Comments (2)
Thank you for your report, TJ!
The issue seems to be related to specifics of your podman installation. It is a bit puzzling that a read-only command that executes cat
under a podman call produces what seems to be a write operation (mkdir).
We will have a look and discuss what we can do here.
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Related Issues (20)
- [BUG] SIGBUS error on HPC using singularity HOT 9
- [FEATURE REQUEST] ARM64 support HOT 2
- [FEATURE REQUEST] Add a prefix to the output files of PGAP. HOT 1
- pgap.py not found with docker container ncbi/pgap HOT 4
- [BUG] Podman: container name is not respected HOT 3
- [BUG] pgap.py --update HOT 3
- [BUG] PGAP fails install when running on singularity. HOT 2
- [BUG] When two input genomes have same basename, the first genome is mistakenly used for the second run. HOT 3
- [FEATURE REQUEST] direct S3 access to input datasets HOT 5
- Running PGAP with Metagenomic Assembled Genome HOT 11
- [BUG] PGAP analysis generates all files except .aa and .gbk HOT 35
- [FEATURE REQUEST] Unable to retrieve additional reference data from https://s3.amazonaws.com/pgap/input-[version].tgz. HOT 2
- Problem with running pgap annotation HOT 1
- [FEATURE REQUEST] Any plans about EGAP (Eukaryotic Genome Annotation Pipeline)? HOT 2
- [FEATURE REQUEST] <Turn Off GO annotation> HOT 7
- [BUG] Binding non-existent file HOT 6
- [BUG] <title>The length of the gene exceeds the length of the conitg HOT 10
- PIPELINE TEST w/ M. genitalium - PermissionError: [Errno 13] Permission denied: '/pgap/output/debug/tmpdir HOT 38
- [BUG] <title>How to run pgap.py with qsub file. HOT 5
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