Trinity job failed

usegalaxy.org support
1

Dear Galaxy Support Team,

I encountered an error while running Trinity on the Galaxy instance. The job failed almost immediately with the following message:

mktemp: failed to create directory via template ‘/tmp/slurm_job_3596145/tmp.XXXXXXXXXX’: No such file or directory

Job details:

  • Tool: Trinity (iuc/trinity 2.15.1+galaxy1)

  • Job API ID: bbd44e69cb8906b54648608049cd8029

  • Dataset UUID: 7b88365f-0613-4327-8caa-6467c1aad1ea

  • History dataset: Trinity on data 45 and data 42: Assembled Transcripts

  • Date: August 29, 2025

It seems the $TMPDIR (or $TRINITY_SCRATCH_DIR) points to /tmp/slurm_job_3596145, but this parent directory does not exist on the compute node. As a result, mktemp fails to create the scratch directory and the Trinity job terminates with exit code 1.

2

Hi @Pedro_Luis_Ramos-Gon

If you are really working at UseGalaxy.org, this might be expected depending on the options used, or even just by chance!

This post has more details (tutorial help, other resource links) but the top summary is here

Current advice

  1. Trinity may work at the UseGalaxy.org server but possibly only for small training types of data that do not involve pooled samples.
  2. Full analysis jobs should consider rnaSPAdes instead at this server.
  3. Other UseGalaxy servers can be alternatives: UseGalaxy.eu and UseGalaxy.org.au are the other two large public options.
  4. You don’t need to start over! Just move your history → FAQ: Transfer entire histories from one Galaxy server to another

I hope this helps to clarify what is going on and provides an alternative! Let us know if you have follow up questions. :slight_smile: