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fritzsedlazeck / Spectre

Copy number caller for long read data including SNV utilization
MIT License
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RemoveN's #10

Closed adbeggs closed 5 months ago

adbeggs commented 6 months ago

Hi all

Have just tried running Remove N's - and has failed

spectre RemoveNs --reference ~/beggsa-clinicalnanopore/genomes/grch38/genome.fa --output-dir . --output-file grch38-spectre-metadata.mdr --save-only

spectre::2024-03-22 09:44:18,068::INFO::spectre.spectre>  Spectre input: RemoveNs --reference /rds/homes/b/beggsa/beggsa-clinicalnanopore/genomes/grch38/genome.fa --output-dir . --output-file grch38-spectre-metadata.mdr --save-only
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
    main_logger.error("Bin size too small") if spectre_args.bin_size < min_bin_size else ""
AttributeError: 'Namespace' object has no attribute 'bin_size'. Did you mean: 'n_size'?