artic_plot_amplicon_depth cmd missing

[emiracherif]

Hi, I had issues with artic_plot_amplicon_depth (AssertionError: error: readgroup not found in provided primer scheme (1)), I tried to get the new primer scheme with artic-tools. But I had the same error.

I was using artic 1.1.3, so I updated to artic 1.2.1, and now I can't find the plotting cmd anymore!

Is the artic_plot_amplicon_depth deprecated in the new artic version? Is there a new cmd to plot amplicons coverage?

Thank you in advance for the help,

Best E.

[will-rowe]

Hi @emiracherif - thanks for getting in touch.

Short answer is yes - the plotting command is removed in the new artic version. Sorry for any inconvenience caused by that - it was causing a lot of trouble for some HPC users to have plotting baked in to the pipeline. The latest version of ARTIC (1.2.1) has initial support for multiqc, which will generate equivalent amplicon plots. So, you should be able to call multiqc . on your pipeline output directory and it will generate a report for you, containing the plot.

Feedback welcome. The upcoming release (1.3.0) of artic will have more information in the multiqc report but it is a work in progress.

[emiracherif]

Hi @will-rowe , Thank you very much for your reply. I'm still having some trouble, though.

I ran multiqc . on one of my artic output_directories, but it seems that multiqc does not find the expected files. So I get this warning/error: [WARNING] multiqc : No analysis results found. Cleaning up..

Am I missing something? Or did I need to put the scheme.bed file in my output directory?

Thanks again Emira

PS: here is the list of my output files: p1_barocde01.1.hdf p1_barocde01.1.vcf p1_barocde01.2.hdf p1_barocde01.2.vcf p1_barocde01.alignreport.er p1_barocde01.alignreport.txt p1_barocde01.consensus.fasta p1_barocde01.coverage_mask.txt p1_barocde01.coverage_mask.txt.1.depths p1_barocde01.coverage_mask.txt.2.depths p1_barocde01.fail.vcf p1_barocde01.merged.vcf p1_barocde01.merged.vcf.gz p1_barocde01.merged.vcf.gz.tbi p1_barocde01.minion.log.txt p1_barocde01.muscle.in.fasta p1_barocde01.muscle.out.fasta p1_barocde01.pass.vcf.gz p1_barocde01.pass.vcf.gz.tbi p1_barocde01.preconsensus.fasta p1_barocde01.primersitereport.txt p1_barocde01.primers.vcf p1_barocde01.primertrimmed.rg.sorted.bam p1_barocde01.primertrimmed.rg.sorted.bam.bai p1_barocde01.sorted.bam p1_barocde01.sorted.bam.bai p1_barocde01.trimmed.rg.sorted.bam p1_barocde01.trimmed.rg.sorted.bam.bai

[will-rowe]

Sorry - I forgot that for v1.2.1 this was enabled by using --strict as it is a new feature and we didn't want it enabled by default (which it will be on the next release). I'm afraid you'll have to rerun with --strict and then call multiqc

[emiracherif]

Thanks! It worked great :)

[will-rowe]

Great!