Finished reading input. ++ echo hyp-3/./s_s_1_sequence_read1.fastq ++ tr , ' ' + fastq_file_set1=hyp-3/./s_s_1_sequence_read1.fastq ++ cd /data/maqgene/reads ++ cat hyp-3/./s_s_1_sequence_read1.fastq ++ wc -l ++ cut -f 1 -d ' ' + TOTAL_LINES=238789852 ++ echo '(238789852 / 5000000) + (238789852 % 5000000 != 0)' ++ bc + num_chunks=48 + 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=2310056006 map_cksum=1393950763 pileup_cksum=1066582800 cns_cksum=2489227137 umdd=50000 dmdd=1000 umid=1000 dmid=1000 max_gene_radius=50000 full_results_dir=/data/maqgene/out/example_user/hyp_3_new outfile_basename=hyp_3_new map_parameters=" -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 200 -A 500 -1 0" assemble_parameters=" -N 2 -q 0 -r 0.0 -m 7 -Q 200 -p " pileup_parameters=" -Q 200 -p -m 7 -q 0" CHUNK_SIZE=5000000 NUM_CHUNKS=48 Will process 238789852 lines of input in 48 chunks make: Entering directory `/data/maqgene/work' # Fri Apr 20 18:23:55 BST 2012: Removing frontend files in case this is a duplicate run ... rm -f /data/maqgene/out/example_user/hyp_3_new/hyp_3_new_{grouped.txt,flat.txt} rm -f /data/maqgene/out/example_user/hyp_3_new/hyp_3_new_uncovered.txt /data/maqgene/out/example_user/hyp_3_new/hyp_3_new_coverage.txt /data/maqgene/out/example_user/hyp_3_new/hyp_3_new_pileup.txt /data/maqgene/out/example_user/hyp_3_new/hyp_3_new_log.txt /data/maqgene/out/example_user/hyp_3_new/hyp_3_new_check.txt /data/maqgene/out/example_user/hyp_3_new/hyp_3_new_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/hyp-3/./s_s_1_sequence_read1.fastq) 1393950763.1.fastq. # : Regrouping fastq reads into chunks of size 5000000. split -l 5000000 -a 5 -d <(cat /data/maqgene/reads/hyp-3/./s_s_2_sequence_read2.fastq) 1393950763.2.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; do mv 1393950763.1.fastq.$stem 1393950763.$stem.1.fastq; done touch 2310056006_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; do mv 1393950763.2.fastq.$stem 1393950763.$stem.2.fastq; done touch 2310056006_split2 # Fri Apr 20 18:26:12 BST 2012: Converting fastq files to bfq ... # Fri Apr 20 18:26:12 BST 2012: Converting fastq files to bfq ... # Fri Apr 20 18:26:12 BST 2012: Converting fastq files to bfq ... # Fri Apr 20 18:26:12 BST 2012: Converting fastq files to bfq ... out | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00003.1.bfq /data/maqgene/bin/maq sol2sanger 1393950763.00005.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00005.1.bfq # Fri Apr 20 18:26:12 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1393950763.00000.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00000.1.bfq # Fri Apr 20 18:26:12 BST 2012: Converting fastq files to bfq ... # Fri Apr 20 18:26:12 BST 2012: Converting fastq files to bfq ... # Fri Apr 20 18:26:12 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1393950763.00001.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00001.1.bfq /data/maqgene/bin/maq sol2sanger 1393950763.00002.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00002.1.bfq /data/maqgene/bin/maq sol2sanger 1393950763.00004.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00004.1.bfq /data/maqgene/bin/maq sol2sanger 1393950763.00006.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00006.1.bfq /data/maqgene/bin/maq sol2sanger 1393950763.00007.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00007.1.bfq /data/maqgene/bin/maq sol2sanger 1393950763.00008.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00008.1.bfq /data/maqgene/bin/maq sol2sanger 1393950763.00009.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00009.1.bfq /data/maqgene/bin/maq sol2sanger 1393950763.00011.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00011.1.bfq /data/maqgene/bin/maq sol2sanger 1393950763.00012.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00012.1.bfq /data/maqgene/bin/maq sol2sanger 1393950763.00013.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00013.1.bfq -- finish writing file '1393950763.00005.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1393950763.00007.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1393950763.00013.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1393950763.00003.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1393950763.00004.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1393950763.00009.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1393950763.00006.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1393950763.00002.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1393950763.00010.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1393950763.00001.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1393950763.00011.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1393950763.00012.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1393950763.00008.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1393950763.00000.1.bfq' -- 1250000 sequences were loaded. # Fri Apr 20 18:26:45 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1393950763.00026.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00026.1.bfq # Fri Apr 20 18:26:46 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1393950763.00027.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00027.1.bfq # Fri Apr 20 18:26:47 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1393950763.00025.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00025.1.bfq # Fri Apr 20 18:26:48 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1393950763.00024.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00024.1.bfq # Fri Apr 20 18:26:49 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1393950763.00023.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00023.1.bfq # Fri Apr 20 18:26:50 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1393950763.00022.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00022.1.bfq # Fri Apr 20 18:26:51 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1393950763.00021.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00021.1.bfq # Fri Apr 20 18:26:52 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1393950763.00020.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00020.1.bfq # Fri Apr 20 18:26:53 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1393950763.00019.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00019.1.bfq # Fri Apr 20 18:26:54 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1393950763.00018.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00018.1.bfq -- finish writing file '1393950763.00027.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1393950763.00026.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1393950763.00022.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1393950763.00023.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1393950763.00025.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1393950763.00024.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1393950763.00021.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1393950763.00019.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1393950763.00018.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1393950763.00020.1.bfq' -- 1250000 sequences were loaded. # Fri Apr 20 18:27:16 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1393950763.00036.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00036.1.bfq # Fri Apr 20 18:27:20 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1393950763.00037.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00037.1.bfq # Fri Apr 20 18:27:21 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1393950763.00035.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00035.1.bfq # Fri Apr 20 18:27:22 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1393950763.00034.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00034.1.bfq # Fri Apr 20 18:27:23 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1393950763.00033.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00033.1.bfq # Fri Apr 20 18:27:24 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1393950763.00032.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00032.1.bfq # Fri Apr 20 18:27:25 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1393950763.00031.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00031.1.bfq # Fri Apr 20 18:27:26 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1393950763.00030.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00030.1.bfq # Fri Apr 20 18:27:27 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1393950763.00029.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00029.1.bfq # Fri Apr 20 18:27:28 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1393950763.00028.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00028.1.bfq # Fri Apr 20 18:27:29 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1393950763.00017.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00017.1.bfq -- finish writing file '1393950763.00036.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1393950763.00035.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1393950763.00037.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1393950763.00034.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1393950763.00033.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1393950763.00029.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1393950763.00017.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1393950763.00030.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1393950763.00031.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1393950763.00032.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1393950763.00028.1.bfq' -- 1250000 sequences were loaded. # Fri Apr 20 18:27:53 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1393950763.00047.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00047.1.bfq # Fri Apr 20 18:28:01 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1393950763.00000.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00000.2.bfq # Fri Apr 20 18:28:01 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1393950763.00046.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00046.1.bfq # Fri Apr 20 18:28:02 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1393950763.00045.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00045.1.bfq -- finish writing file '1393950763.00047.1.bfq' -- 947463 sequences were loaded. # Fri Apr 20 18:28:02 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1393950763.00044.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00044.1.bfq # Fri Apr 20 18:28:03 BST 2012: Converting fastq files to bfq ... # Fri Apr 20 18:28:03 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1393950763.00043.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00043.1.bfq /data/maqgene/bin/maq sol2sanger 1393950763.00001.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00001.2.bfq # Fri Apr 20 18:28:04 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1393950763.00042.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00042.1.bfq # Fri Apr 20 18:28:05 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1393950763.00041.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00041.1.bfq # Fri Apr 20 18:28:06 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1393950763.00040.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00040.1.bfq # Fri Apr 20 18:28:07 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1393950763.00039.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00039.1.bfq # Fri Apr 20 18:28:08 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1393950763.00038.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00038.1.bfq # Fri Apr 20 18:28:09 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1393950763.00016.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00016.1.bfq -- finish writing file '1393950763.00046.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1393950763.00000.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1393950763.00045.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1393950763.00044.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1393950763.00043.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1393950763.00001.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1393950763.00042.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1393950763.00038.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1393950763.00041.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1393950763.00039.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1393950763.00040.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1393950763.00016.1.bfq' -- 1250000 sequences were loaded. # Fri Apr 20 18:28:34 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1393950763.00012.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00012.2.bfq # Fri Apr 20 18:28:46 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1393950763.00013.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00013.2.bfq # Fri Apr 20 18:28:46 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1393950763.00011.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00011.2.bfq # Fri Apr 20 18:28:47 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1393950763.00010.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00010.2.bfq -- finish writing file '1393950763.00012.2.bfq' -- 1250000 sequences were loaded. # Fri Apr 20 18:28:47 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1393950763.00009.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00009.2.bfq # Fri Apr 20 18:28:48 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1393950763.00014.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00014.2.bfq # Fri Apr 20 18:28:49 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1393950763.00008.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00008.2.bfq # Fri Apr 20 18:28:50 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1393950763.00007.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00007.2.bfq # Fri Apr 20 18:28:51 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1393950763.00006.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00006.2.bfq # Fri Apr 20 18:28:52 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1393950763.00005.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00005.2.bfq # Fri Apr 20 18:28:53 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1393950763.00004.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00004.2.bfq # Fri Apr 20 18:28:54 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1393950763.00003.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00003.2.bfq -- finish writing file '1393950763.00011.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1393950763.00013.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1393950763.00009.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1393950763.00014.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1393950763.00010.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1393950763.00006.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1393950763.00007.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1393950763.00008.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1393950763.00003.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1393950763.00005.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1393950763.00004.2.bfq' -- 1250000 sequences were loaded. # Fri Apr 20 18:29:18 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1393950763.00024.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00024.2.bfq # Fri Apr 20 18:29:26 BST 2012: Converting fastq files to bfq ... # Fri Apr 20 18:29:26 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1393950763.00025.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00025.2.bfq /data/maqgene/bin/maq sol2sanger 1393950763.00023.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00023.2.bfq # Fri Apr 20 18:29:27 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1393950763.00022.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00022.2.bfq # Fri Apr 20 18:29:28 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1393950763.00021.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00021.2.bfq /data/maqgene/bin/maq sol2sanger 1393950763.00020.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00020.2.bfq # Fri Apr 20 18:29:29 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1393950763.00019.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00019.2.bfq # Fri Apr 20 18:29:30 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1393950763.00018.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00018.2.bfq # Fri Apr 20 18:29:30 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1393950763.00017.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00017.2.bfq -- finish writing file '1393950763.00024.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1393950763.00023.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1393950763.00025.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1393950763.00018.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1393950763.00019.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1393950763.00022.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1393950763.00021.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1393950763.00020.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1393950763.00017.2.bfq' -- 1250000 sequences were loaded. # Fri Apr 20 18:29:52 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1393950763.00033.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00033.2.bfq # Fri Apr 20 18:29:56 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1393950763.00034.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00034.2.bfq /data/maqgene/bin/maq sol2sanger 1393950763.00032.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00032.2.bfq # Fri Apr 20 18:29:57 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1393950763.00031.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00031.2.bfq # Fri Apr 20 18:29:58 BST 2012: Converting fastq files to bfq ... # Fri Apr 20 18:29:58 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1393950763.00030.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00030.2.bfq /data/maqgene/bin/maq sol2sanger 1393950763.00029.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00029.2.bfq # Fri Apr 20 18:29:59 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1393950763.00028.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00028.2.bfq # Fri Apr 20 18:30:00 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1393950763.00027.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00027.2.bfq # Fri Apr 20 18:30:00 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1393950763.00026.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00026.2.bfq # Fri Apr 20 18:30:01 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1393950763.00016.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00016.2.bfq # Fri Apr 20 18:30:02 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1393950763.00015.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00015.2.bfq # Fri Apr 20 18:30:03 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1393950763.00002.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00002.2.bfq # Fri Apr 20 18:30:04 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1393950763.00015.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00015.1.bfq # Fri Apr 20 18:30:05 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1393950763.00014.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00014.1.bfq -- finish writing file '1393950763.00033.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1393950763.00032.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1393950763.00031.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1393950763.00030.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1393950763.00026.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1393950763.00028.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1393950763.00029.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1393950763.00034.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1393950763.00016.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1393950763.00015.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1393950763.00027.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1393950763.00014.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '1393950763.00002.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1393950763.00015.1.bfq' -- 1250000 sequences were loaded. # Fri Apr 20 18:30:31 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1393950763.00047.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00047.2.bfq -- finish writing file '1393950763.00047.2.bfq' -- 947463 sequences were loaded. # Fri Apr 20 18:30:41 BST 2012: Mapping file(s) 1393950763.00000.1.bfq 1393950763.00000.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 200 -A 500 -1 0 -u 1393950763.00000.unmapped -H 1393950763.00000.mismatch \ 1393950763.00000.map /data/maqgene/genomes/elegans.bfa 1393950763.00000.1.bfq 1393950763.00000.2.bfq 2> /dev/null # Fri Apr 20 18:30:46 BST 2012: Mapping file(s) 1393950763.00001.1.bfq 1393950763.00001.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 200 -A 500 -1 0 -u 1393950763.00001.unmapped -H 1393950763.00001.mismatch \ 1393950763.00001.map /data/maqgene/genomes/elegans.bfa 1393950763.00001.1.bfq 1393950763.00001.2.bfq 2> /dev/null # Fri Apr 20 18:30:46 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1393950763.00046.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00046.2.bfq # Fri Apr 20 18:30:47 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1393950763.00045.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00045.2.bfq # Fri Apr 20 18:30:48 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1393950763.00044.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00044.2.bfq # Fri Apr 20 18:30:49 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1393950763.00043.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00043.2.bfq # Fri Apr 20 18:30:50 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1393950763.00042.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00042.2.bfq # Fri Apr 20 18:30:51 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1393950763.00040.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00040.2.bfq # Fri Apr 20 18:30:51 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1393950763.00041.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00041.2.bfq # Fri Apr 20 18:30:52 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1393950763.00039.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00039.2.bfq # Fri Apr 20 18:30:53 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1393950763.00038.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00038.2.bfq # Fri Apr 20 18:30:53 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1393950763.00037.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00037.2.bfq # Fri Apr 20 18:30:54 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1393950763.00036.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00036.2.bfq # Fri Apr 20 18:30:55 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 1393950763.00035.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 1393950763.00035.2.bfq -- finish writing file '1393950763.00045.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1393950763.00044.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1393950763.00046.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1393950763.00043.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1393950763.00039.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1393950763.00040.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1393950763.00042.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1393950763.00041.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1393950763.00038.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1393950763.00036.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1393950763.00037.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '1393950763.00035.2.bfq' -- 1250000 sequences were loaded. # Fri Apr 20 18:31:56 BST 2012: Mapping file(s) 1393950763.00013.1.bfq 1393950763.00013.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 200 -A 500 -1 0 -u 1393950763.00013.unmapped -H 1393950763.00013.mismatch \ 1393950763.00013.map /data/maqgene/genomes/elegans.bfa 1393950763.00013.1.bfq 1393950763.00013.2.bfq 2> /dev/null /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 200 -A 500 -1 0 -u 1393950763.00012.unmapped -H 1393950763.00012.mismatch \ 1393950763.00012.map /data/maqgene/genomes/elegans.bfa 1393950763.00012.1.bfq 1393950763.00012.2.bfq 2> /dev/null # Fri Apr 20 18:31:57 BST 2012: Mapping file(s) 1393950763.00011.1.bfq 1393950763.00011.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 200 -A 500 -1 0 -u 1393950763.00011.unmapped -H 1393950763.00011.mismatch \ 1393950763.00011.map /data/maqgene/genomes/elegans.bfa 1393950763.00011.1.bfq 1393950763.00011.2.bfq 2> /dev/null # Fri Apr 20 18:31:57 BST 2012: Mapping file(s) 1393950763.00010.1.bfq 1393950763.00010.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 200 -A 500 -1 0 -u 1393950763.00010.unmapped -H 1393950763.00010.mismatch \ 1393950763.00010.map /data/maqgene/genomes/elegans.bfa 1393950763.00010.1.bfq 1393950763.00010.2.bfq 2> /dev/null # Fri Apr 20 18:31:58 BST 2012: Mapping file(s) 1393950763.00008.1.bfq 1393950763.00008.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 200 -A 500 -1 0 -u 1393950763.00008.unmapped -H 1393950763.00008.mismatch \ 1393950763.00008.map /data/maqgene/genomes/elegans.bfa 1393950763.00008.1.bfq 1393950763.00008.2.bfq 2> /dev/null # Fri Apr 20 18:31:58 BST 2012: Mapping file(s) 1393950763.00009.1.bfq 1393950763.00009.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 200 -A 500 -1 0 -u 1393950763.00009.unmapped -H 1393950763.00009.mismatch \ 1393950763.00009.map /data/maqgene/genomes/elegans.bfa 1393950763.00009.1.bfq 1393950763.00009.2.bfq 2> /dev/null # Fri Apr 20 18:31:59 BST 2012: Mapping file(s) 1393950763.00007.1.bfq 1393950763.00007.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 200 -A 500 -1 0 -u 1393950763.00007.unmapped -H 1393950763.00007.mismatch \ 1393950763.00007.map /data/maqgene/genomes/elegans.bfa 1393950763.00007.1.bfq 1393950763.00007.2.bfq 2> /dev/null # Fri Apr 20 18:31:59 BST 2012: Mapping file(s) 1393950763.00006.1.bfq 1393950763.00006.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 200 -A 500 -1 0 -u 1393950763.00006.unmapped -H 1393950763.00006.mismatch \ 1393950763.00006.map /data/maqgene/genomes/elegans.bfa 1393950763.00006.1.bfq 1393950763.00006.2.bfq 2> /dev/null # Fri Apr 20 18:32:00 BST 2012: Mapping file(s) 1393950763.00004.1.bfq 1393950763.00004.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 200 -A 500 -1 0 -u 1393950763.00004.unmapped -H 1393950763.00004.mismatch \ 1393950763.00004.map /data/maqgene/genomes/elegans.bfa 1393950763.00004.1.bfq 1393950763.00004.2.bfq 2> /dev/null # Fri Apr 20 18:32:00 BST 2012: Mapping file(s) 1393950763.00005.1.bfq 1393950763.00005.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 200 -A 500 -1 0 -u 1393950763.00005.unmapped -H 1393950763.00005.mismatch \ 1393950763.00005.map /data/maqgene/genomes/elegans.bfa 1393950763.00005.1.bfq 1393950763.00005.2.bfq 2> /dev/null # Fri Apr 20 18:32:02 BST 2012: Mapping file(s) 1393950763.00003.1.bfq 1393950763.00003.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 200 -A 500 -1 0 -u 1393950763.00003.unmapped -H 1393950763.00003.mismatch \ 1393950763.00003.map /data/maqgene/genomes/elegans.bfa 1393950763.00003.1.bfq 1393950763.00003.2.bfq 2> /dev/null # Fri Apr 20 18:32:04 BST 2012: Mapping file(s) 1393950763.00002.1.bfq 1393950763.00002.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 200 -A 500 -1 0 -u 1393950763.00002.unmapped -H 1393950763.00002.mismatch \ 1393950763.00002.map /data/maqgene/genomes/elegans.bfa 1393950763.00002.1.bfq 1393950763.00002.2.bfq 2> /dev/null # Fri Apr 20 18:39:43 BST 2012: Mapping file(s) 1393950763.00026.1.bfq 1393950763.00026.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 200 -A 500 -1 0 -u 1393950763.00026.unmapped -H 1393950763.00026.mismatch \ 1393950763.00026.map /data/maqgene/genomes/elegans.bfa 1393950763.00026.1.bfq 1393950763.00026.2.bfq 2> /dev/null # Fri Apr 20 18:39:52 BST 2012: Mapping file(s) 1393950763.00025.1.bfq 1393950763.00025.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 200 -A 500 -1 0 -u 1393950763.00025.unmapped -H 1393950763.00025.mismatch \ 1393950763.00025.map /data/maqgene/genomes/elegans.bfa 1393950763.00025.1.bfq 1393950763.00025.2.bfq 2> /dev/null # Fri Apr 20 18:39:52 BST 2012: Mapping file(s) 1393950763.00027.1.bfq 1393950763.00027.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 200 -A 500 -1 0 -u 1393950763.00027.unmapped -H 1393950763.00027.mismatch \ 1393950763.00027.map /data/maqgene/genomes/elegans.bfa 1393950763.00027.1.bfq 1393950763.00027.2.bfq 2> /dev/null # Fri Apr 20 18:39:53 BST 2012: Mapping file(s) 1393950763.00024.1.bfq 1393950763.00024.2.bfq # Fri Apr 20 18:39:53 BST 2012: Mapping file(s) 1393950763.00023.1.bfq 1393950763.00023.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 200 -A 500 -1 0 -u 1393950763.00024.unmapped -H 1393950763.00024.mismatch \ 1393950763.00024.map /data/maqgene/genomes/elegans.bfa 1393950763.00024.1.bfq 1393950763.00024.2.bfq 2> /dev/null /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 200 -A 500 -1 0 -u 1393950763.00023.unmapped -H 1393950763.00023.mismatch \ 1393950763.00023.map /data/maqgene/genomes/elegans.bfa 1393950763.00023.1.bfq 1393950763.00023.2.bfq 2> /dev/null # Fri Apr 20 18:39:54 BST 2012: Mapping file(s) 1393950763.00022.1.bfq 1393950763.00022.2.bfq # Fri Apr 20 18:39:54 BST 2012: Mapping file(s) 1393950763.00021.1.bfq 1393950763.00021.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 200 -A 500 -1 0 -u 1393950763.00022.unmapped -H 1393950763.00022.mismatch \ 1393950763.00022.map /data/maqgene/genomes/elegans.bfa 1393950763.00022.1.bfq 1393950763.00022.2.bfq 2> /dev/null /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 200 -A 500 -1 0 -u 1393950763.00021.unmapped -H 1393950763.00021.mismatch \ 1393950763.00021.map /data/maqgene/genomes/elegans.bfa 1393950763.00021.1.bfq 1393950763.00021.2.bfq 2> /dev/null # Fri Apr 20 18:39:55 BST 2012: Mapping file(s) 1393950763.00019.1.bfq 1393950763.00019.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 200 -A 500 -1 0 -u 1393950763.00019.unmapped -H 1393950763.00019.mismatch \ 1393950763.00019.map /data/maqgene/genomes/elegans.bfa 1393950763.00019.1.bfq 1393950763.00019.2.bfq 2> /dev/null # Fri Apr 20 18:39:55 BST 2012: Mapping file(s) 1393950763.00020.1.bfq 1393950763.00020.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 200 -A 500 -1 0 -u 1393950763.00020.unmapped -H 1393950763.00020.mismatch \ 1393950763.00020.map /data/maqgene/genomes/elegans.bfa 1393950763.00020.1.bfq 1393950763.00020.2.bfq 2> /dev/null # Fri Apr 20 18:39:56 BST 2012: Mapping file(s) 1393950763.00017.1.bfq 1393950763.00017.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 200 -A 500 -1 0 -u 1393950763.00017.unmapped -H 1393950763.00017.mismatch \ 1393950763.00017.map /data/maqgene/genomes/elegans.bfa 1393950763.00017.1.bfq 1393950763.00017.2.bfq 2> /dev/null # Fri Apr 20 18:39:56 BST 2012: Mapping file(s) 1393950763.00018.1.bfq 1393950763.00018.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 200 -A 500 -1 0 -u 1393950763.00018.unmapped -H 1393950763.00018.mismatch \ 1393950763.00018.map /data/maqgene/genomes/elegans.bfa 1393950763.00018.1.bfq 1393950763.00018.2.bfq 2> /dev/null # Fri Apr 20 18:39:57 BST 2012: Mapping file(s) 1393950763.00016.1.bfq 1393950763.00016.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 200 -A 500 -1 0 -u 1393950763.00016.unmapped -H 1393950763.00016.mismatch \ 1393950763.00016.map /data/maqgene/genomes/elegans.bfa 1393950763.00016.1.bfq 1393950763.00016.2.bfq 2> /dev/null # Fri Apr 20 18:39:58 BST 2012: Mapping file(s) 1393950763.00015.1.bfq 1393950763.00015.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 200 -A 500 -1 0 -u 1393950763.00015.unmapped -H 1393950763.00015.mismatch \ 1393950763.00015.map /data/maqgene/genomes/elegans.bfa 1393950763.00015.1.bfq 1393950763.00015.2.bfq 2> /dev/null # Fri Apr 20 18:39:59 BST 2012: Mapping file(s) 1393950763.00014.1.bfq 1393950763.00014.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 200 -A 500 -1 0 -u 1393950763.00014.unmapped -H 1393950763.00014.mismatch \ 1393950763.00014.map /data/maqgene/genomes/elegans.bfa 1393950763.00014.1.bfq 1393950763.00014.2.bfq 2> /dev/null # Fri Apr 20 18:47:48 BST 2012: Mapping file(s) 1393950763.00040.1.bfq 1393950763.00040.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 200 -A 500 -1 0 -u 1393950763.00040.unmapped -H 1393950763.00040.mismatch \ 1393950763.00040.map /data/maqgene/genomes/elegans.bfa 1393950763.00040.1.bfq 1393950763.00040.2.bfq 2> /dev/null # Fri Apr 20 18:47:58 BST 2012: Mapping file(s) 1393950763.00041.1.bfq 1393950763.00041.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 200 -A 500 -1 0 -u 1393950763.00041.unmapped -H 1393950763.00041.mismatch \ 1393950763.00041.map /data/maqgene/genomes/elegans.bfa 1393950763.00041.1.bfq 1393950763.00041.2.bfq 2> /dev/null # Fri Apr 20 18:47:58 BST 2012: Mapping file(s) 1393950763.00039.1.bfq 1393950763.00039.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 200 -A 500 -1 0 -u 1393950763.00039.unmapped -H 1393950763.00039.mismatch \ 1393950763.00039.map /data/maqgene/genomes/elegans.bfa 1393950763.00039.1.bfq 1393950763.00039.2.bfq 2> /dev/null # Fri Apr 20 18:47:59 BST 2012: Mapping file(s) 1393950763.00038.1.bfq 1393950763.00038.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 200 -A 500 -1 0 -u 1393950763.00038.unmapped -H 1393950763.00038.mismatch \ 1393950763.00038.map /data/maqgene/genomes/elegans.bfa 1393950763.00038.1.bfq 1393950763.00038.2.bfq 2> /dev/null # Fri Apr 20 18:47:59 BST 2012: Mapping file(s) 1393950763.00037.1.bfq 1393950763.00037.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 200 -A 500 -1 0 -u 1393950763.00037.unmapped -H 1393950763.00037.mismatch \ 1393950763.00037.map /data/maqgene/genomes/elegans.bfa 1393950763.00037.1.bfq 1393950763.00037.2.bfq 2> /dev/null # Fri Apr 20 18:48:00 BST 2012: Mapping file(s) 1393950763.00036.1.bfq 1393950763.00036.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 200 -A 500 -1 0 -u 1393950763.00036.unmapped -H 1393950763.00036.mismatch \ 1393950763.00036.map /data/maqgene/genomes/elegans.bfa 1393950763.00036.1.bfq 1393950763.00036.2.bfq 2> /dev/null # Fri Apr 20 18:48:00 BST 2012: Mapping file(s) 1393950763.00035.1.bfq 1393950763.00035.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 200 -A 500 -1 0 -u 1393950763.00035.unmapped -H 1393950763.00035.mismatch \ 1393950763.00035.map /data/maqgene/genomes/elegans.bfa 1393950763.00035.1.bfq 1393950763.00035.2.bfq 2> /dev/null # Fri Apr 20 18:48:01 BST 2012: Mapping file(s) 1393950763.00034.1.bfq 1393950763.00034.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 200 -A 500 -1 0 -u 1393950763.00034.unmapped -H 1393950763.00034.mismatch \ 1393950763.00034.map /data/maqgene/genomes/elegans.bfa 1393950763.00034.1.bfq 1393950763.00034.2.bfq 2> /dev/null # Fri Apr 20 18:48:01 BST 2012: Mapping file(s) 1393950763.00033.1.bfq 1393950763.00033.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 200 -A 500 -1 0 -u 1393950763.00033.unmapped -H 1393950763.00033.mismatch \ 1393950763.00033.map /data/maqgene/genomes/elegans.bfa 1393950763.00033.1.bfq 1393950763.00033.2.bfq 2> /dev/null # Fri Apr 20 18:48:02 BST 2012: Mapping file(s) 1393950763.00032.1.bfq 1393950763.00032.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 200 -A 500 -1 0 -u 1393950763.00032.unmapped -H 1393950763.00032.mismatch \ 1393950763.00032.map /data/maqgene/genomes/elegans.bfa 1393950763.00032.1.bfq 1393950763.00032.2.bfq 2> /dev/null # Fri Apr 20 18:48:02 BST 2012: Mapping file(s) 1393950763.00031.1.bfq 1393950763.00031.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 200 -A 500 -1 0 -u 1393950763.00031.unmapped -H 1393950763.00031.mismatch \ 1393950763.00031.map /data/maqgene/genomes/elegans.bfa 1393950763.00031.1.bfq 1393950763.00031.2.bfq 2> /dev/null # Fri Apr 20 18:48:04 BST 2012: Mapping file(s) 1393950763.00030.1.bfq 1393950763.00030.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 200 -A 500 -1 0 -u 1393950763.00030.unmapped -H 1393950763.00030.mismatch \ 1393950763.00030.map /data/maqgene/genomes/elegans.bfa 1393950763.00030.1.bfq 1393950763.00030.2.bfq 2> /dev/null # Fri Apr 20 18:48:05 BST 2012: Mapping file(s) 1393950763.00029.1.bfq 1393950763.00029.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 200 -A 500 -1 0 -u 1393950763.00029.unmapped -H 1393950763.00029.mismatch \ 1393950763.00029.map /data/maqgene/genomes/elegans.bfa 1393950763.00029.1.bfq 1393950763.00029.2.bfq 2> /dev/null # Fri Apr 20 18:48:06 BST 2012: Mapping file(s) 1393950763.00028.1.bfq 1393950763.00028.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 200 -A 500 -1 0 -u 1393950763.00028.unmapped -H 1393950763.00028.mismatch \ 1393950763.00028.map /data/maqgene/genomes/elegans.bfa 1393950763.00028.1.bfq 1393950763.00028.2.bfq 2> /dev/null # Fri Apr 20 18:55:55 BST 2012: Mapping file(s) 1393950763.00047.1.bfq 1393950763.00047.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 200 -A 500 -1 0 -u 1393950763.00047.unmapped -H 1393950763.00047.mismatch \ 1393950763.00047.map /data/maqgene/genomes/elegans.bfa 1393950763.00047.1.bfq 1393950763.00047.2.bfq 2> /dev/null # Fri Apr 20 18:56:05 BST 2012: Mapping file(s) 1393950763.00045.1.bfq 1393950763.00045.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 200 -A 500 -1 0 -u 1393950763.00045.unmapped -H 1393950763.00045.mismatch \ 1393950763.00045.map /data/maqgene/genomes/elegans.bfa 1393950763.00045.1.bfq 1393950763.00045.2.bfq 2> /dev/null # Fri Apr 20 18:56:05 BST 2012: Mapping file(s) 1393950763.00046.1.bfq 1393950763.00046.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 200 -A 500 -1 0 -u 1393950763.00046.unmapped -H 1393950763.00046.mismatch \ 1393950763.00046.map /data/maqgene/genomes/elegans.bfa 1393950763.00046.1.bfq 1393950763.00046.2.bfq 2> /dev/null # Fri Apr 20 18:56:05 BST 2012: Mapping file(s) 1393950763.00043.1.bfq 1393950763.00043.2.bfq # Fri Apr 20 18:56:05 BST 2012: Mapping file(s) 1393950763.00044.1.bfq 1393950763.00044.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 200 -A 500 -1 0 -u 1393950763.00044.unmapped -H 1393950763.00044.mismatch \ 1393950763.00044.map /data/maqgene/genomes/elegans.bfa 1393950763.00044.1.bfq 1393950763.00044.2.bfq 2> /dev/null /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 200 -A 500 -1 0 -u 1393950763.00043.unmapped -H 1393950763.00043.mismatch \ 1393950763.00043.map /data/maqgene/genomes/elegans.bfa 1393950763.00043.1.bfq 1393950763.00043.2.bfq 2> /dev/null # Fri Apr 20 18:56:12 BST 2012: Mapping file(s) 1393950763.00042.1.bfq 1393950763.00042.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 200 -A 500 -1 0 -u 1393950763.00042.unmapped -H 1393950763.00042.mismatch \ 1393950763.00042.map /data/maqgene/genomes/elegans.bfa 1393950763.00042.1.bfq 1393950763.00042.2.bfq 2> /dev/null # Fri Apr 20 19:01:41 BST 2012: Merging all maps ... /data/maqgene/bin/maq mapmerge 1393950763.map 1393950763.00000.map 1393950763.00001.map 1393950763.00002.map 1393950763.00003.map 1393950763.00004.map 1393950763.00005.map 1393950763.00006.map 1393950763.00007.map 1393950763.00008.map 1393950763.00009.map 1393950763.00010.map 1393950763.00011.map 1393950763.00012.map 1393950763.00013.map 1393950763.00014.map 1393950763.00015.map 1393950763.00016.map 1393950763.00017.map 1393950763.00018.map 1393950763.00019.map 1393950763.00020.map 1393950763.00021.map 1393950763.00022.map 1393950763.00023.map 1393950763.00024.map 1393950763.00025.map 1393950763.00026.map 1393950763.00027.map 1393950763.00028.map 1393950763.00029.map 1393950763.00030.map 1393950763.00031.map 1393950763.00032.map 1393950763.00033.map 1393950763.00034.map 1393950763.00035.map 1393950763.00036.map 1393950763.00037.map 1393950763.00038.map 1393950763.00039.map 1393950763.00040.map 1393950763.00041.map 1393950763.00042.map 1393950763.00043.map 1393950763.00044.map 1393950763.00045.map 1393950763.00046.map 1393950763.00047.map # Fri Apr 20 19:01:41 BST 2012: Merging all *.unmapped files ... cat 1393950763.00000.unmapped 1393950763.00001.unmapped 1393950763.00002.unmapped 1393950763.00003.unmapped 1393950763.00004.unmapped 1393950763.00005.unmapped 1393950763.00006.unmapped 1393950763.00007.unmapped 1393950763.00008.unmapped 1393950763.00009.unmapped 1393950763.00010.unmapped 1393950763.00011.unmapped 1393950763.00012.unmapped 1393950763.00013.unmapped 1393950763.00014.unmapped 1393950763.00015.unmapped 1393950763.00016.unmapped 1393950763.00017.unmapped 1393950763.00018.unmapped 1393950763.00019.unmapped 1393950763.00020.unmapped 1393950763.00021.unmapped 1393950763.00022.unmapped 1393950763.00023.unmapped 1393950763.00024.unmapped 1393950763.00025.unmapped 1393950763.00026.unmapped 1393950763.00027.unmapped 1393950763.00028.unmapped 1393950763.00029.unmapped 1393950763.00030.unmapped 1393950763.00031.unmapped 1393950763.00032.unmapped 1393950763.00033.unmapped 1393950763.00034.unmapped 1393950763.00035.unmapped 1393950763.00036.unmapped 1393950763.00037.unmapped 1393950763.00038.unmapped 1393950763.00039.unmapped 1393950763.00040.unmapped 1393950763.00041.unmapped 1393950763.00042.unmapped 1393950763.00043.unmapped 1393950763.00044.unmapped 1393950763.00045.unmapped 1393950763.00046.unmapped 1393950763.00047.unmapped > 1393950763_unmapped.txt # Fri Apr 20 19:01:45 BST 2012: Linking backend file 1393950763_unmapped.txt to /data/maqgene/out/example_user/hyp_3_new/hyp_3_new_unmapped.txt ln -fs /data/maqgene/work/1393950763_unmapped.txt /data/maqgene/out/example_user/hyp_3_new/hyp_3_new_unmapped.txt /data/maqgene/makefile:126: warning: undefined variable `mapcheck_parameters' # Fri Apr 20 19:22:10 BST 2012: Running 'mapcheck' ... /data/maqgene/bin/maq assemble -N 2 -q 0 -r 0.0 -m 7 -Q 200 -p 2489227137.cns \ /data/maqgene/genomes/elegans.bfa 1393950763.map 2> 2489227137_log.txt # Fri Apr 20 19:22:10 BST 2012: Creating pileup ... /data/maqgene/bin/maq mapcheck /data/maqgene/genomes/elegans.bfa 1393950763.map > 1393950763_check.txt \ 2>/dev/null /data/maqgene/bin/maq pileup -Q 200 -p -m 7 -q 0 /data/maqgene/genomes/elegans.bfa 1393950763.map > 1066582800_pileup.txt # Fri Apr 20 19:28:02 BST 2012: Linking backend file 1393950763_check.txt to /data/maqgene/out/example_user/hyp_3_new/hyp_3_new_check.txt ln -fs /data/maqgene/work/1393950763_check.txt /data/maqgene/out/example_user/hyp_3_new/hyp_3_new_check.txt /data/maqgene/bin/filter_matching_lines 1066582800_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 \ > 1066582800_known_snps # Fri Apr 20 19:28:16 BST 2012: Making coverage histogram ... (echo -en "sequencing_depth\tnumber_of_bases\n"; \ cut -f 4 1066582800_pileup.txt \ | /data/maqgene/bin/pileup_histogram 100) > 1066582800_coverage.txt # Fri Apr 20 19:28:16 BST 2012: Getting uncovered regions ... cut -f 1,2,4 1066582800_pileup.txt \ | /data/maqgene/bin/get_uncovered_regions 50 \ > 1066582800_uncovered.txt # Fri Apr 20 19:28:16 BST 2012: Linking backend file 1066582800_pileup.txt to /data/maqgene/out/example_user/hyp_3_new/hyp_3_new_pileup.txt ln -fs /data/maqgene/work/1066582800_pileup.txt /data/maqgene/out/example_user/hyp_3_new/hyp_3_new_pileup.txt # Fri Apr 20 19:29:06 BST 2012: Linking backend file 1066582800_coverage.txt to /data/maqgene/out/example_user/hyp_3_new/hyp_3_new_coverage.txt /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 1066582800_pileup; create table 1066582800_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/1066582800_uncovered.txt /data/maqgene/out/example_user/hyp_3_new/hyp_3_new_uncovered.txt ln -fs /data/maqgene/work/1066582800_coverage.txt /data/maqgene/out/example_user/hyp_3_new/hyp_3_new_coverage.txt cat 1066582800_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 1066582800_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 1066582800_pileup" cat 1066582800_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 1066582800_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 1066582800_pileup" touch 1066582800_pileup # Fri Apr 20 19:30:20 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 1066582800_pileup p using (dna,start)" > /data/maqgene/out/example_user/hyp_3_new/hyp_3_new_snp_read_counts.txt 0 snp read count lines written. # Fri Apr 20 19:31:27 BST 2012: Extracting point mutants from consensus ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 2489227137_snps; create table 2489227137_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) )" # Fri Apr 20 19:31:27 BST 2012: Linking backend file 2489227137_log.txt to /data/maqgene/out/example_user/hyp_3_new/hyp_3_new_log.txt ln -fs /data/maqgene/work/2489227137_log.txt /data/maqgene/out/example_user/hyp_3_new/hyp_3_new_log.txt /data/maqgene/bin/maq cns2snp 2489227137.cns \ | cat -b | /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "load data local infile '/dev/stdin' into table 2489227137_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 2489227137_snps;" # Fri Apr 20 19:31:43 BST 2012: Extracting indels from consensus ... /data/maqgene/bin/maq indelsoa /data/maqgene/genomes/elegans.bfa 1393950763.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 2489227137_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 2489227137_snps;" # Fri Apr 20 19:35:19 BST 2012: Adding placeholders for known SNPs. cat 1066582800_known_snps \ | /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "load data local infile '/dev/stdin' ignore into table 2489227137_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 2489227137_snps;" Found 163293 variants. touch 2489227137_snps # Fri Apr 20 19:35:21 BST 2012: Loading uncovered regions into table ... # Fri Apr 20 19:35:21 BST 2012: Finding all genomic features overlapping variants... cat 1066582800_uncovered.txt \ | /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 1066582800_uncovered; create table 1066582800_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 = 163294; load data local infile '/dev/stdin' into table 1066582800_uncovered (dna, start, end)" /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 2489227137_rel_snps; CREATE TABLE 2489227137_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) )" # Fri Apr 20 19:35:21 BST 2012: Getting masking regions /data/maqgene/bin/associate_regions -b -1 -c -1000000 -m 2 -o >(/usr/bin/mysql -Dmaqgenedb -umaqgene --skip-column-names --batch --raw --local-infile -e "drop table if exists 2489227137_masked_ids; create table 2489227137_masked_ids (query_region_id int(10) NOT NULL, primary key (query_region_id)); load data local infile '/dev/stdin' ignore into table 2489227137_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 2489227137_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 2489227137_rel_snps; flush table 2489227137_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 2489227137_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 5 555 II 16 2282 III 7 598 IV 11 958 V 8 1020 X 8 5356 touch 1066582800_uncovered # Fri Apr 20 19:35:21 BST 2012: Finding mRNA features overlapping uncovered regions ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 1066582800_uncovered_rel; CREATE TABLE 1066582800_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 1066582800_uncovered_rel; flush table 1066582800_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 1066582800_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 2489227137_masked_ids touch 1066582800_uncovered_rel # Fri Apr 20 19:35:24 BST 2012: Calculating translation start offsets for uncovered regions... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 1066582800_offsets_uncovered; create table 1066582800_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 1066582800_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 1066582800_uncovered reg join 1066582800_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 1066582800_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 1066582800_uncovered reg join 1066582800_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 1066582800_offsets_uncovered touch 2489227137_rel_snps # Fri Apr 20 19:35:25 BST 2012: Calculating translation start offsets... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 2489227137_offsets_snps; create table 2489227137_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) );" # Fri Apr 20 19:35:25 BST 2012: Getting intergenic regions /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 2489227137_rel_intergenic; create table 2489227137_rel_intergenic like 2489227137_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 2489227137_rel_intergenic; flush table 2489227137_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 2489227137_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 2489227137_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 2489227137_snps reg join 2489227137_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" # Fri Apr 20 19:35:28 BST 2012: Filtering masked intergenic regions /usr/bin/mysql -Dmaqgenedb -umaqgene --skip-column-names --batch --raw --local-infile -e "delete i.* from 2489227137_rel_intergenic i join 2489227137_masked_ids m using (query_region_id)" touch 2489227137_rel_intergenic # Fri Apr 20 19:35:32 BST 2012: Classifying intergenic relations /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 2489227137_intergenic_assoc; create table 2489227137_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 2489227137_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 2489227137_snps snp join 2489227137_rel_intergenic rel on (snp.id = rel.query_region_id) join elegans_features feature on (rel.target_region_id = feature.id)" touch 2489227137_intergenic_assoc touch 2489227137_offsets_snps # Fri Apr 20 19:35:43 BST 2012: Getting codons affected by point mutations... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 2489227137_codons; create table 2489227137_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 2489227137_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 2489227137_offsets_snps off join 2489227137_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 2489227137_codons /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 2489227137_marked; create table 2489227137_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) );" # Fri Apr 20 19:35:51 BST 2012: Finding exonic indels ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 2489227137_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 2489227137_snps snp join 2489227137_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';" # Fri Apr 20 19:35:51 BST 2012: Finding coding variants ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 2489227137_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 2489227137_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);" # Fri Apr 20 19:35:52 BST 2012: Finding noncoding variants ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 2489227137_marked select snp.id, feature.feature class, 'none' description, feature.attribute parent_feature from 2489227137_snps snp join 2489227137_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');" # Fri Apr 20 19:35:52 BST 2012: Finding splice site variants ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 2489227137_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 2489227137_snps snp join 2489227137_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;" # Fri Apr 20 19:35:53 BST 2012: Finding intergenic and intronic variants ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 2489227137_marked select id, 'nongenic' class, concat(if (relation in ('upstream','into'), - distance, distance),' ',relation) description, attribute from 2489227137_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' );" # Fri Apr 20 19:35:55 BST 2012: Finding uncovered regions in genes ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 2489227137_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 1066582800_uncovered unc join 1066582800_offsets_uncovered b using (id) join 1066582800_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 1066582800_uncovered unc join 1066582800_offsets_uncovered b using (id) join 1066582800_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'" # Fri Apr 20 19:35:55 BST 2012: Variants found: +-----------------+-----------------+ | class | number_variants | +-----------------+-----------------+ | five_prime_UTR | 1317 | | frameshift | 94 | | inframe | 26 | | missense | 6510 | | ncRNA | 887 | | nongenic | 124254 | | non_start | 9 | | premature_stop | 683 | | readthrough | 19 | | silent | 7617 | | SNP | 3470 | | splice_acceptor | 47 | | splice_donor | 46 | | three_prime_UTR | 3580 | | uncovered | 13 | +-----------------+-----------------+ touch 2489227137_marked # Fri Apr 20 19:35:56 BST 2012: Combining results ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 2489227137_combined; create table 2489227137_combined (primary key (id, class, description), key (dna, start)) as select snp.id, 'hyp_3_new' 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 2489227137_snps snp join 1066582800_pileup pile using (dna,start) join 2489227137_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 <= 1 and snp.neighbor_quality >= 3 and pile.read_depth >= 3 and ((pile.read_depth - pile.wt_fwd - pile.wt_rev) / pile.read_depth) >= 0.8) or snp.variant_type = 'indel' ) group by id, class, description union select unc.id id, 'hyp_3_new' 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 1066582800_uncovered unc join 2489227137_marked class on (unc.id = class.id) left join elegans_per_locus using (dna,start) group by id, class, description; alter table 2489227137_combined order by dna, start, length" touch 2489227137_combined # Fri Apr 20 19:36:00 BST 2012: Writing results to grouped file ... /usr/bin/mysql -Dmaqgenedb -umaqgene --skip-column-names --batch --raw --local-infile --column-names -e "select id, mutant_strain, dna, start, length, reference_base, sample_base, consensus_score, loci_multiplicity, mapping_quality, neighbor_quality, number_wildtype_reads, number_variant_reads, sequencing_depth, sample_reads, variant_type, indel_size, group_concat(class) classes, group_concat(description) descriptions, group_concat(concat('{',parent_features,'}')) parent_features from 2489227137_combined group by id order by dna, start;" > /data/maqgene/out/example_user/hyp_3_new/hyp_3_new_grouped.txt # Fri Apr 20 19:36:00 BST 2012: Writing results to flat file ... /usr/bin/mysql -Dmaqgenedb -umaqgene --skip-column-names --batch --raw --local-infile --column-names -e "select * from 2489227137_combined" > /data/maqgene/out/example_user/hyp_3_new/hyp_3_new_flat.txt 2232 lines written. 1378 lines written. rm 1393950763.00012.1.fastq 1393950763.00026.unmapped 1393950763.00040.mismatch 1393950763.00005.mismatch 1393950763.00036.2.bfq 1393950763.00043.unmapped 1393950763.00004.1.bfq 1393950763.00017.2.fastq 1393950763.00026.1.fastq 1393950763.00042.map 1393950763.00023.2.bfq 1393950763.00018.unmapped 1393950763.00002.2.fastq 1393950763.00020.2.fastq 1393950763.00021.mismatch 1393950763.00023.mismatch 1393950763.00024.map 1393950763.00019.2.bfq 1393950763.00007.unmapped 1393950763.00008.mismatch 1393950763.00020.unmapped 1393950763.00047.2.fastq 1393950763.00018.1.fastq 1393950763.00037.2.fastq 1393950763.00024.1.fastq 1393950763.00022.unmapped 1393950763.00046.map 1393950763.00015.2.bfq 1393950763.00033.2.bfq 1393950763.00045.1.fastq 1393950763.00015.mismatch 1393950763.00020.2.bfq 1393950763.00022.1.fastq 1393950763.00023.1.bfq 1393950763.00003.unmapped 1393950763.00025.1.bfq 1393950763.00030.unmapped 1393950763.00037.1.bfq 1393950763.00026.2.fastq 1393950763.00006.map 1393950763.00027.unmapped 1393950763.00035.1.fastq 1393950763.00003.1.fastq 1393950763.00030.1.fastq 1393950763.00014.1.bfq 1393950763.00018.2.fastq 1393950763.00021.unmapped 1393950763.00027.1.fastq 1393950763.00008.unmapped 1393950763.00009.mismatch 1393950763.00031.unmapped 1393950763.00013.unmapped 1393950763.00009.2.bfq 1393950763.00000.map 1393950763.00044.1.bfq 1393950763.00045.2.fastq 1393950763.00022.2.fastq 1393950763.00031.1.fastq 1393950763.00013.1.fastq 1393950763.00038.map 1393950763.00025.2.bfq 1393950763.00012.unmapped 1393950763.00041.1.bfq 1393950763.00001.map 1393950763.00010.map 1393950763.00025.mismatch 1393950763.00008.1.bfq 1393950763.00038.1.bfq 1393950763.00003.2.fastq 1393950763.00035.map 1393950763.00016.map 1393950763.00005.unmapped 1393950763.00039.1.bfq 1393950763.00033.mismatch 1393950763.00027.2.fastq 1393950763.00028.2.bfq 1393950763.00034.map 1393950763.00004.2.bfq 1393950763.00036.unmapped 1393950763.00040.2.bfq 1393950763.00044.1.fastq 1393950763.00005.1.fastq 1393950763.00004.mismatch 1393950763.00029.map 1393950763.00011.map 2310056006_split1 1393950763.00023.unmapped 1393950763.00036.1.fastq 1393950763.00031.2.fastq 1393950763.00013.2.fastq 1393950763.00019.unmapped 1393950763.00017.mismatch 1393950763.00032.1.fastq 1393950763.00023.1.fastq 1393950763.00017.map 1393950763.00022.mismatch 1393950763.00041.2.bfq 1393950763.00019.1.fastq 1393950763.00002.map 1393950763.00020.map 1393950763.00015.unmapped 1393950763.00042.1.bfq 1393950763.00041.mismatch 1393950763.00014.mismatch 1393950763.00047.map 1393950763.00039.2.bfq 1393950763.00024.1.bfq 1393950763.00015.1.fastq 1393950763.00039.mismatch 1393950763.00037.mismatch 1393950763.00005.2.fastq 1393950763.00044.map 1393950763.00037.2.bfq 1393950763.00038.2.bfq 1393950763.00004.unmapped 1393950763.00012.map 1393950763.00046.1.bfq 1393950763.00021.2.bfq 1393950763.00036.2.fastq 1393950763.00035.2.fastq 1393950763.00028.unmapped 1393950763.00032.2.fastq 1393950763.00043.1.fastq 1393950763.00023.2.fastq 1393950763.00014.2.bfq 1393950763.00026.map 1393950763.00040.1.bfq 1393950763.00019.2.fastq 1393950763.00007.2.bfq 1393950763.00028.1.fastq 1393950763.00018.2.bfq 1393950763.00042.2.bfq 1393950763.00007.1.fastq 1393950763.00027.2.bfq 1393950763.00042.mismatch 1393950763.00018.map 1393950763.00024.2.bfq 1393950763.00035.1.bfq 1393950763.00039.unmapped 1393950763.00015.2.fastq 1393950763.00031.2.bfq 1393950763.00025.unmapped 1393950763.00029.mismatch 1393950763.00032.1.bfq 1393950763.00045.map 1393950763.00046.2.bfq 1393950763.00000.1.bfq 1393950763.00022.map 1393950763.00033.unmapped 1393950763.00025.1.fastq 1393950763.00046.mismatch 1393950763.00037.unmapped 1393950763.00043.map 1393950763.00043.mismatch 1393950763.00033.1.fastq 1393950763.00040.unmapped 1393950763.00028.2.fastq 2310056006_split2 1393950763.00044.2.fastq 1393950763.00003.map 1393950763.00006.2.bfq 1393950763.00030.map 1393950763.00001.1.bfq 1393950763.00010.1.bfq 1393950763.00007.map 1393950763.00004.1.fastq 1393950763.00021.1.fastq 1393950763.00027.map 1393950763.00040.1.fastq 1393950763.00016.1.bfq 1393950763.00008.1.fastq 1393950763.00019.1.bfq 1393950763.00029.1.bfq 1393950763.00034.1.bfq 1393950763.00041.unmapped 1393950763.00012.2.fastq 1393950763.00000.2.bfq 1393950763.00014.unmapped 1393950763.00029.unmapped 1393950763.00013.map 1393950763.00025.2.fastq 1393950763.00000.mismatch 1393950763.00041.1.fastq 1393950763.00016.mismatch 1393950763.00033.2.fastq 1393950763.00045.unmapped 1393950763.00017.1.bfq 1393950763.00005.1.bfq 1393950763.00039.1.fastq 1393950763.00038.mismatch 1393950763.00010.2.bfq 1393950763.00024.mismatch 1393950763.00020.1.bfq 1393950763.00028.1.bfq 1393950763.00004.2.fastq 1393950763.00040.2.fastq 1393950763.00001.mismatch 1393950763.00010.mismatch 1393950763.00016.2.bfq 1393950763.00021.map 1393950763.00047.1.bfq 1393950763.00032.mismatch 1393950763.00021.1.bfq 1393950763.00008.map 1393950763.00008.2.bfq 1393950763.00043.2.fastq 1393950763.00005.map 1393950763.00034.2.bfq 1393950763.00009.1.fastq 1393950763.00003.1.bfq 1393950763.00034.mismatch 1393950763.00036.map 1393950763.00029.2.bfq 1393950763.00042.unmapped 1393950763.00012.1.bfq 1393950763.00032.map 1393950763.00007.2.fastq 1393950763.00023.map 1393950763.00011.mismatch 1393950763.00041.2.fastq 1393950763.00024.unmapped 1393950763.00035.mismatch 1393950763.00014.2.fastq 1393950763.00042.1.fastq 1393950763.00035.2.bfq 1393950763.00019.map 1393950763.00017.2.bfq 1393950763.00026.1.bfq 1393950763.00036.1.bfq 1393950763.00039.2.fastq 1393950763.00002.2.bfq 1393950763.00046.unmapped 1393950763.00032.2.bfq 1393950763.00002.mismatch 1393950763.00015.map 1393950763.00047.2.bfq 1393950763.00018.1.bfq 1393950763.00007.1.bfq 1393950763.00033.map 1393950763.00046.1.fastq 1393950763.00047.mismatch 1393950763.00009.map 1393950763.00006.unmapped 1393950763.00012.2.bfq 1393950763.00045.1.bfq 1393950763.00022.1.bfq 1393950763.00012.mismatch 1393950763.00021.2.fastq 1393950763.00019.mismatch 1393950763.00042.2.fastq 1393950763.00006.1.fastq 1393950763.00008.2.fastq 1393950763.00028.map 1393950763.00026.2.bfq 1393950763.00035.unmapped 1393950763.00002.1.bfq 1393950763.00024.2.fastq 1393950763.00026.mismatch 1393950763.00000.unmapped 1393950763.00044.mismatch 1393950763.00030.1.bfq 1393950763.00032.unmapped 1393950763.00044.2.bfq 1393950763.00013.1.bfq 1393950763.00009.unmapped 1393950763.00010.unmapped 1393950763.00027.1.bfq 1393950763.00046.2.fastq 1393950763.00000.1.fastq 1393950763.00018.mismatch 1393950763.00038.unmapped 1393950763.00037.1.fastq 1393950763.00013.2.bfq 1393950763.00004.map 1393950763.00005.2.bfq 1393950763.00025.map 1393950763.00045.2.bfq 1393950763.00001.unmapped 1393950763.00028.mismatch 1393950763.00022.2.bfq 1393950763.00031.1.bfq 1393950763.00038.1.fastq 1393950763.00045.mismatch 1393950763.00016.unmapped 1393950763.00014.1.fastq 1393950763.00006.2.fastq 1393950763.00001.1.fastq 1393950763.00010.1.fastq 1393950763.00011.2.bfq 1393950763.00034.unmapped 1393950763.00016.1.fastq 1393950763.00009.2.fastq 1393950763.00003.2.bfq 1393950763.00040.map 1393950763.00030.2.bfq 1393950763.00006.mismatch 1393950763.00011.1.bfq 1393950763.00006.1.bfq 1393950763.00020.mismatch 1393950763.00034.1.fastq 1393950763.00003.mismatch 1393950763.00039.map 1393950763.00030.mismatch 1393950763.00044.unmapped 1393950763.00000.2.fastq 1393950763.00029.1.fastq 1393950763.00027.mismatch 1393950763.00011.1.fastq 1393950763.00017.unmapped 1393950763.00036.mismatch 1393950763.00033.1.bfq 1393950763.00037.map 1393950763.00043.2.bfq 1393950763.00002.unmapped 1393950763.00009.1.bfq 1393950763.00041.map 1393950763.00038.2.fastq 1393950763.00001.2.bfq 1393950763.00017.1.fastq 1393950763.00014.map 1393950763.00047.unmapped 1393950763.00031.mismatch 1393950763.00007.mismatch 1393950763.00013.mismatch 1393950763.00001.2.fastq 1393950763.00010.2.fastq 1393950763.00002.1.fastq 1393950763.00020.1.fastq 1393950763.00011.unmapped 1393950763.00016.2.fastq 1393950763.00047.1.fastq 1393950763.00030.2.fastq 1393950763.00034.2.fastq 1393950763.00015.1.bfq 1393950763.00031.map 1393950763.00043.1.bfq 1393950763.00029.2.fastq 1393950763.00011.2.fastq make: Leaving directory `/data/maqgene/work' make: Entering directory `/data/maqgene/work' # Fri Apr 20 19:36:03 BST 2012: Cleaning intermediate data ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 2489227137_snps,2489227137_rel,2489227137_masked_ids,2489227137_rel_intergenic,2489227137_intergenic_assoc,2489227137_offsets,2489227137_codons,2489227137_marked,2489227137_combined,1066582800_pileup" rm -f 2489227137_snps 2489227137_rel 2489227137_masked_ids 2489227137_rel_intergenic 2489227137_intergenic_assoc 2489227137_offsets 2489227137_codons 2489227137_marked 2489227137_combined 1066582800_pileup make: Leaving directory `/data/maqgene/work'