Thanks Daehwan for quickly fixing the previous error of TopHat 1.1.0 on SE reads! As I am trying the updated version, I got stuck again at prep_reads with standard 75nt Illumina SE reads. The same command worked well under TopHat 1.0.14 so I think this must be a bug with the new version. The command line and errors are:
tophat -o tophat_cufflinks_test -a 6 -i 50 --solexa1.3-quals -F 0.05 -p 4 -g 20 --coverage-search --microexon-search -j ../../hg19.junc hg19 adipose_75nt.fq
[Mon Oct 4 22:33:39 2010] Beginning TopHat run (v1.1.0)
-----------------------------------------------
[Mon Oct 4 22:33:39 2010] Preparing output location tophat_cufflinks_test/
[Mon Oct 4 22:33:39 2010] Checking for Bowtie index files
[Mon Oct 4 22:33:39 2010] Checking for reference FASTA file
[Mon Oct 4 22:33:39 2010] Checking for Bowtie
Bowtie version: 0.12.7.0
[Mon Oct 4 22:33:39 2010] Checking for Samtools
Samtools version: 0.1.8.0
[Mon Oct 4 22:33:40 2010] Checking reads
min read length: 75bp, max read length: 75bp
format: fastq
quality scale: phred64 (reads generated with GA pipeline version >= 1.3)
[FAILED]
Error: could not execute prep_reads
Anybody has the same problem or can offer a fix? Thanks a lot!
-- Leo
tophat -o tophat_cufflinks_test -a 6 -i 50 --solexa1.3-quals -F 0.05 -p 4 -g 20 --coverage-search --microexon-search -j ../../hg19.junc hg19 adipose_75nt.fq
[Mon Oct 4 22:33:39 2010] Beginning TopHat run (v1.1.0)
-----------------------------------------------
[Mon Oct 4 22:33:39 2010] Preparing output location tophat_cufflinks_test/
[Mon Oct 4 22:33:39 2010] Checking for Bowtie index files
[Mon Oct 4 22:33:39 2010] Checking for reference FASTA file
[Mon Oct 4 22:33:39 2010] Checking for Bowtie
Bowtie version: 0.12.7.0
[Mon Oct 4 22:33:39 2010] Checking for Samtools
Samtools version: 0.1.8.0
[Mon Oct 4 22:33:40 2010] Checking reads
min read length: 75bp, max read length: 75bp
format: fastq
quality scale: phred64 (reads generated with GA pipeline version >= 1.3)
[FAILED]
Error: could not execute prep_reads
Anybody has the same problem or can offer a fix? Thanks a lot!
-- Leo
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