Error with GASV.jar: Can't handle file with 4 columns

[GoogleCodeExporter]

Hi,

I am trying to run GASVPro on DNA-Seq data from a targeted gene panel.

It looks like I can run the first step successfully:

java -jar /opt/GASVPro-1.2/bin/BAMToGASV.jar AGTGGT.filtered.sort.bam

The problem is that I can't successfully run the GASV.jar function with the 
following command:

java -jar /opt/GASVPro-1.2/bin/GASV.jar AGTGGT.filtered.sort.bam.gasv.in

I have tried running BAMToGASV both with and without the additional "-GASVPRO 
True" setting.  Either way, I get the following error message:

ReadInput.java: Error parsing line:
/isi-dcnl/user_data/sneuhausen/Seq/130220/CW_Analysis/GASVPro/Standard_Output/AG
TGGT.filtered.sort.bam_all.deletion     PR      62      9795
        ...unrecognized file format: Can't handle file with 4 columns!
Exception in thread "main" java.lang.NullPointerException
        at gasv.main.ReadInput.readWindowFromSingleFile(Unknown Source)
        at gasv.main.ClusterESP.clusterESP(Unknown Source)
        at gasv.main.GASVMain.main(Unknown Source)

I have also attached a copy of the input file for GASV.jar (which is the same 
in both cases.

I am running the scripts with GASVPro-1.2 on a Linux server.

Can you please help me identify the problem causing this error?

Thanks,
Charles

Original issue reported on code.google.com by cwarde...@gmail.com on 24 Feb 2014 at 7:36

Attachments:

• AGTGGT.filtered.sort.bam.gasv.in

[GoogleCodeExporter]

Thanks for your interest in our software. 

When you run GASV with the formatted output file from BAMToGASV, the *gasv.in 
file, you should use the --batch flag as below.

 java -jar gasv/bin/GASV.jar --batch <YourFile>.gasv.in

If you haven't already take a look at the QuickStart guide (Section 2) in our 
GASV Documentation. We illustrate how to use each part of our pipeline on an 
Example.bam file which you can also download from our google code site.

Let me know if this helps and if you have any other questions about our 
software.

Original comment by sora...@gmail.com on 27 Feb 2014 at 2:12

[GoogleCodeExporter]

Original comment by sora...@gmail.com on 27 Feb 2014 at 2:19

• Changed state: Verified

[GoogleCodeExporter]

Ok, great - this fixed the current problem.

Best,
Charles

Original comment by cwarde...@gmail.com on 3 Mar 2014 at 7:19