Sir,
I am getting error while running newly build CWL tool for BadGenomicsKmers.
CWL tools is below.
#!/usr/bin/env cwl-runner
# This tool description was generated automatically by wdl2cwl ver. 0.2
class: CommandLineTool
cwlVersion: v1.0
requirements:
- class: ShellCommandRequirement
- class: InlineJavascriptRequirement
- class: DockerRequirement
dockerPull: quay.io/biocontainers/gatk4:4.1.6.0--py38_0
- class: InitialWorkDirRequirement
listing:
- $(inputs.ReferenceGenome)
inputs:
- id: ReferenceGenome
type: File
- id: ReferenceGenomeDict
type: File
- id: sampleName
type: string
outputs:
- id: kmers_to_ignore
type: File
outputBinding:
glob: $(inputs.sampleName).txt
baseCommand: []
arguments:
- valueFrom: |-
gatk FindBadGenomicKmersSpark -R $(inputs.ReferenceGenome.path) -O $(inputs.sampleName).txt
shellQuote: false
Generated error is as follows.
10:00:10.659 INFO FindBadGenomicKmersSpark - Shutting down engine
[May 28, 2020 10:00:10 AM GMT] org.broadinstitute.hellbender.tools.spark.sv.evidence.FindBadGenomicKmersSpark done. Elapsed time: 0.22 minutes.
Runtime.totalMemory()=230686720
***********************************************************************
A USER ERROR has occurred: Fasta dict file for reference /ySLAXq/NormalizeFasta.fasta does not exist. Please see http://gatkforums.broadinstitute.org/discussion/1601/how-can-i-prepare-a-fasta-file-to-use-as-reference for help creating it.
***********************************************************************
Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace.
20/05/28 10:00:10 INFO ShutdownHookManager: Shutdown hook called
20/05/28 10:00:10 INFO ShutdownHookManager: Deleting directory /tmp/spark-0ec24ec5-7519-42d9-a6f7-316529086161
Using GATK jar /usr/local/share/gatk4-4.1.6.0-0/gatk-package-4.1.6.0-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /usr/local/share/gatk4-4.1.6.0-0/gatk-package-4.1.6.0-local.jar FindBadGenomicKmersSpark -R /ySLAXq/NormalizeFasta.fasta -O test.txt
INFO [job FindBadGenomicKmers.cwl] Max memory used: 252MiB
ERROR [job FindBadGenomicKmers.cwl] Job error:
("Error collecting output for parameter 'kmers_to_ignore':\nFindBadGenomicKmers.cwl:44:5: Did not find output file with glob pattern: '['test.txt']'", {})
WARNING [job FindBadGenomicKmers.cwl] completed permanentFail
{}
WARNING Final process status is permanentFail
Although tool requirements are set to access directory containing reference genome fasta file and it’s dictionary file. Tool is unable to access reference genome dictionary file.