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fritzsedlazeck / Spectre

Copy number caller for long read data including SNV utilization
MIT License
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RecursionError: maximum recursion depth exceeded in comparison #24

Open adbeggs opened 6 months ago

adbeggs commented 6 months ago

Hi team

Command used:

spectre CNVCaller --coverage mosdepth/"$A".regions.bed.gz --sample-id $A --output-dir spectre2 --reference ~/beggsa-clinicalnanopore/genomes/grch38/genome.fa --metadata ~/beggsa-clinicalnanopore/genomes/grch38/grch38spectremetadata.mdr --blacklist ~/beggsa-clinicalnanopore/genomes/grch38/grch38_blacklist_spectre.bed --snv clair/merge_output.vcf.gz

Output: 

spectre::2024-05-23 16:25:49,087::INFO::spectre.spectre>  Spectre input: CNVCaller --coverage mosdepth/BRCA19.regions.bed.gz --sample-id BRCA19 --output-dir spectre2 --reference /rds/homes/b/beggsa/beggsa-clinicalnanopore/genomes/grch38/genome.fa --metadata /rds/homes/b/beggsa/beggsa-clinicalnanopore/genomes/grch38/grch38spectremetadata.mdr --blacklist /rds/homes/b/beggsa/beggsa-clinicalnanopore/genomes/grch38/grch38_blacklist_spectre.bed --snv clair/merge_output.vcf.gz
spectre::2024-05-23 16:25:49,088::INFO::spectre.spectre>  Spectre version: 0.2.1
spectre::2024-05-23 16:25:49,088::INFO::spectre.spectre>  Starting spectre
spectre::2024-05-23 16:25:49,088::INFO::spectre.spectre>  Evaluate if a new .mdr file needs to be created
spectre::2024-05-23 16:25:49,118::INFO::spectre.spectre>  Using existing metadata file /rds/homes/b/beggsa/beggsa-clinicalnanopore/genomes/grch38/grch38spectremetadata.mdr
spectre::2024-05-23 16:25:49,207::INFO::spectre.spectreCNV>  Spectre calculating for: mosdepth/BRCA19.regions.bed.gz
spectre::2024-05-23 16:25:49,231::INFO::spectre.spectreCNV>  Analysing CN neutral state from SNV data
spectre::2024-05-23 16:25:49,417::DEBUG::spectre.analysis.snv_analysis>  Starting SNV Copy number state compute ...
spectre::2024-05-23 16:25:49,417::DEBUG::spectre.analysis.snv_analysis>  Het sites count per chromosome
spectre::2024-05-23 16:26:11,222::DEBUG::spectre.analysis.snv_analysis>  chr1   348064  34372   35735   5.61x   49.03% het pass | 9.88% het all
spectre::2024-05-23 16:26:11,224::DEBUG::spectre.analysis.snv_analysis>  chr2   360835  35100   34955   5.03x   50.1% het pass | 9.73% het all
spectre::2024-05-23 16:26:11,224::DEBUG::spectre.analysis.snv_analysis>  chr3   301628  29810   29345   5.0x    50.39% het pass | 9.88% het all
spectre::2024-05-23 16:26:11,224::DEBUG::spectre.analysis.snv_analysis>  chr4   311748  29295   34509   5.74x   45.91% het pass | 9.4% het all
spectre::2024-05-23 16:26:11,224::DEBUG::spectre.analysis.snv_analysis>  chr5   267189  26028   25446   5.31x   50.57% het pass | 9.74% het all
spectre::2024-05-23 16:26:11,224::DEBUG::spectre.analysis.snv_analysis>  chr6   267229  26282   26283   4.84x   50.0% het pass | 9.84% het all
spectre::2024-05-23 16:26:11,224::DEBUG::spectre.analysis.snv_analysis>  chr7   244566  25388   24447   5.03x   50.94% het pass | 10.38% het all
spectre::2024-05-23 16:26:11,224::DEBUG::spectre.analysis.snv_analysis>  chr8   222152  21960   21678   4.93x   50.32% het pass | 9.89% het all
spectre::2024-05-23 16:26:11,224::DEBUG::spectre.analysis.snv_analysis>  chr9   185783  19339   17906   5.21x   51.92% het pass | 10.41% het all
spectre::2024-05-23 16:26:11,224::DEBUG::spectre.analysis.snv_analysis>  chr10  210841  21484   20617   5.78x   51.03% het pass | 10.19% het all
spectre::2024-05-23 16:26:11,224::DEBUG::spectre.analysis.snv_analysis>  chr11  214518  20288   23947   4.91x   45.86% het pass | 9.46% het all
spectre::2024-05-23 16:26:11,224::DEBUG::spectre.analysis.snv_analysis>  chr12  203810  19444   20429   4.89x   48.76% het pass | 9.54% het all
spectre::2024-05-23 16:26:11,224::DEBUG::spectre.analysis.snv_analysis>  chr13  166597  15197   20132   5.5x    43.02% het pass | 9.12% het all
spectre::2024-05-23 16:26:11,224::DEBUG::spectre.analysis.snv_analysis>  chr14  139807  13814   14842   5.15x   48.21% het pass | 9.88% het all
spectre::2024-05-23 16:26:11,224::DEBUG::spectre.analysis.snv_analysis>  chr15  124321  12076   12731   4.95x   48.68% het pass | 9.71% het all
spectre::2024-05-23 16:26:11,224::DEBUG::spectre.analysis.snv_analysis>  chr16  125786  13380   12426   7.2x    51.85% het pass | 10.64% het all
spectre::2024-05-23 16:26:11,224::DEBUG::spectre.analysis.snv_analysis>  chr17  116927  12944   11131   5.76x   53.77% het pass | 11.07% het all
spectre::2024-05-23 16:26:11,225::DEBUG::spectre.analysis.snv_analysis>  chr18  124000  11796   13121   5.28x   47.34% het pass | 9.51% het all
spectre::2024-05-23 16:26:11,228::DEBUG::spectre.analysis.snv_analysis>  chr19  86274   9538    7477    5.33x   56.06% het pass | 11.06% het all
spectre::2024-05-23 16:26:11,229::DEBUG::spectre.analysis.snv_analysis>  chr20  106365  14681   8842    6.65x   62.41% het pass | 13.8% het all
spectre::2024-05-23 16:26:11,229::DEBUG::spectre.analysis.snv_analysis>  chr21  68940   9203    7310    7.39x   55.73% het pass | 13.35% het all
spectre::2024-05-23 16:26:11,229::DEBUG::spectre.analysis.snv_analysis>  chr22  62161   8543    5257    6.61x   61.91% het pass | 13.74% het all
spectre::2024-05-23 16:26:11,229::DEBUG::spectre.analysis.snv_analysis>  chrX   183860  16011   14272   4.77x   52.87% het pass | 8.71% het all
spectre::2024-05-23 16:26:11,229::DEBUG::spectre.analysis.snv_analysis>  chrY   5266    815     1541    19.96x  34.59% het pass | 15.48% het all
spectre::2024-05-23 16:26:11,229::DEBUG::spectre.analysis.snv_analysis>  Use chromsomes based on proportion of het sites
spectre::2024-05-23 16:26:11,229::DEBUG::spectre.analysis.snv_analysis>  chr1   5.61
spectre::2024-05-23 16:26:11,229::DEBUG::spectre.analysis.snv_analysis>  chr2   5.03
spectre::2024-05-23 16:26:11,229::DEBUG::spectre.analysis.snv_analysis>  chr3   5.0
spectre::2024-05-23 16:26:11,229::DEBUG::spectre.analysis.snv_analysis>  chr4   5.74
spectre::2024-05-23 16:26:11,229::DEBUG::spectre.analysis.snv_analysis>  chr5   5.31
spectre::2024-05-23 16:26:11,229::DEBUG::spectre.analysis.snv_analysis>  chr6   4.84
spectre::2024-05-23 16:26:11,229::DEBUG::spectre.analysis.snv_analysis>  chr7   5.03
spectre::2024-05-23 16:26:11,229::DEBUG::spectre.analysis.snv_analysis>  chr8   4.93
spectre::2024-05-23 16:26:11,229::DEBUG::spectre.analysis.snv_analysis>  chr9   5.21
spectre::2024-05-23 16:26:11,229::DEBUG::spectre.analysis.snv_analysis>  chr10  5.78
spectre::2024-05-23 16:26:11,229::DEBUG::spectre.analysis.snv_analysis>  chr11  4.91
spectre::2024-05-23 16:26:11,229::DEBUG::spectre.analysis.snv_analysis>  chr12  4.89
spectre::2024-05-23 16:26:11,229::DEBUG::spectre.analysis.snv_analysis>  chr13  5.5
spectre::2024-05-23 16:26:11,229::DEBUG::spectre.analysis.snv_analysis>  chr14  5.15
spectre::2024-05-23 16:26:11,229::DEBUG::spectre.analysis.snv_analysis>  chr15  4.95
spectre::2024-05-23 16:26:11,229::DEBUG::spectre.analysis.snv_analysis>  chr16  7.2
spectre::2024-05-23 16:26:11,229::DEBUG::spectre.analysis.snv_analysis>  chr17  5.76
spectre::2024-05-23 16:26:11,229::DEBUG::spectre.analysis.snv_analysis>  chr18  5.28
spectre::2024-05-23 16:26:11,229::DEBUG::spectre.analysis.snv_analysis>  chr19  5.33
spectre::2024-05-23 16:26:11,229::DEBUG::spectre.analysis.snv_analysis>  chr20  6.65
spectre::2024-05-23 16:26:11,229::DEBUG::spectre.analysis.snv_analysis>  chr21  7.39
spectre::2024-05-23 16:26:11,229::DEBUG::spectre.analysis.snv_analysis>  chr22  6.61
spectre::2024-05-23 16:26:11,229::DEBUG::spectre.analysis.snv_analysis>  chrX   4.77
spectre::2024-05-23 16:26:33,908::DEBUG::spectre.analysis.snv_analysis>  n het sites used for normalization = 1174573
spectre::2024-05-23 16:26:34,094::DEBUG::spectre.analysis.snv_analysis>  p98 HET filter = 8.0
spectre::2024-05-23 16:26:34,643::DEBUG::spectre.analysis.snv_analysis>  HET: 1174573 |  p98 HET 1153663
Traceback (most recent call last):
  File "/rds/projects/b/beggsa-clinicalnanopore/software/condaenvs/spectre2/bin/spectre", line 8, in <module>
    sys.exit(main())
  File "/rds/projects/b/beggsa-clinicalnanopore/software/condaenvs/spectre2/lib/python3.10/site-packages/spectre/spectre.py", line 642, in main
    spectre_run.spectre_exe()
  File "/rds/projects/b/beggsa-clinicalnanopore/software/condaenvs/spectre2/lib/python3.10/site-packages/spectre/spectre.py", line 356, in spectre_exe
    spectre_main.cnv_call()
  File "/rds/projects/b/beggsa-clinicalnanopore/software/condaenvs/spectre2/lib/python3.10/site-packages/spectre/spectreCNV.py", line 71, in cnv_call
    self.snv_analysis.snv_copy_number_state()
  File "/rds/projects/b/beggsa-clinicalnanopore/software/condaenvs/spectre2/lib/python3.10/site-packages/spectre/analysis/snv_analysis.py", line 231, in snv_copy_number_state
    self.snv_multimodal_detect()
  File "/rds/projects/b/beggsa-clinicalnanopore/software/condaenvs/spectre2/lib/python3.10/site-packages/spectre/analysis/snv_analysis.py", line 106, in snv_multimodal_detect
    dist_detected = detect_miltimodal.run()
  File "/rds/projects/b/beggsa-clinicalnanopore/software/condaenvs/spectre2/lib/python3.10/site-packages/spectre/libs/unidip/unidip.py", line 51, in run
    modidxs = self._unidip(0, len(self.dat), True, self.debug)
  File "/rds/projects/b/beggsa-clinicalnanopore/software/condaenvs/spectre2/lib/python3.10/site-packages/spectre/libs/unidip/unidip.py", line 154, in _unidip
    rhidx = self._unidip(start+h_idx[1], end, False, debug)
  File "/rds/projects/b/beggsa-clinicalnanopore/software/condaenvs/spectre2/lib/python3.10/site-packages/spectre/libs/unidip/unidip.py", line 154, in _unidip
    rhidx = self._unidip(start+h_idx[1], end, False, debug)
  File "/rds/projects/b/beggsa-clinicalnanopore/software/condaenvs/spectre2/lib/python3.10/site-packages/spectre/libs/unidip/unidip.py", line 154, in _unidip
    rhidx = self._unidip(start+h_idx[1], end, False, debug)
  [Previous line repeated 975 more times]
  File "/rds/projects/b/beggsa-clinicalnanopore/software/condaenvs/spectre2/lib/python3.10/site-packages/spectre/libs/unidip/unidip.py", line 135, in _unidip
    rmidx = self._unidip(start+modidx[0], start+modidx[1], True, debug)
  File "/rds/projects/b/beggsa-clinicalnanopore/software/condaenvs/spectre2/lib/python3.10/site-packages/spectre/libs/unidip/unidip.py", line 117, in _unidip
    _, pval, modidx = diptst(dat, self.is_hist, self.ntrials)
  File "/rds/projects/b/beggsa-clinicalnanopore/software/condaenvs/spectre2/lib/python3.10/site-packages/spectre/libs/unidip/dip.py", line 55, in diptst
    unif_dips = np.apply_along_axis(dip_fn, 1, unifs, is_hist, True)
  File "<__array_function__ internals>", line 200, in apply_along_axis
  File "/rds/projects/b/beggsa-clinicalnanopore/software/condaenvs/spectre2/lib/python3.10/site-packages/numpy/lib/shape_base.py", line 379, in apply_along_axis
    res = asanyarray(func1d(inarr_view[ind0], *args, **kwargs))
  File "/rds/projects/b/beggsa-clinicalnanopore/software/condaenvs/spectre2/lib/python3.10/site-packages/spectre/libs/unidip/dip.py", line 75, in dip_fn
    counts = collections.Counter(dat)
  File "/rds/projects/b/beggsa-clinicalnanopore/software/condaenvs/spectre2/lib/python3.10/collections/__init__.py", line 577, in __init__
    self.update(iterable, **kwds)
  File "/rds/projects/b/beggsa-clinicalnanopore/software/condaenvs/spectre2/lib/python3.10/collections/__init__.py", line 661, in update
    if isinstance(iterable, _collections_abc.Mapping):
  File "/rds/projects/b/beggsa-clinicalnanopore/software/condaenvs/spectre2/lib/python3.10/abc.py", line 119, in __instancecheck__
    return _abc_instancecheck(cls, instance)
RecursionError: maximum recursion depth exceeded in comparison
abelhj commented 1 month ago

I've run in to this error as well. Is there any workaround?