common-workflow-language / common-workflow-language/cwltool
docker: Error response from daemon: invalid mount config for type "bind": bind source path does not exist
- Dominant language
- Python
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- 376
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- 2d 7h
- Merged PRs (30d)
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Description
We have a few reports about the container failing to start because one of the bind mounts cannot be found, the strange thing is that these are different invocations on different operating systems.
```
(env) decagon@Decagons-MacBook-Pro rnaseq-cwl-training-exercises %
cwltool --tmp-outdir-prefix=/Users/decagon/Documents/ifyProjects/outreachy --tmpdir-prefix=/Users/decagon/Documents/ifyProjects/outreachy main.cwl main-input.yaml
INFO /Users/decagon/env/bin/cwltool 3.0.20210319143721
INFO Resolved 'main.cwl' to 'file:///Users/decagon/Documents/ifyProjects/outreachy/rnaseq-cwl-training-exercises/main.cwl'
WARNING Workflow checker warning:
main.cwl:30:11: Source 'alignment' of type ["File", {"type": "array", "items": "File"}] may be
incompatible
main.cwl:36:7: with sink 'bam_sorted' of type "File"
INFO [workflow ] start
INFO [workflow ] starting step STAR
INFO [step STAR] start
INFO [job STAR] /Users/decagon/Documents/ifyProjects/outreachylby4flmu$ docker \
run \
-i \
--mount=type=bind,source=/Users/decagon/Documents/ifyProjects/outreachylby4flmu,target=/muHyRr \
--mount=type=bind,source=/Users/decagon/Documents/ifyProjects/outreachyd4pal9c6,target=/tmp \
--mount=type=bind,source=/Users/decagon/Documents/ifyProjects/outreachy/rnaseq-cwl-training-exercises/rnaseq/raw_fastq/Mov10_oe_1.subset.fq,target=/var/lib/cwl/stg00e6f5c8-8f2b-4f9a-9558-9da84cf9c6d2/Mov10_oe_1.subset.fq,readonly \
--mount=type=bind,source=/Users/decagon/Documents/ifyProjects/outreachy/rnaseq-cwl-training-exercises/hg19-chr1-STAR-index,target=/var/lib/cwl/stg94179c35-f571-448a-b539-6a6ed7f4020e/hg19-chr1-STAR-index,readonly \
--workdir=/muHyRr \
--read-only=true \
--user=501:20 \
--rm \
--env=TMPDIR=/tmp \
--env=HOME=/muHyRr \
--cidfile=/Users/decagon/Documents/ifyProjects/outreachy99r9o6e7/20210407214207-059030.cid \
quay.io/biocontainers/star:2.7.5c--0 \
STAR \
--runMode \
alignReads \
--genomeDir \
/var/lib/cwl/stg94179c35-f571-448a-b539-6a6ed7f4020e/hg19-chr1-STAR-index \
--outSAMunmapped \
Within \
--runThreadN \
4 \
--readFilesIn \
/var/lib/cwl/stg00e6f5c8-8f2b-4f9a-9558-9da84cf9c6d2/Mov10_oe_1.subset.fq \
--outSAMtype \
BAM \
SortedByCoordinate
docker: Error response from daemon: invalid mount config for type "bind": bind source path does not exist: /host_mnt/Users/decagon/Documents/ifyProjects/outreachylby4flmu.
```
## Expected Behavior
Container should run.
## Actual Behavior
Container fails with docker error.
## Workflow Code
The users who have experienced it see it happening regardless of the workflow being run.
Contributor guide
Assessment
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