Comments (1)
If using a custom primer.bed-file that contains an error the whole artic_ncov_wf:artic_medaka_custom_bed-process fails with error:20.
Looking into the workdir, the process failed at follwoing command command (not given in process-script):
Command failed:artic-tools check_vcf --summaryOut 6238aa8d4c66a472bb0a0b37.vcfreport.txt 6238aa8d4c66a472bb0a0b37.merged.vcf.gz primer_scheme/nCoV-2019/V_custom/nCoV-2019.scheme.bed 2> 6238aa8d4c66a472bb0a0b37.vcfcheck.log
6238aa8d4c66a472bb0a0b37.vcfcheck.log holds then the cause for the error of the command (here a wrong named primer-pair).
from porecov.
Related Issues (20)
- add skip scorpio parameter to pangolin HOT 1
- Only calculate NanoPlot after read filtering step HOT 5
- Add new V5 ARTIC primer BED HOT 5
- Medaka step fails in the -profile fastq_test HOT 3
- summary_report.py fails HOT 7
- publish primersitereport from medaka output
- VarSkipV2b primer does not work as expected HOT 7
- Update Medaka to support R10.4.1 models HOT 14
- Update --help to list up-to-date primer schemes that are supported
- MinKNOW/Guppy update needs new model for R10.4.1 5 kHz HOT 6
- Warning when execution report and timeline already exists HOT 1
- The pipeline fails in artic_ncov_wf_artic_medaka HOT 7
- new pangolin table columns HOT 1
- CovarPlot fails w/ custom BED HOT 5
- Process retry in slurm profile HOT 1
- Publish VCF files HOT 2
- Update medaka to get the latest models HOT 1
- Test Freyja Update function HOT 11
- [Question] CI for Variant Calling HOT 5
- Singularity container execution of pangolin crashes with recent nextflow versions HOT 8
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from porecov.