Comments (1)
Nick-Eagles
commented on June 1, 2024
Mark Miller gave insight into this: he said that jobs submitted containing -pe local 1 very occasionally enter a "random" queue. It appears that manually setting the 'penv' variable in jhpce.config for only those processes using multiple cores fixed the problem. However, there's a small chance the issue isn't gone (the source of the underlying issue isn't entirely clear)
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Related Issues (20)
- [JHPCE] repeated fastqc failure on trimmed paired data HOT 15
- Guide for all setups that are atypical in some way
- Develop a 1 day (max 2) workshop
- Videos documenting how to install and run SPEAQeasy + describing outputs
- Translate course and intro documentation to Spanish
- Add support for MultiQC and maybe other tools
- Add QC metrics generated by Monorail / recount3
- Adapt code to DSL2
- Create a contribution guidelines documentation
- improve storage usage, minimize duplication of FASTQ data HOT 2
- transcript quantification (Salmon/Kallisto) should use trimmed reads HOT 1
- Add support for running SPEAQeasy with one sample
- allow starting the workflow with existing read alignments (sorted BAM/CRAM files) HOT 3
- InferStrandness failure, --force_strand not supported HOT 3
- Construct `rse_tx` for rat HOT 5
- `BuildAnnotationObjects` halts with current version of R
- Add support for more executors
- Improve or clarify what's supported for custom annotation
- PullTranscriptFasta failing HOT 1
- BuildAnnotationObjects fails HOT 19
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