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runNanoSeq.py var and post by NanoSeq 3.5.4 fails for some of samples that NanoSeq 3.5.1 run successfully. #85

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monagai opened this issue Jan 23, 2024 · 2 comments

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@monagai
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monagai commented Jan 23, 2024

I'm trying to use NanoSeq for rat and mouse samples.
runNanoSeq.py var and post by NanoSeq 3.5.4 fails for samples that NanoSeq 3.5.1 run successfully.
It is only a report because I have not clarified the condition of NanoSeq 3.5.4 error.

  1. runNanoSeq.py var fails with part of fragments in 60 threads. (2 samples)

  2. runNanoSeq.py post fails (several samples)

...
Executing: variantcaller.R ./tmpNanoSeq/post/ > ./tmpNanoSeq/post/summary.txt


Executing: nanoseq_results_plotter.R ./tmpNanoSeq/post ./tmpNanoSeq/post/results 

Traceback (most recent call last):
  File "/opt/wtsi-cgp/bin/runNanoSeq.py", line 1156, in <module>
    runCommand(cmd)
  File "/opt/wtsi-cgp/bin/runNanoSeq.py", line 430, in runCommand
    raise ValueError(error)
ValueError: Error in base::table(...) : nothing to tabulate
Calls: table ... standardGeneric -> eval -> eval -> eval -> table -> <Anonymous>
Execution halted
@fa8sanger
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fa8sanger commented Jan 23, 2024 via email

@monagai
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monagai commented Jan 24, 2024

I really thank you for your quick comment.

  1. runNanoSeq.py var fails with part of fragments in 60 threads. (2 samples)

Sorry, this happened for only 1 samples.
There is no error log from var command about it. post command reports error.

I undestand that these error depend on samples.
This issue is a report.
NanoSeq 3.5.4 seems a little bit unstable compared to 3.5.1...

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