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Tophat failed at 'Mapping left_kept_reads to transcriptome'

I am trying to run tophat for color-space data. The error is not very helpful for me to know what's wrong.

Any help is much appreciated.

tophat2 -p 14 -G $gtf --bowtie1 --color --zpacker pigz -o ${f}_tophat \
  --rg-id $f --rg-sample $f --rg-platform 'SOLiD.Wildfire' \
  --rg-library $f --rg-description 'Merged data from three lanes' \
  $bowtieIDX trimmed_joined.${f}.fastq.gz


[2015-06-11 12:25:27] Beginning TopHat run (v2.0.13)
-----------------------------------------------
[2015-06-11 12:25:27] Checking for Bowtie
                  Bowtie version:        1.1.1.0
[2015-06-11 12:25:27] Checking for Bowtie index files (genome)..
[2015-06-11 12:25:27] Checking for reference FASTA file
[2015-06-11 12:25:27] Generating SAM header for /data/rn6/bowtie/rn6.color
[2015-06-11 12:25:35] Reading known junctions from GTF file
[2015-06-11 12:25:42] Preparing reads
         left reads: min. length=25, max. length=75, 106304325 kept reads (105371 discarded)
[2015-06-11 12:44:25] Building transcriptome data files LT1_tophat/tmp/Rattus_norvegicus.Rnor_6.0.80.chrFixed.ercc
[2015-06-11 12:44:39] Building Bowtie index from Rattus_norvegicus.Rnor_6.0.80.chrFixed.ercc.fa
[2015-06-11 12:48:27] Mapping left_kept_reads to transcriptome Rattus_norvegicus.Rnor_6.0.80.chrFixed.ercc with Bowtie
        [FAILED]
Error running bowtie:
Too few quality values for read: 3T3@
        are you sure this is a FASTQ-int file?
terminate called after throwing an instance of 'int'
tophat rna-seq
• 4,128 views • link
updated by Ram Ram • written by biocyberman biocyberman

It looks like your fastq file is corrupt or otherwise malformed.

• 0 views • link
updated by Ram Ram • written by Devon Ryan Devon Ryan

Yes, I also had a hunch on this. BUT it is not my original fastq.gz file. It has something to do with --zpacker param and --unmapped-fifo param. I am not sure what to put for --unmapped-fifo.

• 0 views • link
updated by Ram Ram • written by biocyberman biocyberman

Those are obscure enough parameters that I don't think I've ever seen anyone change them. Try using the defaults first to see if that at least runs.

• 0 views • link
updated by Ram Ram • written by Devon Ryan Devon Ryan

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