cellranger_workflow error

[Matthew Hill]

Hello,

I keep getting error when running cellranger_workflow for scATAC-seq. It pops up the following: 

"Job cellranger_atac_count.run_cellranger_atac_count:NA:1 exited with return code 1 which has not been declared as a valid return code. See 'continueOnReturnCode' runtime attribute for more details."

And when I check the stdout file it says:

[error] The supplied reference path /cromwell_root/genome_dir is not a valid 10x reference on machine 253258f69e51: Reference package has an issue with a required file /cromwell_root/genome_dir/./genes/genes.gtf.gz: Path does not exist Please make sure that you have downloaded the correct 10x reference or generated a custom reference using `mkref`. Cell Ranger ATAC pipelines are compatible with Cell Ranger ATAC 2.0 or Cell Ranger ARC 1.0+ references. Cell Ranger ARC pipelines are compatible with a Cell Ranger ARC 1.0+ reference

I used the exact key word mentioned in the docs for a reference (GRCh38_atac_v1.2.0. And even tried the GRCh38_atac_v1.1.0 but neither worked.

Please let me know what you think. Also, I attached my input csv file just in case that helps. Appreciate your time!

Thanks,

Matt

[Yiming Yang]

Hi Matt,

Sorry for the delay!

This error happened because you used a genome reference built by CellRanger-ATAC v1.2.0, while your job used the default ATAC v2.0.0.

To resolve it, you may do either of the following:

1. Use "GRCh38-2020-A_arc_v2.0.0" reference which was built by CellRanger-ATAC v2.0.0, and use the default ATAC version.

2. Keep your reference as the same, and set "cellranger_atac_version" to "1.2.0" in your workflow page.

In addition, if you use the CellRanger workflow checked out from Dockstore, which is the developing version, you may encounter issues if choosing the second way above, because we haven't updated the docker for CellRanger-ATAC v1.2.0 for the developing version. Otherwise, if you use the workflow checked out from Broad Method Registry, it should be safe for both ways.

Sincerely,

Yiming

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γνῶθι σεαυτόν.

[Matthew Hill]

Hey Yiming,

Thanks! Option 1 worked with Snapshot 28 (not 26). 

Appreciate your help!

Take care,

Matt

[Yiming Yang]

Hi Matt,

Glad that it works for you.

Yes, CellRanger workflow snapshot 26 no longer works on Terra after Terra updated the version of their underlying workflow execution engine (which is Cromwell). So please stick with snapshot 28.

Sincerely,

Yiming

To view this discussion on the web visit https://groups.google.com/d/msgid/cumulus-support/e733db67-b876-4a9d-9f80-c282408e81c5n%40googlegroups.com.