[bug] localization error when using Cromwell via Docker

Question

[bug] localization error when using Cromwell via Docker

vsoch opened this issue 6 years ago · comments

This isn't an issue / bug proper, but rather just an issue that I can link in the documentation to explain the issue with using cromwell inside Docker. I'll open and close likely when I get it fleshed out fully:

Localization via hard link has failed: /cromwell-executions/wgbs/47d02aff-5371-478e-a412-54189e06b303/call-flatten_/inputs/-1474066501/flowcell_1_1_1.fastq.gz -> /opt/data/fastq/flowcell_1_1_1.fastq.gz: Invalid cross-device link

carry on! And thanks to @Bek for the help and pointing this out earlier!

Ulugbek Baymuradov · Answer 1 · Sat Dec 22 2018 07:04:56 GMT+0800 (China Standard Time)

This was due to managing mounted file systems in the case of running a container inside another container. Cromwell running inside a container will try to launch another container for a task when running locally.