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epi2me-labs / wf-clone-validation

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Fail to run and then fail to produce plasmids and test data[Bug]: #10

Closed BenjaminSchwessinger closed 1 year ago

BenjaminSchwessinger commented 2 years ago

What happened?

I really struggled getting this running (docker and singularity failed). Also conda installs didn't work. At the end I got mamba install working with a fixed_conda environment.

Now it runs but doesn't produce plasmid sequences even with

nextflow run epi2me-labs/wf-clone-validation -profile fixed_conda --fastq test_data/test --db_directory XXX -c XXX --no_reconcil.

If finishes and produces a report but does not generate plasmid consensus sequences.

Operating System

ubuntu 20.04

Workflow Execution

Command line

Workflow Execution - EPI2ME Labs Versions

v0.2.4

Workflow Execution - Execution Profile

Conda

Workflow Version

v0.2.4

Relevant log output

Aug.-26 06:52:21.978 [Task monitor] INFO  nextflow.processor.TaskProcessor - [c6/952e62] NOTE: Process `pipeline:assembleCore (1)` terminated with an error exit status (1) -- Execution is retried (4)

Not sure where to find the log file for the actual command run.
sarahjeeeze commented 2 years ago

Hi, usually there should be some clues in the wf-clone-validation-report.html as to why the assembly failed. What is average read quality and length? You may also need to adjust the approx_size and assm_coverage parameters to better fit your data. What were the error messages for docker and singularity failing?

sarahjeeeze commented 1 year ago

Closing through lack of response from original poster