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  • tophat2 error: std out broken pipe

    Hello,

    I am trying to use the latest versions of tophat2 (v2.1), bowtie2(v2.2.6) and samtools (v1.2).

    I get an broken pipe error, that I do not quite understand. (this did appear to work when I changed only the tophat2 to v2.0.9)

    My command:
    tophat -r 100 --mate-std-dev 50 -p 4 --library-type fr-firststrand -o clean -G hg38/gencode.v23.annotation.gtf --transcriptome-index=hg38/clean_hg38/transcriptome_data/known hg38/clean_hg38/hg38_clean 1.fastq.gz 2.fastq.gz

    (This worked with old versions: tophat2(v2.0.9), bowtie2(v2.1), samtools(v0.1.18))

    cat logs/tophat.log

    [2015-10-27 13:56:15] Beginning TopHat run (v2.1.0)
    -----------------------------------------------
    [2015-10-27 13:56:15] Checking for Bowtie
    Bowtie version: 2.2.6.0
    [2015-10-27 13:56:16] Checking for Bowtie index files (transcriptome)..
    [2015-10-27 13:56:16] Checking for Bowtie index files (genome)..
    [2015-10-27 13:56:16] Checking for reference FASTA file
    [2015-10-27 13:56:16] Generating SAM header for ../../../Genomes/hg38/clean_hg38/hg38_clean
    [2015-10-27 13:56:29] Reading known junctions from GTF file
    [2015-10-27 13:57:07] Preparing reads
    [FAILED]
    Error running 'prep_reads'
    gzip: stdout: Broken pipe

    cat logs/prep_reads.log
    prep_reads v2.1.0 (exported)
    ---------------------------

    gzip: stdout: Broken pipe

    gzip: stdout: Broken pipe

    What is wrong here that I need to rectify? Any help and/or advice is much appreciated.

    Many Thanks,
    NS

  • #2
    TopHat was incompatible with new Samtools (v.1.x), which was why older samtools is included in the source. I would start by dropping samtools back to the older version and then running this command again.

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