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Old 10-12-2011, 10:18 AM   #1
victoryhe
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Location: boston

Join Date: Oct 2011
Posts: 7
Unhappy tophat Error running running 'prep_reads'

Hi, Naive here, i'm getting an error from tophat with mac os x 10.6


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tophat -o /tophatoutput/ --solexa1.3-quals /bowtie-0-1.12.7/indexes/mm9 a.fastq

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[Wed Oct 12 13:31:31 2011] Beginning TopHat run (v1.3.2)
-----------------------------------------------
[Wed Oct 12 13:31:31 2011] Preparing output location /tophatoutput/
[Wed Oct 12 13:31:31 2011] Checking for Bowtie index files
[Wed Oct 12 13:31:31 2011] Checking for reference FASTA file
Warning: Could not find FASTA file /bowtie-0-1.12.7/indexes/mm9.fa
[Wed Oct 12 13:31:31 2011] Reconstituting reference FASTA file from Bowtie index
Executing: /bowtie-0-1.12.7/indexes/mm9 > /tmp/mm9.fa
[Wed Oct 12 13:34:42 2011] Checking for Bowtie
Bowtie version: 0.12.7.0
[Wed Oct 12 13:34:42 2011] Checking for Samtools
Samtools Version: 0.1.18
[Wed Oct 12 13:34:42 2011] Generating SAM header for /bowtie-0-1.12.7/indexes/mm9
[Wed Oct 12 13:35:36 2011] Preparing reads
format: fastq
quality scale: phred64 (reads generated with GA pipeline version >= 1.3)
[FAILED]
Error running 'prep_reads'
terminate called after throwing an instance of 'int'

-------

i have never seen such an error before, something wrong on command line?

Last edited by victoryhe; 10-12-2011 at 10:22 AM.
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Old 10-13-2011, 05:09 PM   #2
cedance
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quality scale: phred64 (reads generated with GA pipeline version >= 1.3)
FAILED

Here lies the problem. Are you sure --solexa1.3-quals is right? Could you paste here a complete fastq read (header + read + quality)?
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Old 10-17-2011, 04:53 AM   #3
victoryhe
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thanks! without the solexa option, it works.
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