I am still having difficulty running Maq.
I tried to use S. Typhi CT18 finished sequence in a fasta file & map reads from the file 'Typhi_CT18_solexa.fastq' from Sanger's ftp site using Maq version 0.6.8
But I get the following output which doesn't seem to map any of the reads to the refseq sequence.
maq.pl easyrun -d outdir S_typhiCT18.fasta Typhi_CT18_solexa.fastq
-- CMD: /Users/jozefgecz/Documents/Alison/Maq/maq-0.6.8/maq fasta2bfa
/Users/jozefgecz/Documents/Alison/Maq/maq-0.6.8/S_typhiCT18.fasta outdir/ref.bfa
2> /dev/null
-- CMD: /Users/jozefgecz/Documents/Alison/Maq/maq-0.6.8/maq fastq2bfq -n 2000000
/Users/jozefgecz/Documents/Alison/Maq/maq-0.6.8/Typhi_CT18_solexa.fastq
outdir/read1
-- finish writing file 'outdir/[email protected]'
-- 1879809 sequences were loaded.
-- CMD: (cd outdir; /Users/jozefgecz/Documents/Alison/Maq/maq-0.6.8/maq map -n
2 -e 70 -u [email protected] [email protected] ref.bfa [email protected] 2> [email protected])
-- CMD: (cd outdir; mv [email protected] all.map)
-- CMD: (cd outdir; /Users/jozefgecz/Documents/Alison/Maq/maq-0.6.8/maq mapcheck
ref.bfa all.map > mapcheck.txt)
[ma_mapcheck] processing Salmonella...
-- CMD: (cd outdir; /Users/jozefgecz/Documents/Alison/Maq/maq-0.6.8/maq assemble
-N 2 -Q 60 consensus.cns ref.bfa all.map 2> assemble.log)
-- CMD: /Users/jozefgecz/Documents/Alison/Maq/maq-0.6.8/maq cns2fq
outdir/consensus.cns > outdir/cns.fq
-- CMD: /Users/jozefgecz/Documents/Alison/Maq/maq-0.6.8/maq cns2snp
outdir/consensus.cns > outdir/cns.snp
-- CMD: /Users/jozefgecz/Documents/Alison/Maq/maq-0.6.8/maq cns2win
outdir/consensus.cns > outdir/cns.win
-- CMD: /Users/jozefgecz/Documents/Alison/Maq/maq-0.6.8/maq indelsoa
outdir/ref.bfa outdir/all.map > outdir/cns.indelse
-- CMD: (cd outdir; touch unmap.indel)
-- CMD: /usr/local/bin/maq.pl SNPfilter -q 40 -w 5 -N 2 -f outdir/cns.indelse -d
3 -D 256 -n 20 outdir/cns.snp > outdir/cns.final.snp
-- 0 potential soa-indels pass the filter.
-- CMD: (cd outdir; ln -s cns.final.snp cns.filter.snp)
-- CMD: /usr/local/bin/maq.pl statmap outdir/*.map.log
-- == statmap report ==
-- # single end (SE) reads: 1879809
-- # mapped SE reads: 0 (/ 1879809 = 0%)
-- # 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%)
What am I doing wrong? I just want to trial the Maq program in preparation for when we receive our sequence.
thanks
alig
I tried to use S. Typhi CT18 finished sequence in a fasta file & map reads from the file 'Typhi_CT18_solexa.fastq' from Sanger's ftp site using Maq version 0.6.8
But I get the following output which doesn't seem to map any of the reads to the refseq sequence.
maq.pl easyrun -d outdir S_typhiCT18.fasta Typhi_CT18_solexa.fastq
-- CMD: /Users/jozefgecz/Documents/Alison/Maq/maq-0.6.8/maq fasta2bfa
/Users/jozefgecz/Documents/Alison/Maq/maq-0.6.8/S_typhiCT18.fasta outdir/ref.bfa
2> /dev/null
-- CMD: /Users/jozefgecz/Documents/Alison/Maq/maq-0.6.8/maq fastq2bfq -n 2000000
/Users/jozefgecz/Documents/Alison/Maq/maq-0.6.8/Typhi_CT18_solexa.fastq
outdir/read1
-- finish writing file 'outdir/[email protected]'
-- 1879809 sequences were loaded.
-- CMD: (cd outdir; /Users/jozefgecz/Documents/Alison/Maq/maq-0.6.8/maq map -n
2 -e 70 -u [email protected] [email protected] ref.bfa [email protected] 2> [email protected])
-- CMD: (cd outdir; mv [email protected] all.map)
-- CMD: (cd outdir; /Users/jozefgecz/Documents/Alison/Maq/maq-0.6.8/maq mapcheck
ref.bfa all.map > mapcheck.txt)
[ma_mapcheck] processing Salmonella...
-- CMD: (cd outdir; /Users/jozefgecz/Documents/Alison/Maq/maq-0.6.8/maq assemble
-N 2 -Q 60 consensus.cns ref.bfa all.map 2> assemble.log)
-- CMD: /Users/jozefgecz/Documents/Alison/Maq/maq-0.6.8/maq cns2fq
outdir/consensus.cns > outdir/cns.fq
-- CMD: /Users/jozefgecz/Documents/Alison/Maq/maq-0.6.8/maq cns2snp
outdir/consensus.cns > outdir/cns.snp
-- CMD: /Users/jozefgecz/Documents/Alison/Maq/maq-0.6.8/maq cns2win
outdir/consensus.cns > outdir/cns.win
-- CMD: /Users/jozefgecz/Documents/Alison/Maq/maq-0.6.8/maq indelsoa
outdir/ref.bfa outdir/all.map > outdir/cns.indelse
-- CMD: (cd outdir; touch unmap.indel)
-- CMD: /usr/local/bin/maq.pl SNPfilter -q 40 -w 5 -N 2 -f outdir/cns.indelse -d
3 -D 256 -n 20 outdir/cns.snp > outdir/cns.final.snp
-- 0 potential soa-indels pass the filter.
-- CMD: (cd outdir; ln -s cns.final.snp cns.filter.snp)
-- CMD: /usr/local/bin/maq.pl statmap outdir/*.map.log
-- == statmap report ==
-- # single end (SE) reads: 1879809
-- # mapped SE reads: 0 (/ 1879809 = 0%)
-- # 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%)
What am I doing wrong? I just want to trial the Maq program in preparation for when we receive our sequence.
thanks
alig
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