Spectre
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Crash on SNV module
First attempt since my last round of queries... running with Clair3 SNVs and get:
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 614, in main
spectre_run.spectre_exe()
File "/rds/projects/b/beggsa-clinicalnanopore/software/condaenvs/spectre2/lib/python3.10/site-packages/spectre/spectre.py", line 349, 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 70, 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 230, 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 103, in snv_multimodal_detect
self.het_dump()
File "/rds/projects/b/beggsa-clinicalnanopore/software/condaenvs/spectre2/lib/python3.10/site-packages/spectre/analysis/snv_analysis.py", line 131, in het_dump
het_dump_file = gzip.open(f'{self.spectre_args.out_dir}/debug/het_dump.txt.gz', 'wt')
File "/rds/projects/b/beggsa-clinicalnanopore/software/condaenvs/spectre2/lib/python3.10/gzip.py", line 58, in open
binary_file = GzipFile(filename, gz_mode, compresslevel)
File "/rds/projects/b/beggsa-clinicalnanopore/software/condaenvs/spectre2/lib/python3.10/gzip.py", line 174, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
FileNotFoundError: [Errno 2] No such file or directory: '/rds/projects/b/beggsa-clinicalnanopore/to_share_via_globus/Rare_Disease_Hannah_Titherage_200623/D2325440/20230620_0810_3E_PAO44618_97828260/spectre2a/debug/het_dump.txt.gz'