/data/maqgene/bin/run_maq.sh: line 44: export: `single_CB6930/./WTCHG_52866_04_1.fastq=on': not a valid identifier /data/maqgene/bin/run_maq.sh: line 44: export: `single_CB1122/./WTCHG_52866_02_1.fastq=on': not a valid identifier /data/maqgene/bin/run_maq.sh: line 44: export: `single_CB6930/./WTCHG_52866_04_2.fastq=on': not a valid identifier /data/maqgene/bin/run_maq.sh: line 44: export: `single_CB1122/./WTCHG_52866_02_2.fastq=on': not a valid identifier Finished reading input. ++ echo CB6930/./WTCHG_52866_04_1.fastq,CB1122/./WTCHG_52866_02_1.fastq,CB6930/./WTCHG_52866_04_2.fastq,CB1122/./WTCHG_52866_02_2.fastq ++ tr , ' ' + fastq_file_set1='CB6930/./WTCHG_52866_04_1.fastq CB1122/./WTCHG_52866_02_1.fastq CB6930/./WTCHG_52866_04_2.fastq CB1122/./WTCHG_52866_02_2.fastq' ++ cd /data/maqgene/reads ++ cat CB6930/./WTCHG_52866_04_1.fastq CB1122/./WTCHG_52866_02_1.fastq CB6930/./WTCHG_52866_04_2.fastq CB1122/./WTCHG_52866_02_2.fastq ++ wc -l ++ cut -f 1 -d ' ' + TOTAL_LINES=493830112 ++ echo '(493830112 / 5000000) + (493830112 % 5000000 != 0)' ++ bc + num_chunks=99 + 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=1535661234 map_cksum=2388851596 pileup_cksum=1964021411 cns_cksum=2367457594 umdd=50000 dmdd=1000 umid=1000 dmid=1000 max_gene_radius=50000 full_results_dir=/data/maqgene/out/example_user/CB6930 outfile_basename=CB6930 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=99 Will process 493830112 lines of input in 99 chunks make: Entering directory `/data/maqgene/work' # Wed Apr 10 21:57:13 BST 2013: Removing frontend files in case this is a duplicate run ... rm -f /data/maqgene/out/example_user/CB6930/CB6930_{grouped.txt,flat.txt} rm -f /data/maqgene/out/example_user/CB6930/CB6930_uncovered.txt /data/maqgene/out/example_user/CB6930/CB6930_coverage.txt /data/maqgene/out/example_user/CB6930/CB6930_pileup.txt /data/maqgene/out/example_user/CB6930/CB6930_log.txt /data/maqgene/out/example_user/CB6930/CB6930_check.txt /data/maqgene/out/example_user/CB6930/CB6930_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/./WTCHG_52866_04_1.fastq /data/maqgene/reads/CB1122/./WTCHG_52866_02_1.fastq /data/maqgene/reads/CB6930/./WTCHG_52866_04_2.fastq /data/maqgene/reads/CB1122/./WTCHG_52866_02_2.fastq) 2388851596.1.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; do mv 2388851596.1.fastq.$stem 2388851596.$stem.1.fastq; done touch 1535661234_split1 # Wed Apr 10 21:59:29 BST 2013: Converting fastq files to bfq ... # Wed Apr 10 21:59:29 BST 2013: Converting fastq files to bfq ... # Wed Apr 10 21:59:29 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2388851596.00002.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00002.1.bfq /data/maqgene/bin/maq sol2sanger 2388851596.00000.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00000.1.bfq /data/maqgene/bin/maq sol2sanger 2388851596.00001.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00001.1.bfq # Wed Apr 10 21:59:29 BST 2013: Converting fastq files to bfq ... # Wed Apr 10 21:59:29 BST 2013: Converting fastq files to bfq ... # Wed Apr 10 21:59:29 BST 2013: Converting fastq files to bfq ... # Wed Apr 10 21:59:29 BST 2013: Converting fastq files to bfq ... # Wed Apr 10 21:59:29 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2388851596.00004.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00004.1.bfq # Wed Apr 10 21:59:29 BST 2013: Converting fastq files to bfq ... # Wed Apr 10 21:59:29 BST 2013: Converting fastq files to bfq ... # Wed Apr 10 21:59:29 BST 2013: Converting fastq files to bfq ... # Wed Apr 10 21:59:29 BST 2013: Converting fastq files to bfq ... # Wed Apr 10 21:59:29 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2388851596.00003.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00003.1.bfq /data/maqgene/bin/maq sol2sanger 2388851596.00005.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00005.1.bfq /data/maqgene/bin/maq sol2sanger 2388851596.00006.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00006.1.bfq /data/maqgene/bin/maq sol2sanger 2388851596.00007.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00007.1.bfq /data/maqgene/bin/maq sol2sanger 2388851596.00008.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00008.1.bfq /data/maqgene/bin/maq sol2sanger 2388851596.00009.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00009.1.bfq /data/maqgene/bin/maq sol2sanger 2388851596.00010.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00010.1.bfq /data/maqgene/bin/maq sol2sanger 2388851596.00011.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00011.1.bfq /data/maqgene/bin/maq sol2sanger 2388851596.00012.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00012.1.bfq /data/maqgene/bin/maq sol2sanger 2388851596.00013.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00013.1.bfq -- finish writing file '2388851596.00004.1.bfq' -- 1250000 sequences were loaded. # Wed Apr 10 21:59:58 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2388851596.00014.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00014.1.bfq -- finish writing file '2388851596.00001.1.bfq' -- 1250000 sequences were loaded. # Wed Apr 10 21:59:59 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2388851596.00015.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00015.1.bfq -- finish writing file '2388851596.00007.1.bfq' -- 1250000 sequences were loaded. # Wed Apr 10 21:59:59 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2388851596.00016.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00016.1.bfq -- finish writing file '2388851596.00008.1.bfq' -- 1250000 sequences were loaded. # Wed Apr 10 22:00:00 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2388851596.00017.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00017.1.bfq -- finish writing file '2388851596.00013.1.bfq' -- 1250000 sequences were loaded. # Wed Apr 10 22:00:03 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2388851596.00018.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00018.1.bfq -- finish writing file '2388851596.00003.1.bfq' -- 1250000 sequences were loaded. # Wed Apr 10 22:00:05 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2388851596.00019.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00019.1.bfq -- finish writing file '2388851596.00011.1.bfq' -- 1250000 sequences were loaded. # Wed Apr 10 22:00:05 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2388851596.00020.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00020.1.bfq -- finish writing file '2388851596.00010.1.bfq' -- 1250000 sequences were loaded. # Wed Apr 10 22:00:06 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2388851596.00021.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00021.1.bfq -- finish writing file '2388851596.00006.1.bfq' -- 1250000 sequences were loaded. # Wed Apr 10 22:00:06 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2388851596.00022.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00022.1.bfq -- finish writing file '2388851596.00009.1.bfq' -- 1250000 sequences were loaded. # Wed Apr 10 22:00:06 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2388851596.00023.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00023.1.bfq -- finish writing file '2388851596.00005.1.bfq' -- 1250000 sequences were loaded. # Wed Apr 10 22:00:06 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2388851596.00024.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00024.1.bfq -- finish writing file '2388851596.00012.1.bfq' -- 1250000 sequences were loaded. # Wed Apr 10 22:00:07 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2388851596.00025.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00025.1.bfq -- finish writing file '2388851596.00000.1.bfq' -- 1250000 sequences were loaded. # Wed Apr 10 22:00:07 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2388851596.00026.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00026.1.bfq -- finish writing file '2388851596.00002.1.bfq' -- 1250000 sequences were loaded. # Wed Apr 10 22:00:07 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2388851596.00027.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00027.1.bfq -- finish writing file '2388851596.00017.1.bfq' -- 1250000 sequences were loaded. # Wed Apr 10 22:00:30 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2388851596.00028.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00028.1.bfq -- finish writing file '2388851596.00016.1.bfq' -- 1250000 sequences were loaded. # Wed Apr 10 22:00:32 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2388851596.00029.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00029.1.bfq -- finish writing file '2388851596.00020.1.bfq' -- 1250000 sequences were loaded. # Wed Apr 10 22:00:33 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2388851596.00030.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00030.1.bfq -- finish writing file '2388851596.00014.1.bfq' -- 1250000 sequences were loaded. # Wed Apr 10 22:00:34 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2388851596.00031.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00031.1.bfq -- finish writing file '2388851596.00015.1.bfq' -- 1250000 sequences were loaded. # Wed Apr 10 22:00:34 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2388851596.00032.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00032.1.bfq -- finish writing file '2388851596.00019.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2388851596.00018.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2388851596.00023.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2388851596.00022.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2388851596.00021.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2388851596.00025.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2388851596.00027.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2388851596.00024.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2388851596.00026.1.bfq' -- 1250000 sequences were loaded. # Wed Apr 10 22:00:47 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2388851596.00040.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00040.1.bfq # Wed Apr 10 22:00:47 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2388851596.00041.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00041.1.bfq # Wed Apr 10 22:00:48 BST 2013: Converting fastq files to bfq ... # Wed Apr 10 22:00:48 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2388851596.00038.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00038.1.bfq /data/maqgene/bin/maq sol2sanger 2388851596.00039.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00039.1.bfq # Wed Apr 10 22:00:49 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2388851596.00037.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00037.1.bfq # Wed Apr 10 22:00:49 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2388851596.00036.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00036.1.bfq # Wed Apr 10 22:00:50 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2388851596.00035.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00035.1.bfq # Wed Apr 10 22:00:50 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2388851596.00034.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00034.1.bfq # Wed Apr 10 22:00:51 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2388851596.00033.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00033.1.bfq -- finish writing file '2388851596.00031.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2388851596.00028.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2388851596.00029.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2388851596.00030.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2388851596.00032.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2388851596.00037.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2388851596.00040.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2388851596.00041.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2388851596.00035.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2388851596.00036.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2388851596.00038.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2388851596.00033.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2388851596.00034.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2388851596.00039.1.bfq' -- 1250000 sequences were loaded. # Wed Apr 10 22:01:19 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2388851596.00054.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00054.1.bfq # Wed Apr 10 22:01:22 BST 2013: Converting fastq files to bfq ... # Wed Apr 10 22:01:22 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2388851596.00055.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00055.1.bfq # Wed Apr 10 22:01:22 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2388851596.00053.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00053.1.bfq /data/maqgene/bin/maq sol2sanger 2388851596.00052.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00052.1.bfq # Wed Apr 10 22:01:23 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2388851596.00050.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00050.1.bfq # Wed Apr 10 22:01:23 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2388851596.00051.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00051.1.bfq /data/maqgene/bin/maq sol2sanger 2388851596.00049.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00049.1.bfq # Wed Apr 10 22:01:24 BST 2013: Converting fastq files to bfq ... # Wed Apr 10 22:01:24 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2388851596.00046.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00046.1.bfq /data/maqgene/bin/maq sol2sanger 2388851596.00047.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00047.1.bfq # Wed Apr 10 22:01:24 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2388851596.00048.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00048.1.bfq # Wed Apr 10 22:01:25 BST 2013: Converting fastq files to bfq ... # Wed Apr 10 22:01:25 BST 2013: Converting fastq files to bfq ... # Wed Apr 10 22:01:25 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2388851596.00045.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00045.1.bfq /data/maqgene/bin/maq sol2sanger 2388851596.00044.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00044.1.bfq /data/maqgene/bin/maq sol2sanger 2388851596.00043.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00043.1.bfq # Wed Apr 10 22:01:26 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2388851596.00042.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00042.1.bfq -- finish writing file '2388851596.00054.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2388851596.00051.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2388851596.00046.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2388851596.00053.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2388851596.00049.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2388851596.00055.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2388851596.00052.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2388851596.00050.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2388851596.00048.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2388851596.00047.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2388851596.00043.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2388851596.00045.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2388851596.00044.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2388851596.00042.1.bfq' -- 1250000 sequences were loaded. # Wed Apr 10 22:01:59 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2388851596.00068.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00068.1.bfq # Wed Apr 10 22:02:03 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2388851596.00069.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00069.1.bfq # Wed Apr 10 22:02:03 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2388851596.00067.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00067.1.bfq # Wed Apr 10 22:02:04 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2388851596.00066.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00066.1.bfq # Wed Apr 10 22:02:05 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2388851596.00065.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00065.1.bfq # Wed Apr 10 22:02:06 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2388851596.00064.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00064.1.bfq # Wed Apr 10 22:02:07 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2388851596.00063.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00063.1.bfq # Wed Apr 10 22:02:08 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2388851596.00061.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00061.1.bfq # Wed Apr 10 22:02:08 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2388851596.00062.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00062.1.bfq # Wed Apr 10 22:02:09 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2388851596.00060.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00060.1.bfq # Wed Apr 10 22:02:09 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2388851596.00059.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00059.1.bfq # Wed Apr 10 22:02:10 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2388851596.00058.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00058.1.bfq /data/maqgene/bin/maq sol2sanger 2388851596.00057.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00057.1.bfq # Wed Apr 10 22:02:11 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2388851596.00056.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00056.1.bfq -- finish writing file '2388851596.00068.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2388851596.00069.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2388851596.00067.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2388851596.00064.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2388851596.00065.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2388851596.00056.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2388851596.00066.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2388851596.00062.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2388851596.00061.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2388851596.00063.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2388851596.00060.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2388851596.00059.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2388851596.00058.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2388851596.00057.1.bfq' -- 1250000 sequences were loaded. # Wed Apr 10 22:02:41 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2388851596.00082.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00082.1.bfq # Wed Apr 10 22:02:43 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2388851596.00083.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00083.1.bfq # Wed Apr 10 22:02:44 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2388851596.00081.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00081.1.bfq # Wed Apr 10 22:02:45 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2388851596.00080.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00080.1.bfq # Wed Apr 10 22:02:46 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2388851596.00079.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00079.1.bfq # Wed Apr 10 22:02:47 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2388851596.00078.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00078.1.bfq # Wed Apr 10 22:02:48 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2388851596.00077.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00077.1.bfq # Wed Apr 10 22:02:48 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2388851596.00076.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00076.1.bfq # Wed Apr 10 22:02:48 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2388851596.00075.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00075.1.bfq # Wed Apr 10 22:02:49 BST 2013: Converting fastq files to bfq ... # Wed Apr 10 22:02:49 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2388851596.00074.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00074.1.bfq /data/maqgene/bin/maq sol2sanger 2388851596.00073.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00073.1.bfq # Wed Apr 10 22:02:50 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2388851596.00071.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00071.1.bfq # Wed Apr 10 22:02:50 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2388851596.00072.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00072.1.bfq # Wed Apr 10 22:02:51 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2388851596.00070.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00070.1.bfq -- finish writing file '2388851596.00082.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2388851596.00083.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2388851596.00079.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2388851596.00081.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2388851596.00080.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2388851596.00078.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2388851596.00073.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2388851596.00075.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2388851596.00074.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2388851596.00077.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2388851596.00072.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2388851596.00076.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2388851596.00071.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2388851596.00070.1.bfq' -- 1250000 sequences were loaded. # Wed Apr 10 22:03:22 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2388851596.00096.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00096.1.bfq # Wed Apr 10 22:03:28 BST 2013: Converting fastq files to bfq ... # Wed Apr 10 22:03:28 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2388851596.00097.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00097.1.bfq # Wed Apr 10 22:03:28 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2388851596.00095.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00095.1.bfq /data/maqgene/bin/maq sol2sanger 2388851596.00094.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00094.1.bfq # Wed Apr 10 22:03:29 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2388851596.00093.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00093.1.bfq # Wed Apr 10 22:03:29 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2388851596.00092.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00092.1.bfq # Wed Apr 10 22:03:30 BST 2013: Converting fastq files to bfq ... # Wed Apr 10 22:03:30 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2388851596.00091.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00091.1.bfq /data/maqgene/bin/maq sol2sanger 2388851596.00090.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00090.1.bfq # Wed Apr 10 22:03:31 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2388851596.00089.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00089.1.bfq # Wed Apr 10 22:03:31 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2388851596.00088.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00088.1.bfq # Wed Apr 10 22:03:32 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2388851596.00086.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00086.1.bfq # Wed Apr 10 22:03:32 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2388851596.00087.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00087.1.bfq # Wed Apr 10 22:03:33 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2388851596.00085.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00085.1.bfq # Wed Apr 10 22:03:33 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2388851596.00084.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00084.1.bfq -- finish writing file '2388851596.00096.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2388851596.00095.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2388851596.00094.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2388851596.00097.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2388851596.00085.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2388851596.00093.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2388851596.00092.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2388851596.00086.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2388851596.00090.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2388851596.00088.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2388851596.00091.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2388851596.00089.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2388851596.00087.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2388851596.00084.1.bfq' -- 1250000 sequences were loaded. # Wed Apr 10 22:04:04 BST 2013: Mapping file(s) 2388851596.00011.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00011.unmapped -H 2388851596.00011.mismatch \ 2388851596.00011.map /data/maqgene/genomes/elegans.bfa 2388851596.00011.1.bfq 2> /dev/null # Wed Apr 10 22:04:07 BST 2013: Mapping file(s) 2388851596.00010.1.bfq # Wed Apr 10 22:04:07 BST 2013: Mapping file(s) 2388851596.00012.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00010.unmapped -H 2388851596.00010.mismatch \ 2388851596.00010.map /data/maqgene/genomes/elegans.bfa 2388851596.00010.1.bfq 2> /dev/null /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00012.unmapped -H 2388851596.00012.mismatch \ 2388851596.00012.map /data/maqgene/genomes/elegans.bfa 2388851596.00012.1.bfq 2> /dev/null # Wed Apr 10 22:04:08 BST 2013: Mapping file(s) 2388851596.00009.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00009.unmapped -H 2388851596.00009.mismatch \ 2388851596.00009.map /data/maqgene/genomes/elegans.bfa 2388851596.00009.1.bfq 2> /dev/null # Wed Apr 10 22:04:09 BST 2013: Mapping file(s) 2388851596.00007.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00007.unmapped -H 2388851596.00007.mismatch \ 2388851596.00007.map /data/maqgene/genomes/elegans.bfa 2388851596.00007.1.bfq 2> /dev/null # Wed Apr 10 22:04:09 BST 2013: Mapping file(s) 2388851596.00008.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00008.unmapped -H 2388851596.00008.mismatch \ 2388851596.00008.map /data/maqgene/genomes/elegans.bfa 2388851596.00008.1.bfq 2> /dev/null # Wed Apr 10 22:04:10 BST 2013: Mapping file(s) 2388851596.00006.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00006.unmapped -H 2388851596.00006.mismatch \ 2388851596.00006.map /data/maqgene/genomes/elegans.bfa 2388851596.00006.1.bfq 2> /dev/null # Wed Apr 10 22:04:11 BST 2013: Mapping file(s) 2388851596.00005.1.bfq # Wed Apr 10 22:04:11 BST 2013: Mapping file(s) 2388851596.00004.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00005.unmapped -H 2388851596.00005.mismatch \ 2388851596.00005.map /data/maqgene/genomes/elegans.bfa 2388851596.00005.1.bfq 2> /dev/null /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00004.unmapped -H 2388851596.00004.mismatch \ 2388851596.00004.map /data/maqgene/genomes/elegans.bfa 2388851596.00004.1.bfq 2> /dev/null # Wed Apr 10 22:04:12 BST 2013: Mapping file(s) 2388851596.00003.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00003.unmapped -H 2388851596.00003.mismatch \ 2388851596.00003.map /data/maqgene/genomes/elegans.bfa 2388851596.00003.1.bfq 2> /dev/null # Wed Apr 10 22:04:12 BST 2013: Mapping file(s) 2388851596.00002.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00002.unmapped -H 2388851596.00002.mismatch \ 2388851596.00002.map /data/maqgene/genomes/elegans.bfa 2388851596.00002.1.bfq 2> /dev/null # Wed Apr 10 22:04:13 BST 2013: Mapping file(s) 2388851596.00000.1.bfq # Wed Apr 10 22:04:13 BST 2013: Mapping file(s) 2388851596.00001.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00000.unmapped -H 2388851596.00000.mismatch \ 2388851596.00000.map /data/maqgene/genomes/elegans.bfa 2388851596.00000.1.bfq 2> /dev/null /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00001.unmapped -H 2388851596.00001.mismatch \ 2388851596.00001.map /data/maqgene/genomes/elegans.bfa 2388851596.00001.1.bfq 2> /dev/null # Wed Apr 10 22:04:14 BST 2013: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2388851596.00098.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2388851596.00098.1.bfq -- finish writing file '2388851596.00098.1.bfq' -- 957528 sequences were loaded. # Wed Apr 10 22:08:33 BST 2013: Mapping file(s) 2388851596.00022.1.bfq # Wed Apr 10 22:08:33 BST 2013: Mapping file(s) 2388851596.00021.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00022.unmapped -H 2388851596.00022.mismatch \ 2388851596.00022.map /data/maqgene/genomes/elegans.bfa 2388851596.00022.1.bfq 2> /dev/null /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00021.unmapped -H 2388851596.00021.mismatch \ 2388851596.00021.map /data/maqgene/genomes/elegans.bfa 2388851596.00021.1.bfq 2> /dev/null # Wed Apr 10 22:08:34 BST 2013: Mapping file(s) 2388851596.00020.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00020.unmapped -H 2388851596.00020.mismatch \ 2388851596.00020.map /data/maqgene/genomes/elegans.bfa 2388851596.00020.1.bfq 2> /dev/null # Wed Apr 10 22:08:35 BST 2013: Mapping file(s) 2388851596.00023.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00023.unmapped -H 2388851596.00023.mismatch \ 2388851596.00023.map /data/maqgene/genomes/elegans.bfa 2388851596.00023.1.bfq 2> /dev/null # Wed Apr 10 22:08:36 BST 2013: Mapping file(s) 2388851596.00019.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00019.unmapped -H 2388851596.00019.mismatch \ 2388851596.00019.map /data/maqgene/genomes/elegans.bfa 2388851596.00019.1.bfq 2> /dev/null # Wed Apr 10 22:08:37 BST 2013: Mapping file(s) 2388851596.00018.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00018.unmapped -H 2388851596.00018.mismatch \ 2388851596.00018.map /data/maqgene/genomes/elegans.bfa 2388851596.00018.1.bfq 2> /dev/null # Wed Apr 10 22:08:38 BST 2013: Mapping file(s) 2388851596.00017.1.bfq # Wed Apr 10 22:08:38 BST 2013: Mapping file(s) 2388851596.00016.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00017.unmapped -H 2388851596.00017.mismatch \ 2388851596.00017.map /data/maqgene/genomes/elegans.bfa 2388851596.00017.1.bfq 2> /dev/null /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00016.unmapped -H 2388851596.00016.mismatch \ 2388851596.00016.map /data/maqgene/genomes/elegans.bfa 2388851596.00016.1.bfq 2> /dev/null # Wed Apr 10 22:08:38 BST 2013: Mapping file(s) 2388851596.00015.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00015.unmapped -H 2388851596.00015.mismatch \ 2388851596.00015.map /data/maqgene/genomes/elegans.bfa 2388851596.00015.1.bfq 2> /dev/null # Wed Apr 10 22:08:39 BST 2013: Mapping file(s) 2388851596.00014.1.bfq # Wed Apr 10 22:08:39 BST 2013: Mapping file(s) 2388851596.00024.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00024.unmapped -H 2388851596.00024.mismatch \ 2388851596.00024.map /data/maqgene/genomes/elegans.bfa 2388851596.00024.1.bfq 2> /dev/null /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00014.unmapped -H 2388851596.00014.mismatch \ 2388851596.00014.map /data/maqgene/genomes/elegans.bfa 2388851596.00014.1.bfq 2> /dev/null # Wed Apr 10 22:08:39 BST 2013: Mapping file(s) 2388851596.00013.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00013.unmapped -H 2388851596.00013.mismatch \ 2388851596.00013.map /data/maqgene/genomes/elegans.bfa 2388851596.00013.1.bfq 2> /dev/null # Wed Apr 10 22:08:40 BST 2013: Mapping file(s) 2388851596.00025.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00025.unmapped -H 2388851596.00025.mismatch \ 2388851596.00025.map /data/maqgene/genomes/elegans.bfa 2388851596.00025.1.bfq 2> /dev/null # Wed Apr 10 22:12:43 BST 2013: Mapping file(s) 2388851596.00033.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00033.unmapped -H 2388851596.00033.mismatch \ 2388851596.00033.map /data/maqgene/genomes/elegans.bfa 2388851596.00033.1.bfq 2> /dev/null # Wed Apr 10 22:12:43 BST 2013: Mapping file(s) 2388851596.00032.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00032.unmapped -H 2388851596.00032.mismatch \ 2388851596.00032.map /data/maqgene/genomes/elegans.bfa 2388851596.00032.1.bfq 2> /dev/null # Wed Apr 10 22:12:44 BST 2013: Mapping file(s) 2388851596.00030.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00030.unmapped -H 2388851596.00030.mismatch \ 2388851596.00030.map /data/maqgene/genomes/elegans.bfa 2388851596.00030.1.bfq 2> /dev/null # Wed Apr 10 22:12:44 BST 2013: Mapping file(s) 2388851596.00031.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00031.unmapped -H 2388851596.00031.mismatch \ 2388851596.00031.map /data/maqgene/genomes/elegans.bfa 2388851596.00031.1.bfq 2> /dev/null # Wed Apr 10 22:12:45 BST 2013: Mapping file(s) 2388851596.00029.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00029.unmapped -H 2388851596.00029.mismatch \ 2388851596.00029.map /data/maqgene/genomes/elegans.bfa 2388851596.00029.1.bfq 2> /dev/null # Wed Apr 10 22:12:45 BST 2013: Mapping file(s) 2388851596.00028.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00028.unmapped -H 2388851596.00028.mismatch \ 2388851596.00028.map /data/maqgene/genomes/elegans.bfa 2388851596.00028.1.bfq 2> /dev/null # Wed Apr 10 22:12:46 BST 2013: Mapping file(s) 2388851596.00027.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00027.unmapped -H 2388851596.00027.mismatch \ 2388851596.00027.map /data/maqgene/genomes/elegans.bfa 2388851596.00027.1.bfq 2> /dev/null # Wed Apr 10 22:12:46 BST 2013: Mapping file(s) 2388851596.00026.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00026.unmapped -H 2388851596.00026.mismatch \ 2388851596.00026.map /data/maqgene/genomes/elegans.bfa 2388851596.00026.1.bfq 2> /dev/null # Wed Apr 10 22:12:48 BST 2013: Mapping file(s) 2388851596.00034.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00034.unmapped -H 2388851596.00034.mismatch \ 2388851596.00034.map /data/maqgene/genomes/elegans.bfa 2388851596.00034.1.bfq 2> /dev/null # Wed Apr 10 22:12:53 BST 2013: Mapping file(s) 2388851596.00035.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00035.unmapped -H 2388851596.00035.mismatch \ 2388851596.00035.map /data/maqgene/genomes/elegans.bfa 2388851596.00035.1.bfq 2> /dev/null # Wed Apr 10 22:12:56 BST 2013: Mapping file(s) 2388851596.00036.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00036.unmapped -H 2388851596.00036.mismatch \ 2388851596.00036.map /data/maqgene/genomes/elegans.bfa 2388851596.00036.1.bfq 2> /dev/null # Wed Apr 10 22:14:09 BST 2013: Mapping file(s) 2388851596.00039.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00039.unmapped -H 2388851596.00039.mismatch \ 2388851596.00039.map /data/maqgene/genomes/elegans.bfa 2388851596.00039.1.bfq 2> /dev/null # Wed Apr 10 22:14:10 BST 2013: Mapping file(s) 2388851596.00038.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00038.unmapped -H 2388851596.00038.mismatch \ 2388851596.00038.map /data/maqgene/genomes/elegans.bfa 2388851596.00038.1.bfq 2> /dev/null # Wed Apr 10 22:14:11 BST 2013: Mapping file(s) 2388851596.00037.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00037.unmapped -H 2388851596.00037.mismatch \ 2388851596.00037.map /data/maqgene/genomes/elegans.bfa 2388851596.00037.1.bfq 2> /dev/null # Wed Apr 10 22:17:09 BST 2013: Mapping file(s) 2388851596.00049.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00049.unmapped -H 2388851596.00049.mismatch \ 2388851596.00049.map /data/maqgene/genomes/elegans.bfa 2388851596.00049.1.bfq 2> /dev/null # Wed Apr 10 22:17:09 BST 2013: Mapping file(s) 2388851596.00048.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00048.unmapped -H 2388851596.00048.mismatch \ 2388851596.00048.map /data/maqgene/genomes/elegans.bfa 2388851596.00048.1.bfq 2> /dev/null # Wed Apr 10 22:17:10 BST 2013: Mapping file(s) 2388851596.00047.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00047.unmapped -H 2388851596.00047.mismatch \ 2388851596.00047.map /data/maqgene/genomes/elegans.bfa 2388851596.00047.1.bfq 2> /dev/null # Wed Apr 10 22:17:11 BST 2013: Mapping file(s) 2388851596.00046.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00046.unmapped -H 2388851596.00046.mismatch \ 2388851596.00046.map /data/maqgene/genomes/elegans.bfa 2388851596.00046.1.bfq 2> /dev/null # Wed Apr 10 22:17:12 BST 2013: Mapping file(s) 2388851596.00045.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00045.unmapped -H 2388851596.00045.mismatch \ 2388851596.00045.map /data/maqgene/genomes/elegans.bfa 2388851596.00045.1.bfq 2> /dev/null # Wed Apr 10 22:17:13 BST 2013: Mapping file(s) 2388851596.00044.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00044.unmapped -H 2388851596.00044.mismatch \ 2388851596.00044.map /data/maqgene/genomes/elegans.bfa 2388851596.00044.1.bfq 2> /dev/null # Wed Apr 10 22:17:14 BST 2013: Mapping file(s) 2388851596.00043.1.bfq # Wed Apr 10 22:17:14 BST 2013: Mapping file(s) 2388851596.00042.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00043.unmapped -H 2388851596.00043.mismatch \ 2388851596.00043.map /data/maqgene/genomes/elegans.bfa 2388851596.00043.1.bfq 2> /dev/null /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00042.unmapped -H 2388851596.00042.mismatch \ 2388851596.00042.map /data/maqgene/genomes/elegans.bfa 2388851596.00042.1.bfq 2> /dev/null # Wed Apr 10 22:17:15 BST 2013: Mapping file(s) 2388851596.00041.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00041.unmapped -H 2388851596.00041.mismatch \ 2388851596.00041.map /data/maqgene/genomes/elegans.bfa 2388851596.00041.1.bfq 2> /dev/null # Wed Apr 10 22:17:15 BST 2013: Mapping file(s) 2388851596.00040.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00040.unmapped -H 2388851596.00040.mismatch \ 2388851596.00040.map /data/maqgene/genomes/elegans.bfa 2388851596.00040.1.bfq 2> /dev/null # Wed Apr 10 22:17:27 BST 2013: Mapping file(s) 2388851596.00050.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00050.unmapped -H 2388851596.00050.mismatch \ 2388851596.00050.map /data/maqgene/genomes/elegans.bfa 2388851596.00050.1.bfq 2> /dev/null # Wed Apr 10 22:19:34 BST 2013: Mapping file(s) 2388851596.00053.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00053.unmapped -H 2388851596.00053.mismatch \ 2388851596.00053.map /data/maqgene/genomes/elegans.bfa 2388851596.00053.1.bfq 2> /dev/null # Wed Apr 10 22:19:36 BST 2013: Mapping file(s) 2388851596.00052.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00052.unmapped -H 2388851596.00052.mismatch \ 2388851596.00052.map /data/maqgene/genomes/elegans.bfa 2388851596.00052.1.bfq 2> /dev/null # Wed Apr 10 22:19:38 BST 2013: Mapping file(s) 2388851596.00051.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00051.unmapped -H 2388851596.00051.mismatch \ 2388851596.00051.map /data/maqgene/genomes/elegans.bfa 2388851596.00051.1.bfq 2> /dev/null # Wed Apr 10 22:21:29 BST 2013: Mapping file(s) 2388851596.00062.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00062.unmapped -H 2388851596.00062.mismatch \ 2388851596.00062.map /data/maqgene/genomes/elegans.bfa 2388851596.00062.1.bfq 2> /dev/null # Wed Apr 10 22:21:30 BST 2013: Mapping file(s) 2388851596.00061.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00061.unmapped -H 2388851596.00061.mismatch \ 2388851596.00061.map /data/maqgene/genomes/elegans.bfa 2388851596.00061.1.bfq 2> /dev/null # Wed Apr 10 22:21:31 BST 2013: Mapping file(s) 2388851596.00060.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00060.unmapped -H 2388851596.00060.mismatch \ 2388851596.00060.map /data/maqgene/genomes/elegans.bfa 2388851596.00060.1.bfq 2> /dev/null # Wed Apr 10 22:21:32 BST 2013: Mapping file(s) 2388851596.00059.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00059.unmapped -H 2388851596.00059.mismatch \ 2388851596.00059.map /data/maqgene/genomes/elegans.bfa 2388851596.00059.1.bfq 2> /dev/null # Wed Apr 10 22:21:33 BST 2013: Mapping file(s) 2388851596.00058.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00058.unmapped -H 2388851596.00058.mismatch \ 2388851596.00058.map /data/maqgene/genomes/elegans.bfa 2388851596.00058.1.bfq 2> /dev/null # Wed Apr 10 22:21:34 BST 2013: Mapping file(s) 2388851596.00057.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00057.unmapped -H 2388851596.00057.mismatch \ 2388851596.00057.map /data/maqgene/genomes/elegans.bfa 2388851596.00057.1.bfq 2> /dev/null # Wed Apr 10 22:21:35 BST 2013: Mapping file(s) 2388851596.00056.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00056.unmapped -H 2388851596.00056.mismatch \ 2388851596.00056.map /data/maqgene/genomes/elegans.bfa 2388851596.00056.1.bfq 2> /dev/null # Wed Apr 10 22:21:35 BST 2013: Mapping file(s) 2388851596.00055.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00055.unmapped -H 2388851596.00055.mismatch \ 2388851596.00055.map /data/maqgene/genomes/elegans.bfa 2388851596.00055.1.bfq 2> /dev/null # Wed Apr 10 22:21:36 BST 2013: Mapping file(s) 2388851596.00063.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00063.unmapped -H 2388851596.00063.mismatch \ 2388851596.00063.map /data/maqgene/genomes/elegans.bfa 2388851596.00063.1.bfq 2> /dev/null # Wed Apr 10 22:21:37 BST 2013: Mapping file(s) 2388851596.00054.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00054.unmapped -H 2388851596.00054.mismatch \ 2388851596.00054.map /data/maqgene/genomes/elegans.bfa 2388851596.00054.1.bfq 2> /dev/null # Wed Apr 10 22:24:30 BST 2013: Mapping file(s) 2388851596.00066.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00066.unmapped -H 2388851596.00066.mismatch \ 2388851596.00066.map /data/maqgene/genomes/elegans.bfa 2388851596.00066.1.bfq 2> /dev/null # Wed Apr 10 22:24:31 BST 2013: Mapping file(s) 2388851596.00065.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00065.unmapped -H 2388851596.00065.mismatch \ 2388851596.00065.map /data/maqgene/genomes/elegans.bfa 2388851596.00065.1.bfq 2> /dev/null # Wed Apr 10 22:24:32 BST 2013: Mapping file(s) 2388851596.00064.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00064.unmapped -H 2388851596.00064.mismatch \ 2388851596.00064.map /data/maqgene/genomes/elegans.bfa 2388851596.00064.1.bfq 2> /dev/null # Wed Apr 10 22:24:34 BST 2013: Mapping file(s) 2388851596.00067.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00067.unmapped -H 2388851596.00067.mismatch \ 2388851596.00067.map /data/maqgene/genomes/elegans.bfa 2388851596.00067.1.bfq 2> /dev/null # Wed Apr 10 22:25:20 BST 2013: Mapping file(s) 2388851596.00071.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00071.unmapped -H 2388851596.00071.mismatch \ 2388851596.00071.map /data/maqgene/genomes/elegans.bfa 2388851596.00071.1.bfq 2> /dev/null # Wed Apr 10 22:25:21 BST 2013: Mapping file(s) 2388851596.00070.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00070.unmapped -H 2388851596.00070.mismatch \ 2388851596.00070.map /data/maqgene/genomes/elegans.bfa 2388851596.00070.1.bfq 2> /dev/null # Wed Apr 10 22:25:22 BST 2013: Mapping file(s) 2388851596.00069.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00069.unmapped -H 2388851596.00069.mismatch \ 2388851596.00069.map /data/maqgene/genomes/elegans.bfa 2388851596.00069.1.bfq 2> /dev/null # Wed Apr 10 22:25:23 BST 2013: Mapping file(s) 2388851596.00068.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00068.unmapped -H 2388851596.00068.mismatch \ 2388851596.00068.map /data/maqgene/genomes/elegans.bfa 2388851596.00068.1.bfq 2> /dev/null # Wed Apr 10 22:25:50 BST 2013: Mapping file(s) 2388851596.00075.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00075.unmapped -H 2388851596.00075.mismatch \ 2388851596.00075.map /data/maqgene/genomes/elegans.bfa 2388851596.00075.1.bfq 2> /dev/null # Wed Apr 10 22:25:51 BST 2013: Mapping file(s) 2388851596.00074.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00074.unmapped -H 2388851596.00074.mismatch \ 2388851596.00074.map /data/maqgene/genomes/elegans.bfa 2388851596.00074.1.bfq 2> /dev/null # Wed Apr 10 22:25:52 BST 2013: Mapping file(s) 2388851596.00073.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00073.unmapped -H 2388851596.00073.mismatch \ 2388851596.00073.map /data/maqgene/genomes/elegans.bfa 2388851596.00073.1.bfq 2> /dev/null # Wed Apr 10 22:25:53 BST 2013: Mapping file(s) 2388851596.00072.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00072.unmapped -H 2388851596.00072.mismatch \ 2388851596.00072.map /data/maqgene/genomes/elegans.bfa 2388851596.00072.1.bfq 2> /dev/null # Wed Apr 10 22:28:30 BST 2013: Mapping file(s) 2388851596.00077.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00077.unmapped -H 2388851596.00077.mismatch \ 2388851596.00077.map /data/maqgene/genomes/elegans.bfa 2388851596.00077.1.bfq 2> /dev/null # Wed Apr 10 22:28:32 BST 2013: Mapping file(s) 2388851596.00076.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00076.unmapped -H 2388851596.00076.mismatch \ 2388851596.00076.map /data/maqgene/genomes/elegans.bfa 2388851596.00076.1.bfq 2> /dev/null # Wed Apr 10 22:28:33 BST 2013: Mapping file(s) 2388851596.00078.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00078.unmapped -H 2388851596.00078.mismatch \ 2388851596.00078.map /data/maqgene/genomes/elegans.bfa 2388851596.00078.1.bfq 2> /dev/null # Wed Apr 10 22:28:56 BST 2013: Mapping file(s) 2388851596.00081.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00081.unmapped -H 2388851596.00081.mismatch \ 2388851596.00081.map /data/maqgene/genomes/elegans.bfa 2388851596.00081.1.bfq 2> /dev/null # Wed Apr 10 22:28:57 BST 2013: Mapping file(s) 2388851596.00080.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00080.unmapped -H 2388851596.00080.mismatch \ 2388851596.00080.map /data/maqgene/genomes/elegans.bfa 2388851596.00080.1.bfq 2> /dev/null # Wed Apr 10 22:28:58 BST 2013: Mapping file(s) 2388851596.00079.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00079.unmapped -H 2388851596.00079.mismatch \ 2388851596.00079.map /data/maqgene/genomes/elegans.bfa 2388851596.00079.1.bfq 2> /dev/null # Wed Apr 10 22:28:59 BST 2013: Mapping file(s) 2388851596.00082.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00082.unmapped -H 2388851596.00082.mismatch \ 2388851596.00082.map /data/maqgene/genomes/elegans.bfa 2388851596.00082.1.bfq 2> /dev/null # Wed Apr 10 22:29:51 BST 2013: Mapping file(s) 2388851596.00086.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00086.unmapped -H 2388851596.00086.mismatch \ 2388851596.00086.map /data/maqgene/genomes/elegans.bfa 2388851596.00086.1.bfq 2> /dev/null # Wed Apr 10 22:29:53 BST 2013: Mapping file(s) 2388851596.00085.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00085.unmapped -H 2388851596.00085.mismatch \ 2388851596.00085.map /data/maqgene/genomes/elegans.bfa 2388851596.00085.1.bfq 2> /dev/null # Wed Apr 10 22:29:55 BST 2013: Mapping file(s) 2388851596.00087.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00087.unmapped -H 2388851596.00087.mismatch \ 2388851596.00087.map /data/maqgene/genomes/elegans.bfa 2388851596.00087.1.bfq 2> /dev/null # Wed Apr 10 22:29:55 BST 2013: Mapping file(s) 2388851596.00084.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00084.unmapped -H 2388851596.00084.mismatch \ 2388851596.00084.map /data/maqgene/genomes/elegans.bfa 2388851596.00084.1.bfq 2> /dev/null # Wed Apr 10 22:29:57 BST 2013: Mapping file(s) 2388851596.00088.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00088.unmapped -H 2388851596.00088.mismatch \ 2388851596.00088.map /data/maqgene/genomes/elegans.bfa 2388851596.00088.1.bfq 2> /dev/null # Wed Apr 10 22:29:59 BST 2013: Mapping file(s) 2388851596.00083.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00083.unmapped -H 2388851596.00083.mismatch \ 2388851596.00083.map /data/maqgene/genomes/elegans.bfa 2388851596.00083.1.bfq 2> /dev/null # Wed Apr 10 22:32:41 BST 2013: Mapping file(s) 2388851596.00091.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00091.unmapped -H 2388851596.00091.mismatch \ 2388851596.00091.map /data/maqgene/genomes/elegans.bfa 2388851596.00091.1.bfq 2> /dev/null # Wed Apr 10 22:32:43 BST 2013: Mapping file(s) 2388851596.00090.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00090.unmapped -H 2388851596.00090.mismatch \ 2388851596.00090.map /data/maqgene/genomes/elegans.bfa 2388851596.00090.1.bfq 2> /dev/null # Wed Apr 10 22:32:45 BST 2013: Mapping file(s) 2388851596.00089.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00089.unmapped -H 2388851596.00089.mismatch \ 2388851596.00089.map /data/maqgene/genomes/elegans.bfa 2388851596.00089.1.bfq 2> /dev/null # Wed Apr 10 22:33:11 BST 2013: Mapping file(s) 2388851596.00095.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00095.unmapped -H 2388851596.00095.mismatch \ 2388851596.00095.map /data/maqgene/genomes/elegans.bfa 2388851596.00095.1.bfq 2> /dev/null # Wed Apr 10 22:33:13 BST 2013: Mapping file(s) 2388851596.00094.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00094.unmapped -H 2388851596.00094.mismatch \ 2388851596.00094.map /data/maqgene/genomes/elegans.bfa 2388851596.00094.1.bfq 2> /dev/null # Wed Apr 10 22:33:15 BST 2013: Mapping file(s) 2388851596.00096.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00096.unmapped -H 2388851596.00096.mismatch \ 2388851596.00096.map /data/maqgene/genomes/elegans.bfa 2388851596.00096.1.bfq 2> /dev/null # Wed Apr 10 22:33:16 BST 2013: Mapping file(s) 2388851596.00093.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00093.unmapped -H 2388851596.00093.mismatch \ 2388851596.00093.map /data/maqgene/genomes/elegans.bfa 2388851596.00093.1.bfq 2> /dev/null # Wed Apr 10 22:33:17 BST 2013: Mapping file(s) 2388851596.00092.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00092.unmapped -H 2388851596.00092.mismatch \ 2388851596.00092.map /data/maqgene/genomes/elegans.bfa 2388851596.00092.1.bfq 2> /dev/null # Wed Apr 10 22:33:41 BST 2013: Mapping file(s) 2388851596.00098.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00098.unmapped -H 2388851596.00098.mismatch \ 2388851596.00098.map /data/maqgene/genomes/elegans.bfa 2388851596.00098.1.bfq 2> /dev/null # Wed Apr 10 22:33:41 BST 2013: Mapping file(s) 2388851596.00097.1.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -e 100 -1 0 -u 2388851596.00097.unmapped -H 2388851596.00097.mismatch \ 2388851596.00097.map /data/maqgene/genomes/elegans.bfa 2388851596.00097.1.bfq 2> /dev/null # Wed Apr 10 22:37:21 BST 2013: Merging all *.unmapped files ... # Wed Apr 10 22:37:21 BST 2013: Merging all maps ... cat 2388851596.00000.unmapped 2388851596.00001.unmapped 2388851596.00002.unmapped 2388851596.00003.unmapped 2388851596.00004.unmapped 2388851596.00005.unmapped 2388851596.00006.unmapped 2388851596.00007.unmapped 2388851596.00008.unmapped 2388851596.00009.unmapped 2388851596.00010.unmapped 2388851596.00011.unmapped 2388851596.00012.unmapped 2388851596.00013.unmapped 2388851596.00014.unmapped 2388851596.00015.unmapped 2388851596.00016.unmapped 2388851596.00017.unmapped 2388851596.00018.unmapped 2388851596.00019.unmapped 2388851596.00020.unmapped 2388851596.00021.unmapped 2388851596.00022.unmapped 2388851596.00023.unmapped 2388851596.00024.unmapped 2388851596.00025.unmapped 2388851596.00026.unmapped 2388851596.00027.unmapped 2388851596.00028.unmapped 2388851596.00029.unmapped 2388851596.00030.unmapped 2388851596.00031.unmapped 2388851596.00032.unmapped 2388851596.00033.unmapped 2388851596.00034.unmapped 2388851596.00035.unmapped 2388851596.00036.unmapped 2388851596.00037.unmapped 2388851596.00038.unmapped 2388851596.00039.unmapped 2388851596.00040.unmapped 2388851596.00041.unmapped 2388851596.00042.unmapped 2388851596.00043.unmapped 2388851596.00044.unmapped 2388851596.00045.unmapped 2388851596.00046.unmapped 2388851596.00047.unmapped 2388851596.00048.unmapped 2388851596.00049.unmapped 2388851596.00050.unmapped 2388851596.00051.unmapped 2388851596.00052.unmapped 2388851596.00053.unmapped 2388851596.00054.unmapped 2388851596.00055.unmapped 2388851596.00056.unmapped 2388851596.00057.unmapped 2388851596.00058.unmapped 2388851596.00059.unmapped 2388851596.00060.unmapped 2388851596.00061.unmapped 2388851596.00062.unmapped 2388851596.00063.unmapped 2388851596.00064.unmapped 2388851596.00065.unmapped 2388851596.00066.unmapped 2388851596.00067.unmapped 2388851596.00068.unmapped 2388851596.00069.unmapped 2388851596.00070.unmapped 2388851596.00071.unmapped 2388851596.00072.unmapped 2388851596.00073.unmapped 2388851596.00074.unmapped 2388851596.00075.unmapped 2388851596.00076.unmapped 2388851596.00077.unmapped 2388851596.00078.unmapped 2388851596.00079.unmapped 2388851596.00080.unmapped 2388851596.00081.unmapped 2388851596.00082.unmapped 2388851596.00083.unmapped 2388851596.00084.unmapped 2388851596.00085.unmapped 2388851596.00086.unmapped 2388851596.00087.unmapped 2388851596.00088.unmapped 2388851596.00089.unmapped 2388851596.00090.unmapped 2388851596.00091.unmapped 2388851596.00092.unmapped 2388851596.00093.unmapped 2388851596.00094.unmapped 2388851596.00095.unmapped 2388851596.00096.unmapped 2388851596.00097.unmapped 2388851596.00098.unmapped > 2388851596_unmapped.txt /data/maqgene/bin/maq mapmerge 2388851596.map 2388851596.00000.map 2388851596.00001.map 2388851596.00002.map 2388851596.00003.map 2388851596.00004.map 2388851596.00005.map 2388851596.00006.map 2388851596.00007.map 2388851596.00008.map 2388851596.00009.map 2388851596.00010.map 2388851596.00011.map 2388851596.00012.map 2388851596.00013.map 2388851596.00014.map 2388851596.00015.map 2388851596.00016.map 2388851596.00017.map 2388851596.00018.map 2388851596.00019.map 2388851596.00020.map 2388851596.00021.map 2388851596.00022.map 2388851596.00023.map 2388851596.00024.map 2388851596.00025.map 2388851596.00026.map 2388851596.00027.map 2388851596.00028.map 2388851596.00029.map 2388851596.00030.map 2388851596.00031.map 2388851596.00032.map 2388851596.00033.map 2388851596.00034.map 2388851596.00035.map 2388851596.00036.map 2388851596.00037.map 2388851596.00038.map 2388851596.00039.map 2388851596.00040.map 2388851596.00041.map 2388851596.00042.map 2388851596.00043.map 2388851596.00044.map 2388851596.00045.map 2388851596.00046.map 2388851596.00047.map 2388851596.00048.map 2388851596.00049.map 2388851596.00050.map 2388851596.00051.map 2388851596.00052.map 2388851596.00053.map 2388851596.00054.map 2388851596.00055.map 2388851596.00056.map 2388851596.00057.map 2388851596.00058.map 2388851596.00059.map 2388851596.00060.map 2388851596.00061.map 2388851596.00062.map 2388851596.00063.map 2388851596.00064.map 2388851596.00065.map 2388851596.00066.map 2388851596.00067.map 2388851596.00068.map 2388851596.00069.map 2388851596.00070.map 2388851596.00071.map 2388851596.00072.map 2388851596.00073.map 2388851596.00074.map 2388851596.00075.map 2388851596.00076.map 2388851596.00077.map 2388851596.00078.map 2388851596.00079.map 2388851596.00080.map 2388851596.00081.map 2388851596.00082.map 2388851596.00083.map 2388851596.00084.map 2388851596.00085.map 2388851596.00086.map 2388851596.00087.map 2388851596.00088.map 2388851596.00089.map 2388851596.00090.map 2388851596.00091.map 2388851596.00092.map 2388851596.00093.map 2388851596.00094.map 2388851596.00095.map 2388851596.00096.map 2388851596.00097.map 2388851596.00098.map # Wed Apr 10 22:37:27 BST 2013: Linking backend file 2388851596_unmapped.txt to /data/maqgene/out/example_user/CB6930/CB6930_unmapped.txt ln -fs /data/maqgene/work/2388851596_unmapped.txt /data/maqgene/out/example_user/CB6930/CB6930_unmapped.txt /data/maqgene/makefile:126: warning: undefined variable `mapcheck_parameters' # Wed Apr 10 22:54:17 BST 2013: Generating consensus ... /data/maqgene/bin/maq assemble -N 2 -q 0 -r 0.0 -m 7 -Q 100 -p 2367457594.cns \ /data/maqgene/genomes/elegans.bfa 2388851596.map 2> 2367457594_log.txt # Wed Apr 10 22:54:17 BST 2013: Creating pileup ... # Wed Apr 10 22:54:17 BST 2013: Running 'mapcheck' ... /data/maqgene/bin/maq pileup -Q 100 -m 7 -q 0 /data/maqgene/genomes/elegans.bfa 2388851596.map > 1964021411_pileup.txt /data/maqgene/bin/maq mapcheck /data/maqgene/genomes/elegans.bfa 2388851596.map > 2388851596_check.txt \ 2>/dev/null # Wed Apr 10 22:57:42 BST 2013: Linking backend file 2388851596_check.txt to /data/maqgene/out/example_user/CB6930/CB6930_check.txt ln -fs /data/maqgene/work/2388851596_check.txt /data/maqgene/out/example_user/CB6930/CB6930_check.txt /data/maqgene/bin/filter_matching_lines 1964021411_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 \ > 1964021411_known_snps # Wed Apr 10 22:58:43 BST 2013: Getting uncovered regions ... # Wed Apr 10 22:58:43 BST 2013: Linking backend file 1964021411_pileup.txt to /data/maqgene/out/example_user/CB6930/CB6930_pileup.txt # Wed Apr 10 22:58:43 BST 2013: Making coverage histogram ... cut -f 1,2,4 1964021411_pileup.txt \ | /data/maqgene/bin/get_uncovered_regions 50 \ > 1964021411_uncovered.txt (echo -en "sequencing_depth\tnumber_of_bases\n"; \ cut -f 4 1964021411_pileup.txt \ | /data/maqgene/bin/pileup_histogram 100) > 1964021411_coverage.txt ln -fs /data/maqgene/work/1964021411_pileup.txt /data/maqgene/out/example_user/CB6930/CB6930_pileup.txt # Wed Apr 10 22:59:42 BST 2013: Linking backend file 1964021411_coverage.txt to /data/maqgene/out/example_user/CB6930/CB6930_coverage.txt ln -fs /data/maqgene/work/1964021411_coverage.txt /data/maqgene/out/example_user/CB6930/CB6930_coverage.txt # Wed Apr 10 22:59:42 BST 2013: Filtering and loading pileup for analysis ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 1964021411_pileup; create table 1964021411_pileup ( dna enum('I','II','III','IV','MtDNA','V','X') NOT NULL, start int(10) NOT NULL, ref_base char(1) NOT NULL, read_depth int(5) NOT NULL, sample_reads varchar(100) NOT NULL, A_fwd int(5) NOT NULL, A_rev int(5) NOT NULL, C_fwd int(5) NOT NULL, C_rev int(5) NOT NULL, G_fwd int(5) NOT NULL, G_rev int(5) NOT NULL, T_fwd int(5) NOT NULL, T_rev int(5) NOT NULL, wt_fwd int(5) NOT NULL, wt_rev int(5) NOT NULL, primary key (dna, start) );" cat 1964021411_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 1964021411_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 1964021411_pileup" # Wed Apr 10 22:59:43 BST 2013: Linking backend file 1964021411_uncovered.txt to /data/maqgene/out/example_user/CB6930/CB6930_uncovered.txt ln -fs /data/maqgene/work/1964021411_uncovered.txt /data/maqgene/out/example_user/CB6930/CB6930_uncovered.txt cat 1964021411_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 1964021411_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 1964021411_pileup" touch 1964021411_pileup # Wed Apr 10 23:00:49 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 1964021411_pileup p using (dna,start)" > /data/maqgene/out/example_user/CB6930/CB6930_snp_read_counts.txt 0 snp read count lines written. # Wed Apr 10 23:02:05 BST 2013: Extracting point mutants from consensus ... # Wed Apr 10 23:02:05 BST 2013: Linking backend file 2367457594_log.txt to /data/maqgene/out/example_user/CB6930/CB6930_log.txt /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 2367457594_snps; create table 2367457594_snps ( id int(10) NOT NULL auto_increment, dna char(40) NOT NULL, start int(10) NOT NULL, end int(10) NOT NULL, indel_size int(5) NOT NULL, variant_type enum('indel', 'point') NOT NULL, ref_base char NOT NULL, sample_base char NOT NULL, snp_score int(5) NOT NULL, read_depth int(5) NOT NULL, loci_multiplicity double(5,2) NOT NULL, mapping_quality int(5) NOT NULL, neighbor_quality int(5) NOT NULL, primary key (id), unique key (dna, start), key (indel_size) )" ln -fs /data/maqgene/work/2367457594_log.txt /data/maqgene/out/example_user/CB6930/CB6930_log.txt /data/maqgene/bin/maq cns2snp 2367457594.cns \ | cat -b | /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "load data local infile '/dev/stdin' into table 2367457594_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 2367457594_snps;" # Wed Apr 10 23:02:15 BST 2013: Extracting indels from consensus ... /data/maqgene/bin/maq indelsoa /data/maqgene/genomes/elegans.bfa 2388851596.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 2367457594_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 2367457594_snps;" # Wed Apr 10 23:04:02 BST 2013: Adding placeholders for known SNPs. cat 1964021411_known_snps \ | /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "load data local infile '/dev/stdin' ignore into table 2367457594_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 2367457594_snps;" Found 163353 variants. touch 2367457594_snps # Wed Apr 10 23:04:04 BST 2013: Loading uncovered regions into table ... # Wed Apr 10 23:04:04 BST 2013: Finding all genomic features overlapping variants... cat 1964021411_uncovered.txt \ | /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 1964021411_uncovered; create table 1964021411_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 = 163354; load data local infile '/dev/stdin' into table 1964021411_uncovered (dna, start, end)" # Wed Apr 10 23:04:04 BST 2013: Getting masking regions /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 2367457594_rel_snps; CREATE TABLE 2367457594_rel_snps ( association_id INT(10) NOT NULL, query_region_id INT(10) unsigned NOT NULL, target_region_id INT(10) NOT NULL, distance INT(10) NOT NULL, overlap INT(10) NOT NULL, same_strand enum('SAME', 'OPP') NOT NULL, num_regions_between INT(3) NOT NULL, PRIMARY KEY (association_id), KEY (query_region_id), KEY (target_region_id) )" /data/maqgene/bin/associate_regions -b -1 -c -1000000 -m 2 -o >(/usr/bin/mysql -Dmaqgenedb -umaqgene --skip-column-names --batch --raw --local-infile -e "drop table if exists 2367457594_masked_ids; create table 2367457594_masked_ids (query_region_id int(10) NOT NULL, primary key (query_region_id)); load data local infile '/dev/stdin' ignore into table 2367457594_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 2367457594_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; 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 2367457594_rel_snps; flush table 2367457594_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 2367457594_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 2 240 II 6 982 III 4 243 IV 8 807 V 4 684 X 7 4911 touch 1964021411_uncovered # Wed Apr 10 23:04:04 BST 2013: Finding mRNA features overlapping uncovered regions ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 1964021411_uncovered_rel; CREATE TABLE 1964021411_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 1964021411_uncovered_rel; flush table 1964021411_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 1964021411_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 1964021411_uncovered_rel # Wed Apr 10 23:04:06 BST 2013: Calculating translation start offsets for uncovered regions... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 1964021411_offsets_uncovered; create table 1964021411_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 1964021411_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 1964021411_uncovered reg join 1964021411_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 2367457594_masked_ids /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 1964021411_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 1964021411_uncovered reg join 1964021411_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 1964021411_offsets_uncovered touch 2367457594_rel_snps # Wed Apr 10 23:04:07 BST 2013: Calculating translation start offsets... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 2367457594_offsets_snps; create table 2367457594_offsets_snps ( id int(10) NOT NULL, gene varchar(50) NOT NULL, 5prime_offset int(10) NOT NULL, 3prime_offset int(10) NOT NULL, total_length int(10) NOT NULL, boundary_type char(20) NOT NULL, primary key (id, gene, boundary_type) );" # Wed Apr 10 23:04:07 BST 2013: Getting intergenic regions /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 2367457594_rel_intergenic; create table 2367457594_rel_intergenic like 2367457594_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 2367457594_rel_intergenic; flush table 2367457594_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 2367457594_snps") -t <(/usr/bin/mysql -Dmaqgenedb -umaqgene --skip-column-names --batch --raw --local-infile -e "select id, 'elegans',dna,start,end,strand from elegans_features feature where feature.feature = 'mRNA'") 1>/dev/null; /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 2367457594_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 2367457594_snps reg join 2367457594_rel_snps rel on (reg.id = rel.query_region_id) join elegans_features gene on (rel.target_region_id = gene.id) join elegans_features exon on (exon.attribute = gene.attribute) where exon.feature = 'exon' and gene.feature = 'mRNA' group by reg.id, gene.attribute" # Wed Apr 10 23:04:11 BST 2013: Filtering masked intergenic regions /usr/bin/mysql -Dmaqgenedb -umaqgene --skip-column-names --batch --raw --local-infile -e "delete i.* from 2367457594_rel_intergenic i join 2367457594_masked_ids m using (query_region_id)" touch 2367457594_rel_intergenic # Wed Apr 10 23:04:16 BST 2013: Classifying intergenic relations /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 2367457594_intergenic_assoc; create table 2367457594_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 2367457594_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 2367457594_snps snp join 2367457594_rel_intergenic rel on (snp.id = rel.query_region_id) join elegans_features feature on (rel.target_region_id = feature.id)" touch 2367457594_intergenic_assoc touch 2367457594_offsets_snps # Wed Apr 10 23:04:28 BST 2013: Getting codons affected by point mutations... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 2367457594_codons; create table 2367457594_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 2367457594_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 2367457594_offsets_snps off join 2367457594_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 2367457594_codons /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 2367457594_marked; create table 2367457594_marked ( id int(10) NOT NULL, class varchar(100) NOT NULL, description varchar(100) NOT NULL, parent_feature varchar(100) NOT NULL, primary key (id, class, parent_feature) );" # Wed Apr 10 23:04:35 BST 2013: Finding exonic indels ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 2367457594_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 2367457594_snps snp join 2367457594_rel_snps rel on (snp.id = rel.query_region_id) join elegans_features feature on (rel.target_region_id = feature.id) where feature.feature = 'exon' and snp.variant_type = 'indel';" # Wed Apr 10 23:04:35 BST 2013: Finding coding variants ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 2367457594_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 2367457594_codons trans join elegans_genetic_code reference_codons on (trans.ref_codon = reference_codons.codon) join elegans_genetic_code sample_codons on (trans.sam_codon = sample_codons.codon);" # Wed Apr 10 23:04:36 BST 2013: Finding noncoding variants ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 2367457594_marked select snp.id, feature.feature class, 'none' description, feature.attribute parent_feature from 2367457594_snps snp join 2367457594_rel_snps rel on (snp.id = rel.query_region_id) join elegans_features feature on (rel.target_region_id = feature.id) where feature.feature not in ('exon', 'intron', 'mRNA');" # Wed Apr 10 23:04:36 BST 2013: Finding splice site variants ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 2367457594_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 2367457594_snps snp join 2367457594_rel_snps rel on (snp.id = rel.query_region_id) join elegans_features feature on (rel.target_region_id = feature.id) where feature.feature = 'intron' and rel.distance > -2;" # Wed Apr 10 23:04:36 BST 2013: Finding intergenic and intronic variants ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 2367457594_marked select id, 'nongenic' class, concat(if (relation in ('upstream','into'), - distance, distance),' ',relation) description, attribute from 2367457594_intergenic_assoc where ((relation = 'upstream' and num_regions_between = 0 and distance < 50000) or (relation = 'upstream' and num_regions_between < 2 and distance < 1000) or (relation = 'downstream' and num_regions_between = 0 and distance < 1000) or (relation = 'downstream' and num_regions_between < 2 and distance < 1000) or relation = 'into' );" # Wed Apr 10 23:04:39 BST 2013: Finding uncovered regions in genes ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 2367457594_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 1964021411_uncovered unc join 1964021411_offsets_uncovered b using (id) join 1964021411_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 1964021411_uncovered unc join 1964021411_offsets_uncovered b using (id) join 1964021411_offsets_uncovered e using (id, gene) join elegans_features gene on (e.gene = gene.attribute) where b.boundary_type = 'start' and e.boundary_type = 'end' and gene.strand = '-' and gene.feature = 'mRNA'" # Wed Apr 10 23:04:39 BST 2013: Variants found: +-----------------+-----------------+ | class | number_variants | +-----------------+-----------------+ | five_prime_UTR | 1333 | | frameshift | 93 | | inframe | 18 | | missense | 6381 | | ncRNA | 899 | | nongenic | 126185 | | non_start | 9 | | premature_stop | 694 | | readthrough | 22 | | silent | 7490 | | SNP | 1082 | | splice_acceptor | 46 | | splice_donor | 48 | | three_prime_UTR | 3602 | | uncovered | 9 | +-----------------+-----------------+ touch 2367457594_marked # Wed Apr 10 23:04:39 BST 2013: Combining results ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 2367457594_combined; create table 2367457594_combined (primary key (id, class, description), key (dna, start)) as select snp.id, 'CB6930' 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 2367457594_snps snp join 1964021411_pileup pile using (dna,start) join 2367457594_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' 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 1964021411_uncovered unc join 2367457594_marked class on (unc.id = class.id) left join elegans_per_locus using (dna,start) group by id, class, description; alter table 2367457594_combined order by dna, start, length" touch 2367457594_combined # Wed Apr 10 23:04:40 BST 2013: Writing results to grouped file ... # Wed Apr 10 23:04:40 BST 2013: Writing results to flat file ... /usr/bin/mysql -Dmaqgenedb -umaqgene --skip-column-names --batch --raw --local-infile --column-names -e "select * from 2367457594_combined" > /data/maqgene/out/example_user/CB6930/CB6930_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 2367457594_combined group by id order by dna, start;" > /data/maqgene/out/example_user/CB6930/CB6930_grouped.txt 6691 lines written. 3815 lines written. rm 2388851596.00016.1.bfq 2388851596.00017.1.fastq 2388851596.00014.map 2388851596.00092.1.fastq 2388851596.00055.unmapped 2388851596.00047.unmapped 2388851596.00031.mismatch 2388851596.00023.1.bfq 2388851596.00013.mismatch 2388851596.00002.unmapped 2388851596.00098.map 2388851596.00002.1.fastq 2388851596.00020.1.fastq 2388851596.00054.map 2388851596.00011.1.bfq 2388851596.00019.1.bfq 2388851596.00039.map 2388851596.00044.unmapped 2388851596.00087.mismatch 2388851596.00089.1.bfq 2388851596.00047.1.fastq 2388851596.00068.mismatch 2388851596.00094.map 2388851596.00043.1.bfq 2388851596.00012.unmapped 2388851596.00043.mismatch 2388851596.00063.1.fastq 2388851596.00077.unmapped 2388851596.00068.unmapped 2388851596.00037.map 2388851596.00015.1.bfq 2388851596.00053.map 2388851596.00015.mismatch 2388851596.00071.unmapped 2388851596.00084.1.fastq 2388851596.00048.1.fastq 2388851596.00012.1.fastq 2388851596.00026.unmapped 2388851596.00086.unmapped 2388851596.00028.unmapped 2388851596.00007.mismatch 2388851596.00041.1.bfq 2388851596.00005.mismatch 2388851596.00074.map 2388851596.00082.map 2388851596.00050.mismatch 2388851596.00072.1.bfq 2388851596.00093.1.bfq 2388851596.00097.1.bfq 2388851596.00026.1.fastq 2388851596.00036.mismatch 2388851596.00042.map 2388851596.00007.map 2388851596.00018.unmapped 2388851596.00054.1.fastq 2388851596.00023.mismatch 2388851596.00024.map 2388851596.00026.map 2388851596.00032.unmapped 2388851596.00096.1.bfq 2388851596.00083.1.fastq 2388851596.00018.1.fastq 2388851596.00094.1.bfq 2388851596.00051.mismatch 2388851596.00052.1.bfq 2388851596.00027.1.bfq 2388851596.00002.mismatch 2388851596.00066.1.fastq 2388851596.00046.map 2388851596.00063.map 2388851596.00076.map 2388851596.00040.mismatch 2388851596.00075.1.bfq 2388851596.00043.unmapped 2388851596.00082.mismatch 2388851596.00045.1.fastq 2388851596.00044.1.bfq 2388851596.00084.map 2388851596.00030.1.bfq 2388851596.00087.1.bfq 2388851596.00048.map 2388851596.00022.1.fastq 2388851596.00032.1.bfq 2388851596.00055.mismatch 2388851596.00085.1.bfq 2388851596.00096.unmapped 2388851596.00021.1.bfq 2388851596.00021.mismatch 2388851596.00049.1.fastq 2388851596.00025.1.bfq 2388851596.00059.1.fastq 2388851596.00098.unmapped 2388851596.00096.mismatch 2388851596.00079.1.fastq 2388851596.00008.mismatch 2388851596.00003.unmapped 2388851596.00006.map 2388851596.00060.map 2388851596.00070.map 2388851596.00046.1.bfq 2388851596.00093.unmapped 2388851596.00077.1.fastq 2388851596.00003.1.fastq 2388851596.00067.map 2388851596.00073.1.fastq 2388851596.00069.mismatch 2388851596.00054.1.bfq 2388851596.00027.1.fastq 2388851596.00028.mismatch 2388851596.00057.1.bfq 2388851596.00083.map 2388851596.00064.1.bfq 2388851596.00093.1.fastq 2388851596.00031.unmapped 2388851596.00057.mismatch 2388851596.00065.unmapped 2388851596.00000.map 2388851596.00066.map 2388851596.00056.1.bfq 2388851596.00081.1.bfq 2388851596.00065.mismatch 2388851596.00061.map 2388851596.00037.1.bfq 2388851596.00071.map 2388851596.00075.mismatch 2388851596.00081.map 2388851596.00088.unmapped 2388851596.00091.map 2388851596.00031.1.fastq 2388851596.00013.1.fastq 2388851596.00082.unmapped 2388851596.00089.mismatch 2388851596.00035.1.fastq 2388851596.00038.map 2388851596.00080.map 2388851596.00098.1.bfq 2388851596.00049.map 2388851596.00059.map 2388851596.00074.1.bfq 2388851596.00068.1.fastq 2388851596.00025.mismatch 2388851596.00001.map 2388851596.00010.map 2388851596.00014.1.bfq 2388851596.00008.unmapped 2388851596.00062.1.bfq 2388851596.00009.mismatch 2388851596.00045.unmapped 2388851596.00016.map 2388851596.00077.map 2388851596.00005.unmapped 2388851596.00039.1.bfq 2388851596.00033.mismatch 2388851596.00050.unmapped 2388851596.00076.1.fastq 2388851596.00095.mismatch 2388851596.00034.map 2388851596.00078.1.fastq 2388851596.00036.unmapped 2388851596.00069.unmapped 2388851596.00001.mismatch 2388851596.00007.unmapped 2388851596.00063.1.bfq 2388851596.00053.1.bfq 2388851596.00005.1.fastq 2388851596.00004.mismatch 2388851596.00029.map 2388851596.00011.map 2388851596.00050.1.fastq 2388851596.00023.unmapped 2388851596.00057.unmapped 2388851596.00042.1.bfq 2388851596.00036.1.fastq 2388851596.00056.mismatch 2388851596.00058.mismatch 2388851596.00029.1.bfq 2388851596.00022.unmapped 2388851596.00019.unmapped 2388851596.00062.map 2388851596.00032.1.fastq 2388851596.00072.map 2388851596.00084.1.bfq 2388851596.00023.1.fastq 2388851596.00038.1.bfq 2388851596.00017.map 2388851596.00035.map 2388851596.00068.1.bfq 2388851596.00092.map 2388851596.00089.unmapped 2388851596.00067.1.fastq 2388851596.00019.1.fastq 2388851596.00064.mismatch 2388851596.00020.map 2388851596.00015.unmapped 2388851596.00041.mismatch 2388851596.00051.1.fastq 2388851596.00020.unmapped 2388851596.00044.1.fastq 2388851596.00014.mismatch 2388851596.00047.map 2388851596.00088.1.bfq 2388851596.00024.1.bfq 2388851596.00009.unmapped 2388851596.00078.unmapped 2388851596.00085.mismatch 2388851596.00015.1.fastq 2388851596.00039.mismatch 2388851596.00078.map 2388851596.00060.1.bfq 2388851596.00095.1.bfq 2388851596.00019.mismatch 2388851596.00094.mismatch 2388851596.00012.map 2388851596.00062.unmapped 2388851596.00097.unmapped 2388851596.00090.map 2388851596.00086.1.fastq 2388851596.00072.unmapped 2388851596.00098.mismatch 2388851596.00053.mismatch 2388851596.00036.1.bfq 2388851596.00058.unmapped 2388851596.00067.1.bfq 2388851596.00052.unmapped 2388851596.00025.unmapped 2388851596.00028.1.fastq 2388851596.00075.unmapped 2388851596.00006.1.bfq 1535661234_split1 2388851596.00079.1.bfq 2388851596.00037.mismatch 2388851596.00070.1.bfq 2388851596.00080.1.bfq 2388851596.00042.mismatch 2388851596.00018.map 2388851596.00044.map 2388851596.00052.1.fastq 2388851596.00087.1.fastq 2388851596.00075.1.fastq 2388851596.00024.mismatch 2388851596.00085.unmapped 2388851596.00074.mismatch 2388851596.00043.1.fastq 2388851596.00087.unmapped 2388851596.00045.map 2388851596.00089.map 2388851596.00000.1.bfq 2388851596.00022.map 2388851596.00021.unmapped 2388851596.00083.1.bfq 2388851596.00033.unmapped 2388851596.00025.1.fastq 2388851596.00046.mismatch 2388851596.00086.map 2388851596.00061.1.bfq 2388851596.00028.map 2388851596.00091.1.bfq 2388851596.00048.1.bfq 2388851596.00007.1.fastq 2388851596.00004.unmapped 2388851596.00033.1.fastq 2388851596.00040.unmapped 2388851596.00054.unmapped 2388851596.00079.map 2388851596.00095.1.fastq 2388851596.00003.map 2388851596.00030.map 2388851596.00056.unmapped 2388851596.00010.1.bfq 2388851596.00073.map 2388851596.00004.1.fastq 2388851596.00006.mismatch 2388851596.00027.map 2388851596.00051.1.bfq 2388851596.00040.1.fastq 2388851596.00069.1.fastq 2388851596.00060.mismatch 2388851596.00070.mismatch 2388851596.00080.mismatch 2388851596.00090.mismatch 2388851596.00037.unmapped 2388851596.00012.1.bfq 2388851596.00084.mismatch 2388851596.00056.1.fastq 2388851596.00048.mismatch 2388851596.00087.map 2388851596.00064.unmapped 2388851596.00034.1.bfq 2388851596.00090.1.bfq 2388851596.00041.unmapped 2388851596.00096.1.fastq 2388851596.00076.unmapped 2388851596.00043.map 2388851596.00078.1.bfq 2388851596.00014.unmapped 2388851596.00088.1.fastq 2388851596.00031.map 2388851596.00013.map 2388851596.00076.mismatch 2388851596.00092.1.bfq 2388851596.00082.1.fastq 2388851596.00064.1.fastq 2388851596.00000.mismatch 2388851596.00069.1.bfq 2388851596.00042.unmapped 2388851596.00039.unmapped 2388851596.00041.1.fastq 2388851596.00074.unmapped 2388851596.00061.mismatch 2388851596.00055.1.fastq 2388851596.00014.1.fastq 2388851596.00081.mismatch 2388851596.00068.map 2388851596.00091.mismatch 2388851596.00094.unmapped 2388851596.00021.1.fastq 2388851596.00017.1.bfq 2388851596.00083.mismatch 2388851596.00008.1.fastq 2388851596.00039.1.fastq 2388851596.00038.mismatch 2388851596.00053.unmapped 2388851596.00059.1.bfq 2388851596.00066.mismatch 2388851596.00094.1.fastq 2388851596.00015.map 2388851596.00093.map 2388851596.00047.1.bfq 2388851596.00029.unmapped 2388851596.00016.mismatch 2388851596.00005.map 2388851596.00077.1.bfq 2388851596.00050.map 2388851596.00053.1.fastq 2388851596.00073.unmapped 2388851596.00066.1.bfq 2388851596.00057.1.fastq 2388851596.00095.unmapped 2388851596.00034.mismatch 2388851596.00036.map 2388851596.00002.map 2388851596.00096.map 2388851596.00049.mismatch 2388851596.00059.mismatch 2388851596.00063.unmapped 2388851596.00088.map 2388851596.00079.mismatch 2388851596.00032.map 2388851596.00005.1.bfq 2388851596.00029.mismatch 2388851596.00023.map 2388851596.00011.mismatch 2388851596.00024.unmapped 2388851596.00033.1.bfq 2388851596.00077.mismatch 2388851596.00089.1.fastq 2388851596.00042.1.fastq 2388851596.00028.1.bfq 2388851596.00019.map 2388851596.00055.map 2388851596.00082.1.bfq 2388851596.00001.1.bfq 2388851596.00026.1.bfq 2388851596.00062.mismatch 2388851596.00049.unmapped 2388851596.00021.map 2388851596.00051.map 2388851596.00072.mismatch 2388851596.00024.1.fastq 2388851596.00017.mismatch 2388851596.00008.map 2388851596.00092.mismatch 2388851596.00046.unmapped 2388851596.00088.mismatch 2388851596.00065.1.bfq 2388851596.00009.1.fastq 2388851596.00084.unmapped 2388851596.00020.mismatch 2388851596.00065.map 2388851596.00049.1.bfq 2388851596.00018.1.bfq 2388851596.00066.unmapped 2388851596.00069.map 2388851596.00046.1.fastq 2388851596.00047.mismatch 2388851596.00020.1.bfq 2388851596.00013.unmapped 2388851596.00035.mismatch 2388851596.00097.1.fastq 2388851596.00057.map 2388851596.00006.unmapped 2388851596.00045.1.bfq 2388851596.00060.unmapped 2388851596.00070.unmapped 2388851596.00080.unmapped 2388851596.00090.unmapped 2388851596.00022.1.bfq 2388851596.00058.1.fastq 2388851596.00009.1.bfq 2388851596.00012.mismatch 2388851596.00032.mismatch 2388851596.00030.unmapped 2388851596.00063.mismatch 2388851596.00079.unmapped 2388851596.00071.mismatch 2388851596.00006.1.fastq 2388851596.00060.1.fastq 2388851596.00070.1.fastq 2388851596.00080.1.fastq 2388851596.00090.1.fastq 2388851596.00067.unmapped 2388851596.00000.unmapped 2388851596.00007.1.bfq 2388851596.00026.mismatch 2388851596.00033.map 2388851596.00078.mismatch 2388851596.00052.map 2388851596.00003.1.bfq 2388851596.00008.1.bfq 2388851596.00073.1.bfq 2388851596.00054.mismatch 2388851596.00075.map 2388851596.00009.map 2388851596.00030.1.fastq 2388851596.00091.unmapped 2388851596.00085.1.fastq 2388851596.00000.1.fastq 2388851596.00018.mismatch 2388851596.00041.map 2388851596.00038.unmapped 2388851596.00067.mismatch 2388851596.00061.1.fastq 2388851596.00035.1.bfq 2388851596.00071.1.fastq 2388851596.00081.1.fastq 2388851596.00091.1.fastq 2388851596.00097.map 2388851596.00083.unmapped 2388851596.00001.unmapped 2388851596.00010.unmapped 2388851596.00048.unmapped 2388851596.00035.unmapped 2388851596.00031.1.bfq 2388851596.00002.1.bfq 2388851596.00038.1.fastq 2388851596.00045.mismatch 2388851596.00058.1.bfq 2388851596.00016.unmapped 2388851596.00098.1.fastq 2388851596.00022.mismatch 2388851596.00044.mismatch 2388851596.00051.unmapped 2388851596.00001.1.fastq 2388851596.00010.1.fastq 2388851596.00095.map 2388851596.00025.map 2388851596.00034.unmapped 2388851596.00052.mismatch 2388851596.00058.map 2388851596.00065.1.fastq 2388851596.00055.1.bfq 2388851596.00016.1.fastq 2388851596.00004.map 2388851596.00059.unmapped 2388851596.00004.1.bfq 2388851596.00040.map 2388851596.00011.unmapped 2388851596.00086.1.bfq 2388851596.00076.1.bfq 2388851596.00071.1.bfq 2388851596.00037.1.fastq 2388851596.00034.1.fastq 2388851596.00003.mismatch 2388851596.00056.map 2388851596.00030.mismatch 2388851596.00040.1.bfq 2388851596.00073.mismatch 2388851596.00027.unmapped 2388851596.00086.mismatch 2388851596.00029.1.fastq 2388851596.00027.mismatch 2388851596.00011.1.fastq 2388851596.00085.map 2388851596.00017.unmapped 2388851596.00093.mismatch 2388851596.00092.unmapped 2388851596.00081.unmapped 2388851596.00010.mismatch 2388851596.00050.1.bfq 2388851596.00074.1.fastq 2388851596.00064.map 2388851596.00061.unmapped 2388851596.00062.1.fastq 2388851596.00097.mismatch 2388851596.00072.1.fastq 2388851596.00013.1.bfq make: Leaving directory `/data/maqgene/work' make: Entering directory `/data/maqgene/work' # Wed Apr 10 23:04:43 BST 2013: Cleaning intermediate data ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 2367457594_snps,2367457594_rel,2367457594_masked_ids,2367457594_rel_intergenic,2367457594_intergenic_assoc,2367457594_offsets,2367457594_codons,2367457594_marked,2367457594_combined,1964021411_pileup" rm -f 2367457594_snps 2367457594_rel 2367457594_masked_ids 2367457594_rel_intergenic 2367457594_intergenic_assoc 2367457594_offsets 2367457594_codons 2367457594_marked 2367457594_combined 1964021411_pileup make: Leaving directory `/data/maqgene/work'