A problematic sample crashed diagnostic Ion mining
Closed this issue · 2 comments
Hi there,
I was running Diagnostic ion mining workflow that finished with the following message:
Identifying candidate ions
Building feature histograms
Exception in thread "main" java.lang.NullPointerException
at edu.umich.andykong.ptmshepherd.diagnosticmining.DiagnosticPeakPicker.process(DiagnosticPeakPicker.java:260)
at edu.umich.andykong.ptmshepherd.PTMShepherd.main(PTMShepherd.java:637)
Testing histogram peaks for significance
After this, the processor essentially is not engaged (based on the Task Manager) and after 15 min or so of waiting, I've aborted further execution. Am I not patient enough or is it an actual bug?
I'm using an 18-core workstation with 128 GB RAM and Windows OS.
Log file:
log_2024-05-22_16-31-50.zip
Hi,
No, nothing wrong on your end. It looks like it just hung when it crashed there.
Can you upload the peaksummary.annotated.tsv for me?
Ah, I think I see what the issue is.
WT_plus_1 seems to be a problematic sample. It has no PSMs. I think if you remove that it should run.
Same issue as #1418