Finished reading input. ++ echo CB6945/./WTCHG_15227_read1.fastq,CB6633/./WTCHG_15226_read1.fastq ++ tr , ' ' + fastq_file_set1='CB6945/./WTCHG_15227_read1.fastq CB6633/./WTCHG_15226_read1.fastq' ++ cd /data/maqgene/reads ++ cat CB6945/./WTCHG_15227_read1.fastq CB6633/./WTCHG_15226_read1.fastq ++ wc -l ++ cut -f 1 -d ' ' + TOTAL_LINES=298503380 ++ echo '(298503380 / 5000000) + (298503380 % 5000000 != 0)' ++ bc + num_chunks=60 + 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=18834703 map_cksum=4214583326 pileup_cksum=1879682750 cns_cksum=3000847188 umdd=50000 dmdd=1000 umid=1000 dmid=1000 max_gene_radius=50000 full_results_dir=/data/maqgene/out/example_user/CB6945 outfile_basename=CB6945 map_parameters=" -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0" assemble_parameters=" -N 2 -q 0 -r 0.0 -m 7 -Q 100 -p " pileup_parameters=" -Q 100 -p -m 7 -q 0" CHUNK_SIZE=5000000 NUM_CHUNKS=60 Will process 298503380 lines of input in 60 chunks make: Entering directory `/data/maqgene/work' # Thu Apr 28 10:50:54 BST 2011: Removing frontend files in case this is a duplicate run ... rm -f /data/maqgene/out/example_user/CB6945/CB6945_{grouped.txt,flat.txt} rm -f /data/maqgene/out/example_user/CB6945/CB6945_uncovered.txt /data/maqgene/out/example_user/CB6945/CB6945_coverage.txt /data/maqgene/out/example_user/CB6945/CB6945_pileup.txt /data/maqgene/out/example_user/CB6945/CB6945_log.txt /data/maqgene/out/example_user/CB6945/CB6945_check.txt /data/maqgene/out/example_user/CB6945/CB6945_unmapped.txt make: Leaving directory `/data/maqgene/work' make: Entering directory `/data/maqgene/work' /data/maqgene/makefile:76: warning: undefined variable `date' /data/maqgene/makefile:78: warning: undefined variable `date' # : Regrouping fastq reads into chunks of size 5000000. split -l 5000000 -a 5 -d <(cat /data/maqgene/reads/CB6945/./WTCHG_15227_read1.fastq /data/maqgene/reads/CB6633/./WTCHG_15226_read1.fastq) 4214583326.1.fastq. # : Regrouping fastq reads into chunks of size 5000000. split -l 5000000 -a 5 -d <(cat /data/maqgene/reads/CB6945/./WTCHG_15227_read2.fastq /data/maqgene/reads/CB6633/./WTCHG_15226_read2.fastq) 4214583326.2.fastq. for stem in 00000 00001 00002 00003 00004 00005 00006 00007 00008 00009 00010 00011 00012 00013 00014 00015 00016 00017 00018 00019 00020 00021 00022 00023 00024 00025 00026 00027 00028 00029 00030 00031 00032 00033 00034 00035 00036 00037 00038 00039 00040 00041 00042 00043 00044 00045 00046 00047 00048 00049 00050 00051 00052 00053 00054 00055 00056 00057 00058 00059; do mv 4214583326.1.fastq.$stem 4214583326.$stem.1.fastq; done touch 18834703_split1 for stem in 00000 00001 00002 00003 00004 00005 00006 00007 00008 00009 00010 00011 00012 00013 00014 00015 00016 00017 00018 00019 00020 00021 00022 00023 00024 00025 00026 00027 00028 00029 00030 00031 00032 00033 00034 00035 00036 00037 00038 00039 00040 00041 00042 00043 00044 00045 00046 00047 00048 00049 00050 00051 00052 00053 00054 00055 00056 00057 00058 00059; do mv 4214583326.2.fastq.$stem 4214583326.$stem.2.fastq; done touch 18834703_split2 # Thu Apr 28 10:53:16 BST 2011: Converting fastq files to bfq ... # Thu Apr 28 10:53:16 BST 2011: Converting fastq files to bfq ... # Thu Apr 28 10:53:16 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 4214583326.00008.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00008.1.bfq # Thu Apr 28 10:53:16 BST 2011: Converting fastq files to bfq ... # Thu Apr 28 10:53:16 BST 2011: Converting fastq files to bfq ... # Thu Apr 28 10:53:16 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 4214583326.00005.1.fastq /dev/stdout | \ # Thu Apr 28 10:53:16 BST 2011: Converting fastq files to bfq ... # Thu Apr 28 10:53:16 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 4214583326.00006.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00006.1.bfq # Thu Apr 28 10:53:16 BST 2011: Converting fastq files to bfq ... # Thu Apr 28 10:53:16 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 4214583326.00000.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00000.1.bfq /data/maqgene/bin/maq sol2sanger 4214583326.00001.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00001.1.bfq # Thu Apr 28 10:53:16 BST 2011: Converting fastq files to bfq ... # Thu Apr 28 10:53:16 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 4214583326.00003.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00003.1.bfq # Thu Apr 28 10:53:16 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 4214583326.00002.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00002.1.bfq /data/maqgene/bin/maq sol2sanger 4214583326.00004.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00004.1.bfq /data/maqgene/bin/maq sol2sanger 4214583326.00007.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00007.1.bfq /data/maqgene/bin/maq sol2sanger 4214583326.00009.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00009.1.bfq /data/maqgene/bin/maq sol2sanger 4214583326.00010.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00010.1.bfq /data/maqgene/bin/maq sol2sanger 4214583326.00011.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00011.1.bfq /data/maqgene/bin/maq sol2sanger 4214583326.00012.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00012.1.bfq /data/maqgene/bin/maq sol2sanger 4214583326.00013.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00013.1.bfq -- finish writing file '4214583326.00008.1.bfq' -- 1250000 sequences were loaded. # Thu Apr 28 10:53:33 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 4214583326.00014.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00014.1.bfq -- finish writing file '4214583326.00009.1.bfq' -- 1250000 sequences were loaded. # Thu Apr 28 10:53:33 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 4214583326.00015.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00015.1.bfq -- finish writing file '4214583326.00003.1.bfq' -- 1250000 sequences were loaded. # Thu Apr 28 10:53:43 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 4214583326.00016.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00016.1.bfq -- finish writing file '4214583326.00012.1.bfq' -- 1250000 sequences were loaded. # Thu Apr 28 10:53:46 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 4214583326.00017.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00017.1.bfq -- finish writing file '4214583326.00000.1.bfq' -- 1250000 sequences were loaded. # Thu Apr 28 10:53:46 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 4214583326.00018.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00018.1.bfq -- finish writing file '4214583326.00004.1.bfq' -- 1250000 sequences were loaded. # Thu Apr 28 10:53:46 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 4214583326.00019.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00019.1.bfq -- finish writing file '4214583326.00006.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '4214583326.00002.1.bfq' -- 1250000 sequences were loaded. # Thu Apr 28 10:53:47 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 4214583326.00020.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00020.1.bfq # Thu Apr 28 10:53:47 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 4214583326.00021.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00021.1.bfq -- finish writing file '4214583326.00005.1.bfq' -- 1250000 sequences were loaded. # Thu Apr 28 10:53:47 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 4214583326.00022.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00022.1.bfq -- finish writing file '4214583326.00001.1.bfq' -- 1250000 sequences were loaded. # Thu Apr 28 10:53:47 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 4214583326.00023.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00023.1.bfq -- finish writing file '4214583326.00007.1.bfq' -- 1250000 sequences were loaded. # Thu Apr 28 10:53:47 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 4214583326.00024.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00024.1.bfq -- finish writing file '4214583326.00011.1.bfq' -- 1250000 sequences were loaded. # Thu Apr 28 10:53:48 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 4214583326.00025.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00025.1.bfq -- finish writing file '4214583326.00013.1.bfq' -- 1250000 sequences were loaded. # Thu Apr 28 10:53:48 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 4214583326.00026.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00026.1.bfq -- finish writing file '4214583326.00010.1.bfq' -- 1250000 sequences were loaded. # Thu Apr 28 10:53:52 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 4214583326.00027.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00027.1.bfq -- finish writing file '4214583326.00015.1.bfq' -- 1250000 sequences were loaded. # Thu Apr 28 10:54:02 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 4214583326.00028.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00028.1.bfq -- finish writing file '4214583326.00014.1.bfq' -- 1250000 sequences were loaded. # Thu Apr 28 10:54:02 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 4214583326.00029.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00029.1.bfq -- finish writing file '4214583326.00026.1.bfq' -- 1250000 sequences were loaded. # Thu Apr 28 10:54:12 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 4214583326.00030.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00030.1.bfq -- finish writing file '4214583326.00023.1.bfq' -- 1250000 sequences were loaded. # Thu Apr 28 10:54:13 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 4214583326.00031.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00031.1.bfq -- finish writing file '4214583326.00024.1.bfq' -- 1250000 sequences were loaded. # Thu Apr 28 10:54:13 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 4214583326.00032.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00032.1.bfq -- finish writing file '4214583326.00016.1.bfq' -- 1250000 sequences were loaded. # Thu Apr 28 10:54:14 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 4214583326.00033.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00033.1.bfq -- finish writing file '4214583326.00017.1.bfq' -- 1250000 sequences were loaded. # Thu Apr 28 10:54:15 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 4214583326.00034.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00034.1.bfq -- finish writing file '4214583326.00020.1.bfq' -- 1250000 sequences were loaded. # Thu Apr 28 10:54:16 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 4214583326.00035.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00035.1.bfq -- finish writing file '4214583326.00018.1.bfq' -- 1250000 sequences were loaded. # Thu Apr 28 10:54:16 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 4214583326.00036.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00036.1.bfq -- finish writing file '4214583326.00019.1.bfq' -- 1250000 sequences were loaded. # Thu Apr 28 10:54:16 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 4214583326.00037.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00037.1.bfq -- finish writing file '4214583326.00021.1.bfq' -- 1250000 sequences were loaded. # Thu Apr 28 10:54:17 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 4214583326.00038.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00038.1.bfq -- finish writing file '4214583326.00022.1.bfq' -- 1250000 sequences were loaded. # Thu Apr 28 10:54:17 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 4214583326.00039.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00039.1.bfq -- finish writing file '4214583326.00025.1.bfq' -- 1250000 sequences were loaded. # Thu Apr 28 10:54:18 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 4214583326.00040.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00040.1.bfq -- finish writing file '4214583326.00027.1.bfq' -- 1250000 sequences were loaded. # Thu Apr 28 10:54:22 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 4214583326.00041.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00041.1.bfq -- finish writing file '4214583326.00029.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '4214583326.00028.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '4214583326.00030.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '4214583326.00034.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '4214583326.00032.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '4214583326.00031.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '4214583326.00036.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '4214583326.00033.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '4214583326.00037.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '4214583326.00035.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '4214583326.00038.1.bfq' -- 1250000 sequences were loaded. # Thu Apr 28 10:54:43 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 4214583326.00050.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00050.1.bfq # Thu Apr 28 10:54:43 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 4214583326.00051.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00051.1.bfq -- finish writing file '4214583326.00039.1.bfq' -- 1250000 sequences were loaded. # Thu Apr 28 10:54:43 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 4214583326.00052.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00052.1.bfq -- finish writing file '4214583326.00040.1.bfq' -- 1250000 sequences were loaded. # Thu Apr 28 10:54:43 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 4214583326.00053.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00053.1.bfq # Thu Apr 28 10:54:44 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 4214583326.00054.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00054.1.bfq # Thu Apr 28 10:54:45 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 4214583326.00049.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00049.1.bfq # Thu Apr 28 10:54:46 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 4214583326.00048.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00048.1.bfq -- finish writing file '4214583326.00041.1.bfq' -- 1250000 sequences were loaded. # Thu Apr 28 10:54:47 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 4214583326.00047.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00047.1.bfq # Thu Apr 28 10:54:47 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 4214583326.00046.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00046.1.bfq # Thu Apr 28 10:54:48 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 4214583326.00055.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00055.1.bfq # Thu Apr 28 10:54:49 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 4214583326.00045.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00045.1.bfq # Thu Apr 28 10:54:49 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 4214583326.00044.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00044.1.bfq # Thu Apr 28 10:54:50 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 4214583326.00043.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00043.1.bfq # Thu Apr 28 10:54:51 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 4214583326.00042.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00042.1.bfq -- finish writing file '4214583326.00053.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '4214583326.00054.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '4214583326.00050.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '4214583326.00052.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '4214583326.00051.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '4214583326.00048.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '4214583326.00049.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '4214583326.00047.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '4214583326.00055.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '4214583326.00046.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '4214583326.00045.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '4214583326.00044.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '4214583326.00043.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '4214583326.00042.1.bfq' -- 1250000 sequences were loaded. # Thu Apr 28 10:55:16 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 4214583326.00008.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00008.2.bfq # Thu Apr 28 10:55:19 BST 2011: Converting fastq files to bfq ... # Thu Apr 28 10:55:19 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 4214583326.00009.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00009.2.bfq /data/maqgene/bin/maq sol2sanger 4214583326.00007.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00007.2.bfq # Thu Apr 28 10:55:20 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 4214583326.00006.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00006.2.bfq # Thu Apr 28 10:55:21 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 4214583326.00005.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00005.2.bfq # Thu Apr 28 10:55:21 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 4214583326.00004.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00004.2.bfq # Thu Apr 28 10:55:22 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 4214583326.00003.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00003.2.bfq # Thu Apr 28 10:55:23 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 4214583326.00002.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00002.2.bfq # Thu Apr 28 10:55:23 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 4214583326.00001.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00001.2.bfq # Thu Apr 28 10:55:24 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 4214583326.00000.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00000.2.bfq # Thu Apr 28 10:55:24 BST 2011: Converting fastq files to bfq ... # Thu Apr 28 10:55:24 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 4214583326.00059.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00059.1.bfq /data/maqgene/bin/maq sol2sanger 4214583326.00058.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00058.1.bfq # Thu Apr 28 10:55:25 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 4214583326.00056.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00056.1.bfq # Thu Apr 28 10:55:25 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 4214583326.00057.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00057.1.bfq -- finish writing file '4214583326.00008.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '4214583326.00003.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '4214583326.00009.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '4214583326.00005.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '4214583326.00007.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '4214583326.00059.1.bfq' -- 875845 sequences were loaded. -- finish writing file '4214583326.00002.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '4214583326.00006.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '4214583326.00004.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '4214583326.00001.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '4214583326.00058.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '4214583326.00057.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '4214583326.00000.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '4214583326.00056.1.bfq' -- 1250000 sequences were loaded. # Thu Apr 28 10:55:50 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 4214583326.00022.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00022.2.bfq # Thu Apr 28 10:55:53 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 4214583326.00023.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00023.2.bfq # Thu Apr 28 10:55:53 BST 2011: Converting fastq files to bfq ... # Thu Apr 28 10:55:53 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 4214583326.00020.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00020.2.bfq # Thu Apr 28 10:55:53 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 4214583326.00021.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00021.2.bfq /data/maqgene/bin/maq sol2sanger 4214583326.00019.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00019.2.bfq # Thu Apr 28 10:55:54 BST 2011: Converting fastq files to bfq ... # Thu Apr 28 10:55:54 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 4214583326.00017.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00017.2.bfq # Thu Apr 28 10:55:54 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 4214583326.00018.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00018.2.bfq /data/maqgene/bin/maq sol2sanger 4214583326.00016.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00016.2.bfq # Thu Apr 28 10:55:55 BST 2011: Converting fastq files to bfq ... # Thu Apr 28 10:55:55 BST 2011: Converting fastq files to bfq ... # Thu Apr 28 10:55:55 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 4214583326.00015.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00015.2.bfq /data/maqgene/bin/maq sol2sanger 4214583326.00014.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00014.2.bfq /data/maqgene/bin/maq sol2sanger 4214583326.00013.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00013.2.bfq # Thu Apr 28 10:55:56 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 4214583326.00011.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00011.2.bfq # Thu Apr 28 10:55:56 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 4214583326.00010.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00010.2.bfq # Thu Apr 28 10:55:56 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 4214583326.00012.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00012.2.bfq -- finish writing file '4214583326.00020.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '4214583326.00022.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '4214583326.00018.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '4214583326.00015.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '4214583326.00019.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '4214583326.00012.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '4214583326.00023.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '4214583326.00021.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '4214583326.00013.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '4214583326.00017.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '4214583326.00016.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '4214583326.00014.2.bfq' -- 1250000 sequences were loaded. # Thu Apr 28 10:56:23 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 4214583326.00034.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00034.2.bfq # Thu Apr 28 10:56:23 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 4214583326.00033.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00033.2.bfq -- finish writing file '4214583326.00011.2.bfq' -- 1250000 sequences were loaded. # Thu Apr 28 10:56:23 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 4214583326.00035.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00035.2.bfq -- finish writing file '4214583326.00010.2.bfq' -- 1250000 sequences were loaded. # Thu Apr 28 10:56:23 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 4214583326.00036.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00036.2.bfq # Thu Apr 28 10:56:24 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 4214583326.00037.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00037.2.bfq # Thu Apr 28 10:56:25 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 4214583326.00032.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00032.2.bfq # Thu Apr 28 10:56:26 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 4214583326.00031.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00031.2.bfq # Thu Apr 28 10:56:27 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 4214583326.00030.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00030.2.bfq # Thu Apr 28 10:56:28 BST 2011: Converting fastq files to bfq ... # Thu Apr 28 10:56:28 BST 2011: Converting fastq files to bfq ... # Thu Apr 28 10:56:28 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 4214583326.00027.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00027.2.bfq /data/maqgene/bin/maq sol2sanger 4214583326.00029.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00029.2.bfq /data/maqgene/bin/maq sol2sanger 4214583326.00028.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00028.2.bfq # Thu Apr 28 10:56:29 BST 2011: Converting fastq files to bfq ... # Thu Apr 28 10:56:29 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 4214583326.00026.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00026.2.bfq /data/maqgene/bin/maq sol2sanger 4214583326.00025.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00025.2.bfq # Thu Apr 28 10:56:29 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 4214583326.00024.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00024.2.bfq -- finish writing file '4214583326.00033.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '4214583326.00031.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '4214583326.00034.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '4214583326.00035.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '4214583326.00036.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '4214583326.00032.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '4214583326.00027.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '4214583326.00037.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '4214583326.00028.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '4214583326.00026.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '4214583326.00025.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '4214583326.00030.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '4214583326.00029.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '4214583326.00024.2.bfq' -- 1250000 sequences were loaded. # Thu Apr 28 10:56:55 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 4214583326.00050.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00050.2.bfq # Thu Apr 28 10:56:58 BST 2011: Converting fastq files to bfq ... # Thu Apr 28 10:56:58 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 4214583326.00049.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00049.2.bfq /data/maqgene/bin/maq sol2sanger 4214583326.00051.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00051.2.bfq /data/maqgene/bin/maq sol2sanger 4214583326.00048.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00048.2.bfq # Thu Apr 28 10:56:58 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 4214583326.00047.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00047.2.bfq # Thu Apr 28 10:56:59 BST 2011: Converting fastq files to bfq ... # Thu Apr 28 10:56:59 BST 2011: Converting fastq files to bfq ... # Thu Apr 28 10:56:59 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 4214583326.00045.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00045.2.bfq /data/maqgene/bin/maq sol2sanger 4214583326.00044.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00044.2.bfq /data/maqgene/bin/maq sol2sanger 4214583326.00046.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00046.2.bfq # Thu Apr 28 10:57:00 BST 2011: Converting fastq files to bfq ... # Thu Apr 28 10:57:00 BST 2011: Converting fastq files to bfq ... # Thu Apr 28 10:57:00 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 4214583326.00041.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00041.2.bfq /data/maqgene/bin/maq sol2sanger 4214583326.00043.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00043.2.bfq /data/maqgene/bin/maq sol2sanger 4214583326.00042.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00042.2.bfq # Thu Apr 28 10:57:01 BST 2011: Converting fastq files to bfq ... # Thu Apr 28 10:57:01 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 4214583326.00040.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00040.2.bfq /data/maqgene/bin/maq sol2sanger 4214583326.00039.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00039.2.bfq /data/maqgene/bin/maq sol2sanger 4214583326.00038.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00038.2.bfq -- finish writing file '4214583326.00049.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '4214583326.00050.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '4214583326.00051.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '4214583326.00039.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '4214583326.00048.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '4214583326.00040.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '4214583326.00046.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '4214583326.00045.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '4214583326.00047.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '4214583326.00043.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '4214583326.00044.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '4214583326.00041.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '4214583326.00042.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '4214583326.00038.2.bfq' -- 1250000 sequences were loaded. # Thu Apr 28 10:57:28 BST 2011: Mapping file(s) 4214583326.00003.1.bfq 4214583326.00003.2.bfq # Thu Apr 28 10:57:28 BST 2011: Mapping file(s) 4214583326.00004.1.bfq 4214583326.00004.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 4214583326.00004.unmapped -H 4214583326.00004.mismatch \ 4214583326.00004.map /data/maqgene/genomes/elegans.bfa 4214583326.00004.1.bfq 4214583326.00004.2.bfq 2> /dev/null /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 4214583326.00003.unmapped -H 4214583326.00003.mismatch \ 4214583326.00003.map /data/maqgene/genomes/elegans.bfa 4214583326.00003.1.bfq 4214583326.00003.2.bfq 2> /dev/null # Thu Apr 28 10:57:29 BST 2011: Mapping file(s) 4214583326.00005.1.bfq 4214583326.00005.2.bfq # Thu Apr 28 10:57:29 BST 2011: Mapping file(s) 4214583326.00002.1.bfq 4214583326.00002.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 4214583326.00005.unmapped -H 4214583326.00005.mismatch \ 4214583326.00005.map /data/maqgene/genomes/elegans.bfa 4214583326.00005.1.bfq 4214583326.00005.2.bfq 2> /dev/null /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 4214583326.00002.unmapped -H 4214583326.00002.mismatch \ 4214583326.00002.map /data/maqgene/genomes/elegans.bfa 4214583326.00002.1.bfq 4214583326.00002.2.bfq 2> /dev/null # Thu Apr 28 10:57:30 BST 2011: Mapping file(s) 4214583326.00001.1.bfq 4214583326.00001.2.bfq # Thu Apr 28 10:57:30 BST 2011: Mapping file(s) 4214583326.00000.1.bfq 4214583326.00000.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 4214583326.00001.unmapped -H 4214583326.00001.mismatch \ 4214583326.00001.map /data/maqgene/genomes/elegans.bfa 4214583326.00001.1.bfq 4214583326.00001.2.bfq 2> /dev/null /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 4214583326.00000.unmapped -H 4214583326.00000.mismatch \ 4214583326.00000.map /data/maqgene/genomes/elegans.bfa 4214583326.00000.1.bfq 4214583326.00000.2.bfq 2> /dev/null # Thu Apr 28 10:57:31 BST 2011: Converting fastq files to bfq ... # Thu Apr 28 10:57:31 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 4214583326.00059.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00059.2.bfq /data/maqgene/bin/maq sol2sanger 4214583326.00058.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00058.2.bfq # Thu Apr 28 10:57:32 BST 2011: Converting fastq files to bfq ... # Thu Apr 28 10:57:32 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 4214583326.00057.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00057.2.bfq /data/maqgene/bin/maq sol2sanger 4214583326.00056.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00056.2.bfq # Thu Apr 28 10:57:33 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 4214583326.00055.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00055.2.bfq # Thu Apr 28 10:57:33 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 4214583326.00054.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00054.2.bfq # Thu Apr 28 10:57:34 BST 2011: Converting fastq files to bfq ... # Thu Apr 28 10:57:34 BST 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 4214583326.00053.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00053.2.bfq /data/maqgene/bin/maq sol2sanger 4214583326.00052.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 4214583326.00052.2.bfq -- finish writing file '4214583326.00059.2.bfq' -- 875845 sequences were loaded. -- finish writing file '4214583326.00053.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '4214583326.00052.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '4214583326.00058.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '4214583326.00057.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '4214583326.00055.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '4214583326.00056.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '4214583326.00054.2.bfq' -- 1250000 sequences were loaded. # Thu Apr 28 10:58:04 BST 2011: Mapping file(s) 4214583326.00013.1.bfq 4214583326.00013.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 4214583326.00013.unmapped -H 4214583326.00013.mismatch \ 4214583326.00013.map /data/maqgene/genomes/elegans.bfa 4214583326.00013.1.bfq 4214583326.00013.2.bfq 2> /dev/null # Thu Apr 28 10:58:05 BST 2011: Mapping file(s) 4214583326.00012.1.bfq 4214583326.00012.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 4214583326.00012.unmapped -H 4214583326.00012.mismatch \ 4214583326.00012.map /data/maqgene/genomes/elegans.bfa 4214583326.00012.1.bfq 4214583326.00012.2.bfq 2> /dev/null # Thu Apr 28 10:58:06 BST 2011: Mapping file(s) 4214583326.00011.1.bfq 4214583326.00011.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 4214583326.00011.unmapped -H 4214583326.00011.mismatch \ 4214583326.00011.map /data/maqgene/genomes/elegans.bfa 4214583326.00011.1.bfq 4214583326.00011.2.bfq 2> /dev/null # Thu Apr 28 10:58:07 BST 2011: Mapping file(s) 4214583326.00010.1.bfq 4214583326.00010.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 4214583326.00010.unmapped -H 4214583326.00010.mismatch \ 4214583326.00010.map /data/maqgene/genomes/elegans.bfa 4214583326.00010.1.bfq 4214583326.00010.2.bfq 2> /dev/null # Thu Apr 28 10:58:08 BST 2011: Mapping file(s) 4214583326.00009.1.bfq 4214583326.00009.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 4214583326.00009.unmapped -H 4214583326.00009.mismatch \ 4214583326.00009.map /data/maqgene/genomes/elegans.bfa 4214583326.00009.1.bfq 4214583326.00009.2.bfq 2> /dev/null # Thu Apr 28 10:58:09 BST 2011: Mapping file(s) 4214583326.00008.1.bfq 4214583326.00008.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 4214583326.00008.unmapped -H 4214583326.00008.mismatch \ 4214583326.00008.map /data/maqgene/genomes/elegans.bfa 4214583326.00008.1.bfq 4214583326.00008.2.bfq 2> /dev/null # Thu Apr 28 10:58:10 BST 2011: Mapping file(s) 4214583326.00007.1.bfq 4214583326.00007.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 4214583326.00007.unmapped -H 4214583326.00007.mismatch \ 4214583326.00007.map /data/maqgene/genomes/elegans.bfa 4214583326.00007.1.bfq 4214583326.00007.2.bfq 2> /dev/null # Thu Apr 28 10:58:11 BST 2011: Mapping file(s) 4214583326.00006.1.bfq 4214583326.00006.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 4214583326.00006.unmapped -H 4214583326.00006.mismatch \ 4214583326.00006.map /data/maqgene/genomes/elegans.bfa 4214583326.00006.1.bfq 4214583326.00006.2.bfq 2> /dev/null # Thu Apr 28 11:04:29 BST 2011: Mapping file(s) 4214583326.00017.1.bfq 4214583326.00017.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 4214583326.00017.unmapped -H 4214583326.00017.mismatch \ 4214583326.00017.map /data/maqgene/genomes/elegans.bfa 4214583326.00017.1.bfq 4214583326.00017.2.bfq 2> /dev/null # Thu Apr 28 11:04:30 BST 2011: Mapping file(s) 4214583326.00016.1.bfq 4214583326.00016.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 4214583326.00016.unmapped -H 4214583326.00016.mismatch \ 4214583326.00016.map /data/maqgene/genomes/elegans.bfa 4214583326.00016.1.bfq 4214583326.00016.2.bfq 2> /dev/null # Thu Apr 28 11:04:30 BST 2011: Mapping file(s) 4214583326.00018.1.bfq 4214583326.00018.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 4214583326.00018.unmapped -H 4214583326.00018.mismatch \ 4214583326.00018.map /data/maqgene/genomes/elegans.bfa 4214583326.00018.1.bfq 4214583326.00018.2.bfq 2> /dev/null # Thu Apr 28 11:04:31 BST 2011: Mapping file(s) 4214583326.00019.1.bfq 4214583326.00019.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 4214583326.00019.unmapped -H 4214583326.00019.mismatch \ 4214583326.00019.map /data/maqgene/genomes/elegans.bfa 4214583326.00019.1.bfq 4214583326.00019.2.bfq 2> /dev/null # Thu Apr 28 11:04:32 BST 2011: Mapping file(s) 4214583326.00015.1.bfq 4214583326.00015.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 4214583326.00015.unmapped -H 4214583326.00015.mismatch \ 4214583326.00015.map /data/maqgene/genomes/elegans.bfa 4214583326.00015.1.bfq 4214583326.00015.2.bfq 2> /dev/null # Thu Apr 28 11:04:33 BST 2011: Mapping file(s) 4214583326.00014.1.bfq 4214583326.00014.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 4214583326.00014.unmapped -H 4214583326.00014.mismatch \ 4214583326.00014.map /data/maqgene/genomes/elegans.bfa 4214583326.00014.1.bfq 4214583326.00014.2.bfq 2> /dev/null # Thu Apr 28 11:04:34 BST 2011: Mapping file(s) 4214583326.00020.1.bfq 4214583326.00020.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 4214583326.00020.unmapped -H 4214583326.00020.mismatch \ 4214583326.00020.map /data/maqgene/genomes/elegans.bfa 4214583326.00020.1.bfq 4214583326.00020.2.bfq 2> /dev/null # Thu Apr 28 11:04:35 BST 2011: Mapping file(s) 4214583326.00021.1.bfq 4214583326.00021.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 4214583326.00021.unmapped -H 4214583326.00021.mismatch \ 4214583326.00021.map /data/maqgene/genomes/elegans.bfa 4214583326.00021.1.bfq 4214583326.00021.2.bfq 2> /dev/null # Thu Apr 28 11:04:38 BST 2011: Mapping file(s) 4214583326.00022.1.bfq 4214583326.00022.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 4214583326.00022.unmapped -H 4214583326.00022.mismatch \ 4214583326.00022.map /data/maqgene/genomes/elegans.bfa 4214583326.00022.1.bfq 4214583326.00022.2.bfq 2> /dev/null # Thu Apr 28 11:04:44 BST 2011: Mapping file(s) 4214583326.00024.1.bfq 4214583326.00024.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 4214583326.00024.unmapped -H 4214583326.00024.mismatch \ 4214583326.00024.map /data/maqgene/genomes/elegans.bfa 4214583326.00024.1.bfq 4214583326.00024.2.bfq 2> /dev/null # Thu Apr 28 11:04:45 BST 2011: Mapping file(s) 4214583326.00023.1.bfq 4214583326.00023.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 4214583326.00023.unmapped -H 4214583326.00023.mismatch \ 4214583326.00023.map /data/maqgene/genomes/elegans.bfa 4214583326.00023.1.bfq 4214583326.00023.2.bfq 2> /dev/null # Thu Apr 28 11:04:46 BST 2011: Mapping file(s) 4214583326.00025.1.bfq 4214583326.00025.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 4214583326.00025.unmapped -H 4214583326.00025.mismatch \ 4214583326.00025.map /data/maqgene/genomes/elegans.bfa 4214583326.00025.1.bfq 4214583326.00025.2.bfq 2> /dev/null # Thu Apr 28 11:04:54 BST 2011: Mapping file(s) 4214583326.00027.1.bfq 4214583326.00027.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 4214583326.00027.unmapped -H 4214583326.00027.mismatch \ 4214583326.00027.map /data/maqgene/genomes/elegans.bfa 4214583326.00027.1.bfq 4214583326.00027.2.bfq 2> /dev/null # Thu Apr 28 11:04:55 BST 2011: Mapping file(s) 4214583326.00026.1.bfq 4214583326.00026.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 4214583326.00026.unmapped -H 4214583326.00026.mismatch \ 4214583326.00026.map /data/maqgene/genomes/elegans.bfa 4214583326.00026.1.bfq 4214583326.00026.2.bfq 2> /dev/null # Thu Apr 28 11:10:55 BST 2011: Mapping file(s) 4214583326.00033.1.bfq 4214583326.00033.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 4214583326.00033.unmapped -H 4214583326.00033.mismatch \ 4214583326.00033.map /data/maqgene/genomes/elegans.bfa 4214583326.00033.1.bfq 4214583326.00033.2.bfq 2> /dev/null # Thu Apr 28 11:10:56 BST 2011: Mapping file(s) 4214583326.00032.1.bfq 4214583326.00032.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 4214583326.00032.unmapped -H 4214583326.00032.mismatch \ 4214583326.00032.map /data/maqgene/genomes/elegans.bfa 4214583326.00032.1.bfq 4214583326.00032.2.bfq 2> /dev/null # Thu Apr 28 11:10:57 BST 2011: Mapping file(s) 4214583326.00034.1.bfq 4214583326.00034.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 4214583326.00034.unmapped -H 4214583326.00034.mismatch \ 4214583326.00034.map /data/maqgene/genomes/elegans.bfa 4214583326.00034.1.bfq 4214583326.00034.2.bfq 2> /dev/null # Thu Apr 28 11:10:58 BST 2011: Mapping file(s) 4214583326.00031.1.bfq 4214583326.00031.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 4214583326.00031.unmapped -H 4214583326.00031.mismatch \ 4214583326.00031.map /data/maqgene/genomes/elegans.bfa 4214583326.00031.1.bfq 4214583326.00031.2.bfq 2> /dev/null # Thu Apr 28 11:10:58 BST 2011: Mapping file(s) 4214583326.00030.1.bfq 4214583326.00030.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 4214583326.00030.unmapped -H 4214583326.00030.mismatch \ 4214583326.00030.map /data/maqgene/genomes/elegans.bfa 4214583326.00030.1.bfq 4214583326.00030.2.bfq 2> /dev/null # Thu Apr 28 11:10:59 BST 2011: Mapping file(s) 4214583326.00035.1.bfq 4214583326.00035.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 4214583326.00035.unmapped -H 4214583326.00035.mismatch \ 4214583326.00035.map /data/maqgene/genomes/elegans.bfa 4214583326.00035.1.bfq 4214583326.00035.2.bfq 2> /dev/null # Thu Apr 28 11:11:00 BST 2011: Mapping file(s) 4214583326.00029.1.bfq 4214583326.00029.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 4214583326.00029.unmapped -H 4214583326.00029.mismatch \ 4214583326.00029.map /data/maqgene/genomes/elegans.bfa 4214583326.00029.1.bfq 4214583326.00029.2.bfq 2> /dev/null # Thu Apr 28 11:11:01 BST 2011: Mapping file(s) 4214583326.00028.1.bfq 4214583326.00028.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 4214583326.00028.unmapped -H 4214583326.00028.mismatch \ 4214583326.00028.map /data/maqgene/genomes/elegans.bfa 4214583326.00028.1.bfq 4214583326.00028.2.bfq 2> /dev/null # Thu Apr 28 11:11:02 BST 2011: Mapping file(s) 4214583326.00036.1.bfq 4214583326.00036.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 4214583326.00036.unmapped -H 4214583326.00036.mismatch \ 4214583326.00036.map /data/maqgene/genomes/elegans.bfa 4214583326.00036.1.bfq 4214583326.00036.2.bfq 2> /dev/null # Thu Apr 28 11:11:07 BST 2011: Mapping file(s) 4214583326.00037.1.bfq 4214583326.00037.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 4214583326.00037.unmapped -H 4214583326.00037.mismatch \ 4214583326.00037.map /data/maqgene/genomes/elegans.bfa 4214583326.00037.1.bfq 4214583326.00037.2.bfq 2> /dev/null # Thu Apr 28 11:11:40 BST 2011: Mapping file(s) 4214583326.00039.1.bfq 4214583326.00039.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 4214583326.00039.unmapped -H 4214583326.00039.mismatch \ 4214583326.00039.map /data/maqgene/genomes/elegans.bfa 4214583326.00039.1.bfq 4214583326.00039.2.bfq 2> /dev/null # Thu Apr 28 11:11:41 BST 2011: Mapping file(s) 4214583326.00038.1.bfq 4214583326.00038.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 4214583326.00038.unmapped -H 4214583326.00038.mismatch \ 4214583326.00038.map /data/maqgene/genomes/elegans.bfa 4214583326.00038.1.bfq 4214583326.00038.2.bfq 2> /dev/null # Thu Apr 28 11:12:10 BST 2011: Mapping file(s) 4214583326.00040.1.bfq 4214583326.00040.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 4214583326.00040.unmapped -H 4214583326.00040.mismatch \ 4214583326.00040.map /data/maqgene/genomes/elegans.bfa 4214583326.00040.1.bfq 4214583326.00040.2.bfq 2> /dev/null # Thu Apr 28 11:13:25 BST 2011: Mapping file(s) 4214583326.00041.1.bfq 4214583326.00041.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 4214583326.00041.unmapped -H 4214583326.00041.mismatch \ 4214583326.00041.map /data/maqgene/genomes/elegans.bfa 4214583326.00041.1.bfq 4214583326.00041.2.bfq 2> /dev/null # Thu Apr 28 11:17:31 BST 2011: Mapping file(s) 4214583326.00050.1.bfq 4214583326.00050.2.bfq # Thu Apr 28 11:17:31 BST 2011: Mapping file(s) 4214583326.00049.1.bfq 4214583326.00049.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 4214583326.00050.unmapped -H 4214583326.00050.mismatch \ 4214583326.00050.map /data/maqgene/genomes/elegans.bfa 4214583326.00050.1.bfq 4214583326.00050.2.bfq 2> /dev/null /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 4214583326.00049.unmapped -H 4214583326.00049.mismatch \ 4214583326.00049.map /data/maqgene/genomes/elegans.bfa 4214583326.00049.1.bfq 4214583326.00049.2.bfq 2> /dev/null /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 4214583326.00048.unmapped -H 4214583326.00048.mismatch \ 4214583326.00048.map /data/maqgene/genomes/elegans.bfa 4214583326.00048.1.bfq 4214583326.00048.2.bfq 2> /dev/null # Thu Apr 28 11:17:32 BST 2011: Mapping file(s) 4214583326.00046.1.bfq 4214583326.00046.2.bfq # Thu Apr 28 11:17:32 BST 2011: Mapping file(s) 4214583326.00047.1.bfq 4214583326.00047.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 4214583326.00046.unmapped -H 4214583326.00046.mismatch \ 4214583326.00046.map /data/maqgene/genomes/elegans.bfa 4214583326.00046.1.bfq 4214583326.00046.2.bfq 2> /dev/null /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 4214583326.00047.unmapped -H 4214583326.00047.mismatch \ 4214583326.00047.map /data/maqgene/genomes/elegans.bfa 4214583326.00047.1.bfq 4214583326.00047.2.bfq 2> /dev/null # Thu Apr 28 11:17:33 BST 2011: Mapping file(s) 4214583326.00045.1.bfq 4214583326.00045.2.bfq # Thu Apr 28 11:17:33 BST 2011: Mapping file(s) 4214583326.00044.1.bfq 4214583326.00044.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 4214583326.00045.unmapped -H 4214583326.00045.mismatch \ 4214583326.00045.map /data/maqgene/genomes/elegans.bfa 4214583326.00045.1.bfq 4214583326.00045.2.bfq 2> /dev/null /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 4214583326.00044.unmapped -H 4214583326.00044.mismatch \ 4214583326.00044.map /data/maqgene/genomes/elegans.bfa 4214583326.00044.1.bfq 4214583326.00044.2.bfq 2> /dev/null # Thu Apr 28 11:17:34 BST 2011: Mapping file(s) 4214583326.00043.1.bfq 4214583326.00043.2.bfq # Thu Apr 28 11:17:34 BST 2011: Mapping file(s) 4214583326.00042.1.bfq 4214583326.00042.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 4214583326.00042.unmapped -H 4214583326.00042.mismatch \ 4214583326.00042.map /data/maqgene/genomes/elegans.bfa 4214583326.00042.1.bfq 4214583326.00042.2.bfq 2> /dev/null /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 4214583326.00043.unmapped -H 4214583326.00043.mismatch \ 4214583326.00043.map /data/maqgene/genomes/elegans.bfa 4214583326.00043.1.bfq 4214583326.00043.2.bfq 2> /dev/null # Thu Apr 28 11:17:49 BST 2011: Mapping file(s) 4214583326.00051.1.bfq 4214583326.00051.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 4214583326.00051.unmapped -H 4214583326.00051.mismatch \ 4214583326.00051.map /data/maqgene/genomes/elegans.bfa 4214583326.00051.1.bfq 4214583326.00051.2.bfq 2> /dev/null # Thu Apr 28 11:17:57 BST 2011: Mapping file(s) 4214583326.00052.1.bfq 4214583326.00052.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 4214583326.00052.unmapped -H 4214583326.00052.mismatch \ 4214583326.00052.map /data/maqgene/genomes/elegans.bfa 4214583326.00052.1.bfq 4214583326.00052.2.bfq 2> /dev/null # Thu Apr 28 11:19:01 BST 2011: Mapping file(s) 4214583326.00054.1.bfq 4214583326.00054.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 4214583326.00054.unmapped -H 4214583326.00054.mismatch \ 4214583326.00054.map /data/maqgene/genomes/elegans.bfa 4214583326.00054.1.bfq 4214583326.00054.2.bfq 2> /dev/null # Thu Apr 28 11:19:03 BST 2011: Mapping file(s) 4214583326.00053.1.bfq 4214583326.00053.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 4214583326.00053.unmapped -H 4214583326.00053.mismatch \ 4214583326.00053.map /data/maqgene/genomes/elegans.bfa 4214583326.00053.1.bfq 4214583326.00053.2.bfq 2> /dev/null # Thu Apr 28 11:22:26 BST 2011: Mapping file(s) 4214583326.00055.1.bfq 4214583326.00055.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 4214583326.00055.unmapped -H 4214583326.00055.mismatch \ 4214583326.00055.map /data/maqgene/genomes/elegans.bfa 4214583326.00055.1.bfq 4214583326.00055.2.bfq 2> /dev/null # Thu Apr 28 11:23:57 BST 2011: Mapping file(s) 4214583326.00059.1.bfq 4214583326.00059.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 4214583326.00059.unmapped -H 4214583326.00059.mismatch \ 4214583326.00059.map /data/maqgene/genomes/elegans.bfa 4214583326.00059.1.bfq 4214583326.00059.2.bfq 2> /dev/null # Thu Apr 28 11:23:57 BST 2011: Mapping file(s) 4214583326.00058.1.bfq 4214583326.00058.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 4214583326.00058.unmapped -H 4214583326.00058.mismatch \ 4214583326.00058.map /data/maqgene/genomes/elegans.bfa 4214583326.00058.1.bfq 4214583326.00058.2.bfq 2> /dev/null # Thu Apr 28 11:23:59 BST 2011: Mapping file(s) 4214583326.00057.1.bfq 4214583326.00057.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 4214583326.00057.unmapped -H 4214583326.00057.mismatch \ 4214583326.00057.map /data/maqgene/genomes/elegans.bfa 4214583326.00057.1.bfq 4214583326.00057.2.bfq 2> /dev/null # Thu Apr 28 11:24:01 BST 2011: Mapping file(s) 4214583326.00056.1.bfq 4214583326.00056.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 4214583326.00056.unmapped -H 4214583326.00056.mismatch \ 4214583326.00056.map /data/maqgene/genomes/elegans.bfa 4214583326.00056.1.bfq 4214583326.00056.2.bfq 2> /dev/null # Thu Apr 28 11:28:32 BST 2011: Merging all *.unmapped files ... # Thu Apr 28 11:28:32 BST 2011: Merging all maps ... cat 4214583326.00000.unmapped 4214583326.00001.unmapped 4214583326.00002.unmapped 4214583326.00003.unmapped 4214583326.00004.unmapped 4214583326.00005.unmapped 4214583326.00006.unmapped 4214583326.00007.unmapped 4214583326.00008.unmapped 4214583326.00009.unmapped 4214583326.00010.unmapped 4214583326.00011.unmapped 4214583326.00012.unmapped 4214583326.00013.unmapped 4214583326.00014.unmapped 4214583326.00015.unmapped 4214583326.00016.unmapped 4214583326.00017.unmapped 4214583326.00018.unmapped 4214583326.00019.unmapped 4214583326.00020.unmapped 4214583326.00021.unmapped 4214583326.00022.unmapped 4214583326.00023.unmapped 4214583326.00024.unmapped 4214583326.00025.unmapped 4214583326.00026.unmapped 4214583326.00027.unmapped 4214583326.00028.unmapped 4214583326.00029.unmapped 4214583326.00030.unmapped 4214583326.00031.unmapped 4214583326.00032.unmapped 4214583326.00033.unmapped 4214583326.00034.unmapped 4214583326.00035.unmapped 4214583326.00036.unmapped 4214583326.00037.unmapped 4214583326.00038.unmapped 4214583326.00039.unmapped 4214583326.00040.unmapped 4214583326.00041.unmapped 4214583326.00042.unmapped 4214583326.00043.unmapped 4214583326.00044.unmapped 4214583326.00045.unmapped 4214583326.00046.unmapped 4214583326.00047.unmapped 4214583326.00048.unmapped 4214583326.00049.unmapped 4214583326.00050.unmapped 4214583326.00051.unmapped 4214583326.00052.unmapped 4214583326.00053.unmapped 4214583326.00054.unmapped 4214583326.00055.unmapped 4214583326.00056.unmapped 4214583326.00057.unmapped 4214583326.00058.unmapped 4214583326.00059.unmapped > 4214583326_unmapped.txt /data/maqgene/bin/maq mapmerge 4214583326.map 4214583326.00000.map 4214583326.00001.map 4214583326.00002.map 4214583326.00003.map 4214583326.00004.map 4214583326.00005.map 4214583326.00006.map 4214583326.00007.map 4214583326.00008.map 4214583326.00009.map 4214583326.00010.map 4214583326.00011.map 4214583326.00012.map 4214583326.00013.map 4214583326.00014.map 4214583326.00015.map 4214583326.00016.map 4214583326.00017.map 4214583326.00018.map 4214583326.00019.map 4214583326.00020.map 4214583326.00021.map 4214583326.00022.map 4214583326.00023.map 4214583326.00024.map 4214583326.00025.map 4214583326.00026.map 4214583326.00027.map 4214583326.00028.map 4214583326.00029.map 4214583326.00030.map 4214583326.00031.map 4214583326.00032.map 4214583326.00033.map 4214583326.00034.map 4214583326.00035.map 4214583326.00036.map 4214583326.00037.map 4214583326.00038.map 4214583326.00039.map 4214583326.00040.map 4214583326.00041.map 4214583326.00042.map 4214583326.00043.map 4214583326.00044.map 4214583326.00045.map 4214583326.00046.map 4214583326.00047.map 4214583326.00048.map 4214583326.00049.map 4214583326.00050.map 4214583326.00051.map 4214583326.00052.map 4214583326.00053.map 4214583326.00054.map 4214583326.00055.map 4214583326.00056.map 4214583326.00057.map 4214583326.00058.map 4214583326.00059.map # Thu Apr 28 11:28:33 BST 2011: Linking backend file 4214583326_unmapped.txt to /data/maqgene/out/example_user/CB6945/CB6945_unmapped.txt ln -fs /data/maqgene/work/4214583326_unmapped.txt /data/maqgene/out/example_user/CB6945/CB6945_unmapped.txt /data/maqgene/makefile:126: warning: undefined variable `mapcheck_parameters' # Thu Apr 28 11:51:11 BST 2011: Generating consensus ... # Thu Apr 28 11:51:11 BST 2011: Creating pileup ... /data/maqgene/bin/maq assemble -N 2 -q 0 -r 0.0 -m 7 -Q 100 -p 3000847188.cns \ /data/maqgene/genomes/elegans.bfa 4214583326.map 2> 3000847188_log.txt /data/maqgene/bin/maq pileup -Q 100 -p -m 7 -q 0 /data/maqgene/genomes/elegans.bfa 4214583326.map > 1879682750_pileup.txt # Thu Apr 28 11:51:11 BST 2011: Running 'mapcheck' ... /data/maqgene/bin/maq mapcheck /data/maqgene/genomes/elegans.bfa 4214583326.map > 4214583326_check.txt \ 2>/dev/null # Thu Apr 28 11:57:05 BST 2011: Linking backend file 4214583326_check.txt to /data/maqgene/out/example_user/CB6945/CB6945_check.txt ln -fs /data/maqgene/work/4214583326_check.txt /data/maqgene/out/example_user/CB6945/CB6945_check.txt /data/maqgene/bin/filter_matching_lines 1879682750_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 \ > 1879682750_known_snps # Thu Apr 28 11:57:29 BST 2011: Getting uncovered regions ... # Thu Apr 28 11:57:29 BST 2011: Making coverage histogram ... cut -f 1,2,4 1879682750_pileup.txt \ | /data/maqgene/bin/get_uncovered_regions 50 \ > 1879682750_uncovered.txt # Thu Apr 28 11:57:29 BST 2011: Linking backend file 1879682750_pileup.txt to /data/maqgene/out/example_user/CB6945/CB6945_pileup.txt (echo -en "sequencing_depth\tnumber_of_bases\n"; \ cut -f 4 1879682750_pileup.txt \ | /data/maqgene/bin/pileup_histogram 100) > 1879682750_coverage.txt ln -fs /data/maqgene/work/1879682750_pileup.txt /data/maqgene/out/example_user/CB6945/CB6945_pileup.txt # Thu Apr 28 11:58:04 BST 2011: Filtering and loading pileup for analysis ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 1879682750_pileup; create table 1879682750_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) );" # Thu Apr 28 11:58:04 BST 2011: Linking backend file 1879682750_coverage.txt to /data/maqgene/out/example_user/CB6945/CB6945_coverage.txt ln -fs /data/maqgene/work/1879682750_coverage.txt /data/maqgene/out/example_user/CB6945/CB6945_coverage.txt cat 1879682750_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 1879682750_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 1879682750_pileup" # Thu Apr 28 11:58:05 BST 2011: Linking backend file 1879682750_uncovered.txt to /data/maqgene/out/example_user/CB6945/CB6945_uncovered.txt ln -fs /data/maqgene/work/1879682750_uncovered.txt /data/maqgene/out/example_user/CB6945/CB6945_uncovered.txt cat 1879682750_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 1879682750_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 1879682750_pileup" touch 1879682750_pileup # Thu Apr 28 11:59:08 BST 2011: Writing snp read counts ... /usr/bin/mysql -Dmaqgenedb -umaqgene --skip-column-names --batch --raw --local-infile --column-names -e "select f.id, f.dna, f.start + 1 start, e.snp_name, e.snp_base, if(e.snp_base = 'a', p.A_fwd + p.A_rev, if (e.snp_base = 'c', p.C_fwd + p.C_rev, if (e.snp_base = 'g', p.G_fwd + p.G_rev, if (e.snp_base = 't', p.T_fwd + p.T_rev, -1)))) snp_reads, p.ref_base, p.wt_fwd + p.wt_rev wt_reads, p.read_depth, p.sample_reads from elegans_features f join elegans_snp_changes e on (f.attribute = e.snp_name) join 1879682750_pileup p using (dna,start)" > /data/maqgene/out/example_user/CB6945/CB6945_snp_read_counts.txt 0 snp read count lines written. # Thu Apr 28 12:00:40 BST 2011: Linking backend file 3000847188_log.txt to /data/maqgene/out/example_user/CB6945/CB6945_log.txt /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 3000847188_snps; create table 3000847188_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/3000847188_log.txt /data/maqgene/out/example_user/CB6945/CB6945_log.txt /data/maqgene/bin/maq cns2snp 3000847188.cns \ | cat -b | /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "load data local infile '/dev/stdin' into table 3000847188_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 3000847188_snps;" # Thu Apr 28 12:00:54 BST 2011: Extracting indels from consensus ... /data/maqgene/bin/maq indelsoa /data/maqgene/genomes/elegans.bfa 4214583326.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 3000847188_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 3000847188_snps;" # Thu Apr 28 12:04:38 BST 2011: Adding placeholders for known SNPs. cat 1879682750_known_snps \ | /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "load data local infile '/dev/stdin' ignore into table 3000847188_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 3000847188_snps;" Found 162007 variants. touch 3000847188_snps # Thu Apr 28 12:04:39 BST 2011: Loading uncovered regions into table ... # Thu Apr 28 12:04:39 BST 2011: Finding all genomic features overlapping variants... cat 1879682750_uncovered.txt \ | /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 1879682750_uncovered; create table 1879682750_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 = 162008; load data local infile '/dev/stdin' into table 1879682750_uncovered (dna, start, end)" /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 3000847188_rel_snps; CREATE TABLE 3000847188_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) )" # Thu Apr 28 12:04:39 BST 2011: Getting masking regions /data/maqgene/bin/associate_regions -b -1 -c -1000000 -m 2 -o >(/usr/bin/mysql -Dmaqgenedb -umaqgene --skip-column-names --batch --raw --local-infile -e "drop table if exists 3000847188_masked_ids; create table 3000847188_masked_ids (query_region_id int(10) NOT NULL, primary key (query_region_id)); load data local infile '/dev/stdin' ignore into table 3000847188_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 3000847188_snps") -t <(/usr/bin/mysql -Dmaqgenedb -umaqgene --skip-column-names --batch --raw --local-infile -e "select id,'elegans',dna,start,end,strand from elegans_features feature where feature.feature not in ('mRNA', 'intron')") 1>/dev/null; /data/maqgene/bin/associate_regions -b -1 -c -1000000 -m 0 -o >(/usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "load data local infile '/dev/stdin' into table 3000847188_rel_snps; flush table 3000847188_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 3000847188_snps") -t <(/usr/bin/mysql -Dmaqgenedb -umaqgene --skip-column-names --batch --raw --local-infile -e "select id, 'elegans', dna,start,end,strand from elegans_features where feature in ('SNP','exon','five_prime_UTR','intron','mRNA','three_prime_UTR','ncRNA')") 1>/dev/null Uncovered region statistics: chromosome number_uncovered_regions total_uncovered_length I 758 96113 II 662 88298 III 752 92937 IV 526 61851 V 638 77638 X 127 22658 touch 1879682750_uncovered # Thu Apr 28 12:04:39 BST 2011: Finding mRNA features overlapping uncovered regions ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 1879682750_uncovered_rel; CREATE TABLE 1879682750_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 1879682750_uncovered_rel; flush table 1879682750_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 1879682750_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 3000847188_masked_ids touch 1879682750_uncovered_rel # Thu Apr 28 12:04:42 BST 2011: Calculating translation start offsets for uncovered regions... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 1879682750_offsets_uncovered; create table 1879682750_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 1879682750_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 1879682750_uncovered reg join 1879682750_uncovered_rel rel on (reg.id = rel.query_region_id) join elegans_features gene on (rel.target_region_id = gene.id) join elegans_features exon on (exon.attribute = gene.attribute) where exon.feature = 'exon' and gene.feature = 'mRNA' group by reg.id, gene.attribute" /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 1879682750_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 1879682750_uncovered reg join 1879682750_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 3000847188_rel_snps # Thu Apr 28 12:04:42 BST 2011: Calculating translation start offsets... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 3000847188_offsets_snps; create table 3000847188_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) );" # Thu Apr 28 12:04:42 BST 2011: Getting intergenic regions /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 3000847188_rel_intergenic; create table 3000847188_rel_intergenic like 3000847188_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 3000847188_rel_intergenic; flush table 3000847188_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 3000847188_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 3000847188_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 3000847188_snps reg join 3000847188_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" touch 1879682750_offsets_uncovered # Thu Apr 28 12:04:46 BST 2011: Filtering masked intergenic regions /usr/bin/mysql -Dmaqgenedb -umaqgene --skip-column-names --batch --raw --local-infile -e "delete i.* from 3000847188_rel_intergenic i join 3000847188_masked_ids m using (query_region_id)" touch 3000847188_rel_intergenic # Thu Apr 28 12:04:50 BST 2011: Classifying intergenic relations /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 3000847188_intergenic_assoc; create table 3000847188_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 3000847188_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 3000847188_snps snp join 3000847188_rel_intergenic rel on (snp.id = rel.query_region_id) join elegans_features feature on (rel.target_region_id = feature.id)" touch 3000847188_intergenic_assoc touch 3000847188_offsets_snps # Thu Apr 28 12:05:00 BST 2011: Getting codons affected by point mutations... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 3000847188_codons; create table 3000847188_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 3000847188_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 3000847188_offsets_snps off join 3000847188_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 3000847188_codons /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 3000847188_marked; create table 3000847188_marked ( id int(10) NOT NULL, class varchar(100) NOT NULL, description varchar(100) NOT NULL, parent_feature varchar(100) NOT NULL, primary key (id, class, parent_feature) );" # Thu Apr 28 12:05:06 BST 2011: Finding exonic indels ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 3000847188_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 3000847188_snps snp join 3000847188_rel_snps rel on (snp.id = rel.query_region_id) join elegans_features feature on (rel.target_region_id = feature.id) where feature.feature = 'exon' and snp.variant_type = 'indel';" # Thu Apr 28 12:05:07 BST 2011: Finding coding variants ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 3000847188_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 3000847188_codons trans join elegans_genetic_code reference_codons on (trans.ref_codon = reference_codons.codon) join elegans_genetic_code sample_codons on (trans.sam_codon = sample_codons.codon);" # Thu Apr 28 12:05:07 BST 2011: Finding noncoding variants ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 3000847188_marked select snp.id, feature.feature class, 'none' description, feature.attribute parent_feature from 3000847188_snps snp join 3000847188_rel_snps rel on (snp.id = rel.query_region_id) join elegans_features feature on (rel.target_region_id = feature.id) where feature.feature not in ('exon', 'intron', 'mRNA');" # Thu Apr 28 12:05:07 BST 2011: Finding splice site variants ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 3000847188_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 3000847188_snps snp join 3000847188_rel_snps rel on (snp.id = rel.query_region_id) join elegans_features feature on (rel.target_region_id = feature.id) where feature.feature = 'intron' and rel.distance > -2;" # Thu Apr 28 12:05:08 BST 2011: Finding intergenic and intronic variants ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 3000847188_marked select id, 'nongenic' class, concat(if (relation in ('upstream','into'), - distance, distance),' ',relation) description, attribute from 3000847188_intergenic_assoc where ((relation = 'upstream' and num_regions_between = 0 and distance < 50000) or (relation = 'upstream' and num_regions_between < 2 and distance < 1000) or (relation = 'downstream' and num_regions_between = 0 and distance < 1000) or (relation = 'downstream' and num_regions_between < 2 and distance < 1000) or relation = 'into' );" # Thu Apr 28 12:05:10 BST 2011: Finding uncovered regions in genes ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 3000847188_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 1879682750_uncovered unc join 1879682750_offsets_uncovered b using (id) join 1879682750_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 1879682750_uncovered unc join 1879682750_offsets_uncovered b using (id) join 1879682750_offsets_uncovered e using (id, gene) join elegans_features gene on (e.gene = gene.attribute) where b.boundary_type = 'start' and e.boundary_type = 'end' and gene.strand = '-' and gene.feature = 'mRNA'" # Thu Apr 28 12:05:10 BST 2011: Variants found: +-----------------+-----------------+ | class | number_variants | +-----------------+-----------------+ | five_prime_UTR | 1296 | | frameshift | 89 | | inframe | 26 | | missense | 6135 | | ncRNA | 879 | | nongenic | 125443 | | non_start | 10 | | premature_stop | 687 | | readthrough | 19 | | silent | 7405 | | SNP | 1033 | | splice_acceptor | 46 | | splice_donor | 48 | | three_prime_UTR | 3557 | | uncovered | 2266 | +-----------------+-----------------+ touch 3000847188_marked # Thu Apr 28 12:05:11 BST 2011: Combining results ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 3000847188_combined; create table 3000847188_combined (primary key (id, class, description), key (dna, start)) as select snp.id, 'CB6945' 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 3000847188_snps snp join 1879682750_pileup pile using (dna,start) join 3000847188_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, 'CB6945' 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 1879682750_uncovered unc join 3000847188_marked class on (unc.id = class.id) left join elegans_per_locus using (dna,start) group by id, class, description; alter table 3000847188_combined order by dna, start, length" touch 3000847188_combined # Thu Apr 28 12:05:12 BST 2011: Writing results to grouped file ... /usr/bin/mysql -Dmaqgenedb -umaqgene --skip-column-names --batch --raw --local-infile --column-names -e "select id, mutant_strain, dna, start, length, reference_base, sample_base, consensus_score, loci_multiplicity, mapping_quality, neighbor_quality, number_wildtype_reads, number_variant_reads, sequencing_depth, sample_reads, variant_type, indel_size, group_concat(class) classes, group_concat(description) descriptions, group_concat(concat('{',parent_features,'}')) parent_features from 3000847188_combined group by id order by dna, start;" > /data/maqgene/out/example_user/CB6945/CB6945_grouped.txt # Thu Apr 28 12:05:12 BST 2011: Writing results to flat file ... /usr/bin/mysql -Dmaqgenedb -umaqgene --skip-column-names --batch --raw --local-infile --column-names -e "select * from 3000847188_combined" > /data/maqgene/out/example_user/CB6945/CB6945_flat.txt 6055 lines written. 4176 lines written. rm 4214583326.00007.unmapped 4214583326.00052.1.fastq 4214583326.00017.1.bfq 4214583326.00011.1.bfq 4214583326.00015.2.fastq 4214583326.00037.2.fastq 4214583326.00024.mismatch 4214583326.00048.unmapped 4214583326.00025.unmapped 4214583326.00046.2.bfq 4214583326.00054.1.bfq 4214583326.00000.1.bfq 4214583326.00033.unmapped 4214583326.00025.1.fastq 4214583326.00046.mismatch 4214583326.00057.mismatch 4214583326.00012.mismatch 4214583326.00057.2.bfq 4214583326.00048.2.bfq 4214583326.00055.1.bfq 4214583326.00034.unmapped 4214583326.00037.1.bfq 4214583326.00004.unmapped 4214583326.00033.1.fastq 4214583326.00040.unmapped 4214583326.00028.2.fastq 4214583326.00056.2.fastq 4214583326.00051.map 4214583326.00040.mismatch 4214583326.00006.2.bfq 4214583326.00035.1.fastq 4214583326.00056.unmapped 4214583326.00001.1.bfq 4214583326.00010.1.bfq 4214583326.00004.1.fastq 4214583326.00055.unmapped 4214583326.00027.map 4214583326.00059.map 4214583326.00040.1.fastq 4214583326.00014.1.bfq 4214583326.00016.1.bfq 4214583326.00021.unmapped 4214583326.00008.1.bfq 4214583326.00008.unmapped 4214583326.00009.mismatch 4214583326.00036.mismatch 4214583326.00034.1.bfq 4214583326.00009.2.bfq 4214583326.00048.2.fastq 4214583326.00000.2.bfq 4214583326.00014.unmapped 4214583326.00013.map 4214583326.00025.2.fastq 4214583326.00000.mismatch 4214583326.00053.1.bfq 4214583326.00039.unmapped 4214583326.00041.1.fastq 4214583326.00048.1.bfq 4214583326.00014.1.fastq 4214583326.00016.unmapped 4214583326.00033.2.fastq 4214583326.00058.mismatch 4214583326.00012.unmapped 4214583326.00039.1.fastq 4214583326.00038.mismatch 4214583326.00001.2.bfq 4214583326.00010.2.bfq 4214583326.00038.1.bfq 4214583326.00002.1.bfq 4214583326.00035.map 4214583326.00043.mismatch 18834703_split1 4214583326.00040.2.fastq 4214583326.00001.mismatch 4214583326.00010.mismatch 4214583326.00016.2.bfq 4214583326.00045.1.bfq 4214583326.00047.1.bfq 4214583326.00029.1.bfq 4214583326.00016.mismatch 4214583326.00005.map 4214583326.00053.1.fastq 4214583326.00004.2.bfq 4214583326.00007.map 4214583326.00009.unmapped 4214583326.00036.map 4214583326.00029.2.bfq 4214583326.00042.unmapped 4214583326.00032.map 4214583326.00042.2.bfq 4214583326.00041.unmapped 4214583326.00011.mismatch 4214583326.00041.2.fastq 4214583326.00005.1.fastq 4214583326.00024.unmapped 4214583326.00059.2.fastq 4214583326.00014.2.fastq 4214583326.00017.2.bfq 4214583326.00042.1.fastq 4214583326.00019.map 4214583326.00022.mismatch 4214583326.00028.1.fastq 4214583326.00026.1.bfq 4214583326.00022.2.bfq 4214583326.00024.1.fastq 4214583326.00017.mismatch 4214583326.00002.2.bfq 4214583326.00058.unmapped 4214583326.00046.unmapped 4214583326.00023.map 4214583326.00056.1.fastq 4214583326.00002.mismatch 4214583326.00015.map 4214583326.00020.mismatch 4214583326.00047.2.bfq 4214583326.00032.1.bfq 4214583326.00057.map 4214583326.00005.mismatch 4214583326.00021.1.bfq 4214583326.00059.1.bfq 4214583326.00046.1.fastq 4214583326.00047.mismatch 4214583326.00053.2.fastq 4214583326.00044.map 4214583326.00006.mismatch 4214583326.00037.2.bfq 4214583326.00006.unmapped 4214583326.00012.2.bfq 4214583326.00035.2.fastq 4214583326.00022.1.bfq 4214583326.00050.mismatch 4214583326.00043.1.fastq 4214583326.00042.2.fastq 4214583326.00049.2.fastq 4214583326.00006.1.fastq 4214583326.00028.map 4214583326.00026.2.bfq 4214583326.00024.2.fastq 4214583326.00018.2.bfq 4214583326.00026.mismatch 4214583326.00054.2.bfq 4214583326.00007.1.fastq 4214583326.00000.unmapped 4214583326.00003.1.bfq 4214583326.00056.2.bfq 4214583326.00033.mismatch 4214583326.00054.mismatch 4214583326.00035.1.bfq 4214583326.00027.1.bfq 4214583326.00031.2.bfq 4214583326.00046.2.fastq 4214583326.00053.2.bfq 4214583326.00000.1.fastq 4214583326.00018.mismatch 4214583326.00003.mismatch 4214583326.00038.unmapped 4214583326.00029.mismatch 4214583326.00051.1.bfq 4214583326.00003.2.bfq 4214583326.00033.2.bfq 4214583326.00037.unmapped 4214583326.00025.map 4214583326.00045.2.bfq 18834703_split2 4214583326.00001.unmapped 4214583326.00010.unmapped 4214583326.00048.mismatch 4214583326.00020.2.bfq 4214583326.00012.1.bfq 4214583326.00038.2.bfq 4214583326.00038.1.fastq 4214583326.00045.mismatch 4214583326.00034.1.fastq 4214583326.00043.map 4214583326.00033.map 4214583326.00006.2.fastq 4214583326.00001.1.fastq 4214583326.00010.1.fastq 4214583326.00020.1.bfq 4214583326.00049.mismatch 4214583326.00044.2.fastq 4214583326.00004.map 4214583326.00055.1.fastq 4214583326.00030.2.bfq 4214583326.00011.unmapped 4214583326.00021.1.fastq 4214583326.00052.map 4214583326.00056.map 4214583326.00008.1.fastq 4214583326.00050.2.bfq 4214583326.00035.2.bfq 4214583326.00000.2.fastq 4214583326.00029.1.fastq 4214583326.00053.unmapped 4214583326.00011.1.fastq 4214583326.00017.unmapped 4214583326.00049.1.bfq 4214583326.00005.1.bfq 4214583326.00050.1.bfq 4214583326.00003.unmapped 4214583326.00044.1.bfq 4214583326.00029.unmapped 4214583326.00002.unmapped 4214583326.00020.unmapped 4214583326.00041.map 4214583326.00038.2.fastq 4214583326.00013.2.bfq 4214583326.00017.1.fastq 4214583326.00014.map 4214583326.00016.1.fastq 4214583326.00047.unmapped 4214583326.00031.mismatch 4214583326.00023.1.bfq 4214583326.00013.mismatch 4214583326.00001.2.fastq 4214583326.00010.2.fastq 4214583326.00059.mismatch 4214583326.00002.1.fastq 4214583326.00040.map 4214583326.00020.1.fastq 4214583326.00049.2.bfq 4214583326.00059.2.bfq 4214583326.00019.1.bfq 4214583326.00016.2.fastq 4214583326.00047.1.fastq 4214583326.00055.map 4214583326.00044.1.fastq 4214583326.00034.2.fastq 4214583326.00024.2.bfq 4214583326.00058.2.bfq 4214583326.00021.map 4214583326.00004.mismatch 4214583326.00015.1.bfq 4214583326.00008.map 4214583326.00029.2.fastq 4214583326.00011.2.fastq 4214583326.00012.1.fastq 4214583326.00009.1.fastq 4214583326.00026.unmapped 4214583326.00031.1.bfq 4214583326.00030.1.bfq 4214583326.00018.1.bfq 4214583326.00036.2.bfq 4214583326.00054.unmapped 4214583326.00017.2.fastq 4214583326.00007.2.fastq 4214583326.00043.2.fastq 4214583326.00026.1.fastq 4214583326.00013.unmapped 4214583326.00042.map 4214583326.00035.mismatch 4214583326.00052.2.fastq 4214583326.00018.unmapped 4214583326.00057.1.fastq 4214583326.00002.2.fastq 4214583326.00032.mismatch 4214583326.00020.2.fastq 4214583326.00054.1.fastq 4214583326.00023.mismatch 4214583326.00024.map 4214583326.00019.2.bfq 4214583326.00036.1.bfq 4214583326.00028.1.bfq 4214583326.00058.1.fastq 4214583326.00059.unmapped 4214583326.00047.2.fastq 4214583326.00051.2.bfq 4214583326.00018.1.fastq 4214583326.00019.mismatch 4214583326.00032.2.bfq 4214583326.00045.unmapped 4214583326.00051.mismatch 4214583326.00052.1.bfq 4214583326.00022.unmapped 4214583326.00046.map 4214583326.00015.2.bfq 4214583326.00007.1.bfq 4214583326.00045.1.fastq 4214583326.00015.mismatch 4214583326.00022.1.fastq 4214583326.00009.map 4214583326.00043.1.bfq 4214583326.00021.2.bfq 4214583326.00007.mismatch 4214583326.00025.1.bfq 4214583326.00030.unmapped 4214583326.00026.2.fastq 4214583326.00055.2.fastq 4214583326.00006.map 4214583326.00021.2.fastq 4214583326.00027.unmapped 4214583326.00054.2.fastq 4214583326.00008.2.fastq 4214583326.00040.1.bfq 4214583326.00003.1.fastq 4214583326.00035.unmapped 4214583326.00030.1.fastq 4214583326.00028.2.bfq 4214583326.00034.2.bfq 4214583326.00018.2.fastq 4214583326.00058.map 4214583326.00027.1.fastq 4214583326.00028.mismatch 4214583326.00051.unmapped 4214583326.00004.1.bfq 4214583326.00027.2.bfq 4214583326.00031.unmapped 4214583326.00044.2.bfq 4214583326.00000.map 4214583326.00052.mismatch 4214583326.00056.1.bfq 4214583326.00045.2.fastq 4214583326.00057.2.fastq 4214583326.00022.2.fastq 4214583326.00037.1.fastq 4214583326.00031.1.fastq 4214583326.00013.1.fastq 4214583326.00005.2.bfq 4214583326.00030.map 4214583326.00049.map 4214583326.00038.map 4214583326.00025.2.bfq 4214583326.00014.2.bfq 4214583326.00042.mismatch 4214583326.00053.mismatch 4214583326.00041.1.bfq 4214583326.00025.mismatch 4214583326.00001.map 4214583326.00010.map 4214583326.00055.2.bfq 4214583326.00008.2.bfq 4214583326.00003.2.fastq 4214583326.00037.mismatch 4214583326.00030.2.fastq 4214583326.00011.2.bfq 4214583326.00016.map 4214583326.00057.1.bfq 4214583326.00005.unmapped 4214583326.00039.1.bfq 4214583326.00022.map 4214583326.00050.unmapped 4214583326.00027.2.fastq 4214583326.00009.2.fastq 4214583326.00034.map 4214583326.00036.unmapped 4214583326.00040.2.bfq 4214583326.00039.map 4214583326.00044.unmapped 4214583326.00032.unmapped 4214583326.00011.map 4214583326.00050.1.fastq 4214583326.00023.unmapped 4214583326.00050.map 4214583326.00049.unmapped 4214583326.00036.1.fastq 4214583326.00056.mismatch 4214583326.00031.2.fastq 4214583326.00013.2.fastq 4214583326.00033.1.bfq 4214583326.00019.unmapped 4214583326.00027.mismatch 4214583326.00037.map 4214583326.00012.2.fastq 4214583326.00032.1.fastq 4214583326.00043.2.bfq 4214583326.00023.1.fastq 4214583326.00058.2.fastq 4214583326.00017.map 4214583326.00009.1.bfq 4214583326.00048.1.fastq 4214583326.00041.2.bfq 4214583326.00019.1.fastq 4214583326.00002.map 4214583326.00020.map 4214583326.00015.unmapped 4214583326.00042.1.bfq 4214583326.00041.mismatch 4214583326.00051.1.fastq 4214583326.00007.2.bfq 4214583326.00014.mismatch 4214583326.00047.map 4214583326.00039.2.bfq 4214583326.00052.2.bfq 4214583326.00008.mismatch 4214583326.00024.1.bfq 4214583326.00018.map 4214583326.00057.unmapped 4214583326.00004.2.fastq 4214583326.00023.2.bfq 4214583326.00015.1.fastq 4214583326.00039.mismatch 4214583326.00058.1.bfq 4214583326.00005.2.fastq 4214583326.00050.2.fastq 4214583326.00031.map 4214583326.00012.map 4214583326.00046.1.bfq 4214583326.00053.map 4214583326.00036.2.fastq 4214583326.00030.mismatch 4214583326.00034.mismatch 4214583326.00028.unmapped 4214583326.00032.2.fastq 4214583326.00003.map 4214583326.00023.2.fastq 4214583326.00029.map 4214583326.00013.1.bfq 4214583326.00043.unmapped 4214583326.00026.map 4214583326.00052.unmapped 4214583326.00019.2.fastq 4214583326.00048.map 4214583326.00054.map 4214583326.00039.2.fastq 4214583326.00055.mismatch 4214583326.00051.2.fastq 4214583326.00006.1.bfq 4214583326.00045.map 4214583326.00044.mismatch 4214583326.00021.mismatch 4214583326.00049.1.fastq 4214583326.00059.1.fastq make: Leaving directory `/data/maqgene/work' make: Entering directory `/data/maqgene/work' # Thu Apr 28 12:05:15 BST 2011: Cleaning intermediate data ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 3000847188_snps,3000847188_rel,3000847188_masked_ids,3000847188_rel_intergenic,3000847188_intergenic_assoc,3000847188_offsets,3000847188_codons,3000847188_marked,3000847188_combined,1879682750_pileup" rm -f 3000847188_snps 3000847188_rel 3000847188_masked_ids 3000847188_rel_intergenic 3000847188_intergenic_assoc 3000847188_offsets 3000847188_codons 3000847188_marked 3000847188_combined 1879682750_pileup make: Leaving directory `/data/maqgene/work'