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ssadedin / ximmer

Ximmer is a system for CNV calling on exome and targeted genomic sequencing
http://ssadedin.github.io/ximmer/
GNU Lesser General Public License v2.1
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java.lang.RuntimeException: After comparing the samples specified in the 'samples' block with the available BAM files, no samples remain to analyse #30

Closed hkrzystek closed 5 years ago

hkrzystek commented 5 years ago

Hello @ssadedin ,

I am running into issues with running Ximmer as a native installation on our research cluster computer. This is the current error message I receive.

WARNING: BAM index file /proj/berglab/projects/ncg2-bams/NCG-20091-00.BH7F7YBBXY_L004_AGCCATGC.bai is older than BAM /proj/berglab/projects/ncg2-bams/NCG-20091-00.BH7F7YBBXY_L004_AGCCATGC.bam
WARNING: BAM index file /proj/berglab/projects/ncg2-bams/NCG-20091-00.BH7F7YBBXY_L004_AGCCATGC.bai is older than BAM /proj/berglab/projects/ncg2-bams/NCG-20091-00.BH7F7YBBXY_L004_AGCCATGC.bam
WARNING: BAM index file /proj/berglab/projects/ncg2-bams/NCG-20108-00.BH7F7YBBXY_L004_GTACGCAA.bai is older than BAM /proj/berglab/projects/ncg2-bams/NCG-20108-00.BH7F7YBBXY_L004_GTACGCAA.bam
WARNING: BAM index file /proj/berglab/projects/ncg2-bams/NCG-20108-00.BH7F7YBBXY_L004_GTACGCAA.bai is older than BAM /proj/berglab/projects/ncg2-bams/NCG-20108-00.BH7F7YBBXY_L004_GTACGCAA.bam
WARNING: BAM index file /proj/berglab/projects/ncg2-bams/NCG-20112-00.BH7F7YBBXY_L004_ATTGAGGA.bai is older than BAM /proj/berglab/projects/ncg2-bams/NCG-20112-00.BH7F7YBBXY_L004_ATTGAGGA.bam
WARNING: BAM index file /proj/berglab/projects/ncg2-bams/NCG-20112-00.BH7F7YBBXY_L004_ATTGAGGA.bai is older than BAM /proj/berglab/projects/ncg2-bams/NCG-20112-00.BH7F7YBBXY_L004_ATTGAGGA.bam
WARNING: BAM index file /proj/berglab/projects/ncg2-bams/NCG-20118-00.BH7F7YBBXY_L004_GTCGTAGA.bai is older than BAM /proj/berglab/projects/ncg2-bams/NCG-20118-00.BH7F7YBBXY_L004_GTCGTAGA.bam
WARNING: BAM index file /proj/berglab/projects/ncg2-bams/NCG-20118-00.BH7F7YBBXY_L004_GTCGTAGA.bai is older than BAM /proj/berglab/projects/ncg2-bams/NCG-20118-00.BH7F7YBBXY_L004_GTCGTAGA.bam
WARNING: BAM index file /proj/berglab/projects/ncg2-bams/NCG-20136-00.BH7F7YBBXY_L004_ACAGCAGA.bai is older than BAM /proj/berglab/projects/ncg2-bams/NCG-20136-00.BH7F7YBBXY_L004_ACAGCAGA.bam
WARNING: BAM index file /proj/berglab/projects/ncg2-bams/NCG-20136-00.BH7F7YBBXY_L004_ACAGCAGA.bai is older than BAM /proj/berglab/projects/ncg2-bams/NCG-20136-00.BH7F7YBBXY_L004_ACAGCAGA.bam
WARNING: BAM index file /proj/berglab/projects/ncg2-bams/NCG-20119-00.BH7F7YBBXY_L004_GTGTTCTA.bai is older than BAM /proj/berglab/projects/ncg2-bams/NCG-20119-00.BH7F7YBBXY_L004_GTGTTCTA.bam
WARNING: BAM index file /proj/berglab/projects/ncg2-bams/NCG-20119-00.BH7F7YBBXY_L004_GTGTTCTA.bai is older than BAM /proj/berglab/projects/ncg2-bams/NCG-20119-00.BH7F7YBBXY_L004_GTGTTCTA.bam
WARNING: BAM index file /proj/berglab/projects/ncg2-bams/NCG-20133-00.BH7F7YBBXY_L004_AGCACCTC.bai is older than BAM /proj/berglab/projects/ncg2-bams/NCG-20133-00.BH7F7YBBXY_L004_AGCACCTC.bam
WARNING: BAM index file /proj/berglab/projects/ncg2-bams/NCG-20133-00.BH7F7YBBXY_L004_AGCACCTC.bai is older than BAM /proj/berglab/projects/ncg2-bams/NCG-20133-00.BH7F7YBBXY_L004_AGCACCTC.bam
SimulationRun   [1]     INFO    |12:50:50 Intersecting 14 bam files with 14 samples configured for run 1 
Caught: java.lang.RuntimeException: After comparing the samples specified in the 'samples' block with the available BAM files, no samples remain to analyse. Please check that sample ids are consistent with those in the BAM files supplied
java.lang.RuntimeException: After comparing the samples specified in the 'samples' block with the available BAM files, no samples remain to analyse. Please check that sample ids are consistent with those in the BAM files supplied
        at SimulationRun.resolveBamFiles(SimulationRun.groovy:63)
        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)

I'm not sure what "no samples remain to analyse" means. I entered in 14 samples names in my config.groovy file for the 14 bam files I have, and the sample names match. I can't determine what the issue is.

Thank you, Halina