Closed philsteinberg closed 1 year ago
Looks good! Can you put an example of the MCMC number error in #56? Is it all due to #95?
Added an example log, and yes all of the failed pipelines errored due to Exception: 100% of trees are multiprimary (2500 of 2500), so not enough to report good posterior.
as stated in #95
Description
Launch Strelka2 + Battenberg + PhyloWGS seeds [HSNC single-region] Seed + Sample combination that does not work due to mcmc number #56
Closes #56
Pipeline Run Results
Example
sample:
ILHNLNEV000001-T001-P01-F
seed:51404
input SNV (Strelka2):
/hot/project/disease/HeadNeckTumor/HNSC-000084-LNMEvolution/data/SNV/strelka2/recsnv/vcfs/ILHNLNEV000001-T001-P01-F.vcf
input CNA (Battenberg):
/hot/project/disease/HeadNeckTumor/HNSC-000084-LNMEvolution/data/Battenberg/refit_dpnorm/ILHNLNEV000001-T001-P01-F/ILHNLNEV000001-T001-P01-F_cellularity_ploidy.txt
/hot/project/disease/HeadNeckTumor/HNSC-000084-LNMEvolution/data/Battenberg/refit_dpnorm/ILHNLNEV000001-T001-P01-F/ILHNLNEV000001-T001-P01-F_subclones.txt
config:
/hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/run-strelka2-battenberg-phylowgs/input/config/seed_51404.config
yaml:
/hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/strelka2_battenberg_yamls/single-region/ILHNLNEV000001-T001-P01-F.yaml
output:
/hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/run-strelka2-battenberg-phylowgs/output/call-SRC-1.0.0-rc.1/ILHNLNEV000001-T001-P01-F/PhyloWGS-2205be1/output/
PhyloWGS-2205be1_51404_ILHNLNEV000001-T001-P01-F_Strelka2-Battenberg-mutass.json.gz
PhyloWGS-2205be1_51404_ILHNLNEV000001-T001-P01-F_Strelka2-Battenberg-muts.json.gz
PhyloWGS-2205be1_51404_ILHNLNEV000001-T001-P01-F_Strelka2-Battenberg-summ.json.gz
logs:
/hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/run-strelka2-battenberg-phylowgs/logs/
witness data:
/hot/project/method/AlgorithmEvaluation/BNCH-000082-SRCRNDSeed/pipeline-call-src/run-strelka2-battenberg-phylowgs/witness_results/
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