ERROR: Sample CREATE_INDEX=true appears in more than one BAM file

[kunstner]

Hi @ssadedin, I'm trying to to run ximmer on 8 bam files following the guidelines from the website. For 6 I know the gender, for 2 the gender is unknown.

Unfortunately, ximmer does not work properly on my samples. I always get the following error message

Configured verbose logging Ximmer [1] INFO |1:52:53 Configured verbose logging Ximmer [1] INFO |1:52:53 Simulation enabled in downsample mode Ximmer [1] INFO |1:52:53 No run directory configured: run directory = run Ximmer [1] INFO |1:52:53 Configuration validated! SimulationRun [1] INFO |1:53:13 Resolved BAM files for run 1: [/Users/axel/Downloads/tmp/90_LIED/bams/SampleA.final.bam, /Users/axel/Downloads/tmp/90_LIED/bams/SampleB.final.bam, /Users/axel/Downloads/tmp/90_LIED/bams/SampleC.final.bam, /Users/axel/Downloads/tmp/90_LIED/bams/SampleD.final.bam, /Users/axel/Downloads/tmp/90_LIED/bams/SampleE.final.bam, /Users/axel/Downloads/tmp/90_LIED/bams/SampleF.final.bam, /Users/axel/Downloads/tmp/90_LIED/bams/SampleW.final.bam, /Users/axel/Downloads/tmp/90_LIED/bams/SampleX.final.bam] SimulationRun [1] INFO |1:53:13 Processing BAM Files: /Users/axel/Downloads/tmp/90_LIED/bams/SampleA.final.bam /Users/axel/Downloads/tmp/90_LIED/bams/SampleB.final.bam /Users/axel/Downloads/tmp/90_LIED/bams/SampleC.final.bam /Users/axel/Downloads/tmp/90_LIED/bams/SampleD.final.bam /Users/axel/Downloads/tmp/90_LIED/bams/SampleE.final.bam /Users/axel/Downloads/tmp/90_LIED/bams/SampleF.final.bam /Users/axel/Downloads/tmp/90_LIED/bams/SampleW.final.bam /Users/axel/Downloads/tmp/90_LIED/bams/SampleX.final.bam Caught: java.lang.IllegalArgumentException: Sample CREATE_INDEX=true appears in more than one BAM file. This program only supports a sample appearing in a single BAM file java.lang.IllegalArgumentException: Sample CREATE_INDEX=true appears in more than one BAM file. This program only supports a sample appearing in a single BAM file at SimulationRun$_addBamFiles_closure1.doCall(SimulationRun.groovy:30) at SimulationRun.addBamFiles(SimulationRun.groovy:23) at SimulationRun$addBamFiles$1.callCurrent(Unknown Source) at SimulationRun.resolveBamFiles(SimulationRun.groovy:52) at SimulationRun$resolveBamFiles$0.call(Unknown Source) at SimulationRun$_configureIntegerRuns_closure6.doCall(SimulationRun.groovy:160) at SimulationRun.configureIntegerRuns(SimulationRun.groovy:140) at SimulationRun.configureRuns(SimulationRun.groovy:74) at SimulationRun$configureRuns.call(Unknown Source) at Ximmer.initialiseRuns(Ximmer.groovy:302) at Ximmer.run(Ximmer.groovy:194) at Ximmer$run.call(Unknown Source) at Ximmer.main(Ximmer.groovy:1279)

To run ximmer, I just use ~/usr/docker/ximmer/bin/ximmer -v -c simulation.groovy -o results .

Interestingly, I'm able to run ximmer on a single sample without any problems.

My bam-files are basically created following GATKs best practice for germline SNP calling. SNPs were called using VarScan2 without any issues.

Do you have any suggestions how to deal with this issue?

Thanks a lot, Axel