# HaplotypeCallerSpark

**URL:** <https://cwl.discourse.group/t/haplotypecallerspark/227>\
**Category:** CWL Questions\
**Created:** [November 5, 2020, 7:28am UTC](https://cwl.discourse.group/t/haplotypecallerspark/227 "2020-11-05T07:28:07Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![Ambarish\_Kumar](https://yyz2.discourse-cdn.com/free1/user_avatar/cwl.discourse.group/ambarish_kumar/32/72_2.png) [@Ambarish\_Kumar](https://cwl.discourse.group/u/Ambarish_Kumar)\
**Post date:** [November 5, 2020, 7:28am UTC](https://cwl.discourse.group/t/haplotypecallerspark/227/1 "2020-11-05T07:28:07Z")

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I am getting error while running CWL tool for HaplotypecallerSpark. Error is as follows.

‘’’  
ERROR [job HaplotypeCallerSparkNew.cwl] Job error:  
(“Error collecting output for parameter ‘rawVCF’:\nHaplotypeCallerSparkNew.cwl:37:5: Did not find output file with glob pattern: ‘[‘en.vcf’]’”, {})

‘’’

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**Author:** ![mrc](https://yyz2.discourse-cdn.com/free1/user_avatar/cwl.discourse.group/mrc/32/3_2.png) [@mrc](https://cwl.discourse.group/u/mrc)\
**Post date:** [November 5, 2020, 7:52am UTC](https://cwl.discourse.group/t/haplotypecallerspark/227/2 "2020-11-05T07:52:53Z")

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Hello @Ambarish_Kumar. Can you link or paste in the source for `HaplotypeCallerSparkNew.cwl` and how you are running it? It won’t be possible for anyone to assist you without that. Thanks!

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<div class="post-metadata">

**Author:** ![Ambarish\_Kumar](https://yyz2.discourse-cdn.com/free1/user_avatar/cwl.discourse.group/ambarish_kumar/32/72_2.png) [@Ambarish\_Kumar](https://cwl.discourse.group/u/Ambarish_Kumar)\
**Post date:** [November 5, 2020, 9:02am UTC](https://cwl.discourse.group/t/haplotypecallerspark/227/3 "2020-11-05T09:02:28Z")

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This is the web-link for the tool.

> <https://github.com/ambarishK/bio-cwl-tools/blob/530e671c113e91fe6b9114eda32103bb980450c7/HaplotypeCallerSparkNew.cwl>

I am running it over command-line.

‘’’  
sudo cwltool HaplotypeCallerSparkNew.cwl --inputBAM ebolamutantmarkdup.bam --Reference2bitGenome ebola1.2bit --RefIndex ebola.fasta.fai --sampleName eb --RefDict ebola.dict --BAMindex ebola.bam.bai --output\_filename en.vcf

‘’’  
Input files are contained into following sub-directory.

‘’’

> **[ambarishK/bio-cwl-tools](https://github.com/ambarishK/bio-cwl-tools/tree/release/testdatataset)**
>
> Contribute to ambarishK/bio-cwl-tools development by creating an account on GitHub.

  
‘’’

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<div class="post-metadata">

**Author:** ![Ambarish\_Kumar](https://yyz2.discourse-cdn.com/free1/user_avatar/cwl.discourse.group/ambarish_kumar/32/72_2.png) [@Ambarish\_Kumar](https://cwl.discourse.group/u/Ambarish_Kumar)\
**Post date:** [November 5, 2020, 2:50pm UTC](https://cwl.discourse.group/t/haplotypecallerspark/227/4 "2020-11-05T14:50:36Z")

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I am trying with different outputbinding parameters but error persists.

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**Author:** ![alexiswl](https://yyz2.discourse-cdn.com/free1/user_avatar/cwl.discourse.group/alexiswl/32/93_2.png) [@alexiswl](https://cwl.discourse.group/u/alexiswl)\
**Post date:** [November 11, 2020, 4:45am UTC](https://cwl.discourse.group/t/haplotypecallerspark/227/5 "2020-11-11T04:45:41Z")

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I don’t think this command is running as you expect it:

```auto
arguments:
- valueFrom: |-
    gatk HaplotypeCallerSpark -R $(inputs.Reference2bitGenome.path) -I $(inputs.inputBAM.path) -O $(inputs.output_filename)
  shellQuote: false

```

Will actually run as “gatk HaplotypeCallerSpark -R …” rather than “gatk” “HaplotypeCallerSpark” “-R” …

I would consider using the ‘inputBinding’ for each of your inputs and a ‘baseCommand’ set to `['gatk', 'HaplotypeCallerSpark']`

For the reference, you have put it in as a listing (can you justify why this is necessary), but have specified the `.path` attribute. If you wish to reference the file that you have listing in the working directory, you should use the `.basename` attribute instead.

Alexis