Error with mapping colorspace reads

[galagoz]

Hi all,

I've been trying to analyze old SOLiD-seq data with TopHat-1.4.1/Bowtie-1.0.1/samtools-0.1.19. However, when I run ./tophat bowtie_index/macaca_fascicularis_5.0_genome fastq/E08/SRR2930200.fastq command, I receive the following output:

[Fri Apr  5 17:48:47 2019] Beginning TopHat run (v1.4.1)
-----------------------------------------------
[Fri Apr  5 17:48:47 2019] Preparing output location ./tophat_out/
[Fri Apr  5 17:48:47 2019] Checking for Bowtie index files
[Fri Apr  5 17:48:47 2019] Checking for reference FASTA file
[Fri Apr  5 17:48:47 2019] Checking for Bowtie
    Bowtie version:          1.0.1.0
[Fri Apr  5 17:48:47 2019] Checking for Samtools
    Samtools Version: 0.1.19
[Fri Apr  5 17:48:47 2019] Generating SAM header for ../bowtie_index/macaca_fascicularis_5.0_genome
    format:      fastq
    quality scale:   phred33 (default)
[Fri Apr  5 17:48:49 2019] Preparing reads
    left reads: min. length=51, count=756267
[Fri Apr  5 17:49:05 2019] Mapping left_kept_reads against macaca_fascicularis_5.0_genome with Bowtie 

gzip: stdout: Broken pipe
[Fri Apr  5 17:49:07 2019] Processing bowtie hits
Warning: junction database is empty!
[Fri Apr  5 17:50:55 2019] Processing bowtie hits
    [FAILED]
Error executing: /home/goekberk/tophat-1.4.1.Linux_x86_64/bam_merge ./tophat_out/tmp/left_kept_reads.candidates_and_unspl.bam ./tophat_out/tmp/left_kept_reads.candidates.bam ./tophat_out/tmp/left_kept_reads.unspl.bam

Here are what log files say:

bowtie.left_kept_reads.fixmap.log:

Reads file contained a pattern with more than 1024 quality values. Please truncate reads and quality values and and re-run Bowtie terminate called after throwing an instance of 'int'

long_spanning_read.log:

long_spanning_reads v1.4.1 (exported)
--------------------------------------------
Opening ./tophat_out/tmp/left_kept_reads.bwtout.z for reading
Loading reference sequences...
        reference sequences loaded.
Loading spliced hits...done
Loading junctions...done
Loading deletions...done

prep_reads.log:

prep_reads v1.4.1 (exported)
---------------------------
0 out of 756267 reads have been filtered out

sam_merge.log:

Warning: no input BAM records found.
GList error (GList.hh:970):Invalid list index: 0

Since I'm not that familiar with RNAseq data analysis, I'm not sure how to fix this issue. I'd be glad if you could help me with this issue.

Best regards,
Gökberk