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jhuapl-bio / basestack_consensus

This repository is a Dockerized pipeline for creating consensus viral genomes from Oxford Nanopore data. This pipeline leverages the ARTIC Network bioinformatics pipeline and couples many annotation and reporting tools, resulting in an automatically generated PDF report. The pipeline is built to be deployed in the Basestack platform (https://github.com/jhuapl-bio/Basestack) so that anyone, regardless of bioinformatics expertise, can run it and make use of its automated consensus genomes and reports.
GNU General Public License v3.0
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Permission denied OR Command Error non-fastq files in fastq folder(s) in Module 4 #49

Open Merritt-Brian opened 3 years ago

Merritt-Brian commented 3 years ago

A recursive find is performed for pipeline ingestion at module 4 where it is attempting to find all seq_summary files in the fastq folder following standalone CLI or MinKNOW basecall analysis. Keeping this file in the fastq folder and not the run folder i.e. having multiple sequencing_summary.txt files causes potential issues .

Nanopolish log (Module 4)

[2021-04-29 21:00:57] SAMPLE NTC_NB01:------ processing nanopolish --------
[2021-04-29 21:00:57] SAMPLE NTC_NB01: Starting Module 4 Nanopolish
index: not enough arguments
/opt/basestack_consensus/sequencing_runs/example-run/sequencing_summary_FAN44250_77d58da2.txt: line 1: filename_fastq: command not found

Potentially the issue starts here https://github.com/jhuapl-bio/basestack_consensus/blob/main/pipeline_scripts/artic-module4-draft-consensus-nanopolish.sh#L99

Merritt-Brian commented 3 years ago

Basestack (App) assumes sequencing_summary file is in the base run directory. Recursive checking can be performed from the UI to see if it is present anywhere. But duplicate .txt files will always break the pipeline at module 4