Finished reading input. ++ echo pja-11/./s_s_1_sequence_read1.fastq ++ tr , ' ' + fastq_file_set1=pja-11/./s_s_1_sequence_read1.fastq ++ cd /data/maqgene/reads ++ cat pja-11/./s_s_1_sequence_read1.fastq ++ wc -l ++ cut -f 1 -d ' ' + TOTAL_LINES=161933840 ++ echo '(161933840 / 5000000) + (161933840 % 5000000 != 0)' ++ bc + num_chunks=33 + 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=13454453 map_cksum=2723564971 pileup_cksum=3032792211 cns_cksum=3031615627 umdd=50000 dmdd=1000 umid=1000 dmid=1000 max_gene_radius=50000 full_results_dir=/data/maqgene/out/example_user/pja_11 outfile_basename=pja_11 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=33 Will process 161933840 lines of input in 33 chunks make: Entering directory `/data/maqgene/work' # Wed Mar 28 14:37:02 BST 2012: Removing frontend files in case this is a duplicate run ... rm -f /data/maqgene/out/example_user/pja_11/pja_11_{grouped.txt,flat.txt} rm -f /data/maqgene/out/example_user/pja_11/pja_11_uncovered.txt /data/maqgene/out/example_user/pja_11/pja_11_coverage.txt /data/maqgene/out/example_user/pja_11/pja_11_pileup.txt /data/maqgene/out/example_user/pja_11/pja_11_log.txt /data/maqgene/out/example_user/pja_11/pja_11_check.txt /data/maqgene/out/example_user/pja_11/pja_11_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/pja-11/./s_s_1_sequence_read1.fastq) 2723564971.1.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 00030 00031 00032; do mv 2723564971.1.fastq.$stem 2723564971.$stem.1.fastq; done touch 13454453_split1 # : Regrouping fastq reads into chunks of size 5000000. split -l 5000000 -a 5 -d <(cat /data/maqgene/reads/pja-11/./s_s_2_sequence_read2.fastq) 2723564971.2.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; do mv 2723564971.2.fastq.$stem 2723564971.$stem.2.fastq; done touch 13454453_split2 # Wed Mar 28 14:38:58 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2723564971.00000.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2723564971.00000.1.bfq -- finish writing file '2723564971.00000.1.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 14:39:14 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2723564971.00013.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2723564971.00013.1.bfq -- finish writing file '2723564971.00013.1.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 14:39:30 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2723564971.00014.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2723564971.00014.1.bfq -- finish writing file '2723564971.00014.1.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 14:39:45 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2723564971.00015.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2723564971.00015.1.bfq -- finish writing file '2723564971.00015.1.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 14:39:57 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2723564971.00016.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2723564971.00016.1.bfq # Wed Mar 28 14:40:09 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2723564971.00017.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2723564971.00017.1.bfq -- finish writing file '2723564971.00016.1.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 14:40:09 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2723564971.00012.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2723564971.00012.1.bfq # Wed Mar 28 14:40:10 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2723564971.00018.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2723564971.00018.1.bfq # Wed Mar 28 14:40:11 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2723564971.00011.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2723564971.00011.1.bfq # Wed Mar 28 14:40:12 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2723564971.00010.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2723564971.00010.1.bfq # Wed Mar 28 14:40:13 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2723564971.00009.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2723564971.00009.1.bfq # Wed Mar 28 14:40:15 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2723564971.00008.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2723564971.00008.1.bfq # Wed Mar 28 14:40:17 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2723564971.00007.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2723564971.00007.1.bfq -- finish writing file '2723564971.00017.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2723564971.00012.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2723564971.00018.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2723564971.00010.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2723564971.00011.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2723564971.00009.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2723564971.00008.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2723564971.00007.1.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 14:40:32 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2723564971.00025.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2723564971.00025.1.bfq # Wed Mar 28 14:40:39 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2723564971.00024.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2723564971.00024.1.bfq # Wed Mar 28 14:40:39 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2723564971.00026.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2723564971.00026.1.bfq # Wed Mar 28 14:40:40 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2723564971.00022.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2723564971.00022.1.bfq # Wed Mar 28 14:40:40 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2723564971.00023.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2723564971.00023.1.bfq # Wed Mar 28 14:40:41 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2723564971.00021.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2723564971.00021.1.bfq # Wed Mar 28 14:40:41 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2723564971.00020.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2723564971.00020.1.bfq # Wed Mar 28 14:40:42 BST 2012: Converting fastq files to bfq ... # Wed Mar 28 14:40:42 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2723564971.00019.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2723564971.00019.1.bfq /data/maqgene/bin/maq sol2sanger 2723564971.00006.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2723564971.00006.1.bfq # Wed Mar 28 14:40:43 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2723564971.00004.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2723564971.00004.1.bfq # Wed Mar 28 14:40:43 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2723564971.00005.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2723564971.00005.1.bfq -- finish writing file '2723564971.00025.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2723564971.00026.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2723564971.00023.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2723564971.00022.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2723564971.00005.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2723564971.00020.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2723564971.00024.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2723564971.00019.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2723564971.00004.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2723564971.00021.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2723564971.00006.1.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 14:41:05 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2723564971.00003.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2723564971.00003.2.bfq -- finish writing file '2723564971.00003.2.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 14:41:17 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2723564971.00004.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2723564971.00004.2.bfq -- finish writing file '2723564971.00004.2.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 14:41:27 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2723564971.00005.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2723564971.00005.2.bfq # Wed Mar 28 14:41:29 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2723564971.00006.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2723564971.00006.2.bfq # Wed Mar 28 14:41:30 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2723564971.00002.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2723564971.00002.2.bfq # Wed Mar 28 14:41:31 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2723564971.00001.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2723564971.00001.2.bfq # Wed Mar 28 14:41:32 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2723564971.00000.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2723564971.00000.2.bfq # Wed Mar 28 14:41:33 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2723564971.00032.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2723564971.00032.1.bfq -- finish writing file '2723564971.00032.1.bfq' -- 483460 sequences were loaded. -- finish writing file '2723564971.00005.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '2723564971.00006.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '2723564971.00002.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '2723564971.00001.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '2723564971.00000.2.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 14:41:46 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2723564971.00011.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2723564971.00011.2.bfq # Wed Mar 28 14:41:49 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2723564971.00012.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2723564971.00012.2.bfq # Wed Mar 28 14:41:50 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2723564971.00010.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2723564971.00010.2.bfq # Wed Mar 28 14:41:51 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2723564971.00009.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2723564971.00009.2.bfq # Wed Mar 28 14:41:52 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2723564971.00008.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2723564971.00008.2.bfq # Wed Mar 28 14:41:53 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2723564971.00007.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2723564971.00007.2.bfq # Wed Mar 28 14:41:54 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2723564971.00031.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2723564971.00031.1.bfq # Wed Mar 28 14:41:55 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2723564971.00030.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2723564971.00030.1.bfq # Wed Mar 28 14:41:56 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2723564971.00029.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2723564971.00029.1.bfq # Wed Mar 28 14:41:57 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2723564971.00028.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2723564971.00028.1.bfq # Wed Mar 28 14:41:58 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2723564971.00027.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2723564971.00027.1.bfq -- finish writing file '2723564971.00011.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '2723564971.00010.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '2723564971.00009.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '2723564971.00012.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '2723564971.00008.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '2723564971.00031.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2723564971.00007.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '2723564971.00030.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2723564971.00029.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2723564971.00028.1.bfq' -- 1250000 sequences were loaded. -- finish writing file '2723564971.00027.1.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 14:42:16 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2723564971.00022.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2723564971.00022.2.bfq -- finish writing file '2723564971.00022.2.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 14:42:28 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2723564971.00023.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2723564971.00023.2.bfq # Wed Mar 28 14:42:30 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2723564971.00024.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2723564971.00024.2.bfq # Wed Mar 28 14:42:31 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2723564971.00021.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2723564971.00021.2.bfq # Wed Mar 28 14:42:32 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2723564971.00020.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2723564971.00020.2.bfq # Wed Mar 28 14:42:33 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2723564971.00019.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2723564971.00019.2.bfq # Wed Mar 28 14:42:34 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2723564971.00018.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2723564971.00018.2.bfq -- finish writing file '2723564971.00023.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '2723564971.00021.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '2723564971.00024.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '2723564971.00020.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '2723564971.00019.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '2723564971.00018.2.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 14:42:47 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2723564971.00029.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2723564971.00029.2.bfq # Wed Mar 28 14:42:50 BST 2012: Converting fastq files to bfq ... # Wed Mar 28 14:42:50 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2723564971.00030.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2723564971.00030.2.bfq /data/maqgene/bin/maq sol2sanger 2723564971.00028.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2723564971.00028.2.bfq # Wed Mar 28 14:42:51 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2723564971.00027.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2723564971.00027.2.bfq # Wed Mar 28 14:42:52 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2723564971.00026.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2723564971.00026.2.bfq # Wed Mar 28 14:42:53 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2723564971.00025.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2723564971.00025.2.bfq # Wed Mar 28 14:42:54 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2723564971.00017.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2723564971.00017.2.bfq # Wed Mar 28 14:42:55 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2723564971.00016.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2723564971.00016.2.bfq # Wed Mar 28 14:42:56 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2723564971.00015.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2723564971.00015.2.bfq # Wed Mar 28 14:42:57 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2723564971.00014.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2723564971.00014.2.bfq # Wed Mar 28 14:42:58 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2723564971.00013.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2723564971.00013.2.bfq # Wed Mar 28 14:42:59 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2723564971.00003.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2723564971.00003.1.bfq -- finish writing file '2723564971.00029.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '2723564971.00030.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '2723564971.00028.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '2723564971.00026.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '2723564971.00027.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '2723564971.00017.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '2723564971.00016.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '2723564971.00025.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '2723564971.00015.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '2723564971.00013.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '2723564971.00014.2.bfq' -- 1250000 sequences were loaded. -- finish writing file '2723564971.00003.1.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 14:43:17 BST 2012: Mapping file(s) 2723564971.00011.1.bfq 2723564971.00011.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 2723564971.00011.unmapped -H 2723564971.00011.mismatch \ 2723564971.00011.map /data/maqgene/genomes/elegans.bfa 2723564971.00011.1.bfq 2723564971.00011.2.bfq 2> /dev/null # Wed Mar 28 14:43:35 BST 2012: Mapping file(s) 2723564971.00012.1.bfq 2723564971.00012.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 2723564971.00012.unmapped -H 2723564971.00012.mismatch \ 2723564971.00012.map /data/maqgene/genomes/elegans.bfa 2723564971.00012.1.bfq 2723564971.00012.2.bfq 2> /dev/null # Wed Mar 28 14:43:37 BST 2012: Mapping file(s) 2723564971.00010.1.bfq 2723564971.00010.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 2723564971.00010.unmapped -H 2723564971.00010.mismatch \ 2723564971.00010.map /data/maqgene/genomes/elegans.bfa 2723564971.00010.1.bfq 2723564971.00010.2.bfq 2> /dev/null # Wed Mar 28 14:43:39 BST 2012: Mapping file(s) 2723564971.00009.1.bfq 2723564971.00009.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 2723564971.00009.unmapped -H 2723564971.00009.mismatch \ 2723564971.00009.map /data/maqgene/genomes/elegans.bfa 2723564971.00009.1.bfq 2723564971.00009.2.bfq 2> /dev/null # Wed Mar 28 14:43:41 BST 2012: Mapping file(s) 2723564971.00008.1.bfq 2723564971.00008.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 2723564971.00008.unmapped -H 2723564971.00008.mismatch \ 2723564971.00008.map /data/maqgene/genomes/elegans.bfa 2723564971.00008.1.bfq 2723564971.00008.2.bfq 2> /dev/null # Wed Mar 28 14:43:43 BST 2012: Mapping file(s) 2723564971.00007.1.bfq 2723564971.00007.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 2723564971.00007.unmapped -H 2723564971.00007.mismatch \ 2723564971.00007.map /data/maqgene/genomes/elegans.bfa 2723564971.00007.1.bfq 2723564971.00007.2.bfq 2> /dev/null # Wed Mar 28 14:48:35 BST 2012: Mapping file(s) 2723564971.00016.1.bfq 2723564971.00016.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 2723564971.00016.unmapped -H 2723564971.00016.mismatch \ 2723564971.00016.map /data/maqgene/genomes/elegans.bfa 2723564971.00016.1.bfq 2723564971.00016.2.bfq 2> /dev/null # Wed Mar 28 14:48:36 BST 2012: Mapping file(s) 2723564971.00015.1.bfq 2723564971.00015.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 2723564971.00015.unmapped -H 2723564971.00015.mismatch \ 2723564971.00015.map /data/maqgene/genomes/elegans.bfa 2723564971.00015.1.bfq 2723564971.00015.2.bfq 2> /dev/null # Wed Mar 28 14:48:37 BST 2012: Mapping file(s) 2723564971.00014.1.bfq 2723564971.00014.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 2723564971.00014.unmapped -H 2723564971.00014.mismatch \ 2723564971.00014.map /data/maqgene/genomes/elegans.bfa 2723564971.00014.1.bfq 2723564971.00014.2.bfq 2> /dev/null # Wed Mar 28 14:48:38 BST 2012: Mapping file(s) 2723564971.00013.1.bfq 2723564971.00013.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 2723564971.00013.unmapped -H 2723564971.00013.mismatch \ 2723564971.00013.map /data/maqgene/genomes/elegans.bfa 2723564971.00013.1.bfq 2723564971.00013.2.bfq 2> /dev/null # Wed Mar 28 14:48:39 BST 2012: Mapping file(s) 2723564971.00006.1.bfq 2723564971.00006.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 2723564971.00006.unmapped -H 2723564971.00006.mismatch \ 2723564971.00006.map /data/maqgene/genomes/elegans.bfa 2723564971.00006.1.bfq 2723564971.00006.2.bfq 2> /dev/null # Wed Mar 28 14:48:39 BST 2012: Mapping file(s) 2723564971.00005.1.bfq 2723564971.00005.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 2723564971.00005.unmapped -H 2723564971.00005.mismatch \ 2723564971.00005.map /data/maqgene/genomes/elegans.bfa 2723564971.00005.1.bfq 2723564971.00005.2.bfq 2> /dev/null # Wed Mar 28 14:54:01 BST 2012: Mapping file(s) 2723564971.00023.1.bfq 2723564971.00023.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 2723564971.00023.unmapped -H 2723564971.00023.mismatch \ 2723564971.00023.map /data/maqgene/genomes/elegans.bfa 2723564971.00023.1.bfq 2723564971.00023.2.bfq 2> /dev/null # Wed Mar 28 14:54:01 BST 2012: Mapping file(s) 2723564971.00022.1.bfq 2723564971.00022.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 2723564971.00022.unmapped -H 2723564971.00022.mismatch \ 2723564971.00022.map /data/maqgene/genomes/elegans.bfa 2723564971.00022.1.bfq 2723564971.00022.2.bfq 2> /dev/null # Wed Mar 28 14:54:01 BST 2012: Mapping file(s) 2723564971.00021.1.bfq 2723564971.00021.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 2723564971.00021.unmapped -H 2723564971.00021.mismatch \ 2723564971.00021.map /data/maqgene/genomes/elegans.bfa 2723564971.00021.1.bfq 2723564971.00021.2.bfq 2> /dev/null # Wed Mar 28 14:54:02 BST 2012: Mapping file(s) 2723564971.00024.1.bfq 2723564971.00024.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 2723564971.00024.unmapped -H 2723564971.00024.mismatch \ 2723564971.00024.map /data/maqgene/genomes/elegans.bfa 2723564971.00024.1.bfq 2723564971.00024.2.bfq 2> /dev/null # Wed Mar 28 14:54:03 BST 2012: Mapping file(s) 2723564971.00020.1.bfq 2723564971.00020.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 2723564971.00020.unmapped -H 2723564971.00020.mismatch \ 2723564971.00020.map /data/maqgene/genomes/elegans.bfa 2723564971.00020.1.bfq 2723564971.00020.2.bfq 2> /dev/null # Wed Mar 28 14:54:04 BST 2012: Mapping file(s) 2723564971.00019.1.bfq 2723564971.00019.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 2723564971.00019.unmapped -H 2723564971.00019.mismatch \ 2723564971.00019.map /data/maqgene/genomes/elegans.bfa 2723564971.00019.1.bfq 2723564971.00019.2.bfq 2> /dev/null # Wed Mar 28 14:54:05 BST 2012: Mapping file(s) 2723564971.00018.1.bfq 2723564971.00018.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 2723564971.00018.unmapped -H 2723564971.00018.mismatch \ 2723564971.00018.map /data/maqgene/genomes/elegans.bfa 2723564971.00018.1.bfq 2723564971.00018.2.bfq 2> /dev/null # Wed Mar 28 14:54:06 BST 2012: Mapping file(s) 2723564971.00017.1.bfq 2723564971.00017.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 2723564971.00017.unmapped -H 2723564971.00017.mismatch \ 2723564971.00017.map /data/maqgene/genomes/elegans.bfa 2723564971.00017.1.bfq 2723564971.00017.2.bfq 2> /dev/null # Wed Mar 28 14:54:07 BST 2012: Mapping file(s) 2723564971.00004.1.bfq 2723564971.00004.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 2723564971.00004.unmapped -H 2723564971.00004.mismatch \ 2723564971.00004.map /data/maqgene/genomes/elegans.bfa 2723564971.00004.1.bfq 2723564971.00004.2.bfq 2> /dev/null # Wed Mar 28 14:54:08 BST 2012: Mapping file(s) 2723564971.00000.1.bfq 2723564971.00000.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 2723564971.00000.unmapped -H 2723564971.00000.mismatch \ 2723564971.00000.map /data/maqgene/genomes/elegans.bfa 2723564971.00000.1.bfq 2723564971.00000.2.bfq 2> /dev/null # Wed Mar 28 14:54:09 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2723564971.00032.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2723564971.00032.2.bfq -- finish writing file '2723564971.00032.2.bfq' -- 483460 sequences were loaded. # Wed Mar 28 15:00:06 BST 2012: Mapping file(s) 2723564971.00003.1.bfq 2723564971.00003.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 2723564971.00003.unmapped -H 2723564971.00003.mismatch \ 2723564971.00003.map /data/maqgene/genomes/elegans.bfa 2723564971.00003.1.bfq 2723564971.00003.2.bfq 2> /dev/null # Wed Mar 28 15:04:45 BST 2012: Mapping file(s) 2723564971.00032.1.bfq 2723564971.00032.2.bfq # Wed Mar 28 15:04:45 BST 2012: Mapping file(s) 2723564971.00030.1.bfq 2723564971.00030.2.bfq # Wed Mar 28 15:04:45 BST 2012: Mapping file(s) 2723564971.00028.1.bfq 2723564971.00028.2.bfq # Wed Mar 28 15:04:45 BST 2012: Mapping file(s) 2723564971.00027.1.bfq 2723564971.00027.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 2723564971.00032.unmapped -H 2723564971.00032.mismatch \ 2723564971.00032.map /data/maqgene/genomes/elegans.bfa 2723564971.00032.1.bfq 2723564971.00032.2.bfq 2> /dev/null # Wed Mar 28 15:04:45 BST 2012: Mapping file(s) 2723564971.00026.1.bfq 2723564971.00026.2.bfq # Wed Mar 28 15:04:45 BST 2012: Mapping file(s) 2723564971.00025.1.bfq 2723564971.00025.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 2723564971.00030.unmapped -H 2723564971.00030.mismatch \ 2723564971.00030.map /data/maqgene/genomes/elegans.bfa 2723564971.00030.1.bfq 2723564971.00030.2.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 2723564971.00029.unmapped -H 2723564971.00029.mismatch \ 2723564971.00029.map /data/maqgene/genomes/elegans.bfa 2723564971.00029.1.bfq 2723564971.00029.2.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 2723564971.00028.unmapped -H 2723564971.00028.mismatch \ 2723564971.00028.map /data/maqgene/genomes/elegans.bfa 2723564971.00028.1.bfq 2723564971.00028.2.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 2723564971.00027.unmapped -H 2723564971.00027.mismatch \ 2723564971.00027.map /data/maqgene/genomes/elegans.bfa 2723564971.00027.1.bfq 2723564971.00027.2.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 2723564971.00026.unmapped -H 2723564971.00026.mismatch \ 2723564971.00026.map /data/maqgene/genomes/elegans.bfa 2723564971.00026.1.bfq 2723564971.00026.2.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 2723564971.00025.unmapped -H 2723564971.00025.mismatch \ 2723564971.00025.map /data/maqgene/genomes/elegans.bfa 2723564971.00025.1.bfq 2723564971.00025.2.bfq 2> /dev/null # Wed Mar 28 15:10:08 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2723564971.00031.2.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2723564971.00031.2.bfq # Wed Mar 28 15:10:08 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2723564971.00002.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2723564971.00002.1.bfq -- finish writing file '2723564971.00031.2.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 15:10:20 BST 2012: Converting fastq files to bfq ... /data/maqgene/bin/maq sol2sanger 2723564971.00001.1.fastq /dev/stdout | \ /data/maqgene/bin/maq fastq2bfq /dev/stdin 2723564971.00001.1.bfq # Wed Mar 28 15:10:20 BST 2012: Mapping file(s) 2723564971.00031.1.bfq 2723564971.00031.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 2723564971.00031.unmapped -H 2723564971.00031.mismatch \ 2723564971.00031.map /data/maqgene/genomes/elegans.bfa 2723564971.00031.1.bfq 2723564971.00031.2.bfq 2> /dev/null -- finish writing file '2723564971.00002.1.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 15:10:20 BST 2012: Mapping file(s) 2723564971.00002.1.bfq 2723564971.00002.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 2723564971.00002.unmapped -H 2723564971.00002.mismatch \ 2723564971.00002.map /data/maqgene/genomes/elegans.bfa 2723564971.00002.1.bfq 2723564971.00002.2.bfq 2> /dev/null -- finish writing file '2723564971.00001.1.bfq' -- 1250000 sequences were loaded. # Wed Mar 28 15:10:32 BST 2012: Mapping file(s) 2723564971.00001.1.bfq 2723564971.00001.2.bfq /data/maqgene/bin/maq map -m 0.00001 -C 250 -n 2 -2 0 -a 500 -e 100 -A 500 -1 0 -u 2723564971.00001.unmapped -H 2723564971.00001.mismatch \ 2723564971.00001.map /data/maqgene/genomes/elegans.bfa 2723564971.00001.1.bfq 2723564971.00001.2.bfq 2> /dev/null # Wed Mar 28 15:15:10 BST 2012: Merging all *.unmapped files ... # Wed Mar 28 15:15:10 BST 2012: Merging all maps ... cat 2723564971.00000.unmapped 2723564971.00001.unmapped 2723564971.00002.unmapped 2723564971.00003.unmapped 2723564971.00004.unmapped 2723564971.00005.unmapped 2723564971.00006.unmapped 2723564971.00007.unmapped 2723564971.00008.unmapped 2723564971.00009.unmapped 2723564971.00010.unmapped 2723564971.00011.unmapped 2723564971.00012.unmapped 2723564971.00013.unmapped 2723564971.00014.unmapped 2723564971.00015.unmapped 2723564971.00016.unmapped 2723564971.00017.unmapped 2723564971.00018.unmapped 2723564971.00019.unmapped 2723564971.00020.unmapped 2723564971.00021.unmapped 2723564971.00022.unmapped 2723564971.00023.unmapped 2723564971.00024.unmapped 2723564971.00025.unmapped 2723564971.00026.unmapped 2723564971.00027.unmapped 2723564971.00028.unmapped 2723564971.00029.unmapped 2723564971.00030.unmapped 2723564971.00031.unmapped 2723564971.00032.unmapped > 2723564971_unmapped.txt /data/maqgene/bin/maq mapmerge 2723564971.map 2723564971.00000.map 2723564971.00001.map 2723564971.00002.map 2723564971.00003.map 2723564971.00004.map 2723564971.00005.map 2723564971.00006.map 2723564971.00007.map 2723564971.00008.map 2723564971.00009.map 2723564971.00010.map 2723564971.00011.map 2723564971.00012.map 2723564971.00013.map 2723564971.00014.map 2723564971.00015.map 2723564971.00016.map 2723564971.00017.map 2723564971.00018.map 2723564971.00019.map 2723564971.00020.map 2723564971.00021.map 2723564971.00022.map 2723564971.00023.map 2723564971.00024.map 2723564971.00025.map 2723564971.00026.map 2723564971.00027.map 2723564971.00028.map 2723564971.00029.map 2723564971.00030.map 2723564971.00031.map 2723564971.00032.map # Wed Mar 28 15:15:14 BST 2012: Linking backend file 2723564971_unmapped.txt to /data/maqgene/out/example_user/pja_11/pja_11_unmapped.txt ln -fs /data/maqgene/work/2723564971_unmapped.txt /data/maqgene/out/example_user/pja_11/pja_11_unmapped.txt /data/maqgene/makefile:126: warning: undefined variable `mapcheck_parameters' # Wed Mar 28 15:27:26 BST 2012: Running 'mapcheck' ... # Wed Mar 28 15:27:26 BST 2012: Creating pileup ... # Wed Mar 28 15:27:26 BST 2012: Generating consensus ... /data/maqgene/bin/maq mapcheck /data/maqgene/genomes/elegans.bfa 2723564971.map > 2723564971_check.txt \ 2>/dev/null /data/maqgene/bin/maq assemble -N 2 -q 0 -r 0.0 -m 7 -Q 100 -p 3031615627.cns \ /data/maqgene/genomes/elegans.bfa 2723564971.map 2> 3031615627_log.txt /data/maqgene/bin/maq pileup -Q 100 -p -m 7 -q 0 /data/maqgene/genomes/elegans.bfa 2723564971.map > 3032792211_pileup.txt # Wed Mar 28 15:31:17 BST 2012: Linking backend file 2723564971_check.txt to /data/maqgene/out/example_user/pja_11/pja_11_check.txt ln -fs /data/maqgene/work/2723564971_check.txt /data/maqgene/out/example_user/pja_11/pja_11_check.txt /data/maqgene/bin/filter_matching_lines 3032792211_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 \ > 3032792211_known_snps # Wed Mar 28 15:31:56 BST 2012: Getting uncovered regions ... # Wed Mar 28 15:31:56 BST 2012: Making coverage histogram ... # Wed Mar 28 15:31:56 BST 2012: Linking backend file 3032792211_pileup.txt to /data/maqgene/out/example_user/pja_11/pja_11_pileup.txt cut -f 1,2,4 3032792211_pileup.txt \ | /data/maqgene/bin/get_uncovered_regions 50 \ > 3032792211_uncovered.txt (echo -en "sequencing_depth\tnumber_of_bases\n"; \ cut -f 4 3032792211_pileup.txt \ | /data/maqgene/bin/pileup_histogram 100) > 3032792211_coverage.txt ln -fs /data/maqgene/work/3032792211_pileup.txt /data/maqgene/out/example_user/pja_11/pja_11_pileup.txt # Wed Mar 28 15:32:41 BST 2012: Linking backend file 3032792211_coverage.txt to /data/maqgene/out/example_user/pja_11/pja_11_coverage.txt ln -fs /data/maqgene/work/3032792211_coverage.txt /data/maqgene/out/example_user/pja_11/pja_11_coverage.txt # Wed Mar 28 15:32:41 BST 2012: Filtering and loading pileup for analysis ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 3032792211_pileup; create table 3032792211_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) );" # Wed Mar 28 15:32:42 BST 2012: Linking backend file 3032792211_uncovered.txt to /data/maqgene/out/example_user/pja_11/pja_11_uncovered.txt ln -fs /data/maqgene/work/3032792211_uncovered.txt /data/maqgene/out/example_user/pja_11/pja_11_uncovered.txt cat 3032792211_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 3032792211_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 3032792211_pileup" # Wed Mar 28 15:33:42 BST 2012: Extracting point mutants from consensus ... # Wed Mar 28 15:33:42 BST 2012: Linking backend file 3031615627_log.txt to /data/maqgene/out/example_user/pja_11/pja_11_log.txt /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 3031615627_snps; create table 3031615627_snps ( id int(10) NOT NULL auto_increment, dna char(40) NOT NULL, start int(10) NOT NULL, end int(10) NOT NULL, indel_size int(5) NOT NULL, variant_type enum('indel', 'point') NOT NULL, ref_base char NOT NULL, sample_base char NOT NULL, snp_score int(5) NOT NULL, read_depth int(5) NOT NULL, loci_multiplicity double(5,2) NOT NULL, mapping_quality int(5) NOT NULL, neighbor_quality int(5) NOT NULL, primary key (id), unique key (dna, start), key (indel_size) )" ln -fs /data/maqgene/work/3031615627_log.txt /data/maqgene/out/example_user/pja_11/pja_11_log.txt /data/maqgene/bin/maq cns2snp 3031615627.cns \ | cat -b | /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "load data local infile '/dev/stdin' into table 3031615627_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 3031615627_snps;" cat 3032792211_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 3032792211_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 3032792211_pileup" touch 3032792211_pileup # Wed Mar 28 15:33:46 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 3032792211_pileup p using (dna,start)" > /data/maqgene/out/example_user/pja_11/pja_11_snp_read_counts.txt 0 snp read count lines written. # Wed Mar 28 15:33:59 BST 2012: Extracting indels from consensus ... /data/maqgene/bin/maq indelsoa /data/maqgene/genomes/elegans.bfa 2723564971.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 3031615627_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 3031615627_snps;" # Wed Mar 28 15:36:16 BST 2012: Adding placeholders for known SNPs. cat 3032792211_known_snps \ | /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "load data local infile '/dev/stdin' ignore into table 3031615627_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 3031615627_snps;" Found 173355 variants. touch 3031615627_snps # Wed Mar 28 15:36:17 BST 2012: Loading uncovered regions into table ... # Wed Mar 28 15:36:17 BST 2012: Finding all genomic features overlapping variants... cat 3032792211_uncovered.txt \ | /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 3032792211_uncovered; create table 3032792211_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 = 173356; load data local infile '/dev/stdin' into table 3032792211_uncovered (dna, start, end)" /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 3031615627_rel_snps; CREATE TABLE 3031615627_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) )" # Wed Mar 28 15:36:17 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 3031615627_masked_ids; create table 3031615627_masked_ids (query_region_id int(10) NOT NULL, primary key (query_region_id)); load data local infile '/dev/stdin' ignore into table 3031615627_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 3031615627_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 3031615627_rel_snps; flush table 3031615627_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 3031615627_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 7 663 II 15 2461 III 8 781 IV 16 1447 V 16 1688 X 11 5663 touch 3032792211_uncovered # Wed Mar 28 15:36:18 BST 2012: Finding mRNA features overlapping uncovered regions ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 3032792211_uncovered_rel; CREATE TABLE 3032792211_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 3032792211_uncovered_rel; flush table 3032792211_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 3032792211_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 3032792211_uncovered_rel # Wed Mar 28 15:36:20 BST 2012: Calculating translation start offsets for uncovered regions... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 3032792211_offsets_uncovered; create table 3032792211_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 3032792211_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 3032792211_uncovered reg join 3032792211_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 3032792211_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 3032792211_uncovered reg join 3032792211_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 3031615627_masked_ids touch 3032792211_offsets_uncovered touch 3031615627_rel_snps # Wed Mar 28 15:36:21 BST 2012: Getting intergenic regions # Wed Mar 28 15:36:21 BST 2012: Calculating translation start offsets... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 3031615627_rel_intergenic; create table 3031615627_rel_intergenic like 3031615627_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 3031615627_rel_intergenic; flush table 3031615627_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 3031615627_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 "drop table if exists 3031615627_offsets_snps; create table 3031615627_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 "insert into 3031615627_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 3031615627_snps reg join 3031615627_rel_snps rel on (reg.id = rel.query_region_id) join elegans_features gene on (rel.target_region_id = gene.id) join elegans_features exon on (exon.attribute = gene.attribute) where exon.feature = 'exon' and gene.feature = 'mRNA' group by reg.id, gene.attribute" # Wed Mar 28 15:36:25 BST 2012: Filtering masked intergenic regions /usr/bin/mysql -Dmaqgenedb -umaqgene --skip-column-names --batch --raw --local-infile -e "delete i.* from 3031615627_rel_intergenic i join 3031615627_masked_ids m using (query_region_id)" touch 3031615627_rel_intergenic # Wed Mar 28 15:36:34 BST 2012: Classifying intergenic relations /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 3031615627_intergenic_assoc; create table 3031615627_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 3031615627_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 3031615627_snps snp join 3031615627_rel_intergenic rel on (snp.id = rel.query_region_id) join elegans_features feature on (rel.target_region_id = feature.id)" touch 3031615627_intergenic_assoc touch 3031615627_offsets_snps # Wed Mar 28 15:36:46 BST 2012: Getting codons affected by point mutations... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 3031615627_codons; create table 3031615627_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 3031615627_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 3031615627_offsets_snps off join 3031615627_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 3031615627_codons /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 3031615627_marked; create table 3031615627_marked ( id int(10) NOT NULL, class varchar(100) NOT NULL, description varchar(100) NOT NULL, parent_feature varchar(100) NOT NULL, primary key (id, class, parent_feature) );" # Wed Mar 28 15:36:53 BST 2012: Finding exonic indels ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 3031615627_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 3031615627_snps snp join 3031615627_rel_snps rel on (snp.id = rel.query_region_id) join elegans_features feature on (rel.target_region_id = feature.id) where feature.feature = 'exon' and snp.variant_type = 'indel';" # Wed Mar 28 15:36:53 BST 2012: Finding coding variants ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 3031615627_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 3031615627_codons trans join elegans_genetic_code reference_codons on (trans.ref_codon = reference_codons.codon) join elegans_genetic_code sample_codons on (trans.sam_codon = sample_codons.codon);" # Wed Mar 28 15:36:53 BST 2012: Finding noncoding variants ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 3031615627_marked select snp.id, feature.feature class, 'none' description, feature.attribute parent_feature from 3031615627_snps snp join 3031615627_rel_snps rel on (snp.id = rel.query_region_id) join elegans_features feature on (rel.target_region_id = feature.id) where feature.feature not in ('exon', 'intron', 'mRNA');" # Wed Mar 28 15:36:54 BST 2012: Finding splice site variants ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 3031615627_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 3031615627_snps snp join 3031615627_rel_snps rel on (snp.id = rel.query_region_id) join elegans_features feature on (rel.target_region_id = feature.id) where feature.feature = 'intron' and rel.distance > -2;" # Wed Mar 28 15:36:55 BST 2012: Finding intergenic and intronic variants ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 3031615627_marked select id, 'nongenic' class, concat(if (relation in ('upstream','into'), - distance, distance),' ',relation) description, attribute from 3031615627_intergenic_assoc where ((relation = 'upstream' and num_regions_between = 0 and distance < 50000) or (relation = 'upstream' and num_regions_between < 2 and distance < 1000) or (relation = 'downstream' and num_regions_between = 0 and distance < 1000) or (relation = 'downstream' and num_regions_between < 2 and distance < 1000) or relation = 'into' );" # Wed Mar 28 15:36:57 BST 2012: Finding uncovered regions in genes ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "insert into 3031615627_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 3032792211_uncovered unc join 3032792211_offsets_uncovered b using (id) join 3032792211_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 3032792211_uncovered unc join 3032792211_offsets_uncovered b using (id) join 3032792211_offsets_uncovered e using (id, gene) join elegans_features gene on (e.gene = gene.attribute) where b.boundary_type = 'start' and e.boundary_type = 'end' and gene.strand = '-' and gene.feature = 'mRNA'" # Wed Mar 28 15:36:57 BST 2012: Variants found: +-----------------+-----------------+ | class | number_variants | +-----------------+-----------------+ | five_prime_UTR | 1388 | | frameshift | 61 | | inframe | 22 | | missense | 9893 | | ncRNA | 911 | | nongenic | 103187 | | non_start | 12 | | premature_stop | 602 | | readthrough | 34 | | silent | 10087 | | SNP | 39224 | | splice_acceptor | 47 | | splice_donor | 46 | | three_prime_UTR | 3665 | | uncovered | 20 | +-----------------+-----------------+ touch 3031615627_marked # Wed Mar 28 15:36:58 BST 2012: Combining results ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 3031615627_combined; create table 3031615627_combined (primary key (id, class, description), key (dna, start)) as select snp.id, 'pja_11' 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 3031615627_snps snp join 3032792211_pileup pile using (dna,start) join 3031615627_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, 'pja_11' 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 3032792211_uncovered unc join 3031615627_marked class on (unc.id = class.id) left join elegans_per_locus using (dna,start) group by id, class, description; alter table 3031615627_combined order by dna, start, length" touch 3031615627_combined # Wed Mar 28 15:37:04 BST 2012: Writing results to grouped file ... # Wed Mar 28 15:37:04 BST 2012: Writing results to flat file ... /usr/bin/mysql -Dmaqgenedb -umaqgene --skip-column-names --batch --raw --local-infile --column-names -e "select id, mutant_strain, dna, start, length, reference_base, sample_base, consensus_score, loci_multiplicity, mapping_quality, neighbor_quality, number_wildtype_reads, number_variant_reads, sequencing_depth, sample_reads, variant_type, indel_size, group_concat(class) classes, group_concat(description) descriptions, group_concat(concat('{',parent_features,'}')) parent_features from 3031615627_combined group by id order by dna, start;" > /data/maqgene/out/example_user/pja_11/pja_11_grouped.txt /usr/bin/mysql -Dmaqgenedb -umaqgene --skip-column-names --batch --raw --local-infile --column-names -e "select * from 3031615627_combined" > /data/maqgene/out/example_user/pja_11/pja_11_flat.txt 64941 lines written. 48490 lines written. rm 2723564971.00024.1.fastq 2723564971.00017.mismatch 2723564971.00002.2.bfq 2723564971.00020.2.bfq 2723564971.00015.map 2723564971.00020.mismatch 2723564971.00018.1.bfq 2723564971.00009.1.fastq 2723564971.00006.unmapped 2723564971.00012.2.bfq 2723564971.00022.1.bfq 2723564971.00007.2.fastq 2723564971.00012.mismatch 2723564971.00016.mismatch 2723564971.00006.1.fastq 2723564971.00028.map 2723564971.00008.unmapped 2723564971.00024.2.fastq 2723564971.00026.mismatch 2723564971.00000.unmapped 2723564971.00003.1.bfq 2723564971.00032.2.bfq 2723564971.00018.2.bfq 2723564971.00007.1.bfq 2723564971.00008.2.bfq 2723564971.00000.1.fastq 2723564971.00018.mismatch 2723564971.00027.mismatch 2723564971.00009.map 2723564971.00027.2.bfq 2723564971.00001.unmapped 2723564971.00010.unmapped 2723564971.00031.1.bfq 2723564971.00013.1.bfq 2723564971.00016.unmapped 2723564971.00001.mismatch 2723564971.00021.2.fastq 2723564971.00006.2.fastq 2723564971.00001.1.fastq 2723564971.00010.1.fastq 2723564971.00019.2.bfq 2723564971.00008.2.fastq 2723564971.00016.1.fastq 2723564971.00004.map 2723564971.00003.2.bfq 2723564971.00029.unmapped 2723564971.00030.2.bfq 2723564971.00011.unmapped 2723564971.00025.map 2723564971.00003.mismatch 2723564971.00030.mismatch 2723564971.00000.2.fastq 2723564971.00029.1.fastq 2723564971.00016.2.fastq 2723564971.00011.1.fastq 2723564971.00017.unmapped 2723564971.00005.mismatch 2723564971.00008.1.bfq 2723564971.00005.2.bfq 2723564971.00020.unmapped 2723564971.00031.2.bfq 2723564971.00013.2.bfq 2723564971.00017.1.fastq 2723564971.00014.map 13454453_split1 2723564971.00031.mismatch 2723564971.00013.mismatch 2723564971.00001.2.fastq 2723564971.00010.2.fastq 2723564971.00002.1.fastq 2723564971.00020.1.fastq 2723564971.00019.1.bfq 2723564971.00022.map 2723564971.00009.2.fastq 2723564971.00012.unmapped 2723564971.00015.1.bfq 2723564971.00029.2.fastq 2723564971.00011.2.fastq 2723564971.00012.1.fastq 2723564971.00026.unmapped 2723564971.00026.2.bfq 2723564971.00009.1.bfq 2723564971.00017.2.fastq 2723564971.00009.2.bfq 2723564971.00026.1.fastq 2723564971.00011.1.bfq 2723564971.00023.2.bfq 2723564971.00018.unmapped 2723564971.00007.mismatch 2723564971.00002.2.fastq 2723564971.00032.mismatch 2723564971.00020.2.fastq 2723564971.00023.mismatch 2723564971.00024.map 2723564971.00021.map 2723564971.00028.1.bfq 2723564971.00018.1.fastq 2723564971.00019.mismatch 2723564971.00022.unmapped 2723564971.00015.2.bfq 2723564971.00025.1.bfq 2723564971.00012.2.fastq 2723564971.00015.mismatch 2723564971.00022.1.fastq 2723564971.00029.map 2723564971.00003.unmapped 2723564971.00030.unmapped 2723564971.00030.1.bfq 2723564971.00027.unmapped 2723564971.00003.1.fastq 2723564971.00030.1.fastq 2723564971.00028.2.bfq 2723564971.00007.unmapped 2723564971.00008.mismatch 2723564971.00021.2.bfq 2723564971.00018.2.fastq 2723564971.00027.1.fastq 2723564971.00028.mismatch 2723564971.00021.1.bfq 2723564971.00004.1.bfq 13454453_split2 2723564971.00013.unmapped 2723564971.00000.map 2723564971.00022.2.fastq 2723564971.00031.1.fastq 2723564971.00013.1.fastq 2723564971.00025.2.bfq 2723564971.00002.unmapped 2723564971.00026.2.fastq 2723564971.00001.map 2723564971.00010.map 2723564971.00003.2.fastq 2723564971.00030.2.fastq 2723564971.00016.map 2723564971.00005.unmapped 2723564971.00014.1.bfq 2723564971.00027.2.fastq 2723564971.00021.unmapped 2723564971.00004.2.bfq 2723564971.00009.mismatch 2723564971.00005.1.fastq 2723564971.00004.mismatch 2723564971.00032.unmapped 2723564971.00011.map 2723564971.00023.unmapped 2723564971.00031.2.fastq 2723564971.00013.2.fastq 2723564971.00019.unmapped 2723564971.00023.1.bfq 2723564971.00032.1.fastq 2723564971.00023.1.fastq 2723564971.00017.map 2723564971.00008.map 2723564971.00029.1.bfq 2723564971.00019.1.fastq 2723564971.00002.map 2723564971.00020.map 2723564971.00015.unmapped 2723564971.00025.mismatch 2723564971.00014.mismatch 2723564971.00024.1.bfq 2723564971.00015.1.fastq 2723564971.00005.2.fastq 2723564971.00009.unmapped 2723564971.00012.map 2723564971.00028.unmapped 2723564971.00032.2.fastq 2723564971.00023.2.fastq 2723564971.00027.map 2723564971.00026.map 2723564971.00022.mismatch 2723564971.00019.2.fastq 2723564971.00028.1.fastq 2723564971.00022.2.bfq 2723564971.00006.1.bfq 2723564971.00023.map 2723564971.00018.map 2723564971.00024.2.bfq 2723564971.00015.2.fastq 2723564971.00024.mismatch 2723564971.00025.unmapped 2723564971.00000.1.bfq 2723564971.00025.1.fastq 2723564971.00014.2.bfq 2723564971.00004.unmapped 2723564971.00028.2.fastq 2723564971.00002.mismatch 2723564971.00003.map 2723564971.00006.2.bfq 2723564971.00030.map 2723564971.00001.1.bfq 2723564971.00007.1.fastq 2723564971.00004.1.fastq 2723564971.00006.mismatch 2723564971.00016.1.bfq 2723564971.00021.mismatch 2723564971.00006.map 2723564971.00032.1.bfq 2723564971.00000.2.bfq 2723564971.00031.map 2723564971.00013.map 2723564971.00025.2.fastq 2723564971.00000.mismatch 2723564971.00014.1.fastq 2723564971.00014.unmapped 2723564971.00017.1.bfq 2723564971.00027.1.bfq 2723564971.00007.2.bfq 2723564971.00001.2.bfq 2723564971.00010.2.bfq 2723564971.00002.1.bfq 2723564971.00020.1.bfq 2723564971.00012.1.bfq 2723564971.00004.2.fastq 2723564971.00007.map 2723564971.00010.1.bfq 2723564971.00021.1.fastq 2723564971.00010.mismatch 2723564971.00016.2.bfq 2723564971.00008.1.fastq 2723564971.00031.unmapped 2723564971.00005.map 2723564971.00029.2.bfq 2723564971.00011.2.bfq 2723564971.00032.map 2723564971.00029.mismatch 2723564971.00011.mismatch 2723564971.00024.unmapped 2723564971.00014.2.fastq 2723564971.00019.map 2723564971.00017.2.bfq 2723564971.00026.1.bfq 2723564971.00005.1.bfq make: Leaving directory `/data/maqgene/work' make: Entering directory `/data/maqgene/work' # Wed Mar 28 15:37:06 BST 2012: Cleaning intermediate data ... /usr/bin/mysql -umaqgene -Dmaqgenedb --local-infile -e "drop table if exists 3031615627_snps,3031615627_rel,3031615627_masked_ids,3031615627_rel_intergenic,3031615627_intergenic_assoc,3031615627_offsets,3031615627_codons,3031615627_marked,3031615627_combined,3032792211_pileup" rm -f 3031615627_snps 3031615627_rel 3031615627_masked_ids 3031615627_rel_intergenic 3031615627_intergenic_assoc 3031615627_offsets 3031615627_codons 3031615627_marked 3031615627_combined 3032792211_pileup make: Leaving directory `/data/maqgene/work'