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Error executing process > 'pipeline:process_bams:combine_bams_and_tags (1)' #81
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I got the same error, with the same exit error (255) and command error ([ERRO] xopen: no content), and the folder |
I pulled out a few of the many thousand input FASTQ files and the command cleared the step. Seems to be something about input girth? |
I gave |
We've found there's a bug in the version of csvtk thats being used in the workflow (shenwei356/csvtk#259). We've replaced the use of csvtk in our development branch. |
@cjw85 Thanks. I can confirm that the latest prerelease version solves this issue. |
We have not made any updates to the code since this issue was reported. |
You mean the "development branch" is not the prerelease one? Well, then for whatever reason the latest version in prerelease did not stop at that point anymore. |
My apologies, yes the |
I'm not fully following. At the time of encountering the issue, I had 20 symlinked TSVs in the input folder, each 452MB in size. So nothing seems like it was empty. I moved to Singularity and somehow the problem went away, despite me not switching to prerelease. |
We used the same code, but the wf-single-cell software returned the same error. It seems that the problem has not been resolved, and we were using version v1.1.0. Similarly, using the '-profile singularity' option resulted in another error. |
Try I still don't get how me switching to singularity helped, but somehow it did. |
The fox for this issue is now included in V2.0.0. |
Operating System
Other Linux (please specify below)
Other Linux
No response
Workflow Version
v1.1.0
Workflow Execution
Command line
EPI2ME Version
No response
CLI command run
Workflow Execution - CLI Execution Profile
standard (default)
What happened?
I am rerunning a sample that has previously worked fine on older versions of the workflow, most recently
-r prerelease
under v1.0.3 finishing on March 7th. I am encountering an error which I have previously not seen. I checked the git blame and it seems the part of the workflow that is causing the explosion was recently modified.It seems the samtools part of the command runs fine. There is a
tags
folder with 20 symlinked TSVs, each 452MB in size. There is achr_tags
folder but it's empty.Relevant log output
Application activity log entry
No response
Were you able to successfully run the latest version of the workflow with the demo data?
yes
Other demo data information
The text was updated successfully, but these errors were encountered: