Comments (4)
The command has an extra argument artic-ncov2019/primer_schemes/
which should not be present, i.e. it should be:
artic minion --threads 8 --scheme-directory ~/artic-ncov2019/primer_schemes --read-file sample01.fastq --sequencing-summary /data/COVID_SET1/COVID-19/merged_fastq_files/ nCoV-2019/V3 sample01
from fieldbioinformatics.
Additionally, unless you are using --medaka
you will need to add the --fast5-directory
argument, and the --sequencing-summary
should point to a sequencing summary not a directory.
from fieldbioinformatics.
Thank you so much for response
The issue is resolved.
If you can let me know document of output results explanation from artic workflow
from fieldbioinformatics.
Hi @shashibioinfo143 - sorry for missing this.
You can find details on the output files in the SOP - I'll update the docs to give more details too.
Closing this issue now as the original problem is resolved.
from fieldbioinformatics.
Related Issues (20)
- artic pipeline not installing properly: ModuleNotFoundError: No module named 'importlib.metadata' HOT 1
- Longshot `thread 'main' panicked at 'assertion failed: p <= 0.0'` error: possible to update longshot? HOT 3
- vcf_filter.py filtering parameters and align_trim.py for alternative primer scheme
- Error with medaka consensus HOT 1
- Unable to install artic on mac
- artic_vcf_merge Fails HOT 2
- What is the default mindepth ? HOT 4
- pipeline has stopped working...! HOT 5
- Conda recipe for 1.2.3 not working HOT 8
- no version information available (required by samtools) HOT 5
- Overlapping variants in fail.vcf and pass.vcf cause preconsensus to be masked and thus bcftools complains when applying the "pass" variant HOT 2
- Artic v5 mismatched primer names in bedfile causes "dropped" amplicons HOT 1
- Update medaka version HOT 2
- KeyError: 'SupportFraction' when running margin_cons.py
- Clarify what's meant by 'Suppress variant'
- Conda environment set up HOT 3
- Custom bed file with "primer gaps" causes workflow to crash at artic-tools vcf_checker step HOT 1
- Error: bcftools consensus fail with overlapping variants HOT 5
- htslib =1.17 dependency PLEASE UPDATE HOT 1
- PyVCF assigns a QUAL value of '.' instead of zero
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from fieldbioinformatics.