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

docker: Error response from daemon: invalid mount config for type "bind": bind source path does not exist

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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

Open the contributing guide

Assessment

This issue has not been assessed yet.

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