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  • ViralFusionSeq Troubleshooting

    Hi all,

    I'm attempting to use ViralFusionSeq on Ubuntu 12.04 for identifying viral integration sites in the human genome with RNA-Seq data, but am running into errors. The "1.VFS.sys.check.pl" as well as "2.run.example.dataset.pl" script both run successfully, so it seems properly configured.

    When attempting to validate my fastq files via the "misc/prep.fastq.2.Illumina.1.8.gz.pl" I get the following error:

    Code:
    $ perl misc/prep.fastq.2.Illumina.1.8.gz.pl Sample1_F1.fastq,Sample1_F2.fastq,Sample1_F3.fastq,Sample1_F4.fastq,Sample1_F5.fastq Sample1_R1.fastq,Sample1_R2.fastq,Sample1_R3.fastq,Sample1_R4.fastq,Sample1_R5.fastq
    Do you want to gzip the fastq files?
    If your system is short of disk space, select YES. Gzip will save approximate 2/3 of the space required
    For maximum VFS performance, select NO
    NO
    Will let the fastq(s)un-compressed
    Validating fastq file: Sample1_F1.fastq,Sample1_F2.fastq,Sample1_F3.fastq,Sample1_F4.fastq,Sample1_F5.fastq Undefined subroutine &main::process_error called at misc/prep.fastq.2.Illumina.1.8.gz.pl line 117, <STDIN> line 1.
    Any help troubleshooting this error is greatly appreciated, thank you!

  • #2
    Update - Error Fixed

    Was a simple fix. I'm used to TopHat handling unmerged sequence files, but this script required the sequence files to be merged.

    Code:
    $ cat Sample1_F1.fastq Sample1_F2.fastq Sample1_F3.fastq Sample1_F4.fastq Sample1_F5.fastq > Sample1_F.fastq
    $ cat Sample1_R1.fastq Sample1_R2.fastq Sample1_R3.fastq Sample1_R4.fastq Sample1_R5.fastq > Sample1_R.fastq
    
    $ perl misc/prep.fastq.2.Illumina.1.8.gz.pl Sample1_F.fastq Sample1_R.fastq
    
    Do you want to gzip the fastq files?
    If your system is short of disk space, select YES. Gzip will save approximate 2/3 of the space required
    For maximum VFS performance, select NO
    NO
    Will let the fastq(s)un-compressed
    Validating fastq file: Sample1_F.fastq OK
    Validating fastq file: Sample1_R.fastq OK
    Converting Sample1_F.fastq to Sample1_F.vfs_in.fq
    Converting Sample1_R.fastq to Sample1_R.vfs_in.fq

    Comment

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