Error executing process > 'pipeline:process_bams:tag_bams (14)

[Jason-Eigenbrood]

Operating System

Other Linux (please specify below)

Other Linux

Linux 4.18.0-372.32.1.el8_6.x86_64

Workflow Version

v.1.01

Workflow Execution

Command line

EPI2ME Version

No response

CLI command run

nextflow run epi2me-labs/wf-single-cell \ -profile singularity \ -c wf.config \ -params-file nextflow.params.yaml \ -resume

wf.config.txt sRunWorkflow.sh.txt nextflow.params.yaml.txt

Workflow Execution - CLI Execution Profile

custom

What happened?

test.wf.32271319.out.txt test.wf.32271319.err.txt nextflow.log.txt Here are the relevant out files.

Relevant log output

Log outputs are in files above.

Application activity log entry

Used cluster.

Were you able to successfully run the latest version of the workflow with the demo data?

yes

Other demo data information

None.

[nrhorner]

Hi @Jason-Eigenbrood I believe this is a bug that is fixed in v1.0.3. Could you please try this version using

nextflow run epi2me-labs/wf-single-cell -r v1.0.3'

Thanks

[Jason-Eigenbrood]

Hi Neil,

Will do thank you. Should I restart entire workflow or resume?

---

From: Neil Horner @.> Sent: Wednesday, February 14, 2024 8:28:59 AM To: epi2me-labs/wf-single-cell @.> Cc: Jason Eigenbrood @.>; Mention @.> Subject: Re: [epi2me-labs/wf-single-cell] Error executing process > 'pipeline:process_bams:tag_bams (14) (Issue #76)

Hi @Jason-Eigenbroodhttps://github.com/Jason-Eigenbrood I believe this is a bug that is fixed in v1.0.3. Could you please try this version using

nextflow run epi2me-labs/wf-single-cell -r v1.0.3'

Thanks

— Reply to this email directly, view it on GitHubhttps://github.com/epi2me-labs/wf-single-cell/issues/76#issuecomment-1943283482, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BBKHAQAPQZB6WORGB5FXBW3YTRYUVAVCNFSM6AAAAABDGQABBWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSNBTGI4DGNBYGI. You are receiving this because you were mentioned.Message ID: @.***>

[nrhorner]

Hi Jason,

You can give-resume a try but I'm unsure at which stage the workflow will resume at.

[Jason-Eigenbrood]

Hi Neil,

-resume did not work but once I restarted the workflow everything ran great until pipeline:process_bams:stringtie, which got stuck at 95%. I see same issue on another thread so I will also comment there!

[nrhorner]

Hi @Jason-Eigenbrood thanks for the update. I will close this ticket then