Finished reading input. ++ echo CB6871/./s_1_1_sequence_read1.fastq,ot340/./ot340_chrI_11m_12m_read1.fastq,CB6841/./s_1_1_sequence_read1.fastq ++ tr , ' ' + fastq_file_set1='CB6871/./s_1_1_sequence_read1.fastq ot340/./ot340_chrI_11m_12m_read1.fastq CB6841/./s_1_1_sequence_read1.fastq' ++ cd /data/maqgene/reads ++ wc -l ++ cat CB6871/./s_1_1_sequence_read1.fastq ot340/./ot340_chrI_11m_12m_read1.fastq CB6841/./s_1_1_sequence_read1.fastq ++ cut -f 1 -d ' ' + TOTAL_LINES=244199632 ++ echo '(244199632 / 5000000) + (244199632 % 5000000 != 0)' ++ bc + num_chunks=49 + 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=942262979 map_cksum=3228754180 pileup_cksum=2885205677 cns_cksum=743643928 umdd=50000 dmdd=1000 umid=1000 dmid=1000 max_gene_radius=50000 full_results_dir=/data/maqgene/out/example_user/CB6841 outfile_basename=CB6841 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=49 Will process 244199632 lines of input in 49 chunks make: Entering directory `/data/maqgene/work' # Thu Feb 3 17:56:53 GMT 2011: Removing frontend files in case this is a duplicate run ... rm -f /data/maqgene/out/example_user/CB6841/CB6841_{grouped.txt,flat.txt} rm -f /data/maqgene/out/example_user/CB6841/CB6841_uncovered.txt /data/maqgene/out/example_user/CB6841/CB6841_coverage.txt /data/maqgene/out/example_user/CB6841/CB6841_pileup.txt /data/maqgene/out/example_user/CB6841/CB6841_log.txt /data/maqgene/out/example_user/CB6841/CB6841_check.txt /data/maqgene/out/example_user/CB6841/CB6841_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/CB6871/./s_1_1_sequence_read1.fastq /data/maqgene/reads/ot340/./ot340_chrI_11m_12m_read1.fastq /data/maqgene/reads/CB6841/./s_1_1_sequence_read1.fastq) 3228754180.1.fastq. split -l 5000000 -a 5 -d <(cat /data/maqgene/reads/CB6871/./s_1_2_sequence_read2.fastq /data/maqgene/reads/ot340/./ot340_chrI_11m_12m_read2.fastq /data/maqgene/reads/CB6841/./s_1_2_sequence_read2.fastq) 3228754180.2.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; do mv 3228754180.1.fastq.$stem 3228754180.$stem.1.fastq; done touch 942262979_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; do mv 3228754180.2.fastq.$stem 3228754180.$stem.2.fastq; done touch 942262979_split2 # Thu Feb 3 17:58:57 GMT 2011: Converting fastq files to bfq ... # Thu Feb 3 17:58:57 GMT 2011: Converting fastq files to bfq ... # Thu Feb 3 17:58:57 GMT 2011: Converting fastq files to bfq ... out | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00003.1.bfq # Thu Feb 3 17:58:57 GMT 2011: Converting fastq files to bfq ... # Thu Feb 3 17:58:57 GMT 2011: Converting fastq files to bfq ... # Thu Feb 3 17:58:57 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3228754180.00004.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00004.1.bfq /data/maqgene/bin/maq sol2sanger 3228754180.00006.1.fastq /dev/stdout | \ # Thu Feb 3 17:58:57 GMT 2011: Converting fastq files to bfq ... # Thu Feb 3 17:58:57 GMT 2011: Converting fastq files to bfq ... # Thu Feb 3 17:58:57 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3228754180.00000.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00000.1.bfq # Thu Feb 3 17:58:57 GMT 2011: Converting fastq files to bfq ... # Thu Feb 3 17:58:57 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3228754180.00001.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00001.1.bfq /data/maqgene/bin/maq sol2sanger 3228754180.00002.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00002.1.bfq /data/maqgene/bin/maq sol2sanger 3228754180.00005.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00005.1.bfq /data/maqgene/bin/maq sol2sanger 3228754180.00007.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00007.1.bfq /data/maqgene/bin/maq sol2sanger 3228754180.00008.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00008.1.bfq /data/maqgene/bin/maq sol2sanger 3228754180.00009.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00009.1.bfq /data/maqgene/bin/maq sol2sanger 3228754180.00010.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00010.1.bfq /data/maqgene/bin/maq sol2sanger 3228754180.00011.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00011.1.bfq /data/maqgene/bin/maq sol2sanger 3228754180.00012.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00012.1.bfq /data/maqgene/bin/maq sol2sanger 3228754180.00013.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00013.1.bfq -- finish writing file '3228754180.00011.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 17:59:16 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3228754180.00014.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00014.1.bfq -- finish writing file '3228754180.00004.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 17:59:18 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3228754180.00015.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00015.1.bfq -- finish writing file '3228754180.00003.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 17:59:20 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3228754180.00016.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00016.1.bfq -- finish writing file '3228754180.00012.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 17:59:21 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3228754180.00017.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00017.1.bfq -- finish writing file '3228754180.00000.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 17:59:27 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3228754180.00018.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00018.1.bfq -- finish writing file '3228754180.00009.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 17:59:27 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3228754180.00019.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00019.1.bfq -- finish writing file '3228754180.00001.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3228754180.00005.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 17:59:27 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3228754180.00021.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00021.1.bfq # Thu Feb 3 17:59:27 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3228754180.00020.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00020.1.bfq -- finish writing file '3228754180.00002.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 17:59:27 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3228754180.00022.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00022.1.bfq -- finish writing file '3228754180.00010.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 17:59:27 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3228754180.00023.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00023.1.bfq -- finish writing file '3228754180.00008.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 17:59:27 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3228754180.00024.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00024.1.bfq -- finish writing file '3228754180.00013.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 17:59:27 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3228754180.00025.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00025.1.bfq -- finish writing file '3228754180.00007.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 17:59:28 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3228754180.00026.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00026.1.bfq -- finish writing file '3228754180.00006.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 17:59:28 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3228754180.00027.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00027.1.bfq -- finish writing file '3228754180.00016.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 17:59:42 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3228754180.00028.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00028.1.bfq -- finish writing file '3228754180.00014.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 17:59:48 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3228754180.00029.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00029.1.bfq -- finish writing file '3228754180.00015.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 17:59:51 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3228754180.00030.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00030.1.bfq -- finish writing file '3228754180.00017.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 17:59:52 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3228754180.00031.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00031.1.bfq -- finish writing file '3228754180.00025.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 17:59:54 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3228754180.00032.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00032.1.bfq -- finish writing file '3228754180.00020.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 17:59:54 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3228754180.00033.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00033.1.bfq -- finish writing file '3228754180.00018.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 17:59:55 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3228754180.00034.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00034.1.bfq -- finish writing file '3228754180.00026.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 17:59:56 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3228754180.00035.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00035.1.bfq -- finish writing file '3228754180.00027.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 17:59:59 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3228754180.00036.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00036.1.bfq -- finish writing file '3228754180.00021.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 17:59:59 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3228754180.00037.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00037.1.bfq -- finish writing file '3228754180.00023.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 17:59:59 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3228754180.00038.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00038.1.bfq -- finish writing file '3228754180.00019.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 17:59:59 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3228754180.00039.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00039.1.bfq -- finish writing file '3228754180.00022.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 18:00:00 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3228754180.00040.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00040.1.bfq -- finish writing file '3228754180.00024.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 18:00:00 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3228754180.00041.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00041.1.bfq -- finish writing file '3228754180.00029.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 18:00:09 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3228754180.00042.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00042.1.bfq -- finish writing file '3228754180.00028.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 18:00:12 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3228754180.00043.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00043.1.bfq -- finish writing file '3228754180.00033.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 18:00:15 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3228754180.00044.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00044.1.bfq -- finish writing file '3228754180.00034.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 18:00:21 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3228754180.00045.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00045.1.bfq -- finish writing file '3228754180.00030.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 18:00:21 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3228754180.00046.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00046.1.bfq -- finish writing file '3228754180.00031.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 18:00:21 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3228754180.00047.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00047.1.bfq -- finish writing file '3228754180.00032.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 18:00:23 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3228754180.00048.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00048.1.bfq -- finish writing file '3228754180.00038.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 18:00:24 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3228754180.00000.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00000.2.bfq -- finish writing file '3228754180.00035.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 18:00:27 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3228754180.00001.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00001.2.bfq -- finish writing file '3228754180.00041.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 18:00:27 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3228754180.00002.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00002.2.bfq -- finish writing file '3228754180.00037.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3228754180.00040.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3228754180.00036.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3228754180.00039.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3228754180.00043.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3228754180.00042.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3228754180.00044.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 18:00:39 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3228754180.00008.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00008.2.bfq # Thu Feb 3 18:00:39 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3228754180.00009.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00009.2.bfq # Thu Feb 3 18:00:40 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3228754180.00007.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00007.2.bfq /data/maqgene/bin/maq sol2sanger 3228754180.00006.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00006.2.bfq -- finish writing file '3228754180.00048.1.bfq' -- 1049908 sequences were loaded. # Thu Feb 3 18:00:41 GMT 2011: Converting fastq files to bfq ... # Thu Feb 3 18:00:41 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3228754180.00005.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00005.2.bfq /data/maqgene/bin/maq sol2sanger 3228754180.00004.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00004.2.bfq -- finish writing file '3228754180.00046.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 18:00:41 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3228754180.00010.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00010.2.bfq -- finish writing file '3228754180.00045.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 18:00:42 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3228754180.00011.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00011.2.bfq # Thu Feb 3 18:00:42 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3228754180.00003.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00003.2.bfq # Thu Feb 3 18:00:43 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3228754180.00012.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00012.2.bfq -- finish writing file '3228754180.00047.1.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 18:00:47 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3228754180.00013.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00013.2.bfq -- finish writing file '3228754180.00000.2.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 18:00:48 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3228754180.00014.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00014.2.bfq -- finish writing file '3228754180.00001.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '3228754180.00002.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '3228754180.00009.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '3228754180.00007.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '3228754180.00004.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '3228754180.00003.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '3228754180.00006.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '3228754180.00008.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '3228754180.00005.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '3228754180.00010.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '3228754180.00011.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '3228754180.00013.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '3228754180.00012.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '3228754180.00014.2.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 18:01:08 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3228754180.00027.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00027.2.bfq # Thu Feb 3 18:01:09 GMT 2011: Converting fastq files to bfq ... # Thu Feb 3 18:01:09 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3228754180.00028.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00028.2.bfq # Thu Feb 3 18:01:09 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3228754180.00026.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00026.2.bfq /data/maqgene/bin/maq sol2sanger 3228754180.00025.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00025.2.bfq # Thu Feb 3 18:01:09 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3228754180.00024.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00024.2.bfq # Thu Feb 3 18:01:10 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3228754180.00023.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00023.2.bfq # Thu Feb 3 18:01:10 GMT 2011: Converting fastq files to bfq ... # Thu Feb 3 18:01:10 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3228754180.00022.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00022.2.bfq /data/maqgene/bin/maq sol2sanger 3228754180.00021.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00021.2.bfq # Thu Feb 3 18:01:11 GMT 2011: Converting fastq files to bfq ... # Thu Feb 3 18:01:11 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3228754180.00020.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00020.2.bfq /data/maqgene/bin/maq sol2sanger 3228754180.00019.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00019.2.bfq # Thu Feb 3 18:01:11 GMT 2011: Converting fastq files to bfq ... # Thu Feb 3 18:01:11 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3228754180.00018.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00018.2.bfq /data/maqgene/bin/maq sol2sanger 3228754180.00017.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00017.2.bfq # Thu Feb 3 18:01:12 GMT 2011: Converting fastq files to bfq ... # Thu Feb 3 18:01:12 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3228754180.00016.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00016.2.bfq /data/maqgene/bin/maq sol2sanger 3228754180.00015.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00015.2.bfq -- finish writing file '3228754180.00027.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '3228754180.00025.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '3228754180.00015.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '3228754180.00019.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '3228754180.00028.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '3228754180.00024.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '3228754180.00023.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '3228754180.00020.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '3228754180.00022.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '3228754180.00026.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '3228754180.00016.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '3228754180.00018.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '3228754180.00021.2.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 18:01:39 GMT 2011: Converting fastq files to bfq ... # Thu Feb 3 18:01:39 GMT 2011: Converting fastq files to bfq ... # Thu Feb 3 18:01:39 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3228754180.00038.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00038.2.bfq /data/maqgene/bin/maq sol2sanger 3228754180.00040.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00040.2.bfq /data/maqgene/bin/maq sol2sanger 3228754180.00039.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00039.2.bfq -- finish writing file '3228754180.00017.2.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 18:01:40 GMT 2011: Converting fastq files to bfq ... # Thu Feb 3 18:01:40 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3228754180.00041.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00041.2.bfq /data/maqgene/bin/maq sol2sanger 3228754180.00037.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00037.2.bfq # Thu Feb 3 18:01:40 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3228754180.00036.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00036.2.bfq # Thu Feb 3 18:01:41 GMT 2011: Converting fastq files to bfq ... # Thu Feb 3 18:01:41 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3228754180.00042.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00042.2.bfq /data/maqgene/bin/maq sol2sanger 3228754180.00035.2.fastq /dev/stdout | \ # Thu Feb 3 18:01:41 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3228754180.00034.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00034.2.bfq # Thu Feb 3 18:01:42 GMT 2011: Converting fastq files to bfq ... # Thu Feb 3 18:01:42 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3228754180.00033.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00033.2.bfq /data/maqgene/bin/maq sol2sanger 3228754180.00032.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00032.2.bfq # Thu Feb 3 18:01:42 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3228754180.00031.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00031.2.bfq # Thu Feb 3 18:01:43 GMT 2011: Converting fastq files to bfq ... # Thu Feb 3 18:01:43 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3228754180.00030.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00030.2.bfq /data/maqgene/bin/maq sol2sanger 3228754180.00029.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00029.2.bfq -- finish writing file '3228754180.00036.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '3228754180.00039.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '3228754180.00031.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '3228754180.00037.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '3228754180.00029.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '3228754180.00034.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '3228754180.00032.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '3228754180.00041.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '3228754180.00040.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '3228754180.00038.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '3228754180.00035.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '3228754180.00042.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '3228754180.00033.2.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 18:02:09 GMT 2011: Mapping file(s) 3228754180.00005.1.bfq 3228754180.00005.2.bfq # Thu Feb 3 18:02:09 GMT 2011: Mapping file(s) 3228754180.00006.1.bfq 3228754180.00006.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3228754180.00005.unmapped -H 3228754180.00005.mismatch \ 3228754180.00005.map /data/maqgene/genomes/elegans.bfa 3228754180.00005.1.bfq 3228754180.00005.2.bfq 2> /dev/null /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3228754180.00006.unmapped -H 3228754180.00006.mismatch \ 3228754180.00006.map /data/maqgene/genomes/elegans.bfa 3228754180.00006.1.bfq 3228754180.00006.2.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 3228754180.00004.unmapped -H 3228754180.00004.mismatch \ 3228754180.00004.map /data/maqgene/genomes/elegans.bfa 3228754180.00004.1.bfq 3228754180.00004.2.bfq 2> /dev/null -- finish writing file '3228754180.00030.2.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 18:02:10 GMT 2011: Mapping file(s) 3228754180.00003.1.bfq 3228754180.00003.2.bfq # Thu Feb 3 18:02:10 GMT 2011: Mapping file(s) 3228754180.00002.1.bfq 3228754180.00002.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3228754180.00003.unmapped -H 3228754180.00003.mismatch \ 3228754180.00003.map /data/maqgene/genomes/elegans.bfa 3228754180.00003.1.bfq 3228754180.00003.2.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 3228754180.00002.unmapped -H 3228754180.00002.mismatch \ 3228754180.00002.map /data/maqgene/genomes/elegans.bfa 3228754180.00002.1.bfq 3228754180.00002.2.bfq 2> /dev/null # Thu Feb 3 18:02:11 GMT 2011: Mapping file(s) 3228754180.00007.1.bfq 3228754180.00007.2.bfq # Thu Feb 3 18:02:11 GMT 2011: Mapping file(s) 3228754180.00001.1.bfq 3228754180.00001.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3228754180.00007.unmapped -H 3228754180.00007.mismatch \ 3228754180.00007.map /data/maqgene/genomes/elegans.bfa 3228754180.00007.1.bfq 3228754180.00007.2.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 3228754180.00001.unmapped -H 3228754180.00001.mismatch \ 3228754180.00001.map /data/maqgene/genomes/elegans.bfa 3228754180.00001.1.bfq 3228754180.00001.2.bfq 2> /dev/null # Thu Feb 3 18:02:12 GMT 2011: Mapping file(s) 3228754180.00000.1.bfq 3228754180.00000.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3228754180.00000.unmapped -H 3228754180.00000.mismatch \ 3228754180.00000.map /data/maqgene/genomes/elegans.bfa 3228754180.00000.1.bfq 3228754180.00000.2.bfq 2> /dev/null # Thu Feb 3 18:02:12 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3228754180.00048.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00048.2.bfq # Thu Feb 3 18:02:13 GMT 2011: Converting fastq files to bfq ... # Thu Feb 3 18:02:13 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3228754180.00047.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00047.2.bfq /data/maqgene/bin/maq sol2sanger 3228754180.00046.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00046.2.bfq # Thu Feb 3 18:02:14 GMT 2011: Converting fastq files to bfq ... # Thu Feb 3 18:02:14 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3228754180.00045.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00045.2.bfq /data/maqgene/bin/maq sol2sanger 3228754180.00044.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00044.2.bfq # Thu Feb 3 18:02:14 GMT 2011: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3228754180.00043.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3228754180.00043.2.bfq -- finish writing file '3228754180.00048.2.bfq' -- 1049908 sequences were loaded. # Thu Feb 3 18:02:28 GMT 2011: Mapping file(s) 3228754180.00008.1.bfq 3228754180.00008.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3228754180.00008.unmapped -H 3228754180.00008.mismatch \ 3228754180.00008.map /data/maqgene/genomes/elegans.bfa 3228754180.00008.1.bfq 3228754180.00008.2.bfq 2> /dev/null -- finish writing file '3228754180.00044.2.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 18:02:33 GMT 2011: Mapping file(s) 3228754180.00009.1.bfq 3228754180.00009.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3228754180.00009.unmapped -H 3228754180.00009.mismatch \ 3228754180.00009.map /data/maqgene/genomes/elegans.bfa 3228754180.00009.1.bfq 3228754180.00009.2.bfq 2> /dev/null -- finish writing file '3228754180.00047.2.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 18:02:35 GMT 2011: Mapping file(s) 3228754180.00010.1.bfq 3228754180.00010.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3228754180.00010.unmapped -H 3228754180.00010.mismatch \ 3228754180.00010.map /data/maqgene/genomes/elegans.bfa 3228754180.00010.1.bfq 3228754180.00010.2.bfq 2> /dev/null -- finish writing file '3228754180.00045.2.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 18:02:38 GMT 2011: Mapping file(s) 3228754180.00011.1.bfq 3228754180.00011.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3228754180.00011.unmapped -H 3228754180.00011.mismatch \ 3228754180.00011.map /data/maqgene/genomes/elegans.bfa 3228754180.00011.1.bfq 3228754180.00011.2.bfq 2> /dev/null -- finish writing file '3228754180.00046.2.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 18:02:42 GMT 2011: Mapping file(s) 3228754180.00012.1.bfq 3228754180.00012.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3228754180.00012.unmapped -H 3228754180.00012.mismatch \ 3228754180.00012.map /data/maqgene/genomes/elegans.bfa 3228754180.00012.1.bfq 3228754180.00012.2.bfq 2> /dev/null -- finish writing file '3228754180.00043.2.bfq' -- 1250000 sequences were loaded. # Thu Feb 3 18:02:44 GMT 2011: Mapping file(s) 3228754180.00013.1.bfq 3228754180.00013.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3228754180.00013.unmapped -H 3228754180.00013.mismatch \ 3228754180.00013.map /data/maqgene/genomes/elegans.bfa 3228754180.00013.1.bfq 3228754180.00013.2.bfq 2> /dev/null # Thu Feb 3 18:08:35 GMT 2011: Mapping file(s) 3228754180.00015.1.bfq 3228754180.00015.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3228754180.00015.unmapped -H 3228754180.00015.mismatch \ 3228754180.00015.map /data/maqgene/genomes/elegans.bfa 3228754180.00015.1.bfq 3228754180.00015.2.bfq 2> /dev/null # Thu Feb 3 18:08:37 GMT 2011: Mapping file(s) 3228754180.00014.1.bfq 3228754180.00014.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3228754180.00014.unmapped -H 3228754180.00014.mismatch \ 3228754180.00014.map /data/maqgene/genomes/elegans.bfa 3228754180.00014.1.bfq 3228754180.00014.2.bfq 2> /dev/null # Thu Feb 3 18:08:41 GMT 2011: Mapping file(s) 3228754180.00016.1.bfq 3228754180.00016.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3228754180.00016.unmapped -H 3228754180.00016.mismatch \ 3228754180.00016.map /data/maqgene/genomes/elegans.bfa 3228754180.00016.1.bfq 3228754180.00016.2.bfq 2> /dev/null # Thu Feb 3 18:08:41 GMT 2011: Mapping file(s) 3228754180.00017.1.bfq 3228754180.00017.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3228754180.00017.unmapped -H 3228754180.00017.mismatch \ 3228754180.00017.map /data/maqgene/genomes/elegans.bfa 3228754180.00017.1.bfq 3228754180.00017.2.bfq 2> /dev/null # Thu Feb 3 18:08:55 GMT 2011: Mapping file(s) 3228754180.00019.1.bfq 3228754180.00019.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3228754180.00019.unmapped -H 3228754180.00019.mismatch \ 3228754180.00019.map /data/maqgene/genomes/elegans.bfa 3228754180.00019.1.bfq 3228754180.00019.2.bfq 2> /dev/null # Thu Feb 3 18:08:56 GMT 2011: Mapping file(s) 3228754180.00018.1.bfq 3228754180.00018.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3228754180.00018.unmapped -H 3228754180.00018.mismatch \ 3228754180.00018.map /data/maqgene/genomes/elegans.bfa 3228754180.00018.1.bfq 3228754180.00018.2.bfq 2> /dev/null # Thu Feb 3 18:08:56 GMT 2011: Mapping file(s) 3228754180.00020.1.bfq 3228754180.00020.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3228754180.00020.unmapped -H 3228754180.00020.mismatch \ 3228754180.00020.map /data/maqgene/genomes/elegans.bfa 3228754180.00020.1.bfq 3228754180.00020.2.bfq 2> /dev/null # Thu Feb 3 18:08:59 GMT 2011: Mapping file(s) 3228754180.00021.1.bfq 3228754180.00021.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3228754180.00021.unmapped -H 3228754180.00021.mismatch \ 3228754180.00021.map /data/maqgene/genomes/elegans.bfa 3228754180.00021.1.bfq 3228754180.00021.2.bfq 2> /dev/null # Thu Feb 3 18:09:08 GMT 2011: Mapping file(s) 3228754180.00022.1.bfq 3228754180.00022.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3228754180.00022.unmapped -H 3228754180.00022.mismatch \ 3228754180.00022.map /data/maqgene/genomes/elegans.bfa 3228754180.00022.1.bfq 3228754180.00022.2.bfq 2> /dev/null # Thu Feb 3 18:09:15 GMT 2011: Mapping file(s) 3228754180.00023.1.bfq 3228754180.00023.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3228754180.00023.unmapped -H 3228754180.00023.mismatch \ 3228754180.00023.map /data/maqgene/genomes/elegans.bfa 3228754180.00023.1.bfq 3228754180.00023.2.bfq 2> /dev/null # Thu Feb 3 18:09:30 GMT 2011: Mapping file(s) 3228754180.00026.1.bfq 3228754180.00026.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3228754180.00026.unmapped -H 3228754180.00026.mismatch \ 3228754180.00026.map /data/maqgene/genomes/elegans.bfa 3228754180.00026.1.bfq 3228754180.00026.2.bfq 2> /dev/null # Thu Feb 3 18:09:31 GMT 2011: Mapping file(s) 3228754180.00025.1.bfq 3228754180.00025.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3228754180.00025.unmapped -H 3228754180.00025.mismatch \ 3228754180.00025.map /data/maqgene/genomes/elegans.bfa 3228754180.00025.1.bfq 3228754180.00025.2.bfq 2> /dev/null # Thu Feb 3 18:09:32 GMT 2011: Mapping file(s) 3228754180.00024.1.bfq 3228754180.00024.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3228754180.00024.unmapped -H 3228754180.00024.mismatch \ 3228754180.00024.map /data/maqgene/genomes/elegans.bfa 3228754180.00024.1.bfq 3228754180.00024.2.bfq 2> /dev/null # Thu Feb 3 18:09:47 GMT 2011: Mapping file(s) 3228754180.00027.1.bfq 3228754180.00027.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3228754180.00027.unmapped -H 3228754180.00027.mismatch \ 3228754180.00027.map /data/maqgene/genomes/elegans.bfa 3228754180.00027.1.bfq 3228754180.00027.2.bfq 2> /dev/null # Thu Feb 3 18:14:56 GMT 2011: Mapping file(s) 3228754180.00028.1.bfq 3228754180.00028.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3228754180.00028.unmapped -H 3228754180.00028.mismatch \ 3228754180.00028.map /data/maqgene/genomes/elegans.bfa 3228754180.00028.1.bfq 3228754180.00028.2.bfq 2> /dev/null # Thu Feb 3 18:15:11 GMT 2011: Mapping file(s) 3228754180.00031.1.bfq 3228754180.00031.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3228754180.00031.unmapped -H 3228754180.00031.mismatch \ 3228754180.00031.map /data/maqgene/genomes/elegans.bfa 3228754180.00031.1.bfq 3228754180.00031.2.bfq 2> /dev/null # Thu Feb 3 18:15:11 GMT 2011: Mapping file(s) 3228754180.00030.1.bfq 3228754180.00030.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3228754180.00030.unmapped -H 3228754180.00030.mismatch \ 3228754180.00030.map /data/maqgene/genomes/elegans.bfa 3228754180.00030.1.bfq 3228754180.00030.2.bfq 2> /dev/null # Thu Feb 3 18:15:12 GMT 2011: Mapping file(s) 3228754180.00032.1.bfq 3228754180.00032.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3228754180.00032.unmapped -H 3228754180.00032.mismatch \ 3228754180.00032.map /data/maqgene/genomes/elegans.bfa 3228754180.00032.1.bfq 3228754180.00032.2.bfq 2> /dev/null # Thu Feb 3 18:15:13 GMT 2011: Mapping file(s) 3228754180.00029.1.bfq 3228754180.00029.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3228754180.00029.unmapped -H 3228754180.00029.mismatch \ 3228754180.00029.map /data/maqgene/genomes/elegans.bfa 3228754180.00029.1.bfq 3228754180.00029.2.bfq 2> /dev/null # Thu Feb 3 18:15:19 GMT 2011: Mapping file(s) 3228754180.00033.1.bfq 3228754180.00033.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3228754180.00033.unmapped -H 3228754180.00033.mismatch \ 3228754180.00033.map /data/maqgene/genomes/elegans.bfa 3228754180.00033.1.bfq 3228754180.00033.2.bfq 2> /dev/null # Thu Feb 3 18:15:19 GMT 2011: Mapping file(s) 3228754180.00034.1.bfq 3228754180.00034.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3228754180.00034.unmapped -H 3228754180.00034.mismatch \ 3228754180.00034.map /data/maqgene/genomes/elegans.bfa 3228754180.00034.1.bfq 3228754180.00034.2.bfq 2> /dev/null # Thu Feb 3 18:15:23 GMT 2011: Mapping file(s) 3228754180.00035.1.bfq 3228754180.00035.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3228754180.00035.unmapped -H 3228754180.00035.mismatch \ 3228754180.00035.map /data/maqgene/genomes/elegans.bfa 3228754180.00035.1.bfq 3228754180.00035.2.bfq 2> /dev/null # Thu Feb 3 18:15:25 GMT 2011: Mapping file(s) 3228754180.00036.1.bfq 3228754180.00036.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3228754180.00036.unmapped -H 3228754180.00036.mismatch \ 3228754180.00036.map /data/maqgene/genomes/elegans.bfa 3228754180.00036.1.bfq 3228754180.00036.2.bfq 2> /dev/null # Thu Feb 3 18:15:27 GMT 2011: Mapping file(s) 3228754180.00037.1.bfq 3228754180.00037.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3228754180.00037.unmapped -H 3228754180.00037.mismatch \ 3228754180.00037.map /data/maqgene/genomes/elegans.bfa 3228754180.00037.1.bfq 3228754180.00037.2.bfq 2> /dev/null # Thu Feb 3 18:15:40 GMT 2011: Mapping file(s) 3228754180.00038.1.bfq 3228754180.00038.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3228754180.00038.unmapped -H 3228754180.00038.mismatch \ 3228754180.00038.map /data/maqgene/genomes/elegans.bfa 3228754180.00038.1.bfq 3228754180.00038.2.bfq 2> /dev/null # Thu Feb 3 18:15:50 GMT 2011: Mapping file(s) 3228754180.00039.1.bfq 3228754180.00039.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3228754180.00039.unmapped -H 3228754180.00039.mismatch \ 3228754180.00039.map /data/maqgene/genomes/elegans.bfa 3228754180.00039.1.bfq 3228754180.00039.2.bfq 2> /dev/null # Thu Feb 3 18:16:01 GMT 2011: Mapping file(s) 3228754180.00040.1.bfq 3228754180.00040.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3228754180.00040.unmapped -H 3228754180.00040.mismatch \ 3228754180.00040.map /data/maqgene/genomes/elegans.bfa 3228754180.00040.1.bfq 3228754180.00040.2.bfq 2> /dev/null # Thu Feb 3 18:16:14 GMT 2011: Mapping file(s) 3228754180.00041.1.bfq 3228754180.00041.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3228754180.00041.unmapped -H 3228754180.00041.mismatch \ 3228754180.00041.map /data/maqgene/genomes/elegans.bfa 3228754180.00041.1.bfq 3228754180.00041.2.bfq 2> /dev/null # Thu Feb 3 18:21:54 GMT 2011: Mapping file(s) 3228754180.00048.1.bfq 3228754180.00048.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3228754180.00048.unmapped -H 3228754180.00048.mismatch \ 3228754180.00048.map /data/maqgene/genomes/elegans.bfa 3228754180.00048.1.bfq 3228754180.00048.2.bfq 2> /dev/null # Thu Feb 3 18:21:54 GMT 2011: Mapping file(s) 3228754180.00047.1.bfq 3228754180.00047.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3228754180.00047.unmapped -H 3228754180.00047.mismatch \ 3228754180.00047.map /data/maqgene/genomes/elegans.bfa 3228754180.00047.1.bfq 3228754180.00047.2.bfq 2> /dev/null # Thu Feb 3 18:22:01 GMT 2011: Mapping file(s) 3228754180.00046.1.bfq 3228754180.00046.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3228754180.00046.unmapped -H 3228754180.00046.mismatch \ 3228754180.00046.map /data/maqgene/genomes/elegans.bfa 3228754180.00046.1.bfq 3228754180.00046.2.bfq 2> /dev/null # Thu Feb 3 18:22:01 GMT 2011: Mapping file(s) 3228754180.00045.1.bfq 3228754180.00045.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3228754180.00045.unmapped -H 3228754180.00045.mismatch \ 3228754180.00045.map /data/maqgene/genomes/elegans.bfa 3228754180.00045.1.bfq 3228754180.00045.2.bfq 2> /dev/null # Thu Feb 3 18:22:01 GMT 2011: Mapping file(s) 3228754180.00044.1.bfq 3228754180.00044.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3228754180.00044.unmapped -H 3228754180.00044.mismatch \ 3228754180.00044.map /data/maqgene/genomes/elegans.bfa 3228754180.00044.1.bfq 3228754180.00044.2.bfq 2> /dev/null # Thu Feb 3 18:22:09 GMT 2011: Mapping file(s) 3228754180.00043.1.bfq 3228754180.00043.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3228754180.00043.unmapped -H 3228754180.00043.mismatch \ 3228754180.00043.map /data/maqgene/genomes/elegans.bfa 3228754180.00043.1.bfq 3228754180.00043.2.bfq 2> /dev/null # Thu Feb 3 18:22:09 GMT 2011: Mapping file(s) 3228754180.00042.1.bfq 3228754180.00042.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3228754180.00042.unmapped -H 3228754180.00042.mismatch \ 3228754180.00042.map /data/maqgene/genomes/elegans.bfa 3228754180.00042.1.bfq 3228754180.00042.2.bfq 2> /dev/null # Thu Feb 3 18:27:44 GMT 2011: Merging all maps ... # Thu Feb 3 18:27:44 GMT 2011: Merging all *.unmapped files ... /data/maqgene/bin/maq mapmerge 3228754180.map 3228754180.00000.map 3228754180.00001.map 3228754180.00002.map 3228754180.00003.map 3228754180.00004.map 3228754180.00005.map 3228754180.00006.map 3228754180.00007.map 3228754180.00008.map 3228754180.00009.map 3228754180.00010.map 3228754180.00011.map 3228754180.00012.map 3228754180.00013.map 3228754180.00014.map 3228754180.00015.map 3228754180.00016.map 3228754180.00017.map 3228754180.00018.map 3228754180.00019.map 3228754180.00020.map 3228754180.00021.map 3228754180.00022.map 3228754180.00023.map 3228754180.00024.map 3228754180.00025.map 3228754180.00026.map 3228754180.00027.map 3228754180.00028.map 3228754180.00029.map 3228754180.00030.map 3228754180.00031.map 3228754180.00032.map 3228754180.00033.map 3228754180.00034.map 3228754180.00035.map 3228754180.00036.map 3228754180.00037.map 3228754180.00038.map 3228754180.00039.map 3228754180.00040.map 3228754180.00041.map 3228754180.00042.map 3228754180.00043.map 3228754180.00044.map 3228754180.00045.map 3228754180.00046.map 3228754180.00047.map 3228754180.00048.map cat 3228754180.00000.unmapped 3228754180.00001.unmapped 3228754180.00002.unmapped 3228754180.00003.unmapped 3228754180.00004.unmapped 3228754180.00005.unmapped 3228754180.00006.unmapped 3228754180.00007.unmapped 3228754180.00008.unmapped 3228754180.00009.unmapped 3228754180.00010.unmapped 3228754180.00011.unmapped 3228754180.00012.unmapped 3228754180.00013.unmapped 3228754180.00014.unmapped 3228754180.00015.unmapped 3228754180.00016.unmapped 3228754180.00017.unmapped 3228754180.00018.unmapped 3228754180.00019.unmapped 3228754180.00020.unmapped 3228754180.00021.unmapped 3228754180.00022.unmapped 3228754180.00023.unmapped 3228754180.00024.unmapped 3228754180.00025.unmapped 3228754180.00026.unmapped 3228754180.00027.unmapped 3228754180.00028.unmapped 3228754180.00029.unmapped 3228754180.00030.unmapped 3228754180.00031.unmapped 3228754180.00032.unmapped 3228754180.00033.unmapped 3228754180.00034.unmapped 3228754180.00035.unmapped 3228754180.00036.unmapped 3228754180.00037.unmapped 3228754180.00038.unmapped 3228754180.00039.unmapped 3228754180.00040.unmapped 3228754180.00041.unmapped 3228754180.00042.unmapped 3228754180.00043.unmapped 3228754180.00044.unmapped 3228754180.00045.unmapped 3228754180.00046.unmapped 3228754180.00047.unmapped 3228754180.00048.unmapped > 3228754180_unmapped.txt # Thu Feb 3 18:27:50 GMT 2011: Linking backend file 3228754180_unmapped.txt to /data/maqgene/out/example_user/CB6841/CB6841_unmapped.txt ln -fs /data/maqgene/work/3228754180_unmapped.txt /data/maqgene/out/example_user/CB6841/CB6841_unmapped.txt /data/maqgene/makefile:126: warning: undefined variable `mapcheck_parameters' # Thu Feb 3 18:44:58 GMT 2011: Running 'mapcheck' ... # Thu Feb 3 18:44:58 GMT 2011: Generating consensus ... /data/maqgene/bin/maq mapcheck /data/maqgene/genomes/elegans.bfa 3228754180.map > 3228754180_check.txt \ 2>/dev/null # Thu Feb 3 18:44:58 GMT 2011: Creating pileup ... /data/maqgene/bin/maq assemble -N 2 -q 0 -r 0.0 -m 7 -Q 100 -p 743643928.cns \ /data/maqgene/genomes/elegans.bfa 3228754180.map 2> 743643928_log.txt /data/maqgene/bin/maq pileup -Q 100 -p -m 7 -q 0 /data/maqgene/genomes/elegans.bfa 3228754180.map > 2885205677_pileup.txt # Thu Feb 3 18:49:49 GMT 2011: Linking backend file 3228754180_check.txt to /data/maqgene/out/example_user/CB6841/CB6841_check.txt ln -fs /data/maqgene/work/3228754180_check.txt /data/maqgene/out/example_user/CB6841/CB6841_check.txt /data/maqgene/bin/filter_matching_lines 2885205677_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 \ > 2885205677_known_snps # Thu Feb 3 18:50:06 GMT 2011: Making coverage histogram ... (echo -en "sequencing_depth\tnumber_of_bases\n"; \ cut -f 4 2885205677_pileup.txt \ | /data/maqgene/bin/pileup_histogram 100) > 2885205677_coverage.txt cut -f 1,2,4 2885205677_pileup.txt \ | /data/maqgene/bin/get_uncovered_regions 50 \ > 2885205677_uncovered.txt # Thu Feb 3 18:50:06 GMT 2011: Linking backend file 2885205677_pileup.txt to /data/maqgene/out/example_user/CB6841/CB6841_pileup.txt ln -fs /data/maqgene/work/2885205677_pileup.txt /data/maqgene/out/example_user/CB6841/CB6841_pileup.txt # Thu Feb 3 18:50:43 GMT 2011: Linking backend file 2885205677_coverage.txt to /data/maqgene/out/example_user/CB6841/CB6841_coverage.txt ln -fs /data/maqgene/work/2885205677_coverage.txt /data/maqgene/out/example_user/CB6841/CB6841_coverage.txt # Thu Feb 3 18:50:44 GMT 2011: Filtering and loading pileup for analysis ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 2885205677_pileup; create table 2885205677_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 2885205677_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 2885205677_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 2885205677_pileup" # Thu Feb 3 18:50:44 GMT 2011: Linking backend file 2885205677_uncovered.txt to /data/maqgene/out/example_user/CB6841/CB6841_uncovered.txt ln -fs /data/maqgene/work/2885205677_uncovered.txt /data/maqgene/out/example_user/CB6841/CB6841_uncovered.txt cat 2885205677_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 2885205677_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 2885205677_pileup" touch 2885205677_pileup # Thu Feb 3 18:51:43 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 2885205677_pileup p using (dna,start)" > /data/maqgene/out/example_user/CB6841/CB6841_snp_read_counts.txt 0 snp read count lines written. # Thu Feb 3 18:52:44 GMT 2011: Extracting point mutants from consensus ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 743643928_snps; create table 743643928_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) )" # Thu Feb 3 18:52:44 GMT 2011: Linking backend file 743643928_log.txt to /data/maqgene/out/example_user/CB6841/CB6841_log.txt ln -fs /data/maqgene/work/743643928_log.txt /data/maqgene/out/example_user/CB6841/CB6841_log.txt /data/maqgene/bin/maq cns2snp 743643928.cns \ | cat -b | /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "load data local infile '/dev/stdin' into table 743643928_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 743643928_snps;" # Thu Feb 3 18:52:57 GMT 2011: Extracting indels from consensus ... /data/maqgene/bin/maq indelsoa /data/maqgene/genomes/elegans.bfa 3228754180.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 743643928_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 743643928_snps;" # Thu Feb 3 18:55:40 GMT 2011: Adding placeholders for known SNPs. cat 2885205677_known_snps \ | /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "load data local infile '/dev/stdin' ignore into table 743643928_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 743643928_snps;" Found 161306 variants. touch 743643928_snps # Thu Feb 3 18:55:41 GMT 2011: Loading uncovered regions into table ... cat 2885205677_uncovered.txt \ | /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 2885205677_uncovered; create table 2885205677_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 = 161307; load data local infile '/dev/stdin' into table 2885205677_uncovered (dna, start, end)" # Thu Feb 3 18:55:41 GMT 2011: Finding all genomic features overlapping variants... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 743643928_rel_snps; CREATE TABLE 743643928_rel_snps ( association_id INT(10) NOT NULL, query_region_id INT(10) unsigned NOT NULL, target_region_id INT(10) NOT NULL, distance INT(10) NOT NULL, overlap INT(10) NOT NULL, same_strand enum('SAME', 'OPP') NOT NULL, num_regions_between INT(3) NOT NULL, PRIMARY KEY (association_id), KEY (query_region_id), KEY (target_region_id) )" # Thu Feb 3 18:55:41 GMT 2011: Getting masking regions /data/maqgene/bin/associate_regions -b -1 -c -1000000 -m 2 -o >(/usr/bin/mysql -Dmaqgenedb -umaqgene --skip-column-names --batch --raw --local-infile -e "drop table if exists 743643928_masked_ids; create table 743643928_masked_ids (query_region_id int(10) NOT NULL, primary key (query_region_id)); load data local infile '/dev/stdin' ignore into table 743643928_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 743643928_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 743643928_rel_snps; flush table 743643928_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 743643928_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 7 655 II 12 2098 III 6 787 IV 11 1156 V 6 817 X 9 5493 touch 2885205677_uncovered # Thu Feb 3 18:55:42 GMT 2011: Finding mRNA features overlapping uncovered regions ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 2885205677_uncovered_rel; CREATE TABLE 2885205677_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 2885205677_uncovered_rel; flush table 2885205677_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 2885205677_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 2885205677_uncovered_rel # Thu Feb 3 18:55:44 GMT 2011: Calculating translation start offsets for uncovered regions... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 2885205677_offsets_uncovered; create table 2885205677_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 2885205677_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 2885205677_uncovered reg join 2885205677_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 743643928_masked_ids /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 2885205677_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 2885205677_uncovered reg join 2885205677_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 2885205677_offsets_uncovered touch 743643928_rel_snps # Thu Feb 3 18:55:45 GMT 2011: Calculating translation start offsets... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 743643928_offsets_snps; create table 743643928_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 18:55:45 GMT 2011: Getting intergenic regions /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 743643928_rel_intergenic; create table 743643928_rel_intergenic like 743643928_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 743643928_rel_intergenic; flush table 743643928_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 743643928_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 743643928_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 743643928_snps reg join 743643928_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 18:55:48 GMT 2011: Filtering masked intergenic regions /usr/bin/mysql -Dmaqgenedb -umaqgene --skip-column-names --batch --raw --local-infile -e "delete i.* from 743643928_rel_intergenic i join 743643928_masked_ids m using (query_region_id)" touch 743643928_rel_intergenic # Thu Feb 3 18:55:52 GMT 2011: Classifying intergenic relations /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 743643928_intergenic_assoc; create table 743643928_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 743643928_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 743643928_snps snp join 743643928_rel_intergenic rel on (snp.id = rel.query_region_id) join elegans_features feature on (rel.target_region_id = feature.id)" touch 743643928_intergenic_assoc touch 743643928_offsets_snps # Thu Feb 3 18:56:04 GMT 2011: Getting codons affected by point mutations... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 743643928_codons; create table 743643928_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 743643928_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 743643928_offsets_snps off join 743643928_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 743643928_codons /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 743643928_marked; create table 743643928_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 18:56:11 GMT 2011: Finding exonic indels ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 743643928_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 743643928_snps snp join 743643928_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 18:56:11 GMT 2011: Finding coding variants ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 743643928_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 743643928_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 18:56:11 GMT 2011: Finding noncoding variants ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 743643928_marked select snp.id, feature.feature class, 'none' description, feature.attribute parent_feature from 743643928_snps snp join 743643928_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 18:56:12 GMT 2011: Finding splice site variants ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 743643928_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 743643928_snps snp join 743643928_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 18:56:12 GMT 2011: Finding intergenic and intronic variants ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 743643928_marked select id, 'nongenic' class, concat(if (relation in ('upstream','into'), - distance, distance),' ',relation) description, attribute from 743643928_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 18:56:14 GMT 2011: Finding uncovered regions in genes ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 743643928_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 2885205677_uncovered unc join 2885205677_offsets_uncovered b using (id) join 2885205677_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 2885205677_uncovered unc join 2885205677_offsets_uncovered b using (id) join 2885205677_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 18:56:14 GMT 2011: Variants found: +-----------------+-----------------+ | class | number_variants | +-----------------+-----------------+ | five_prime_UTR | 1297 | | frameshift | 93 | | inframe | 24 | | missense | 6135 | | ncRNA | 870 | | nongenic | 124737 | | non_start | 9 | | premature_stop | 690 | | readthrough | 19 | | silent | 7406 | | SNP | 1028 | | splice_acceptor | 48 | | splice_donor | 48 | | three_prime_UTR | 3553 | | uncovered | 14 | +-----------------+-----------------+ touch 743643928_marked # Thu Feb 3 18:56:15 GMT 2011: Combining results ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 743643928_combined; create table 743643928_combined (primary key (id, class, description), key (dna, start)) as select snp.id, 'CB6841' 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 743643928_snps snp join 2885205677_pileup pile using (dna,start) join 743643928_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, 'CB6841' 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 2885205677_uncovered unc join 743643928_marked class on (unc.id = class.id) left join elegans_per_locus using (dna,start) group by id, class, description; alter table 743643928_combined order by dna, start, length" touch 743643928_combined # Thu Feb 3 18:56:16 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 743643928_combined group by id order by dna, start;" > /data/maqgene/out/example_user/CB6841/CB6841_grouped.txt # Thu Feb 3 18:56:16 GMT 2011: Writing results to flat file ... /usr/bin/mysql -Dmaqgenedb -umaqgene --skip-column-names --batch --raw --local-infile --column-names -e "select * from 743643928_combined" > /data/maqgene/out/example_user/CB6841/CB6841_flat.txt 3667 lines written. 2131 lines written. rm 3228754180.00026.1.bfq 3228754180.00039.2.fastq 3228754180.00024.1.fastq 3228754180.00017.mismatch 3228754180.00028.map 3228754180.00046.unmapped 942262979_split1 3228754180.00026.mismatch 3228754180.00007.1.fastq 3228754180.00002.mismatch 3228754180.00015.map 3228754180.00047.2.bfq 3228754180.00018.1.bfq 3228754180.00031.mismatch 3228754180.00007.2.bfq 3228754180.00035.1.bfq 3228754180.00046.1.fastq 3228754180.00047.mismatch 3228754180.00031.2.bfq 3228754180.00006.unmapped 3228754180.00037.unmapped 3228754180.00010.1.bfq 3228754180.00048.mismatch 3228754180.00012.mismatch 3228754180.00038.2.bfq 3228754180.00048.2.bfq 3228754180.00042.2.fastq 3228754180.00006.1.fastq 3228754180.00046.2.fastq 3228754180.00026.2.bfq 3228754180.00040.1.fastq 3228754180.00024.2.fastq 3228754180.00000.unmapped 3228754180.00044.2.fastq 3228754180.00003.1.bfq 3228754180.00030.1.bfq 3228754180.00007.map 3228754180.00018.2.bfq 3228754180.00008.1.bfq 3228754180.00021.1.fastq 3228754180.00027.1.bfq 3228754180.00043.2.bfq 3228754180.00008.1.fastq 3228754180.00000.1.fastq 3228754180.00018.mismatch 3228754180.00038.unmapped 3228754180.00045.2.bfq 3228754180.00001.unmapped 3228754180.00022.2.bfq 3228754180.00031.1.bfq 3228754180.00044.1.bfq 3228754180.00038.1.fastq 3228754180.00045.mismatch 3228754180.00029.2.bfq 3228754180.00016.unmapped 3228754180.00013.2.bfq 3228754180.00022.mismatch 3228754180.00033.map 3228754180.00021.2.fastq 3228754180.00006.2.fastq 3228754180.00016.1.fastq 3228754180.00001.1.fastq 3228754180.00010.1.fastq 3228754180.00034.unmapped 3228754180.00040.map 3228754180.00004.map 3228754180.00003.2.bfq 3228754180.00029.unmapped 3228754180.00030.2.bfq 3228754180.00034.1.fastq 3228754180.00003.mismatch 3228754180.00036.map 3228754180.00000.2.bfq 3228754180.00021.map 3228754180.00000.2.fastq 3228754180.00027.mismatch 3228754180.00011.1.fastq 3228754180.00008.map 3228754180.00017.unmapped 3228754180.00043.2.fastq 3228754180.00005.1.bfq 3228754180.00002.2.bfq 3228754180.00048.1.bfq 3228754180.00009.1.fastq 942262979_split2 3228754180.00002.unmapped 3228754180.00020.unmapped 3228754180.00041.map 3228754180.00038.2.fastq 3228754180.00014.map 3228754180.00020.1.bfq 3228754180.00047.unmapped 3228754180.00007.2.fastq 3228754180.00023.1.bfq 3228754180.00013.mismatch 3228754180.00001.2.fastq 3228754180.00010.2.fastq 3228754180.00035.mismatch 3228754180.00002.1.fastq 3228754180.00037.map 3228754180.00035.2.bfq 3228754180.00019.1.bfq 3228754180.00047.1.fastq 3228754180.00012.unmapped 3228754180.00034.2.fastq 3228754180.00037.1.bfq 3228754180.00032.2.bfq 3228754180.00015.1.bfq 3228754180.00029.2.fastq 3228754180.00011.2.fastq 3228754180.00007.1.bfq 3228754180.00012.1.fastq 3228754180.00026.unmapped 3228754180.00005.mismatch 3228754180.00009.map 3228754180.00030.1.fastq 3228754180.00027.2.bfq 3228754180.00017.2.fastq 3228754180.00026.1.fastq 3228754180.00036.mismatch 3228754180.00042.map 3228754180.00023.2.bfq 3228754180.00018.unmapped 3228754180.00002.2.fastq 3228754180.00032.mismatch 3228754180.00020.2.fastq 3228754180.00017.1.fastq 3228754180.00023.mismatch 3228754180.00024.map 3228754180.00008.2.fastq 3228754180.00019.2.bfq 3228754180.00047.2.fastq 3228754180.00022.1.fastq 3228754180.00018.1.fastq 3228754180.00019.mismatch 3228754180.00045.unmapped 3228754180.00040.1.bfq 3228754180.00022.unmapped 3228754180.00046.map 3228754180.00025.map 3228754180.00015.2.bfq 3228754180.00044.2.bfq 3228754180.00037.2.bfq 3228754180.00010.unmapped 3228754180.00045.1.fastq 3228754180.00015.mismatch 3228754180.00016.2.fastq 3228754180.00037.1.fastq 3228754180.00003.unmapped 3228754180.00005.2.bfq 3228754180.00030.unmapped 3228754180.00044.mismatch 3228754180.00026.2.fastq 3228754180.00012.2.fastq 3228754180.00006.map 3228754180.00027.unmapped 3228754180.00028.2.bfq 3228754180.00003.1.fastq 3228754180.00037.2.fastq 3228754180.00011.2.bfq 3228754180.00018.2.fastq 3228754180.00027.1.fastq 3228754180.00028.mismatch 3228754180.00036.1.bfq 3228754180.00020.2.bfq 3228754180.00009.2.fastq 3228754180.00004.1.bfq 3228754180.00008.mismatch 3228754180.00031.unmapped 3228754180.00013.unmapped 3228754180.00030.mismatch 3228754180.00000.map 3228754180.00041.2.fastq 3228754180.00039.map 3228754180.00044.unmapped 3228754180.00045.2.fastq 3228754180.00022.2.fastq 3228754180.00031.1.fastq 3228754180.00013.1.fastq 3228754180.00008.2.bfq 3228754180.00043.mismatch 3228754180.00033.1.bfq 3228754180.00038.map 3228754180.00029.1.fastq 3228754180.00025.2.bfq 3228754180.00036.2.bfq 3228754180.00009.1.bfq 3228754180.00041.1.bfq 3228754180.00001.map 3228754180.00048.1.fastq 3228754180.00014.1.bfq 3228754180.00003.2.fastq 3228754180.00007.mismatch 3228754180.00030.2.fastq 3228754180.00016.map 3228754180.00005.unmapped 3228754180.00039.1.bfq 3228754180.00033.mismatch 3228754180.00027.2.fastq 3228754180.00011.unmapped 3228754180.00034.map 3228754180.00036.unmapped 3228754180.00040.2.bfq 3228754180.00011.1.bfq 3228754180.00005.1.fastq 3228754180.00004.mismatch 3228754180.00032.unmapped 3228754180.00011.map 3228754180.00023.unmapped 3228754180.00048.unmapped 3228754180.00025.1.bfq 3228754180.00036.1.fastq 3228754180.00031.2.fastq 3228754180.00013.2.fastq 3228754180.00019.unmapped 3228754180.00032.1.fastq 3228754180.00034.mismatch 3228754180.00023.1.fastq 3228754180.00017.map 3228754180.00043.map 3228754180.00040.mismatch 3228754180.00029.map 3228754180.00043.unmapped 3228754180.00019.1.fastq 3228754180.00002.map 3228754180.00020.map 3228754180.00015.unmapped 3228754180.00048.map 3228754180.00042.1.bfq 3228754180.00041.mismatch 3228754180.00014.mismatch 3228754180.00047.map 3228754180.00021.mismatch 3228754180.00024.1.bfq 3228754180.00007.unmapped 3228754180.00021.2.bfq 3228754180.00015.1.fastq 3228754180.00039.mismatch 3228754180.00005.2.fastq 3228754180.00022.1.bfq 3228754180.00012.map 3228754180.00046.1.bfq 3228754180.00036.2.fastq 3228754180.00028.unmapped 3228754180.00032.2.fastq 3228754180.00023.2.fastq 3228754180.00026.map 3228754180.00019.2.fastq 3228754180.00014.2.bfq 3228754180.00012.2.bfq 3228754180.00028.1.fastq 3228754180.00042.2.bfq 3228754180.00043.1.bfq 3228754180.00006.1.bfq 3228754180.00001.1.bfq 3228754180.00035.1.fastq 3228754180.00042.mismatch 3228754180.00018.map 3228754180.00024.2.bfq 3228754180.00015.2.fastq 3228754180.00024.mismatch 3228754180.00021.unmapped 3228754180.00025.unmapped 3228754180.00033.2.bfq 3228754180.00008.unmapped 3228754180.00009.mismatch 3228754180.00035.unmapped 3228754180.00045.map 3228754180.00046.2.bfq 3228754180.00009.2.bfq 3228754180.00000.1.bfq 3228754180.00022.map 3228754180.00048.2.fastq 3228754180.00033.unmapped 3228754180.00025.1.fastq 3228754180.00046.mismatch 3228754180.00041.2.bfq 3228754180.00004.unmapped 3228754180.00033.1.fastq 3228754180.00040.unmapped 3228754180.00028.2.fastq 3228754180.00003.map 3228754180.00029.1.bfq 3228754180.00006.2.bfq 3228754180.00030.map 3228754180.00025.mismatch 3228754180.00004.1.fastq 3228754180.00006.mismatch 3228754180.00027.map 3228754180.00035.map 3228754180.00016.1.bfq 3228754180.00045.1.bfq 3228754180.00034.1.bfq 3228754180.00032.1.bfq 3228754180.00041.unmapped 3228754180.00044.1.fastq 3228754180.00021.1.bfq 3228754180.00010.map 3228754180.00014.unmapped 3228754180.00004.2.bfq 3228754180.00031.map 3228754180.00013.map 3228754180.00009.unmapped 3228754180.00025.2.fastq 3228754180.00000.mismatch 3228754180.00028.1.bfq 3228754180.00039.unmapped 3228754180.00041.1.fastq 3228754180.00014.1.fastq 3228754180.00033.2.fastq 3228754180.00017.1.bfq 3228754180.00038.1.bfq 3228754180.00039.1.fastq 3228754180.00038.mismatch 3228754180.00001.2.bfq 3228754180.00010.2.bfq 3228754180.00002.1.bfq 3228754180.00004.2.fastq 3228754180.00013.1.bfq 3228754180.00040.2.fastq 3228754180.00001.mismatch 3228754180.00010.mismatch 3228754180.00016.2.bfq 3228754180.00047.1.bfq 3228754180.00039.2.bfq 3228754180.00016.mismatch 3228754180.00034.2.bfq 3228754180.00037.mismatch 3228754180.00020.mismatch 3228754180.00020.1.fastq 3228754180.00044.map 3228754180.00042.unmapped 3228754180.00012.1.bfq 3228754180.00032.map 3228754180.00029.mismatch 3228754180.00023.map 3228754180.00011.mismatch 3228754180.00024.unmapped 3228754180.00035.2.fastq 3228754180.00014.2.fastq 3228754180.00043.1.fastq 3228754180.00042.1.fastq 3228754180.00019.map 3228754180.00005.map 3228754180.00017.2.bfq make: Leaving directory `/data/maqgene/work' make: Entering directory `/data/maqgene/work' # Thu Feb 3 18:56:17 GMT 2011: Cleaning intermediate data ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 743643928_snps,743643928_rel,743643928_masked_ids,743643928_rel_intergenic,743643928_intergenic_assoc,743643928_offsets,743643928_codons,743643928_marked,743643928_combined,2885205677_pileup" rm -f 743643928_snps 743643928_rel 743643928_masked_ids 743643928_rel_intergenic 743643928_intergenic_assoc 743643928_offsets 743643928_codons 743643928_marked 743643928_combined 2885205677_pileup make: Leaving directory `/data/maqgene/work'