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bioinformatics-centre / BayesTyper

A method for variant graph genotyping based on exact alignment of k-mers
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Classifying kmers error with bayesTyper genotype #13

Closed stephaniemyan closed 5 years ago

stephaniemyan commented 5 years ago

Hi,

I'm trying to genotype variant clusters using bayesTyper genotype and running into the following error:

[05/03/2019 14:03:52] You are using BayesTyper (v1.4)

[05/03/2019 14:03:52] Seeding pseudo-random number generator with 1551812632 ...
[05/03/2019 14:03:52] Setting the kmer size to 55 ...

[05/03/2019 14:03:52] Parsed information for 1 sample(s)

[05/03/2019 14:03:52] Parsing reference genome ...
[05/03/2019 14:04:03] Parsed 65 reference genome chromosomes(s) (3095211400 nucleotides)

[05/03/2019 14:04:03] Parsing decoy sequence(s) ...
[05/03/2019 14:04:03] Parsed 2515 decoy sequence(s) (10503663 nucleotides)

[05/03/2019 14:04:11] Maximum resident set size: 3.28256 Gb

[05/03/2019 14:04:11] Parsing variant clusters ...
[05/03/2019 14:04:42] Parsed 1811780 variant clusters (5202843 variants)

[05/03/2019 14:04:49] Parsing parameter kmers ...
[05/03/2019 14:04:51] Parsed 1000000 kmers

[05/03/2019 14:04:51] Maximum resident set size: 24.6832 Gb

[05/03/2019 14:04:51] Counting kmers in variant cluster paths ...
[05/03/2019 14:09:35] Counting kmers in inter-cluster regions and decoy sequence(s) ...

[05/03/2019 14:11:06] Parsing KMC table containing 3219629908 kmers for sample altai_neand.res ...

[05/03/2019 14:16:03] Classifying kmers in variant cluster paths ...
bayesTyper: /isdata/kroghgrp/jasi/bayesTyper/code/releases/v1.4_static/BayesTyper-1.4/src/bayesTyper/KmerHash.cpp:306: std::vector<std::vector<std::vector<KmerStats> > > ObservedKmerCountsHash<sample_bin>::calculateKmerStats(const std::vector<Sample>&) [with unsigned char sample_bin = 3u]: Assertion `!(*hash_it).second.isExcluded()' failed.
Aborted

This is the command I'm using:

bayesTyper genotype -v bayestyper_unit_1/variant_clusters.bin -c bayestyper_cluster_data -s samples.tsv -g ../vcf/bayestyper_GRCh38_bundle_v1.3/GRCh38_canon.fa -d ../vcf/bayestyper_GRCh38_bundle_v1.3/GRCh38_decoy.fa -o bayestyper_unit_1/bayestyper -z -p 12

Could you tell me what the error is referring to and how to debug it?

Thanks, Steph

jonassibbesen commented 5 years ago

Hi Steph,

Thanks for writing. This error is due to a bug that was introduced in the version 1.4. Updating to v1.4.1 should fix the issue.

Please let me know if v1.4.1 does not fix the issue.

Cheers,

Jonas

stephaniemyan commented 5 years ago

It works with v1.4.1, thanks so much!