Closed dnhare closed 3 years ago
@dnhare Can you tell me which primer scheme you're using? The script that parses the primer file expects the ARTIC primer BED name field format (i.e. nCoV-2019_1_LEFT
, nCoV-2019_1_RIGHT
).
The input file used to generate the failing plot is qc_sequencing/<samplename>.amplicon_coverage.bed
. Can you check the following:
amplicon_id
column filled with an identifier and not an empty fieldCould you copy and paste the first few lines of a qc_sequencing/*.amplicon_coverage.bed
file?
Thank you very much for your prompt response.
We're using ARTIC V3 primer scheme. The path to the primer_bed in the config.yaml file is: ~/artic-ncov2019/primer_schemes/nCoV-2019/V3/nCoV-2019.primer.bed
Unfortunately, the issue seems to be that we are not generating a qc_sequencing directory, or .amplicon.coverage.bed files.
Are these supposed to be outputs after executing the snakemake script, or outputs from the artic pipeline?
This error can occur when the pipeline fails to find any samples. Can you double-check that your bam files are named using the pattern defined in your config.yaml?
On Aug 5, 2021, at 12:01 PM, dnhare @.***> wrote:
Thank you very much for your prompt response.
We're using ARTIC V3 primer scheme. The path to the primer_bed in the config.yaml file is: ~/artic-ncov2019/primer_schemes/nCoV-2019/V3/nCoV-2019.primer.bed
Unfortunately, the issue seems to be that we are not generating a qc_sequencing directory, or .amplicon.coverage.bed files.
Are these supposed to be outputs after executing the snakemake script, or outputs from the artic pipeline?
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Thank you @jts
As far as I can tell my bam files are in the pattern specified in my config.yaml (I haven't changed the default pattern of "{data_root}/{sample}.sorted.bam")
The bam files are named in the data_root directory as numbered files e.g. "18.sorted.bam"
There are also corresponding .bam.bai files in that directory e.g. "18.bam.bai" etc.
Do you think this naming structure could be preventing the pipeline from finding any samples?
I've tried renaming some of the bam files and adjusting the config.yaml file accordingly to see if that makes a difference, but I get the same error.
Thanks for your help!
@jts @rdeborja This was solved by specifying the absolute path to the sample directory in the config.yaml file, and removing '~'
Thanks for your help with this.
Thanks for letting us know @dnhare. Great tip in case anyone else encounters the same issue.
Hi there,
I've recently installed ncov-tools but the snakemake script repeatedly fails to execute due to the following error. I'd greatly appreciate any advice as to how to correct this error.
Many thanks.
Dan
Error: At least one layer must contain all faceting variables:
amplicon_id
.amplicon_id
amplicon_id
Backtrace: █