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lds2_indexer not found during rnaseq_collapse #267
Description
I am running EGAPX 1.0 on a SLURM cluster using Singularity.
The pipeline fails at:
egapx:rnaseq_short_plane:rnaseq_short_plane:rnaseq_collapse:run_rnaseq_collapse
with the following error:
Info: (106.11) Registry file of application "lds2_indexer" is not found
The .command.run file contains:
container: '/path/egapx/local_cache/ncbi-egapx-1.0.img'
and my io.config specifies:
singularity.enabled = true
process.container = '/path/egapx/local_cache/ncbi-egapx-1.0.img'
However, I have the impression that the Singularity container may not actually be invoked for this process, or that lds2_indexer is being searched for outside the container.
Could you please confirm whether this is the expected way to configure the EGAPX container, and how I can verify that lds2_indexer is being executed from inside the container?
Thanks
Gaetan
Activity
boukn commentedon Sep 4, 2026
This is a completely ignorable error message. The "Info" tag means its not an Error or Warning. Its a deep internal ncbi code thing that can be entirely ignored.
This is not the same thing as nextflow, bash, or singularity, being unable to find and run the application. That this message printed means that the application was found and did started running.
As for the naseq_collapse failure, I would need the logs from the failed work-dir?