Error: disk space?

[sophie-03]

Hi, I’m trying to run cactus but am getting an error regarding disk space - however I’ve made sure I have plenty of space available so I don’t think its actually an error with disk space. I’m hoping you can help find what the issue is, this is the error file I get: cactus.err.txt

[glennhickey]

OSError: [Errno 28] No space left on device is pretty unambiguous. I'm guessing what's happening is that you have lots of room where you are running cactus from, but cactus is using /tmp for all its temporary files and you're running out of space there.

You can tell cactus to write its temporary files somewhere else with the --workDir option or by using one of the environment variables mentioned below.

--workDir WORKDIR     Absolute path to directory where temporary files
                        generated during the Toil run should be placed.
                        Standard output and error from batch system jobs
                        (unless --noStdOutErr) will be placed in this
                        directory. A cache directory may be placed in this
                        directory. Temp files and folders will be placed in a
                        directory toil-<workflowID> within workDir. The
                        workflowID is generated by Toil and will be reported
                        in the workflow logs. Default is determined by the
                        variables (TMPDIR, TEMP, TMP) via mkdtemp. This
                        directory needs to exist on all machines running jobs;
                        if capturing standard output and error from batch
                        system jobs is desired, it will generally need to be
                        on a shared file system. When sharing a cache between
                        containers on a host, this directory must be shared
                        between the containers.

[alptaciroglu]

I am having a similar problem. I tried changing workDir, but didn't work. Attaching log file here in case it is useful. cactusLogFile_031220.txt

[alptaciroglu]

Any updates on this?

[glennhickey]

You're running out of disk. Since this is happening within Docker, it is probably happening wherever Docker is storing data on your system (and is outside of Cactus's control).

[glennhickey]

Sorry, I take that back. This is a bug. Cactus is calling sort in this command, which is using your system's temp directory rather than the one specified in workDir.

[alptaciroglu]

Thanks for the update!