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morrislab / phylowgs

Application for inferring subclonal composition and evolution from whole-genome sequencing data.
GNU General Public License v3.0
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Assert error when creating ssm_data.txt #69

Closed pspealman closed 6 years ago

pspealman commented 7 years ago

sample1_head.vcf.txt I've encountered a problem while trying to generate the ssm_data.txt file using a .vcf file generated using GATK's HaplotypeCaller on haploid yeast data.

Using the attached file ('sample1_head.vcf), and the command: python ../phylowgs/parser/create_phylowgs_inputs.py --vcf-type sample1=sanger sample1=sample1_head.vcf

Results in the following error: Traceback (most recent call last): File "../phylowgs/parser/create_phylowgs_inputs.py", line 1354, in <module> main() File "../phylowgs/parser/create_phylowgs_inputs.py", line 1299, in main variant_ids, ref_read_counts, total_read_counts = parse_variants(samples, vcf_files, vcf_types, args.tumor_sample, args.missing_variant_confidence) File "../phylowgs/parser/create_phylowgs_inputs.py", line 1200, in parse_variants total_read_counts = impute_missing_total_reads(total_read_counts, missing_variant_confidence) File "../phylowgs/parser/create_phylowgs_inputs.py", line 1109, in impute_missing_total_reads assert np.sum(sample_means <= 0) == np.sum(np.isnan(sample_means)) == 0 AssertionError

I feel like I'm missing something obvious. Any help or direction would be greatly appreciated.

jwintersinger commented 6 years ago

Hi Pieter,

Please let me know via e-mail if you have any further issues like this. Thanks! :)