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artic-network / fieldbioinformatics

The ARTIC field bioinformatics pipeline
MIT License
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Artic_vcf_merge failed #103

Closed idolawoye closed 2 years ago

idolawoye commented 2 years ago

Hi, I am getting the following error when I run the minion command:

Command failed:artic_vcf_merge CERI-KRISP-K032245_ONT /home/idowu/Downloads/Bioinfo/fieldbioinformatics/test-data/primer-schemes/nCoV-2019/V3/nCoV-2019.scheme.bed 2> CERI-KRISP-K032245_ONT.primersitereport.txt nCoV-2019_2:CERI-KRISP-K032245_ONT.nCoV-2019_2.vcf nCoV-2019_1:CERI-KRISP-K032245_ONT.nCoV-2019_1.vcf

The command I entered was:

artic minion --threads 10 --normalise 200 --skip-nanopolish --scheme-directory ~/Downloads/Bioinfo/fieldbioinformatics/test-data/primer-schemes --strict --read-file ../CERI-KRISP-K032245_ONT.fastq.gz nCoV-2019/V3 CERI-KRISP-K032245_ONT

I don't know what seems to be wrong here

BioWilko commented 2 years ago

That's because without using nanopolish or medaka there is no variant caller in the pipeline therefore no vcf files to merge.

If you do not have access to the fast5 files I suggest you use the command:

artic minion --threads 10 --normalise 200 --medaka --medaka-model <insert medaka model here> --scheme-directory ~/Downloads/Bioinfo/fieldbioinformatics/test-data/primer-schemes --strict --read-file ../CERI-KRISP-K032245_ONT.fastq.gz nCoV-2019/V3 CERI-KRISP-K032245_ONT

ONTs medaka repo explains how to determine your medaka model

idolawoye commented 2 years ago

Thanks!