Finished reading input. ++ echo ot340/./ot340_chrI_11m_12m_read1.fastq,CB6841/./s_1_1_sequence_read1.fastq,CB6878/./s_7_1_sequence_read1.fastq ++ tr , ' ' + fastq_file_set1='ot340/./ot340_chrI_11m_12m_read1.fastq CB6841/./s_1_1_sequence_read1.fastq CB6878/./s_7_1_sequence_read1.fastq' ++ cd /data/maqgene/reads ++ wc -l ++ cat ot340/./ot340_chrI_11m_12m_read1.fastq CB6841/./s_1_1_sequence_read1.fastq CB6878/./s_7_1_sequence_read1.fastq ++ cut -f 1 -d ' ' + TOTAL_LINES=223597348 ++ echo '(223597348 / 5000000) + (223597348 % 5000000 != 0)' ++ bc + num_chunks=45 + 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=4151819774 map_cksum=1453441340 pileup_cksum=3703570229 cns_cksum=2225133155 umdd=50000 dmdd=1000 umid=1000 dmid=1000 max_gene_radius=50000 full_results_dir=/data/maqgene/out/example_user/CB6878 outfile_basename=CB6878 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=45 Will process 223597348 lines of input in 45 chunks make: Entering directory `/data/maqgene/work' # Thu Feb 3 19:25:41 GMT 2011: Removing frontend files in case this is a duplicate run ... rm -f /data/maqgene/out/example_user/CB6878/CB6878_{grouped.txt,flat.txt} rm -f /data/maqgene/out/example_user/CB6878/CB6878_uncovered.txt /data/maqgene/out/example_user/CB6878/CB6878_coverage.txt /data/maqgene/out/example_user/CB6878/CB6878_pileup.txt /data/maqgene/out/example_user/CB6878/CB6878_log.txt /data/maqgene/out/example_user/CB6878/CB6878_check.txt /data/maqgene/out/example_user/CB6878/CB6878_unmapped.txt make: Leaving directory `/data/maqgene/work' make: Entering directory `/data/maqgene/work' /data/maqgene/makefile:76: warning: undefined variable `date' /data/maqgene/makefile:78: warning: undefined variable `date' # : Regrouping fastq reads into chunks of size 5000000. split -l 5000000 -a 5 -d <(cat /data/maqgene/reads/ot340/./ot340_chrI_11m_12m_read1.fastq /data/maqgene/reads/CB6841/./s_1_1_sequence_read1.fastq /data/maqgene/reads/CB6878/./s_7_1_sequence_read1.fastq) 1453441340.1.fastq. # : Regrouping fastq reads into chunks of size 5000000. split -l 5000000 -a 5 -d <(cat /data/maqgene/reads/ot340/./ot340_chrI_11m_12m_read2.fastq /data/maqgene/reads/CB6841/./s_1_2_sequence_read2.fastq /data/maqgene/reads/CB6878/./s_7_2_sequence_read2.fastq) 1453441340.2.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; do mv 1453441340.1.fastq.$stem 1453441340.$stem.1.fastq; done touch 4151819774_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; do mv 1453441340.2.fastq.$stem 1453441340.$stem.2.fastq; done touch 4151819774_split2 # Thu Feb 3 19:28:11 GMT 2011: Converting fastq files to bfq ... # Thu Feb 3 19:28:11 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1453441340.00000.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1453441340.00000.1.bfq # Thu Feb 3 19:28:11 GMT 2011: Converting fastq files to bfq ... # Thu Feb 3 19:28:11 GMT 2011: Converting fastq files to bfq ... # Thu Feb 3 19:28:11 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1453441340.00002.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1453441340.00002.1.bfq /data/maqgene/bin/maq sol2sanger 1453441340.00001.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1453441340.00001.1.bfq /data/maqgene/bin/maq sol2sanger 1453441340.00003.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1453441340.00003.1.bfq # Thu Feb 3 19:28:11 GMT 2011: Converting fastq files to bfq ... out | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1453441340.00004.1.bfq # Thu Feb 3 19:28:11 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1453441340.00005.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1453441340.00005.1.bfq /data/maqgene/bin/maq sol2sanger 1453441340.00006.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1453441340.00006.1.bfq /data/maqgene/bin/maq sol2sanger 1453441340.00007.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1453441340.00007.1.bfq # Thu Feb 3 19:28:11 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1453441340.00008.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1453441340.00008.1.bfq # Thu Feb 3 19:28:11 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1453441340.00009.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1453441340.00009.1.bfq # Thu Feb 3 19:28:11 GMT 2011: Converting fastq files to bfq ... # Thu Feb 3 19:28:11 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1453441340.00012.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1453441340.00012.1.bfq # Thu Feb 3 19:28:11 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1453441340.00013.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1453441340.00013.1.bfq # Thu Feb 3 19:28:11 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1453441340.00010.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1453441340.00010.1.bfq /data/maqgene/bin/maq sol2sanger 1453441340.00011.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1453441340.00011.1.bfq -- finish writing file '1453441340.00005.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 19:28:37 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1453441340.00014.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1453441340.00014.1.bfq -- finish writing file '1453441340.00000.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 19:28:38 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1453441340.00015.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1453441340.00015.1.bfq -- finish writing file '1453441340.00002.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 19:28:39 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1453441340.00016.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1453441340.00016.1.bfq -- finish writing file '1453441340.00013.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 19:28:41 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1453441340.00017.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1453441340.00017.1.bfq -- finish writing file '1453441340.00011.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 19:28:41 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1453441340.00018.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1453441340.00018.1.bfq -- finish writing file '1453441340.00007.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 19:28:41 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1453441340.00019.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1453441340.00019.1.bfq -- finish writing file '1453441340.00006.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 19:28:42 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1453441340.00020.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1453441340.00020.1.bfq -- finish writing file '1453441340.00004.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 19:28:42 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1453441340.00021.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1453441340.00021.1.bfq -- finish writing file '1453441340.00012.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 19:28:42 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1453441340.00022.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1453441340.00022.1.bfq -- finish writing file '1453441340.00009.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 19:28:42 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1453441340.00023.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1453441340.00023.1.bfq -- finish writing file '1453441340.00001.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 19:28:43 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1453441340.00024.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1453441340.00024.1.bfq -- finish writing file '1453441340.00008.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 19:28:43 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1453441340.00025.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1453441340.00025.1.bfq -- finish writing file '1453441340.00010.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 19:28:45 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1453441340.00026.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1453441340.00026.1.bfq -- finish writing file '1453441340.00003.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 19:28:48 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1453441340.00027.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1453441340.00027.1.bfq -- finish writing file '1453441340.00015.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1453441340.00020.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1453441340.00014.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1453441340.00025.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1453441340.00021.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1453441340.00023.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1453441340.00016.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1453441340.00017.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1453441340.00018.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1453441340.00024.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1453441340.00022.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1453441340.00019.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1453441340.00027.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1453441340.00026.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 19:29:29 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1453441340.00040.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1453441340.00040.1.bfq -- finish writing file '1453441340.00040.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 19:29:48 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1453441340.00041.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1453441340.00041.1.bfq # Thu Feb 3 19:29:55 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1453441340.00042.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1453441340.00042.1.bfq # Thu Feb 3 19:29:55 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1453441340.00039.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1453441340.00039.1.bfq # Thu Feb 3 19:29:56 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1453441340.00038.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1453441340.00038.1.bfq # Thu Feb 3 19:29:57 GMT 2011: Converting fastq files to bfq ... # Thu Feb 3 19:29:57 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1453441340.00036.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1453441340.00036.1.bfq /data/maqgene/bin/maq sol2sanger 1453441340.00037.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1453441340.00037.1.bfq # Thu Feb 3 19:29:58 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1453441340.00035.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1453441340.00035.1.bfq # Thu Feb 3 19:29:59 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1453441340.00033.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1453441340.00033.1.bfq # Thu Feb 3 19:29:59 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1453441340.00034.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1453441340.00034.1.bfq -- finish writing file '1453441340.00041.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1453441340.00038.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1453441340.00042.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1453441340.00039.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1453441340.00035.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1453441340.00036.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1453441340.00037.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1453441340.00034.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1453441340.00033.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 19:30:29 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1453441340.00005.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1453441340.00005.2.bfq # Thu Feb 3 19:30:35 GMT 2011: Converting fastq files to bfq ... # Thu Feb 3 19:30:35 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1453441340.00006.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1453441340.00006.2.bfq /data/maqgene/bin/maq sol2sanger 1453441340.00004.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1453441340.00004.2.bfq # Thu Feb 3 19:30:36 GMT 2011: Converting fastq files to bfq ... # Thu Feb 3 19:30:36 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1453441340.00002.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1453441340.00002.2.bfq /data/maqgene/bin/maq sol2sanger 1453441340.00003.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1453441340.00003.2.bfq # Thu Feb 3 19:30:37 GMT 2011: Converting fastq files to bfq ... # Thu Feb 3 19:30:37 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1453441340.00000.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1453441340.00000.2.bfq /data/maqgene/bin/maq sol2sanger 1453441340.00001.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1453441340.00001.2.bfq # Thu Feb 3 19:30:38 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1453441340.00044.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1453441340.00044.1.bfq # Thu Feb 3 19:30:38 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1453441340.00043.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1453441340.00043.1.bfq # Thu Feb 3 19:30:39 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1453441340.00032.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1453441340.00032.1.bfq # Thu Feb 3 19:30:39 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1453441340.00031.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1453441340.00031.1.bfq -- finish writing file '1453441340.00005.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1453441340.00044.1.bfq' -- 899337 sequences were loaded. -- finish writing file '1453441340.00006.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1453441340.00001.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1453441340.00000.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1453441340.00032.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1453441340.00004.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1453441340.00002.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1453441340.00003.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1453441340.00031.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1453441340.00043.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 19:31:13 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1453441340.00016.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1453441340.00016.2.bfq # Thu Feb 3 19:31:25 GMT 2011: Converting fastq files to bfq ... # Thu Feb 3 19:31:25 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1453441340.00017.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1453441340.00017.2.bfq /data/maqgene/bin/maq sol2sanger 1453441340.00015.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1453441340.00015.2.bfq # Thu Feb 3 19:31:26 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1453441340.00014.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1453441340.00014.2.bfq # Thu Feb 3 19:31:26 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1453441340.00013.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1453441340.00013.2.bfq -- finish writing file '1453441340.00016.2.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 19:31:27 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1453441340.00012.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1453441340.00012.2.bfq # Thu Feb 3 19:31:27 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1453441340.00011.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1453441340.00011.2.bfq # Thu Feb 3 19:31:28 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1453441340.00018.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1453441340.00018.2.bfq # Thu Feb 3 19:31:28 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1453441340.00010.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1453441340.00010.2.bfq # Thu Feb 3 19:31:29 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1453441340.00009.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1453441340.00009.2.bfq # Thu Feb 3 19:31:29 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1453441340.00008.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1453441340.00008.2.bfq -- finish writing file '1453441340.00015.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1453441340.00018.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1453441340.00013.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1453441340.00017.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1453441340.00011.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1453441340.00012.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1453441340.00014.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1453441340.00009.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1453441340.00008.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1453441340.00010.2.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 19:32:05 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1453441340.00027.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1453441340.00027.2.bfq -- finish writing file '1453441340.00027.2.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 19:32:19 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1453441340.00028.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1453441340.00028.2.bfq # Thu Feb 3 19:32:20 GMT 2011: Converting fastq files to bfq ... # Thu Feb 3 19:32:20 GMT 2011: Converting fastq files to bfq ... # Thu Feb 3 19:32:20 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1453441340.00029.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1453441340.00029.2.bfq /data/maqgene/bin/maq sol2sanger 1453441340.00026.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1453441340.00026.2.bfq /data/maqgene/bin/maq sol2sanger 1453441340.00025.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1453441340.00025.2.bfq # Thu Feb 3 19:32:21 GMT 2011: Converting fastq files to bfq ... # Thu Feb 3 19:32:21 GMT 2011: Converting fastq files to bfq ... out | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1453441340.00024.2.bfq # Thu Feb 3 19:32:21 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1453441340.00023.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1453441340.00023.2.bfq /data/maqgene/bin/maq sol2sanger 1453441340.00022.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1453441340.00022.2.bfq # Thu Feb 3 19:32:22 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1453441340.00020.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1453441340.00020.2.bfq # Thu Feb 3 19:32:22 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1453441340.00021.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1453441340.00021.2.bfq # Thu Feb 3 19:32:22 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1453441340.00019.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1453441340.00019.2.bfq # Thu Feb 3 19:32:23 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1453441340.00007.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1453441340.00007.2.bfq # Thu Feb 3 19:32:23 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1453441340.00030.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1453441340.00030.1.bfq # Thu Feb 3 19:32:23 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1453441340.00029.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1453441340.00029.1.bfq # Thu Feb 3 19:32:24 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1453441340.00028.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1453441340.00028.1.bfq -- finish writing file '1453441340.00028.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1453441340.00025.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1453441340.00029.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1453441340.00023.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1453441340.00007.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1453441340.00026.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1453441340.00022.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1453441340.00024.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1453441340.00029.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1453441340.00020.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1453441340.00030.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1453441340.00019.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1453441340.00028.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1453441340.00021.2.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 19:33:12 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1453441340.00042.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1453441340.00042.2.bfq -- finish writing file '1453441340.00042.2.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 19:33:28 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1453441340.00043.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1453441340.00043.2.bfq -- finish writing file '1453441340.00043.2.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 19:33:43 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1453441340.00044.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1453441340.00044.2.bfq -- finish writing file '1453441340.00044.2.bfq' -- 899337 sequences were loaded. # Thu Feb 3 19:33:53 GMT 2011: Mapping file(s) 1453441340.00000.1.bfq 1453441340.00000.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1453441340.00000.unmapped -H 1453441340.00000.mismatch \ 1453441340.00000.map /data/maqgene/genomes/elegans.bfa 1453441340.00000.1.bfq 1453441340.00000.2.bfq 2> /dev/null # Thu Feb 3 19:34:00 GMT 2011: Mapping file(s) 1453441340.00001.1.bfq 1453441340.00001.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1453441340.00001.unmapped -H 1453441340.00001.mismatch \ 1453441340.00001.map /data/maqgene/genomes/elegans.bfa 1453441340.00001.1.bfq 1453441340.00001.2.bfq 2> /dev/null # Thu Feb 3 19:34:02 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1453441340.00041.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1453441340.00041.2.bfq # Thu Feb 3 19:34:04 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1453441340.00040.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1453441340.00040.2.bfq # Thu Feb 3 19:34:05 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1453441340.00039.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1453441340.00039.2.bfq # Thu Feb 3 19:34:06 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1453441340.00038.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1453441340.00038.2.bfq # Thu Feb 3 19:34:07 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1453441340.00037.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1453441340.00037.2.bfq # Thu Feb 3 19:34:08 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1453441340.00036.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1453441340.00036.2.bfq # Thu Feb 3 19:34:09 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1453441340.00035.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1453441340.00035.2.bfq # Thu Feb 3 19:34:10 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1453441340.00034.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1453441340.00034.2.bfq -- finish writing file '1453441340.00040.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1453441340.00039.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1453441340.00036.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1453441340.00041.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1453441340.00035.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1453441340.00038.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1453441340.00037.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1453441340.00034.2.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 19:40:06 GMT 2011: Mapping file(s) 1453441340.00009.1.bfq 1453441340.00009.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1453441340.00009.unmapped -H 1453441340.00009.mismatch \ 1453441340.00009.map /data/maqgene/genomes/elegans.bfa 1453441340.00009.1.bfq 1453441340.00009.2.bfq 2> /dev/null # Thu Feb 3 19:40:07 GMT 2011: Mapping file(s) 1453441340.00008.1.bfq 1453441340.00008.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1453441340.00008.unmapped -H 1453441340.00008.mismatch \ 1453441340.00008.map /data/maqgene/genomes/elegans.bfa 1453441340.00008.1.bfq 1453441340.00008.2.bfq 2> /dev/null # Thu Feb 3 19:40:08 GMT 2011: Mapping file(s) 1453441340.00007.1.bfq 1453441340.00007.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1453441340.00007.unmapped -H 1453441340.00007.mismatch \ 1453441340.00007.map /data/maqgene/genomes/elegans.bfa 1453441340.00007.1.bfq 1453441340.00007.2.bfq 2> /dev/null # Thu Feb 3 19:40:09 GMT 2011: Mapping file(s) 1453441340.00006.1.bfq 1453441340.00006.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1453441340.00006.unmapped -H 1453441340.00006.mismatch \ 1453441340.00006.map /data/maqgene/genomes/elegans.bfa 1453441340.00006.1.bfq 1453441340.00006.2.bfq 2> /dev/null # Thu Feb 3 19:40:10 GMT 2011: Mapping file(s) 1453441340.00005.1.bfq 1453441340.00005.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1453441340.00005.unmapped -H 1453441340.00005.mismatch \ 1453441340.00005.map /data/maqgene/genomes/elegans.bfa 1453441340.00005.1.bfq 1453441340.00005.2.bfq 2> /dev/null # Thu Feb 3 19:41:56 GMT 2011: Mapping file(s) 1453441340.00011.1.bfq 1453441340.00011.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1453441340.00011.unmapped -H 1453441340.00011.mismatch \ 1453441340.00011.map /data/maqgene/genomes/elegans.bfa 1453441340.00011.1.bfq 1453441340.00011.2.bfq 2> /dev/null # Thu Feb 3 19:41:58 GMT 2011: Mapping file(s) 1453441340.00010.1.bfq 1453441340.00010.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1453441340.00010.unmapped -H 1453441340.00010.mismatch \ 1453441340.00010.map /data/maqgene/genomes/elegans.bfa 1453441340.00010.1.bfq 1453441340.00010.2.bfq 2> /dev/null # Thu Feb 3 19:42:00 GMT 2011: Mapping file(s) 1453441340.00004.1.bfq 1453441340.00004.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1453441340.00004.unmapped -H 1453441340.00004.mismatch \ 1453441340.00004.map /data/maqgene/genomes/elegans.bfa 1453441340.00004.1.bfq 1453441340.00004.2.bfq 2> /dev/null # Thu Feb 3 19:42:01 GMT 2011: Mapping file(s) 1453441340.00003.1.bfq 1453441340.00003.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1453441340.00003.unmapped -H 1453441340.00003.mismatch \ 1453441340.00003.map /data/maqgene/genomes/elegans.bfa 1453441340.00003.1.bfq 1453441340.00003.2.bfq 2> /dev/null # Thu Feb 3 19:42:02 GMT 2011: Mapping file(s) 1453441340.00002.1.bfq 1453441340.00002.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1453441340.00002.unmapped -H 1453441340.00002.mismatch \ 1453441340.00002.map /data/maqgene/genomes/elegans.bfa 1453441340.00002.1.bfq 1453441340.00002.2.bfq 2> /dev/null # Thu Feb 3 19:42:03 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1453441340.00033.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1453441340.00033.2.bfq # Thu Feb 3 19:42:04 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1453441340.00032.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1453441340.00032.2.bfq # Thu Feb 3 19:42:05 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1453441340.00031.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1453441340.00031.2.bfq -- finish writing file '1453441340.00033.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1453441340.00032.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1453441340.00031.2.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 19:46:42 GMT 2011: Mapping file(s) 1453441340.00017.1.bfq 1453441340.00017.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1453441340.00017.unmapped -H 1453441340.00017.mismatch \ 1453441340.00017.map /data/maqgene/genomes/elegans.bfa 1453441340.00017.1.bfq 1453441340.00017.2.bfq 2> /dev/null # Thu Feb 3 19:46:43 GMT 2011: Mapping file(s) 1453441340.00016.1.bfq 1453441340.00016.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1453441340.00016.unmapped -H 1453441340.00016.mismatch \ 1453441340.00016.map /data/maqgene/genomes/elegans.bfa 1453441340.00016.1.bfq 1453441340.00016.2.bfq 2> /dev/null # Thu Feb 3 19:46:44 GMT 2011: Mapping file(s) 1453441340.00018.1.bfq 1453441340.00018.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1453441340.00018.unmapped -H 1453441340.00018.mismatch \ 1453441340.00018.map /data/maqgene/genomes/elegans.bfa 1453441340.00018.1.bfq 1453441340.00018.2.bfq 2> /dev/null # Thu Feb 3 19:46:45 GMT 2011: Mapping file(s) 1453441340.00015.1.bfq 1453441340.00015.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1453441340.00015.unmapped -H 1453441340.00015.mismatch \ 1453441340.00015.map /data/maqgene/genomes/elegans.bfa 1453441340.00015.1.bfq 1453441340.00015.2.bfq 2> /dev/null # Thu Feb 3 19:46:46 GMT 2011: Mapping file(s) 1453441340.00014.1.bfq 1453441340.00014.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1453441340.00014.unmapped -H 1453441340.00014.mismatch \ 1453441340.00014.map /data/maqgene/genomes/elegans.bfa 1453441340.00014.1.bfq 1453441340.00014.2.bfq 2> /dev/null # Thu Feb 3 19:46:47 GMT 2011: Mapping file(s) 1453441340.00013.1.bfq 1453441340.00013.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1453441340.00013.unmapped -H 1453441340.00013.mismatch \ 1453441340.00013.map /data/maqgene/genomes/elegans.bfa 1453441340.00013.1.bfq 1453441340.00013.2.bfq 2> /dev/null # Thu Feb 3 19:46:48 GMT 2011: Mapping file(s) 1453441340.00012.1.bfq 1453441340.00012.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1453441340.00012.unmapped -H 1453441340.00012.mismatch \ 1453441340.00012.map /data/maqgene/genomes/elegans.bfa 1453441340.00012.1.bfq 1453441340.00012.2.bfq 2> /dev/null # Thu Feb 3 19:46:49 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1453441340.00030.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1453441340.00030.2.bfq -- finish writing file '1453441340.00030.2.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 19:47:37 GMT 2011: Mapping file(s) 1453441340.00020.1.bfq 1453441340.00020.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1453441340.00020.unmapped -H 1453441340.00020.mismatch \ 1453441340.00020.map /data/maqgene/genomes/elegans.bfa 1453441340.00020.1.bfq 1453441340.00020.2.bfq 2> /dev/null # Thu Feb 3 19:47:38 GMT 2011: Mapping file(s) 1453441340.00019.1.bfq 1453441340.00019.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1453441340.00019.unmapped -H 1453441340.00019.mismatch \ 1453441340.00019.map /data/maqgene/genomes/elegans.bfa 1453441340.00019.1.bfq 1453441340.00019.2.bfq 2> /dev/null # Thu Feb 3 19:48:12 GMT 2011: Mapping file(s) 1453441340.00023.1.bfq 1453441340.00023.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1453441340.00023.unmapped -H 1453441340.00023.mismatch \ 1453441340.00023.map /data/maqgene/genomes/elegans.bfa 1453441340.00023.1.bfq 1453441340.00023.2.bfq 2> /dev/null # Thu Feb 3 19:48:13 GMT 2011: Mapping file(s) 1453441340.00022.1.bfq 1453441340.00022.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1453441340.00022.unmapped -H 1453441340.00022.mismatch \ 1453441340.00022.map /data/maqgene/genomes/elegans.bfa 1453441340.00022.1.bfq 1453441340.00022.2.bfq 2> /dev/null # Thu Feb 3 19:48:14 GMT 2011: Mapping file(s) 1453441340.00021.1.bfq 1453441340.00021.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1453441340.00021.unmapped -H 1453441340.00021.mismatch \ 1453441340.00021.map /data/maqgene/genomes/elegans.bfa 1453441340.00021.1.bfq 1453441340.00021.2.bfq 2> /dev/null # Thu Feb 3 19:48:21 GMT 2011: Mapping file(s) 1453441340.00024.1.bfq 1453441340.00024.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1453441340.00024.unmapped -H 1453441340.00024.mismatch \ 1453441340.00024.map /data/maqgene/genomes/elegans.bfa 1453441340.00024.1.bfq 1453441340.00024.2.bfq 2> /dev/null # Thu Feb 3 19:50:03 GMT 2011: Mapping file(s) 1453441340.00025.1.bfq 1453441340.00025.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1453441340.00025.unmapped -H 1453441340.00025.mismatch \ 1453441340.00025.map /data/maqgene/genomes/elegans.bfa 1453441340.00025.1.bfq 1453441340.00025.2.bfq 2> /dev/null # Thu Feb 3 19:52:58 GMT 2011: Mapping file(s) 1453441340.00030.1.bfq 1453441340.00030.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1453441340.00030.unmapped -H 1453441340.00030.mismatch \ 1453441340.00030.map /data/maqgene/genomes/elegans.bfa 1453441340.00030.1.bfq 1453441340.00030.2.bfq 2> /dev/null # Thu Feb 3 19:53:00 GMT 2011: Mapping file(s) 1453441340.00029.1.bfq 1453441340.00029.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1453441340.00029.unmapped -H 1453441340.00029.mismatch \ 1453441340.00029.map /data/maqgene/genomes/elegans.bfa 1453441340.00029.1.bfq 1453441340.00029.2.bfq 2> /dev/null # Thu Feb 3 19:53:02 GMT 2011: Mapping file(s) 1453441340.00028.1.bfq 1453441340.00028.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1453441340.00028.unmapped -H 1453441340.00028.mismatch \ 1453441340.00028.map /data/maqgene/genomes/elegans.bfa 1453441340.00028.1.bfq 1453441340.00028.2.bfq 2> /dev/null # Thu Feb 3 19:53:03 GMT 2011: Mapping file(s) 1453441340.00027.1.bfq 1453441340.00027.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1453441340.00027.unmapped -H 1453441340.00027.mismatch \ 1453441340.00027.map /data/maqgene/genomes/elegans.bfa 1453441340.00027.1.bfq 1453441340.00027.2.bfq 2> /dev/null # Thu Feb 3 19:53:04 GMT 2011: Mapping file(s) 1453441340.00026.1.bfq 1453441340.00026.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1453441340.00026.unmapped -H 1453441340.00026.mismatch \ 1453441340.00026.map /data/maqgene/genomes/elegans.bfa 1453441340.00026.1.bfq 1453441340.00026.2.bfq 2> /dev/null # Thu Feb 3 19:53:28 GMT 2011: Mapping file(s) 1453441340.00032.1.bfq 1453441340.00032.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1453441340.00032.unmapped -H 1453441340.00032.mismatch \ 1453441340.00032.map /data/maqgene/genomes/elegans.bfa 1453441340.00032.1.bfq 1453441340.00032.2.bfq 2> /dev/null # Thu Feb 3 19:53:30 GMT 2011: Mapping file(s) 1453441340.00031.1.bfq 1453441340.00031.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1453441340.00031.unmapped -H 1453441340.00031.mismatch \ 1453441340.00031.map /data/maqgene/genomes/elegans.bfa 1453441340.00031.1.bfq 1453441340.00031.2.bfq 2> /dev/null # Thu Feb 3 19:54:28 GMT 2011: Mapping file(s) 1453441340.00036.1.bfq 1453441340.00036.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1453441340.00036.unmapped -H 1453441340.00036.mismatch \ 1453441340.00036.map /data/maqgene/genomes/elegans.bfa 1453441340.00036.1.bfq 1453441340.00036.2.bfq 2> /dev/null # Thu Feb 3 19:54:28 GMT 2011: Mapping file(s) 1453441340.00035.1.bfq 1453441340.00035.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1453441340.00035.unmapped -H 1453441340.00035.mismatch \ 1453441340.00035.map /data/maqgene/genomes/elegans.bfa 1453441340.00035.1.bfq 1453441340.00035.2.bfq 2> /dev/null # Thu Feb 3 19:54:29 GMT 2011: Mapping file(s) 1453441340.00037.1.bfq 1453441340.00037.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1453441340.00037.unmapped -H 1453441340.00037.mismatch \ 1453441340.00037.map /data/maqgene/genomes/elegans.bfa 1453441340.00037.1.bfq 1453441340.00037.2.bfq 2> /dev/null # Thu Feb 3 19:54:30 GMT 2011: Mapping file(s) 1453441340.00034.1.bfq 1453441340.00034.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1453441340.00034.unmapped -H 1453441340.00034.mismatch \ 1453441340.00034.map /data/maqgene/genomes/elegans.bfa 1453441340.00034.1.bfq 1453441340.00034.2.bfq 2> /dev/null # Thu Feb 3 19:54:31 GMT 2011: Mapping file(s) 1453441340.00033.1.bfq 1453441340.00033.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1453441340.00033.unmapped -H 1453441340.00033.mismatch \ 1453441340.00033.map /data/maqgene/genomes/elegans.bfa 1453441340.00033.1.bfq 1453441340.00033.2.bfq 2> /dev/null # Thu Feb 3 19:54:34 GMT 2011: Mapping file(s) 1453441340.00038.1.bfq 1453441340.00038.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1453441340.00038.unmapped -H 1453441340.00038.mismatch \ 1453441340.00038.map /data/maqgene/genomes/elegans.bfa 1453441340.00038.1.bfq 1453441340.00038.2.bfq 2> /dev/null # Thu Feb 3 19:58:58 GMT 2011: Mapping file(s) 1453441340.00041.1.bfq 1453441340.00041.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1453441340.00041.unmapped -H 1453441340.00041.mismatch \ 1453441340.00041.map /data/maqgene/genomes/elegans.bfa 1453441340.00041.1.bfq 1453441340.00041.2.bfq 2> /dev/null # Thu Feb 3 19:59:00 GMT 2011: Mapping file(s) 1453441340.00040.1.bfq 1453441340.00040.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1453441340.00040.unmapped -H 1453441340.00040.mismatch \ 1453441340.00040.map /data/maqgene/genomes/elegans.bfa 1453441340.00040.1.bfq 1453441340.00040.2.bfq 2> /dev/null # Thu Feb 3 19:59:02 GMT 2011: Mapping file(s) 1453441340.00039.1.bfq 1453441340.00039.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1453441340.00039.unmapped -H 1453441340.00039.mismatch \ 1453441340.00039.map /data/maqgene/genomes/elegans.bfa 1453441340.00039.1.bfq 1453441340.00039.2.bfq 2> /dev/null # Thu Feb 3 19:59:55 GMT 2011: Mapping file(s) 1453441340.00044.1.bfq 1453441340.00044.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1453441340.00044.unmapped -H 1453441340.00044.mismatch \ 1453441340.00044.map /data/maqgene/genomes/elegans.bfa 1453441340.00044.1.bfq 1453441340.00044.2.bfq 2> /dev/null # Thu Feb 3 20:00:19 GMT 2011: Mapping file(s) 1453441340.00043.1.bfq 1453441340.00043.2.bfq # Thu Feb 3 20:00:19 GMT 2011: Mapping file(s) 1453441340.00042.1.bfq 1453441340.00042.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 1453441340.00043.unmapped -H 1453441340.00043.mismatch \ 1453441340.00043.map /data/maqgene/genomes/elegans.bfa 1453441340.00043.1.bfq 1453441340.00043.2.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 1453441340.00042.unmapped -H 1453441340.00042.mismatch \ 1453441340.00042.map /data/maqgene/genomes/elegans.bfa 1453441340.00042.1.bfq 1453441340.00042.2.bfq 2> /dev/null # Thu Feb 3 20:04:51 GMT 2011: Merging all maps ... /data/maqgene/bin/maq mapmerge 1453441340.map 1453441340.00000.map 1453441340.00001.map 1453441340.00002.map 1453441340.00003.map 1453441340.00004.map 1453441340.00005.map 1453441340.00006.map 1453441340.00007.map 1453441340.00008.map 1453441340.00009.map 1453441340.00010.map 1453441340.00011.map 1453441340.00012.map 1453441340.00013.map 1453441340.00014.map 1453441340.00015.map 1453441340.00016.map 1453441340.00017.map 1453441340.00018.map 1453441340.00019.map 1453441340.00020.map 1453441340.00021.map 1453441340.00022.map 1453441340.00023.map 1453441340.00024.map 1453441340.00025.map 1453441340.00026.map 1453441340.00027.map 1453441340.00028.map 1453441340.00029.map 1453441340.00030.map 1453441340.00031.map 1453441340.00032.map 1453441340.00033.map 1453441340.00034.map 1453441340.00035.map 1453441340.00036.map 1453441340.00037.map 1453441340.00038.map 1453441340.00039.map 1453441340.00040.map 1453441340.00041.map 1453441340.00042.map 1453441340.00043.map 1453441340.00044.map # Thu Feb 3 20:04:51 GMT 2011: Merging all *.unmapped files ... cat 1453441340.00000.unmapped 1453441340.00001.unmapped 1453441340.00002.unmapped 1453441340.00003.unmapped 1453441340.00004.unmapped 1453441340.00005.unmapped 1453441340.00006.unmapped 1453441340.00007.unmapped 1453441340.00008.unmapped 1453441340.00009.unmapped 1453441340.00010.unmapped 1453441340.00011.unmapped 1453441340.00012.unmapped 1453441340.00013.unmapped 1453441340.00014.unmapped 1453441340.00015.unmapped 1453441340.00016.unmapped 1453441340.00017.unmapped 1453441340.00018.unmapped 1453441340.00019.unmapped 1453441340.00020.unmapped 1453441340.00021.unmapped 1453441340.00022.unmapped 1453441340.00023.unmapped 1453441340.00024.unmapped 1453441340.00025.unmapped 1453441340.00026.unmapped 1453441340.00027.unmapped 1453441340.00028.unmapped 1453441340.00029.unmapped 1453441340.00030.unmapped 1453441340.00031.unmapped 1453441340.00032.unmapped 1453441340.00033.unmapped 1453441340.00034.unmapped 1453441340.00035.unmapped 1453441340.00036.unmapped 1453441340.00037.unmapped 1453441340.00038.unmapped 1453441340.00039.unmapped 1453441340.00040.unmapped 1453441340.00041.unmapped 1453441340.00042.unmapped 1453441340.00043.unmapped 1453441340.00044.unmapped > 1453441340_unmapped.txt # Thu Feb 3 20:04:56 GMT 2011: Linking backend file 1453441340_unmapped.txt to /data/maqgene/out/example_user/CB6878/CB6878_unmapped.txt ln -fs /data/maqgene/work/1453441340_unmapped.txt /data/maqgene/out/example_user/CB6878/CB6878_unmapped.txt /data/maqgene/makefile:126: warning: undefined variable `mapcheck_parameters' # Thu Feb 3 20:20:17 GMT 2011: Generating consensus ... /data/maqgene/bin/maq assemble -N 2 -q 0 -r 0.0 -m 7 -Q 100 -p 2225133155.cns \ /data/maqgene/genomes/elegans.bfa 1453441340.map 2> 2225133155_log.txt # Thu Feb 3 20:29:58 GMT 2011: Running 'mapcheck' ... /data/maqgene/bin/maq mapcheck /data/maqgene/genomes/elegans.bfa 1453441340.map > 1453441340_check.txt \ 2>/dev/null # Thu Feb 3 20:29:58 GMT 2011: Creating pileup ... /data/maqgene/bin/maq pileup -Q 100 -p -m 7 -q 0 /data/maqgene/genomes/elegans.bfa 1453441340.map > 3703570229_pileup.txt # Thu Feb 3 20:34:50 GMT 2011: Linking backend file 2225133155_log.txt to /data/maqgene/out/example_user/CB6878/CB6878_log.txt ln -fs /data/maqgene/work/2225133155_log.txt /data/maqgene/out/example_user/CB6878/CB6878_log.txt ln -fs /data/maqgene/work/1453441340_check.txt /data/maqgene/out/example_user/CB6878/CB6878_check.txt /data/maqgene/bin/filter_matching_lines 3703570229_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 \ > 3703570229_known_snps # Thu Feb 3 20:34:59 GMT 2011: Getting uncovered regions ... cut -f 1,2,4 3703570229_pileup.txt \ | /data/maqgene/bin/get_uncovered_regions 50 \ > 3703570229_uncovered.txt # Thu Feb 3 20:34:59 GMT 2011: Making coverage histogram ... (echo -en "sequencing_depth\tnumber_of_bases\n"; \ cut -f 4 3703570229_pileup.txt \ | /data/maqgene/bin/pileup_histogram 100) > 3703570229_coverage.txt # Thu Feb 3 20:34:59 GMT 2011: Linking backend file 3703570229_pileup.txt to /data/maqgene/out/example_user/CB6878/CB6878_pileup.txt ln -fs /data/maqgene/work/3703570229_pileup.txt /data/maqgene/out/example_user/CB6878/CB6878_pileup.txt # Thu Feb 3 20:35:32 GMT 2011: Linking backend file 3703570229_coverage.txt to /data/maqgene/out/example_user/CB6878/CB6878_coverage.txt ln -fs /data/maqgene/work/3703570229_coverage.txt /data/maqgene/out/example_user/CB6878/CB6878_coverage.txt # Thu Feb 3 20:35:33 GMT 2011: Filtering and loading pileup for analysis ... # Thu Feb 3 20:35:33 GMT 2011: Extracting point mutants from consensus ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 3703570229_pileup; create table 3703570229_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) );" /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 2225133155_snps; create table 2225133155_snps ( id int(10) NOT NULL auto_increment, dna char(40) NOT NULL, start int(10) NOT NULL, end int(10) NOT NULL, indel_size int(5) NOT NULL, variant_type enum('indel', 'point') NOT NULL, ref_base char NOT NULL, sample_base char NOT NULL, snp_score int(5) NOT NULL, read_depth int(5) NOT NULL, loci_multiplicity double(5,2) NOT NULL, mapping_quality int(5) NOT NULL, neighbor_quality int(5) NOT NULL, primary key (id), unique key (dna, start), key (indel_size) )" cat 3703570229_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 3703570229_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 3703570229_pileup" /data/maqgene/bin/maq cns2snp 2225133155.cns \ | cat -b | /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "load data local infile '/dev/stdin' into table 2225133155_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 2225133155_snps;" # Thu Feb 3 20:35:37 GMT 2011: Linking backend file 3703570229_uncovered.txt to /data/maqgene/out/example_user/CB6878/CB6878_uncovered.txt ln -fs /data/maqgene/work/3703570229_uncovered.txt /data/maqgene/out/example_user/CB6878/CB6878_uncovered.txt # Thu Feb 3 20:35:48 GMT 2011: Extracting indels from consensus ... /data/maqgene/bin/maq indelsoa /data/maqgene/genomes/elegans.bfa 1453441340.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 2225133155_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 2225133155_snps;" cat 3703570229_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 3703570229_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 3703570229_pileup" touch 3703570229_pileup # Thu Feb 3 20:36:34 GMT 2011: Writing snp read counts ... /usr/bin/mysql -Dmaqgenedb -umaqgene --skip-column-names --batch --raw --local-infile --column-names -e "select f.id, f.dna, f.start + 1 start, e.snp_name, e.snp_base, if(e.snp_base = 'a', p.A_fwd + p.A_rev, if (e.snp_base = 'c', p.C_fwd + p.C_rev, if (e.snp_base = 'g', p.G_fwd + p.G_rev, if (e.snp_base = 't', p.T_fwd + p.T_rev, -1)))) snp_reads, p.ref_base, p.wt_fwd + p.wt_rev wt_reads, p.read_depth, p.sample_reads from elegans_features f join elegans_snp_changes e on (f.attribute = e.snp_name) join 3703570229_pileup p using (dna,start)" > /data/maqgene/out/example_user/CB6878/CB6878_snp_read_counts.txt 0 snp read count lines written. # Thu Feb 3 20:37:55 GMT 2011: Adding placeholders for known SNPs. cat 3703570229_known_snps \ | /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "load data local infile '/dev/stdin' ignore into table 2225133155_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 2225133155_snps;" Found 161375 variants. touch 2225133155_snps # Thu Feb 3 20:37:56 GMT 2011: Loading uncovered regions into table ... cat 3703570229_uncovered.txt \ | /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 3703570229_uncovered; create table 3703570229_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 = 161376; load data local infile '/dev/stdin' into table 3703570229_uncovered (dna, start, end)" # Thu Feb 3 20:37:56 GMT 2011: Finding all genomic features overlapping variants... # Thu Feb 3 20:37:56 GMT 2011: Getting masking regions /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 2225133155_rel_snps; CREATE TABLE 2225133155_rel_snps ( association_id INT(10) NOT NULL, query_region_id INT(10) unsigned NOT NULL, target_region_id INT(10) NOT NULL, distance INT(10) NOT NULL, overlap INT(10) NOT NULL, same_strand enum('SAME', 'OPP') NOT NULL, num_regions_between INT(3) NOT NULL, PRIMARY KEY (association_id), KEY (query_region_id), KEY (target_region_id) )" /data/maqgene/bin/associate_regions -b -1 -c -1000000 -m 2 -o >(/usr/bin/mysql -Dmaqgenedb -umaqgene --skip-column-names --batch --raw --local-infile -e "drop table if exists 2225133155_masked_ids; create table 2225133155_masked_ids (query_region_id int(10) NOT NULL, primary key (query_region_id)); load data local infile '/dev/stdin' ignore into table 2225133155_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 2225133155_snps") -t <(/usr/bin/mysql -Dmaqgenedb -umaqgene --skip-column-names --batch --raw --local-infile -e "select id,'elegans',dna,start,end,strand from elegans_features feature where feature.feature not in ('mRNA', 'intron')") 1>/dev/null; /data/maqgene/bin/associate_regions -b -1 -c -1000000 -m 0 -o >(/usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "load data local infile '/dev/stdin' into table 2225133155_rel_snps; flush table 2225133155_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 2225133155_snps") -t <(/usr/bin/mysql -Dmaqgenedb -umaqgene --skip-column-names --batch --raw --local-infile -e "select id, 'elegans', dna,start,end,strand from elegans_features where feature in ('SNP','exon','five_prime_UTR','intron','mRNA','three_prime_UTR','ncRNA')") 1>/dev/null Uncovered region statistics: chromosome number_uncovered_regions total_uncovered_length I 6 603 II 13 2181 III 7 809 IV 9 820 V 9 1107 X 12 5764 touch 3703570229_uncovered # Thu Feb 3 20:37:56 GMT 2011: Finding mRNA features overlapping uncovered regions ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 3703570229_uncovered_rel; CREATE TABLE 3703570229_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 3703570229_uncovered_rel; flush table 3703570229_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 3703570229_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 2225133155_masked_ids touch 3703570229_uncovered_rel # Thu Feb 3 20:37:59 GMT 2011: Calculating translation start offsets for uncovered regions... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 3703570229_offsets_uncovered; create table 3703570229_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 3703570229_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 3703570229_uncovered reg join 3703570229_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 3703570229_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 3703570229_uncovered reg join 3703570229_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 3703570229_offsets_uncovered touch 2225133155_rel_snps # Thu Feb 3 20:38:00 GMT 2011: Calculating translation start offsets... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 2225133155_offsets_snps; create table 2225133155_offsets_snps ( id int(10) NOT NULL, gene varchar(50) NOT NULL, 5prime_offset int(10) NOT NULL, 3prime_offset int(10) NOT NULL, total_length int(10) NOT NULL, boundary_type char(20) NOT NULL, primary key (id, gene, boundary_type) );" # Thu Feb 3 20:38:00 GMT 2011: Getting intergenic regions /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 2225133155_rel_intergenic; create table 2225133155_rel_intergenic like 2225133155_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 2225133155_rel_intergenic; flush table 2225133155_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 2225133155_snps") -t <(/usr/bin/mysql -Dmaqgenedb -umaqgene --skip-column-names --batch --raw --local-infile -e "select id, 'elegans',dna,start,end,strand from elegans_features feature where feature.feature = 'mRNA'") 1>/dev/null; /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 2225133155_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 2225133155_snps reg join 2225133155_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" # Thu Feb 3 20:38:03 GMT 2011: Filtering masked intergenic regions /usr/bin/mysql -Dmaqgenedb -umaqgene --skip-column-names --batch --raw --local-infile -e "delete i.* from 2225133155_rel_intergenic i join 2225133155_masked_ids m using (query_region_id)" touch 2225133155_rel_intergenic # Thu Feb 3 20:38:07 GMT 2011: Classifying intergenic relations /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 2225133155_intergenic_assoc; create table 2225133155_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 2225133155_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 2225133155_snps snp join 2225133155_rel_intergenic rel on (snp.id = rel.query_region_id) join elegans_features feature on (rel.target_region_id = feature.id)" touch 2225133155_intergenic_assoc touch 2225133155_offsets_snps # Thu Feb 3 20:38:17 GMT 2011: Getting codons affected by point mutations... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 2225133155_codons; create table 2225133155_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 2225133155_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 2225133155_offsets_snps off join 2225133155_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 2225133155_codons /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 2225133155_marked; create table 2225133155_marked ( id int(10) NOT NULL, class varchar(100) NOT NULL, description varchar(100) NOT NULL, parent_feature varchar(100) NOT NULL, primary key (id, class, parent_feature) );" # Thu Feb 3 20:38:22 GMT 2011: Finding exonic indels ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 2225133155_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 2225133155_snps snp join 2225133155_rel_snps rel on (snp.id = rel.query_region_id) join elegans_features feature on (rel.target_region_id = feature.id) where feature.feature = 'exon' and snp.variant_type = 'indel';" # Thu Feb 3 20:38:22 GMT 2011: Finding coding variants ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 2225133155_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 2225133155_codons trans join elegans_genetic_code reference_codons on (trans.ref_codon = reference_codons.codon) join elegans_genetic_code sample_codons on (trans.sam_codon = sample_codons.codon);" # Thu Feb 3 20:38:23 GMT 2011: Finding noncoding variants ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 2225133155_marked select snp.id, feature.feature class, 'none' description, feature.attribute parent_feature from 2225133155_snps snp join 2225133155_rel_snps rel on (snp.id = rel.query_region_id) join elegans_features feature on (rel.target_region_id = feature.id) where feature.feature not in ('exon', 'intron', 'mRNA');" # Thu Feb 3 20:38:23 GMT 2011: Finding splice site variants ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 2225133155_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 2225133155_snps snp join 2225133155_rel_snps rel on (snp.id = rel.query_region_id) join elegans_features feature on (rel.target_region_id = feature.id) where feature.feature = 'intron' and rel.distance > -2;" # Thu Feb 3 20:38:23 GMT 2011: Finding intergenic and intronic variants ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 2225133155_marked select id, 'nongenic' class, concat(if (relation in ('upstream','into'), - distance, distance),' ',relation) description, attribute from 2225133155_intergenic_assoc where ((relation = 'upstream' and num_regions_between = 0 and distance < 50000) or (relation = 'upstream' and num_regions_between < 2 and distance < 1000) or (relation = 'downstream' and num_regions_between = 0 and distance < 1000) or (relation = 'downstream' and num_regions_between < 2 and distance < 1000) or relation = 'into' );" # Thu Feb 3 20:38:26 GMT 2011: Finding uncovered regions in genes ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 2225133155_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 3703570229_uncovered unc join 3703570229_offsets_uncovered b using (id) join 3703570229_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 3703570229_uncovered unc join 3703570229_offsets_uncovered b using (id) join 3703570229_offsets_uncovered e using (id, gene) join elegans_features gene on (e.gene = gene.attribute) where b.boundary_type = 'start' and e.boundary_type = 'end' and gene.strand = '-' and gene.feature = 'mRNA'" # Thu Feb 3 20:38:26 GMT 2011: Variants found: +-----------------+-----------------+ | class | number_variants | +-----------------+-----------------+ | five_prime_UTR | 1304 | | frameshift | 88 | | inframe | 26 | | missense | 6143 | | ncRNA | 871 | | nongenic | 124798 | | non_start | 10 | | premature_stop | 687 | | readthrough | 20 | | silent | 7403 | | SNP | 1032 | | splice_acceptor | 47 | | splice_donor | 46 | | three_prime_UTR | 3559 | | uncovered | 14 | +-----------------+-----------------+ touch 2225133155_marked # Thu Feb 3 20:38:27 GMT 2011: Combining results ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 2225133155_combined; create table 2225133155_combined (primary key (id, class, description), key (dna, start)) as select snp.id, 'CB6878' 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 2225133155_snps snp join 3703570229_pileup pile using (dna,start) join 2225133155_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, 'CB6878' 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 3703570229_uncovered unc join 2225133155_marked class on (unc.id = class.id) left join elegans_per_locus using (dna,start) group by id, class, description; alter table 2225133155_combined order by dna, start, length" touch 2225133155_combined # Thu Feb 3 20:38:27 GMT 2011: Writing results to flat file ... /usr/bin/mysql -Dmaqgenedb -umaqgene --skip-column-names --batch --raw --local-infile --column-names -e "select * from 2225133155_combined" > /data/maqgene/out/example_user/CB6878/CB6878_flat.txt # Thu Feb 3 20:38:27 GMT 2011: Writing results to grouped file ... /usr/bin/mysql -Dmaqgenedb -umaqgene --skip-column-names --batch --raw --local-infile --column-names -e "select id, mutant_strain, dna, start, length, reference_base, sample_base, consensus_score, loci_multiplicity, mapping_quality, neighbor_quality, number_wildtype_reads, number_variant_reads, sequencing_depth, sample_reads, variant_type, indel_size, group_concat(class) classes, group_concat(description) descriptions, group_concat(concat('{',parent_features,'}')) parent_features from 2225133155_combined group by id order by dna, start;" > /data/maqgene/out/example_user/CB6878/CB6878_grouped.txt 3692 lines written. 2211 lines written. rm 1453441340.00026.mismatch 1453441340.00007.mismatch 1453441340.00041.1.bfq 1453441340.00014.map 1453441340.00003.1.bfq 1453441340.00013.1.bfq 1453441340.00007.2.bfq 1453441340.00018.2.bfq 1453441340.00027.1.bfq 1453441340.00000.1.fastq 1453441340.00018.mismatch 1453441340.00044.mismatch 1453441340.00006.unmapped 1453441340.00001.unmapped 1453441340.00010.unmapped 1453441340.00022.2.bfq 1453441340.00031.1.bfq 1453441340.00038.1.fastq 1453441340.00022.mismatch 1453441340.00033.map 1453441340.00034.2.bfq 1453441340.00006.2.fastq 1453441340.00044.1.bfq 1453441340.00043.unmapped 1453441340.00001.1.fastq 1453441340.00010.1.fastq 1453441340.00034.unmapped 1453441340.00030.1.bfq 1453441340.00016.1.fastq 1453441340.00004.map 1453441340.00003.2.bfq 1453441340.00040.map 1453441340.00030.2.bfq 1453441340.00011.unmapped 1453441340.00021.mismatch 1453441340.00034.1.fastq 1453441340.00003.mismatch 1453441340.00008.mismatch 1453441340.00021.2.bfq 1453441340.00030.mismatch 1453441340.00014.mismatch 1453441340.00037.2.fastq 1453441340.00000.2.fastq 1453441340.00008.1.bfq 1453441340.00029.1.fastq 1453441340.00027.mismatch 1453441340.00011.1.fastq 1453441340.00017.unmapped 1453441340.00005.1.bfq 1453441340.00015.unmapped 1453441340.00020.unmapped 1453441340.00038.2.fastq 1453441340.00017.1.fastq 1453441340.00031.mismatch 1453441340.00023.1.bfq 1453441340.00013.mismatch 1453441340.00029.2.bfq 1453441340.00001.2.fastq 1453441340.00010.2.fastq 1453441340.00002.unmapped 1453441340.00002.1.fastq 1453441340.00031.2.bfq 1453441340.00020.1.fastq 1453441340.00037.1.bfq 1453441340.00019.1.bfq 1453441340.00016.2.fastq 1453441340.00035.1.fastq 1453441340.00012.unmapped 1453441340.00034.2.fastq 1453441340.00014.1.bfq 1453441340.00021.unmapped 1453441340.00015.1.bfq 1453441340.00003.2.fastq 1453441340.00029.2.fastq 1453441340.00011.2.fastq 1453441340.00008.unmapped 1453441340.00009.mismatch 4151819774_split1 1453441340.00012.1.fastq 1453441340.00026.unmapped 1453441340.00009.2.bfq 1453441340.00005.mismatch 1453441340.00041.mismatch 1453441340.00017.2.fastq 1453441340.00026.1.fastq 1453441340.00036.mismatch 1453441340.00042.map 1453441340.00023.2.bfq 1453441340.00018.unmapped 1453441340.00002.2.fastq 1453441340.00032.mismatch 1453441340.00020.2.fastq 1453441340.00016.unmapped 1453441340.00023.mismatch 1453441340.00024.map 1453441340.00019.2.bfq 1453441340.00029.1.bfq 1453441340.00028.1.bfq 1453441340.00042.2.bfq 1453441340.00018.1.fastq 1453441340.00019.mismatch 1453441340.00022.unmapped 1453441340.00015.2.bfq 1453441340.00035.map 1453441340.00012.2.fastq 1453441340.00015.mismatch 1453441340.00044.1.fastq 1453441340.00022.1.fastq 1453441340.00010.map 1453441340.00009.unmapped 1453441340.00003.unmapped 1453441340.00025.1.bfq 1453441340.00030.unmapped 1453441340.00026.2.fastq 1453441340.00006.map 1453441340.00027.unmapped 1453441340.00003.1.fastq 1453441340.00030.1.fastq 1453441340.00028.2.bfq 1453441340.00037.unmapped 1453441340.00018.2.fastq 1453441340.00027.1.fastq 1453441340.00028.mismatch 1453441340.00004.1.bfq 1453441340.00019.map 1453441340.00031.unmapped 1453441340.00013.unmapped 1453441340.00025.unmapped 1453441340.00000.map 1453441340.00037.mismatch 1453441340.00022.2.fastq 1453441340.00031.1.fastq 1453441340.00044.map 1453441340.00013.1.fastq 1453441340.00037.2.bfq 1453441340.00038.map 1453441340.00000.1.bfq 1453441340.00025.2.bfq 1453441340.00035.2.fastq 1453441340.00025.mismatch 1453441340.00001.map 1453441340.00043.1.fastq 1453441340.00038.1.bfq 1453441340.00042.2.fastq 1453441340.00014.2.bfq 1453441340.00030.2.fastq 1453441340.00005.unmapped 1453441340.00039.1.bfq 1453441340.00033.mismatch 1453441340.00034.map 1453441340.00007.1.fastq 1453441340.00004.2.bfq 1453441340.00036.unmapped 1453441340.00040.2.bfq 1453441340.00005.1.fastq 1453441340.00004.mismatch 1453441340.00029.map 1453441340.00035.1.bfq 1453441340.00011.map 1453441340.00040.mismatch 1453441340.00023.unmapped 1453441340.00027.2.fastq 1453441340.00036.1.fastq 1453441340.00031.2.fastq 1453441340.00013.2.fastq 1453441340.00019.unmapped 1453441340.00032.1.bfq 1453441340.00032.1.fastq 1453441340.00023.1.fastq 1453441340.00017.map 1453441340.00000.unmapped 1453441340.00041.2.bfq 1453441340.00038.2.bfq 1453441340.00019.1.fastq 1453441340.00002.map 1453441340.00020.map 1453441340.00043.map 1453441340.00042.1.bfq 1453441340.00039.2.bfq 1453441340.00024.1.bfq 1453441340.00007.unmapped 1453441340.00044.2.fastq 1453441340.00015.1.fastq 1453441340.00039.mismatch 1453441340.00007.map 1453441340.00021.1.fastq 1453441340.00032.unmapped 1453441340.00008.1.fastq 1453441340.00011.1.bfq 1453441340.00012.map 1453441340.00005.2.fastq 1453441340.00036.2.fastq 1453441340.00028.unmapped 1453441340.00032.2.fastq 1453441340.00023.2.fastq 1453441340.00026.map 1453441340.00029.unmapped 1453441340.00013.2.bfq 1453441340.00019.2.fastq 1453441340.00028.1.fastq 1453441340.00038.unmapped 1453441340.00006.1.bfq 1453441340.00042.mismatch 1453441340.00018.map 1453441340.00024.2.bfq 1453441340.00015.2.fastq 1453441340.00024.mismatch 1453441340.00008.map 1453441340.00043.2.fastq 1453441340.00033.unmapped 1453441340.00025.1.fastq 1453441340.00009.1.fastq 1453441340.00004.unmapped 1453441340.00033.1.fastq 1453441340.00040.unmapped 1453441340.00007.2.fastq 1453441340.00028.2.fastq 1453441340.00043.2.bfq 1453441340.00003.map 1453441340.00006.2.bfq 1453441340.00030.map 1453441340.00016.map 1453441340.00001.1.bfq 1453441340.00010.1.bfq 1453441340.00043.1.bfq 1453441340.00004.1.fastq 1453441340.00006.mismatch 1453441340.00027.map 1453441340.00036.1.bfq 1453441340.00040.1.fastq 1453441340.00016.1.bfq 1453441340.00032.2.bfq 4151819774_split2 1453441340.00021.map 1453441340.00041.unmapped 1453441340.00007.1.bfq 1453441340.00000.2.bfq 1453441340.00014.unmapped 1453441340.00031.map 1453441340.00013.map 1453441340.00025.2.fastq 1453441340.00000.mismatch 1453441340.00040.2.fastq 1453441340.00039.unmapped 1453441340.00009.map 1453441340.00041.1.fastq 1453441340.00027.2.bfq 1453441340.00014.1.fastq 1453441340.00033.2.fastq 1453441340.00041.map 1453441340.00017.1.bfq 1453441340.00033.1.bfq 1453441340.00039.1.fastq 1453441340.00038.mismatch 1453441340.00001.mismatch 1453441340.00021.2.fastq 1453441340.00001.2.bfq 1453441340.00010.2.bfq 1453441340.00002.1.bfq 1453441340.00020.1.bfq 1453441340.00008.2.fastq 1453441340.00004.2.fastq 1453441340.00035.unmapped 1453441340.00010.mismatch 1453441340.00034.1.bfq 1453441340.00016.2.bfq 1453441340.00040.1.bfq 1453441340.00016.mismatch 1453441340.00005.map 1453441340.00035.mismatch 1453441340.00025.map 1453441340.00044.2.bfq 1453441340.00034.mismatch 1453441340.00036.map 1453441340.00042.unmapped 1453441340.00021.1.bfq 1453441340.00012.1.bfq 1453441340.00032.map 1453441340.00029.mismatch 1453441340.00023.map 1453441340.00037.1.fastq 1453441340.00041.2.fastq 1453441340.00024.unmapped 1453441340.00005.2.bfq 1453441340.00014.2.fastq 1453441340.00042.1.fastq 1453441340.00017.2.bfq 1453441340.00026.1.bfq 1453441340.00035.2.bfq 1453441340.00039.2.fastq 1453441340.00024.1.fastq 1453441340.00017.mismatch 1453441340.00002.2.bfq 1453441340.00011.mismatch 1453441340.00008.2.bfq 1453441340.00011.2.bfq 1453441340.00002.mismatch 1453441340.00015.map 1453441340.00020.mismatch 1453441340.00022.map 1453441340.00018.1.bfq 1453441340.00009.2.fastq 1453441340.00039.map 1453441340.00044.unmapped 1453441340.00012.2.bfq 1453441340.00022.1.bfq 1453441340.00043.mismatch 1453441340.00012.mismatch 1453441340.00037.map 1453441340.00033.2.bfq 1453441340.00036.2.bfq 1453441340.00006.1.fastq 1453441340.00028.map 1453441340.00009.1.bfq 1453441340.00026.2.bfq 1453441340.00020.2.bfq 1453441340.00024.2.fastq make: Leaving directory `/data/maqgene/work' make: Entering directory `/data/maqgene/work' # Thu Feb 3 20:38:28 GMT 2011: Cleaning intermediate data ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 2225133155_snps,2225133155_rel,2225133155_masked_ids,2225133155_rel_intergenic,2225133155_intergenic_assoc,2225133155_offsets,2225133155_codons,2225133155_marked,2225133155_combined,3703570229_pileup" rm -f 2225133155_snps 2225133155_rel 2225133155_masked_ids 2225133155_rel_intergenic 2225133155_intergenic_assoc 2225133155_offsets 2225133155_codons 2225133155_marked 2225133155_combined 3703570229_pileup make: Leaving directory `/data/maqgene/work'