Comments (1)
maxulysse
commented on September 24, 2024
Hi @grendon, I'm not sure this is due to the singularity container.
These WARNINGS in the .command.err seems concerning to me:
WARNING 2023-04-18 15:20:56 CollectAlignmentSummaryMetrics No Read length histograms to plot.
WARNING 2023-04-18 15:20:56 CollectBaseDistributionByCycle No valid bases found in input file. No plot will be produced.
WARNING 2023-04-18 15:20:56 CollectInsertSizeMetrics All data categories were discarded because they contained < 0.05 of the total aligned paired data.
WARNING 2023-04-18 15:20:56 CollectInsertSizeMetrics Total mapped pairs in all categories: 0.0
WARNING 2023-04-18 15:20:56 MeanQualityByCycle No valid bases found in input file. No plot will be produced.
WARNING 2023-04-18 15:20:56 QualityScoreDistribution No valid bases found in input file. No plot will be produced.
[Tue Apr 18 15:20:56 GMT 2023] picard.analysis.CollectMultipleMetrics done. Elapsed time: 0.00 minutes.
Can you check if the files are not empty, and if not, that singularity is properly configured so that Nextflow can read the files properly?
from viralrecon.
Related Issues (20)
- Artic v5 mismatched primer names in artic-ncov2019 repo cause certain amplicons to be erroneously filtered/removed
- Add QIAseq DIRECT SARS-CoV-2 Kit amplicons
- Argument input-fasta is missing in NFCORE_VIRALRECON:ILLUMINA:CONSENSUS_BCFTOOLS:CONSENSUS_QC:NEXTCLADE_RUN" HOT 4
- Problem installing viralrecon
- Adding "aggregate" and "plot" methods in the freyja subworkflow HOT 4
- Error running version 2.6.0 with Nanopore data in process NFCORE_VIRALRECON:NANOPORE:ARTIC_MINION
- Unable to download the python script HOT 3
- Split authors in generated RO crate
- Adding "--grouplineages" parameter in the nf-core/viralrecon HOT 3
- Make cutadapt primer's position ext.arg
- Properly deal with multiqc in the config files before the next release HOT 3
- Temp file problem in VARIANTS_IVAR:BCFTOOLS_SORT HOT 1
- Allow skipping `freyja boot` HOT 1
- `MOSDEPTH_AMPLICON` doesn't run in `dev` branch HOT 1
- Non-SCV2 amplicon run returns consensus genomes with no low-coverage masking HOT 5
- nf-core/viralrecon run halted due to R version clash HOT 6
- Error when running illumina command
- ivariant filtering problem using 'tsv file' generated by 'ivar variant' command. HOT 7
- variant discrepancy between in ivar and snpeff annotated file HOT 2
- Old container for FASTQC processes in current release (2.6.0) is old and now fails on AWS Batch HOT 4
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from viralrecon.