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

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 * style="background-color: #EEE"|[[Image:C14.jpg|128px]] Genetics of human eye development
 * style="background-color: #F2F2F2" align="center"|  |Main project page
 * style="background-color: #F2F2F2" align="center"|  |Main project page


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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.


 * Heather 13:24, 29 June 2009 (EDT):

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.
 * Heather 17:57, 29 June 2009 (EDT):


 * }