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Molmed / checkQC

CheckQC inspects the content of an Illumina runfolder and determines if it passes a set of quality criteria
http://checkqc.readthedocs.io/
GNU General Public License v3.0
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Issues for NovaSeq SP with interop==1.1.9 #88

Closed matrulda closed 4 years ago

matrulda commented 4 years ago

It looks like the latest release of interop (1.1.9) does not work for (at least) NovaSeq SP. 


Traceback (most recent call last):
  File "/home/MOLMED/matas618/.conda/envs/checkqc/bin/checkqc", line 11, in <module>
    load_entry_point('checkQC', 'console_scripts', 'checkqc')()
  File "/home/MOLMED/matas618/.conda/envs/checkqc/lib/python3.6/site-packages/click/core.py", line 722, in __call__
    return self.main(*args, **kwargs)
  File "/home/MOLMED/matas618/.conda/envs/checkqc/lib/python3.6/site-packages/click/core.py", line 697, in main
    rv = self.invoke(ctx)
  File "/home/MOLMED/matas618/.conda/envs/checkqc/lib/python3.6/site-packages/click/core.py", line 895, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/home/MOLMED/matas618/.conda/envs/checkqc/lib/python3.6/site-packages/click/core.py", line 535, in invoke
    return callback(*args, **kwargs)
  File "/home/MOLMED/matas618/workspace/checkQC/checkQC/app.py", line 41, in start
    app.run()
  File "/home/MOLMED/matas618/workspace/checkQC/checkQC/app.py", line 104, in run
    reports = self.configure_and_run()
  File "/home/MOLMED/matas618/workspace/checkQC/checkQC/app.py", line 87, in configure_and_run
    reports = qc_engine.run()
  File "/home/MOLMED/matas618/workspace/checkQC/checkQC/qc_engine.py", line 61, in run
    reports = self._compile_reports()
  File "/home/MOLMED/matas618/workspace/checkQC/checkQC/qc_engine.py", line 103, in _compile_reports
    handler_report = handler.report()
  File "/home/MOLMED/matas618/workspace/checkQC/checkQC/handlers/qc_handler.py", line 240, in report
    sorted_errors_and_warnings = sorted(errors_and_warnings, key=lambda x: x.ordering)
  File "/home/MOLMED/matas618/workspace/checkQC/checkQC/handlers/undetermined_percentage_handler.py", line 75, in check_qc
    if self.error() != self.UNKNOWN and percentage_undetermined > compute_threshold(self.error()):
  File "/home/MOLMED/matas618/workspace/checkQC/checkQC/handlers/undetermined_percentage_handler.py", line 66, in compute_threshold
    return value + mean_phix_per_lane[lane_nbr]
KeyError: 2

We might have to update the interop requirements, but this will be further investigated first.

The solution for now is to use interop 1.1.5.