Etchevers:Notebook/STRA6 in eye development/2009/06/29

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Linux running Maq for a 3-day weekend

For SOX2:

~$ cd maq-0.7.1
~/maq-0.7.1$ maq.pl easyrun -d outdirSOX2 refhg19.fasta GDZ_SOX2.fastq

-- CMD: xx/maq-0.7.1/maq fasta2bfa xx/maq-0.7.1/refhg19.fasta outdirSOX2/ref.bfa 2> /dev/null read() on closed filehandle $fh at /usr/local/bin/maq.pl line 833.

    • Cannot guess the format of file 'xx/maq-0.7.1/GDZ_SOX2.fastq'. at /usr/local/bin/maq.pl line 107.
~/maq-0.7.1$ maq.pl easyrun -d outdirSOX2 refhg19.fasta GDZ3_SOX2.fastq

-- CMD: xx/maq-0.7.1/maq fasta2bfa /home/heather/maq-0.7.1/refhg19.fasta outdirSOX2/ref.bfa 2> /dev/null -- CMD: xx/maq-0.7.1/maq fastq2bfq -n 2000000 /home/heather/maq-0.7.1/GDZ3_SOX2.fastq outdirSOX2/read1 -- finish writing file 'outdirSOX2/read1@1.bfq' -- finish writing file 'outdirSOX2/read1@2000001.bfq' -- 3786087 sequences were loaded. -- CMD: (cd outdirSOX2; xx/maq-0.7.1/maq map -n 2 -e 70 -u unmap1@1.txt aln1@1.map ref.bfa read1@1.bfq 2> aln1@1.map.log) -- CMD: (cd outdirSOX2; xx/maq-0.7.1/maq map -n 2 -e 70 -u unmap1@2000001.txt aln1@2000001.map ref.bfa read1@2000001.bfq 2> aln1@2000001.map.log)

-- CMD: (cd outdirSOX2; xx/maq-0.7.1/maq mapmerge all.map aln1@1.map aln1@2000001.map) -- CMD: (cd outdirSOX2; xx/maq-0.7.1/maq mapcheck ref.bfa all.map > mapcheck.txt) [ma_mapcheck] processing chr1... [ma_mapcheck] processing chr2... [ma_mapcheck] processing chr3... [ma_mapcheck] processing chr4... [ma_mapcheck] processing chr5... [ma_mapcheck] processing chr6... [ma_mapcheck] processing chr7... [ma_mapcheck] processing chr8... [ma_mapcheck] processing chr9... [ma_mapcheck] processing chr10... [ma_mapcheck] processing chr11... [ma_mapcheck] processing chr12... [ma_mapcheck] processing chr13... [ma_mapcheck] processing chr14... [ma_mapcheck] processing chr15... [ma_mapcheck] processing chr16... [ma_mapcheck] processing chr17... [ma_mapcheck] processing chr18... [ma_mapcheck] processing chr19... [ma_mapcheck] processing chr20... [ma_mapcheck] processing chr21... [ma_mapcheck] processing chr22... [ma_mapcheck] processing chrX... [ma_mapcheck] processing chrY... [ma_mapcheck] processing chrM... -- CMD: (cd outdirSOX2; xx/maq-0.7.1/maq assemble -N 2 -Q 60 consensus.cns ref.bfa all.map 2> assemble.log) -- CMD: xx/maq-0.7.1/maq cns2fq outdirSOX2/consensus.cns > outdirSOX2/cns.fq -- CMD: xx/maq-0.7.1/maq cns2snp outdirSOX2/consensus.cns > outdirSOX2/cns.snp -- CMD: xx/maq-0.7.1/maq cns2win outdirSOX2/consensus.cns > outdirSOX2/cns.win -- CMD: xx/maq-0.7.1/maq indelsoa outdirSOX2/ref.bfa outdirSOX2/all.map > outdirSOX2/cns.indelse -- CMD: (cd outdirSOX2; touch unmap.indel) -- CMD: /usr/local/bin/maq.pl SNPfilter -q 40 -w 5 -N 2 -f outdirSOX2/cns.indelse -d 3 -D 256 -n 20 outdirSOX2/cns.snp > outdirSOX2/cns.final.snp -- 0 potential soa-indels pass the filter. -- CMD: (cd outdirSOX2; ln -s cns.final.snp cns.filter.snp) -- CMD: /usr/local/bin/maq.pl statmap outdirSOX2/*.map.log

-- == statmap report ==

-- # single end (SE) reads: 3786087 -- # mapped SE reads: 3267657 (/ 3786087 = 86.3%) -- # paired end (PE) reads: 0 -- # mapped PE reads: 0 (/ 0 = NA%) -- # reads that are mapped in pairs: 0 (/ 0 = NA%) -- # Q>=30 reads that are moved to meet mate-pair requirement: 0 (/ 0 = NA%) -- # Q<30 reads that are moved to meet mate-pair requirement: 0 (NA%)

~/maq-0.7.1$

For RAX and OTX2:

~/maq-0.7.1$ maq.pl easyrun -d outdirRAX refhg19.fasta GDZ4_RAX.fastq

-- CMD: xx/maq-0.7.1/maq fasta2bfa /home/heather/maq-0.7.1/refhg19.fasta outdirRAX/ref.bfa 2> /dev/null -- CMD: xx/maq-0.7.1/maq fastq2bfq -n 2000000 /home/heather/maq-0.7.1/GDZ4_RAX.fastq outdirRAX/read1 -- finish writing file 'outdirRAX/read1@1.bfq' -- finish writing file 'outdirRAX/read1@2000001.bfq' -- finish writing file 'outdirRAX/read1@4000001.bfq' -- 4981790 sequences were loaded. -- CMD: (cd outdirRAX; /home/heather/maq-0.7.1/maq map -n 2 -e 70 -u unmap1@4000001.txt aln1@4000001.map ref.bfa read1@4000001.bfq 2> aln1@4000001.map.log) -- CMD: (cd outdirRAX; /home/heather/maq-0.7.1/maq map -n 2 -e 70 -u unmap1@1.txt aln1@1.map ref.bfa read1@1.bfq 2> aln1@1.map.log) -- CMD: (cd outdirRAX; /home/heather/maq-0.7.1/maq map -n 2 -e 70 -u unmap1@2000001.txt aln1@2000001.map ref.bfa read1@2000001.bfq 2> aln1@2000001.map.log) -- CMD: (cd outdirRAX; /home/heather/maq-0.7.1/maq mapmerge all.map aln1@4000001.map aln1@1.map aln1@2000001.map) -- CMD: (cd outdirRAX; /home/heather/maq-0.7.1/maq mapcheck ref.bfa all.map > mapcheck.txt) -- CMD: (cd outdirRAX; /home/heather/maq-0.7.1/maq assemble -N 2 -Q 60 consensus.cns ref.bfa all.map 2> assemble.log) -- CMD: xx/maq-0.7.1/maq cns2fq outdirRAX/consensus.cns > outdirRAX/cns.fq -- CMD: xx/maq-0.7.1/maq cns2snp outdirRAX/consensus.cns > outdirRAX/cns.snp -- CMD: xx/maq-0.7.1/maq cns2win outdirRAX/consensus.cns > outdirRAX/cns.win -- CMD: xx/maq-0.7.1/maq indelsoa outdirRAX/ref.bfa outdirRAX/all.map > outdirRAX/cns.indelse -- CMD: (cd outdirRAX; touch unmap.indel) -- CMD: /usr/local/bin/maq.pl SNPfilter -q 40 -w 5 -N 2 -f outdirRAX/cns.indelse -d 3 -D 256 -n 20 outdirRAX/cns.snp > outdirRAX/cns.final.snp -- 0 potential soa-indels pass the filter. -- CMD: (cd outdirRAX; ln -s cns.final.snp cns.filter.snp) -- CMD: /usr/local/bin/maq.pl statmap outdirRAX/*.map.log

-- == statmap report ==

-- # single end (SE) reads: 4981790 -- # mapped SE reads: 1486402 (/ 4981790 = 29.83%) -- # paired end (PE) reads: 0 -- # mapped PE reads: 0 (/ 0 = NA%) -- # reads that are mapped in pairs: 0 (/ 0 = NA%) -- # Q>=30 reads that are moved to meet mate-pair requirement: 0 (/ 0 = NA%) -- # Q<30 reads that are moved to meet mate-pair requirement: 0 (NA%)

~/maq-0.7.1$ cd outdirRAX
~/maq-0.7.1/outdirRAX$ ls

all.map cns.filter.snp read1@1.bfq aln1@1.map cns.final.snp read1@2000001.bfq aln1@1.map.log cns.fq read1@4000001.bfq aln1@2000001.map cns.indelse ref.bfa aln1@2000001.map.log cns.snp unmap1@1.txt aln1@4000001.map cns.win unmap1@2000001.txt aln1@4000001.map.log consensus.cns unmap1@4000001.txt assemble.log mapcheck.txt unmap.indel

~/maq-0.7.1/outdirRAX$ cd ..
~/maq-0.7.1$ maq.pl easyrun -d outdirOTX2-1 refhg19.fasta GDZ_OTX2.fastq

-- CMD: xx/maq-0.7.1/maq fasta2bfa xx/maq-0.7.1/refhg19.fasta outdirOTX2-1/ref.bfa 2> /dev/null read() on closed filehandle $fh at /usr/local/bin/maq.pl line 833.

    • Cannot guess the format of file 'xx/maq-0.7.1/GDZ_OTX2.fastq'. at /usr/local/bin/maq.pl line 107.
~/maq-0.7.1$ ls

aclocal.m4 csmap2ntmap.cc main.h outdirSOX2 algo.hh csmap2ntmap.o main.o pair_stat.cc aln1@4000001.map dword.hh Makefile pair_stat.o altchr.cc eland2maq.cc Makefile.am pileup.cc altchr.o eland2maq.o Makefile.generic pileup.o assemble.cc fasta2bfa.c Makefile.in PROBLEMS assemble.h fasta2bfa.o mapcheck.cc rbcc.cc assemble.o fastq2bfq.c mapcheck.o rbcc.o assopt.c fastq2bfq.o maq read.cc assopt.o FUTURES maq.1 read.h AUTHORS GDZ1_OTX2.fastq maqmap.c README autogen.sh GDZ2_OTX2-2.fastq maqmap_conv.c read.o aux_utils.c GDZ3_SOX2.fastq maqmap_conv.o refhg19.fasta aux_utils.o GDZ4_RAX.fastq maqmap.h rmdup.cc bfa.c GDZ5_PAX6.fastq maqmap.o rmdup.o bfa.h genran.c maq.pdf scripts bfa.o genran.h maq.pod seq.c break_pair.c genran.o match_aux.cc seq.h break_pair.o get_pos.c match_aux.o seq.o ChangeLog get_pos.o match.cc SeqResults cleanup.sh glfgen.cc match.hh simulate.c config.guess glfgen.o match.o simulate.o config.h glf.h merge.cc sort_mapping.cc config.h.in HumGen merge.o sort_mapping.o config.log indel_call.cc missing stamp-h1 config.status indel_call.o NEWS stdaln.c config.sub indel_pe.cc OTX2-1.txt stdaln.h configure indel_pe.o outdir stdaln.o configure.ac indel_soa.cc outdirOTX-2 stdhash.hh const.c indel_soa.o outdirOTX2-1 submap.c const.h INSTALL outdirOTX2-2 submap.o const.o install-sh outdirPAX6 subsnp.cc COPYING main.c outdirRAX subsnp.o

~/maq-0.7.1$ maq.pl easyrun -d outdirOTX2-1 refhg19.fasta GDZ2_OTX2.fastq

-- CMD: xx/maq-0.7.1/maq fasta2bfa /home/heather/maq-0.7.1/refhg19.fasta outdirOTX2-1/ref.bfa 2> /dev/null '^C** fail to run command 'xx/maq-0.7.1/maq fasta2bfa /home/heather/maq-0.7.1/refhg19.fasta outdirOTX2-1/ref.bfa 2> /dev/null' at /usr/local/bin/maq.pl line 842.

~/maq-0.7.1$ maq.pl easyrun -d outdirOTX2 refhg19.fasta GDZ1_OTX2.fastq

-- CMD: xx/maq-0.7.1/maq fasta2bfa /home/heather/maq-0.7.1/refhg19.fasta outdirOTX2/ref.bfa 2> /dev/null

-- CMD: xx/maq-0.7.1/maq fastq2bfq -n 2000000 /home/heather/maq-0.7.1/GDZ1_OTX2.fastq outdirOTX2/read1 -- finish writing file 'outdirOTX2/read1@1.bfq' -- finish writing file 'outdirOTX2/read1@2000001.bfq' -- finish writing file 'outdirOTX2/read1@4000001.bfq' -- 4780016 sequences were loaded. -- CMD: (cd outdirOTX2; xx/maq-0.7.1/maq map -n 2 -e 70 -u unmap1@4000001.txt aln1@4000001.map ref.bfa read1@4000001.bfq 2> aln1@4000001.map.log) -- CMD: (cd outdirOTX2; xx/maq-0.7.1/maq map -n 2 -e 70 -u unmap1@1.txt aln1@1.map ref.bfa read1@1.bfq 2> aln1@1.map.log) -- CMD: (cd outdirOTX2; xx/maq-0.7.1/maq map -n 2 -e 70 -u unmap1@2000001.txt aln1@2000001.map ref.bfa read1@2000001.bfq 2> aln1@2000001.map.log)

The following when I reflexively used Ctrl-C for copy to paste here! so redo the following CMDs manually:

^C** fail to run command '(cd outdirOTX2; xx/maq-0.7.1/maq map -n 2 -e 70 -u unmap1@2000001.txt aln1@2000001.map ref.bfa read1@2000001.bfq 2> aln1@2000001.map.log)' at /usr/local/bin/maq.pl line 842.

~/maq-0.7.1$ cd outdirOTX2; xx/maq-0.7.1/maq map -n 2 -e 70 -u unmap1@2000001.txt aln1@2000001.map ref.bfa read1@2000001.bfq 2> aln1@2000001.map.log

And this is still running.

I wish I knew how to get the carriage returns recognized as such.

After a few hours, I retyped in the above with only one space between each word and it elicited a much better response:

~/maq-0.7.1/outdirOTX2$ maq map -n 2 -e 70 -u unmap1@2000001.txt aln1@2000001.map ref.bfa read1@2000001.bfq > aln1@2000001.map.log

-- maq-0.7.1 [ma_load_reads] loading reads... [ma_load_reads] set length of the first read as 71. [ma_load_reads] 2000000*2 reads loaded. [ma_longread2read] encoding reads... 4000000 sequences processed. [ma_match] set the minimum insert size as 72. [match_core] Total length of the reference: 3095693983 [match_core] round 1/3... [match_core] making index... [match_search] 0% processed in 12.273 sec: 0 / 0 = 0.000 [match_search] 1% processed in 246.179 sec: 686496 / 28632775 = 0.024

Off to bed, then.