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Old 07-16-2013, 07:28 AM   #1
eligar97
Junior Member
 
Location: Ohio

Join Date: Jul 2013
Posts: 2
Default Viral Alignment- ViralFusionSeq

Hi everyone. I am a high school intern and I am working in aligning viral genomes to RNAseq data. I am very new to bioinformatics, and am still learning how to manage alignment software. I have been using the software ViralFusionSeq to locate viral integration sites. Unfortunately, I am having major technical difficulties. I am constantly getting the same error message when I try to run the sample dataset. I have installed all of the cpan modules and 3rd party software, but I still get this error:

Thread 1 terminated abnormally: main=HASH(0x2b212422a238) at viral.fusion.pl line 621.
Thread 2 terminated abnormally: main=HASH(0x2b212822a240) at viral.fusion.pl line 622.
Use of uninitialized value $ReturnData[0] in join or string at viral.fusion.pl
line 624 (#1)
(W uninitialized) An undefined value was used as if it were already
defined. It was interpreted as a "" or a 0, but maybe it was a mistake.
To suppress this warning assign a defined value to your variables.

To help you figure out what was undefined, perl will try to tell you the
name of the variable (if any) that was undefined. In some cases it cannot
do this, so it also tells you what operation you used the undefined value
in. Note, however, that perl optimizes your program and the operation
displayed in the warning may not necessarily appear literally in your
program. For example, "that $foo" is usually optimized into "that "
. $foo, and the warning will refer to the concatenation (.) operator,
even though there is no . in your program.

Use of uninitialized value $ReturnData2[0] in join or string at viral.fusion.pl
line 627 (#1)


Does anyone who has used this software have any ideas as to why I have this error?

Thanks for your help.
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