Has anyone seen this error before? I had Tophat working fine, but wanted to use the newly provided Illumina bowtie_index and I'm now getting this error:
[Thu Aug 4 13:56:11 2011] Beginning TopHat run (v1.3.0)
-----------------------------------------------
[Thu Aug 4 13:56:11 2011] Preparing output location /m/illumina/tophat/
[Thu Aug 4 13:56:11 2011] Checking for Bowtie index files
[Thu Aug 4 13:56:11 2011] Checking for reference FASTA file
[Thu Aug 4 13:56:11 2011] Checking for Bowtie
Bowtie version: 0.12.7.0
[Thu Aug 4 13:56:11 2011] Checking for Samtools
Samtools Version: 0.1.8
[Thu Aug 4 13:56:11 2011] Generating SAM header for /m/ref/genome
[Thu Aug 4 13:56:40 2011] Preparing reads
format: fastq
quality scale: phred33 (default)
[FAILED]
Error retrieving prep_reads info.
OR!!! In two of my samples, I get this error message:
Error: qual length (103) differs from seq length (63) for fastq record !
In case it matters, there is a slice of my pre-maq ill2sanger .txt file and post-maq .fastq file attached.
My apologies if this has been answered before.
[Thu Aug 4 13:56:11 2011] Beginning TopHat run (v1.3.0)
-----------------------------------------------
[Thu Aug 4 13:56:11 2011] Preparing output location /m/illumina/tophat/
[Thu Aug 4 13:56:11 2011] Checking for Bowtie index files
[Thu Aug 4 13:56:11 2011] Checking for reference FASTA file
[Thu Aug 4 13:56:11 2011] Checking for Bowtie
Bowtie version: 0.12.7.0
[Thu Aug 4 13:56:11 2011] Checking for Samtools
Samtools Version: 0.1.8
[Thu Aug 4 13:56:11 2011] Generating SAM header for /m/ref/genome
[Thu Aug 4 13:56:40 2011] Preparing reads
format: fastq
quality scale: phred33 (default)
[FAILED]
Error retrieving prep_reads info.
OR!!! In two of my samples, I get this error message:
Error: qual length (103) differs from seq length (63) for fastq record !
In case it matters, there is a slice of my pre-maq ill2sanger .txt file and post-maq .fastq file attached.
My apologies if this has been answered before.
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