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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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KILLED error when running ximmer through docker #34

Open emyli14 opened 4 years ago

emyli14 commented 4 years ago

Hi, I' trying to run ximmer (analysis only) using docker and a minimal configuration file and am encountering the following error regardless of the bam files and target regions used. Any help resolving this would be greatly appreciated. Thanks!

Code:

docker run  \
  -v /<file path>/reference_files:/reference \
  -e XIMMER_REF=/reference/hg19_reordered.fasta \
  -v /<file path>/:/data \
    ximmer ximmer \
  -c /data/Genetics/CNVs/ximmer/minimal_configuration_file \
  -v \
  -o /data/Genetics/CNVs/ximmer/output_test \
  -nosim

Config file:

bam_files=[
"data/Exome_sequencing_files/BAM_files/2014/sample1.bam",
"data/Exome_sequencing_files/BAM_files/2014/sample2.bam",
"data/Exome_sequencing_files/BAM_files/2014/sample3.bam",
"data/Exome_sequencing_files/BAM_files/2014/sample4.bam"
]
target_regions="data/Genetics/CNVs/xhmm/exome_target_files/AgilentSureSelect_v4_Covered.bed"
concurrency=20
callers {
    xhmm {}
    exomedepth {}
}

Output:

Using reference sequence: /reference/hg19_reordered.fasta

  | |/ /(_)___ ___  ____ ___  ___  _____
  |   // / __ `__ \/ __ `__ \/ _ \/ ___/
 /   |/ / / / / / / / / / / /  __/ /    
/_/|_/_/_/ /_/ /_/_/ /_/ /_/\___/_/     

Install directory detected as: /usr/local/ximmer

Reference has been set to /reference/hg19_reordered.fasta
**************************************************

#     #  ###  #     #  #     #  #######  ######   
 #   #    #   ##   ##  ##   ##  #        #     #  
  # #     #   # # # #  # # # #  #        #     #  
   #      #   #  #  #  #  #  #  #####    ######   
  # #     #   #     #  #     #  #        #   #    
 #   #    #   #     #  #     #  #        #    #   
#     #  ###  #     #  #     #  #######  #     #  

**************************************************
Configured verbose logging
Ximmer  [1] INFO    |10:01:29 Configured verbose logging 
Ximmer  [1] INFO    |10:01:29 Simulation disabled. 
Ximmer  [1] INFO    |10:01:30 No run directory configured: run directory = run 
Ximmer  [1] INFO    |10:01:30 Configuration validated! 
SimulationRun   [1] INFO    |10:02:32 Resolved BAM files for run 1: [data/Exome_sequencing_files/BAM_files/2014/mq1-100830.remdup.uniqMap.SS4.bam, data/Exome_sequencing_files/BAM_files/2014/mq1-MQ130002.remdup.uniqMap.SS4.bam, data/Exome_sequencing_files/BAM_files/2014/mq1-MQ130073.remdup.uniqMap.SS4.bam, data/Exome_sequencing_files/BAM_files/2014/mq1-MQ140002.remdup.uniqMap.SS4.bam] 
SimulationRun   [1] INFO    |10:02:32 Processing BAM Files: 
data/Exome_sequencing_files/BAM_files/2014/mq1-100830.remdup.uniqMap.SS4.bam
data/Exome_sequencing_files/BAM_files/2014/mq1-MQ130002.remdup.uniqMap.SS4.bam
data/Exome_sequencing_files/BAM_files/2014/mq1-MQ130073.remdup.uniqMap.SS4.bam
data/Exome_sequencing_files/BAM_files/2014/mq1-MQ140002.remdup.uniqMap.SS4.bam 
Ximmer  [1] INFO    |10:02:33 Simulation disabled: analysis will be performed directly from source files 
Ximmer  [1] INFO    |10:02:33 No true positive CNVs configured for run 1 
Ximmer  [1] INFO    |10:02:33 Analysis has caller configuration: xhmm 
Ximmer  [1] INFO    |10:02:33 Anaysis keys are: [] 
Ximmer  [1] INFO    |10:02:33 Write file /data/Genetics/CNVs/ximmer/output_test/run1/analysis/xhmm.default.params.txt with caller parameters 
Ximmer  [1] INFO    |10:02:33 Analysis has caller configuration: exomedepth 
Ximmer  [1] INFO    |10:02:33 Anaysis keys are: [] 
Ximmer  [1] INFO    |10:02:33 Write file /data/Genetics/CNVs/ximmer/output_test/run1/analysis/ed.default.params.txt with caller parameters 
Ximmer  [1] INFO    |10:02:33 Executing Bpipe command: bash /usr/local/ximmer/eval/bpipe run -n 20 -p TOOLS=/usr/local/ximmer/eval/pipeline/tools -p DGV_CNVS=/usr/local/ximmer/cache/dgvMerged.txt.gz -p XIMMER_SRC=/usr/local/ximmer/src/main/groovy -p callers=xhmm,ed -p refgene=/usr/local/ximmer/cache/refGene.txt.gz -p simulation=false -p batches=analysis -p target_bed=/data/Genetics/CNVs/xhmm/exome_target_files/AgilentSureSelect_v4_Covered.bed -p sample_id_mask="" -p imgpath=run1/#batch#/report/ /usr/local/ximmer/eval/pipeline/exome_cnv_pipeline.groovy /data/Exome_sequencing_files/BAM_files/2014/mq1-100830.remdup.uniqMap.SS4.bam /data/Exome_sequencing_files/BAM_files/2014/mq1-MQ130002.remdup.uniqMap.SS4.bam /data/Exome_sequencing_files/BAM_files/2014/mq1-MQ130073.remdup.uniqMap.SS4.bam /data/Exome_sequencing_files/BAM_files/2014/mq1-MQ140002.remdup.uniqMap.SS4.bam 
/usr/local/ximmer/bin/ximmer: line 42:    23 Killed                  $BASE/eval/pipeline/tools/groovy/2.4.6/bin/groovy -cp $BASE/src/main/groovy:$BASE/src/main/resources:$BASE/eval/pipeline/tools/groovy-ngs-utils/1.0.9/groovy-ngs-utils.jar $BASE/src/main/groovy/Ximmer.groovy $*