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artic-network / fieldbioinformatics

The ARTIC field bioinformatics pipeline
MIT License
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Error with medaka consensus #115

Closed lqhungpt closed 2 years ago

lqhungpt commented 2 years ago

When I ran artic with command line on my MacBook M1 Pro chip as bellow:

artic minion --medaka --medaka-model r941_min_high_g360 --normalise 50 --threads 32 --scheme-directory ~/fieldbioinformatics/test-data/primer-schemes/ --read-file /Users/hungluong/passv12.trimmed.fastq.gz ncv1/V1 abcd

I got error after running medaka consensus as bellow:

Running: medaka consensus --model r941_min_high_g360 --threads 32 --chunk_len 800 --chunk_ovlp 400 --RG 2 abcd.trimmed.rg.sorted.bam abcd.2.hdf Command failed:medaka consensus --model r941_min_high_g360 --threads 32 --chunk_len 800 --chunk_ovlp 400 --RG 2 abcd.trimmed.rg.sorted.bam abcd.2.hdf

BioWilko commented 2 years ago

Hi @lqhungpt without any more information I can't really help, if you run medaka consensus --model r941_min_high_g360 --threads 32 --chunk_len 800 --chunk_ovlp 400 --RG 2 abcd.trimmed.rg.sorted.bam abcd.2.hdf in the directory you ran the pipeline when encountering this error initially you should get a much more informative error.