3525698466.00093.unmapped 3525698466.00035.mismatch 3525698466.00010.mismatch 3525698466.00003.map 3525698466.00030.map 3525698466.00148.unmapped 3525698466.00001.1.bfq 3525698466.00010.1.bfq 3525698466.00073.map 3525698466.00140.map 3525698466.00122.map 3525698466.00004.1.fastq 3525698466.00008.mismatch 3525698466.00145.map 3525698466.00132.1.fastq 3525698466.00040.1.fastq 3525698466.00078.mismatch 3525698466.00070.mismatch 3525698466.00028.1.fastq 3525698466.00093.map 3525698466.00056.1.fastq 3525698466.00146.mismatch 3525698466.00109.1.fastq 3525698466.00075.map 3525698466.00064.unmapped 3525698466.00159.mismatch 3525698466.00103.map 3525698466.00041.map 3525698466.00011.1.bfq 3525698466.00110.1.bfq 3525698466.00130.map 3525698466.00000.mismatch 3525698466.00107.mismatch 3525698466.00039.unmapped 3525698466.00041.1.fastq 3525698466.00127.1.bfq 3525698466.00071.mismatch 3525698466.00014.1.fastq 3525698466.00081.mismatch 3525698466.00099.map 3525698466.00091.mismatch 3525698466.00140.1.fastq 3525698466.00105.1.bfq 3525698466.00017.1.bfq 3525698466.00040.1.bfq 3525698466.00092.1.bfq 3525698466.00099.unmapped 3525698466.00084.1.fastq 3525698466.00057.mismatch 3525698466.00154.1.bfq 3525698466.00113.unmapped 3525698466.00025.map 3525698466.00039.1.fastq 3525698466.00002.1.bfq 3525698466.00020.1.bfq 3525698466.00113.map 3525698466.00053.unmapped 3525698466.00001.mismatch 3525698466.00100.mismatch 3525698466.00037.map 3525698466.00139.unmapped 3525698466.00114.1.fastq 3525698466.00133.map 3525698466.00038.1.fastq 3525698466.00141.1.fastq 3525698466.00117.1.bfq 3525698466.00140.1.bfq 3525698466.00158.1.fastq 3525698466.00102.1.bfq 3525698466.00021.1.bfq 3525698466.00032.map 3525698466.00101.mismatch 3525698466.00023.map 3525698466.00011.mismatch 3525698466.00110.mismatch 3525698466.00035.unmapped 3525698466.00157.mismatch 3525698466.00019.map 3525698466.00083.1.bfq 3525698466.00072.mismatch 3525698466.00153.unmapped 3525698466.00024.1.fastq 3525698466.00017.mismatch 3525698466.00104.1.fastq 3525698466.00088.unmapped 3525698466.00054.1.bfq 3525698466.00112.1.bfq 3525698466.00002.mismatch 3525698466.00020.mismatch 3525698466.00132.unmapped 3525698466.00132.map 3525698466.00018.1.bfq 3525698466.00046.mismatch 3525698466.00087.1.fastq 3525698466.00098.mismatch 3525698466.00119.map 3525698466.00067.map 3525698466.00142.1.fastq 3525698466.00074.1.fastq 3525698466.00117.mismatch 3525698466.00124.1.fastq 3525698466.00048.1.fastq 3525698466.00009.unmapped 3525698466.00045.1.bfq 3525698466.00086.unmapped 3525698466.00080.unmapped 3525698466.00028.unmapped 3525698466.00022.1.bfq 3525698466.00151.unmapped 3525698466.00102.mismatch 3525698466.00137.1.bfq 3525698466.00014.map 3525698466.00146.unmapped 3525698466.00120.mismatch 3525698466.00111.mismatch 3525698466.00118.1.bfq 3525698466.00006.1.fastq 3525698466.00065.map 3525698466.00119.unmapped 3525698466.00147.unmapped 3525698466.00123.unmapped 3525698466.00159.unmapped 3525698466.00147.mismatch 3525698466.00106.mismatch 3525698466.00037.1.fastq 3525698466.00056.map 3525698466.00000.unmapped 3525698466.00109.unmapped 3525698466.00003.1.bfq 3525698466.00126.1.fastq 3525698466.00030.1.bfq 3525698466.00073.1.bfq 3525698466.00054.mismatch 3525698466.00081.unmapped 3525698466.00112.mismatch 3525698466.00027.1.bfq 3525698466.00121.mismatch 3525698466.00034.mismatch 3525698466.00018.mismatch 3525698466.00103.1.fastq 3525698466.00161.mismatch 3525698466.00042.map 3525698466.00128.map 3525698466.00058.mismatch 3525698466.00029.map 3525698466.00084.1.bfq 3525698466.00051.1.bfq 3525698466.00036.unmapped 3525698466.00058.map 3525698466.00001.unmapped 3525698466.00010.unmapped 3525698466.00103.1.bfq 3525698466.00008.1.bfq 3525698466.00068.map 3525698466.00029.unmapped 3525698466.00031.1.bfq 3525698466.00055.mismatch 3525698466.00066.mismatch 3525698466.00044.1.fastq 3525698466.00128.unmapped 3525698466.00021.mismatch 3525698466.00022.mismatch 3525698466.00033.map 3525698466.00118.mismatch 3525698466.00068.1.bfq 3525698466.00108.map 3525698466.00043.1.fastq 3525698466.00145.1.fastq 3525698466.00004.map 3525698466.00040.map 3525698466.00101.unmapped 3525698466.00011.unmapped 3525698466.00110.unmapped 3525698466.00137.map 3525698466.00015.unmapped 3525698466.00034.1.fastq 3525698466.00003.mismatch 3525698466.00149.map 3525698466.00030.mismatch 3525698466.00138.1.fastq 3525698466.00073.mismatch 3525698466.00029.1.fastq 3525698466.00027.mismatch 3525698466.00017.unmapped 3525698466.00092.unmapped 3525698466.00096.unmapped 3525698466.00037.1.bfq 3525698466.00116.1.fastq 3525698466.00104.map 3525698466.00002.unmapped 3525698466.00062.1.fastq 3525698466.00111.unmapped 3525698466.00161.1.fastq 3525698466.00143.1.fastq 3525698466.00074.map 3525698466.00002.1.fastq 3525698466.00032.1.bfq 3525698466.00156.map 3525698466.00098.unmapped 3525698466.00031.mismatch 3525698466.00023.1.bfq 3525698466.00013.mismatch 3525698466.00137.1.fastq 3525698466.00130.mismatch 3525698466.00049.map 3525698466.00059.map 3525698466.00155.1.fastq 3525698466.00108.mismatch 3525698466.00084.map 3525698466.00099.1.fastq 3525698466.00129.1.fastq 3525698466.00127.mismatch 3525698466.00019.1.bfq 3525698466.00082.mismatch 3525698466.00009.mismatch 3525698466.00099.mismatch 3525698466.00094.map 3525698466.00077.map 3525698466.00102.unmapped 3525698466.00021.unmapped 3525698466.00007.mismatch 3525698466.00115.unmapped 3525698466.00069.unmapped 3525698466.00141.map 3525698466.00113.mismatch 3525698466.00131.mismatch 3525698466.00097.mismatch 3525698466.00116.mismatch 3525698466.00024.1.bfq 3525698466.00094.1.fastq 3525698466.00029.1.bfq 3525698466.00054.unmapped 3525698466.00076.mismatch 3525698466.00147.1.fastq 3525698466.00023.1.fastq 3525698466.00018.unmapped 3525698466.00031.map 3525698466.00032.mismatch 3525698466.00074.mismatch 3525698466.00024.map 3525698466.00140.unmapped 3525698466.00028.1.bfq 3525698466.00109.mismatch 3525698466.00066.unmapped 3525698466.00092.mismatch 3525698466.00124.map 3525698466.00022.unmapped 3525698466.00087.map 3525698466.00118.unmapped 3525698466.00160.1.bfq 3525698466.00037.mismatch 3525698466.00142.map 3525698466.00123.mismatch 3525698466.00154.unmapped 3525698466.00077.1.bfq 3525698466.00128.1.bfq 3525698466.00119.mismatch 3525698466.00003.unmapped 3525698466.00096.map 3525698466.00030.unmapped 3525698466.00073.unmapped 3525698466.00058.1.bfq 3525698466.00006.map 3525698466.00027.unmapped 3525698466.00060.map 3525698466.00063.1.fastq 3525698466.00156.1.bfq 3525698466.00054.1.fastq 3525698466.00012.1.fastq 3525698466.00160.1.fastq 3525698466.00049.1.bfq 3525698466.00059.1.bfq 3525698466.00015.mismatch 3525698466.00044.mismatch 3525698466.00076.1.fastq 3525698466.00028.mismatch 3525698466.00103.unmapped 3525698466.00004.1.bfq 3525698466.00110.map 3525698466.00031.unmapped 3525698466.00013.unmapped 3525698466.00130.unmapped 3525698466.00106.map 3525698466.00056.1.bfq 3525698466.00127.unmapped 3525698466.00085.unmapped 3525698466.00061.map 3525698466.00144.1.fastq 3525698466.00051.unmapped 3525698466.00068.unmapped 3525698466.00133.1.bfq 3525698466.00038.map 3525698466.00057.unmapped 3525698466.00128.mismatch 3525698466.00112.unmapped 3525698466.00122.mismatch 3525698466.00104.1.bfq 3525698466.00086.1.fastq 3525698466.00049.mismatch 3525698466.00131.unmapped 3525698466.00069.1.bfq 3525698466.00014.1.bfq 3525698466.00052.1.fastq 3525698466.00096.1.bfq 3525698466.00012.mismatch 3525698466.00130.1.bfq 3525698466.00016.map 3525698466.00160.unmapped 3525698466.00160.map 3525698466.00033.mismatch 3525698466.00034.map 3525698466.00094.1.bfq 3525698466.00138.map 3525698466.00037.unmapped 3525698466.00005.1.fastq 3525698466.00004.mismatch 3525698466.00032.unmapped 3525698466.00050.1.fastq 3525698466.00023.unmapped 3525698466.00137.mismatch 3525698466.00114.1.bfq 3525698466.00036.1.fastq 3525698466.00096.1.fastq 3525698466.00018.1.fastq 3525698466.00116.map 3525698466.00043.map 3525698466.00019.unmapped 3525698466.00062.map 3525698466.00014.unmapped 3525698466.00161.map 3525698466.00158.mismatch 3525698466.00143.map 3525698466.00109.1.bfq 3525698466.00069.mismatch 3525698466.00134.map 3525698466.00159.1.bfq 3525698466.00105.1.fastq 3525698466.00155.map 3525698466.00129.map 3525698466.00042.1.bfq 3525698466.00041.mismatch 3525698466.00051.1.fastq 3525698466.00014.mismatch 3525698466.00047.map 3525698466.00144.unmapped 3525698466.00136.1.fastq 3525698466.00015.1.fastq 3525698466.00084.mismatch 3525698466.00041.1.bfq 3525698466.00150.1.fastq 3525698466.00069.1.fastq 3525698466.00094.mismatch 3525698466.00111.1.bfq 3525698466.00091.1.bfq 3525698466.00087.1.bfq 3525698466.00149.1.bfq 3525698466.00084.unmapped 3525698466.00038.unmapped 3525698466.00114.mismatch 3525698466.00002.map 3525698466.00065.unmapped 3525698466.00142.1.bfq 3525698466.00141.mismatch 3525698466.00124.1.bfq 3525698466.00088.map 3525698466.00093.mismatch 3525698466.00115.1.fastq 3525698466.00082.map 3525698466.00151.1.fastq 3525698466.00036.mismatch 3525698466.00145.mismatch 3525698466.00045.1.fastq 3525698466.00055.map 3525698466.00006.1.bfq 3525698466.00021.map 3525698466.00060.1.bfq 3525698466.00042.mismatch 3525698466.00101.1.bfq 3525698466.00008.map 3525698466.00070.unmapped 3525698466.00075.1.fastq 3525698466.00024.mismatch 3525698466.00083.1.fastq 3525698466.00058.unmapped 3525698466.00043.1.bfq 3525698466.00094.unmapped 3525698466.00106.1.bfq 3525698466.00033.unmapped 3525698466.00077.mismatch 3525698466.00025.1.fastq 3525698466.00087.mismatch 3525698466.00061.1.bfq 3525698466.00142.mismatch 3525698466.00086.1.bfq 3525698466.00124.mismatch 3525698466.00004.unmapped 3525698466.00059.unmapped 3525698466.00038.1.bfq 3525698466.00040.unmapped 3525698466.00079.unmapped 3525698466.00137.unmapped 3525698466.00095.1.fastq 3525698466.00063.map 3525698466.00091.unmapped 3525698466.00152.1.fastq 3525698466.00089.map 3525698466.00056.unmapped 3525698466.00122.1.bfq 3525698466.00006.mismatch 3525698466.00076.map 3525698466.00125.1.fastq 3525698466.00133.unmapped 3525698466.00060.mismatch 3525698466.00016.1.bfq 3525698466.00090.unmapped 3525698466.00148.1.fastq 3525698466.00133.1.fastq 3525698466.00066.1.fastq 3525698466.00049.unmapped 3525698466.00009.map 3525698466.00104.unmapped 3525698466.00072.1.bfq 3525698466.00041.unmapped 3525698466.00138.1.bfq 3525698466.00085.1.fastq 3525698466.00074.unmapped 3525698466.00064.1.fastq 3525698466.00019.mismatch 3525698466.00097.map 3525698466.00077.unmapped 3525698466.00093.1.bfq 3525698466.00085.1.bfq 3525698466.00061.mismatch 3525698466.00062.1.bfq 3525698466.00112.map 3525698466.00079.map 3525698466.00161.1.bfq 3525698466.00156.unmapped 3525698466.00143.1.bfq 3525698466.00088.1.bfq 3525698466.00038.mismatch 3525698466.00047.1.fastq 3525698466.00114.unmapped 3525698466.00071.unmapped 3525698466.00129.1.bfq 3525698466.00078.map 3525698466.00141.unmapped 3525698466.00055.1.bfq 3525698466.00107.1.bfq 3525698466.00082.1.bfq 3525698466.00149.unmapped 3525698466.00047.1.bfq 3525698466.00034.1.bfq 3525698466.00005.mismatch 3525698466.00016.mismatch 3525698466.00005.map 3525698466.00078.unmapped 3525698466.00157.map 3525698466.00109.map 3525698466.00160.mismatch 3525698466.00053.1.fastq 3525698466.00099.1.bfq 2769662419_split1 3525698466.00086.mismatch 3525698466.00044.map 3525698466.00042.unmapped 3525698466.00139.1.fastq 3525698466.00138.mismatch 3525698466.00029.mismatch 3525698466.00024.unmapped 3525698466.00105.map 3525698466.00026.1.bfq 3525698466.00062.mismatch 3525698466.00051.map 3525698466.00135.unmapped 3525698466.00154.mismatch 3525698466.00035.1.fastq 3525698466.00143.mismatch 3525698466.00106.1.fastq 3525698466.00087.unmapped 3525698466.00134.mismatch 3525698466.00136.map 3525698466.00046.unmapped 3525698466.00155.mismatch 3525698466.00144.map 3525698466.00129.mismatch 3525698466.00142.unmapped 3525698466.00150.map 3525698466.00153.1.fastq 3525698466.00124.unmapped 3525698466.00045.mismatch 3525698466.00088.1.fastq 3525698466.00047.mismatch 3525698466.00108.1.bfq 3525698466.00097.1.fastq 3525698466.00067.1.bfq 3525698466.00126.1.bfq 3525698466.00079.1.bfq 3525698466.00149.mismatch 3525698466.00009.1.bfq 3525698466.00012.1.bfq 3525698466.00006.unmapped 3525698466.00135.1.fastq 3525698466.00158.map 3525698466.00060.unmapped 3525698466.00083.mismatch 3525698466.00103.mismatch 3525698466.00121.1.bfq 3525698466.00115.map 3525698466.00117.map 3525698466.00095.1.bfq 3525698466.00151.map 3525698466.00007.1.fastq 3525698466.00097.1.bfq 3525698466.00018.map 3525698466.00070.1.fastq 3525698466.00080.1.fastq 3525698466.00146.1.fastq 3525698466.00026.mismatch 3525698466.00026.map 3525698466.00052.map 3525698466.00106.unmapped 3525698466.00063.1.bfq 3525698466.00060.1.fastq 3525698466.00159.1.fastq 3525698466.00020.unmapped 3525698466.00061.unmapped 3525698466.00158.unmapped 3525698466.00076.1.bfq 3525698466.00043.mismatch 3525698466.00000.1.fastq 3525698466.00107.1.fastq 3525698466.00042.1.fastq 3525698466.00097.unmapped 3525698466.00040.mismatch 3525698466.00071.1.fastq 3525698466.00081.1.fastq 3525698466.00157.1.bfq 3525698466.00085.map 3525698466.00126.mismatch 3525698466.00048.map 3525698466.00064.mismatch 3525698466.00025.mismatch 3525698466.00057.1.fastq 3525698466.00156.1.fastq 3525698466.00147.map 3525698466.00043.unmapped 3525698466.00049.1.fastq 3525698466.00059.1.fastq 3525698466.00007.unmapped 3525698466.00079.1.fastq 3525698466.00001.1.fastq 3525698466.00010.1.fastq 3525698466.00095.map 3525698466.00152.map 3525698466.00138.unmapped 3525698466.00077.1.fastq 3525698466.00016.1.fastq 3525698466.00033.1.bfq 3525698466.00115.mismatch 3525698466.00072.unmapped 3525698466.00125.map 3525698466.00098.1.bfq 3525698466.00126.map 3525698466.00050.map 3525698466.00063.mismatch 3525698466.00090.1.fastq 3525698466.00145.unmapped 3525698466.00083.map 3525698466.00039.1.bfq 3525698466.00116.unmapped 3525698466.00120.unmapped 3525698466.00062.unmapped 3525698466.00065.mismatch 3525698466.00131.map 3525698466.00161.unmapped 3525698466.00110.1.fastq 3525698466.00066.map 3525698466.00143.unmapped 3525698466.00005.1.bfq 3525698466.00100.map 3525698466.00034.unmapped 3525698466.00157.1.fastq 3525698466.00064.map 3525698466.00013.map 3525698466.00155.unmapped 3525698466.00036.1.bfq 3525698466.00129.unmapped 3525698466.00082.unmapped 3525698466.00082.1.fastq 3525698466.00067.1.fastq 3525698466.00092.1.fastq 3525698466.00158.1.bfq 3525698466.00047.unmapped 3525698466.00140.mismatch 3525698466.00107.unmapped 3525698466.00039.map 3525698466.00090.1.bfq 3525698466.00111.1.fastq 3525698466.00061.1.fastq 3525698466.00008.unmapped 3525698466.00098.1.fastq 3525698466.00079.mismatch 3525698466.00100.1.fastq 3525698466.00134.1.bfq 3525698466.00149.1.fastq 3525698466.00136.1.bfq 3525698466.00117.1.fastq 3525698466.00078.1.fastq 3525698466.00015.1.bfq 3525698466.00053.map 3525698466.00102.1.fastq 3525698466.00021.1.fastq 3525698466.00026.unmapped 3525698466.00139.1.bfq 3525698466.00139.map 3525698466.00016.unmapped 3525698466.00012.unmapped 3525698466.00050.mismatch 3525698466.00100.1.bfq 3525698466.00134.unmapped 3525698466.00096.mismatch 3525698466.00057.1.bfq 3525698466.00048.1.bfq 3525698466.00115.1.bfq 3525698466.00089.unmapped 3525698466.00147.1.bfq 3525698466.00035.map 3525698466.00055.unmapped 3525698466.00112.1.fastq 3525698466.00121.1.fastq 3525698466.00121.unmapped 3525698466.00108.unmapped 3525698466.00133.mismatch 3525698466.00046.1.fastq 3525698466.00105.mismatch 3525698466.00091.1.fastq 3525698466.00153.map 3525698466.00051.mismatch 3525698466.00052.1.bfq 3525698466.00023.mismatch 3525698466.00085.mismatch 3525698466.00046.map 3525698466.00067.unmapped 3525698466.00075.1.bfq 3525698466.00136.mismatch 3525698466.00050.1.bfq 3525698466.00056.mismatch 3525698466.00067.mismatch 3525698466.00144.mismatch make: Leaving directory `/data/maqgene/work' make: Entering directory `/data/maqgene/work' # Mon Apr 22 15:22:30 BST 2013: Cleaning intermediate data ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 2734059306_snps,2734059306_rel,2734059306_masked_ids,2734059306_rel_intergenic,2734059306_intergenic_assoc,2734059306_offsets,2734059306_codons,2734059306_marked,2734059306_combined,2929290487_pileup" rm -f 2734059306_snps 2734059306_rel 2734059306_masked_ids 2734059306_rel_intergenic 2734059306_intergenic_assoc 2734059306_offsets 2734059306_codons 2734059306_marked 2734059306_combined 2929290487_pileup make: Leaving directory `/data/maqgene/work'