Finished reading input. ++ echo CB6945.3/./s_12_1_sequence_read1.fastq ++ tr , ' ' + fastq_file_set1=CB6945.3/./s_12_1_sequence_read1.fastq ++ cd /data/maqgene/reads ++ cat CB6945.3/./s_12_1_sequence_read1.fastq ++ wc -l ++ cut -f 1 -d ' ' + TOTAL_LINES=148743936 ++ echo '(148743936 / 5000000) + (148743936 % 5000000 != 0)' ++ bc + num_chunks=30 + set +x make -j 14 -l 14 --always-make -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=733656107 map_cksum=3312216658 pileup_cksum=1657516583 cns_cksum=1058872118 umdd=50000 dmdd=1000 umid=1000 dmid=1000 max_gene_radius=50000 full_results_dir=/data/maqgene/out/example_user/CB6945_3 outfile_basename=CB6945_3 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=30 Will process 148743936 lines of input in 30 chunks make: Entering directory `/data/maqgene/work' # Fri Jan 13 14:02:43 GMT 2012: Removing frontend files in case this is a duplicate run ... rm -f /data/maqgene/out/example_user/CB6945_3/CB6945_3_{grouped.txt,flat.txt} rm -f /data/maqgene/out/example_user/CB6945_3/CB6945_3_uncovered.txt /data/maqgene/out/example_user/CB6945_3/CB6945_3_coverage.txt /data/maqgene/out/example_user/CB6945_3/CB6945_3_pileup.txt /data/maqgene/out/example_user/CB6945_3/CB6945_3_log.txt /data/maqgene/out/example_user/CB6945_3/CB6945_3_check.txt /data/maqgene/out/example_user/CB6945_3/CB6945_3_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/CB6945.3/./s_12_1_sequence_read1.fastq) 3312216658.1.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; do mv 3312216658.1.fastq.$stem 3312216658.$stem.1.fastq; done touch 733656107_split1 # : Regrouping fastq reads into chunks of size 5000000. split -l 5000000 -a 5 -d <(cat /data/maqgene/reads/CB6945.3/./s_12_2_sequence_read2.fastq) 3312216658.2.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; do mv 3312216658.2.fastq.$stem 3312216658.$stem.2.fastq; done touch 733656107_split2 # Fri Jan 13 14:06:06 GMT 2012: Converting fastq files to bfq ... # Fri Jan 13 14:06:06 GMT 2012: Converting fastq files to bfq ... # Fri Jan 13 14:06:06 GMT 2012: Converting fastq files to bfq ... # Fri Jan 13 14:06:06 GMT 2012: Converting fastq files to bfq ... # Fri Jan 13 14:06:06 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3312216658.00009.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3312216658.00009.1.bfq # Fri Jan 13 14:06:06 GMT 2012: Converting fastq files to bfq ... # Fri Jan 13 14:06:06 GMT 2012: Converting fastq files to bfq ... # Fri Jan 13 14:06:06 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3312216658.00000.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3312216658.00000.1.bfq # Fri Jan 13 14:06:06 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3312216658.00001.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3312216658.00001.1.bfq /data/maqgene/bin/maq sol2sanger 3312216658.00002.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3312216658.00002.1.bfq /data/maqgene/bin/maq sol2sanger 3312216658.00004.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3312216658.00004.1.bfq # Fri Jan 13 14:06:06 GMT 2012: Converting fastq files to bfq ... # Fri Jan 13 14:06:06 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3312216658.00005.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3312216658.00005.1.bfq /data/maqgene/bin/maq sol2sanger 3312216658.00003.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3312216658.00003.1.bfq /data/maqgene/bin/maq sol2sanger 3312216658.00006.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3312216658.00006.1.bfq /data/maqgene/bin/maq sol2sanger 3312216658.00007.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3312216658.00007.1.bfq /data/maqgene/bin/maq sol2sanger 3312216658.00008.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3312216658.00008.1.bfq /data/maqgene/bin/maq sol2sanger 3312216658.00010.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3312216658.00010.1.bfq /data/maqgene/bin/maq sol2sanger 3312216658.00011.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3312216658.00011.1.bfq /data/maqgene/bin/maq sol2sanger 3312216658.00012.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3312216658.00012.1.bfq # Fri Jan 13 14:06:07 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3312216658.00013.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3312216658.00013.1.bfq -- finish writing file '3312216658.00012.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3312216658.00013.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3312216658.00003.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3312216658.00011.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3312216658.00002.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3312216658.00008.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3312216658.00004.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3312216658.00006.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3312216658.00007.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3312216658.00001.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3312216658.00009.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3312216658.00010.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3312216658.00005.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3312216658.00000.1.bfq' -- 1250000 sequences were loaded. # Fri Jan 13 14:06:55 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3312216658.00026.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3312216658.00026.1.bfq -- finish writing file '3312216658.00026.1.bfq' -- 1250000 sequences were loaded. # Fri Jan 13 14:07:15 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3312216658.00027.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3312216658.00027.1.bfq -- finish writing file '3312216658.00027.1.bfq' -- 1250000 sequences were loaded. # Fri Jan 13 14:07:30 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3312216658.00028.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3312216658.00028.1.bfq -- finish writing file '3312216658.00028.1.bfq' -- 1250000 sequences were loaded. # Fri Jan 13 14:07:49 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3312216658.00029.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3312216658.00029.1.bfq -- finish writing file '3312216658.00029.1.bfq' -- 935984 sequences were loaded. # Fri Jan 13 14:08:01 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3312216658.00000.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3312216658.00000.2.bfq # Fri Jan 13 14:08:02 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3312216658.00001.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3312216658.00001.2.bfq # Fri Jan 13 14:08:03 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3312216658.00025.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3312216658.00025.1.bfq # Fri Jan 13 14:08:04 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3312216658.00024.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3312216658.00024.1.bfq # Fri Jan 13 14:08:05 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3312216658.00023.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3312216658.00023.1.bfq # Fri Jan 13 14:08:06 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3312216658.00022.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3312216658.00022.1.bfq # Fri Jan 13 14:08:08 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3312216658.00021.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3312216658.00021.1.bfq # Fri Jan 13 14:08:10 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3312216658.00020.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3312216658.00020.1.bfq -- finish writing file '3312216658.00000.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '3312216658.00001.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '3312216658.00025.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3312216658.00024.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3312216658.00023.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3312216658.00022.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3312216658.00021.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3312216658.00020.1.bfq' -- 1250000 sequences were loaded. # Fri Jan 13 14:08:39 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3312216658.00008.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3312216658.00008.2.bfq # Fri Jan 13 14:08:56 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3312216658.00009.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3312216658.00009.2.bfq # Fri Jan 13 14:08:57 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3312216658.00007.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3312216658.00007.2.bfq # Fri Jan 13 14:08:58 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3312216658.00006.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3312216658.00006.2.bfq # Fri Jan 13 14:08:59 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3312216658.00005.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3312216658.00005.2.bfq # Fri Jan 13 14:09:00 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3312216658.00004.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3312216658.00004.2.bfq -- finish writing file '3312216658.00008.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '3312216658.00009.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '3312216658.00007.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '3312216658.00006.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '3312216658.00005.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '3312216658.00004.2.bfq' -- 1250000 sequences were loaded. # Fri Jan 13 14:09:24 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3312216658.00014.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3312216658.00014.2.bfq -- finish writing file '3312216658.00014.2.bfq' -- 1250000 sequences were loaded. # Fri Jan 13 14:09:37 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3312216658.00015.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3312216658.00015.2.bfq # Fri Jan 13 14:09:42 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3312216658.00016.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3312216658.00016.2.bfq # Fri Jan 13 14:09:43 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3312216658.00013.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3312216658.00013.2.bfq # Fri Jan 13 14:09:44 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3312216658.00012.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3312216658.00012.2.bfq # Fri Jan 13 14:09:45 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3312216658.00011.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3312216658.00011.2.bfq # Fri Jan 13 14:09:46 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3312216658.00010.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3312216658.00010.2.bfq # Fri Jan 13 14:09:48 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3312216658.00003.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3312216658.00003.2.bfq # Fri Jan 13 14:09:50 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3312216658.00002.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3312216658.00002.2.bfq -- finish writing file '3312216658.00015.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '3312216658.00013.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '3312216658.00016.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '3312216658.00012.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '3312216658.00011.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '3312216658.00010.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '3312216658.00003.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '3312216658.00002.2.bfq' -- 1250000 sequences were loaded. # Fri Jan 13 14:10:09 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3312216658.00023.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3312216658.00023.2.bfq # Fri Jan 13 14:10:12 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3312216658.00024.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3312216658.00024.2.bfq # Fri Jan 13 14:10:13 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3312216658.00022.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3312216658.00022.2.bfq # Fri Jan 13 14:10:14 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3312216658.00021.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3312216658.00021.2.bfq # Fri Jan 13 14:10:15 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3312216658.00020.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3312216658.00020.2.bfq # Fri Jan 13 14:10:16 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3312216658.00019.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3312216658.00019.2.bfq # Fri Jan 13 14:10:17 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3312216658.00018.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3312216658.00018.2.bfq # Fri Jan 13 14:10:18 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3312216658.00017.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3312216658.00017.2.bfq # Fri Jan 13 14:10:19 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3312216658.00019.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3312216658.00019.1.bfq # Fri Jan 13 14:10:20 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3312216658.00018.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3312216658.00018.1.bfq # Fri Jan 13 14:10:21 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3312216658.00017.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3312216658.00017.1.bfq -- finish writing file '3312216658.00023.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '3312216658.00024.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '3312216658.00022.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '3312216658.00021.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '3312216658.00020.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '3312216658.00019.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '3312216658.00017.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '3312216658.00018.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '3312216658.00019.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3312216658.00017.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3312216658.00018.1.bfq' -- 1250000 sequences were loaded. # Fri Jan 13 14:10:46 GMT 2012: Mapping file(s) 3312216658.00004.1.bfq 3312216658.00004.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3312216658.00004.unmapped -H 3312216658.00004.mismatch \ 3312216658.00004.map /data/maqgene/genomes/elegans.bfa 3312216658.00004.1.bfq 3312216658.00004.2.bfq 2> /dev/null # Fri Jan 13 14:11:07 GMT 2012: Mapping file(s) 3312216658.00005.1.bfq 3312216658.00005.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3312216658.00005.unmapped -H 3312216658.00005.mismatch \ 3312216658.00005.map /data/maqgene/genomes/elegans.bfa 3312216658.00005.1.bfq 3312216658.00005.2.bfq 2> /dev/null # Fri Jan 13 14:11:09 GMT 2012: Mapping file(s) 3312216658.00003.1.bfq 3312216658.00003.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3312216658.00003.unmapped -H 3312216658.00003.mismatch \ 3312216658.00003.map /data/maqgene/genomes/elegans.bfa 3312216658.00003.1.bfq 3312216658.00003.2.bfq 2> /dev/null # Fri Jan 13 14:11:11 GMT 2012: Mapping file(s) 3312216658.00002.1.bfq 3312216658.00002.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3312216658.00002.unmapped -H 3312216658.00002.mismatch \ 3312216658.00002.map /data/maqgene/genomes/elegans.bfa 3312216658.00002.1.bfq 3312216658.00002.2.bfq 2> /dev/null # Fri Jan 13 14:11:12 GMT 2012: Mapping file(s) 3312216658.00001.1.bfq 3312216658.00001.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3312216658.00001.unmapped -H 3312216658.00001.mismatch \ 3312216658.00001.map /data/maqgene/genomes/elegans.bfa 3312216658.00001.1.bfq 3312216658.00001.2.bfq 2> /dev/null # Fri Jan 13 14:11:12 GMT 2012: Mapping file(s) 3312216658.00000.1.bfq 3312216658.00000.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3312216658.00000.unmapped -H 3312216658.00000.mismatch \ 3312216658.00000.map /data/maqgene/genomes/elegans.bfa 3312216658.00000.1.bfq 3312216658.00000.2.bfq 2> /dev/null # Fri Jan 13 14:11:13 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3312216658.00029.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3312216658.00029.2.bfq # Fri Jan 13 14:11:14 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3312216658.00027.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3312216658.00027.2.bfq # Fri Jan 13 14:11:14 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3312216658.00028.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3312216658.00028.2.bfq # Fri Jan 13 14:11:15 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3312216658.00026.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3312216658.00026.2.bfq # Fri Jan 13 14:11:16 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3312216658.00025.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3312216658.00025.2.bfq # Fri Jan 13 14:11:16 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3312216658.00016.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3312216658.00016.1.bfq -- finish writing file '3312216658.00029.2.bfq' -- 935984 sequences were loaded. -- finish writing file '3312216658.00028.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '3312216658.00027.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '3312216658.00025.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '3312216658.00026.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '3312216658.00016.1.bfq' -- 1250000 sequences were loaded. # Fri Jan 13 14:17:13 GMT 2012: Mapping file(s) 3312216658.00012.1.bfq 3312216658.00012.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3312216658.00012.unmapped -H 3312216658.00012.mismatch \ 3312216658.00012.map /data/maqgene/genomes/elegans.bfa 3312216658.00012.1.bfq 3312216658.00012.2.bfq 2> /dev/null # Fri Jan 13 14:17:15 GMT 2012: Mapping file(s) 3312216658.00011.1.bfq 3312216658.00011.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3312216658.00011.unmapped -H 3312216658.00011.mismatch \ 3312216658.00011.map /data/maqgene/genomes/elegans.bfa 3312216658.00011.1.bfq 3312216658.00011.2.bfq 2> /dev/null # Fri Jan 13 14:18:08 GMT 2012: Mapping file(s) 3312216658.00017.1.bfq 3312216658.00017.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3312216658.00017.unmapped -H 3312216658.00017.mismatch \ 3312216658.00017.map /data/maqgene/genomes/elegans.bfa 3312216658.00017.1.bfq 3312216658.00017.2.bfq 2> /dev/null # Fri Jan 13 14:18:10 GMT 2012: Mapping file(s) 3312216658.00016.1.bfq 3312216658.00016.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3312216658.00016.unmapped -H 3312216658.00016.mismatch \ 3312216658.00016.map /data/maqgene/genomes/elegans.bfa 3312216658.00016.1.bfq 3312216658.00016.2.bfq 2> /dev/null # Fri Jan 13 14:18:12 GMT 2012: Mapping file(s) 3312216658.00013.1.bfq 3312216658.00013.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3312216658.00013.unmapped -H 3312216658.00013.mismatch \ 3312216658.00013.map /data/maqgene/genomes/elegans.bfa 3312216658.00013.1.bfq 3312216658.00013.2.bfq 2> /dev/null # Fri Jan 13 14:18:53 GMT 2012: Mapping file(s) 3312216658.00019.1.bfq 3312216658.00019.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3312216658.00019.unmapped -H 3312216658.00019.mismatch \ 3312216658.00019.map /data/maqgene/genomes/elegans.bfa 3312216658.00019.1.bfq 3312216658.00019.2.bfq 2> /dev/null # Fri Jan 13 14:18:54 GMT 2012: Mapping file(s) 3312216658.00018.1.bfq 3312216658.00018.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3312216658.00018.unmapped -H 3312216658.00018.mismatch \ 3312216658.00018.map /data/maqgene/genomes/elegans.bfa 3312216658.00018.1.bfq 3312216658.00018.2.bfq 2> /dev/null # Fri Jan 13 14:18:55 GMT 2012: Mapping file(s) 3312216658.00010.1.bfq 3312216658.00010.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3312216658.00010.unmapped -H 3312216658.00010.mismatch \ 3312216658.00010.map /data/maqgene/genomes/elegans.bfa 3312216658.00010.1.bfq 3312216658.00010.2.bfq 2> /dev/null # Fri Jan 13 14:18:56 GMT 2012: Mapping file(s) 3312216658.00009.1.bfq 3312216658.00009.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3312216658.00009.unmapped -H 3312216658.00009.mismatch \ 3312216658.00009.map /data/maqgene/genomes/elegans.bfa 3312216658.00009.1.bfq 3312216658.00009.2.bfq 2> /dev/null # Fri Jan 13 14:18:57 GMT 2012: Mapping file(s) 3312216658.00008.1.bfq 3312216658.00008.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3312216658.00008.unmapped -H 3312216658.00008.mismatch \ 3312216658.00008.map /data/maqgene/genomes/elegans.bfa 3312216658.00008.1.bfq 3312216658.00008.2.bfq 2> /dev/null # Fri Jan 13 14:26:24 GMT 2012: Mapping file(s) 3312216658.00028.1.bfq 3312216658.00028.2.bfq # Fri Jan 13 14:26:24 GMT 2012: Mapping file(s) 3312216658.00027.1.bfq 3312216658.00027.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3312216658.00028.unmapped -H 3312216658.00028.mismatch \ 3312216658.00028.map /data/maqgene/genomes/elegans.bfa 3312216658.00028.1.bfq 3312216658.00028.2.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 3312216658.00027.unmapped -H 3312216658.00027.mismatch \ 3312216658.00027.map /data/maqgene/genomes/elegans.bfa 3312216658.00027.1.bfq 3312216658.00027.2.bfq 2> /dev/null # Fri Jan 13 14:26:25 GMT 2012: Mapping file(s) 3312216658.00025.1.bfq 3312216658.00025.2.bfq # Fri Jan 13 14:26:25 GMT 2012: Mapping file(s) 3312216658.00026.1.bfq 3312216658.00026.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3312216658.00025.unmapped -H 3312216658.00025.mismatch \ 3312216658.00025.map /data/maqgene/genomes/elegans.bfa 3312216658.00025.1.bfq 3312216658.00025.2.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 3312216658.00026.unmapped -H 3312216658.00026.mismatch \ 3312216658.00026.map /data/maqgene/genomes/elegans.bfa 3312216658.00026.1.bfq 3312216658.00026.2.bfq 2> /dev/null # Fri Jan 13 14:31:36 GMT 2012: Mapping file(s) 3312216658.00020.1.bfq 3312216658.00020.2.bfq # Fri Jan 13 14:31:36 GMT 2012: Mapping file(s) 3312216658.00006.1.bfq 3312216658.00006.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3312216658.00020.unmapped -H 3312216658.00020.mismatch \ 3312216658.00020.map /data/maqgene/genomes/elegans.bfa 3312216658.00020.1.bfq 3312216658.00020.2.bfq 2> /dev/null # Fri Jan 13 14:31:36 GMT 2012: Mapping file(s) 3312216658.00022.1.bfq 3312216658.00022.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3312216658.00006.unmapped -H 3312216658.00006.mismatch \ 3312216658.00006.map /data/maqgene/genomes/elegans.bfa 3312216658.00006.1.bfq 3312216658.00006.2.bfq 2> /dev/null # Fri Jan 13 14:31:36 GMT 2012: Mapping file(s) 3312216658.00029.1.bfq 3312216658.00029.2.bfq # Fri Jan 13 14:31:36 GMT 2012: Mapping file(s) 3312216658.00021.1.bfq 3312216658.00021.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3312216658.00022.unmapped -H 3312216658.00022.mismatch \ 3312216658.00022.map /data/maqgene/genomes/elegans.bfa 3312216658.00022.1.bfq 3312216658.00022.2.bfq 2> /dev/null # Fri Jan 13 14:31:36 GMT 2012: Mapping file(s) 3312216658.00024.1.bfq 3312216658.00024.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3312216658.00029.unmapped -H 3312216658.00029.mismatch \ 3312216658.00029.map /data/maqgene/genomes/elegans.bfa 3312216658.00029.1.bfq 3312216658.00029.2.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 3312216658.00024.unmapped -H 3312216658.00024.mismatch \ 3312216658.00024.map /data/maqgene/genomes/elegans.bfa 3312216658.00024.1.bfq 3312216658.00024.2.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 3312216658.00021.unmapped -H 3312216658.00021.mismatch \ 3312216658.00021.map /data/maqgene/genomes/elegans.bfa 3312216658.00021.1.bfq 3312216658.00021.2.bfq 2> /dev/null # Fri Jan 13 14:31:36 GMT 2012: Mapping file(s) 3312216658.00007.1.bfq 3312216658.00007.2.bfq # Fri Jan 13 14:31:36 GMT 2012: Mapping file(s) 3312216658.00023.1.bfq 3312216658.00023.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3312216658.00023.unmapped -H 3312216658.00023.mismatch \ 3312216658.00023.map /data/maqgene/genomes/elegans.bfa 3312216658.00023.1.bfq 3312216658.00023.2.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 3312216658.00007.unmapped -H 3312216658.00007.mismatch \ 3312216658.00007.map /data/maqgene/genomes/elegans.bfa 3312216658.00007.1.bfq 3312216658.00007.2.bfq 2> /dev/null # Fri Jan 13 14:31:37 GMT 2012: Converting fastq files to bfq ... # Fri Jan 13 14:31:37 GMT 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 3312216658.00014.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3312216658.00014.1.bfq /data/maqgene/bin/maq sol2sanger 3312216658.00015.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 3312216658.00015.1.bfq -- finish writing file '3312216658.00014.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '3312216658.00015.1.bfq' -- 1250000 sequences were loaded. # Fri Jan 13 14:37:54 GMT 2012: Mapping file(s) 3312216658.00015.1.bfq 3312216658.00015.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3312216658.00015.unmapped -H 3312216658.00015.mismatch \ 3312216658.00015.map /data/maqgene/genomes/elegans.bfa 3312216658.00015.1.bfq 3312216658.00015.2.bfq 2> /dev/null # Fri Jan 13 14:37:54 GMT 2012: Mapping file(s) 3312216658.00014.1.bfq 3312216658.00014.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 3312216658.00014.unmapped -H 3312216658.00014.mismatch \ 3312216658.00014.map /data/maqgene/genomes/elegans.bfa 3312216658.00014.1.bfq 3312216658.00014.2.bfq 2> /dev/null # Fri Jan 13 14:42:54 GMT 2012: Merging all maps ... # Fri Jan 13 14:42:54 GMT 2012: Merging all *.unmapped files ... /data/maqgene/bin/maq mapmerge 3312216658.map 3312216658.00000.map 3312216658.00001.map 3312216658.00002.map 3312216658.00003.map 3312216658.00004.map 3312216658.00005.map 3312216658.00006.map 3312216658.00007.map 3312216658.00008.map 3312216658.00009.map 3312216658.00010.map 3312216658.00011.map 3312216658.00012.map 3312216658.00013.map 3312216658.00014.map 3312216658.00015.map 3312216658.00016.map 3312216658.00017.map 3312216658.00018.map 3312216658.00019.map 3312216658.00020.map 3312216658.00021.map 3312216658.00022.map 3312216658.00023.map 3312216658.00024.map 3312216658.00025.map 3312216658.00026.map 3312216658.00027.map 3312216658.00028.map 3312216658.00029.map cat 3312216658.00000.unmapped 3312216658.00001.unmapped 3312216658.00002.unmapped 3312216658.00003.unmapped 3312216658.00004.unmapped 3312216658.00005.unmapped 3312216658.00006.unmapped 3312216658.00007.unmapped 3312216658.00008.unmapped 3312216658.00009.unmapped 3312216658.00010.unmapped 3312216658.00011.unmapped 3312216658.00012.unmapped 3312216658.00013.unmapped 3312216658.00014.unmapped 3312216658.00015.unmapped 3312216658.00016.unmapped 3312216658.00017.unmapped 3312216658.00018.unmapped 3312216658.00019.unmapped 3312216658.00020.unmapped 3312216658.00021.unmapped 3312216658.00022.unmapped 3312216658.00023.unmapped 3312216658.00024.unmapped 3312216658.00025.unmapped 3312216658.00026.unmapped 3312216658.00027.unmapped 3312216658.00028.unmapped 3312216658.00029.unmapped > 3312216658_unmapped.txt # Fri Jan 13 14:42:57 GMT 2012: Linking backend file 3312216658_unmapped.txt to /data/maqgene/out/example_user/CB6945_3/CB6945_3_unmapped.txt ln -fs /data/maqgene/work/3312216658_unmapped.txt /data/maqgene/out/example_user/CB6945_3/CB6945_3_unmapped.txt /data/maqgene/makefile:126: warning: undefined variable `mapcheck_parameters' # Fri Jan 13 14:59:55 GMT 2012: Generating consensus ... /data/maqgene/bin/maq assemble -N 2 -q 0 -r 0.0 -m 7 -Q 100 -p 1058872118.cns \ /data/maqgene/genomes/elegans.bfa 3312216658.map 2> 1058872118_log.txt # Fri Jan 13 15:06:11 GMT 2012: Running 'mapcheck' ... # Fri Jan 13 15:06:11 GMT 2012: Linking backend file 1058872118_log.txt to /data/maqgene/out/example_user/CB6945_3/CB6945_3_log.txt /data/maqgene/bin/maq mapcheck /data/maqgene/genomes/elegans.bfa 3312216658.map > 3312216658_check.txt \ 2>/dev/null /data/maqgene/bin/maq pileup -Q 100 -p -m 7 -q 0 /data/maqgene/genomes/elegans.bfa 3312216658.map > 1657516583_pileup.txt ln -fs /data/maqgene/work/1058872118_log.txt /data/maqgene/out/example_user/CB6945_3/CB6945_3_log.txt # Fri Jan 13 15:09:56 GMT 2012: Linking backend file 3312216658_check.txt to /data/maqgene/out/example_user/CB6945_3/CB6945_3_check.txt ln -fs /data/maqgene/work/3312216658_check.txt /data/maqgene/out/example_user/CB6945_3/CB6945_3_check.txt /data/maqgene/bin/filter_matching_lines 1657516583_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 \ > 1657516583_known_snps # Fri Jan 13 15:10:15 GMT 2012: Making coverage histogram ... (echo -en "sequencing_depth\tnumber_of_bases\n"; \ cut -f 4 1657516583_pileup.txt \ | /data/maqgene/bin/pileup_histogram 100) > 1657516583_coverage.txt cut -f 1,2,4 1657516583_pileup.txt \ | /data/maqgene/bin/get_uncovered_regions 50 \ > 1657516583_uncovered.txt # Fri Jan 13 15:10:15 GMT 2012: Linking backend file 1657516583_pileup.txt to /data/maqgene/out/example_user/CB6945_3/CB6945_3_pileup.txt ln -fs /data/maqgene/work/1657516583_pileup.txt /data/maqgene/out/example_user/CB6945_3/CB6945_3_pileup.txt # Fri Jan 13 15:10:55 GMT 2012: Filtering and loading pileup for analysis ... # Fri Jan 13 15:10:55 GMT 2012: Extracting point mutants from consensus ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 1657516583_pileup; create table 1657516583_pileup ( dna enum('I','II','III','IV','MtDNA','V','X') NOT NULL, start int(10) NOT NULL, ref_base char(1) NOT NULL, read_depth int(5) NOT NULL, sample_reads varchar(100) NOT NULL, A_fwd int(5) NOT NULL, A_rev int(5) NOT NULL, C_fwd int(5) NOT NULL, C_rev int(5) NOT NULL, G_fwd int(5) NOT NULL, G_rev int(5) NOT NULL, T_fwd int(5) NOT NULL, T_rev int(5) NOT NULL, wt_fwd int(5) NOT NULL, wt_rev int(5) NOT NULL, primary key (dna, start) );" /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 1058872118_snps; create table 1058872118_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 Jan 13 15:10:55 GMT 2012: Linking backend file 1657516583_coverage.txt to /data/maqgene/out/example_user/CB6945_3/CB6945_3_coverage.txt ln -fs /data/maqgene/work/1657516583_coverage.txt /data/maqgene/out/example_user/CB6945_3/CB6945_3_coverage.txt cat 1657516583_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 1657516583_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 1657516583_pileup" /data/maqgene/bin/maq cns2snp 1058872118.cns \ | cat -b | /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "load data local infile '/dev/stdin' into table 1058872118_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 1058872118_snps;" # Fri Jan 13 15:10:57 GMT 2012: Linking backend file 1657516583_uncovered.txt to /data/maqgene/out/example_user/CB6945_3/CB6945_3_uncovered.txt ln -fs /data/maqgene/work/1657516583_uncovered.txt /data/maqgene/out/example_user/CB6945_3/CB6945_3_uncovered.txt # Fri Jan 13 15:11:13 GMT 2012: Extracting indels from consensus ... /data/maqgene/bin/maq indelsoa /data/maqgene/genomes/elegans.bfa 3312216658.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 1058872118_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 1058872118_snps;" cat 1657516583_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 1657516583_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 1657516583_pileup" touch 1657516583_pileup # Fri Jan 13 15:11:52 GMT 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 1657516583_pileup p using (dna,start)" > /data/maqgene/out/example_user/CB6945_3/CB6945_3_snp_read_counts.txt 0 snp read count lines written. # Fri Jan 13 15:13:29 GMT 2012: Adding placeholders for known SNPs. cat 1657516583_known_snps \ | /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "load data local infile '/dev/stdin' ignore into table 1058872118_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 1058872118_snps;" Found 160546 variants. touch 1058872118_snps # Fri Jan 13 15:13:31 GMT 2012: Loading uncovered regions into table ... # Fri Jan 13 15:13:31 GMT 2012: Finding all genomic features overlapping variants... cat 1657516583_uncovered.txt \ | /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 1657516583_uncovered; create table 1657516583_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 = 160547; load data local infile '/dev/stdin' into table 1657516583_uncovered (dna, start, end)" # Fri Jan 13 15:13:31 GMT 2012: Getting masking regions /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 1058872118_rel_snps; CREATE TABLE 1058872118_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 1058872118_masked_ids; create table 1058872118_masked_ids (query_region_id int(10) NOT NULL, primary key (query_region_id)); load data local infile '/dev/stdin' ignore into table 1058872118_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 1058872118_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 1058872118_rel_snps; flush table 1058872118_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 1058872118_snps") -t <(/usr/bin/mysql -Dmaqgenedb -umaqgene --skip-column-names --batch --raw --local-infile -e "select id, 'elegans', dna,start,end,strand from elegans_features where feature in ('SNP','exon','five_prime_UTR','intron','mRNA','three_prime_UTR','ncRNA')") 1>/dev/null Uncovered region statistics: chromosome number_uncovered_regions total_uncovered_length I 7 899 II 17 2258 III 8 896 IV 14 1233 V 11 1552 X 14 5666 touch 1657516583_uncovered # Fri Jan 13 15:13:32 GMT 2012: Finding mRNA features overlapping uncovered regions ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 1657516583_uncovered_rel; CREATE TABLE 1657516583_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 1657516583_uncovered_rel; flush table 1657516583_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 1657516583_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 1058872118_masked_ids touch 1657516583_uncovered_rel # Fri Jan 13 15:13:34 GMT 2012: Calculating translation start offsets for uncovered regions... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 1657516583_offsets_uncovered; create table 1657516583_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 1657516583_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 1657516583_uncovered reg join 1657516583_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 1657516583_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 1657516583_uncovered reg join 1657516583_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 1657516583_offsets_uncovered touch 1058872118_rel_snps # Fri Jan 13 15:13:35 GMT 2012: Calculating translation start offsets... # Fri Jan 13 15:13:35 GMT 2012: Getting intergenic regions /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 1058872118_offsets_snps; create table 1058872118_offsets_snps ( id int(10) NOT NULL, gene varchar(50) NOT NULL, 5prime_offset int(10) NOT NULL, 3prime_offset int(10) NOT NULL, total_length int(10) NOT NULL, boundary_type char(20) NOT NULL, primary key (id, gene, boundary_type) );" /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 1058872118_rel_intergenic; create table 1058872118_rel_intergenic like 1058872118_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 1058872118_rel_intergenic; flush table 1058872118_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 1058872118_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 1058872118_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 1058872118_snps reg join 1058872118_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 Jan 13 15:13:40 GMT 2012: Filtering masked intergenic regions /usr/bin/mysql -Dmaqgenedb -umaqgene --skip-column-names --batch --raw --local-infile -e "delete i.* from 1058872118_rel_intergenic i join 1058872118_masked_ids m using (query_region_id)" touch 1058872118_rel_intergenic # Fri Jan 13 15:13:46 GMT 2012: Classifying intergenic relations /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 1058872118_intergenic_assoc; create table 1058872118_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 1058872118_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 1058872118_snps snp join 1058872118_rel_intergenic rel on (snp.id = rel.query_region_id) join elegans_features feature on (rel.target_region_id = feature.id)" touch 1058872118_intergenic_assoc touch 1058872118_offsets_snps # Fri Jan 13 15:13:57 GMT 2012: Getting codons affected by point mutations... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 1058872118_codons; create table 1058872118_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 1058872118_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 1058872118_offsets_snps off join 1058872118_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 1058872118_codons /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 1058872118_marked; create table 1058872118_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 Jan 13 15:14:05 GMT 2012: Finding exonic indels ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 1058872118_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 1058872118_snps snp join 1058872118_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 Jan 13 15:14:06 GMT 2012: Finding coding variants ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 1058872118_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 1058872118_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 Jan 13 15:14:06 GMT 2012: Finding noncoding variants ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 1058872118_marked select snp.id, feature.feature class, 'none' description, feature.attribute parent_feature from 1058872118_snps snp join 1058872118_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 Jan 13 15:14:07 GMT 2012: Finding splice site variants ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 1058872118_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 1058872118_snps snp join 1058872118_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 Jan 13 15:14:07 GMT 2012: Finding intergenic and intronic variants ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 1058872118_marked select id, 'nongenic' class, concat(if (relation in ('upstream','into'), - distance, distance),' ',relation) description, attribute from 1058872118_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 Jan 13 15:14:09 GMT 2012: Finding uncovered regions in genes ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 1058872118_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 1657516583_uncovered unc join 1657516583_offsets_uncovered b using (id) join 1657516583_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 1657516583_uncovered unc join 1657516583_offsets_uncovered b using (id) join 1657516583_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 Jan 13 15:14:10 GMT 2012: Variants found: +-----------------+-----------------+ | class | number_variants | +-----------------+-----------------+ | five_prime_UTR | 1287 | | frameshift | 57 | | inframe | 14 | | missense | 6149 | | ncRNA | 874 | | nongenic | 124083 | | non_start | 9 | | premature_stop | 690 | | readthrough | 19 | | silent | 7419 | | SNP | 1022 | | splice_acceptor | 46 | | splice_donor | 46 | | three_prime_UTR | 3547 | | uncovered | 22 | +-----------------+-----------------+ touch 1058872118_marked # Fri Jan 13 15:14:11 GMT 2012: Combining results ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 1058872118_combined; create table 1058872118_combined (primary key (id, class, description), key (dna, start)) as select snp.id, 'CB6945_3' 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 1058872118_snps snp join 1657516583_pileup pile using (dna,start) join 1058872118_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, 'CB6945_3' 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 1657516583_uncovered unc join 1058872118_marked class on (unc.id = class.id) left join elegans_per_locus using (dna,start) group by id, class, description; alter table 1058872118_combined order by dna, start, length" touch 1058872118_combined # Fri Jan 13 15:14:13 GMT 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 1058872118_combined group by id order by dna, start;" > /data/maqgene/out/example_user/CB6945_3/CB6945_3_grouped.txt # Fri Jan 13 15:14:13 GMT 2012: Writing results to flat file ... /usr/bin/mysql -Dmaqgenedb -umaqgene --skip-column-names --batch --raw --local-infile --column-names -e "select * from 1058872118_combined" > /data/maqgene/out/example_user/CB6945_3/CB6945_3_flat.txt 3349 lines written. 1994 lines written. rm 3312216658.00007.1.fastq 3312216658.00013.unmapped 3312216658.00026.2.bfq 3312216658.00022.2.fastq 3312216658.00013.1.fastq 3312216658.00025.mismatch 3312216658.00001.map 3312216658.00010.map 3312216658.00014.1.bfq 3312216658.00003.2.fastq 3312216658.00016.map 3312216658.00005.unmapped 3312216658.00027.2.fastq 3312216658.00004.2.bfq 3312216658.00007.map 3312216658.00005.1.fastq 3312216658.00004.mismatch 3312216658.00029.map 3312216658.00021.1.fastq 3312216658.00011.map 3312216658.00023.unmapped 3312216658.00008.1.fastq 3312216658.00013.2.fastq 3312216658.00019.unmapped 3312216658.00023.1.fastq 3312216658.00019.1.fastq 3312216658.00002.map 3312216658.00020.map 3312216658.00015.unmapped 3312216658.00011.2.fastq 3312216658.00014.mismatch 733656107_split2 3312216658.00024.1.bfq 3312216658.00015.1.fastq 3312216658.00005.2.fastq 3312216658.00021.map 3312216658.00028.unmapped 3312216658.00009.1.fastq 3312216658.00023.2.fastq 3312216658.00026.map 3312216658.00009.2.fastq 3312216658.00019.2.fastq 3312216658.00028.1.fastq 3312216658.00007.2.fastq 3312216658.00006.1.bfq 3312216658.00018.map 3312216658.00024.2.bfq 3312216658.00012.map 3312216658.00015.2.fastq 3312216658.00024.mismatch 3312216658.00025.unmapped 3312216658.00000.1.bfq 3312216658.00022.map 3312216658.00007.1.bfq 3312216658.00025.1.fastq 3312216658.00009.map 3312216658.00004.unmapped 3312216658.00028.2.fastq 3312216658.00003.map 3312216658.00006.2.bfq 3312216658.00001.1.bfq 3312216658.00010.1.bfq 3312216658.00021.2.fastq 3312216658.00007.2.bfq 3312216658.00004.1.fastq 3312216658.00006.mismatch 3312216658.00027.map 3312216658.00008.2.fastq 3312216658.00016.1.bfq 3312216658.00002.1.bfq 3312216658.00000.2.bfq 3312216658.00014.unmapped 3312216658.00029.1.bfq 3312216658.00013.map 3312216658.00025.2.fastq 3312216658.00000.mismatch 3312216658.00021.1.bfq 3312216658.00005.mismatch 3312216658.00008.1.bfq 3312216658.00014.1.fastq 3312216658.00005.2.bfq 3312216658.00017.1.bfq 3312216658.00001.2.bfq 3312216658.00010.2.bfq 3312216658.00020.1.bfq 3312216658.00004.2.fastq 3312216658.00017.map 3312216658.00001.mismatch 3312216658.00010.mismatch 3312216658.00016.2.bfq 3312216658.00008.map 3312216658.00016.mismatch 3312216658.00005.map 3312216658.00029.2.bfq 3312216658.00011.2.bfq 3312216658.00012.1.bfq 3312216658.00029.mismatch 3312216658.00023.map 3312216658.00011.mismatch 3312216658.00024.unmapped 3312216658.00014.2.fastq 3312216658.00019.map 3312216658.00017.2.bfq 3312216658.00026.1.bfq 3312216658.00009.1.bfq 3312216658.00024.1.fastq 3312216658.00017.mismatch 3312216658.00002.2.bfq 3312216658.00020.2.bfq 3312216658.00007.mismatch 3312216658.00002.mismatch 3312216658.00015.map 3312216658.00020.mismatch 3312216658.00018.1.bfq 3312216658.00006.unmapped 3312216658.00012.2.bfq 3312216658.00022.1.bfq 3312216658.00012.mismatch 3312216658.00006.1.fastq 3312216658.00028.map 3312216658.00024.2.fastq 3312216658.00026.mismatch 3312216658.00000.unmapped 3312216658.00003.1.bfq 3312216658.00021.mismatch 3312216658.00018.2.bfq 3312216658.00007.unmapped 3312216658.00027.1.bfq 3312216658.00008.mismatch 3312216658.00021.2.bfq 3312216658.00000.1.fastq 3312216658.00018.mismatch 3312216658.00008.2.bfq 3312216658.00025.map 3312216658.00001.unmapped 3312216658.00010.unmapped 3312216658.00022.2.bfq 3312216658.00013.1.bfq 3312216658.00016.unmapped 3312216658.00022.mismatch 3312216658.00006.2.fastq 3312216658.00001.1.fastq 3312216658.00010.1.fastq 3312216658.00016.1.fastq 3312216658.00004.map 3312216658.00003.2.bfq 3312216658.00029.unmapped 3312216658.00011.unmapped 3312216658.00003.mismatch 3312216658.00027.2.bfq 3312216658.00000.2.fastq 3312216658.00021.unmapped 3312216658.00029.1.fastq 3312216658.00027.mismatch 3312216658.00011.1.fastq 3312216658.00017.unmapped 3312216658.00008.unmapped 3312216658.00005.1.bfq 3312216658.00009.mismatch 3312216658.00000.map 3312216658.00009.2.bfq 3312216658.00002.unmapped 3312216658.00020.unmapped 3312216658.00013.2.bfq 3312216658.00017.1.fastq 3312216658.00014.map 3312216658.00023.1.bfq 3312216658.00013.mismatch 3312216658.00001.2.fastq 3312216658.00010.2.fastq 3312216658.00002.1.fastq 3312216658.00020.1.fastq 3312216658.00019.1.bfq 3312216658.00016.2.fastq 3312216658.00012.unmapped 3312216658.00025.2.bfq 3312216658.00015.1.bfq 3312216658.00029.2.fastq 3312216658.00012.1.fastq 3312216658.00026.unmapped 3312216658.00011.1.bfq 3312216658.00009.unmapped 3312216658.00017.2.fastq 3312216658.00026.1.fastq 3312216658.00023.2.bfq 3312216658.00018.unmapped 3312216658.00002.2.fastq 3312216658.00020.2.fastq 3312216658.00023.mismatch 3312216658.00024.map 3312216658.00019.2.bfq 3312216658.00028.1.bfq 3312216658.00018.1.fastq 3312216658.00019.mismatch 3312216658.00022.unmapped 3312216658.00015.2.bfq 3312216658.00012.2.fastq 3312216658.00015.mismatch 3312216658.00022.1.fastq 733656107_split1 3312216658.00003.unmapped 3312216658.00025.1.bfq 3312216658.00026.2.fastq 3312216658.00006.map 3312216658.00027.unmapped 3312216658.00003.1.fastq 3312216658.00014.2.bfq 3312216658.00028.2.bfq 3312216658.00018.2.fastq 3312216658.00027.1.fastq 3312216658.00028.mismatch 3312216658.00004.1.bfq make: Leaving directory `/data/maqgene/work' make: Entering directory `/data/maqgene/work' # Fri Jan 13 15:14:15 GMT 2012: Cleaning intermediate data ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 1058872118_snps,1058872118_rel,1058872118_masked_ids,1058872118_rel_intergenic,1058872118_intergenic_assoc,1058872118_offsets,1058872118_codons,1058872118_marked,1058872118_combined,1657516583_pileup" rm -f 1058872118_snps 1058872118_rel 1058872118_masked_ids 1058872118_rel_intergenic 1058872118_intergenic_assoc 1058872118_offsets 1058872118_codons 1058872118_marked 1058872118_combined 1657516583_pileup make: Leaving directory `/data/maqgene/work'