Bug (maybe) : terminated with an error exit status (1)

[thanadol-git]

Hi!

I tried to repeat the work I did last summer. It turned out that I always get terminated with an error exit status (1). This error message in our output file. Well, I don't really know what could be the problem to resolve it. Can it be the version of either NextFlow or QuantMS during the time? Please let me know if you have any idea.

I attached the whole output to the file below.

Thanks!

job_output.log

[jpfeuffer]

It could be that we are stricter with SDRF validation now.
I think there might have been some changes in when parameters are taken from the sdrf vs from the workflow parameters.
@ypriverol and @enryH might know more

[jpfeuffer]

You are missing the precursor tolerance specification. Originally we allowed specifying it in the parameters or the SDRF. I don't know what the current rule is. I think it was documented somewhere.

[daichengxin]

Yes, SDRF validation has become more stringent. The precursor mass tolerance should be a valid value, such as 0.05 Da, 20 ppm

ValueError: Cannot read precursor mass tolerance: not available.

[ypriverol]

@daichengxin can we move or reference to this issue from sdrf-pipelines.

[enryH]

I referenced it to a similar issue.

[thanadol-git]

Hi, Problem solved. Thanks a lot.