#!/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
Here is it input file.
ReferenceGenome:
class: File
path: /home/ngsap2/NormalizeFasta.fasta
ReferenceGenomeDict:
class: File
path: /home/ngsap2/NormalizeFasta.dict
sampleName: test
Sir, FindBadGenomicKmers.cwl is generating error. Please debug it.
Error is as follows.
[May 29, 2020 7:51:35 AM GMT] org.broadinstitute.hellbender.tools.spark.sv.evidence.FindBadGenomicKmersSpark done. Elapsed time: 0.12 minutes.
Runtime.totalMemory()=412090368
***********************************************************************
A USER ERROR has occurred: Fasta dict file for reference /MFmpnF/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.
20/05/29 07:51:35 INFO ShutdownHookManager: Shutdown hook called
20/05/29 07:51:35 INFO ShutdownHookManager: Deleting directory /tmp/spark-0f863957-1caf-4a4d-9015-1d2cd153a345
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 /MFmpnF/NormalizeFasta.fasta -O test.txt
INFO [job FindBadGenomicKmers.cwl] Max memory used: 268MiB
ERROR [job FindBadGenomicKmers.cwl] Job error:
("Error collecting output for parameter 'kmers_to_ignore':\nFindBadGenomicKmers.cwl:45:5: Did not find output file with glob pattern: '['test.txt']'", {})
WARNING [job FindBadGenomicKmers.cwl] completed permanentFail
{}
WARNING Final process status is permanentFail