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Universc "essential container in task exited" #230

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adamrtalbot opened this issue Jun 2, 2023 · 2 comments
Open

Universc "essential container in task exited" #230

adamrtalbot opened this issue Jun 2, 2023 · 2 comments
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@adamrtalbot
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Description of the bug

During full sized tests using aligner universc, the UNIVERSC process failed with "Essential container in task exited". Unfortunately the logs for the process are empty.

Tower run: https://tower.nf/orgs/nf-core/workspaces/AWSmegatests/watch/PEq66ZO67hldJ

Command used and terminal output

nextflow run 'https://github.com/nf-core/scrnaseq' \
		 -name serene_goodall_2 \
		 -params-file 'https://api.tower.nf/ephemeral/d_mdXl0JaaqLAOtycNO_cQ.json' \
		 -with-tower \
		 -r 6cccb9d37afa873b6799cd09f8589b5b129c8ac1 \
		 -profile test_full,public_aws_ecr \
		 -resume 4fe7371e-2261-44a1-a640-79d6ccd002c9

Relevant files

nf-1dwmFGI1UUZphr.txt
nf-1dwmFGI1UUZphr.log

System information

scrnaseq version: 2.3.1 (#6cccb9d37afa873b6799cd09f8589b5b129c8ac1)
Nextflow: 23.04.1 build 5866

@adamrtalbot adamrtalbot added the bug Something isn't working label Jun 2, 2023
@adamrtalbot adamrtalbot changed the title Universc "essential container in task exited" on full sized tests Universc "essential container in task exited" Jun 2, 2023
@adamrtalbot
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This actually occurs on the test data as well:

nextflow run . -profile test,docker --aligner universc --outdir results

@adamrtalbot
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The log file is added to _log in the working directory:

script running in /universc/launch_universc.sh...
SOURCE '/universc/universc' is an absolute symlink to '/universc/launch_universc.sh'
... script called from /universc
Running launch_universc.sh in '/universc'
UniverSC Copyright (C) 2019 Tom Kelly; Kai Battenberg
This program comes with ABSOLUTELY NO WARRANTY; for details type 'cat LICENSE'. This is free software, and you are welcome to redistribute it under certain conditions; type 'cat LICENSE' for details.
Cell Ranger is called as third-party dependency and is not maintained by this project. Please ensure you comply with the End User License Agreement for all software installed where applicable; for details type 'cat README.md'.
Error: option -t needs to be a technology listed or custom_<barcode>_<UMI>

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