I know there are several posts about 'prep_reads', but they concern the Sanger/Phred quality issue. I think mye problem is different.
I am trying to map single-end illumina reads. They are sequenced with the CASAVA 1.8 and later pipeline, so I have kept the default values regarding quality scores.
I have mapped such reads without problems before, but now I always get error at the prep_reads stage:
And inside the prep_reads log:
Any tips on what is wrong?
I am trying to map single-end illumina reads. They are sequenced with the CASAVA 1.8 and later pipeline, so I have kept the default values regarding quality scores.
I have mapped such reads without problems before, but now I always get error at the prep_reads stage:
Code:
[2013-06-02 12:53:23] Beginning TopHat run (v2.0.7) ----------------------------------------------- [2013-06-02 12:53:23] Checking for Bowtie Bowtie version: 2.0.6.0 [2013-06-02 12:53:23] Checking for Samtools Samtools version: 0.1.18.0 [2013-06-02 12:53:23] Checking for Bowtie index files [2013-06-02 12:53:23] Checking for reference FASTA file [2013-06-02 12:53:23] Generating SAM header for sycon-genome format: fastq quality scale: phred33 (default) [2013-06-02 12:53:24] Preparing reads [FAILED] Error running 'prep_reads' Usage: prep_reads <reads1.fa/fq,...,readsN.fa/fq>
And inside the prep_reads log:
Code:
/cluster/home/jonbra/bin/prep_reads: unrecognized option '--max-seg-multihits'
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