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:
Any help troubleshooting this error is greatly appreciated, thank you!
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.
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