Downstream SAINTexpress non-zero exit code

Question

Downstream SAINTexpress non-zero exit code

Closed this issue a month ago · 4 comments

- Upload your log file
(If a log file hasn't been generated, go to the 'Run' tab in FragPipe, click 'Export Log', zip the resulting "log_[date_time].txt" file to avoid truncation, then attach the zipped file by drag & drop here.)
log_2024-06-14_10-09-21.zip
Downstream_log_2024-06-14_10_10_45.zip

- Describe the issue or question:

I successfully ran 9 DDA bio-replicates through FragPipe, but when attempting to run downstream SAINTexpress, it failed to finish creating necessary documents because of a "exit code:3". Not sure how to fix this.
Thanks.

Answer 1 · 2024-06-14T14:31:02.000Z

Could you rename your experiment group name to follow SAINT's requirement? I think the control group needs to be named to CONTROL.

@anesvi Do we have a tutorial or document somewhere in GitHub? I only found it in the short course material.

Best,

Fengchao

Answer 2 · 2024-06-14T14:39:04.000Z

I have two types of control groups, do they need to be named differently to discriminate between them?

Answer 3 · 2024-06-14T14:46:56.000Z

I guess one SAINT analysis can only have one control groups? @guoci

Best,

Fengchao

Answer 4 · 2024-06-14T15:23:08.000Z

You are correct. I used CONTROL for my empty vector and used other identifiers for everything else and SAINTexpress worked. Thanks for the help.