gvcf_manifest issues

[meghatron21]

Hi.

I have been trying to use GLnexus with a list of gvcfs. I have tried all different ways to point to the vcfs with a vcf on each line and I keep getting the following error when running via DNAnexusy.

2021-01-07 18:08:50 GLnexus STDERR ResolutionError: Unable to resolve "DRR132536.cancer.vcf" to a data object or folder name in '/' 2021-01-07 18:08:50 GLnexus STDERR ResolutionError: Unable to resolve "DRR131656.cancer.vcf" to a data object or folder name in '/'

• GLnexus (failed) job-Fzqk8jj06F16vzZgFXzygy7b mpagadala 2021-01-07 18:08:19 (runtime 0:00:25) AppInternalError: Please consult the job log; the job's reported error could not be parsed from the file job_error.json

This is the command: dx run ../tools/GLnexus -i gvcf_manifest=cancer.list.txt -i output_name=PRJDB6952.cancer -i bed_ranges_to_genotype=../hg38.chromsizes

Thanks!

[mlin]

Hi, for the DNAnexus applet each line of the manifest is supposed to be the DNAnexus file immutable id (file-xxxx), not the file name. In addition to being immutable this speeds things up because it does not have to make API calls to resolve names to the file id's to download. Hope this helps

[meghatron21]

Thanks for the response. When I run the manifest with the file ids, it says it cannot find the corresponding vcf.gz.tbi. Do I have to include a separate line for the vcf.gz.tbi?

[mlin]

Sorry i missed this. I'm not sure where that message would be coming from as GLnexus does not consume tabix indexes. Can you paste the exact invocation and error messages?