[2013-11-19 07:32:34] Beginning TopHat run (v2.0.4)
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[2013-11-19 07:32:34] Checking for Bowtie
Bowtie version: 0.12.7.0
[2013-11-19 07:32:34] Checking for Samtools
Samtools version: 0.1.18.0
[2013-11-19 07:32:34] Checking for Bowtie index files
[2013-11-19 07:32:34] Checking for Bowtie index files
[2013-11-19 07:32:34] Checking for reference FASTA file
[2013-11-19 07:32:34] Generating SAM RNA_seq_suit/bowtie_index/mm9
format: fastq
quality scale: phred33 (default)
[2013-11-19 07:32:37] Reading known junctions from GTF file
[2013-11-19 07:32:43] Pre-filtering multi-mapped left reads
[2013-11-19 07:32:43] Mapping SRRXXX_1 to genome mm9 with Bowtie
[2013-11-19 10:21:54] Pre-filtering multi-mapped right reads
[2013-11-19 10:21:54] Mapping SRRXXX_2 to genome mm9 with Bowtie
[2013-11-19 13:34:48] Preparing reads
[FAILED]
Error running 'prep_reads'
Error: beginning of quality values record not found! (@831)
Thanks for your time!
-----------------------------------------------
[2013-11-19 07:32:34] Checking for Bowtie
Bowtie version: 0.12.7.0
[2013-11-19 07:32:34] Checking for Samtools
Samtools version: 0.1.18.0
[2013-11-19 07:32:34] Checking for Bowtie index files
[2013-11-19 07:32:34] Checking for Bowtie index files
[2013-11-19 07:32:34] Checking for reference FASTA file
[2013-11-19 07:32:34] Generating SAM RNA_seq_suit/bowtie_index/mm9
format: fastq
quality scale: phred33 (default)
[2013-11-19 07:32:37] Reading known junctions from GTF file
[2013-11-19 07:32:43] Pre-filtering multi-mapped left reads
[2013-11-19 07:32:43] Mapping SRRXXX_1 to genome mm9 with Bowtie
[2013-11-19 10:21:54] Pre-filtering multi-mapped right reads
[2013-11-19 10:21:54] Mapping SRRXXX_2 to genome mm9 with Bowtie
[2013-11-19 13:34:48] Preparing reads
[FAILED]
Error running 'prep_reads'
Error: beginning of quality values record not found! (@831)
Thanks for your time!
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