Error "OSError: AF_UNIX path too long"
Bug report
Error in rule GTDBtk_bins_single
when prodigal
is run by GTDB-Tk
:
OSError: AF_UNIX path too long
...
EXCEPTION: ProdigalException
MESSAGE: An exception was caught while running Prodigal:
Log files and screenshots
Steps to reproduce
Code version: v0.1-68-gb6f9da0e
Command
# command used to launch IMP3
# placeholders for paths as these are not relevant
TMPDIR=path/to/tmp/ snakemake -s path/to/Snakefile -rp --rerun-incomplete --cores 12 --configfile path/to/sample.yaml --use-conda --conda-prefix path/to/conda &> path/to/smk.log
Possible fixes
This seems to be related to the length of the tmp folder path stored in the bash
variable $TMPDIR
.
The error could be reproduced when defining the tmp
folder as a sub-folder in the output path (resulting in 85 characters).
After, setting it to /tmp
(TMPDIR=/tmp snakemake ...
) the prodigal
jobs could be run without an issue.