I am trying to map illumina paired-end datasets using tophat2. Everything seems to work fine but I suddenly get an errormessage concerning bowtie:
[2013-02-15 16:16:36] Beginning TopHat run (v2.0.7)
-----------------------------------------------
[2013-02-15 16:16:36] Checking for Bowtie
Bowtie version: 2.0.6.0
[2013-02-15 16:16:36] Checking for Samtools
Samtools version: 0.1.18.0
[2013-02-15 16:16:36] Checking for Bowtie index files
[2013-02-15 16:16:36] Checking for reference FASTA file
[2013-02-15 16:16:36] Generating SAM header for /usit/abel/u1/jonbra/Sycon-diff-expr-test/sycon_genome
format: fastq
quality scale: phred33 (default)
[2013-02-15 16:16:42] Preparing reads
left reads: min. length=101, max. length=101, 20383888 kept reads (10376 discarded)
[2013-02-15 16:23:29] Mapping left_kept_reads to genome sycon_genome with Bowtie2
[FAILED]
Error running bowtie:
[2013-02-15 16:16:36] Beginning TopHat run (v2.0.7)
-----------------------------------------------
[2013-02-15 16:16:36] Checking for Bowtie
Bowtie version: 2.0.6.0
[2013-02-15 16:16:36] Checking for Samtools
Samtools version: 0.1.18.0
[2013-02-15 16:16:36] Checking for Bowtie index files
[2013-02-15 16:16:36] Checking for reference FASTA file
[2013-02-15 16:16:36] Generating SAM header for /usit/abel/u1/jonbra/Sycon-diff-expr-test/sycon_genome
format: fastq
quality scale: phred33 (default)
[2013-02-15 16:16:42] Preparing reads
left reads: min. length=101, max. length=101, 20383888 kept reads (10376 discarded)
[2013-02-15 16:23:29] Mapping left_kept_reads to genome sycon_genome with Bowtie2
[FAILED]
Error running bowtie:
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