Closed dburkhardt closed 1 year ago
Scott recently fixed a bug like this on the method outputs in the past couple of days (#209). There was some inconsistency in how method outputs were interpreted. Might just be a further fix of the same type needed there?
Well good news is this is currently passing on @olgabot's PR: https://github.com/singlecellopenproblems/SingleCellOpenProblems/actions/runs/684539619
I think I'll pull that one into master and we can address the caching later. Right now, her run-benchmarks job took 1hr40min which is only marginally longer than with caching
results.zip
So this issue is coming up with the
docker-jupyter-kernels
branch. Not sure if it will propagate for other folks. Right now, as of https://github.com/singlecellopenproblems/SingleCellOpenProblems/commit/2787beb4bf76a9665980f97539faf011e5f5b0f1, theparse_nextflow.py
script is failing. This script parses the output of theresults
directory and prepares JSON files for the website. Because we're not updating the website during the jam, this isn't an essential issue and my plan is to bypass.The error is:
The problem is that some of the entries in
results/pipeline_info/execution_trace.txt
don't record a0
exit status and instead show up like this:This means that these entries are filtered out by https://github.com/singlecellopenproblems/SingleCellOpenProblems/blob/2787beb4bf76a9665980f97539faf011e5f5b0f1/workflow/parse_nextflow.py#L62
and when
parse_metric_results(results)
looks for the corresponding method runtime information, it's missing.Now it's not clear why this line in
execution_trace.txt
doesn't have the correct information about the run info. My guess is this is a bug in the way Nextflow is caching the run. There are a total of threerun_method
entries (out of 55) that are missing info:However, there are several more that are missing as well. I'm uploading the
results
directory from that run.It's important to note that the metrics computed on these runs are also in the
results/metrics
directory from the run, suggesting that in fact therun_method
process completed successfully.In summary, the
execution_trace.txt
is missing about runs that ostensibly completed successfully.Relevant files results.zip