AMPLISEQ:RENAME_RAW_DATA_FILES pipeline break

[Dedaniya08]

Description of the bug

The pipeline break when rename the raw data files, when running the AMPLISEQ: RENAME_RAW_DATA_FILES. in Azure Computer instance.

Command used and terminal output

$ nextflow run nf-core/ampliseq -r 2.11.0 -profile docker -c ./final_run_folder/nextflow.config,./final_run_folder/conf/test_modified.config, -params-file params.yaml --multiple_sequencing_runs -w ./working_dirr/

Relevant files

error.txt

System information

Azure Computer Instance:

• Nextflow version ( 24.10.0.5928)
• Standard_F64s_V2 (64 cores, 128 GB RAM, 512 GB disk)
• Executor (local)
• Container engine: Docker
• OS (debain ubuntu)
• nf-core/ampliseq (2.11.0)

[erikrikarddaniel]

In the error file it says Cannot run program "/bin/bash" which sounds critical to me, but I don't know a thing about Azure computing. I think your problem relates to how you set up your run and is not a bug in the pipeline. I would therefore recommend you to post your issue at the nf-core Slack: https://nf-co.re/join/slack, since there are people there that knows more about cloud computing in general as well as Azure in particular.

[ewels]

The key bit is this: Device or resource busy - this is usually due to some file system problems, eg. the disk being very slow etc. Difficult to say more without having more information about the infrastructure setup on Azure and config used. Things like azure instance types, whether Seqera Fusion / other solution was used, attached storage types and so on.

[d4straub]

Closing this because that wont be solved here unfortunately, partially also discussed in #813