/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_CB6930-2/./WTCHG_54189_04_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 CB6930-2/./WTCHG_54189_04_1.fastq,CB6930-2/./WTCHG_54189_04_2.fastq,CB1122-2/./WTCHG_54189_02_1.fastq,CB1122-2/./WTCHG_54189_02_2.fastq ++ tr , ' ' + fastq_file_set1='CB6930-2/./WTCHG_54189_04_1.fastq CB6930-2/./WTCHG_54189_04_2.fastq CB1122-2/./WTCHG_54189_02_1.fastq CB1122-2/./WTCHG_54189_02_2.fastq' ++ cd /data/maqgene/reads ++ cat CB6930-2/./WTCHG_54189_04_1.fastq CB6930-2/./WTCHG_54189_04_2.fastq CB1122-2/./WTCHG_54189_02_1.fastq CB1122-2/./WTCHG_54189_02_2.fastq ++ wc -l ++ cut -f 1 -d ' ' + TOTAL_LINES=531727360 ++ echo '(531727360 / 5000000) + (531727360 % 5000000 != 0)' ++ bc + num_chunks=107 + 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=4083184944 map_cksum=235486258 pileup_cksum=3049876794 cns_cksum=3421280319 umdd=50000 dmdd=1000 umid=1000 dmid=1000 max_gene_radius=50000 full_results_dir=/data/maqgene/out/example_user/CB6930_2 outfile_basename=CB6930_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=107 Will process 531727360 lines of input in 107 chunks make: Entering directory `/data/maqgene/work' # Sun Apr 21 23:13:07 BST 2013: Removing frontend files in case this is a duplicate run ... rm -f /data/maqgene/out/example_user/CB6930_2/CB6930_2_{grouped.txt,flat.txt} rm -f /data/maqgene/out/example_user/CB6930_2/CB6930_2_uncovered.txt /data/maqgene/out/example_user/CB6930_2/CB6930_2_coverage.txt /data/maqgene/out/example_user/CB6930_2/CB6930_2_pileup.txt /data/maqgene/out/example_user/CB6930_2/CB6930_2_log.txt /data/maqgene/out/example_user/CB6930_2/CB6930_2_check.txt /data/maqgene/out/example_user/CB6930_2/CB6930_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/CB6930-2/./WTCHG_54189_04_1.fastq /data/maqgene/reads/CB6930-2/./WTCHG_54189_04_2.fastq /data/maqgene/reads/CB1122-2/./WTCHG_54189_02_1.fastq /data/maqgene/reads/CB1122-2/./WTCHG_54189_02_2.fastq) 235486258.1.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; do mv 235486258.1.fastq.$stem 235486258.$stem.1.fastq; done touch 4083184944_split1 # Sun Apr 21 23:17:16 BST 2013: Converting fastq files to bfq ... # Sun Apr 21 23:17:16 BST 2013: Converting fastq files to bfq ... # Sun Apr 21 23:17:16 BST 2013: Converting fastq files to bfq ... # Sun Apr 21 23:17:16 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00001.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00001.1.bfq # Sun Apr 21 23:17:16 BST 2013: Converting fastq files to bfq ... # Sun Apr 21 23:17:16 BST 2013: Converting fastq files to bfq ... # Sun Apr 21 23:17:16 BST 2013: Converting fastq files to bfq ... # Sun Apr 21 23:17:16 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00003.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00003.1.bfq /data/maqgene/bin/maq sol2sanger 235486258.00004.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00004.1.bfq # Sun Apr 21 23:17:16 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00005.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00005.1.bfq /data/maqgene/bin/maq sol2sanger 235486258.00006.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00006.1.bfq /data/maqgene/bin/maq sol2sanger 235486258.00007.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00007.1.bfq /data/maqgene/bin/maq sol2sanger 235486258.00008.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00008.1.bfq /data/maqgene/bin/maq sol2sanger 235486258.00009.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00009.1.bfq /data/maqgene/bin/maq sol2sanger 235486258.00010.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00010.1.bfq /data/maqgene/bin/maq sol2sanger 235486258.00011.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00011.1.bfq # Sun Apr 21 23:17:16 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00002.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00002.1.bfq # Sun Apr 21 23:17:16 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00000.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00000.1.bfq # Sun Apr 21 23:17:17 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00013.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00013.1.bfq # Sun Apr 21 23:17:17 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00012.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00012.1.bfq -- finish writing file '235486258.00009.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '235486258.00007.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '235486258.00010.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '235486258.00002.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '235486258.00003.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '235486258.00000.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '235486258.00013.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '235486258.00006.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '235486258.00001.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '235486258.00011.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '235486258.00004.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '235486258.00012.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '235486258.00005.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '235486258.00008.1.bfq' -- 1250000 sequences were loaded. # Sun Apr 21 23:18:10 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00026.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00026.1.bfq -- finish writing file '235486258.00026.1.bfq' -- 1250000 sequences were loaded. # Sun Apr 21 23:18:38 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00027.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00027.1.bfq -- finish writing file '235486258.00027.1.bfq' -- 1250000 sequences were loaded. # Sun Apr 21 23:19:00 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00028.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00028.1.bfq # Sun Apr 21 23:19:23 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00029.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00029.1.bfq # Sun Apr 21 23:19:24 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00025.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00025.1.bfq # Sun Apr 21 23:19:25 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00024.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00024.1.bfq # Sun Apr 21 23:19:26 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00023.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00023.1.bfq # Sun Apr 21 23:19:27 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00022.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00022.1.bfq # Sun Apr 21 23:19:29 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00021.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00021.1.bfq # Sun Apr 21 23:19:31 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00020.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00020.1.bfq # Sun Apr 21 23:19:33 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00019.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00019.1.bfq -- finish writing file '235486258.00028.1.bfq' -- 1250000 sequences were loaded. # Sun Apr 21 23:19:33 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00018.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00018.1.bfq -- finish writing file '235486258.00029.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '235486258.00024.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '235486258.00023.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '235486258.00022.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '235486258.00020.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '235486258.00021.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '235486258.00025.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '235486258.00019.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '235486258.00018.1.bfq' -- 1250000 sequences were loaded. # Sun Apr 21 23:20:15 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00038.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00038.1.bfq -- finish writing file '235486258.00038.1.bfq' -- 1250000 sequences were loaded. # Sun Apr 21 23:20:48 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00039.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00039.1.bfq # Sun Apr 21 23:20:54 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00040.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00040.1.bfq # Sun Apr 21 23:20:56 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00037.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00037.1.bfq # Sun Apr 21 23:20:58 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00036.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00036.1.bfq # Sun Apr 21 23:21:00 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00035.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00035.1.bfq # Sun Apr 21 23:21:02 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00034.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00034.1.bfq -- finish writing file '235486258.00040.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '235486258.00039.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '235486258.00037.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '235486258.00036.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '235486258.00034.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '235486258.00035.1.bfq' -- 1250000 sequences were loaded. # Sun Apr 21 23:21:41 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00045.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00045.1.bfq # Sun Apr 21 23:21:59 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00046.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00046.1.bfq # Sun Apr 21 23:22:00 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00044.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00044.1.bfq # Sun Apr 21 23:22:01 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00043.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00043.1.bfq # Sun Apr 21 23:22:02 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00042.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00042.1.bfq # Sun Apr 21 23:22:03 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00041.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00041.1.bfq # Sun Apr 21 23:22:05 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00033.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00033.1.bfq # Sun Apr 21 23:22:07 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00032.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00032.1.bfq -- finish writing file '235486258.00045.1.bfq' -- 1250000 sequences were loaded. # Sun Apr 21 23:22:07 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00031.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00031.1.bfq -- finish writing file '235486258.00046.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '235486258.00044.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '235486258.00042.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '235486258.00043.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '235486258.00041.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '235486258.00033.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '235486258.00032.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '235486258.00031.1.bfq' -- 1250000 sequences were loaded. # Sun Apr 21 23:22:46 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00054.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00054.1.bfq -- finish writing file '235486258.00054.1.bfq' -- 1250000 sequences were loaded. # Sun Apr 21 23:23:11 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00055.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00055.1.bfq # Sun Apr 21 23:23:19 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00056.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00056.1.bfq # Sun Apr 21 23:23:21 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00053.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00053.1.bfq # Sun Apr 21 23:23:23 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00052.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00052.1.bfq # Sun Apr 21 23:23:25 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00051.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00051.1.bfq # Sun Apr 21 23:23:27 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00050.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00050.1.bfq -- finish writing file '235486258.00055.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '235486258.00052.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '235486258.00053.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '235486258.00056.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '235486258.00051.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '235486258.00050.1.bfq' -- 1250000 sequences were loaded. # Sun Apr 21 23:24:09 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00061.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00061.1.bfq # Sun Apr 21 23:24:14 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00062.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00062.1.bfq # Sun Apr 21 23:24:15 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00060.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00060.1.bfq # Sun Apr 21 23:24:16 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00059.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00059.1.bfq # Sun Apr 21 23:24:17 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00058.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00058.1.bfq # Sun Apr 21 23:24:18 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00057.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00057.1.bfq -- finish writing file '235486258.00061.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '235486258.00057.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '235486258.00059.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '235486258.00058.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '235486258.00062.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '235486258.00060.1.bfq' -- 1250000 sequences were loaded. # Sun Apr 21 23:24:57 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00067.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00067.1.bfq # Sun Apr 21 23:25:20 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00068.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00068.1.bfq -- finish writing file '235486258.00067.1.bfq' -- 1250000 sequences were loaded. # Sun Apr 21 23:25:20 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00066.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00066.1.bfq # Sun Apr 21 23:25:21 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00069.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00069.1.bfq # Sun Apr 21 23:25:22 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00065.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00065.1.bfq # Sun Apr 21 23:25:23 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00064.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00064.1.bfq -- finish writing file '235486258.00069.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '235486258.00068.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '235486258.00066.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '235486258.00065.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '235486258.00064.1.bfq' -- 1250000 sequences were loaded. # Sun Apr 21 23:26:08 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00073.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00073.1.bfq # Sun Apr 21 23:26:20 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00074.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00074.1.bfq # Sun Apr 21 23:26:21 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00072.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00072.1.bfq # Sun Apr 21 23:26:22 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00071.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00071.1.bfq # Sun Apr 21 23:26:23 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00070.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00070.1.bfq # Sun Apr 21 23:26:24 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00063.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00063.1.bfq -- finish writing file '235486258.00073.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '235486258.00074.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '235486258.00072.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '235486258.00071.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '235486258.00063.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '235486258.00070.1.bfq' -- 1250000 sequences were loaded. # Sun Apr 21 23:27:06 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00079.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00079.1.bfq # Sun Apr 21 23:27:29 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00080.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00080.1.bfq # Sun Apr 21 23:27:30 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00078.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00078.1.bfq # Sun Apr 21 23:27:31 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00077.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00077.1.bfq # Sun Apr 21 23:27:32 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00076.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00076.1.bfq # Sun Apr 21 23:27:33 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00075.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00075.1.bfq -- finish writing file '235486258.00079.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '235486258.00080.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '235486258.00078.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '235486258.00076.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '235486258.00077.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '235486258.00075.1.bfq' -- 1250000 sequences were loaded. # Sun Apr 21 23:28:12 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00085.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00085.1.bfq # Sun Apr 21 23:28:29 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00086.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00086.1.bfq # Sun Apr 21 23:28:31 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00084.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00084.1.bfq # Sun Apr 21 23:28:33 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00083.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00083.1.bfq # Sun Apr 21 23:28:35 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00082.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00082.1.bfq -- finish writing file '235486258.00085.1.bfq' -- 1250000 sequences were loaded. # Sun Apr 21 23:28:37 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00081.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00081.1.bfq # Sun Apr 21 23:28:39 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00087.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00087.1.bfq -- finish writing file '235486258.00082.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '235486258.00084.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '235486258.00086.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '235486258.00083.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '235486258.00081.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '235486258.00087.1.bfq' -- 1250000 sequences were loaded. # Sun Apr 21 23:29:17 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00092.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00092.1.bfq # Sun Apr 21 23:29:35 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00093.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00093.1.bfq # Sun Apr 21 23:29:36 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00091.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00091.1.bfq # Sun Apr 21 23:29:37 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00090.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00090.1.bfq # Sun Apr 21 23:29:38 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00089.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00089.1.bfq # Sun Apr 21 23:29:39 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00088.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00088.1.bfq -- finish writing file '235486258.00092.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '235486258.00093.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '235486258.00088.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '235486258.00089.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '235486258.00091.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '235486258.00090.1.bfq' -- 1250000 sequences were loaded. # Sun Apr 21 23:30:21 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00098.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00098.1.bfq # Sun Apr 21 23:30:30 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00099.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00099.1.bfq # Sun Apr 21 23:30:32 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00097.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00097.1.bfq # Sun Apr 21 23:30:34 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00096.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00096.1.bfq -- finish writing file '235486258.00098.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '235486258.00099.1.bfq' -- 1250000 sequences were loaded. # Sun Apr 21 23:31:05 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00101.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00101.1.bfq -- finish writing file '235486258.00097.1.bfq' -- 1250000 sequences were loaded. # Sun Apr 21 23:31:05 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00100.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00100.1.bfq # Sun Apr 21 23:31:07 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00102.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00102.1.bfq -- finish writing file '235486258.00096.1.bfq' -- 1250000 sequences were loaded. # Sun Apr 21 23:31:08 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00095.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00095.1.bfq # Sun Apr 21 23:31:10 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00103.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00103.1.bfq # Sun Apr 21 23:31:12 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00094.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00094.1.bfq # Sun Apr 21 23:31:14 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00049.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00049.1.bfq -- finish writing file '235486258.00101.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '235486258.00100.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '235486258.00102.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '235486258.00095.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '235486258.00103.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '235486258.00094.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '235486258.00049.1.bfq' -- 1250000 sequences were loaded. # Sun Apr 21 23:31:56 BST 2013: Mapping file(s) 235486258.00002.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00002.unmapped -H 235486258.00002.mismatch \ 235486258.00002.map /data/maqgene/genomes/elegans.bfa 235486258.00002.1.bfq 2> /dev/null # Sun Apr 21 23:32:21 BST 2013: Mapping file(s) 235486258.00003.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00003.unmapped -H 235486258.00003.mismatch \ 235486258.00003.map /data/maqgene/genomes/elegans.bfa 235486258.00003.1.bfq 2> /dev/null # Sun Apr 21 23:32:22 BST 2013: Mapping file(s) 235486258.00001.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00001.unmapped -H 235486258.00001.mismatch \ 235486258.00001.map /data/maqgene/genomes/elegans.bfa 235486258.00001.1.bfq 2> /dev/null # Sun Apr 21 23:32:23 BST 2013: Mapping file(s) 235486258.00000.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00000.unmapped -H 235486258.00000.mismatch \ 235486258.00000.map /data/maqgene/genomes/elegans.bfa 235486258.00000.1.bfq 2> /dev/null # Sun Apr 21 23:32:24 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00106.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00106.1.bfq # Sun Apr 21 23:32:25 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00105.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00105.1.bfq # Sun Apr 21 23:32:26 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00104.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00104.1.bfq # Sun Apr 21 23:32:27 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00048.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00048.1.bfq # Sun Apr 21 23:32:28 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00047.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00047.1.bfq # Sun Apr 21 23:32:29 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00030.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00030.1.bfq -- finish writing file '235486258.00106.1.bfq' -- 431840 sequences were loaded. -- finish writing file '235486258.00105.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '235486258.00048.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '235486258.00030.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '235486258.00047.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '235486258.00104.1.bfq' -- 1250000 sequences were loaded. # Sun Apr 21 23:38:15 BST 2013: Mapping file(s) 235486258.00009.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00009.unmapped -H 235486258.00009.mismatch \ 235486258.00009.map /data/maqgene/genomes/elegans.bfa 235486258.00009.1.bfq 2> /dev/null # Sun Apr 21 23:38:16 BST 2013: Mapping file(s) 235486258.00008.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00008.unmapped -H 235486258.00008.mismatch \ 235486258.00008.map /data/maqgene/genomes/elegans.bfa 235486258.00008.1.bfq 2> /dev/null # Sun Apr 21 23:38:17 BST 2013: Mapping file(s) 235486258.00007.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00007.unmapped -H 235486258.00007.mismatch \ 235486258.00007.map /data/maqgene/genomes/elegans.bfa 235486258.00007.1.bfq 2> /dev/null # Sun Apr 21 23:38:19 BST 2013: Mapping file(s) 235486258.00006.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00006.unmapped -H 235486258.00006.mismatch \ 235486258.00006.map /data/maqgene/genomes/elegans.bfa 235486258.00006.1.bfq 2> /dev/null # Sun Apr 21 23:38:19 BST 2013: Mapping file(s) 235486258.00005.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00005.unmapped -H 235486258.00005.mismatch \ 235486258.00005.map /data/maqgene/genomes/elegans.bfa 235486258.00005.1.bfq 2> /dev/null # Sun Apr 21 23:38:20 BST 2013: Mapping file(s) 235486258.00004.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00004.unmapped -H 235486258.00004.mismatch \ 235486258.00004.map /data/maqgene/genomes/elegans.bfa 235486258.00004.1.bfq 2> /dev/null # Sun Apr 21 23:46:41 BST 2013: Mapping file(s) 235486258.00020.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00020.unmapped -H 235486258.00020.mismatch \ 235486258.00020.map /data/maqgene/genomes/elegans.bfa 235486258.00020.1.bfq 2> /dev/null # Sun Apr 21 23:46:43 BST 2013: Mapping file(s) 235486258.00019.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00019.unmapped -H 235486258.00019.mismatch \ 235486258.00019.map /data/maqgene/genomes/elegans.bfa 235486258.00019.1.bfq 2> /dev/null # Sun Apr 21 23:46:45 BST 2013: Mapping file(s) 235486258.00018.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00018.unmapped -H 235486258.00018.mismatch \ 235486258.00018.map /data/maqgene/genomes/elegans.bfa 235486258.00018.1.bfq 2> /dev/null # Sun Apr 21 23:47:32 BST 2013: Mapping file(s) 235486258.00023.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00023.unmapped -H 235486258.00023.mismatch \ 235486258.00023.map /data/maqgene/genomes/elegans.bfa 235486258.00023.1.bfq 2> /dev/null # Sun Apr 21 23:47:34 BST 2013: Mapping file(s) 235486258.00022.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00022.unmapped -H 235486258.00022.mismatch \ 235486258.00022.map /data/maqgene/genomes/elegans.bfa 235486258.00022.1.bfq 2> /dev/null # Sun Apr 21 23:47:36 BST 2013: Mapping file(s) 235486258.00021.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00021.unmapped -H 235486258.00021.mismatch \ 235486258.00021.map /data/maqgene/genomes/elegans.bfa 235486258.00021.1.bfq 2> /dev/null # Sun Apr 21 23:52:58 BST 2013: Mapping file(s) 235486258.00026.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00026.unmapped -H 235486258.00026.mismatch \ 235486258.00026.map /data/maqgene/genomes/elegans.bfa 235486258.00026.1.bfq 2> /dev/null # Sun Apr 21 23:53:00 BST 2013: Mapping file(s) 235486258.00025.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00025.unmapped -H 235486258.00025.mismatch \ 235486258.00025.map /data/maqgene/genomes/elegans.bfa 235486258.00025.1.bfq 2> /dev/null # Sun Apr 21 23:53:02 BST 2013: Mapping file(s) 235486258.00024.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00024.unmapped -H 235486258.00024.mismatch \ 235486258.00024.map /data/maqgene/genomes/elegans.bfa 235486258.00024.1.bfq 2> /dev/null # Sun Apr 21 23:56:38 BST 2013: Mapping file(s) 235486258.00029.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00029.unmapped -H 235486258.00029.mismatch \ 235486258.00029.map /data/maqgene/genomes/elegans.bfa 235486258.00029.1.bfq 2> /dev/null # Sun Apr 21 23:56:39 BST 2013: Mapping file(s) 235486258.00028.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00028.unmapped -H 235486258.00028.mismatch \ 235486258.00028.map /data/maqgene/genomes/elegans.bfa 235486258.00028.1.bfq 2> /dev/null # Sun Apr 21 23:56:40 BST 2013: Mapping file(s) 235486258.00027.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00027.unmapped -H 235486258.00027.mismatch \ 235486258.00027.map /data/maqgene/genomes/elegans.bfa 235486258.00027.1.bfq 2> /dev/null # Sun Apr 21 23:56:41 BST 2013: Mapping file(s) 235486258.00013.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00013.unmapped -H 235486258.00013.mismatch \ 235486258.00013.map /data/maqgene/genomes/elegans.bfa 235486258.00013.1.bfq 2> /dev/null # Sun Apr 21 23:56:42 BST 2013: Mapping file(s) 235486258.00012.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00012.unmapped -H 235486258.00012.mismatch \ 235486258.00012.map /data/maqgene/genomes/elegans.bfa 235486258.00012.1.bfq 2> /dev/null # Mon Apr 22 00:04:19 BST 2013: Mapping file(s) 235486258.00036.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00036.unmapped -H 235486258.00036.mismatch \ 235486258.00036.map /data/maqgene/genomes/elegans.bfa 235486258.00036.1.bfq 2> /dev/null # Mon Apr 22 00:04:19 BST 2013: Mapping file(s) 235486258.00035.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00035.unmapped -H 235486258.00035.mismatch \ 235486258.00035.map /data/maqgene/genomes/elegans.bfa 235486258.00035.1.bfq 2> /dev/null # Mon Apr 22 00:04:20 BST 2013: Mapping file(s) 235486258.00037.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00037.unmapped -H 235486258.00037.mismatch \ 235486258.00037.map /data/maqgene/genomes/elegans.bfa 235486258.00037.1.bfq 2> /dev/null # Mon Apr 22 00:04:21 BST 2013: Mapping file(s) 235486258.00034.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00034.unmapped -H 235486258.00034.mismatch \ 235486258.00034.map /data/maqgene/genomes/elegans.bfa 235486258.00034.1.bfq 2> /dev/null # Mon Apr 22 00:04:22 BST 2013: Mapping file(s) 235486258.00033.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00033.unmapped -H 235486258.00033.mismatch \ 235486258.00033.map /data/maqgene/genomes/elegans.bfa 235486258.00033.1.bfq 2> /dev/null # Mon Apr 22 00:04:23 BST 2013: Mapping file(s) 235486258.00032.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00032.unmapped -H 235486258.00032.mismatch \ 235486258.00032.map /data/maqgene/genomes/elegans.bfa 235486258.00032.1.bfq 2> /dev/null # Mon Apr 22 00:10:55 BST 2013: Mapping file(s) 235486258.00039.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00039.unmapped -H 235486258.00039.mismatch \ 235486258.00039.map /data/maqgene/genomes/elegans.bfa 235486258.00039.1.bfq 2> /dev/null # Mon Apr 22 00:10:57 BST 2013: Mapping file(s) 235486258.00038.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00038.unmapped -H 235486258.00038.mismatch \ 235486258.00038.map /data/maqgene/genomes/elegans.bfa 235486258.00038.1.bfq 2> /dev/null # Mon Apr 22 00:10:59 BST 2013: Mapping file(s) 235486258.00031.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00031.unmapped -H 235486258.00031.mismatch \ 235486258.00031.map /data/maqgene/genomes/elegans.bfa 235486258.00031.1.bfq 2> /dev/null # Mon Apr 22 00:13:00 BST 2013: Mapping file(s) 235486258.00043.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00043.unmapped -H 235486258.00043.mismatch \ 235486258.00043.map /data/maqgene/genomes/elegans.bfa 235486258.00043.1.bfq 2> /dev/null # Mon Apr 22 00:13:02 BST 2013: Mapping file(s) 235486258.00042.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00042.unmapped -H 235486258.00042.mismatch \ 235486258.00042.map /data/maqgene/genomes/elegans.bfa 235486258.00042.1.bfq 2> /dev/null # Mon Apr 22 00:13:04 BST 2013: Mapping file(s) 235486258.00041.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00041.unmapped -H 235486258.00041.mismatch \ 235486258.00041.map /data/maqgene/genomes/elegans.bfa 235486258.00041.1.bfq 2> /dev/null # Mon Apr 22 00:18:16 BST 2013: Mapping file(s) 235486258.00047.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00047.unmapped -H 235486258.00047.mismatch \ 235486258.00047.map /data/maqgene/genomes/elegans.bfa 235486258.00047.1.bfq 2> /dev/null # Mon Apr 22 00:18:18 BST 2013: Mapping file(s) 235486258.00046.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00046.unmapped -H 235486258.00046.mismatch \ 235486258.00046.map /data/maqgene/genomes/elegans.bfa 235486258.00046.1.bfq 2> /dev/null # Mon Apr 22 00:18:20 BST 2013: Mapping file(s) 235486258.00045.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00045.unmapped -H 235486258.00045.mismatch \ 235486258.00045.map /data/maqgene/genomes/elegans.bfa 235486258.00045.1.bfq 2> /dev/null # Mon Apr 22 00:21:16 BST 2013: Mapping file(s) 235486258.00049.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00049.unmapped -H 235486258.00049.mismatch \ 235486258.00049.map /data/maqgene/genomes/elegans.bfa 235486258.00049.1.bfq 2> /dev/null # Mon Apr 22 00:21:17 BST 2013: Mapping file(s) 235486258.00048.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00048.unmapped -H 235486258.00048.mismatch \ 235486258.00048.map /data/maqgene/genomes/elegans.bfa 235486258.00048.1.bfq 2> /dev/null # Mon Apr 22 00:21:18 BST 2013: Mapping file(s) 235486258.00044.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00044.unmapped -H 235486258.00044.mismatch \ 235486258.00044.map /data/maqgene/genomes/elegans.bfa 235486258.00044.1.bfq 2> /dev/null # Mon Apr 22 00:21:19 BST 2013: Mapping file(s) 235486258.00040.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00040.unmapped -H 235486258.00040.mismatch \ 235486258.00040.map /data/maqgene/genomes/elegans.bfa 235486258.00040.1.bfq 2> /dev/null # Mon Apr 22 00:21:20 BST 2013: Mapping file(s) 235486258.00030.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00030.unmapped -H 235486258.00030.mismatch \ 235486258.00030.map /data/maqgene/genomes/elegans.bfa 235486258.00030.1.bfq 2> /dev/null # Mon Apr 22 00:28:12 BST 2013: Mapping file(s) 235486258.00054.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00054.unmapped -H 235486258.00054.mismatch \ 235486258.00054.map /data/maqgene/genomes/elegans.bfa 235486258.00054.1.bfq 2> /dev/null # Mon Apr 22 00:28:13 BST 2013: Mapping file(s) 235486258.00053.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00053.unmapped -H 235486258.00053.mismatch \ 235486258.00053.map /data/maqgene/genomes/elegans.bfa 235486258.00053.1.bfq 2> /dev/null # Mon Apr 22 00:28:14 BST 2013: Mapping file(s) 235486258.00052.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00052.unmapped -H 235486258.00052.mismatch \ 235486258.00052.map /data/maqgene/genomes/elegans.bfa 235486258.00052.1.bfq 2> /dev/null # Mon Apr 22 00:28:15 BST 2013: Mapping file(s) 235486258.00051.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00051.unmapped -H 235486258.00051.mismatch \ 235486258.00051.map /data/maqgene/genomes/elegans.bfa 235486258.00051.1.bfq 2> /dev/null # Mon Apr 22 00:28:16 BST 2013: Mapping file(s) 235486258.00050.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00050.unmapped -H 235486258.00050.mismatch \ 235486258.00050.map /data/maqgene/genomes/elegans.bfa 235486258.00050.1.bfq 2> /dev/null # Mon Apr 22 00:34:23 BST 2013: Mapping file(s) 235486258.00060.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00060.unmapped -H 235486258.00060.mismatch \ 235486258.00060.map /data/maqgene/genomes/elegans.bfa 235486258.00060.1.bfq 2> /dev/null # Mon Apr 22 00:34:24 BST 2013: Mapping file(s) 235486258.00059.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00059.unmapped -H 235486258.00059.mismatch \ 235486258.00059.map /data/maqgene/genomes/elegans.bfa 235486258.00059.1.bfq 2> /dev/null # Mon Apr 22 00:34:25 BST 2013: Mapping file(s) 235486258.00058.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00058.unmapped -H 235486258.00058.mismatch \ 235486258.00058.map /data/maqgene/genomes/elegans.bfa 235486258.00058.1.bfq 2> /dev/null # Mon Apr 22 00:34:26 BST 2013: Mapping file(s) 235486258.00057.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00057.unmapped -H 235486258.00057.mismatch \ 235486258.00057.map /data/maqgene/genomes/elegans.bfa 235486258.00057.1.bfq 2> /dev/null # Mon Apr 22 00:34:27 BST 2013: Mapping file(s) 235486258.00056.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00056.unmapped -H 235486258.00056.mismatch \ 235486258.00056.map /data/maqgene/genomes/elegans.bfa 235486258.00056.1.bfq 2> /dev/null # Mon Apr 22 00:40:48 BST 2013: Mapping file(s) 235486258.00064.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00064.unmapped -H 235486258.00064.mismatch \ 235486258.00064.map /data/maqgene/genomes/elegans.bfa 235486258.00064.1.bfq 2> /dev/null # Mon Apr 22 00:40:50 BST 2013: Mapping file(s) 235486258.00063.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00063.unmapped -H 235486258.00063.mismatch \ 235486258.00063.map /data/maqgene/genomes/elegans.bfa 235486258.00063.1.bfq 2> /dev/null # Mon Apr 22 00:40:52 BST 2013: Mapping file(s) 235486258.00062.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00062.unmapped -H 235486258.00062.mismatch \ 235486258.00062.map /data/maqgene/genomes/elegans.bfa 235486258.00062.1.bfq 2> /dev/null # Mon Apr 22 00:42:08 BST 2013: Mapping file(s) 235486258.00067.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00067.unmapped -H 235486258.00067.mismatch \ 235486258.00067.map /data/maqgene/genomes/elegans.bfa 235486258.00067.1.bfq 2> /dev/null # Mon Apr 22 00:42:11 BST 2013: Mapping file(s) 235486258.00066.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00066.unmapped -H 235486258.00066.mismatch \ 235486258.00066.map /data/maqgene/genomes/elegans.bfa 235486258.00066.1.bfq 2> /dev/null # Mon Apr 22 00:42:13 BST 2013: Mapping file(s) 235486258.00065.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00065.unmapped -H 235486258.00065.mismatch \ 235486258.00065.map /data/maqgene/genomes/elegans.bfa 235486258.00065.1.bfq 2> /dev/null # Mon Apr 22 00:48:25 BST 2013: Mapping file(s) 235486258.00070.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00070.unmapped -H 235486258.00070.mismatch \ 235486258.00070.map /data/maqgene/genomes/elegans.bfa 235486258.00070.1.bfq 2> /dev/null # Mon Apr 22 00:48:27 BST 2013: Mapping file(s) 235486258.00069.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00069.unmapped -H 235486258.00069.mismatch \ 235486258.00069.map /data/maqgene/genomes/elegans.bfa 235486258.00069.1.bfq 2> /dev/null # Mon Apr 22 00:48:29 BST 2013: Mapping file(s) 235486258.00068.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00068.unmapped -H 235486258.00068.mismatch \ 235486258.00068.map /data/maqgene/genomes/elegans.bfa 235486258.00068.1.bfq 2> /dev/null # Mon Apr 22 00:50:20 BST 2013: Mapping file(s) 235486258.00073.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00073.unmapped -H 235486258.00073.mismatch \ 235486258.00073.map /data/maqgene/genomes/elegans.bfa 235486258.00073.1.bfq 2> /dev/null # Mon Apr 22 00:50:22 BST 2013: Mapping file(s) 235486258.00072.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00072.unmapped -H 235486258.00072.mismatch \ 235486258.00072.map /data/maqgene/genomes/elegans.bfa 235486258.00072.1.bfq 2> /dev/null # Mon Apr 22 00:50:24 BST 2013: Mapping file(s) 235486258.00071.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00071.unmapped -H 235486258.00071.mismatch \ 235486258.00071.map /data/maqgene/genomes/elegans.bfa 235486258.00071.1.bfq 2> /dev/null # Mon Apr 22 00:55:55 BST 2013: Mapping file(s) 235486258.00076.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00076.unmapped -H 235486258.00076.mismatch \ 235486258.00076.map /data/maqgene/genomes/elegans.bfa 235486258.00076.1.bfq 2> /dev/null # Mon Apr 22 00:55:57 BST 2013: Mapping file(s) 235486258.00075.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00075.unmapped -H 235486258.00075.mismatch \ 235486258.00075.map /data/maqgene/genomes/elegans.bfa 235486258.00075.1.bfq 2> /dev/null # Mon Apr 22 00:55:59 BST 2013: Mapping file(s) 235486258.00074.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00074.unmapped -H 235486258.00074.mismatch \ 235486258.00074.map /data/maqgene/genomes/elegans.bfa 235486258.00074.1.bfq 2> /dev/null # Mon Apr 22 00:58:45 BST 2013: Mapping file(s) 235486258.00079.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00079.unmapped -H 235486258.00079.mismatch \ 235486258.00079.map /data/maqgene/genomes/elegans.bfa 235486258.00079.1.bfq 2> /dev/null # Mon Apr 22 00:58:46 BST 2013: Mapping file(s) 235486258.00078.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00078.unmapped -H 235486258.00078.mismatch \ 235486258.00078.map /data/maqgene/genomes/elegans.bfa 235486258.00078.1.bfq 2> /dev/null # Mon Apr 22 00:58:47 BST 2013: Mapping file(s) 235486258.00077.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00077.unmapped -H 235486258.00077.mismatch \ 235486258.00077.map /data/maqgene/genomes/elegans.bfa 235486258.00077.1.bfq 2> /dev/null # Mon Apr 22 00:58:48 BST 2013: Mapping file(s) 235486258.00061.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00061.unmapped -H 235486258.00061.mismatch \ 235486258.00061.map /data/maqgene/genomes/elegans.bfa 235486258.00061.1.bfq 2> /dev/null # Mon Apr 22 00:58:49 BST 2013: Mapping file(s) 235486258.00055.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00055.unmapped -H 235486258.00055.mismatch \ 235486258.00055.map /data/maqgene/genomes/elegans.bfa 235486258.00055.1.bfq 2> /dev/null # Mon Apr 22 01:06:01 BST 2013: Mapping file(s) 235486258.00085.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00085.unmapped -H 235486258.00085.mismatch \ 235486258.00085.map /data/maqgene/genomes/elegans.bfa 235486258.00085.1.bfq 2> /dev/null # Mon Apr 22 01:06:02 BST 2013: Mapping file(s) 235486258.00084.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00084.unmapped -H 235486258.00084.mismatch \ 235486258.00084.map /data/maqgene/genomes/elegans.bfa 235486258.00084.1.bfq 2> /dev/null # Mon Apr 22 01:06:03 BST 2013: Mapping file(s) 235486258.00083.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00083.unmapped -H 235486258.00083.mismatch \ 235486258.00083.map /data/maqgene/genomes/elegans.bfa 235486258.00083.1.bfq 2> /dev/null # Mon Apr 22 01:06:04 BST 2013: Mapping file(s) 235486258.00082.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00082.unmapped -H 235486258.00082.mismatch \ 235486258.00082.map /data/maqgene/genomes/elegans.bfa 235486258.00082.1.bfq 2> /dev/null # Mon Apr 22 01:06:05 BST 2013: Mapping file(s) 235486258.00081.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00081.unmapped -H 235486258.00081.mismatch \ 235486258.00081.map /data/maqgene/genomes/elegans.bfa 235486258.00081.1.bfq 2> /dev/null # Mon Apr 22 01:06:05 BST 2013: Mapping file(s) 235486258.00080.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00080.unmapped -H 235486258.00080.mismatch \ 235486258.00080.map /data/maqgene/genomes/elegans.bfa 235486258.00080.1.bfq 2> /dev/null # Mon Apr 22 01:13:47 BST 2013: Mapping file(s) 235486258.00092.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00092.unmapped -H 235486258.00092.mismatch \ 235486258.00092.map /data/maqgene/genomes/elegans.bfa 235486258.00092.1.bfq 2> /dev/null # Mon Apr 22 01:13:48 BST 2013: Mapping file(s) 235486258.00091.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00091.unmapped -H 235486258.00091.mismatch \ 235486258.00091.map /data/maqgene/genomes/elegans.bfa 235486258.00091.1.bfq 2> /dev/null # Mon Apr 22 01:13:49 BST 2013: Mapping file(s) 235486258.00090.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00090.unmapped -H 235486258.00090.mismatch \ 235486258.00090.map /data/maqgene/genomes/elegans.bfa 235486258.00090.1.bfq 2> /dev/null # Mon Apr 22 01:13:50 BST 2013: Mapping file(s) 235486258.00089.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00089.unmapped -H 235486258.00089.mismatch \ 235486258.00089.map /data/maqgene/genomes/elegans.bfa 235486258.00089.1.bfq 2> /dev/null # Mon Apr 22 01:13:51 BST 2013: Mapping file(s) 235486258.00088.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00088.unmapped -H 235486258.00088.mismatch \ 235486258.00088.map /data/maqgene/genomes/elegans.bfa 235486258.00088.1.bfq 2> /dev/null # Mon Apr 22 01:19:38 BST 2013: Mapping file(s) 235486258.00095.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00095.unmapped -H 235486258.00095.mismatch \ 235486258.00095.map /data/maqgene/genomes/elegans.bfa 235486258.00095.1.bfq 2> /dev/null # Mon Apr 22 01:19:39 BST 2013: Mapping file(s) 235486258.00094.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00094.unmapped -H 235486258.00094.mismatch \ 235486258.00094.map /data/maqgene/genomes/elegans.bfa 235486258.00094.1.bfq 2> /dev/null # Mon Apr 22 01:19:40 BST 2013: Mapping file(s) 235486258.00093.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00093.unmapped -H 235486258.00093.mismatch \ 235486258.00093.map /data/maqgene/genomes/elegans.bfa 235486258.00093.1.bfq 2> /dev/null # Mon Apr 22 01:19:41 BST 2013: Mapping file(s) 235486258.00087.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00087.unmapped -H 235486258.00087.mismatch \ 235486258.00087.map /data/maqgene/genomes/elegans.bfa 235486258.00087.1.bfq 2> /dev/null # Mon Apr 22 01:19:42 BST 2013: Mapping file(s) 235486258.00086.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00086.unmapped -H 235486258.00086.mismatch \ 235486258.00086.map /data/maqgene/genomes/elegans.bfa 235486258.00086.1.bfq 2> /dev/null # Mon Apr 22 01:25:43 BST 2013: Mapping file(s) 235486258.00101.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00101.unmapped -H 235486258.00101.mismatch \ 235486258.00101.map /data/maqgene/genomes/elegans.bfa 235486258.00101.1.bfq 2> /dev/null # Mon Apr 22 01:25:44 BST 2013: Mapping file(s) 235486258.00100.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00100.unmapped -H 235486258.00100.mismatch \ 235486258.00100.map /data/maqgene/genomes/elegans.bfa 235486258.00100.1.bfq 2> /dev/null # Mon Apr 22 01:25:45 BST 2013: Mapping file(s) 235486258.00099.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00099.unmapped -H 235486258.00099.mismatch \ 235486258.00099.map /data/maqgene/genomes/elegans.bfa 235486258.00099.1.bfq 2> /dev/null # Mon Apr 22 01:25:46 BST 2013: Mapping file(s) 235486258.00098.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00098.unmapped -H 235486258.00098.mismatch \ 235486258.00098.map /data/maqgene/genomes/elegans.bfa 235486258.00098.1.bfq 2> /dev/null # Mon Apr 22 01:25:47 BST 2013: Mapping file(s) 235486258.00097.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00097.unmapped -H 235486258.00097.mismatch \ 235486258.00097.map /data/maqgene/genomes/elegans.bfa 235486258.00097.1.bfq 2> /dev/null # Mon Apr 22 01:31:44 BST 2013: Mapping file(s) 235486258.00105.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00105.unmapped -H 235486258.00105.mismatch \ 235486258.00105.map /data/maqgene/genomes/elegans.bfa 235486258.00105.1.bfq 2> /dev/null # Mon Apr 22 01:31:46 BST 2013: Mapping file(s) 235486258.00104.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00104.unmapped -H 235486258.00104.mismatch \ 235486258.00104.map /data/maqgene/genomes/elegans.bfa 235486258.00104.1.bfq 2> /dev/null # Mon Apr 22 01:31:48 BST 2013: Mapping file(s) 235486258.00103.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00103.unmapped -H 235486258.00103.mismatch \ 235486258.00103.map /data/maqgene/genomes/elegans.bfa 235486258.00103.1.bfq 2> /dev/null # Mon Apr 22 01:36:48 BST 2013: Mapping file(s) 235486258.00102.1.bfq # Mon Apr 22 01:36:48 BST 2013: Mapping file(s) 235486258.00106.1.bfq # Mon Apr 22 01:36:48 BST 2013: Mapping file(s) 235486258.00096.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00106.unmapped -H 235486258.00106.mismatch \ 235486258.00106.map /data/maqgene/genomes/elegans.bfa 235486258.00106.1.bfq 2> /dev/null /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00102.unmapped -H 235486258.00102.mismatch \ 235486258.00102.map /data/maqgene/genomes/elegans.bfa 235486258.00102.1.bfq 2> /dev/null /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00096.unmapped -H 235486258.00096.mismatch \ 235486258.00096.map /data/maqgene/genomes/elegans.bfa 235486258.00096.1.bfq 2> /dev/null # Mon Apr 22 01:36:48 BST 2013: Mapping file(s) 235486258.00011.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00011.unmapped -H 235486258.00011.mismatch \ 235486258.00011.map /data/maqgene/genomes/elegans.bfa 235486258.00011.1.bfq 2> /dev/null # Mon Apr 22 01:36:56 BST 2013: Mapping file(s) 235486258.00010.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00010.unmapped -H 235486258.00010.mismatch \ 235486258.00010.map /data/maqgene/genomes/elegans.bfa 235486258.00010.1.bfq 2> /dev/null # Mon Apr 22 01:36:56 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00017.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00017.1.bfq -- finish writing file '235486258.00017.1.bfq' -- 1250000 sequences were loaded. # Mon Apr 22 01:43:57 BST 2013: Mapping file(s) 235486258.00017.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00017.unmapped -H 235486258.00017.mismatch \ 235486258.00017.map /data/maqgene/genomes/elegans.bfa 235486258.00017.1.bfq 2> /dev/null /data/maqgene/bin/maq sol2sanger 235486258.00015.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00015.1.bfq # Mon Apr 22 01:43:57 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00016.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00016.1.bfq # Mon Apr 22 01:43:57 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 235486258.00014.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 235486258.00014.1.bfq -- finish writing file '235486258.00014.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '235486258.00016.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '235486258.00015.1.bfq' -- 1250000 sequences were loaded. # Mon Apr 22 01:49:53 BST 2013: Mapping file(s) 235486258.00015.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00016.unmapped -H 235486258.00016.mismatch \ 235486258.00016.map /data/maqgene/genomes/elegans.bfa 235486258.00016.1.bfq 2> /dev/null /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00015.unmapped -H 235486258.00015.mismatch \ 235486258.00015.map /data/maqgene/genomes/elegans.bfa 235486258.00015.1.bfq 2> /dev/null # Mon Apr 22 01:49:53 BST 2013: Mapping file(s) 235486258.00014.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 235486258.00014.unmapped -H 235486258.00014.mismatch \ 235486258.00014.map /data/maqgene/genomes/elegans.bfa 235486258.00014.1.bfq 2> /dev/null # Mon Apr 22 01:56:54 BST 2013: Merging all maps ... # Mon Apr 22 01:56:54 BST 2013: Merging all *.unmapped files ... /data/maqgene/bin/maq mapmerge 235486258.map 235486258.00000.map 235486258.00001.map 235486258.00002.map 235486258.00003.map 235486258.00004.map 235486258.00005.map 235486258.00006.map 235486258.00007.map 235486258.00008.map 235486258.00009.map 235486258.00010.map 235486258.00011.map 235486258.00012.map 235486258.00013.map 235486258.00014.map 235486258.00015.map 235486258.00016.map 235486258.00017.map 235486258.00018.map 235486258.00019.map 235486258.00020.map 235486258.00021.map 235486258.00022.map 235486258.00023.map 235486258.00024.map 235486258.00025.map 235486258.00026.map 235486258.00027.map 235486258.00028.map 235486258.00029.map 235486258.00030.map 235486258.00031.map 235486258.00032.map 235486258.00033.map 235486258.00034.map 235486258.00035.map 235486258.00036.map 235486258.00037.map 235486258.00038.map 235486258.00039.map 235486258.00040.map 235486258.00041.map 235486258.00042.map 235486258.00043.map 235486258.00044.map 235486258.00045.map 235486258.00046.map 235486258.00047.map 235486258.00048.map 235486258.00049.map 235486258.00050.map 235486258.00051.map 235486258.00052.map 235486258.00053.map 235486258.00054.map 235486258.00055.map 235486258.00056.map 235486258.00057.map 235486258.00058.map 235486258.00059.map 235486258.00060.map 235486258.00061.map 235486258.00062.map 235486258.00063.map 235486258.00064.map 235486258.00065.map 235486258.00066.map 235486258.00067.map 235486258.00068.map 235486258.00069.map 235486258.00070.map 235486258.00071.map 235486258.00072.map 235486258.00073.map 235486258.00074.map 235486258.00075.map 235486258.00076.map 235486258.00077.map 235486258.00078.map 235486258.00079.map 235486258.00080.map 235486258.00081.map 235486258.00082.map 235486258.00083.map 235486258.00084.map 235486258.00085.map 235486258.00086.map 235486258.00087.map 235486258.00088.map 235486258.00089.map 235486258.00090.map 235486258.00091.map 235486258.00092.map 235486258.00093.map 235486258.00094.map 235486258.00095.map 235486258.00096.map 235486258.00097.map 235486258.00098.map 235486258.00099.map 235486258.00100.map 235486258.00101.map 235486258.00102.map 235486258.00103.map 235486258.00104.map 235486258.00105.map 235486258.00106.map cat 235486258.00000.unmapped 235486258.00001.unmapped 235486258.00002.unmapped 235486258.00003.unmapped 235486258.00004.unmapped 235486258.00005.unmapped 235486258.00006.unmapped 235486258.00007.unmapped 235486258.00008.unmapped 235486258.00009.unmapped 235486258.00010.unmapped 235486258.00011.unmapped 235486258.00012.unmapped 235486258.00013.unmapped 235486258.00014.unmapped 235486258.00015.unmapped 235486258.00016.unmapped 235486258.00017.unmapped 235486258.00018.unmapped 235486258.00019.unmapped 235486258.00020.unmapped 235486258.00021.unmapped 235486258.00022.unmapped 235486258.00023.unmapped 235486258.00024.unmapped 235486258.00025.unmapped 235486258.00026.unmapped 235486258.00027.unmapped 235486258.00028.unmapped 235486258.00029.unmapped 235486258.00030.unmapped 235486258.00031.unmapped 235486258.00032.unmapped 235486258.00033.unmapped 235486258.00034.unmapped 235486258.00035.unmapped 235486258.00036.unmapped 235486258.00037.unmapped 235486258.00038.unmapped 235486258.00039.unmapped 235486258.00040.unmapped 235486258.00041.unmapped 235486258.00042.unmapped 235486258.00043.unmapped 235486258.00044.unmapped 235486258.00045.unmapped 235486258.00046.unmapped 235486258.00047.unmapped 235486258.00048.unmapped 235486258.00049.unmapped 235486258.00050.unmapped 235486258.00051.unmapped 235486258.00052.unmapped 235486258.00053.unmapped 235486258.00054.unmapped 235486258.00055.unmapped 235486258.00056.unmapped 235486258.00057.unmapped 235486258.00058.unmapped 235486258.00059.unmapped 235486258.00060.unmapped 235486258.00061.unmapped 235486258.00062.unmapped 235486258.00063.unmapped 235486258.00064.unmapped 235486258.00065.unmapped 235486258.00066.unmapped 235486258.00067.unmapped 235486258.00068.unmapped 235486258.00069.unmapped 235486258.00070.unmapped 235486258.00071.unmapped 235486258.00072.unmapped 235486258.00073.unmapped 235486258.00074.unmapped 235486258.00075.unmapped 235486258.00076.unmapped 235486258.00077.unmapped 235486258.00078.unmapped 235486258.00079.unmapped 235486258.00080.unmapped 235486258.00081.unmapped 235486258.00082.unmapped 235486258.00083.unmapped 235486258.00084.unmapped 235486258.00085.unmapped 235486258.00086.unmapped 235486258.00087.unmapped 235486258.00088.unmapped 235486258.00089.unmapped 235486258.00090.unmapped 235486258.00091.unmapped 235486258.00092.unmapped 235486258.00093.unmapped 235486258.00094.unmapped 235486258.00095.unmapped 235486258.00096.unmapped 235486258.00097.unmapped 235486258.00098.unmapped 235486258.00099.unmapped 235486258.00100.unmapped 235486258.00101.unmapped 235486258.00102.unmapped 235486258.00103.unmapped 235486258.00104.unmapped 235486258.00105.unmapped 235486258.00106.unmapped > 235486258_unmapped.txt # Mon Apr 22 01:57:12 BST 2013: Linking backend file 235486258_unmapped.txt to /data/maqgene/out/example_user/CB6930_2/CB6930_2_unmapped.txt ln -fs /data/maqgene/work/235486258_unmapped.txt /data/maqgene/out/example_user/CB6930_2/CB6930_2_unmapped.txt /data/maqgene/makefile:126: warning: undefined variable `mapcheck_parameters' # Mon Apr 22 02:28:02 BST 2013: Creating pileup ... /data/maqgene/bin/maq pileup -Q 100 -m 7 -q 0 /data/maqgene/genomes/elegans.bfa 235486258.map > 3049876794_pileup.txt # Mon Apr 22 02:28:02 BST 2013: Generating consensus ... /data/maqgene/bin/maq mapcheck /data/maqgene/genomes/elegans.bfa 235486258.map > 235486258_check.txt \ 2>/dev/null /data/maqgene/bin/maq assemble -N 2 -q 0 -r 0.0 -m 7 -Q 100 -p 3421280319.cns \ /data/maqgene/genomes/elegans.bfa 235486258.map 2> 3421280319_log.txt # Mon Apr 22 02:34:06 BST 2013: Linking backend file 235486258_check.txt to /data/maqgene/out/example_user/CB6930_2/CB6930_2_check.txt ln -fs /data/maqgene/work/235486258_check.txt /data/maqgene/out/example_user/CB6930_2/CB6930_2_check.txt /data/maqgene/bin/filter_matching_lines 3049876794_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 \ > 3049876794_known_snps # Mon Apr 22 02:36:09 BST 2013: Linking backend file 3049876794_pileup.txt to /data/maqgene/out/example_user/CB6930_2/CB6930_2_pileup.txt # Mon Apr 22 02:36:09 BST 2013: Making coverage histogram ... cut -f 1,2,4 3049876794_pileup.txt \ | /data/maqgene/bin/get_uncovered_regions 50 \ > 3049876794_uncovered.txt (echo -en "sequencing_depth\tnumber_of_bases\n"; \ cut -f 4 3049876794_pileup.txt \ | /data/maqgene/bin/pileup_histogram 100) > 3049876794_coverage.txt ln -fs /data/maqgene/work/3049876794_pileup.txt /data/maqgene/out/example_user/CB6930_2/CB6930_2_pileup.txt # Mon Apr 22 02:41:51 BST 2013: Linking backend file 3049876794_coverage.txt to /data/maqgene/out/example_user/CB6930_2/CB6930_2_coverage.txt ln -fs /data/maqgene/work/3049876794_coverage.txt /data/maqgene/out/example_user/CB6930_2/CB6930_2_coverage.txt # Mon Apr 22 02:41:51 BST 2013: Linking backend file 3421280319_log.txt to /data/maqgene/out/example_user/CB6930_2/CB6930_2_log.txt # Mon Apr 22 02:41:51 BST 2013: Linking backend file 3049876794_uncovered.txt to /data/maqgene/out/example_user/CB6930_2/CB6930_2_uncovered.txt ln -fs /data/maqgene/work/3421280319_log.txt /data/maqgene/out/example_user/CB6930_2/CB6930_2_log.txt /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 3049876794_pileup; create table 3049876794_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) );" ln -fs /data/maqgene/work/3049876794_uncovered.txt /data/maqgene/out/example_user/CB6930_2/CB6930_2_uncovered.txt # Mon Apr 22 02:41:51 BST 2013: Extracting point mutants from consensus ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 3421280319_snps; create table 3421280319_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) )" cat 3049876794_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 3049876794_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 3049876794_pileup" /data/maqgene/bin/maq cns2snp 3421280319.cns \ | cat -b | /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "load data local infile '/dev/stdin' into table 3421280319_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 3421280319_snps;" # Mon Apr 22 02:42:06 BST 2013: Extracting indels from consensus ... /data/maqgene/bin/maq indelsoa /data/maqgene/genomes/elegans.bfa 235486258.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 3421280319_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 3421280319_snps;" cat 3049876794_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 3049876794_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 3049876794_pileup" touch 3049876794_pileup # Mon Apr 22 02:44:26 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 3049876794_pileup p using (dna,start)" > /data/maqgene/out/example_user/CB6930_2/CB6930_2_snp_read_counts.txt 0 snp read count lines written. # Mon Apr 22 02:45:21 BST 2013: Adding placeholders for known SNPs. cat 3049876794_known_snps \ | /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "load data local infile '/dev/stdin' ignore into table 3421280319_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 3421280319_snps;" Found 163175 variants. touch 3421280319_snps # Mon Apr 22 02:45:24 BST 2013: Getting masking regions # Mon Apr 22 02:45:24 BST 2013: Finding all genomic features overlapping variants... /data/maqgene/bin/associate_regions -b -1 -c -1000000 -m 2 -o >(/usr/bin/mysql -Dmaqgenedb -umaqgene --skip-column-names --batch --raw --local-infile -e "drop table if exists 3421280319_masked_ids; create table 3421280319_masked_ids (query_region_id int(10) NOT NULL, primary key (query_region_id)); load data local infile '/dev/stdin' ignore into table 3421280319_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 3421280319_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; cat 3049876794_uncovered.txt \ | /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 3049876794_uncovered; create table 3049876794_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 = 163176; load data local infile '/dev/stdin' into table 3049876794_uncovered (dna, start, end)" /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 3421280319_rel_snps; CREATE TABLE 3421280319_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 3421280319_rel_snps; flush table 3421280319_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 3421280319_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 2 180 II 6 980 III 4 243 IV 5 501 V 4 558 X 4 4855 touch 3049876794_uncovered # Mon Apr 22 02:45:24 BST 2013: Finding mRNA features overlapping uncovered regions ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 3049876794_uncovered_rel; CREATE TABLE 3049876794_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 3049876794_uncovered_rel; flush table 3049876794_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 3049876794_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 3421280319_masked_ids touch 3049876794_uncovered_rel # Mon Apr 22 02:45:29 BST 2013: Calculating translation start offsets for uncovered regions... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 3049876794_offsets_uncovered; create table 3049876794_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 3049876794_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 3049876794_uncovered reg join 3049876794_uncovered_rel rel on (reg.id = rel.query_region_id) join elegans_features gene on (rel.target_region_id = gene.id) join elegans_features exon on (exon.attribute = gene.attribute) where exon.feature = 'exon' and gene.feature = 'mRNA' group by reg.id, gene.attribute" /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 3049876794_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 3049876794_uncovered reg join 3049876794_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 3049876794_offsets_uncovered touch 3421280319_rel_snps # Mon Apr 22 02:45:31 BST 2013: Getting intergenic regions /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 3421280319_rel_intergenic; create table 3421280319_rel_intergenic like 3421280319_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 3421280319_rel_intergenic; flush table 3421280319_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 3421280319_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 3421280319_offsets_snps; create table 3421280319_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 3421280319_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 3421280319_snps reg join 3421280319_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 02:45:38 BST 2013: Filtering masked intergenic regions /usr/bin/mysql -Dmaqgenedb -umaqgene --skip-column-names --batch --raw --local-infile -e "delete i.* from 3421280319_rel_intergenic i join 3421280319_masked_ids m using (query_region_id)" touch 3421280319_rel_intergenic # Mon Apr 22 02:45:50 BST 2013: Classifying intergenic relations /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 3421280319_intergenic_assoc; create table 3421280319_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 3421280319_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 3421280319_snps snp join 3421280319_rel_intergenic rel on (snp.id = rel.query_region_id) join elegans_features feature on (rel.target_region_id = feature.id)" touch 3421280319_intergenic_assoc touch 3421280319_offsets_snps # Mon Apr 22 02:46:13 BST 2013: Getting codons affected by point mutations... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 3421280319_codons; create table 3421280319_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 3421280319_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 3421280319_offsets_snps off join 3421280319_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 3421280319_codons /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 3421280319_marked; create table 3421280319_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 02:46:27 BST 2013: Finding exonic indels ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 3421280319_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 3421280319_snps snp join 3421280319_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 02:46:28 BST 2013: Finding coding variants ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 3421280319_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 3421280319_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 02:46:28 BST 2013: Finding noncoding variants ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 3421280319_marked select snp.id, feature.feature class, 'none' description, feature.attribute parent_feature from 3421280319_snps snp join 3421280319_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 02:46:30 BST 2013: Finding splice site variants ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 3421280319_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 3421280319_snps snp join 3421280319_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 02:46:30 BST 2013: Finding intergenic and intronic variants ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 3421280319_marked select id, 'nongenic' class, concat(if (relation in ('upstream','into'), - distance, distance),' ',relation) description, attribute from 3421280319_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 02:46:35 BST 2013: Finding uncovered regions in genes ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 3421280319_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 3049876794_uncovered unc join 3049876794_offsets_uncovered b using (id) join 3049876794_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 3049876794_uncovered unc join 3049876794_offsets_uncovered b using (id) join 3049876794_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 02:46:35 BST 2013: Variants found: +-----------------+-----------------+ | class | number_variants | +-----------------+-----------------+ | five_prime_UTR | 1326 | | frameshift | 95 | | inframe | 21 | | missense | 6343 | | ncRNA | 890 | | nongenic | 126087 | | non_start | 9 | | premature_stop | 695 | | readthrough | 21 | | silent | 7472 | | SNP | 1076 | | splice_acceptor | 49 | | splice_donor | 52 | | three_prime_UTR | 3602 | | uncovered | 7 | +-----------------+-----------------+ touch 3421280319_marked # Mon Apr 22 02:46:37 BST 2013: Combining results ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 3421280319_combined; create table 3421280319_combined (primary key (id, class, description), key (dna, start)) as select snp.id, 'CB6930_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 3421280319_snps snp join 3049876794_pileup pile using (dna,start) join 3421280319_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, 'CB6930_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 3049876794_uncovered unc join 3421280319_marked class on (unc.id = class.id) left join elegans_per_locus using (dna,start) group by id, class, description; alter table 3421280319_combined order by dna, start, length" touch 3421280319_combined # Mon Apr 22 02:46:41 BST 2013: Writing results to grouped file ... /usr/bin/mysql -Dmaqgenedb -umaqgene --skip-column-names --batch --raw --local-infile --column-names -e "select * from 3421280319_combined" > /data/maqgene/out/example_user/CB6930_2/CB6930_2_flat.txt /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 3421280319_combined group by id order by dna, start;" > /data/maqgene/out/example_user/CB6930_2/CB6930_2_grouped.txt 6428 lines written. 3698 lines written. rm 235486258.00103.1.fastq 235486258.00081.map 235486258.00032.unmapped 235486258.00091.map 235486258.00031.1.fastq 235486258.00013.1.fastq 235486258.00007.1.fastq 235486258.00063.1.bfq 235486258.00098.unmapped 235486258.00038.map 235486258.00054.unmapped 235486258.00053.mismatch 235486258.00035.1.bfq 235486258.00054.1.bfq 235486258.00068.1.fastq 235486258.00025.mismatch 235486258.00001.map 235486258.00010.map 235486258.00063.mismatch 235486258.00099.1.bfq 235486258.00006.map 235486258.00032.1.bfq 235486258.00016.map 235486258.00037.unmapped 235486258.00073.mismatch 235486258.00033.mismatch 235486258.00010.1.bfq 235486258.00050.unmapped 235486258.00048.mismatch 235486258.00087.map 235486258.00089.1.bfq 235486258.00097.1.bfq 235486258.00011.1.bfq 235486258.00095.mismatch 235486258.00034.map 235486258.00036.unmapped 235486258.00069.mismatch 235486258.00096.1.fastq 235486258.00043.map 235486258.00105.map 235486258.00078.1.bfq 235486258.00005.1.fastq 235486258.00088.1.fastq 235486258.00029.map 235486258.00101.map 235486258.00011.map 235486258.00050.1.fastq 235486258.00023.unmapped 235486258.00082.1.fastq 235486258.00046.1.bfq 235486258.00043.1.bfq 235486258.00036.1.fastq 235486258.00056.mismatch 235486258.00079.map 235486258.00019.unmapped 235486258.00055.1.fastq 235486258.00062.map 235486258.00032.1.fastq 235486258.00072.map 235486258.00021.1.fastq 235486258.00065.1.fastq 235486258.00078.map 235486258.00092.map 235486258.00083.mismatch 235486258.00008.1.fastq 235486258.00009.1.bfq 235486258.00019.1.fastq 235486258.00105.1.fastq 235486258.00104.mismatch 235486258.00014.map 235486258.00020.map 235486258.00105.unmapped 235486258.00015.unmapped 235486258.00098.1.bfq 235486258.00041.mismatch 235486258.00051.1.fastq 235486258.00014.mismatch 235486258.00047.map 235486258.00069.1.fastq 235486258.00065.mismatch 235486258.00024.1.bfq 235486258.00029.unmapped 235486258.00042.1.bfq 235486258.00015.1.fastq 235486258.00039.mismatch 235486258.00089.unmapped 235486258.00084.unmapped 235486258.00080.mismatch 235486258.00057.1.fastq 235486258.00068.unmapped 235486258.00002.map 235486258.00049.mismatch 235486258.00094.mismatch 235486258.00059.mismatch 235486258.00102.map 235486258.00070.1.bfq 235486258.00088.map 235486258.00079.mismatch 235486258.00093.mismatch 235486258.00005.1.bfq 235486258.00062.1.bfq 235486258.00082.map 4083184944_split1 235486258.00084.1.bfq 235486258.00063.map 235486258.00028.unmapped 235486258.00000.mismatch 235486258.00089.1.fastq 235486258.00028.1.bfq 235486258.00026.map 235486258.00079.1.bfq 235486258.00052.unmapped 235486258.00008.map 235486258.00028.1.fastq 235486258.00054.map 235486258.00077.unmapped 235486258.00083.unmapped 235486258.00075.unmapped 235486258.00006.1.bfq 235486258.00009.1.fastq 235486258.00060.1.bfq 235486258.00077.mismatch 235486258.00021.1.bfq 235486258.00042.mismatch 235486258.00018.map 235486258.00052.1.fastq 235486258.00066.unmapped 235486258.00103.unmapped 235486258.00069.map 235486258.00066.1.bfq 235486258.00091.unmapped 235486258.00020.1.bfq 235486258.00075.1.fastq 235486258.00024.mismatch 235486258.00029.1.bfq 235486258.00067.map 235486258.00025.unmapped 235486258.00035.mismatch 235486258.00097.1.fastq 235486258.00057.map 235486258.00072.1.bfq 235486258.00021.map 235486258.00012.map 235486258.00007.map 235486258.00099.mismatch 235486258.00105.1.bfq 235486258.00058.1.fastq 235486258.00098.mismatch 235486258.00025.1.fastq 235486258.00046.mismatch 235486258.00079.unmapped 235486258.00061.1.bfq 235486258.00095.unmapped 235486258.00100.mismatch 235486258.00091.1.bfq 235486258.00099.map 235486258.00089.map 235486258.00049.unmapped 235486258.00000.unmapped 235486258.00004.unmapped 235486258.00033.1.fastq 235486258.00007.1.bfq 235486258.00040.unmapped 235486258.00033.map 235486258.00078.mismatch 235486258.00095.1.fastq 235486258.00003.map 235486258.00030.map 235486258.00056.unmapped 235486258.00027.mismatch 235486258.00073.map 235486258.00009.map 235486258.00004.1.fastq 235486258.00006.mismatch 235486258.00027.map 235486258.00040.1.fastq 235486258.00060.mismatch 235486258.00070.mismatch 235486258.00085.1.fastq 235486258.00090.mismatch 235486258.00036.1.bfq 235486258.00056.1.fastq 235486258.00047.unmapped 235486258.00064.unmapped 235486258.00104.unmapped 235486258.00055.map 235486258.00082.1.bfq 235486258.00019.map 235486258.00097.map 235486258.00041.unmapped 235486258.00045.unmapped 235486258.00103.map 235486258.00063.unmapped 235486258.00035.unmapped 235486258.00014.unmapped 235486258.00023.map 235486258.00002.1.bfq 235486258.00064.1.fastq 235486258.00098.1.fastq 235486258.00039.unmapped 235486258.00041.1.fastq 235486258.00051.unmapped 235486258.00034.1.bfq 235486258.00091.mismatch 235486258.00061.mismatch 235486258.00071.mismatch 235486258.00014.1.fastq 235486258.00081.mismatch 235486258.00068.map 235486258.00010.unmapped 235486258.00017.1.bfq 235486258.00055.1.bfq 235486258.00064.1.bfq 235486258.00039.1.fastq 235486258.00038.mismatch 235486258.00065.unmapped 235486258.00037.1.fastq 235486258.00104.1.fastq 235486258.00070.map 235486258.00053.unmapped 235486258.00026.mismatch 235486258.00094.1.fastq 235486258.00001.mismatch 235486258.00010.mismatch 235486258.00086.mismatch 235486258.00020.unmapped 235486258.00085.map 235486258.00016.mismatch 235486258.00005.map 235486258.00069.1.bfq 235486258.00050.map 235486258.00053.1.fastq 235486258.00074.1.fastq 235486258.00074.1.bfq 235486258.00017.map 235486258.00034.mismatch 235486258.00036.map 235486258.00042.unmapped 235486258.00102.1.bfq 235486258.00022.map 235486258.00032.map 235486258.00029.mismatch 235486258.00101.mismatch 235486258.00011.mismatch 235486258.00098.map 235486258.00024.unmapped 235486258.00026.1.fastq 235486258.00023.1.bfq 235486258.00012.1.bfq 235486258.00083.1.bfq 235486258.00042.1.fastq 235486258.00076.1.fastq 235486258.00039.map 235486258.00044.unmapped 235486258.00087.mismatch 235486258.00062.mismatch 235486258.00037.1.bfq 235486258.00051.map 235486258.00072.mismatch 235486258.00096.1.bfq 235486258.00024.1.fastq 235486258.00017.mismatch 235486258.00100.map 235486258.00092.mismatch 235486258.00046.unmapped 235486258.00063.1.fastq 235486258.00099.unmapped 235486258.00092.1.bfq 235486258.00037.map 235486258.00075.mismatch 235486258.00002.mismatch 235486258.00015.map 235486258.00020.mismatch 235486258.00005.unmapped 235486258.00018.1.bfq 235486258.00084.1.fastq 235486258.00100.1.bfq 235486258.00048.1.fastq 235486258.00046.1.fastq 235486258.00047.mismatch 235486258.00086.unmapped 235486258.00007.mismatch 235486258.00041.1.bfq 235486258.00081.1.bfq 235486258.00008.1.bfq 235486258.00067.1.fastq 235486258.00006.unmapped 235486258.00011.unmapped 235486258.00027.1.bfq 235486258.00094.1.bfq 235486258.00060.unmapped 235486258.00070.unmapped 235486258.00080.unmapped 235486258.00090.unmapped 235486258.00022.1.bfq 235486258.00102.mismatch 235486258.00012.mismatch 235486258.00106.mismatch 235486258.00088.1.bfq 235486258.00058.map 235486258.00043.mismatch 235486258.00028.map 235486258.00071.1.bfq 235486258.00060.1.fastq 235486258.00070.1.fastq 235486258.00080.1.fastq 235486258.00083.1.fastq 235486258.00016.1.bfq 235486258.00093.1.bfq 235486258.00053.map 235486258.00101.1.bfq 235486258.00048.map 235486258.00087.unmapped 235486258.00052.map 235486258.00106.unmapped 235486258.00096.mismatch 235486258.00066.1.fastq 235486258.00059.unmapped 235486258.00042.map 235486258.00066.mismatch 235486258.00040.mismatch 235486258.00054.mismatch 235486258.00075.map 235486258.00071.unmapped 235486258.00043.unmapped 235486258.00081.unmapped 235486258.00048.1.bfq 235486258.00082.mismatch 235486258.00057.1.bfq 235486258.00033.1.bfq 235486258.00084.map 235486258.00000.1.fastq 235486258.00106.1.fastq 235486258.00080.1.bfq 235486258.00065.map 235486258.00038.unmapped 235486258.00055.mismatch 235486258.00085.1.bfq 235486258.00073.1.bfq 235486258.00061.1.fastq 235486258.00045.map 235486258.00071.1.fastq 235486258.00081.1.fastq 235486258.00049.1.fastq 235486258.00091.1.fastq 235486258.00059.1.fastq 235486258.00007.unmapped 235486258.00001.unmapped 235486258.00079.1.fastq 235486258.00008.mismatch 235486258.00103.1.bfq 235486258.00000.1.bfq 235486258.00065.1.bfq 235486258.00031.1.bfq 235486258.00106.1.bfq 235486258.00038.1.fastq 235486258.00045.mismatch 235486258.00021.unmapped 235486258.00030.1.bfq 235486258.00016.unmapped 235486258.00077.1.fastq 235486258.00072.unmapped 235486258.00001.1.fastq 235486258.00010.1.fastq 235486258.00095.map 235486258.00034.unmapped 235486258.00060.map 235486258.00090.1.fastq 235486258.00077.1.bfq 235486258.00039.1.bfq 235486258.00016.1.fastq 235486258.00004.map 235486258.00013.1.bfq 235486258.00040.map 235486258.00101.unmapped 235486258.00057.mismatch 235486258.00066.map 235486258.00085.mismatch 235486258.00034.1.fastq 235486258.00003.mismatch 235486258.00056.map 235486258.00030.mismatch 235486258.00096.unmapped 235486258.00021.mismatch 235486258.00013.map 235486258.00062.unmapped 235486258.00029.1.fastq 235486258.00101.1.fastq 235486258.00011.1.fastq 235486258.00082.unmapped 235486258.00017.unmapped 235486258.00089.mismatch 235486258.00035.1.fastq 235486258.00092.unmapped 235486258.00050.1.bfq 235486258.00064.map 235486258.00104.map 235486258.00049.map 235486258.00002.unmapped 235486258.00059.map 235486258.00062.1.fastq 235486258.00014.1.bfq 235486258.00041.map 235486258.00099.1.fastq 235486258.00072.1.fastq 235486258.00093.map 235486258.00083.map 235486258.00017.1.fastq 235486258.00103.mismatch 235486258.00092.1.fastq 235486258.00008.unmapped 235486258.00031.mismatch 235486258.00009.mismatch 235486258.00013.mismatch 235486258.00100.1.fastq 235486258.00077.map 235486258.00064.mismatch 235486258.00002.1.fastq 235486258.00020.1.fastq 235486258.00040.1.bfq 235486258.00019.1.bfq 235486258.00026.1.bfq 235486258.00075.1.bfq 235486258.00104.1.bfq 235486258.00086.1.bfq 235486258.00078.1.fastq 235486258.00047.1.fastq 235486258.00068.mismatch 235486258.00094.map 235486258.00076.unmapped 235486258.00059.1.bfq 235486258.00102.unmapped 235486258.00097.mismatch 235486258.00053.1.bfq 235486258.00012.unmapped 235486258.00076.mismatch 235486258.00074.unmapped 235486258.00057.unmapped 235486258.00015.1.bfq 235486258.00003.1.bfq 235486258.00031.map 235486258.00058.mismatch 235486258.00074.mismatch 235486258.00087.1.bfq 235486258.00102.1.fastq 235486258.00056.1.bfq 235486258.00076.map 235486258.00012.1.fastq 235486258.00026.unmapped 235486258.00023.1.fastq 235486258.00038.1.bfq 235486258.00035.map 235486258.00068.1.bfq 235486258.00005.mismatch 235486258.00050.mismatch 235486258.00045.1.bfq 235486258.00076.1.bfq 235486258.00067.1.bfq 235486258.00036.mismatch 235486258.00067.unmapped 235486258.00033.unmapped 235486258.00018.unmapped 235486258.00004.mismatch 235486258.00044.1.fastq 235486258.00032.mismatch 235486258.00067.mismatch 235486258.00054.1.fastq 235486258.00023.mismatch 235486258.00024.map 235486258.00009.unmapped 235486258.00058.1.bfq 235486258.00051.1.bfq 235486258.00095.1.bfq 235486258.00018.1.fastq 235486258.00019.mismatch 235486258.00105.mismatch 235486258.00025.map 235486258.00096.map 235486258.00051.mismatch 235486258.00052.1.bfq 235486258.00069.unmapped 235486258.00022.unmapped 235486258.00046.map 235486258.00055.unmapped 235486258.00100.unmapped 235486258.00097.unmapped 235486258.00022.mismatch 235486258.00086.1.fastq 235486258.00078.unmapped 235486258.00004.1.bfq 235486258.00045.1.fastq 235486258.00015.mismatch 235486258.00022.1.fastq 235486258.00058.unmapped 235486258.00001.1.bfq 235486258.00074.map 235486258.00044.mismatch 235486258.00094.unmapped 235486258.00088.unmapped 235486258.00003.unmapped 235486258.00025.1.bfq 235486258.00030.unmapped 235486258.00073.unmapped 235486258.00088.mismatch 235486258.00049.1.bfq 235486258.00061.unmapped 235486258.00027.unmapped 235486258.00037.mismatch 235486258.00006.1.fastq 235486258.00080.map 235486258.00090.map 235486258.00044.map 235486258.00093.unmapped 235486258.00084.mismatch 235486258.00003.1.fastq 235486258.00030.1.fastq 235486258.00073.1.fastq 235486258.00087.1.fastq 235486258.00044.1.bfq 235486258.00027.1.fastq 235486258.00028.mismatch 235486258.00085.unmapped 235486258.00093.1.fastq 235486258.00043.1.fastq 235486258.00090.1.bfq 235486258.00031.unmapped 235486258.00013.unmapped 235486258.00048.unmapped 235486258.00000.map 235486258.00106.map 235486258.00052.mismatch 235486258.00018.mismatch 235486258.00047.1.bfq 235486258.00086.map 235486258.00061.map 235486258.00071.map make: Leaving directory `/data/maqgene/work' make: Entering directory `/data/maqgene/work' # Mon Apr 22 02:46:46 BST 2013: Cleaning intermediate data ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 3421280319_snps,3421280319_rel,3421280319_masked_ids,3421280319_rel_intergenic,3421280319_intergenic_assoc,3421280319_offsets,3421280319_codons,3421280319_marked,3421280319_combined,3049876794_pileup" rm -f 3421280319_snps 3421280319_rel 3421280319_masked_ids 3421280319_rel_intergenic 3421280319_intergenic_assoc 3421280319_offsets 3421280319_codons 3421280319_marked 3421280319_combined 3049876794_pileup make: Leaving directory `/data/maqgene/work'