Finished reading input. ++ echo CB6997-1/./s_s_1_sequence_read1.fastq ++ tr , ' ' + fastq_file_set1=CB6997-1/./s_s_1_sequence_read1.fastq ++ cd /data/maqgene/reads ++ wc -l ++ cat CB6997-1/./s_s_1_sequence_read1.fastq ++ cut -f 1 -d ' ' + TOTAL_LINES=246029168 ++ bc ++ echo '(246029168 / 5000000) + (246029168 % 5000000 != 0)' + num_chunks=50 + 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=100166623 map_cksum=336440 pileup_cksum=428440209 cns_cksum=2658399291 umdd=50000 dmdd=1000 umid=1000 dmid=1000 max_gene_radius=50000 full_results_dir=/data/maqgene/out/example_user/CB6997_1 outfile_basename=CB6997_1 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=50 Will process 246029168 lines of input in 50 chunks make: Entering directory `/data/maqgene/work' # Wed Mar 28 10:51:05 BST 2012: Removing frontend files in case this is a duplicate run ... rm -f /data/maqgene/out/example_user/CB6997_1/CB6997_1_{grouped.txt,flat.txt} rm -f /data/maqgene/out/example_user/CB6997_1/CB6997_1_uncovered.txt /data/maqgene/out/example_user/CB6997_1/CB6997_1_coverage.txt /data/maqgene/out/example_user/CB6997_1/CB6997_1_pileup.txt /data/maqgene/out/example_user/CB6997_1/CB6997_1_log.txt /data/maqgene/out/example_user/CB6997_1/CB6997_1_check.txt /data/maqgene/out/example_user/CB6997_1/CB6997_1_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/CB6997-1/./s_s_1_sequence_read1.fastq) 336440.1.fastq. # : Regrouping fastq reads into chunks of size 5000000. split -l 5000000 -a 5 -d <(cat /data/maqgene/reads/CB6997-1/./s_s_2_sequence_read2.fastq) 336440.2.fastq. for stem in 00000 00001 00002 00003 00004 00005 00006 00007 00008 00009 00010 00011 00012 00013 00014 00015 00016 00017 00018 00019 00020 00021 00022 00023 00024 00025 00026 00027 00028 00029 00030 00031 00032 00033 00034 00035 00036 00037 00038 00039 00040 00041 00042 00043 00044 00045 00046 00047 00048 00049; do mv 336440.1.fastq.$stem 336440.$stem.1.fastq; done touch 100166623_split1 for stem in 00000 00001 00002 00003 00004 00005 00006 00007 00008 00009 00010 00011 00012 00013 00014 00015 00016 00017 00018 00019 00020 00021 00022 00023 00024 00025 00026 00027 00028 00029 00030 00031 00032 00033 00034 00035 00036 00037 00038 00039 00040 00041 00042 00043 00044 00045 00046 00047 00048 00049; do mv 336440.2.fastq.$stem 336440.$stem.2.fastq; done touch 100166623_split2 # Wed Mar 28 10:53:10 BST 2012: Converting fastq files to bfq ... # Wed Mar 28 10:53:10 BST 2012: Converting fastq files to bfq ... # Wed Mar 28 10:53:10 BST 2012: Converting fastq files to bfq ... # Wed Mar 28 10:53:10 BST 2012: Converting fastq files to bfq ... # Wed Mar 28 10:53:10 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 336440.00001.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00001.1.bfq /data/maqgene/bin/maq sol2sanger 336440.00000.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00000.1.bfq # Wed Mar 28 10:53:10 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 336440.00002.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00002.1.bfq /data/maqgene/bin/maq sol2sanger 336440.00003.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00003.1.bfq # Wed Mar 28 10:53:10 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 336440.00004.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00004.1.bfq /data/maqgene/bin/maq sol2sanger 336440.00005.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00005.1.bfq /data/maqgene/bin/maq sol2sanger 336440.00006.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00006.1.bfq # Wed Mar 28 10:53:10 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 336440.00007.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00007.1.bfq # Wed Mar 28 10:53:10 BST 2012: Converting fastq files to bfq ... # Wed Mar 28 10:53:10 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 336440.00008.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00008.1.bfq # Wed Mar 28 10:53:10 BST 2012: Converting fastq files to bfq ... | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00009.1.bfq # Wed Mar 28 10:53:10 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 336440.00011.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00011.1.bfq /data/maqgene/bin/maq sol2sanger 336440.00012.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00012.1.bfq # Wed Mar 28 10:53:10 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 336440.00013.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00013.1.bfq # Wed Mar 28 10:53:10 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 336440.00010.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00010.1.bfq -- finish writing file '336440.00011.1.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 10:53:31 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 336440.00014.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00014.1.bfq -- finish writing file '336440.00013.1.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 10:53:32 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 336440.00015.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00015.1.bfq -- finish writing file '336440.00006.1.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 10:53:34 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 336440.00016.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00016.1.bfq -- finish writing file '336440.00007.1.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 10:53:35 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 336440.00017.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00017.1.bfq -- finish writing file '336440.00012.1.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 10:53:35 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 336440.00018.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00018.1.bfq -- finish writing file '336440.00003.1.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 10:53:37 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 336440.00019.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00019.1.bfq -- finish writing file '336440.00000.1.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 10:53:38 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 336440.00020.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00020.1.bfq -- finish writing file '336440.00002.1.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 10:53:39 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 336440.00021.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00021.1.bfq -- finish writing file '336440.00005.1.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 10:53:39 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 336440.00022.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00022.1.bfq -- finish writing file '336440.00009.1.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 10:53:39 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 336440.00023.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00023.1.bfq -- finish writing file '336440.00008.1.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 10:53:39 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 336440.00024.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00024.1.bfq -- finish writing file '336440.00010.1.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 10:53:39 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 336440.00025.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00025.1.bfq -- finish writing file '336440.00001.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '336440.00004.1.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 10:53:40 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 336440.00026.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00026.1.bfq # Wed Mar 28 10:53:40 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 336440.00027.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00027.1.bfq -- finish writing file '336440.00018.1.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 10:53:52 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 336440.00028.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00028.1.bfq -- finish writing file '336440.00015.1.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 10:53:55 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 336440.00029.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00029.1.bfq -- finish writing file '336440.00021.1.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 10:53:56 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 336440.00030.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00030.1.bfq -- finish writing file '336440.00014.1.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 10:53:59 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 336440.00031.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00031.1.bfq -- finish writing file '336440.00019.1.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 10:54:00 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 336440.00032.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00032.1.bfq -- finish writing file '336440.00016.1.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 10:54:03 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 336440.00033.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00033.1.bfq -- finish writing file '336440.00020.1.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 10:54:03 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 336440.00034.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00034.1.bfq -- finish writing file '336440.00017.1.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 10:54:04 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 336440.00035.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00035.1.bfq -- finish writing file '336440.00023.1.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 10:54:04 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 336440.00036.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00036.1.bfq -- finish writing file '336440.00024.1.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 10:54:06 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 336440.00037.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00037.1.bfq -- finish writing file '336440.00022.1.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 10:54:06 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 336440.00038.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00038.1.bfq -- finish writing file '336440.00027.1.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 10:54:08 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 336440.00039.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00039.1.bfq -- finish writing file '336440.00025.1.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 10:54:08 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 336440.00040.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00040.1.bfq -- finish writing file '336440.00026.1.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 10:54:10 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 336440.00041.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00041.1.bfq -- finish writing file '336440.00028.1.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 10:54:20 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 336440.00042.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00042.1.bfq -- finish writing file '336440.00029.1.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 10:54:21 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 336440.00043.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00043.1.bfq -- finish writing file '336440.00030.1.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 10:54:23 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 336440.00044.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00044.1.bfq -- finish writing file '336440.00032.1.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 10:54:24 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 336440.00045.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00045.1.bfq -- finish writing file '336440.00034.1.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 10:54:25 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 336440.00046.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00046.1.bfq -- finish writing file '336440.00033.1.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 10:54:25 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 336440.00047.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00047.1.bfq -- finish writing file '336440.00031.1.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 10:54:25 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 336440.00048.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00048.1.bfq -- finish writing file '336440.00035.1.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 10:54:30 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 336440.00049.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00049.1.bfq -- finish writing file '336440.00036.1.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 10:54:31 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 336440.00000.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00000.2.bfq -- finish writing file '336440.00037.1.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 10:54:33 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 336440.00001.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00001.2.bfq -- finish writing file '336440.00039.1.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 10:54:34 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 336440.00002.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00002.2.bfq -- finish writing file '336440.00040.1.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 10:54:35 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 336440.00003.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00003.2.bfq -- finish writing file '336440.00049.1.bfq' -- 257292 sequences were loaded. # Wed Mar 28 10:54:35 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 336440.00004.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00004.2.bfq -- finish writing file '336440.00038.1.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 10:54:35 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 336440.00005.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00005.2.bfq -- finish writing file '336440.00041.1.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 10:54:36 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 336440.00006.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00006.2.bfq -- finish writing file '336440.00043.1.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 10:54:46 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 336440.00007.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00007.2.bfq -- finish writing file '336440.00042.1.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 10:54:46 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 336440.00008.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00008.2.bfq -- finish writing file '336440.00045.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '336440.00044.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '336440.00048.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '336440.00046.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '336440.00047.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '336440.00001.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '336440.00003.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '336440.00000.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '336440.00005.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '336440.00006.2.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 10:54:57 BST 2012: Converting fastq files to bfq ... # Wed Mar 28 10:54:57 BST 2012: Converting fastq files to bfq ... # Wed Mar 28 10:54:57 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 336440.00015.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00015.2.bfq /data/maqgene/bin/maq sol2sanger 336440.00017.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00017.2.bfq /data/maqgene/bin/maq sol2sanger 336440.00016.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00016.2.bfq -- finish writing file '336440.00004.2.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 10:54:57 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 336440.00018.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00018.2.bfq -- finish writing file '336440.00002.2.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 10:54:58 BST 2012: Converting fastq files to bfq ... # Wed Mar 28 10:54:58 BST 2012: Converting fastq files to bfq ... # Wed Mar 28 10:54:58 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 336440.00019.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00019.2.bfq /data/maqgene/bin/maq sol2sanger 336440.00014.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00014.2.bfq /data/maqgene/bin/maq sol2sanger 336440.00013.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00013.2.bfq # Wed Mar 28 10:54:59 BST 2012: Converting fastq files to bfq ... # Wed Mar 28 10:54:59 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 336440.00012.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00012.2.bfq # Wed Mar 28 10:54:59 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 336440.00020.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00020.2.bfq /data/maqgene/bin/maq sol2sanger 336440.00011.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00011.2.bfq # Wed Mar 28 10:55:00 BST 2012: Converting fastq files to bfq ... # Wed Mar 28 10:55:00 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 336440.00009.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00009.2.bfq /data/maqgene/bin/maq sol2sanger 336440.00010.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00010.2.bfq -- finish writing file '336440.00007.2.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 10:55:04 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 336440.00021.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00021.2.bfq -- finish writing file '336440.00008.2.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 10:55:05 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 336440.00022.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00022.2.bfq -- finish writing file '336440.00013.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '336440.00016.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '336440.00015.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '336440.00014.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '336440.00017.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '336440.00012.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '336440.00018.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '336440.00020.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '336440.00011.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '336440.00019.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '336440.00010.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '336440.00022.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '336440.00009.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '336440.00021.2.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 10:55:26 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 336440.00035.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00035.2.bfq # Wed Mar 28 10:55:27 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 336440.00036.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00036.2.bfq # Wed Mar 28 10:55:27 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 336440.00034.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00034.2.bfq # Wed Mar 28 10:55:27 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 336440.00033.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00033.2.bfq # Wed Mar 28 10:55:28 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 336440.00032.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00032.2.bfq /data/maqgene/bin/maq sol2sanger 336440.00031.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00031.2.bfq # Wed Mar 28 10:55:28 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 336440.00030.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00030.2.bfq # Wed Mar 28 10:55:29 BST 2012: Converting fastq files to bfq ... # Wed Mar 28 10:55:29 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 336440.00029.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00029.2.bfq /data/maqgene/bin/maq sol2sanger 336440.00028.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00028.2.bfq # Wed Mar 28 10:55:29 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 336440.00027.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00027.2.bfq # Wed Mar 28 10:55:30 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 336440.00026.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00026.2.bfq # Wed Mar 28 10:55:30 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 336440.00024.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00024.2.bfq # Wed Mar 28 10:55:30 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 336440.00025.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00025.2.bfq # Wed Mar 28 10:55:31 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 336440.00023.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00023.2.bfq -- finish writing file '336440.00030.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '336440.00036.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '336440.00035.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '336440.00033.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '336440.00029.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '336440.00031.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '336440.00034.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '336440.00024.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '336440.00026.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '336440.00023.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '336440.00032.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '336440.00028.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '336440.00027.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '336440.00025.2.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 10:55:54 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 336440.00049.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00049.2.bfq -- finish writing file '336440.00049.2.bfq' -- 257292 sequences were loaded. # Wed Mar 28 10:55:57 BST 2012: Mapping file(s) 336440.00000.1.bfq 336440.00000.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 336440.00000.unmapped -H 336440.00000.mismatch \ 336440.00000.map /data/maqgene/genomes/elegans.bfa 336440.00000.1.bfq 336440.00000.2.bfq 2> /dev/null # Wed Mar 28 10:55:58 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 336440.00048.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00048.2.bfq # Wed Mar 28 10:55:58 BST 2012: Mapping file(s) 336440.00001.1.bfq 336440.00001.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 336440.00001.unmapped -H 336440.00001.mismatch \ 336440.00001.map /data/maqgene/genomes/elegans.bfa 336440.00001.1.bfq 336440.00001.2.bfq 2> /dev/null # Wed Mar 28 10:55:59 BST 2012: Converting fastq files to bfq ... # Wed Mar 28 10:55:59 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 336440.00046.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00046.2.bfq /data/maqgene/bin/maq sol2sanger 336440.00047.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00047.2.bfq # Wed Mar 28 10:56:00 BST 2012: Converting fastq files to bfq ... # Wed Mar 28 10:56:00 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 336440.00044.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00044.2.bfq /data/maqgene/bin/maq sol2sanger 336440.00045.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00045.2.bfq # Wed Mar 28 10:56:01 BST 2012: Converting fastq files to bfq ... # Wed Mar 28 10:56:01 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 336440.00043.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00043.2.bfq /data/maqgene/bin/maq sol2sanger 336440.00042.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00042.2.bfq # Wed Mar 28 10:56:02 BST 2012: Converting fastq files to bfq ... # Wed Mar 28 10:56:02 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 336440.00041.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00041.2.bfq /data/maqgene/bin/maq sol2sanger 336440.00040.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00040.2.bfq # Wed Mar 28 10:56:03 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 336440.00039.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00039.2.bfq /data/maqgene/bin/maq sol2sanger 336440.00038.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00038.2.bfq # Wed Mar 28 10:56:04 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 336440.00037.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 336440.00037.2.bfq -- finish writing file '336440.00047.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '336440.00038.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '336440.00048.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '336440.00046.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '336440.00045.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '336440.00044.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '336440.00041.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '336440.00043.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '336440.00040.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '336440.00042.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '336440.00039.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '336440.00037.2.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 10:56:27 BST 2012: Mapping file(s) 336440.00012.1.bfq 336440.00012.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 336440.00012.unmapped -H 336440.00012.mismatch \ 336440.00012.map /data/maqgene/genomes/elegans.bfa 336440.00012.1.bfq 336440.00012.2.bfq 2> /dev/null # Wed Mar 28 10:56:29 BST 2012: Mapping file(s) 336440.00013.1.bfq 336440.00013.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 336440.00013.unmapped -H 336440.00013.mismatch \ 336440.00013.map /data/maqgene/genomes/elegans.bfa 336440.00013.1.bfq 336440.00013.2.bfq 2> /dev/null # Wed Mar 28 10:56:31 BST 2012: Mapping file(s) 336440.00011.1.bfq 336440.00011.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 336440.00011.unmapped -H 336440.00011.mismatch \ 336440.00011.map /data/maqgene/genomes/elegans.bfa 336440.00011.1.bfq 336440.00011.2.bfq 2> /dev/null # Wed Mar 28 10:56:32 BST 2012: Mapping file(s) 336440.00010.1.bfq 336440.00010.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 336440.00010.unmapped -H 336440.00010.mismatch \ 336440.00010.map /data/maqgene/genomes/elegans.bfa 336440.00010.1.bfq 336440.00010.2.bfq 2> /dev/null # Wed Mar 28 10:56:32 BST 2012: Mapping file(s) 336440.00008.1.bfq 336440.00008.2.bfq # Wed Mar 28 10:56:32 BST 2012: Mapping file(s) 336440.00009.1.bfq 336440.00009.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 336440.00008.unmapped -H 336440.00008.mismatch \ 336440.00008.map /data/maqgene/genomes/elegans.bfa 336440.00008.1.bfq 336440.00008.2.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 336440.00009.unmapped -H 336440.00009.mismatch \ 336440.00009.map /data/maqgene/genomes/elegans.bfa 336440.00009.1.bfq 336440.00009.2.bfq 2> /dev/null # Wed Mar 28 10:56:33 BST 2012: Mapping file(s) 336440.00007.1.bfq 336440.00007.2.bfq # Wed Mar 28 10:56:33 BST 2012: Mapping file(s) 336440.00005.1.bfq 336440.00005.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 336440.00007.unmapped -H 336440.00007.mismatch \ 336440.00007.map /data/maqgene/genomes/elegans.bfa 336440.00007.1.bfq 336440.00007.2.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 336440.00005.unmapped -H 336440.00005.mismatch \ 336440.00005.map /data/maqgene/genomes/elegans.bfa 336440.00005.1.bfq 336440.00005.2.bfq 2> /dev/null # Wed Mar 28 10:56:33 BST 2012: Mapping file(s) 336440.00006.1.bfq 336440.00006.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 336440.00006.unmapped -H 336440.00006.mismatch \ 336440.00006.map /data/maqgene/genomes/elegans.bfa 336440.00006.1.bfq 336440.00006.2.bfq 2> /dev/null # Wed Mar 28 10:56:34 BST 2012: Mapping file(s) 336440.00004.1.bfq 336440.00004.2.bfq # Wed Mar 28 10:56:34 BST 2012: Mapping file(s) 336440.00002.1.bfq 336440.00002.2.bfq # Wed Mar 28 10:56:34 BST 2012: Mapping file(s) 336440.00003.1.bfq 336440.00003.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 336440.00004.unmapped -H 336440.00004.mismatch \ 336440.00004.map /data/maqgene/genomes/elegans.bfa 336440.00004.1.bfq 336440.00004.2.bfq 2> /dev/null /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 336440.00003.unmapped -H 336440.00003.mismatch \ 336440.00003.map /data/maqgene/genomes/elegans.bfa 336440.00003.1.bfq 336440.00003.2.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 336440.00002.unmapped -H 336440.00002.mismatch \ 336440.00002.map /data/maqgene/genomes/elegans.bfa 336440.00002.1.bfq 336440.00002.2.bfq 2> /dev/null # Wed Mar 28 11:02:18 BST 2012: Mapping file(s) 336440.00014.1.bfq 336440.00014.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 336440.00014.unmapped -H 336440.00014.mismatch \ 336440.00014.map /data/maqgene/genomes/elegans.bfa 336440.00014.1.bfq 336440.00014.2.bfq 2> /dev/null # Wed Mar 28 11:02:29 BST 2012: Mapping file(s) 336440.00015.1.bfq 336440.00015.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 336440.00015.unmapped -H 336440.00015.mismatch \ 336440.00015.map /data/maqgene/genomes/elegans.bfa 336440.00015.1.bfq 336440.00015.2.bfq 2> /dev/null # Wed Mar 28 11:02:40 BST 2012: Mapping file(s) 336440.00016.1.bfq 336440.00016.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 336440.00016.unmapped -H 336440.00016.mismatch \ 336440.00016.map /data/maqgene/genomes/elegans.bfa 336440.00016.1.bfq 336440.00016.2.bfq 2> /dev/null # Wed Mar 28 11:02:47 BST 2012: Mapping file(s) 336440.00017.1.bfq 336440.00017.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 336440.00017.unmapped -H 336440.00017.mismatch \ 336440.00017.map /data/maqgene/genomes/elegans.bfa 336440.00017.1.bfq 336440.00017.2.bfq 2> /dev/null # Wed Mar 28 11:02:50 BST 2012: Mapping file(s) 336440.00018.1.bfq 336440.00018.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 336440.00018.unmapped -H 336440.00018.mismatch \ 336440.00018.map /data/maqgene/genomes/elegans.bfa 336440.00018.1.bfq 336440.00018.2.bfq 2> /dev/null # Wed Mar 28 11:02:58 BST 2012: Mapping file(s) 336440.00019.1.bfq 336440.00019.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 336440.00019.unmapped -H 336440.00019.mismatch \ 336440.00019.map /data/maqgene/genomes/elegans.bfa 336440.00019.1.bfq 336440.00019.2.bfq 2> /dev/null # Wed Mar 28 11:03:03 BST 2012: Mapping file(s) 336440.00020.1.bfq 336440.00020.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 336440.00020.unmapped -H 336440.00020.mismatch \ 336440.00020.map /data/maqgene/genomes/elegans.bfa 336440.00020.1.bfq 336440.00020.2.bfq 2> /dev/null # Wed Mar 28 11:03:03 BST 2012: Mapping file(s) 336440.00021.1.bfq 336440.00021.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 336440.00021.unmapped -H 336440.00021.mismatch \ 336440.00021.map /data/maqgene/genomes/elegans.bfa 336440.00021.1.bfq 336440.00021.2.bfq 2> /dev/null # Wed Mar 28 11:03:04 BST 2012: Mapping file(s) 336440.00022.1.bfq 336440.00022.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 336440.00022.unmapped -H 336440.00022.mismatch \ 336440.00022.map /data/maqgene/genomes/elegans.bfa 336440.00022.1.bfq 336440.00022.2.bfq 2> /dev/null # Wed Mar 28 11:03:12 BST 2012: Mapping file(s) 336440.00023.1.bfq 336440.00023.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 336440.00023.unmapped -H 336440.00023.mismatch \ 336440.00023.map /data/maqgene/genomes/elegans.bfa 336440.00023.1.bfq 336440.00023.2.bfq 2> /dev/null # Wed Mar 28 11:03:19 BST 2012: Mapping file(s) 336440.00024.1.bfq 336440.00024.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 336440.00024.unmapped -H 336440.00024.mismatch \ 336440.00024.map /data/maqgene/genomes/elegans.bfa 336440.00024.1.bfq 336440.00024.2.bfq 2> /dev/null # Wed Mar 28 11:03:23 BST 2012: Mapping file(s) 336440.00025.1.bfq 336440.00025.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 336440.00025.unmapped -H 336440.00025.mismatch \ 336440.00025.map /data/maqgene/genomes/elegans.bfa 336440.00025.1.bfq 336440.00025.2.bfq 2> /dev/null # Wed Mar 28 11:03:29 BST 2012: Mapping file(s) 336440.00026.1.bfq 336440.00026.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 336440.00026.unmapped -H 336440.00026.mismatch \ 336440.00026.map /data/maqgene/genomes/elegans.bfa 336440.00026.1.bfq 336440.00026.2.bfq 2> /dev/null # Wed Mar 28 11:03:41 BST 2012: Mapping file(s) 336440.00027.1.bfq 336440.00027.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 336440.00027.unmapped -H 336440.00027.mismatch \ 336440.00027.map /data/maqgene/genomes/elegans.bfa 336440.00027.1.bfq 336440.00027.2.bfq 2> /dev/null # Wed Mar 28 11:08:29 BST 2012: Mapping file(s) 336440.00028.1.bfq 336440.00028.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 336440.00028.unmapped -H 336440.00028.mismatch \ 336440.00028.map /data/maqgene/genomes/elegans.bfa 336440.00028.1.bfq 336440.00028.2.bfq 2> /dev/null # Wed Mar 28 11:08:34 BST 2012: Mapping file(s) 336440.00029.1.bfq 336440.00029.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 336440.00029.unmapped -H 336440.00029.mismatch \ 336440.00029.map /data/maqgene/genomes/elegans.bfa 336440.00029.1.bfq 336440.00029.2.bfq 2> /dev/null # Wed Mar 28 11:08:40 BST 2012: Mapping file(s) 336440.00030.1.bfq 336440.00030.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 336440.00030.unmapped -H 336440.00030.mismatch \ 336440.00030.map /data/maqgene/genomes/elegans.bfa 336440.00030.1.bfq 336440.00030.2.bfq 2> /dev/null # Wed Mar 28 11:08:54 BST 2012: Mapping file(s) 336440.00031.1.bfq 336440.00031.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 336440.00031.unmapped -H 336440.00031.mismatch \ 336440.00031.map /data/maqgene/genomes/elegans.bfa 336440.00031.1.bfq 336440.00031.2.bfq 2> /dev/null # Wed Mar 28 11:09:03 BST 2012: Mapping file(s) 336440.00032.1.bfq 336440.00032.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 336440.00032.unmapped -H 336440.00032.mismatch \ 336440.00032.map /data/maqgene/genomes/elegans.bfa 336440.00032.1.bfq 336440.00032.2.bfq 2> /dev/null # Wed Mar 28 11:09:08 BST 2012: Mapping file(s) 336440.00033.1.bfq 336440.00033.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 336440.00033.unmapped -H 336440.00033.mismatch \ 336440.00033.map /data/maqgene/genomes/elegans.bfa 336440.00033.1.bfq 336440.00033.2.bfq 2> /dev/null # Wed Mar 28 11:09:09 BST 2012: Mapping file(s) 336440.00034.1.bfq 336440.00034.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 336440.00034.unmapped -H 336440.00034.mismatch \ 336440.00034.map /data/maqgene/genomes/elegans.bfa 336440.00034.1.bfq 336440.00034.2.bfq 2> /dev/null # Wed Mar 28 11:09:13 BST 2012: Mapping file(s) 336440.00035.1.bfq 336440.00035.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 336440.00035.unmapped -H 336440.00035.mismatch \ 336440.00035.map /data/maqgene/genomes/elegans.bfa 336440.00035.1.bfq 336440.00035.2.bfq 2> /dev/null # Wed Mar 28 11:09:19 BST 2012: Mapping file(s) 336440.00036.1.bfq 336440.00036.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 336440.00036.unmapped -H 336440.00036.mismatch \ 336440.00036.map /data/maqgene/genomes/elegans.bfa 336440.00036.1.bfq 336440.00036.2.bfq 2> /dev/null # Wed Mar 28 11:09:24 BST 2012: Mapping file(s) 336440.00037.1.bfq 336440.00037.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 336440.00037.unmapped -H 336440.00037.mismatch \ 336440.00037.map /data/maqgene/genomes/elegans.bfa 336440.00037.1.bfq 336440.00037.2.bfq 2> /dev/null # Wed Mar 28 11:09:36 BST 2012: Mapping file(s) 336440.00038.1.bfq 336440.00038.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 336440.00038.unmapped -H 336440.00038.mismatch \ 336440.00038.map /data/maqgene/genomes/elegans.bfa 336440.00038.1.bfq 336440.00038.2.bfq 2> /dev/null # Wed Mar 28 11:09:42 BST 2012: Mapping file(s) 336440.00039.1.bfq 336440.00039.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 336440.00039.unmapped -H 336440.00039.mismatch \ 336440.00039.map /data/maqgene/genomes/elegans.bfa 336440.00039.1.bfq 336440.00039.2.bfq 2> /dev/null # Wed Mar 28 11:09:44 BST 2012: Mapping file(s) 336440.00040.1.bfq 336440.00040.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 336440.00040.unmapped -H 336440.00040.mismatch \ 336440.00040.map /data/maqgene/genomes/elegans.bfa 336440.00040.1.bfq 336440.00040.2.bfq 2> /dev/null # Wed Mar 28 11:11:08 BST 2012: Mapping file(s) 336440.00041.1.bfq 336440.00041.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 336440.00041.unmapped -H 336440.00041.mismatch \ 336440.00041.map /data/maqgene/genomes/elegans.bfa 336440.00041.1.bfq 336440.00041.2.bfq 2> /dev/null # Wed Mar 28 11:15:10 BST 2012: Mapping file(s) 336440.00045.1.bfq 336440.00045.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 336440.00045.unmapped -H 336440.00045.mismatch \ 336440.00045.map /data/maqgene/genomes/elegans.bfa 336440.00045.1.bfq 336440.00045.2.bfq 2> /dev/null # Wed Mar 28 11:15:11 BST 2012: Mapping file(s) 336440.00046.1.bfq 336440.00046.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 336440.00046.unmapped -H 336440.00046.mismatch \ 336440.00046.map /data/maqgene/genomes/elegans.bfa 336440.00046.1.bfq 336440.00046.2.bfq 2> /dev/null # Wed Mar 28 11:15:12 BST 2012: Mapping file(s) 336440.00044.1.bfq 336440.00044.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 336440.00044.unmapped -H 336440.00044.mismatch \ 336440.00044.map /data/maqgene/genomes/elegans.bfa 336440.00044.1.bfq 336440.00044.2.bfq 2> /dev/null # Wed Mar 28 11:15:12 BST 2012: Mapping file(s) 336440.00043.1.bfq 336440.00043.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 336440.00043.unmapped -H 336440.00043.mismatch \ 336440.00043.map /data/maqgene/genomes/elegans.bfa 336440.00043.1.bfq 336440.00043.2.bfq 2> /dev/null # Wed Mar 28 11:15:13 BST 2012: Mapping file(s) 336440.00047.1.bfq 336440.00047.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 336440.00047.unmapped -H 336440.00047.mismatch \ 336440.00047.map /data/maqgene/genomes/elegans.bfa 336440.00047.1.bfq 336440.00047.2.bfq 2> /dev/null # Wed Mar 28 11:15:14 BST 2012: Mapping file(s) 336440.00042.1.bfq 336440.00042.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 336440.00042.unmapped -H 336440.00042.mismatch \ 336440.00042.map /data/maqgene/genomes/elegans.bfa 336440.00042.1.bfq 336440.00042.2.bfq 2> /dev/null # Wed Mar 28 11:15:33 BST 2012: Mapping file(s) 336440.00048.1.bfq 336440.00048.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 336440.00048.unmapped -H 336440.00048.mismatch \ 336440.00048.map /data/maqgene/genomes/elegans.bfa 336440.00048.1.bfq 336440.00048.2.bfq 2> /dev/null # Wed Mar 28 11:15:39 BST 2012: Mapping file(s) 336440.00049.1.bfq 336440.00049.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 336440.00049.unmapped -H 336440.00049.mismatch \ 336440.00049.map /data/maqgene/genomes/elegans.bfa 336440.00049.1.bfq 336440.00049.2.bfq 2> /dev/null # Wed Mar 28 11:20:32 BST 2012: Merging all maps ... /data/maqgene/bin/maq mapmerge 336440.map 336440.00000.map 336440.00001.map 336440.00002.map 336440.00003.map 336440.00004.map 336440.00005.map 336440.00006.map 336440.00007.map 336440.00008.map 336440.00009.map 336440.00010.map 336440.00011.map 336440.00012.map 336440.00013.map 336440.00014.map 336440.00015.map 336440.00016.map 336440.00017.map 336440.00018.map 336440.00019.map 336440.00020.map 336440.00021.map 336440.00022.map 336440.00023.map 336440.00024.map 336440.00025.map 336440.00026.map 336440.00027.map 336440.00028.map 336440.00029.map 336440.00030.map 336440.00031.map 336440.00032.map 336440.00033.map 336440.00034.map 336440.00035.map 336440.00036.map 336440.00037.map 336440.00038.map 336440.00039.map 336440.00040.map 336440.00041.map 336440.00042.map 336440.00043.map 336440.00044.map 336440.00045.map 336440.00046.map 336440.00047.map 336440.00048.map 336440.00049.map # Wed Mar 28 11:20:32 BST 2012: Merging all *.unmapped files ... cat 336440.00000.unmapped 336440.00001.unmapped 336440.00002.unmapped 336440.00003.unmapped 336440.00004.unmapped 336440.00005.unmapped 336440.00006.unmapped 336440.00007.unmapped 336440.00008.unmapped 336440.00009.unmapped 336440.00010.unmapped 336440.00011.unmapped 336440.00012.unmapped 336440.00013.unmapped 336440.00014.unmapped 336440.00015.unmapped 336440.00016.unmapped 336440.00017.unmapped 336440.00018.unmapped 336440.00019.unmapped 336440.00020.unmapped 336440.00021.unmapped 336440.00022.unmapped 336440.00023.unmapped 336440.00024.unmapped 336440.00025.unmapped 336440.00026.unmapped 336440.00027.unmapped 336440.00028.unmapped 336440.00029.unmapped 336440.00030.unmapped 336440.00031.unmapped 336440.00032.unmapped 336440.00033.unmapped 336440.00034.unmapped 336440.00035.unmapped 336440.00036.unmapped 336440.00037.unmapped 336440.00038.unmapped 336440.00039.unmapped 336440.00040.unmapped 336440.00041.unmapped 336440.00042.unmapped 336440.00043.unmapped 336440.00044.unmapped 336440.00045.unmapped 336440.00046.unmapped 336440.00047.unmapped 336440.00048.unmapped 336440.00049.unmapped > 336440_unmapped.txt # Wed Mar 28 11:20:34 BST 2012: Linking backend file 336440_unmapped.txt to /data/maqgene/out/example_user/CB6997_1/CB6997_1_unmapped.txt ln -fs /data/maqgene/work/336440_unmapped.txt /data/maqgene/out/example_user/CB6997_1/CB6997_1_unmapped.txt /data/maqgene/makefile:126: warning: undefined variable `mapcheck_parameters' # Wed Mar 28 11:39:16 BST 2012: Running 'mapcheck' ... # Wed Mar 28 11:39:16 BST 2012: Generating consensus ... /data/maqgene/bin/maq pileup -Q 100 -p -m 7 -q 0 /data/maqgene/genomes/elegans.bfa 336440.map > 428440209_pileup.txt /data/maqgene/bin/maq assemble -N 2 -q 0 -r 0.0 -m 7 -Q 100 -p 2658399291.cns \ /data/maqgene/genomes/elegans.bfa 336440.map 2> 2658399291_log.txt /data/maqgene/bin/maq mapcheck /data/maqgene/genomes/elegans.bfa 336440.map > 336440_check.txt \ 2>/dev/null # Wed Mar 28 11:45:09 BST 2012: Linking backend file 336440_check.txt to /data/maqgene/out/example_user/CB6997_1/CB6997_1_check.txt ln -fs /data/maqgene/work/336440_check.txt /data/maqgene/out/example_user/CB6997_1/CB6997_1_check.txt /data/maqgene/bin/filter_matching_lines 428440209_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 \ > 428440209_known_snps # Wed Mar 28 11:45:30 BST 2012: Getting uncovered regions ... # Wed Mar 28 11:45:30 BST 2012: Linking backend file 428440209_pileup.txt to /data/maqgene/out/example_user/CB6997_1/CB6997_1_pileup.txt # Wed Mar 28 11:45:30 BST 2012: Making coverage histogram ... cut -f 1,2,4 428440209_pileup.txt \ | /data/maqgene/bin/get_uncovered_regions 50 \ > 428440209_uncovered.txt (echo -en "sequencing_depth\tnumber_of_bases\n"; \ cut -f 4 428440209_pileup.txt \ | /data/maqgene/bin/pileup_histogram 100) > 428440209_coverage.txt ln -fs /data/maqgene/work/428440209_pileup.txt /data/maqgene/out/example_user/CB6997_1/CB6997_1_pileup.txt # Wed Mar 28 11:48:40 BST 2012: Filtering and loading pileup for analysis ... # Wed Mar 28 11:48:40 BST 2012: Extracting point mutants from consensus ... # Wed Mar 28 11:48:40 BST 2012: Linking backend file 428440209_coverage.txt to /data/maqgene/out/example_user/CB6997_1/CB6997_1_coverage.txt # Wed Mar 28 11:48:40 BST 2012: Linking backend file 2658399291_log.txt to /data/maqgene/out/example_user/CB6997_1/CB6997_1_log.txt # Wed Mar 28 11:48:40 BST 2012: Linking backend file 428440209_uncovered.txt to /data/maqgene/out/example_user/CB6997_1/CB6997_1_uncovered.txt /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 2658399291_snps; create table 2658399291_snps ( id int(10) NOT NULL auto_increment, dna char(40) NOT NULL, start int(10) NOT NULL, end int(10) NOT NULL, indel_size int(5) NOT NULL, variant_type enum('indel', 'point') NOT NULL, ref_base char NOT NULL, sample_base char NOT NULL, snp_score int(5) NOT NULL, read_depth int(5) NOT NULL, loci_multiplicity double(5,2) NOT NULL, mapping_quality int(5) NOT NULL, neighbor_quality int(5) NOT NULL, primary key (id), unique key (dna, start), key (indel_size) )" ln -fs /data/maqgene/work/428440209_coverage.txt /data/maqgene/out/example_user/CB6997_1/CB6997_1_coverage.txt ln -fs /data/maqgene/work/428440209_uncovered.txt /data/maqgene/out/example_user/CB6997_1/CB6997_1_uncovered.txt /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 428440209_pileup; create table 428440209_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) );" ln -fs /data/maqgene/work/2658399291_log.txt /data/maqgene/out/example_user/CB6997_1/CB6997_1_log.txt cat 428440209_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 428440209_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 428440209_pileup" /data/maqgene/bin/maq cns2snp 2658399291.cns \ | cat -b | /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "load data local infile '/dev/stdin' into table 2658399291_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 2658399291_snps;" # Wed Mar 28 11:48:56 BST 2012: Extracting indels from consensus ... /data/maqgene/bin/maq indelsoa /data/maqgene/genomes/elegans.bfa 336440.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 2658399291_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 2658399291_snps;" cat 428440209_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 428440209_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 428440209_pileup" touch 428440209_pileup # Wed Mar 28 11:49:56 BST 2012: Writing snp read counts ... /usr/bin/mysql -Dmaqgenedb -umaqgene --skip-column-names --batch --raw --local-infile --column-names -e "select f.id, f.dna, f.start + 1 start, e.snp_name, e.snp_base, if(e.snp_base = 'a', p.A_fwd + p.A_rev, if (e.snp_base = 'c', p.C_fwd + p.C_rev, if (e.snp_base = 'g', p.G_fwd + p.G_rev, if (e.snp_base = 't', p.T_fwd + p.T_rev, -1)))) snp_reads, p.ref_base, p.wt_fwd + p.wt_rev wt_reads, p.read_depth, p.sample_reads from elegans_features f join elegans_snp_changes e on (f.attribute = e.snp_name) join 428440209_pileup p using (dna,start)" > /data/maqgene/out/example_user/CB6997_1/CB6997_1_snp_read_counts.txt 0 snp read count lines written. # Wed Mar 28 11:52:33 BST 2012: Adding placeholders for known SNPs. cat 428440209_known_snps \ | /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "load data local infile '/dev/stdin' ignore into table 2658399291_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 2658399291_snps;" Found 160744 variants. touch 2658399291_snps # Wed Mar 28 11:52:34 BST 2012: Loading uncovered regions into table ... # Wed Mar 28 11:52:34 BST 2012: Finding all genomic features overlapping variants... cat 428440209_uncovered.txt \ | /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 428440209_uncovered; create table 428440209_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 = 160745; load data local infile '/dev/stdin' into table 428440209_uncovered (dna, start, end)" # Wed Mar 28 11:52:34 BST 2012: Getting masking regions /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 2658399291_rel_snps; CREATE TABLE 2658399291_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 2658399291_masked_ids; create table 2658399291_masked_ids (query_region_id int(10) NOT NULL, primary key (query_region_id)); load data local infile '/dev/stdin' ignore into table 2658399291_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 2658399291_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 2658399291_rel_snps; flush table 2658399291_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 2658399291_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 4 657 II 16 2383 III 8 874 IV 17 1689 V 14 1478 X 10 5538 touch 428440209_uncovered # Wed Mar 28 11:52:34 BST 2012: Finding mRNA features overlapping uncovered regions ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 428440209_uncovered_rel; CREATE TABLE 428440209_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 428440209_uncovered_rel; flush table 428440209_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 428440209_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 2658399291_masked_ids touch 428440209_uncovered_rel # Wed Mar 28 11:52:37 BST 2012: Calculating translation start offsets for uncovered regions... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 428440209_offsets_uncovered; create table 428440209_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 428440209_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 428440209_uncovered reg join 428440209_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 428440209_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 428440209_uncovered reg join 428440209_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 428440209_offsets_uncovered touch 2658399291_rel_snps # Wed Mar 28 11:52:37 BST 2012: Calculating translation start offsets... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 2658399291_offsets_snps; create table 2658399291_offsets_snps ( id int(10) NOT NULL, gene varchar(50) NOT NULL, 5prime_offset int(10) NOT NULL, 3prime_offset int(10) NOT NULL, total_length int(10) NOT NULL, boundary_type char(20) NOT NULL, primary key (id, gene, boundary_type) );" # Wed Mar 28 11:52:37 BST 2012: Getting intergenic regions /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 2658399291_rel_intergenic; create table 2658399291_rel_intergenic like 2658399291_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 2658399291_rel_intergenic; flush table 2658399291_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 2658399291_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 2658399291_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 2658399291_snps reg join 2658399291_rel_snps rel on (reg.id = rel.query_region_id) join elegans_features gene on (rel.target_region_id = gene.id) join elegans_features exon on (exon.attribute = gene.attribute) where exon.feature = 'exon' and gene.feature = 'mRNA' group by reg.id, gene.attribute" # Wed Mar 28 11:52:42 BST 2012: Filtering masked intergenic regions /usr/bin/mysql -Dmaqgenedb -umaqgene --skip-column-names --batch --raw --local-infile -e "delete i.* from 2658399291_rel_intergenic i join 2658399291_masked_ids m using (query_region_id)" touch 2658399291_rel_intergenic # Wed Mar 28 11:52:46 BST 2012: Classifying intergenic relations /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 2658399291_intergenic_assoc; create table 2658399291_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 2658399291_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 2658399291_snps snp join 2658399291_rel_intergenic rel on (snp.id = rel.query_region_id) join elegans_features feature on (rel.target_region_id = feature.id)" touch 2658399291_intergenic_assoc touch 2658399291_offsets_snps # Wed Mar 28 11:52:58 BST 2012: Getting codons affected by point mutations... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 2658399291_codons; create table 2658399291_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 2658399291_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 2658399291_offsets_snps off join 2658399291_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 2658399291_codons /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 2658399291_marked; create table 2658399291_marked ( id int(10) NOT NULL, class varchar(100) NOT NULL, description varchar(100) NOT NULL, parent_feature varchar(100) NOT NULL, primary key (id, class, parent_feature) );" # Wed Mar 28 11:53:06 BST 2012: Finding exonic indels ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 2658399291_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 2658399291_snps snp join 2658399291_rel_snps rel on (snp.id = rel.query_region_id) join elegans_features feature on (rel.target_region_id = feature.id) where feature.feature = 'exon' and snp.variant_type = 'indel';" # Wed Mar 28 11:53:06 BST 2012: Finding coding variants ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 2658399291_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 2658399291_codons trans join elegans_genetic_code reference_codons on (trans.ref_codon = reference_codons.codon) join elegans_genetic_code sample_codons on (trans.sam_codon = sample_codons.codon);" # Wed Mar 28 11:53:06 BST 2012: Finding noncoding variants ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 2658399291_marked select snp.id, feature.feature class, 'none' description, feature.attribute parent_feature from 2658399291_snps snp join 2658399291_rel_snps rel on (snp.id = rel.query_region_id) join elegans_features feature on (rel.target_region_id = feature.id) where feature.feature not in ('exon', 'intron', 'mRNA');" # Wed Mar 28 11:53:07 BST 2012: Finding splice site variants ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 2658399291_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 2658399291_snps snp join 2658399291_rel_snps rel on (snp.id = rel.query_region_id) join elegans_features feature on (rel.target_region_id = feature.id) where feature.feature = 'intron' and rel.distance > -2;" # Wed Mar 28 11:53:07 BST 2012: Finding intergenic and intronic variants ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 2658399291_marked select id, 'nongenic' class, concat(if (relation in ('upstream','into'), - distance, distance),' ',relation) description, attribute from 2658399291_intergenic_assoc where ((relation = 'upstream' and num_regions_between = 0 and distance < 50000) or (relation = 'upstream' and num_regions_between < 2 and distance < 1000) or (relation = 'downstream' and num_regions_between = 0 and distance < 1000) or (relation = 'downstream' and num_regions_between < 2 and distance < 1000) or relation = 'into' );" # Wed Mar 28 11:53:10 BST 2012: Finding uncovered regions in genes ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 2658399291_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 428440209_uncovered unc join 428440209_offsets_uncovered b using (id) join 428440209_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 428440209_uncovered unc join 428440209_offsets_uncovered b using (id) join 428440209_offsets_uncovered e using (id, gene) join elegans_features gene on (e.gene = gene.attribute) where b.boundary_type = 'start' and e.boundary_type = 'end' and gene.strand = '-' and gene.feature = 'mRNA'" # Wed Mar 28 11:53:10 BST 2012: Variants found: +-----------------+-----------------+ | class | number_variants | +-----------------+-----------------+ | five_prime_UTR | 1299 | | frameshift | 87 | | inframe | 27 | | missense | 6115 | | ncRNA | 867 | | nongenic | 124258 | | non_start | 9 | | premature_stop | 689 | | readthrough | 19 | | silent | 7401 | | SNP | 1025 | | splice_acceptor | 46 | | splice_donor | 47 | | three_prime_UTR | 3563 | | uncovered | 20 | +-----------------+-----------------+ touch 2658399291_marked # Wed Mar 28 11:53:11 BST 2012: Combining results ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 2658399291_combined; create table 2658399291_combined (primary key (id, class, description), key (dna, start)) as select snp.id, 'CB6997_1' 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 2658399291_snps snp join 428440209_pileup pile using (dna,start) join 2658399291_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, 'CB6997_1' 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 428440209_uncovered unc join 2658399291_marked class on (unc.id = class.id) left join elegans_per_locus using (dna,start) group by id, class, description; alter table 2658399291_combined order by dna, start, length" touch 2658399291_combined # Wed Mar 28 11:53:13 BST 2012: Writing results to grouped file ... # Wed Mar 28 11:53:13 BST 2012: Writing results to flat 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 2658399291_combined group by id order by dna, start;" > /data/maqgene/out/example_user/CB6997_1/CB6997_1_grouped.txt /usr/bin/mysql -Dmaqgenedb -umaqgene --skip-column-names --batch --raw --local-infile --column-names -e "select * from 2658399291_combined" > /data/maqgene/out/example_user/CB6997_1/CB6997_1_flat.txt 3698 lines written. 2192 lines written. rm 336440.00028.2.bfq 336440.00030.2.fastq 336440.00016.map 336440.00005.unmapped 336440.00017.map 336440.00039.1.bfq 336440.00021.2.fastq 336440.00027.2.fastq 336440.00037.map 336440.00034.map 336440.00004.2.bfq 336440.00018.1.fastq 336440.00036.unmapped 336440.00040.2.bfq 336440.00009.2.fastq 336440.00005.1.fastq 336440.00004.mismatch 336440.00029.map 336440.00011.map 336440.00040.mismatch 336440.00047.map 336440.00039.map 336440.00044.unmapped 336440.00036.1.fastq 336440.00013.2.fastq 336440.00019.unmapped 336440.00032.1.fastq 336440.00023.1.fastq 336440.00043.mismatch 336440.00042.1.fastq 336440.00029.1.fastq 336440.00043.2.bfq 336440.00041.2.bfq 336440.00019.1.fastq 336440.00002.map 336440.00009.1.bfq 336440.00020.map 336440.00012.2.fastq 336440.00048.1.fastq 336440.00042.1.bfq 336440.00041.mismatch 336440.00014.mismatch 336440.00007.mismatch 336440.00039.2.bfq 336440.00024.1.bfq 336440.00015.1.fastq 336440.00039.mismatch 336440.00044.2.bfq 336440.00005.2.fastq 336440.00012.map 336440.00026.map 336440.00046.1.bfq 336440.00036.2.fastq 336440.00028.unmapped 336440.00032.2.fastq 336440.00023.2.fastq 336440.00034.mismatch 336440.00019.2.fastq 336440.00043.unmapped 336440.00028.1.fastq 336440.00042.2.bfq 336440.00006.1.bfq 336440.00048.map 336440.00039.2.fastq 336440.00018.map 336440.00024.2.bfq 336440.00021.mismatch 336440.00049.1.fastq 336440.00015.2.fastq 336440.00007.unmapped 336440.00008.mismatch 336440.00021.2.bfq 336440.00025.unmapped 336440.00037.2.fastq 336440.00049.mismatch 336440.00026.1.bfq 336440.00045.map 336440.00024.1.fastq 336440.00011.1.bfq 336440.00033.1.bfq 336440.00022.map 336440.00033.unmapped 336440.00015.unmapped 336440.00025.1.fastq 336440.00046.mismatch 336440.00004.unmapped 336440.00040.unmapped 336440.00028.2.fastq 336440.00002.unmapped 336440.00003.map 336440.00012.2.bfq 336440.00006.2.bfq 336440.00030.map 336440.00001.1.bfq 336440.00010.1.bfq 336440.00004.1.fastq 336440.00006.mismatch 336440.00027.map 336440.00035.1.fastq 336440.00016.1.bfq 336440.00049.map 336440.00033.mismatch 336440.00024.mismatch 336440.00021.unmapped 336440.00034.1.bfq 336440.00042.2.fastq 336440.00041.unmapped 336440.00008.unmapped 336440.00009.mismatch 336440.00000.2.bfq 336440.00014.unmapped 336440.00000.map 336440.00031.map 336440.00013.map 336440.00009.2.bfq 336440.00025.2.fastq 336440.00048.2.fastq 336440.00000.mismatch 336440.00039.unmapped 336440.00041.1.fastq 336440.00031.1.bfq 336440.00014.1.fastq 336440.00033.2.fastq 336440.00017.1.bfq 336440.00016.unmapped 336440.00039.1.fastq 336440.00038.mismatch 336440.00001.2.bfq 336440.00010.2.bfq 336440.00002.1.bfq 100166623_split1 336440.00004.2.fastq 336440.00043.1.bfq 336440.00040.2.fastq 336440.00001.mismatch 336440.00010.mismatch 336440.00016.2.bfq 336440.00048.1.bfq 336440.00047.1.bfq 336440.00016.mismatch 336440.00005.map 336440.00045.1.bfq 336440.00034.2.bfq 336440.00046.2.bfq 336440.00036.map 336440.00044.1.fastq 336440.00029.2.bfq 336440.00042.unmapped 336440.00012.1.bfq 336440.00032.map 336440.00009.unmapped 336440.00029.mismatch 336440.00023.map 336440.00011.mismatch 336440.00041.2.fastq 336440.00024.unmapped 336440.00014.2.fastq 336440.00019.map 336440.00049.2.fastq 336440.00017.2.bfq 336440.00017.mismatch 336440.00002.2.bfq 336440.00046.unmapped 336440.00002.mismatch 336440.00015.map 336440.00020.mismatch 336440.00047.2.bfq 336440.00018.1.bfq 336440.00046.1.fastq 336440.00047.mismatch 336440.00049.1.bfq 336440.00037.mismatch 336440.00029.1.bfq 336440.00006.unmapped 336440.00044.map 336440.00047.unmapped 336440.00037.2.bfq 336440.00022.1.bfq 336440.00035.map 336440.00000.1.bfq 336440.00012.mismatch 336440.00035.2.fastq 336440.00031.2.fastq 336440.00006.1.fastq 336440.00028.map 336440.00043.1.fastq 336440.00026.2.bfq 336440.00014.2.bfq 336440.00024.2.fastq 336440.00000.unmapped 336440.00003.1.bfq 336440.00008.1.bfq 336440.00030.1.bfq 336440.00026.mismatch 336440.00007.1.fastq 336440.00018.2.bfq 336440.00027.1.bfq 336440.00031.mismatch 336440.00000.1.fastq 336440.00018.mismatch 336440.00035.1.bfq 336440.00038.unmapped 336440.00031.2.bfq 336440.00042.mismatch 100166623_split2 336440.00045.2.bfq 336440.00001.unmapped 336440.00010.unmapped 336440.00032.1.bfq 336440.00022.2.bfq 336440.00014.1.bfq 336440.00037.unmapped 336440.00038.1.fastq 336440.00045.mismatch 336440.00048.mismatch 336440.00011.2.bfq 336440.00022.mismatch 336440.00006.2.fastq 336440.00038.2.bfq 336440.00001.1.fastq 336440.00010.1.fastq 336440.00038.1.bfq 336440.00034.unmapped 336440.00043.map 336440.00020.2.bfq 336440.00040.1.fastq 336440.00016.1.fastq 336440.00004.map 336440.00003.2.bfq 336440.00040.map 336440.00030.2.bfq 336440.00011.unmapped 336440.00044.2.fastq 336440.00037.1.bfq 336440.00034.1.fastq 336440.00003.mismatch 336440.00030.mismatch 336440.00007.map 336440.00021.1.fastq 336440.00000.2.fastq 336440.00027.mismatch 336440.00011.1.fastq 336440.00008.1.fastq 336440.00017.unmapped 336440.00005.1.bfq 336440.00020.unmapped 336440.00041.map 336440.00038.2.fastq 336440.00017.1.fastq 336440.00014.map 336440.00029.unmapped 336440.00037.1.fastq 336440.00023.1.bfq 336440.00013.mismatch 336440.00013.2.bfq 336440.00001.2.fastq 336440.00010.2.fastq 336440.00002.1.fastq 336440.00020.1.fastq 336440.00048.unmapped 336440.00019.1.bfq 336440.00044.1.bfq 336440.00016.2.fastq 336440.00045.unmapped 336440.00047.1.fastq 336440.00049.2.bfq 336440.00012.unmapped 336440.00034.2.fastq 336440.00029.2.fastq 336440.00011.2.fastq 336440.00021.map 336440.00032.unmapped 336440.00033.1.fastq 336440.00012.1.fastq 336440.00026.unmapped 336440.00008.map 336440.00007.2.bfq 336440.00043.2.fastq 336440.00005.mismatch 336440.00013.1.bfq 336440.00009.1.fastq 336440.00036.2.bfq 336440.00017.2.fastq 336440.00026.1.fastq 336440.00036.mismatch 336440.00042.map 336440.00023.2.bfq 336440.00018.unmapped 336440.00020.1.bfq 336440.00046.2.fastq 336440.00007.2.fastq 336440.00002.2.fastq 336440.00032.mismatch 336440.00020.2.fastq 336440.00013.unmapped 336440.00023.mismatch 336440.00035.mismatch 336440.00019.2.bfq 336440.00028.1.bfq 336440.00035.2.bfq 336440.00047.2.fastq 336440.00036.1.bfq 336440.00024.map 336440.00049.unmapped 336440.00022.unmapped 336440.00046.map 336440.00015.2.bfq 336440.00045.1.fastq 336440.00015.mismatch 336440.00007.1.bfq 336440.00033.map 336440.00022.1.fastq 336440.00003.unmapped 336440.00009.map 336440.00025.1.bfq 336440.00030.unmapped 336440.00027.2.bfq 336440.00026.2.fastq 336440.00006.map 336440.00015.1.bfq 336440.00027.unmapped 336440.00003.1.fastq 336440.00030.1.fastq 336440.00019.mismatch 336440.00008.2.fastq 336440.00018.2.fastq 336440.00035.unmapped 336440.00027.1.fastq 336440.00028.mismatch 336440.00048.2.bfq 336440.00004.1.bfq 336440.00033.2.bfq 336440.00040.1.bfq 336440.00031.unmapped 336440.00044.mismatch 336440.00025.map 336440.00032.2.bfq 336440.00045.2.fastq 336440.00022.2.fastq 336440.00031.1.fastq 336440.00013.1.fastq 336440.00021.1.bfq 336440.00038.map 336440.00025.2.bfq 336440.00005.2.bfq 336440.00041.1.bfq 336440.00025.mismatch 336440.00001.map 336440.00010.map 336440.00008.2.bfq 336440.00023.unmapped 336440.00003.2.fastq make: Leaving directory `/data/maqgene/work' make: Entering directory `/data/maqgene/work' # Wed Mar 28 11:53:14 BST 2012: Cleaning intermediate data ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 2658399291_snps,2658399291_rel,2658399291_masked_ids,2658399291_rel_intergenic,2658399291_intergenic_assoc,2658399291_offsets,2658399291_codons,2658399291_marked,2658399291_combined,428440209_pileup" rm -f 2658399291_snps 2658399291_rel 2658399291_masked_ids 2658399291_rel_intergenic 2658399291_intergenic_assoc 2658399291_offsets 2658399291_codons 2658399291_marked 2658399291_combined 428440209_pileup make: Leaving directory `/data/maqgene/work'