Re: [svtoolkit-help] Mismatched read pair records

[Bob H. <han...@br...>]

It looks like you included bam 100.bam twice in the input list.
This is then (I suspect) detected as two read pairs with the same read 
name, which is not supported.
-Bob

On 11/1/12 8:30 PM, yw wrote:
> Hi there,
> I have been tried to run Genome-STRIP with my data these days. I believe
> I have successfully installed the software. The install test was okay.
> And I tried with 30 BAM files and got the results. However, When I came
> to more BAM files, something went wrong.
> I can't figure out what is wrong with my BAM files. Anyone has any
> suggestions? Thx.
>
> Here is the error message:
>
> java -Xmx4g
> -Djava.io.tmpdir=/home/wbxie/software/svtoolkit/installtest/all_tmpdir
> -cp
> /home/wbxie/software/svtoolkit/lib/SVToolkit.jar:/home/wbxie/software/svtoolkit/lib/gatk/GenomeAnalysisTK.jar:/home/wbxie/software/svtoolkit/lib/gatk/Queue.jar
> -verbose:gc org.broadinstitute.sv.main.SVDiscovery -T SVDiscovery -R
> /home/wbxie/software/svtoolkit/installtest/data/rice_all_genomes_v7.fasta -I
> /home/wbxie/wild_rice/bwa_map/100.bam -I
> /home/wbxie/wild_rice/bwa_map/100.bam -I
> /home/wbxie/wild_rice/bwa_map/101.bam -I
>
[snip]