wf-human-variation produces TypeError: unsupported operand type(s) for /: 'NoneType' and 'NoneType' during data normalisation.

[vmkalbskopf]

While running the wf-human-variation pipeline, ont-spectre produced an error implying that either the vcf file and reference files were empty or that the script did not load them correctly. I have attached the relevant files (but only a small sample of the vcf file as it is sensitive human data). The reference is the standard GRCh38.p14 file, and I checked it manually myself. Should this bug be filed on the wf-human-variation repo instead?

spectre::INFO> Spectre version: 0.2.2
spectre::INFO> Spectre enabled
spectre::INFO> Extraction of metadata is activated
spectre::INFO> Extracting metadata from resource: data/grch38_metadata.mdr
spectre::INFO> Using blacklist from resource: data/grch38_blacklist_0.3.bed
spectre::INFO> Spectre calculating for: work/6a/95c8185412eee91e54c8bc26ea21af/readstats and bin size: 1000
spectre::INFO> Data normalization and outlier removal (right tail)
spectre::INFO> Parsing VCF to AF freqs file
spectre::INFO> Thresholds for coverage, lower (Q10.0): None, upper(Q90.0): None
multiprocessing.pool.RemoteTraceback: 
"""
Traceback (most recent call last):
  File "/opt/custflow/epi2meuser/conda/lib/python3.8/multiprocessing/pool.py", line 125, in worker
    result = (True, func(*args, **kwds))
  File "/opt/custflow/epi2meuser/conda/lib/python3.8/multiprocessing/pool.py", line 48, in mapstar
    return list(map(*args))
  File "/opt/custflow/epi2meuser/conda/lib/python3.8/site-packages/spectre/main.py", line 120, in outside_spectre_worker
    worker.cnv_call()
  File "/opt/custflow/epi2meuser/conda/lib/python3.8/site-packages/spectre/spectreCNV.py", line 101, in cnv_call
    self.cnv_analysis.data_normalization()
  File "/opt/custflow/epi2meuser/conda/lib/python3.8/site-packages/spectre/analysis/analysis.py", line 172, in data_normalization
    self.lower_2n_threshold = coverage_lower_threshold / genome_median * self.ploidy
TypeError: unsupported operand type(s) for /: 'NoneType' and 'NoneType'
"""

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/opt/custflow/epi2meuser/conda/bin/spectre", line 10, in <module>
    sys.exit(run_main())
  File "/opt/custflow/epi2meuser/conda/lib/python3.8/site-packages/spectre/main.py", line 506, in run_main
    spectre_run.spectre_exe()
  File "/opt/custflow/epi2meuser/conda/lib/python3.8/site-packages/spectre/main.py", line 274, in spectre_exe
    results = pool.map(outside_spectre_worker, tuple(spectre_instructions))
  File "/opt/custflow/epi2meuser/conda/lib/python3.8/multiprocessing/pool.py", line 364, in map
    return self._map_async(func, iterable, mapstar, chunksize).get()
  File "/opt/custflow/epi2meuser/conda/lib/python3.8/multiprocessing/pool.py", line 771, in get
    raise self._value
TypeError: unsupported operand type(s) for /: 'NoneType' and 'NoneType'

B_22064.thresholds.bed.txt

800_lines.vcf.txt

B_22064.regions.filt.bed.txt

B_22064.mosdepth.global.dist.txt B_22064.mosdepth.summary.txt

[snurk]

Dear @vmkalbskopf, thank you very much for the bug report! While we are looking into it, can you please see if discussion in https://github.com/epi2me-labs/wf-human-variation/issues/198 is relevant, I think this was the only time we saw this error message before.

[vmkalbskopf]

From what I can see in that bug report, spectre should not be used when the sequencing data was generated using adaptive sampling. However, I am using whole genome sequencing, so I don't think it is relevant. But that is an interesting coincidence...

I am going to try running QDNAseq in the meantime.