common-workflow-language / common-workflow-language/cwltool

bind source path does not exist - cwltool keeps waiting / running does not stop

Open
#1,887 2 comments 2 reactions 0 assignees View on GitHub
Dominant language
Python
Stars
376
Forks
255
Avg merge
2d 7h
Merged PRs (30d)
12

Description

## Expected Behavior
The cwltool execution should stop
Ticket is in a way related to https://github.com/common-workflow-language/cwltool/issues/1433

## Actual Behavior
It just hangs

## Workflow Code

Any kind of system that can cause a `Error response from daemon: invalid mount config for type "bind": bind source path does not exist`

## Full Traceback
```pytb
INFO [job fastqc.cwl] /Volumes/Git/m-unlock/cwl/tests/quality/TEMPsni_4q21$ docker \
run \
-i \
--mount=type=bind,source=/Volumes/Git/m-unlock/cwl/tests/quality/TEMPsni_4q21,target=/UGPAAz \
--mount=type=bind,source=/Volumes/Git/m-unlock/cwl/tests/quality/TEMPzo3plhh_,target=/tmp \
--mount=type=bind,source=/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpbjuirt14,target=/var/lib/cwl/stga89df90a-6e44-4402-b5f1-c31fe009096c/forward.fastq.gz,readonly \
--mount=type=bind,source=/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpl03c7t5g,target=/var/lib/cwl/stga1bc4c48-0a08-41e4-b81a-605af80f6c6c/reverse.fastq.gz,readonly \
--workdir=/UGPAAz \
--read-only=true \
--net=none \
--user=501:20 \
--rm \
--cidfile=/Volumes/Git/m-unlock/cwl/tests/quality/TEMP3vfjc209/20230817154231-366180.cid \
--env=TMPDIR=/tmp \
--env=HOME=/UGPAAz \
docker-registry.wur.nl/m-unlock/docker/fastqc:0.11.9 \
fastqc \
--outdir \
FASTQC \
--threads \
1 \
/var/lib/cwl/stga89df90a-6e44-4402-b5f1-c31fe009096c/forward.fastq.gz \
/var/lib/cwl/stga1bc4c48-0a08-41e4-b81a-605af80f6c6c/reverse.fastq.gz
docker: Error response from daemon: invalid mount config for type "bind": bind source path does not exist: /host_mnt/private/var/folders/jt/8knvb4rn6zzb5pn7247hc8gh0000gn/T/tmpbjuirt14.
See 'docker run --help'.
```

## Your Environment
* cwltool version: 3.1.20230624081518

Contributor guide

Open the contributing guide

Assessment

This issue has not been assessed yet.

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.