Finished reading input. ++ echo CB7037/./s_s_1_sequence_read1.fastq,CB6997-1/./s_s_1_sequence_read1.fastq ++ tr , ' ' + fastq_file_set1='CB7037/./s_s_1_sequence_read1.fastq CB6997-1/./s_s_1_sequence_read1.fastq' ++ cd /data/maqgene/reads ++ wc -l ++ cat CB7037/./s_s_1_sequence_read1.fastq CB6997-1/./s_s_1_sequence_read1.fastq ++ cut -f 1 -d ' ' + TOTAL_LINES=450741284 ++ echo '(450741284 / 5000000) + (450741284 % 5000000 != 0)' ++ bc + num_chunks=91 + 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=4252044719 map_cksum=1210298692 pileup_cksum=1351391557 cns_cksum=1483950234 umdd=50000 dmdd=1000 umid=1000 dmid=1000 max_gene_radius=50000 full_results_dir=/data/maqgene/out/example_user/CB7073 outfile_basename=CB7073 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=91 Will process 450741284 lines of input in 91 chunks make: Entering directory `/data/maqgene/work' # Wed Mar 28 11:57:29 BST 2012: Removing frontend files in case this is a duplicate run ... rm -f /data/maqgene/out/example_user/CB7073/CB7073_{grouped.txt,flat.txt} rm -f /data/maqgene/out/example_user/CB7073/CB7073_uncovered.txt /data/maqgene/out/example_user/CB7073/CB7073_coverage.txt /data/maqgene/out/example_user/CB7073/CB7073_pileup.txt /data/maqgene/out/example_user/CB7073/CB7073_log.txt /data/maqgene/out/example_user/CB7073/CB7073_check.txt /data/maqgene/out/example_user/CB7073/CB7073_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. # : Regrouping fastq reads into chunks of size 5000000. split -l 5000000 -a 5 -d <(cat /data/maqgene/reads/CB7037/./s_s_1_sequence_read1.fastq /data/maqgene/reads/CB6997-1/./s_s_1_sequence_read1.fastq) 1210298692.1.fastq. split -l 5000000 -a 5 -d <(cat /data/maqgene/reads/CB7037/./s_s_2_sequence_read2.fastq /data/maqgene/reads/CB6997-1/./s_s_2_sequence_read2.fastq) 1210298692.2.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 00060 00061 00062 00063 00064 00065 00066 00067 00068 00069 00070 00071 00072 00073 00074 00075 00076 00077 00078 00079 00080 00081 00082 00083 00084 00085 00086 00087 00088 00089 00090; do mv 1210298692.1.fastq.$stem 1210298692.$stem.1.fastq; done touch 4252044719_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 00060 00061 00062 00063 00064 00065 00066 00067 00068 00069 00070 00071 00072 00073 00074 00075 00076 00077 00078 00079 00080 00081 00082 00083 00084 00085 00086 00087 00088 00089 00090; do mv 1210298692.2.fastq.$stem 1210298692.$stem.2.fastq; done touch 4252044719_split2 # Wed Mar 28 12:01:52 BST 2012: Converting fastq files to bfq ... # Wed Mar 28 12:01:52 BST 2012: Converting fastq files to bfq ... # Wed Mar 28 12:01:52 BST 2012: Converting fastq files to bfq ... # Wed Mar 28 12:01:52 BST 2012: Converting fastq files to bfq ... # Wed Mar 28 12:01:52 BST 2012: Converting fastq files to bfq ... # Wed Mar 28 12:01:52 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00000.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00000.1.bfq # Wed Mar 28 12:01:52 BST 2012: Converting fastq files to bfq ... # Wed Mar 28 12:01:52 BST 2012: Converting fastq files to bfq ... # Wed Mar 28 12:01:52 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00001.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00001.1.bfq /data/maqgene/bin/maq sol2sanger 1210298692.00002.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00002.1.bfq /data/maqgene/bin/maq sol2sanger 1210298692.00003.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00003.1.bfq /data/maqgene/bin/maq sol2sanger 1210298692.00004.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00004.1.bfq /data/maqgene/bin/maq sol2sanger 1210298692.00005.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00005.1.bfq /data/maqgene/bin/maq sol2sanger 1210298692.00006.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00006.1.bfq /data/maqgene/bin/maq sol2sanger 1210298692.00007.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00007.1.bfq /data/maqgene/bin/maq sol2sanger 1210298692.00008.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00008.1.bfq /data/maqgene/bin/maq sol2sanger 1210298692.00009.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00009.1.bfq /data/maqgene/bin/maq sol2sanger 1210298692.00010.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00010.1.bfq /data/maqgene/bin/maq sol2sanger 1210298692.00011.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00011.1.bfq /data/maqgene/bin/maq sol2sanger 1210298692.00012.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00012.1.bfq /data/maqgene/bin/maq sol2sanger 1210298692.00013.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00013.1.bfq -- finish writing file '1210298692.00005.1.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 12:02:13 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00014.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00014.1.bfq -- finish writing file '1210298692.00004.1.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 12:02:14 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00015.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00015.1.bfq -- finish writing file '1210298692.00012.1.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 12:02:14 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00016.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00016.1.bfq -- finish writing file '1210298692.00013.1.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 12:02:16 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00017.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00017.1.bfq -- finish writing file '1210298692.00011.1.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 12:02:19 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00018.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00018.1.bfq -- finish writing file '1210298692.00002.1.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 12:02:20 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00019.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00019.1.bfq -- finish writing file '1210298692.00003.1.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 12:02:21 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00020.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00020.1.bfq -- finish writing file '1210298692.00007.1.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 12:02:21 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00021.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00021.1.bfq -- finish writing file '1210298692.00010.1.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 12:02:21 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00022.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00022.1.bfq -- finish writing file '1210298692.00006.1.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 12:02:22 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00023.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00023.1.bfq -- finish writing file '1210298692.00001.1.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 12:02:22 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00024.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00024.1.bfq -- finish writing file '1210298692.00009.1.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 12:02:22 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00025.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00025.1.bfq -- finish writing file '1210298692.00008.1.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 12:02:23 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00026.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00026.1.bfq -- finish writing file '1210298692.00000.1.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 12:02:23 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00027.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00027.1.bfq -- finish writing file '1210298692.00015.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00017.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00016.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00019.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00014.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00025.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00018.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00020.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00021.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00026.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00023.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00024.1.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 12:02:45 BST 2012: Converting fastq files to bfq ... # Wed Mar 28 12:02:45 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00038.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00038.1.bfq # Wed Mar 28 12:02:45 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00037.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00037.1.bfq /data/maqgene/bin/maq sol2sanger 1210298692.00036.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00036.1.bfq # Wed Mar 28 12:02:46 BST 2012: Converting fastq files to bfq ... # Wed Mar 28 12:02:46 BST 2012: Converting fastq files to bfq ... # Wed Mar 28 12:02:46 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00035.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00035.1.bfq /data/maqgene/bin/maq sol2sanger 1210298692.00039.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00039.1.bfq /data/maqgene/bin/maq sol2sanger 1210298692.00034.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00034.1.bfq -- finish writing file '1210298692.00022.1.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 12:02:46 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00033.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00033.1.bfq -- finish writing file '1210298692.00027.1.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 12:02:47 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00040.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00040.1.bfq # Wed Mar 28 12:02:47 BST 2012: Converting fastq files to bfq ... # Wed Mar 28 12:02:47 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00032.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00032.1.bfq /data/maqgene/bin/maq sol2sanger 1210298692.00031.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00031.1.bfq # Wed Mar 28 12:02:48 BST 2012: Converting fastq files to bfq ... # Wed Mar 28 12:02:48 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00030.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00030.1.bfq /data/maqgene/bin/maq sol2sanger 1210298692.00041.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00041.1.bfq /data/maqgene/bin/maq sol2sanger 1210298692.00029.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00029.1.bfq # Wed Mar 28 12:02:49 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00028.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00028.1.bfq -- finish writing file '1210298692.00032.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00036.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00038.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00037.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00034.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00033.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00031.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00035.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00029.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00039.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00040.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00041.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00028.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00030.1.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 12:03:13 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00054.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00054.1.bfq # Wed Mar 28 12:03:20 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00051.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00051.1.bfq # Wed Mar 28 12:03:20 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00053.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00053.1.bfq # Wed Mar 28 12:03:20 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00055.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00055.1.bfq /data/maqgene/bin/maq sol2sanger 1210298692.00052.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00052.1.bfq # Wed Mar 28 12:03:21 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00050.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00050.1.bfq # Wed Mar 28 12:03:21 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00049.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00049.1.bfq # Wed Mar 28 12:03:21 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00048.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00048.1.bfq # Wed Mar 28 12:03:22 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00046.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00046.1.bfq # Wed Mar 28 12:03:22 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00045.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00045.1.bfq # Wed Mar 28 12:03:22 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00047.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00047.1.bfq # Wed Mar 28 12:03:23 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00042.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00042.1.bfq # Wed Mar 28 12:03:23 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00044.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00044.1.bfq # Wed Mar 28 12:03:23 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00043.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00043.1.bfq -- finish writing file '1210298692.00054.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00049.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00042.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00046.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00055.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00053.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00051.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00050.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00047.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00045.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00052.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00048.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00044.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00043.1.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 12:03:47 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00068.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00068.1.bfq # Wed Mar 28 12:03:55 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00069.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00069.1.bfq # Wed Mar 28 12:03:56 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00067.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00067.1.bfq # Wed Mar 28 12:03:57 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00066.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00066.1.bfq # Wed Mar 28 12:03:58 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00065.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00065.1.bfq # Wed Mar 28 12:03:59 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00064.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00064.1.bfq -- finish writing file '1210298692.00068.1.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 12:04:00 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00063.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00063.1.bfq -- finish writing file '1210298692.00069.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00067.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00065.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00064.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00063.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00066.1.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 12:04:12 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00075.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00075.1.bfq # Wed Mar 28 12:04:15 BST 2012: Converting fastq files to bfq ... # Wed Mar 28 12:04:15 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00076.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00076.1.bfq # Wed Mar 28 12:04:15 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00074.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00074.1.bfq /data/maqgene/bin/maq sol2sanger 1210298692.00073.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00073.1.bfq # Wed Mar 28 12:04:16 BST 2012: Converting fastq files to bfq ... # Wed Mar 28 12:04:16 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00071.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00071.1.bfq /data/maqgene/bin/maq sol2sanger 1210298692.00072.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00072.1.bfq # Wed Mar 28 12:04:17 BST 2012: Converting fastq files to bfq ... # Wed Mar 28 12:04:17 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00070.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00070.1.bfq /data/maqgene/bin/maq sol2sanger 1210298692.00062.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00062.1.bfq # Wed Mar 28 12:04:17 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00061.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00061.1.bfq # Wed Mar 28 12:04:18 BST 2012: Converting fastq files to bfq ... # Wed Mar 28 12:04:18 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00060.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00060.1.bfq /data/maqgene/bin/maq sol2sanger 1210298692.00059.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00059.1.bfq # Wed Mar 28 12:04:19 BST 2012: Converting fastq files to bfq ... # Wed Mar 28 12:04:19 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00056.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00056.1.bfq /data/maqgene/bin/maq sol2sanger 1210298692.00057.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00057.1.bfq # Wed Mar 28 12:04:19 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00058.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00058.1.bfq -- finish writing file '1210298692.00076.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00075.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00073.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00074.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00072.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00070.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00061.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00062.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00071.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00058.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00057.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00056.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00060.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00059.1.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 12:04:42 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00089.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00089.1.bfq -- finish writing file '1210298692.00089.1.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 12:04:55 BST 2012: Converting fastq files to bfq ... # Wed Mar 28 12:04:55 BST 2012: Converting fastq files to bfq ... # Wed Mar 28 12:04:55 BST 2012: Converting fastq files to bfq ... # Wed Mar 28 12:04:55 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00088.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00088.1.bfq # Wed Mar 28 12:04:55 BST 2012: Converting fastq files to bfq ... # Wed Mar 28 12:04:55 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00087.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00087.1.bfq # Wed Mar 28 12:04:55 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00090.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00090.1.bfq /data/maqgene/bin/maq sol2sanger 1210298692.00086.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00086.1.bfq /data/maqgene/bin/maq sol2sanger 1210298692.00085.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00085.1.bfq /data/maqgene/bin/maq sol2sanger 1210298692.00084.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00084.1.bfq /data/maqgene/bin/maq sol2sanger 1210298692.00083.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00083.1.bfq # Wed Mar 28 12:04:56 BST 2012: Converting fastq files to bfq ... # Wed Mar 28 12:04:56 BST 2012: Converting fastq files to bfq ... # Wed Mar 28 12:04:56 BST 2012: Converting fastq files to bfq ... # Wed Mar 28 12:04:56 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00000.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00000.2.bfq /data/maqgene/bin/maq sol2sanger 1210298692.00082.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00082.1.bfq /data/maqgene/bin/maq sol2sanger 1210298692.00081.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00081.1.bfq /data/maqgene/bin/maq sol2sanger 1210298692.00080.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00080.1.bfq # Wed Mar 28 12:04:57 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00077.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00077.1.bfq # Wed Mar 28 12:04:57 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00079.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00079.1.bfq # Wed Mar 28 12:04:57 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00078.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00078.1.bfq -- finish writing file '1210298692.00090.1.bfq' -- 185321 sequences were loaded. # Wed Mar 28 12:04:57 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00001.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00001.2.bfq -- finish writing file '1210298692.00077.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00087.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00086.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00084.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00088.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00085.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00078.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00081.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00080.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00083.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00082.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00001.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00079.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00000.2.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 12:05:22 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00014.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00014.2.bfq # Wed Mar 28 12:05:31 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00015.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00015.2.bfq # Wed Mar 28 12:05:31 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00013.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00013.2.bfq # Wed Mar 28 12:05:32 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00012.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00012.2.bfq # Wed Mar 28 12:05:33 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00011.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00011.2.bfq # Wed Mar 28 12:05:34 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00010.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00010.2.bfq -- finish writing file '1210298692.00014.2.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 12:05:34 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00009.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00009.2.bfq -- finish writing file '1210298692.00013.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00015.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00012.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00011.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00010.2.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 12:05:46 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00020.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00020.2.bfq # Wed Mar 28 12:05:46 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00019.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00019.2.bfq -- finish writing file '1210298692.00009.2.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 12:05:47 BST 2012: Converting fastq files to bfq ... # Wed Mar 28 12:05:47 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00018.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00018.2.bfq /data/maqgene/bin/maq sol2sanger 1210298692.00021.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00021.2.bfq # Wed Mar 28 12:05:48 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00017.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00017.2.bfq # Wed Mar 28 12:05:48 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00022.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00022.2.bfq # Wed Mar 28 12:05:49 BST 2012: Converting fastq files to bfq ... # Wed Mar 28 12:05:49 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00008.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00008.2.bfq /data/maqgene/bin/maq sol2sanger 1210298692.00016.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00016.2.bfq # Wed Mar 28 12:05:50 BST 2012: Converting fastq files to bfq ... # Wed Mar 28 12:05:50 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00006.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00006.2.bfq /data/maqgene/bin/maq sol2sanger 1210298692.00007.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00007.2.bfq # Wed Mar 28 12:05:51 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00004.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00004.2.bfq # Wed Mar 28 12:05:51 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00005.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00005.2.bfq # Wed Mar 28 12:05:52 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00003.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00003.2.bfq # Wed Mar 28 12:05:52 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00002.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00002.2.bfq -- finish writing file '1210298692.00020.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00021.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00019.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00018.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00017.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00022.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00016.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00008.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00004.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00005.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00007.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00006.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00002.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00003.2.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 12:06:13 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00035.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00035.2.bfq # Wed Mar 28 12:06:15 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00036.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00036.2.bfq # Wed Mar 28 12:06:16 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00034.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00034.2.bfq # Wed Mar 28 12:06:17 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00033.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00033.2.bfq # Wed Mar 28 12:06:18 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00032.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00032.2.bfq # Wed Mar 28 12:06:19 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00031.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00031.2.bfq # Wed Mar 28 12:06:20 BST 2012: Converting fastq files to bfq ... # Wed Mar 28 12:06:20 BST 2012: Converting fastq files to bfq ... # Wed Mar 28 12:06:20 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00028.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00028.2.bfq /data/maqgene/bin/maq sol2sanger 1210298692.00030.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00030.2.bfq /data/maqgene/bin/maq sol2sanger 1210298692.00029.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00029.2.bfq # Wed Mar 28 12:06:21 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00027.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00027.2.bfq # Wed Mar 28 12:06:21 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00026.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00026.2.bfq # Wed Mar 28 12:06:22 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00025.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00025.2.bfq # Wed Mar 28 12:06:22 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00024.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00024.2.bfq # Wed Mar 28 12:06:23 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00023.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00023.2.bfq -- finish writing file '1210298692.00036.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00035.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00034.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00031.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00033.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00029.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00025.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00032.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00024.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00028.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00026.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00030.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00027.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00023.2.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 12:06:45 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00049.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00049.2.bfq # Wed Mar 28 12:06:51 BST 2012: Converting fastq files to bfq ... # Wed Mar 28 12:06:51 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00050.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00050.2.bfq /data/maqgene/bin/maq sol2sanger 1210298692.00048.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00048.2.bfq # Wed Mar 28 12:06:52 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00047.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00047.2.bfq # Wed Mar 28 12:06:52 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00046.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00046.2.bfq # Wed Mar 28 12:06:53 BST 2012: Converting fastq files to bfq ... # Wed Mar 28 12:06:53 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00045.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00045.2.bfq /data/maqgene/bin/maq sol2sanger 1210298692.00044.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00044.2.bfq # Wed Mar 28 12:06:54 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00042.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00042.2.bfq # Wed Mar 28 12:06:54 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00043.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00043.2.bfq # Wed Mar 28 12:06:55 BST 2012: Converting fastq files to bfq ... # Wed Mar 28 12:06:55 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00041.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00041.2.bfq /data/maqgene/bin/maq sol2sanger 1210298692.00040.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00040.2.bfq -- finish writing file '1210298692.00049.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00048.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00050.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00045.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00044.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00041.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00046.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00047.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00043.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00040.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00042.2.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 12:07:14 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00060.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00060.2.bfq # Wed Mar 28 12:07:16 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00059.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00059.2.bfq # Wed Mar 28 12:07:16 BST 2012: Converting fastq files to bfq ... # Wed Mar 28 12:07:16 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00061.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00061.2.bfq /data/maqgene/bin/maq sol2sanger 1210298692.00058.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00058.2.bfq # Wed Mar 28 12:07:17 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00057.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00057.2.bfq # Wed Mar 28 12:07:17 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00056.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00056.2.bfq # Wed Mar 28 12:07:18 BST 2012: Converting fastq files to bfq ... # Wed Mar 28 12:07:18 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00055.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00055.2.bfq /data/maqgene/bin/maq sol2sanger 1210298692.00054.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00054.2.bfq # Wed Mar 28 12:07:19 BST 2012: Converting fastq files to bfq ... # Wed Mar 28 12:07:19 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00052.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00052.2.bfq /data/maqgene/bin/maq sol2sanger 1210298692.00053.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00053.2.bfq # Wed Mar 28 12:07:20 BST 2012: Converting fastq files to bfq ... # Wed Mar 28 12:07:20 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00039.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00039.2.bfq /data/maqgene/bin/maq sol2sanger 1210298692.00051.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00051.2.bfq # Wed Mar 28 12:07:21 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00038.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00038.2.bfq # Wed Mar 28 12:07:22 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00037.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00037.2.bfq -- finish writing file '1210298692.00060.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00057.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00061.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00038.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00039.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00055.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00056.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00059.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00058.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00053.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00054.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00052.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00051.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00037.2.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 12:07:44 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00074.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00074.2.bfq # Wed Mar 28 12:07:46 BST 2012: Converting fastq files to bfq ... # Wed Mar 28 12:07:46 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00073.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00073.2.bfq # Wed Mar 28 12:07:46 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00072.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00072.2.bfq /data/maqgene/bin/maq sol2sanger 1210298692.00075.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00075.2.bfq # Wed Mar 28 12:07:47 BST 2012: Converting fastq files to bfq ... # Wed Mar 28 12:07:47 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00071.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00071.2.bfq /data/maqgene/bin/maq sol2sanger 1210298692.00070.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00070.2.bfq # Wed Mar 28 12:07:48 BST 2012: Converting fastq files to bfq ... # Wed Mar 28 12:07:48 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00068.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00068.2.bfq /data/maqgene/bin/maq sol2sanger 1210298692.00069.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00069.2.bfq # Wed Mar 28 12:07:49 BST 2012: Converting fastq files to bfq ... # Wed Mar 28 12:07:49 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00067.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00067.2.bfq /data/maqgene/bin/maq sol2sanger 1210298692.00066.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00066.2.bfq # Wed Mar 28 12:07:50 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00064.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00064.2.bfq # Wed Mar 28 12:07:50 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00065.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00065.2.bfq # Wed Mar 28 12:07:51 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00063.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00063.2.bfq # Wed Mar 28 12:07:52 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00062.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00062.2.bfq -- finish writing file '1210298692.00074.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00075.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00067.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00069.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00072.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00073.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00071.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00068.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00070.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00064.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00066.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00065.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00062.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00063.2.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 12:08:13 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00088.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00088.2.bfq # Wed Mar 28 12:08:21 BST 2012: Converting fastq files to bfq ... # Wed Mar 28 12:08:21 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00087.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00087.2.bfq /data/maqgene/bin/maq sol2sanger 1210298692.00089.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00089.2.bfq # Wed Mar 28 12:08:21 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00086.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00086.2.bfq # Wed Mar 28 12:08:22 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00085.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00085.2.bfq # Wed Mar 28 12:08:22 BST 2012: Converting fastq files to bfq ... # Wed Mar 28 12:08:22 BST 2012: Converting fastq files to bfq ... out | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00083.2.bfq /data/maqgene/bin/maq sol2sanger 1210298692.00084.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00084.2.bfq # Wed Mar 28 12:08:23 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00080.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00080.2.bfq # Wed Mar 28 12:08:23 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00081.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00081.2.bfq # Wed Mar 28 12:08:23 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00082.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00082.2.bfq # Wed Mar 28 12:08:24 BST 2012: Converting fastq files to bfq ... # Wed Mar 28 12:08:24 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00078.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00078.2.bfq /data/maqgene/bin/maq sol2sanger 1210298692.00077.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00077.2.bfq # Wed Mar 28 12:08:24 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00079.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00079.2.bfq # Wed Mar 28 12:08:25 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1210298692.00076.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00076.2.bfq -- finish writing file '1210298692.00088.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00086.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00077.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00079.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00078.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00087.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00089.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00085.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00084.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00082.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00080.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00076.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00083.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1210298692.00081.2.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 12:08:47 BST 2012: Mapping file(s) 1210298692.00011.1.bfq 1210298692.00011.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1210298692.00011.unmapped -H 1210298692.00011.mismatch \ 1210298692.00011.map /data/maqgene/genomes/elegans.bfa 1210298692.00011.1.bfq 1210298692.00011.2.bfq 2> /dev/null # Wed Mar 28 12:08:56 BST 2012: Mapping file(s) 1210298692.00012.1.bfq 1210298692.00012.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1210298692.00012.unmapped -H 1210298692.00012.mismatch \ 1210298692.00012.map /data/maqgene/genomes/elegans.bfa 1210298692.00012.1.bfq 1210298692.00012.2.bfq 2> /dev/null # Wed Mar 28 12:08:56 BST 2012: Mapping file(s) 1210298692.00010.1.bfq 1210298692.00010.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1210298692.00010.unmapped -H 1210298692.00010.mismatch \ 1210298692.00010.map /data/maqgene/genomes/elegans.bfa 1210298692.00010.1.bfq 1210298692.00010.2.bfq 2> /dev/null # Wed Mar 28 12:08:57 BST 2012: Mapping file(s) 1210298692.00009.1.bfq 1210298692.00009.2.bfq # Wed Mar 28 12:08:57 BST 2012: Mapping file(s) 1210298692.00008.1.bfq 1210298692.00008.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1210298692.00009.unmapped -H 1210298692.00009.mismatch \ 1210298692.00009.map /data/maqgene/genomes/elegans.bfa 1210298692.00009.1.bfq 1210298692.00009.2.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 1210298692.00008.unmapped -H 1210298692.00008.mismatch \ 1210298692.00008.map /data/maqgene/genomes/elegans.bfa 1210298692.00008.1.bfq 1210298692.00008.2.bfq 2> /dev/null # Wed Mar 28 12:08:58 BST 2012: Mapping file(s) 1210298692.00006.1.bfq 1210298692.00006.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1210298692.00006.unmapped -H 1210298692.00006.mismatch \ 1210298692.00006.map /data/maqgene/genomes/elegans.bfa 1210298692.00006.1.bfq 1210298692.00006.2.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 1210298692.00007.unmapped -H 1210298692.00007.mismatch \ 1210298692.00007.map /data/maqgene/genomes/elegans.bfa 1210298692.00007.1.bfq 1210298692.00007.2.bfq 2> /dev/null # Wed Mar 28 12:08:59 BST 2012: Mapping file(s) 1210298692.00005.1.bfq 1210298692.00005.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1210298692.00005.unmapped -H 1210298692.00005.mismatch \ 1210298692.00005.map /data/maqgene/genomes/elegans.bfa 1210298692.00005.1.bfq 1210298692.00005.2.bfq 2> /dev/null # Wed Mar 28 12:08:59 BST 2012: Mapping file(s) 1210298692.00004.1.bfq 1210298692.00004.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1210298692.00004.unmapped -H 1210298692.00004.mismatch \ 1210298692.00004.map /data/maqgene/genomes/elegans.bfa 1210298692.00004.1.bfq 1210298692.00004.2.bfq 2> /dev/null # Wed Mar 28 12:09:00 BST 2012: Mapping file(s) 1210298692.00003.1.bfq 1210298692.00003.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1210298692.00003.unmapped -H 1210298692.00003.mismatch \ 1210298692.00003.map /data/maqgene/genomes/elegans.bfa 1210298692.00003.1.bfq 1210298692.00003.2.bfq 2> /dev/null # Wed Mar 28 12:09:00 BST 2012: Mapping file(s) 1210298692.00002.1.bfq 1210298692.00002.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1210298692.00002.unmapped -H 1210298692.00002.mismatch \ 1210298692.00002.map /data/maqgene/genomes/elegans.bfa 1210298692.00002.1.bfq 1210298692.00002.2.bfq 2> /dev/null # Wed Mar 28 12:14:52 BST 2012: Mapping file(s) 1210298692.00020.1.bfq 1210298692.00020.2.bfq # Wed Mar 28 12:14:52 BST 2012: Mapping file(s) 1210298692.00021.1.bfq 1210298692.00021.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1210298692.00021.unmapped -H 1210298692.00021.mismatch \ 1210298692.00021.map /data/maqgene/genomes/elegans.bfa 1210298692.00021.1.bfq 1210298692.00021.2.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 1210298692.00020.unmapped -H 1210298692.00020.mismatch \ 1210298692.00020.map /data/maqgene/genomes/elegans.bfa 1210298692.00020.1.bfq 1210298692.00020.2.bfq 2> /dev/null # Wed Mar 28 12:14:53 BST 2012: Mapping file(s) 1210298692.00019.1.bfq 1210298692.00019.2.bfq # Wed Mar 28 12:14:53 BST 2012: Mapping file(s) 1210298692.00018.1.bfq 1210298692.00018.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1210298692.00019.unmapped -H 1210298692.00019.mismatch \ 1210298692.00019.map /data/maqgene/genomes/elegans.bfa 1210298692.00019.1.bfq 1210298692.00019.2.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 1210298692.00018.unmapped -H 1210298692.00018.mismatch \ 1210298692.00018.map /data/maqgene/genomes/elegans.bfa 1210298692.00018.1.bfq 1210298692.00018.2.bfq 2> /dev/null # Wed Mar 28 12:14:53 BST 2012: Mapping file(s) 1210298692.00017.1.bfq 1210298692.00017.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1210298692.00017.unmapped -H 1210298692.00017.mismatch \ 1210298692.00017.map /data/maqgene/genomes/elegans.bfa 1210298692.00017.1.bfq 1210298692.00017.2.bfq 2> /dev/null # Wed Mar 28 12:14:54 BST 2012: Mapping file(s) 1210298692.00022.1.bfq 1210298692.00022.2.bfq # Wed Mar 28 12:14:54 BST 2012: Mapping file(s) 1210298692.00016.1.bfq 1210298692.00016.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1210298692.00022.unmapped -H 1210298692.00022.mismatch \ 1210298692.00022.map /data/maqgene/genomes/elegans.bfa 1210298692.00022.1.bfq 1210298692.00022.2.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 1210298692.00016.unmapped -H 1210298692.00016.mismatch \ 1210298692.00016.map /data/maqgene/genomes/elegans.bfa 1210298692.00016.1.bfq 1210298692.00016.2.bfq 2> /dev/null # Wed Mar 28 12:14:55 BST 2012: Mapping file(s) 1210298692.00015.1.bfq 1210298692.00015.2.bfq # Wed Mar 28 12:14:55 BST 2012: Mapping file(s) 1210298692.00014.1.bfq 1210298692.00014.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1210298692.00015.unmapped -H 1210298692.00015.mismatch \ 1210298692.00015.map /data/maqgene/genomes/elegans.bfa 1210298692.00015.1.bfq 1210298692.00015.2.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 1210298692.00014.unmapped -H 1210298692.00014.mismatch \ 1210298692.00014.map /data/maqgene/genomes/elegans.bfa 1210298692.00014.1.bfq 1210298692.00014.2.bfq 2> /dev/null # Wed Mar 28 12:14:56 BST 2012: Mapping file(s) 1210298692.00013.1.bfq 1210298692.00013.2.bfq # Wed Mar 28 12:14:56 BST 2012: Mapping file(s) 1210298692.00001.1.bfq 1210298692.00001.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1210298692.00013.unmapped -H 1210298692.00013.mismatch \ 1210298692.00013.map /data/maqgene/genomes/elegans.bfa 1210298692.00013.1.bfq 1210298692.00013.2.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 1210298692.00001.unmapped -H 1210298692.00001.mismatch \ 1210298692.00001.map /data/maqgene/genomes/elegans.bfa 1210298692.00001.1.bfq 1210298692.00001.2.bfq 2> /dev/null # Wed Mar 28 12:14:57 BST 2012: Converting fastq files to bfq ... # Wed Mar 28 12:14:57 BST 2012: Mapping file(s) 1210298692.00000.1.bfq 1210298692.00000.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1210298692.00000.unmapped -H 1210298692.00000.mismatch \ 1210298692.00000.map /data/maqgene/genomes/elegans.bfa 1210298692.00000.1.bfq 1210298692.00000.2.bfq 2> /dev/null /data/maqgene/bin/maq sol2sanger 1210298692.00090.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1210298692.00090.2.bfq -- finish writing file '1210298692.00090.2.bfq' -- 185321 sequences were loaded. # Wed Mar 28 12:15:00 BST 2012: Mapping file(s) 1210298692.00023.1.bfq 1210298692.00023.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1210298692.00023.unmapped -H 1210298692.00023.mismatch \ 1210298692.00023.map /data/maqgene/genomes/elegans.bfa 1210298692.00023.1.bfq 1210298692.00023.2.bfq 2> /dev/null # Wed Mar 28 12:21:18 BST 2012: Mapping file(s) 1210298692.00036.1.bfq 1210298692.00036.2.bfq # Wed Mar 28 12:21:18 BST 2012: Mapping file(s) 1210298692.00035.1.bfq 1210298692.00035.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1210298692.00036.unmapped -H 1210298692.00036.mismatch \ 1210298692.00036.map /data/maqgene/genomes/elegans.bfa 1210298692.00036.1.bfq 1210298692.00036.2.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 1210298692.00035.unmapped -H 1210298692.00035.mismatch \ 1210298692.00035.map /data/maqgene/genomes/elegans.bfa 1210298692.00035.1.bfq 1210298692.00035.2.bfq 2> /dev/null # Wed Mar 28 12:21:19 BST 2012: Mapping file(s) 1210298692.00034.1.bfq 1210298692.00034.2.bfq # Wed Mar 28 12:21:19 BST 2012: Mapping file(s) 1210298692.00033.1.bfq 1210298692.00033.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1210298692.00034.unmapped -H 1210298692.00034.mismatch \ 1210298692.00034.map /data/maqgene/genomes/elegans.bfa 1210298692.00034.1.bfq 1210298692.00034.2.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 1210298692.00033.unmapped -H 1210298692.00033.mismatch \ 1210298692.00033.map /data/maqgene/genomes/elegans.bfa 1210298692.00033.1.bfq 1210298692.00033.2.bfq 2> /dev/null # Wed Mar 28 12:21:20 BST 2012: Mapping file(s) 1210298692.00032.1.bfq 1210298692.00032.2.bfq # Wed Mar 28 12:21:20 BST 2012: Mapping file(s) 1210298692.00031.1.bfq 1210298692.00031.2.bfq 00032.unmapped -H 1210298692.00032.mismatch \ 1210298692.00032.map /data/maqgene/genomes/elegans.bfa 1210298692.00032.1.bfq 1210298692.00032.2.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 1210298692.00031.unmapped -H 1210298692.00031.mismatch \ 1210298692.00031.map /data/maqgene/genomes/elegans.bfa 1210298692.00031.1.bfq 1210298692.00031.2.bfq 2> /dev/null # Wed Mar 28 12:21:20 BST 2012: Mapping file(s) 1210298692.00030.1.bfq 1210298692.00030.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1210298692.00030.unmapped -H 1210298692.00030.mismatch \ 1210298692.00030.map /data/maqgene/genomes/elegans.bfa 1210298692.00030.1.bfq 1210298692.00030.2.bfq 2> /dev/null # Wed Mar 28 12:21:21 BST 2012: Mapping file(s) 1210298692.00037.1.bfq 1210298692.00037.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1210298692.00037.unmapped -H 1210298692.00037.mismatch \ 1210298692.00037.map /data/maqgene/genomes/elegans.bfa 1210298692.00037.1.bfq 1210298692.00037.2.bfq 2> /dev/null # Wed Mar 28 12:21:21 BST 2012: Mapping file(s) 1210298692.00029.1.bfq 1210298692.00029.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1210298692.00029.unmapped -H 1210298692.00029.mismatch \ 1210298692.00029.map /data/maqgene/genomes/elegans.bfa 1210298692.00029.1.bfq 1210298692.00029.2.bfq 2> /dev/null # Wed Mar 28 12:21:22 BST 2012: Mapping file(s) 1210298692.00027.1.bfq 1210298692.00027.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1210298692.00027.unmapped -H 1210298692.00027.mismatch \ 1210298692.00027.map /data/maqgene/genomes/elegans.bfa 1210298692.00027.1.bfq 1210298692.00027.2.bfq 2> /dev/null # Wed Mar 28 12:21:22 BST 2012: Mapping file(s) 1210298692.00028.1.bfq 1210298692.00028.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1210298692.00028.unmapped -H 1210298692.00028.mismatch \ 1210298692.00028.map /data/maqgene/genomes/elegans.bfa 1210298692.00028.1.bfq 1210298692.00028.2.bfq 2> /dev/null # Wed Mar 28 12:21:23 BST 2012: Mapping file(s) 1210298692.00026.1.bfq 1210298692.00026.2.bfq # Wed Mar 28 12:21:23 BST 2012: Mapping file(s) 1210298692.00025.1.bfq 1210298692.00025.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1210298692.00026.unmapped -H 1210298692.00026.mismatch \ 1210298692.00026.map /data/maqgene/genomes/elegans.bfa 1210298692.00026.1.bfq 1210298692.00026.2.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 1210298692.00025.unmapped -H 1210298692.00025.mismatch \ 1210298692.00025.map /data/maqgene/genomes/elegans.bfa 1210298692.00025.1.bfq 1210298692.00025.2.bfq 2> /dev/null # Wed Mar 28 12:21:24 BST 2012: Mapping file(s) 1210298692.00024.1.bfq 1210298692.00024.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1210298692.00024.unmapped -H 1210298692.00024.mismatch \ 1210298692.00024.map /data/maqgene/genomes/elegans.bfa 1210298692.00024.1.bfq 1210298692.00024.2.bfq 2> /dev/null # Wed Mar 28 12:27:58 BST 2012: Mapping file(s) 1210298692.00050.1.bfq 1210298692.00050.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1210298692.00050.unmapped -H 1210298692.00050.mismatch \ 1210298692.00050.map /data/maqgene/genomes/elegans.bfa 1210298692.00050.1.bfq 1210298692.00050.2.bfq 2> /dev/null # Wed Mar 28 12:27:59 BST 2012: Mapping file(s) 1210298692.00049.1.bfq 1210298692.00049.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1210298692.00049.unmapped -H 1210298692.00049.mismatch \ 1210298692.00049.map /data/maqgene/genomes/elegans.bfa 1210298692.00049.1.bfq 1210298692.00049.2.bfq 2> /dev/null # Wed Mar 28 12:28:00 BST 2012: Mapping file(s) 1210298692.00048.1.bfq 1210298692.00048.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1210298692.00048.unmapped -H 1210298692.00048.mismatch \ 1210298692.00048.map /data/maqgene/genomes/elegans.bfa 1210298692.00048.1.bfq 1210298692.00048.2.bfq 2> /dev/null # Wed Mar 28 12:28:01 BST 2012: Mapping file(s) 1210298692.00047.1.bfq 1210298692.00047.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1210298692.00047.unmapped -H 1210298692.00047.mismatch \ 1210298692.00047.map /data/maqgene/genomes/elegans.bfa 1210298692.00047.1.bfq 1210298692.00047.2.bfq 2> /dev/null # Wed Mar 28 12:28:02 BST 2012: Mapping file(s) 1210298692.00046.1.bfq 1210298692.00046.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1210298692.00046.unmapped -H 1210298692.00046.mismatch \ 1210298692.00046.map /data/maqgene/genomes/elegans.bfa 1210298692.00046.1.bfq 1210298692.00046.2.bfq 2> /dev/null # Wed Mar 28 12:28:03 BST 2012: Mapping file(s) 1210298692.00045.1.bfq 1210298692.00045.2.bfq # Wed Mar 28 12:28:03 BST 2012: Mapping file(s) 1210298692.00044.1.bfq 1210298692.00044.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1210298692.00045.unmapped -H 1210298692.00045.mismatch \ 1210298692.00045.map /data/maqgene/genomes/elegans.bfa 1210298692.00045.1.bfq 1210298692.00045.2.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 1210298692.00044.unmapped -H 1210298692.00044.mismatch \ 1210298692.00044.map /data/maqgene/genomes/elegans.bfa 1210298692.00044.1.bfq 1210298692.00044.2.bfq 2> /dev/null # Wed Mar 28 12:28:04 BST 2012: Mapping file(s) 1210298692.00043.1.bfq 1210298692.00043.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1210298692.00043.unmapped -H 1210298692.00043.mismatch \ 1210298692.00043.map /data/maqgene/genomes/elegans.bfa 1210298692.00043.1.bfq 1210298692.00043.2.bfq 2> /dev/null # Wed Mar 28 12:28:05 BST 2012: Mapping file(s) 1210298692.00042.1.bfq 1210298692.00042.2.bfq # Wed Mar 28 12:28:05 BST 2012: Mapping file(s) 1210298692.00041.1.bfq 1210298692.00041.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1210298692.00042.unmapped -H 1210298692.00042.mismatch \ 1210298692.00042.map /data/maqgene/genomes/elegans.bfa 1210298692.00042.1.bfq 1210298692.00042.2.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 1210298692.00041.unmapped -H 1210298692.00041.mismatch \ 1210298692.00041.map /data/maqgene/genomes/elegans.bfa 1210298692.00041.1.bfq 1210298692.00041.2.bfq 2> /dev/null # Wed Mar 28 12:28:06 BST 2012: Mapping file(s) 1210298692.00040.1.bfq 1210298692.00040.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1210298692.00040.unmapped -H 1210298692.00040.mismatch \ 1210298692.00040.map /data/maqgene/genomes/elegans.bfa 1210298692.00040.1.bfq 1210298692.00040.2.bfq 2> /dev/null # Wed Mar 28 12:28:07 BST 2012: Mapping file(s) 1210298692.00038.1.bfq 1210298692.00038.2.bfq # Wed Mar 28 12:28:07 BST 2012: Mapping file(s) 1210298692.00039.1.bfq 1210298692.00039.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1210298692.00038.unmapped -H 1210298692.00038.mismatch \ 1210298692.00038.map /data/maqgene/genomes/elegans.bfa 1210298692.00038.1.bfq 1210298692.00038.2.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 1210298692.00039.unmapped -H 1210298692.00039.mismatch \ 1210298692.00039.map /data/maqgene/genomes/elegans.bfa 1210298692.00039.1.bfq 1210298692.00039.2.bfq 2> /dev/null # Wed Mar 28 12:28:07 BST 2012: Mapping file(s) 1210298692.00051.1.bfq 1210298692.00051.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1210298692.00051.unmapped -H 1210298692.00051.mismatch \ 1210298692.00051.map /data/maqgene/genomes/elegans.bfa 1210298692.00051.1.bfq 1210298692.00051.2.bfq 2> /dev/null # Wed Mar 28 12:34:20 BST 2012: Mapping file(s) 1210298692.00064.1.bfq 1210298692.00064.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1210298692.00064.unmapped -H 1210298692.00064.mismatch \ 1210298692.00064.map /data/maqgene/genomes/elegans.bfa 1210298692.00064.1.bfq 1210298692.00064.2.bfq 2> /dev/null # Wed Mar 28 12:34:39 BST 2012: Mapping file(s) 1210298692.00063.1.bfq 1210298692.00063.2.bfq # Wed Mar 28 12:34:39 BST 2012: Mapping file(s) 1210298692.00065.1.bfq 1210298692.00065.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1210298692.00065.unmapped -H 1210298692.00065.mismatch \ 1210298692.00065.map /data/maqgene/genomes/elegans.bfa 1210298692.00065.1.bfq 1210298692.00065.2.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 1210298692.00063.unmapped -H 1210298692.00063.mismatch \ 1210298692.00063.map /data/maqgene/genomes/elegans.bfa 1210298692.00063.1.bfq 1210298692.00063.2.bfq 2> /dev/null # Wed Mar 28 12:34:40 BST 2012: Mapping file(s) 1210298692.00062.1.bfq 1210298692.00062.2.bfq # Wed Mar 28 12:34:40 BST 2012: Mapping file(s) 1210298692.00061.1.bfq 1210298692.00061.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1210298692.00062.unmapped -H 1210298692.00062.mismatch \ 1210298692.00062.map /data/maqgene/genomes/elegans.bfa 1210298692.00062.1.bfq 1210298692.00062.2.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 1210298692.00061.unmapped -H 1210298692.00061.mismatch \ 1210298692.00061.map /data/maqgene/genomes/elegans.bfa 1210298692.00061.1.bfq 1210298692.00061.2.bfq 2> /dev/null # Wed Mar 28 12:34:41 BST 2012: Mapping file(s) 1210298692.00060.1.bfq 1210298692.00060.2.bfq # Wed Mar 28 12:34:41 BST 2012: Mapping file(s) 1210298692.00059.1.bfq 1210298692.00059.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1210298692.00060.unmapped -H 1210298692.00060.mismatch \ 1210298692.00060.map /data/maqgene/genomes/elegans.bfa 1210298692.00060.1.bfq 1210298692.00060.2.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 1210298692.00059.unmapped -H 1210298692.00059.mismatch \ 1210298692.00059.map /data/maqgene/genomes/elegans.bfa 1210298692.00059.1.bfq 1210298692.00059.2.bfq 2> /dev/null # Wed Mar 28 12:34:42 BST 2012: Mapping file(s) 1210298692.00058.1.bfq 1210298692.00058.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1210298692.00058.unmapped -H 1210298692.00058.mismatch \ 1210298692.00058.map /data/maqgene/genomes/elegans.bfa 1210298692.00058.1.bfq 1210298692.00058.2.bfq 2> /dev/null # Wed Mar 28 12:34:42 BST 2012: Mapping file(s) 1210298692.00057.1.bfq 1210298692.00057.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1210298692.00057.unmapped -H 1210298692.00057.mismatch \ 1210298692.00057.map /data/maqgene/genomes/elegans.bfa 1210298692.00057.1.bfq 1210298692.00057.2.bfq 2> /dev/null # Wed Mar 28 12:34:43 BST 2012: Mapping file(s) 1210298692.00056.1.bfq 1210298692.00056.2.bfq # Wed Mar 28 12:34:43 BST 2012: Mapping file(s) 1210298692.00055.1.bfq 1210298692.00055.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1210298692.00056.unmapped -H 1210298692.00056.mismatch \ 1210298692.00056.map /data/maqgene/genomes/elegans.bfa 1210298692.00056.1.bfq 1210298692.00056.2.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 1210298692.00055.unmapped -H 1210298692.00055.mismatch \ 1210298692.00055.map /data/maqgene/genomes/elegans.bfa 1210298692.00055.1.bfq 1210298692.00055.2.bfq 2> /dev/null # Wed Mar 28 12:34:44 BST 2012: Mapping file(s) 1210298692.00054.1.bfq 1210298692.00054.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1210298692.00054.unmapped -H 1210298692.00054.mismatch \ 1210298692.00054.map /data/maqgene/genomes/elegans.bfa 1210298692.00054.1.bfq 1210298692.00054.2.bfq 2> /dev/null # Wed Mar 28 12:34:45 BST 2012: Mapping file(s) 1210298692.00053.1.bfq 1210298692.00053.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1210298692.00053.unmapped -H 1210298692.00053.mismatch \ 1210298692.00053.map /data/maqgene/genomes/elegans.bfa 1210298692.00053.1.bfq 1210298692.00053.2.bfq 2> /dev/null # Wed Mar 28 12:34:45 BST 2012: Mapping file(s) 1210298692.00052.1.bfq 1210298692.00052.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1210298692.00052.unmapped -H 1210298692.00052.mismatch \ 1210298692.00052.map /data/maqgene/genomes/elegans.bfa 1210298692.00052.1.bfq 1210298692.00052.2.bfq 2> /dev/null # Wed Mar 28 12:40:57 BST 2012: Mapping file(s) 1210298692.00078.1.bfq 1210298692.00078.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1210298692.00078.unmapped -H 1210298692.00078.mismatch \ 1210298692.00078.map /data/maqgene/genomes/elegans.bfa 1210298692.00078.1.bfq 1210298692.00078.2.bfq 2> /dev/null # Wed Mar 28 12:41:30 BST 2012: Mapping file(s) 1210298692.00079.1.bfq 1210298692.00079.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1210298692.00079.unmapped -H 1210298692.00079.mismatch \ 1210298692.00079.map /data/maqgene/genomes/elegans.bfa 1210298692.00079.1.bfq 1210298692.00079.2.bfq 2> /dev/null # Wed Mar 28 12:41:31 BST 2012: Mapping file(s) 1210298692.00077.1.bfq 1210298692.00077.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1210298692.00077.unmapped -H 1210298692.00077.mismatch \ 1210298692.00077.map /data/maqgene/genomes/elegans.bfa 1210298692.00077.1.bfq 1210298692.00077.2.bfq 2> /dev/null # Wed Mar 28 12:41:32 BST 2012: Mapping file(s) 1210298692.00076.1.bfq 1210298692.00076.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1210298692.00076.unmapped -H 1210298692.00076.mismatch \ 1210298692.00076.map /data/maqgene/genomes/elegans.bfa 1210298692.00076.1.bfq 1210298692.00076.2.bfq 2> /dev/null # Wed Mar 28 12:41:33 BST 2012: Mapping file(s) 1210298692.00075.1.bfq 1210298692.00075.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1210298692.00075.unmapped -H 1210298692.00075.mismatch \ 1210298692.00075.map /data/maqgene/genomes/elegans.bfa 1210298692.00075.1.bfq 1210298692.00075.2.bfq 2> /dev/null # Wed Mar 28 12:41:34 BST 2012: Mapping file(s) 1210298692.00074.1.bfq 1210298692.00074.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1210298692.00074.unmapped -H 1210298692.00074.mismatch \ 1210298692.00074.map /data/maqgene/genomes/elegans.bfa 1210298692.00074.1.bfq 1210298692.00074.2.bfq 2> /dev/null # Wed Mar 28 12:42:00 BST 2012: Mapping file(s) 1210298692.00073.1.bfq 1210298692.00073.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1210298692.00073.unmapped -H 1210298692.00073.mismatch \ 1210298692.00073.map /data/maqgene/genomes/elegans.bfa 1210298692.00073.1.bfq 1210298692.00073.2.bfq 2> /dev/null # Wed Mar 28 12:42:01 BST 2012: Mapping file(s) 1210298692.00072.1.bfq 1210298692.00072.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1210298692.00072.unmapped -H 1210298692.00072.mismatch \ 1210298692.00072.map /data/maqgene/genomes/elegans.bfa 1210298692.00072.1.bfq 1210298692.00072.2.bfq 2> /dev/null # Wed Mar 28 12:42:02 BST 2012: Mapping file(s) 1210298692.00071.1.bfq 1210298692.00071.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1210298692.00071.unmapped -H 1210298692.00071.mismatch \ 1210298692.00071.map /data/maqgene/genomes/elegans.bfa 1210298692.00071.1.bfq 1210298692.00071.2.bfq 2> /dev/null # Wed Mar 28 12:42:03 BST 2012: Mapping file(s) 1210298692.00070.1.bfq 1210298692.00070.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1210298692.00070.unmapped -H 1210298692.00070.mismatch \ 1210298692.00070.map /data/maqgene/genomes/elegans.bfa 1210298692.00070.1.bfq 1210298692.00070.2.bfq 2> /dev/null # Wed Mar 28 12:42:04 BST 2012: Mapping file(s) 1210298692.00069.1.bfq 1210298692.00069.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1210298692.00069.unmapped -H 1210298692.00069.mismatch \ 1210298692.00069.map /data/maqgene/genomes/elegans.bfa 1210298692.00069.1.bfq 1210298692.00069.2.bfq 2> /dev/null # Wed Mar 28 12:42:06 BST 2012: Mapping file(s) 1210298692.00068.1.bfq 1210298692.00068.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1210298692.00068.unmapped -H 1210298692.00068.mismatch \ 1210298692.00068.map /data/maqgene/genomes/elegans.bfa 1210298692.00068.1.bfq 1210298692.00068.2.bfq 2> /dev/null # Wed Mar 28 12:42:08 BST 2012: Mapping file(s) 1210298692.00067.1.bfq 1210298692.00067.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1210298692.00067.unmapped -H 1210298692.00067.mismatch \ 1210298692.00067.map /data/maqgene/genomes/elegans.bfa 1210298692.00067.1.bfq 1210298692.00067.2.bfq 2> /dev/null # Wed Mar 28 12:48:42 BST 2012: Mapping file(s) 1210298692.00090.1.bfq 1210298692.00090.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1210298692.00090.unmapped -H 1210298692.00090.mismatch \ 1210298692.00090.map /data/maqgene/genomes/elegans.bfa 1210298692.00090.1.bfq 1210298692.00090.2.bfq 2> /dev/null # Wed Mar 28 12:50:24 BST 2012: Mapping file(s) 1210298692.00089.1.bfq 1210298692.00089.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1210298692.00089.unmapped -H 1210298692.00089.mismatch \ 1210298692.00089.map /data/maqgene/genomes/elegans.bfa 1210298692.00089.1.bfq 1210298692.00089.2.bfq 2> /dev/null # Wed Mar 28 12:54:50 BST 2012: Mapping file(s) 1210298692.00088.1.bfq 1210298692.00088.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1210298692.00088.unmapped -H 1210298692.00088.mismatch \ 1210298692.00088.map /data/maqgene/genomes/elegans.bfa 1210298692.00088.1.bfq 1210298692.00088.2.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 1210298692.00087.unmapped -H 1210298692.00087.mismatch \ 1210298692.00087.map /data/maqgene/genomes/elegans.bfa 1210298692.00087.1.bfq 1210298692.00087.2.bfq 2> /dev/null # Wed Mar 28 12:58:43 BST 2012: Mapping file(s) 1210298692.00083.1.bfq 1210298692.00083.2.bfq # Wed Mar 28 12:58:43 BST 2012: Mapping file(s) 1210298692.00086.1.bfq 1210298692.00086.2.bfq # Wed Mar 28 12:58:43 BST 2012: Mapping file(s) 1210298692.00082.1.bfq 1210298692.00082.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1210298692.00084.unmapped -H 1210298692.00084.mismatch \ 1210298692.00084.map /data/maqgene/genomes/elegans.bfa 1210298692.00084.1.bfq 1210298692.00084.2.bfq 2> /dev/null # Wed Mar 28 12:58:43 BST 2012: Mapping file(s) 1210298692.00085.1.bfq 1210298692.00085.2.bfq # Wed Mar 28 12:58:43 BST 2012: Mapping file(s) 1210298692.00066.1.bfq 1210298692.00066.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1210298692.00086.unmapped -H 1210298692.00086.mismatch \ 1210298692.00086.map /data/maqgene/genomes/elegans.bfa 1210298692.00086.1.bfq 1210298692.00086.2.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 1210298692.00085.unmapped -H 1210298692.00085.mismatch \ 1210298692.00085.map /data/maqgene/genomes/elegans.bfa 1210298692.00085.1.bfq 1210298692.00085.2.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 1210298692.00083.unmapped -H 1210298692.00083.mismatch \ 1210298692.00083.map /data/maqgene/genomes/elegans.bfa 1210298692.00083.1.bfq 1210298692.00083.2.bfq 2> /dev/null # Wed Mar 28 12:58:43 BST 2012: Mapping file(s) 1210298692.00081.1.bfq 1210298692.00081.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1210298692.00082.unmapped -H 1210298692.00082.mismatch \ 1210298692.00082.map /data/maqgene/genomes/elegans.bfa 1210298692.00082.1.bfq 1210298692.00082.2.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 1210298692.00081.unmapped -H 1210298692.00081.mismatch \ 1210298692.00081.map /data/maqgene/genomes/elegans.bfa 1210298692.00081.1.bfq 1210298692.00081.2.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 1210298692.00066.unmapped -H 1210298692.00066.mismatch \ 1210298692.00066.map /data/maqgene/genomes/elegans.bfa 1210298692.00066.1.bfq 1210298692.00066.2.bfq 2> /dev/null # Wed Mar 28 12:58:43 BST 2012: Mapping file(s) 1210298692.00080.1.bfq 1210298692.00080.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1210298692.00080.unmapped -H 1210298692.00080.mismatch \ 1210298692.00080.map /data/maqgene/genomes/elegans.bfa 1210298692.00080.1.bfq 1210298692.00080.2.bfq 2> /dev/null # Wed Mar 28 13:04:15 BST 2012: Merging all maps ... /data/maqgene/bin/maq mapmerge 1210298692.map 1210298692.00000.map 1210298692.00001.map 1210298692.00002.map 1210298692.00003.map 1210298692.00004.map 1210298692.00005.map 1210298692.00006.map 1210298692.00007.map 1210298692.00008.map 1210298692.00009.map 1210298692.00010.map 1210298692.00011.map 1210298692.00012.map 1210298692.00013.map 1210298692.00014.map 1210298692.00015.map 1210298692.00016.map 1210298692.00017.map 1210298692.00018.map 1210298692.00019.map 1210298692.00020.map 1210298692.00021.map 1210298692.00022.map 1210298692.00023.map 1210298692.00024.map 1210298692.00025.map 1210298692.00026.map 1210298692.00027.map 1210298692.00028.map 1210298692.00029.map 1210298692.00030.map 1210298692.00031.map 1210298692.00032.map 1210298692.00033.map 1210298692.00034.map 1210298692.00035.map 1210298692.00036.map 1210298692.00037.map 1210298692.00038.map 1210298692.00039.map 1210298692.00040.map 1210298692.00041.map 1210298692.00042.map 1210298692.00043.map 1210298692.00044.map 1210298692.00045.map 1210298692.00046.map 1210298692.00047.map 1210298692.00048.map 1210298692.00049.map 1210298692.00050.map 1210298692.00051.map 1210298692.00052.map 1210298692.00053.map 1210298692.00054.map 1210298692.00055.map 1210298692.00056.map 1210298692.00057.map 1210298692.00058.map 1210298692.00059.map 1210298692.00060.map 1210298692.00061.map 1210298692.00062.map 1210298692.00063.map 1210298692.00064.map 1210298692.00065.map 1210298692.00066.map 1210298692.00067.map 1210298692.00068.map 1210298692.00069.map 1210298692.00070.map 1210298692.00071.map 1210298692.00072.map 1210298692.00073.map 1210298692.00074.map 1210298692.00075.map 1210298692.00076.map 1210298692.00077.map 1210298692.00078.map 1210298692.00079.map 1210298692.00080.map 1210298692.00081.map 1210298692.00082.map 1210298692.00083.map 1210298692.00084.map 1210298692.00085.map 1210298692.00086.map 1210298692.00087.map 1210298692.00088.map 1210298692.00089.map 1210298692.00090.map # Wed Mar 28 13:04:15 BST 2012: Merging all *.unmapped files ... cat 1210298692.00000.unmapped 1210298692.00001.unmapped 1210298692.00002.unmapped 1210298692.00003.unmapped 1210298692.00004.unmapped 1210298692.00005.unmapped 1210298692.00006.unmapped 1210298692.00007.unmapped 1210298692.00008.unmapped 1210298692.00009.unmapped 1210298692.00010.unmapped 1210298692.00011.unmapped 1210298692.00012.unmapped 1210298692.00013.unmapped 1210298692.00014.unmapped 1210298692.00015.unmapped 1210298692.00016.unmapped 1210298692.00017.unmapped 1210298692.00018.unmapped 1210298692.00019.unmapped 1210298692.00020.unmapped 1210298692.00021.unmapped 1210298692.00022.unmapped 1210298692.00023.unmapped 1210298692.00024.unmapped 1210298692.00025.unmapped 1210298692.00026.unmapped 1210298692.00027.unmapped 1210298692.00028.unmapped 1210298692.00029.unmapped 1210298692.00030.unmapped 1210298692.00031.unmapped 1210298692.00032.unmapped 1210298692.00033.unmapped 1210298692.00034.unmapped 1210298692.00035.unmapped 1210298692.00036.unmapped 1210298692.00037.unmapped 1210298692.00038.unmapped 1210298692.00039.unmapped 1210298692.00040.unmapped 1210298692.00041.unmapped 1210298692.00042.unmapped 1210298692.00043.unmapped 1210298692.00044.unmapped 1210298692.00045.unmapped 1210298692.00046.unmapped 1210298692.00047.unmapped 1210298692.00048.unmapped 1210298692.00049.unmapped 1210298692.00050.unmapped 1210298692.00051.unmapped 1210298692.00052.unmapped 1210298692.00053.unmapped 1210298692.00054.unmapped 1210298692.00055.unmapped 1210298692.00056.unmapped 1210298692.00057.unmapped 1210298692.00058.unmapped 1210298692.00059.unmapped 1210298692.00060.unmapped 1210298692.00061.unmapped 1210298692.00062.unmapped 1210298692.00063.unmapped 1210298692.00064.unmapped 1210298692.00065.unmapped 1210298692.00066.unmapped 1210298692.00067.unmapped 1210298692.00068.unmapped 1210298692.00069.unmapped 1210298692.00070.unmapped 1210298692.00071.unmapped 1210298692.00072.unmapped 1210298692.00073.unmapped 1210298692.00074.unmapped 1210298692.00075.unmapped 1210298692.00076.unmapped 1210298692.00077.unmapped 1210298692.00078.unmapped 1210298692.00079.unmapped 1210298692.00080.unmapped 1210298692.00081.unmapped 1210298692.00082.unmapped 1210298692.00083.unmapped 1210298692.00084.unmapped 1210298692.00085.unmapped 1210298692.00086.unmapped 1210298692.00087.unmapped 1210298692.00088.unmapped 1210298692.00089.unmapped 1210298692.00090.unmapped > 1210298692_unmapped.txt # Wed Mar 28 13:04:26 BST 2012: Linking backend file 1210298692_unmapped.txt to /data/maqgene/out/example_user/CB7073/CB7073_unmapped.txt ln -fs /data/maqgene/work/1210298692_unmapped.txt /data/maqgene/out/example_user/CB7073/CB7073_unmapped.txt /data/maqgene/makefile:126: warning: undefined variable `mapcheck_parameters' # Wed Mar 28 13:42:21 BST 2012: Generating consensus ... /data/maqgene/bin/maq assemble -N 2 -q 0 -r 0.0 -m 7 -Q 100 -p 1483950234.cns \ /data/maqgene/genomes/elegans.bfa 1210298692.map 2> 1483950234_log.txt # Wed Mar 28 13:58:29 BST 2012: Running 'mapcheck' ... /data/maqgene/bin/maq mapcheck /data/maqgene/genomes/elegans.bfa 1210298692.map > 1210298692_check.txt \ 2>/dev/null # Wed Mar 28 14:09:01 BST 2012: Linking backend file 1483950234_log.txt to /data/maqgene/out/example_user/CB7073/CB7073_log.txt ln -fs /data/maqgene/work/1483950234_log.txt /data/maqgene/out/example_user/CB7073/CB7073_log.txt # Wed Mar 28 14:09:01 BST 2012: Linking backend file 1210298692_check.txt to /data/maqgene/out/example_user/CB7073/CB7073_check.txt ln -fs /data/maqgene/work/1210298692_check.txt /data/maqgene/out/example_user/CB7073/CB7073_check.txt # Wed Mar 28 14:09:01 BST 2012: Creating pileup ... /data/maqgene/bin/maq pileup -Q 100 -p -m 7 -q 0 /data/maqgene/genomes/elegans.bfa 1210298692.map > 1351391557_pileup.txt /data/maqgene/bin/filter_matching_lines 1351391557_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 \ > 1351391557_known_snps # Wed Mar 28 14:20:22 BST 2012: Linking backend file 1351391557_pileup.txt to /data/maqgene/out/example_user/CB7073/CB7073_pileup.txt ln -fs /data/maqgene/work/1351391557_pileup.txt /data/maqgene/out/example_user/CB7073/CB7073_pileup.txt # Wed Mar 28 14:20:22 BST 2012: Filtering and loading pileup for analysis ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 1351391557_pileup; create table 1351391557_pileup ( dna enum('I','II','III','IV','MtDNA','V','X') NOT NULL, start int(10) NOT NULL, ref_base char(1) NOT NULL, read_depth int(5) NOT NULL, sample_reads varchar(100) NOT NULL, A_fwd int(5) NOT NULL, A_rev int(5) NOT NULL, C_fwd int(5) NOT NULL, C_rev int(5) NOT NULL, G_fwd int(5) NOT NULL, G_rev int(5) NOT NULL, T_fwd int(5) NOT NULL, T_rev int(5) NOT NULL, wt_fwd int(5) NOT NULL, wt_rev int(5) NOT NULL, primary key (dna, start) );" cat 1351391557_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 1351391557_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 1351391557_pileup" cat 1351391557_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 1351391557_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 1351391557_pileup" touch 1351391557_pileup # Wed Mar 28 14:22:07 BST 2012: Extracting point mutants from consensus ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 1483950234_snps; create table 1483950234_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) )" /data/maqgene/bin/maq cns2snp 1483950234.cns \ | cat -b | /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "load data local infile '/dev/stdin' into table 1483950234_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 1483950234_snps;" # Wed Mar 28 14:22:22 BST 2012: Extracting indels from consensus ... /data/maqgene/bin/maq indelsoa /data/maqgene/genomes/elegans.bfa 1210298692.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 1483950234_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 1483950234_snps;" # Wed Mar 28 14:29:44 BST 2012: Adding placeholders for known SNPs. cat 1351391557_known_snps \ | /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "load data local infile '/dev/stdin' ignore into table 1483950234_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 1483950234_snps;" Found 160915 variants. touch 1483950234_snps # Wed Mar 28 14:29:46 BST 2012: 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 1351391557_pileup p using (dna,start)" > /data/maqgene/out/example_user/CB7073/CB7073_snp_read_counts.txt 0 snp read count lines written. # Wed Mar 28 14:29:46 BST 2012: 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 1483950234_masked_ids; create table 1483950234_masked_ids (query_region_id int(10) NOT NULL, primary key (query_region_id)); load data local infile '/dev/stdin' ignore into table 1483950234_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 1483950234_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; touch 1483950234_masked_ids # Wed Mar 28 14:29:49 BST 2012: Finding all genomic features overlapping variants... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 1483950234_rel_snps; CREATE TABLE 1483950234_rel_snps ( association_id INT(10) NOT NULL, query_region_id INT(10) unsigned NOT NULL, target_region_id INT(10) NOT NULL, distance INT(10) NOT NULL, overlap INT(10) NOT NULL, same_strand enum('SAME', 'OPP') NOT NULL, num_regions_between INT(3) NOT NULL, PRIMARY KEY (association_id), KEY (query_region_id), KEY (target_region_id) )" /data/maqgene/bin/associate_regions -b -1 -c -1000000 -m 0 -o >(/usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "load data local infile '/dev/stdin' into table 1483950234_rel_snps; flush table 1483950234_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 1483950234_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 touch 1483950234_rel_snps # Wed Mar 28 14:29:53 BST 2012: Making coverage histogram ... (echo -en "sequencing_depth\tnumber_of_bases\n"; \ cut -f 4 1351391557_pileup.txt \ | /data/maqgene/bin/pileup_histogram 100) > 1351391557_coverage.txt # Wed Mar 28 14:31:24 BST 2012: Getting intergenic regions /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 1483950234_rel_intergenic; create table 1483950234_rel_intergenic like 1483950234_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 1483950234_rel_intergenic; flush table 1483950234_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 1483950234_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; # Wed Mar 28 14:31:29 BST 2012: Filtering masked intergenic regions /usr/bin/mysql -Dmaqgenedb -umaqgene --skip-column-names --batch --raw --local-infile -e "delete i.* from 1483950234_rel_intergenic i join 1483950234_masked_ids m using (query_region_id)" touch 1483950234_rel_intergenic # Wed Mar 28 14:31:34 BST 2012: Linking backend file 1351391557_coverage.txt to /data/maqgene/out/example_user/CB7073/CB7073_coverage.txt ln -fs /data/maqgene/work/1351391557_coverage.txt /data/maqgene/out/example_user/CB7073/CB7073_coverage.txt # Wed Mar 28 14:31:34 BST 2012: Classifying intergenic relations /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 1483950234_intergenic_assoc; create table 1483950234_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 1483950234_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 1483950234_snps snp join 1483950234_rel_intergenic rel on (snp.id = rel.query_region_id) join elegans_features feature on (rel.target_region_id = feature.id)" touch 1483950234_intergenic_assoc # Wed Mar 28 14:31:44 BST 2012: Calculating translation start offsets... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 1483950234_offsets_snps; create table 1483950234_offsets_snps ( id int(10) NOT NULL, gene varchar(50) NOT NULL, 5prime_offset int(10) NOT NULL, 3prime_offset int(10) NOT NULL, total_length int(10) NOT NULL, boundary_type char(20) NOT NULL, primary key (id, gene, boundary_type) );" /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 1483950234_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 1483950234_snps reg join 1483950234_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 1483950234_offsets_snps # Wed Mar 28 14:32:07 BST 2012: Getting uncovered regions ... cut -f 1,2,4 1351391557_pileup.txt \ | /data/maqgene/bin/get_uncovered_regions 50 \ > 1351391557_uncovered.txt # Wed Mar 28 14:33:39 BST 2012: Getting codons affected by point mutations... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 1483950234_codons; create table 1483950234_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 1483950234_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 1483950234_offsets_snps off join 1483950234_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 1483950234_codons # Wed Mar 28 14:33:49 BST 2012: Linking backend file 1351391557_uncovered.txt to /data/maqgene/out/example_user/CB7073/CB7073_uncovered.txt ln -fs /data/maqgene/work/1351391557_uncovered.txt /data/maqgene/out/example_user/CB7073/CB7073_uncovered.txt # Wed Mar 28 14:33:49 BST 2012: Loading uncovered regions into table ... cat 1351391557_uncovered.txt \ | /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 1351391557_uncovered; create table 1351391557_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 = 160916; load data local infile '/dev/stdin' into table 1351391557_uncovered (dna, start, end)" Uncovered region statistics: chromosome number_uncovered_regions total_uncovered_length I 3 598 II 13 2108 III 5 704 IV 8 754 V 7 894 X 9 5448 touch 1351391557_uncovered # Wed Mar 28 14:33:49 BST 2012: Finding mRNA features overlapping uncovered regions ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 1351391557_uncovered_rel; CREATE TABLE 1351391557_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 1351391557_uncovered_rel; flush table 1351391557_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 1351391557_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 1351391557_uncovered_rel # Wed Mar 28 14:33:51 BST 2012: Calculating translation start offsets for uncovered regions... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 1351391557_offsets_uncovered; create table 1351391557_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 1351391557_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 1351391557_uncovered reg join 1351391557_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 1351391557_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 1351391557_uncovered reg join 1351391557_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 1351391557_offsets_uncovered /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 1483950234_marked; create table 1483950234_marked ( id int(10) NOT NULL, class varchar(100) NOT NULL, description varchar(100) NOT NULL, parent_feature varchar(100) NOT NULL, primary key (id, class, parent_feature) );" # Wed Mar 28 14:33:52 BST 2012: Finding exonic indels ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 1483950234_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 1483950234_snps snp join 1483950234_rel_snps rel on (snp.id = rel.query_region_id) join elegans_features feature on (rel.target_region_id = feature.id) where feature.feature = 'exon' and snp.variant_type = 'indel';" # Wed Mar 28 14:33:52 BST 2012: Finding coding variants ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 1483950234_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 1483950234_codons trans join elegans_genetic_code reference_codons on (trans.ref_codon = reference_codons.codon) join elegans_genetic_code sample_codons on (trans.sam_codon = sample_codons.codon);" # Wed Mar 28 14:33:52 BST 2012: Finding noncoding variants ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 1483950234_marked select snp.id, feature.feature class, 'none' description, feature.attribute parent_feature from 1483950234_snps snp join 1483950234_rel_snps rel on (snp.id = rel.query_region_id) join elegans_features feature on (rel.target_region_id = feature.id) where feature.feature not in ('exon', 'intron', 'mRNA');" # Wed Mar 28 14:33:53 BST 2012: Finding splice site variants ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 1483950234_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 1483950234_snps snp join 1483950234_rel_snps rel on (snp.id = rel.query_region_id) join elegans_features feature on (rel.target_region_id = feature.id) where feature.feature = 'intron' and rel.distance > -2;" # Wed Mar 28 14:33:54 BST 2012: Finding intergenic and intronic variants ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 1483950234_marked select id, 'nongenic' class, concat(if (relation in ('upstream','into'), - distance, distance),' ',relation) description, attribute from 1483950234_intergenic_assoc where ((relation = 'upstream' and num_regions_between = 0 and distance < 50000) or (relation = 'upstream' and num_regions_between < 2 and distance < 1000) or (relation = 'downstream' and num_regions_between = 0 and distance < 1000) or (relation = 'downstream' and num_regions_between < 2 and distance < 1000) or relation = 'into' );" # Wed Mar 28 14:33:57 BST 2012: Finding uncovered regions in genes ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 1483950234_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 1351391557_uncovered unc join 1351391557_offsets_uncovered b using (id) join 1351391557_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 1351391557_uncovered unc join 1351391557_offsets_uncovered b using (id) join 1351391557_offsets_uncovered e using (id, gene) join elegans_features gene on (e.gene = gene.attribute) where b.boundary_type = 'start' and e.boundary_type = 'end' and gene.strand = '-' and gene.feature = 'mRNA'" # Wed Mar 28 14:33:57 BST 2012: Variants found: +-----------------+-----------------+ | class | number_variants | +-----------------+-----------------+ | five_prime_UTR | 1293 | | frameshift | 101 | | inframe | 30 | | missense | 6112 | | ncRNA | 870 | | nongenic | 124391 | | non_start | 9 | | premature_stop | 688 | | readthrough | 19 | | silent | 7403 | | SNP | 1034 | | splice_acceptor | 46 | | splice_donor | 46 | | three_prime_UTR | 3559 | | uncovered | 11 | +-----------------+-----------------+ touch 1483950234_marked # Wed Mar 28 14:33:59 BST 2012: Combining results ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 1483950234_combined; create table 1483950234_combined (primary key (id, class, description), key (dna, start)) as select snp.id, 'CB7073' 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 1483950234_snps snp join 1351391557_pileup pile using (dna,start) join 1483950234_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, 'CB7073' 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 1351391557_uncovered unc join 1483950234_marked class on (unc.id = class.id) left join elegans_per_locus using (dna,start) group by id, class, description; alter table 1483950234_combined order by dna, start, length" touch 1483950234_combined # Wed Mar 28 14:34:05 BST 2012: Writing results to grouped file ... /usr/bin/mysql -Dmaqgenedb -umaqgene --skip-column-names --batch --raw --local-infile --column-names -e "select id, mutant_strain, dna, start, length, reference_base, sample_base, consensus_score, loci_multiplicity, mapping_quality, neighbor_quality, number_wildtype_reads, number_variant_reads, sequencing_depth, sample_reads, variant_type, indel_size, group_concat(class) classes, group_concat(description) descriptions, group_concat(concat('{',parent_features,'}')) parent_features from 1483950234_combined group by id order by dna, start;" > /data/maqgene/out/example_user/CB7073/CB7073_grouped.txt 2341 lines written. # Wed Mar 28 14:34:05 BST 2012: Writing results to flat file ... /usr/bin/mysql -Dmaqgenedb -umaqgene --skip-column-names --batch --raw --local-infile --column-names -e "select * from 1483950234_combined" > /data/maqgene/out/example_user/CB7073/CB7073_flat.txt 4003 lines written. rm 1210298692.00017.2.fastq 1210298692.00086.1.fastq 1210298692.00059.map 1210298692.00026.1.fastq 1210298692.00036.mismatch 1210298692.00042.map 1210298692.00023.2.bfq 1210298692.00077.2.fastq 1210298692.00018.unmapped 1210298692.00008.mismatch 1210298692.00002.2.fastq 1210298692.00032.mismatch 1210298692.00058.unmapped 1210298692.00054.1.fastq 1210298692.00023.mismatch 1210298692.00024.map 1210298692.00019.2.bfq 1210298692.00084.2.bfq 1210298692.00057.mismatch 1210298692.00024.2.bfq 1210298692.00088.1.bfq 1210298692.00047.2.fastq 1210298692.00080.1.bfq 1210298692.00018.1.fastq 1210298692.00019.mismatch 1210298692.00041.mismatch 1210298692.00062.1.bfq 1210298692.00045.unmapped 1210298692.00065.1.fastq 1210298692.00078.unmapped 1210298692.00082.2.bfq 1210298692.00051.mismatch 1210298692.00037.mismatch 1210298692.00022.unmapped 1210298692.00064.map 1210298692.00046.map 1210298692.00015.2.bfq 1210298692.00037.2.bfq 1210298692.00045.1.bfq 4252044719_split2 1210298692.00087.1.fastq 1210298692.00045.1.fastq 1210298692.00015.mismatch 1210298692.00035.2.fastq 1210298692.00005.2.bfq 1210298692.00022.1.fastq 1210298692.00085.unmapped 1210298692.00074.2.bfq 1210298692.00074.mismatch 1210298692.00043.1.fastq 1210298692.00084.2.fastq 1210298692.00089.map 1210298692.00083.map 1210298692.00014.2.bfq 1210298692.00003.unmapped 1210298692.00041.2.bfq 1210298692.00025.1.bfq 1210298692.00030.unmapped 1210298692.00026.2.fastq 1210298692.00073.unmapped 1210298692.00059.unmapped 1210298692.00086.map 1210298692.00006.map 1210298692.00069.unmapped 1210298692.00037.unmapped 1210298692.00027.unmapped 1210298692.00009.1.bfq 1210298692.00070.map 1210298692.00054.2.fastq 1210298692.00007.1.fastq 1210298692.00074.map 1210298692.00003.1.fastq 1210298692.00030.1.fastq 1210298692.00048.unmapped 1210298692.00073.1.fastq 1210298692.00018.2.fastq 1210298692.00078.2.fastq 1210298692.00048.mismatch 1210298692.00027.1.fastq 1210298692.00028.mismatch 1210298692.00065.mismatch 1210298692.00053.2.bfq 1210298692.00043.1.bfq 1210298692.00052.unmapped 1210298692.00063.mismatch 1210298692.00013.unmapped 1210298692.00029.mismatch 1210298692.00051.1.bfq 1210298692.00000.map 1210298692.00048.2.bfq 1210298692.00059.1.bfq 1210298692.00052.mismatch 1210298692.00086.2.bfq 1210298692.00040.1.bfq 1210298692.00056.1.bfq 1210298692.00079.2.bfq 1210298692.00045.2.fastq 1210298692.00060.1.bfq 1210298692.00075.mismatch 1210298692.00068.mismatch 1210298692.00090.2.bfq 1210298692.00022.2.fastq 1210298692.00073.2.bfq 1210298692.00031.1.fastq 1210298692.00053.1.bfq 1210298692.00013.1.fastq 1210298692.00038.2.bfq 1210298692.00088.2.bfq 1210298692.00084.1.bfq 1210298692.00076.1.bfq 1210298692.00022.mismatch 1210298692.00043.map 1210298692.00038.map 1210298692.00040.mismatch 1210298692.00025.2.bfq 1210298692.00088.1.fastq 1210298692.00065.2.bfq 1210298692.00064.1.bfq 1210298692.00082.1.fastq 1210298692.00054.map 1210298692.00076.unmapped 1210298692.00068.1.fastq 1210298692.00001.map 1210298692.00010.map 1210298692.00044.2.fastq 1210298692.00003.2.fastq 1210298692.00055.1.fastq 1210298692.00086.2.fastq 1210298692.00007.map 1210298692.00016.map 1210298692.00021.1.fastq 1210298692.00048.2.fastq 1210298692.00089.mismatch 1210298692.00039.1.bfq 1210298692.00033.mismatch 1210298692.00013.1.bfq 1210298692.00027.2.fastq 1210298692.00008.1.fastq 1210298692.00050.2.bfq 1210298692.00060.2.bfq 1210298692.00034.map 1210298692.00031.unmapped 1210298692.00036.unmapped 1210298692.00040.2.bfq 1210298692.00066.mismatch 1210298692.00051.map 1210298692.00067.map 1210298692.00005.1.fastq 1210298692.00004.mismatch 1210298692.00029.map 1210298692.00050.1.fastq 1210298692.00069.1.fastq 1210298692.00027.2.bfq 1210298692.00012.1.bfq 1210298692.00054.unmapped 1210298692.00029.unmapped 1210298692.00079.1.bfq 1210298692.00036.1.fastq 1210298692.00056.mismatch 1210298692.00031.2.fastq 1210298692.00013.2.fastq 1210298692.00005.unmapped 1210298692.00019.unmapped 1210298692.00011.2.bfq 1210298692.00084.unmapped 1210298692.00062.map 1210298692.00032.1.fastq 1210298692.00057.1.fastq 1210298692.00072.map 1210298692.00068.unmapped 1210298692.00023.1.fastq 1210298692.00017.map 1210298692.00049.mismatch 1210298692.00080.2.bfq 1210298692.00059.mismatch 1210298692.00021.1.bfq 1210298692.00079.mismatch 1210298692.00089.2.bfq 1210298692.00068.2.fastq 1210298692.00005.1.bfq 1210298692.00059.2.bfq 1210298692.00019.1.fastq 1210298692.00064.mismatch 1210298692.00002.map 1210298692.00020.map 1210298692.00042.1.bfq 1210298692.00020.2.fastq 1210298692.00051.1.fastq 1210298692.00077.mismatch 1210298692.00089.1.fastq 1210298692.00089.2.fastq 1210298692.00028.1.bfq 1210298692.00082.map 1210298692.00014.mismatch 1210298692.00047.map 1210298692.00039.2.bfq 1210298692.00087.2.fastq 1210298692.00072.1.bfq 1210298692.00035.mismatch 1210298692.00021.map 1210298692.00077.2.bfq 1210298692.00064.2.bfq 1210298692.00015.1.fastq 1210298692.00039.mismatch 1210298692.00050.unmapped 1210298692.00043.2.fastq 1210298692.00008.2.bfq 1210298692.00070.unmapped 1210298692.00083.unmapped 1210298692.00005.2.fastq 1210298692.00009.1.fastq 1210298692.00050.2.fastq 1210298692.00000.unmapped 1210298692.00012.map 1210298692.00046.1.bfq 1210298692.00066.unmapped 1210298692.00036.2.fastq 1210298692.00069.map 1210298692.00007.2.fastq 1210298692.00032.2.fastq 1210298692.00053.mismatch 1210298692.00023.2.fastq 1210298692.00052.2.fastq 1210298692.00078.1.bfq 1210298692.00076.map 1210298692.00057.map 1210298692.00026.map 1210298692.00035.2.bfq 1210298692.00085.2.bfq 1210298692.00055.2.bfq 1210298692.00056.2.bfq 1210298692.00019.2.fastq 1210298692.00036.1.bfq 1210298692.00028.1.fastq 1210298692.00049.unmapped 1210298692.00058.1.fastq 1210298692.00061.mismatch 1210298692.00051.2.fastq 1210298692.00079.unmapped 1210298692.00006.1.bfq 1210298692.00051.2.bfq 1210298692.00038.1.bfq 1210298692.00071.1.bfq 1210298692.00028.2.bfq 1210298692.00009.2.bfq 1210298692.00013.map 1210298692.00055.map 1210298692.00042.mismatch 1210298692.00018.map 1210298692.00052.1.fastq 1210298692.00083.1.bfq 1210298692.00010.2.bfq 1210298692.00015.2.fastq 1210298692.00007.1.bfq 1210298692.00075.1.fastq 1210298692.00024.mismatch 1210298692.00082.1.bfq 1210298692.00078.mismatch 1210298692.00052.1.bfq 1210298692.00025.unmapped 1210298692.00053.map 1210298692.00086.1.bfq 1210298692.00027.1.bfq 1210298692.00088.2.fastq 1210298692.00037.map 1210298692.00009.map 1210298692.00045.map 1210298692.00018.2.bfq 1210298692.00046.2.bfq 1210298692.00082.2.fastq 1210298692.00000.1.bfq 1210298692.00022.map 1210298692.00085.1.fastq 1210298692.00033.unmapped 1210298692.00025.1.fastq 1210298692.00046.mismatch 1210298692.00058.1.bfq 1210298692.00055.2.fastq 1210298692.00063.2.bfq 1210298692.00042.2.bfq 1210298692.00065.unmapped 1210298692.00021.2.fastq 1210298692.00090.1.bfq 1210298692.00077.1.bfq 1210298692.00011.unmapped 1210298692.00008.2.fastq 1210298692.00004.unmapped 1210298692.00026.mismatch 1210298692.00033.1.fastq 1210298692.00035.unmapped 1210298692.00028.2.fastq 1210298692.00002.1.bfq 1210298692.00010.2.fastq 1210298692.00003.map 1210298692.00006.2.bfq 1210298692.00030.map 1210298692.00056.unmapped 1210298692.00058.map 1210298692.00001.1.bfq 1210298692.00010.1.bfq 1210298692.00073.map 1210298692.00070.2.bfq 1210298692.00044.mismatch 1210298692.00032.unmapped 1210298692.00087.map 1210298692.00049.2.bfq 1210298692.00004.1.fastq 1210298692.00069.2.fastq 1210298692.00027.map 1210298692.00040.1.fastq 1210298692.00026.2.bfq 1210298692.00060.mismatch 1210298692.00070.mismatch 1210298692.00080.mismatch 1210298692.00090.mismatch 1210298692.00044.2.bfq 1210298692.00075.2.fastq 1210298692.00055.1.bfq 1210298692.00033.2.bfq 1210298692.00042.unmapped 1210298692.00056.1.fastq 1210298692.00057.2.fastq 1210298692.00064.unmapped 1210298692.00034.1.bfq 1210298692.00020.2.bfq 1210298692.00037.1.fastq 1210298692.00041.unmapped 1210298692.00040.unmapped 1210298692.00004.map 1210298692.00085.mismatch 1210298692.00000.2.bfq 1210298692.00014.unmapped 1210298692.00060.unmapped 1210298692.00031.map 1210298692.00076.1.fastq 1210298692.00025.2.fastq 1210298692.00081.map 1210298692.00064.1.fastq 1210298692.00000.mismatch 1210298692.00067.1.bfq 1210298692.00081.2.bfq 1210298692.00039.unmapped 1210298692.00071.map 1210298692.00041.1.fastq 1210298692.00069.1.bfq 1210298692.00087.1.bfq 1210298692.00071.2.bfq 1210298692.00075.unmapped 1210298692.00074.1.fastq 1210298692.00065.2.fastq 1210298692.00071.mismatch 1210298692.00014.1.fastq 1210298692.00081.mismatch 1210298692.00068.map 1210298692.00033.2.fastq 1210298692.00083.mismatch 1210298692.00080.map 1210298692.00023.unmapped 1210298692.00016.1.bfq 1210298692.00063.unmapped 1210298692.00039.1.fastq 1210298692.00038.mismatch 1210298692.00069.2.bfq 1210298692.00001.2.bfq 1210298692.00009.2.fastq 1210298692.00066.1.bfq 1210298692.00020.1.bfq 1210298692.00004.2.fastq 1210298692.00053.unmapped 1210298692.00031.2.bfq 1210298692.00040.2.fastq 1210298692.00001.mismatch 1210298692.00010.mismatch 1210298692.00016.2.bfq 1210298692.00075.2.bfq 1210298692.00039.map 1210298692.00047.1.bfq 1210298692.00044.unmapped 1210298692.00067.1.fastq 1210298692.00033.1.bfq 1210298692.00089.1.bfq 1210298692.00005.map 1210298692.00087.2.bfq 4252044719_split1 1210298692.00053.1.fastq 1210298692.00043.mismatch 1210298692.00063.1.fastq 1210298692.00013.2.bfq 1210298692.00034.mismatch 1210298692.00036.map 1210298692.00029.2.bfq 1210298692.00036.2.bfq 1210298692.00020.unmapped 1210298692.00032.1.bfq 1210298692.00011.map 1210298692.00058.2.fastq 1210298692.00064.2.fastq 1210298692.00084.1.fastq 1210298692.00032.map 1210298692.00048.1.fastq 1210298692.00023.map 1210298692.00011.mismatch 1210298692.00041.2.fastq 1210298692.00024.unmapped 1210298692.00065.1.bfq 1210298692.00086.unmapped 1210298692.00028.unmapped 1210298692.00014.2.fastq 1210298692.00041.1.bfq 1210298692.00061.unmapped 1210298692.00042.1.fastq 1210298692.00014.map 1210298692.00019.map 1210298692.00017.2.bfq 1210298692.00007.2.bfq 1210298692.00043.2.bfq 1210298692.00025.mismatch 1210298692.00048.map 1210298692.00062.mismatch 1210298692.00039.2.fastq 1210298692.00072.mismatch 1210298692.00024.1.fastq 1210298692.00017.mismatch 1210298692.00057.1.bfq 1210298692.00002.2.bfq 1210298692.00046.unmapped 1210298692.00006.mismatch 1210298692.00083.2.bfq 1210298692.00061.1.bfq 1210298692.00030.2.fastq 1210298692.00084.mismatch 1210298692.00002.mismatch 1210298692.00015.map 1210298692.00020.mismatch 1210298692.00047.2.bfq 1210298692.00085.2.fastq 1210298692.00070.1.fastq 1210298692.00083.1.fastq 1210298692.00062.2.bfq 1210298692.00046.1.fastq 1210298692.00047.mismatch 1210298692.00053.2.fastq 1210298692.00052.2.bfq 1210298692.00087.unmapped 1210298692.00051.unmapped 1210298692.00066.1.fastq 1210298692.00063.map 1210298692.00086.mismatch 1210298692.00034.2.bfq 1210298692.00006.unmapped 1210298692.00081.1.bfq 1210298692.00012.2.bfq 1210298692.00043.unmapped 1210298692.00074.1.bfq 1210298692.00082.mismatch 1210298692.00080.unmapped 1210298692.00090.unmapped 1210298692.00022.1.bfq 1210298692.00084.map 1210298692.00073.mismatch 1210298692.00088.unmapped 1210298692.00030.1.bfq 1210298692.00012.mismatch 1210298692.00088.map 1210298692.00042.2.fastq 1210298692.00085.map 1210298692.00077.map 1210298692.00006.1.fastq 1210298692.00028.map 1210298692.00021.mismatch 1210298692.00049.1.fastq 1210298692.00060.1.fastq 1210298692.00059.1.fastq 1210298692.00080.1.fastq 1210298692.00090.1.fastq 1210298692.00079.1.fastq 1210298692.00024.2.fastq 1210298692.00017.1.bfq 1210298692.00008.map 1210298692.00054.2.bfq 1210298692.00037.2.fastq 1210298692.00052.map 1210298692.00035.1.bfq 1210298692.00003.1.bfq 1210298692.00048.1.bfq 1210298692.00082.unmapped 1210298692.00077.1.fastq 1210298692.00073.1.bfq 1210298692.00054.mismatch 1210298692.00075.map 1210298692.00071.unmapped 1210298692.00081.unmapped 1210298692.00008.1.bfq 1210298692.00069.mismatch 1210298692.00015.unmapped 1210298692.00032.2.bfq 1210298692.00046.2.fastq 1210298692.00060.map 1210298692.00000.1.fastq 1210298692.00018.mismatch 1210298692.00074.2.fastq 1210298692.00038.unmapped 1210298692.00007.mismatch 1210298692.00061.1.fastq 1210298692.00071.1.fastq 1210298692.00081.1.fastq 1210298692.00066.map 1210298692.00025.map 1210298692.00045.2.bfq 1210298692.00057.2.bfq 1210298692.00001.unmapped 1210298692.00010.unmapped 1210298692.00034.unmapped 1210298692.00054.1.bfq 1210298692.00022.2.bfq 1210298692.00037.1.bfq 1210298692.00031.1.bfq 1210298692.00007.unmapped 1210298692.00038.1.fastq 1210298692.00045.mismatch 1210298692.00024.1.bfq 1210298692.00056.2.fastq 1210298692.00016.unmapped 1210298692.00021.2.bfq 1210298692.00033.map 1210298692.00006.2.fastq 1210298692.00035.1.fastq 1210298692.00010.1.fastq 1210298692.00060.2.fastq 1210298692.00070.2.fastq 1210298692.00080.2.fastq 1210298692.00090.2.fastq 1210298692.00076.mismatch 1210298692.00067.unmapped 1210298692.00049.map 1210298692.00074.unmapped 1210298692.00014.1.bfq 1210298692.00079.map 1210298692.00016.1.fastq 1210298692.00021.unmapped 1210298692.00003.2.bfq 1210298692.00063.2.fastq 1210298692.00040.map 1210298692.00030.2.bfq 1210298692.00008.unmapped 1210298692.00009.mismatch 1210298692.00018.1.bfq 1210298692.00034.1.fastq 1210298692.00003.mismatch 1210298692.00056.map 1210298692.00030.mismatch 1210298692.00073.2.fastq 1210298692.00076.2.bfq 1210298692.00055.mismatch 1210298692.00072.2.bfq 1210298692.00038.2.fastq 1210298692.00000.2.fastq 1210298692.00026.1.bfq 1210298692.00062.unmapped 1210298692.00029.1.fastq 1210298692.00027.mismatch 1210298692.00011.1.fastq 1210298692.00090.map 1210298692.00078.1.fastq 1210298692.00017.unmapped 1210298692.00004.1.bfq 1210298692.00061.2.fastq 1210298692.00071.2.fastq 1210298692.00081.2.fastq 1210298692.00050.1.bfq 1210298692.00011.1.bfq 1210298692.00075.1.bfq 1210298692.00087.mismatch 1210298692.00002.unmapped 1210298692.00067.mismatch 1210298692.00062.1.fastq 1210298692.00057.unmapped 1210298692.00041.map 1210298692.00072.1.fastq 1210298692.00063.1.bfq 1210298692.00078.2.bfq 1210298692.00017.1.fastq 1210298692.00029.1.bfq 1210298692.00058.mismatch 1210298692.00055.unmapped 1210298692.00047.unmapped 1210298692.00031.mismatch 1210298692.00023.1.bfq 1210298692.00013.mismatch 1210298692.00058.2.bfq 1210298692.00001.2.fastq 1210298692.00001.1.fastq 1210298692.00076.2.fastq 1210298692.00044.map 1210298692.00002.1.fastq 1210298692.00035.map 1210298692.00020.1.fastq 1210298692.00068.1.bfq 1210298692.00068.2.bfq 1210298692.00083.2.fastq 1210298692.00067.2.bfq 1210298692.00019.1.bfq 1210298692.00089.unmapped 1210298692.00016.2.fastq 1210298692.00049.1.bfq 1210298692.00047.1.fastq 1210298692.00066.2.fastq 1210298692.00044.1.bfq 1210298692.00061.map 1210298692.00012.unmapped 1210298692.00034.2.fastq 1210298692.00044.1.fastq 1210298692.00050.map 1210298692.00061.2.bfq 1210298692.00004.2.bfq 1210298692.00085.1.bfq 1210298692.00015.1.bfq 1210298692.00012.2.fastq 1210298692.00029.2.fastq 1210298692.00011.2.fastq 1210298692.00012.1.fastq 1210298692.00009.unmapped 1210298692.00026.unmapped 1210298692.00088.mismatch 1210298692.00078.map 1210298692.00070.1.bfq 1210298692.00049.2.fastq 1210298692.00067.2.fastq 1210298692.00059.2.fastq 1210298692.00065.map 1210298692.00005.mismatch 1210298692.00077.unmapped 1210298692.00079.2.fastq 1210298692.00062.2.fastq 1210298692.00050.mismatch 1210298692.00016.mismatch 1210298692.00072.2.fastq 1210298692.00066.2.bfq 1210298692.00072.unmapped make: Leaving directory `/data/maqgene/work' make: Entering directory `/data/maqgene/work' # Wed Mar 28 14:34:09 BST 2012: Cleaning intermediate data ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 1483950234_snps,1483950234_rel,1483950234_masked_ids,1483950234_rel_intergenic,1483950234_intergenic_assoc,1483950234_offsets,1483950234_codons,1483950234_marked,1483950234_combined,1351391557_pileup" rm -f 1483950234_snps 1483950234_rel 1483950234_masked_ids 1483950234_rel_intergenic 1483950234_intergenic_assoc 1483950234_offsets 1483950234_codons 1483950234_marked 1483950234_combined 1351391557_pileup make: Leaving directory `/data/maqgene/work'