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Old 08-25-2014, 06:49 AM   #1
RobJackson28
Junior Member
 
Location: Thunder Bay, Ontario, Canada

Join Date: Aug 2014
Posts: 2
Question 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!
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Old 08-25-2014, 11:27 AM   #2
RobJackson28
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Location: Thunder Bay, Ontario, Canada

Join Date: Aug 2014
Posts: 2
Default

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
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