Open nmshahir opened 5 months ago
Hi, I encountered the same issue as you. Did you manage to resolve it? If so, could you please share how you did it? Thank you!
I've ran into the same issue but it appeared only when adding the genetic map.
wget https://raw.githubusercontent.com/nf-core/test-datasets/phaseimpute/hum_data/panel/chr21/1000GP.chr21.s.norel.vcf.gz
wget https://raw.githubusercontent.com/nf-core/test-datasets/phaseimpute/hum_data/panel/chr21/1000GP.chr21.s.norel.vcf.gz.csi
wget https://raw.githubusercontent.com/nf-core/test-datasets/phaseimpute/hum_data/reference_genome/GRCh38_21.map
SHAPEIT5_phase_common \
--input 1000GP.chr21.s.norel.vcf.gz \
--map GRCh38_21.map \
--region chr21:16570070-16609998 \
--thread 2 \
--output 1000GP_chr21_16570070-16609998_chunks.vcf.gz
I'm using SHAPEIT5 to phase a large panel (300K+) using phase_common and it keeps stopping at the PBWT step? This is the relevant error:
The parameters used are below:
Please advise?