You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
i have tried installing VCF-kit as you mentioned in github site and i downloaded the reference genome as mentioned.
run1:
command: vk primer indel --ref=WBcel235 QX1211.indels.vcf.gz
Using reference located at /home/shanmu/.genome/WBcel235/WBcel235.fa.gz
--size ignored; size is set dynamically when genotyping indels.
Applied 2 variants
Cannot find thermo path '/primer3_config/
similarly i have installed vcfkit through docker and ran the programme as below
Run2:
sudo docker run -v /root/.genome/:/data -v /media/shanmu/shanmu_hdd1/chickpea_minicore/merged_298/filtered_passed/docker/VCF-kit/test_data:/datapath -it andersenlab/vcf-kit vk primer indel /datapath/QX1211.indels.vcf.gz --ref=/data/WBcel235
Genome 'WBcel235' does not exist
run 3:
sudo docker run -v /home/shanmu/.genome/:/data -v /media/shanmu/shanmu_hdd1/chickpea_minicore/merged_298/filtered_passed/docker/VCF-kit/test_data:/datapath -it andersenlab/vcf-kit vk primer indel /datapath/QX1211.indels.vcf.gz --ref=/data/WBcel235
--size ignored; size is set dynamically when genotyping indels.
[E::fai_build3_core] Failed to open the file /data/WBcel235
[faidx] Could not load fai index of /data/WBcel235
[E::fai_build3_core] Failed to open the file /data/WBcel235
[faidx] Could not load fai index of /data/WBcel235
Note: the --sample option not given, applying all records regardless of the genotype
Applied 0 variants
Cannot find thermo path '/primer3_config/
The text was updated successfully, but these errors were encountered:
i have tried installing VCF-kit as you mentioned in github site and i downloaded the reference genome as mentioned.
run1:
command: vk primer indel --ref=WBcel235 QX1211.indels.vcf.gz
Applied 2 variants
similarly i have installed vcfkit through docker and ran the programme as below
Run2:
sudo docker run -v /root/.genome/:/data -v /media/shanmu/shanmu_hdd1/chickpea_minicore/merged_298/filtered_passed/docker/VCF-kit/test_data:/datapath -it andersenlab/vcf-kit vk primer indel /datapath/QX1211.indels.vcf.gz --ref=/data/WBcel235
run 3:
sudo docker run -v /home/shanmu/.genome/:/data -v /media/shanmu/shanmu_hdd1/chickpea_minicore/merged_298/filtered_passed/docker/VCF-kit/test_data:/datapath -it andersenlab/vcf-kit vk primer indel /datapath/QX1211.indels.vcf.gz --ref=/data/WBcel235
[E::fai_build3_core] Failed to open the file /data/WBcel235
[faidx] Could not load fai index of /data/WBcel235
[E::fai_build3_core] Failed to open the file /data/WBcel235
[faidx] Could not load fai index of /data/WBcel235
Note: the --sample option not given, applying all records regardless of the genotype
Applied 0 variants
The text was updated successfully, but these errors were encountered: