Hey guys,
i'm going to align 50nt illumina paired end with TopHat.
When i start the run with : tophat -r 100 -p 2 bowtie index readfiles all looks quite nice.
The first output i get is:
[Mon May 23 10:31:32 2011] Beginning TopHat run (v1.2.0)
-----------------------------------------------
[Mon May 23 10:31:32 2011] Preparing output location ./tophat_out/
[Mon May 23 10:31:32 2011] Checking for Bowtie index files
[Mon May 23 10:31:32 2011] Checking for reference FASTA file
[Mon May 23 10:31:32 2011] Checking for Bowtie
Bowtie version: 0.12.7.0
[Mon May 23 10:31:32 2011] Checking for Samtools
Samtools Version: 0.1.16
[Mon May 23 10:31:32 2011] Checking reads
min read length: 50bp, max read length: 50bp
format: fastq
quality scale: phred33 (default)
BUT: after that the programm terminates and no computation was done. Any hints how to solve the problem?
Thanks in advance,
Philip
i'm going to align 50nt illumina paired end with TopHat.
When i start the run with : tophat -r 100 -p 2 bowtie index readfiles all looks quite nice.
The first output i get is:
[Mon May 23 10:31:32 2011] Beginning TopHat run (v1.2.0)
-----------------------------------------------
[Mon May 23 10:31:32 2011] Preparing output location ./tophat_out/
[Mon May 23 10:31:32 2011] Checking for Bowtie index files
[Mon May 23 10:31:32 2011] Checking for reference FASTA file
[Mon May 23 10:31:32 2011] Checking for Bowtie
Bowtie version: 0.12.7.0
[Mon May 23 10:31:32 2011] Checking for Samtools
Samtools Version: 0.1.16
[Mon May 23 10:31:32 2011] Checking reads
min read length: 50bp, max read length: 50bp
format: fastq
quality scale: phred33 (default)
BUT: after that the programm terminates and no computation was done. Any hints how to solve the problem?
Thanks in advance,
Philip
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