sh: 0: Illegal option -j

[jguhlin]

I fixed the issue of the missing TephraDB files by copying them manually and changing the configuration (Apparently singularity wants the user to be root, but that needs the --fakeroot command to work, which is difficult) -- I think you could rebuild it to work around that at some point.

But now I am receiving an illegal option -j

`INFO - ======== Tephra version: 0.12.5 (started at: 10-06-2020 05:41:14) ======== INFO - Configuration - Log file for monitoring progress and errors: tephra_full.log INFO - Configuration - Genome file: polished_1.fasta.masked INFO - Configuration - Repeat database: consensi.fa.classified INFO - Configuration - Number of threads: 24 INFO - Command - 'tephra findltrs' started at: 10-06-2020 05:41:14. sh: 0: Illegal option -j ERROR - 'gt suffixerator' failed with exit value: 2. Here is the output:

INFO - Command - 'tephra findltrs' completed at: 10-06-2020 05:41:15. INFO - Command - 'tephra findtrims' started at: 10-06-2020 05:41:15.

[ERROR]: Copy failed: No such file or directory INFO - Command - 'tephra findtrims' completed at: 10-06-2020 05:41:16. INFO - Command - 'tephra findhelitrons' started at: 10-06-2020 05:41:16.

[ERROR]: Could not open file: /db/polished_1_tephra_hscan_helitrons.hel.fa INFO - Command - 'tephra findhelitrons' completed at: 10-06-2020 05:41:38. INFO - Command - 'tephra findtirs' started at: 10-06-2020 05:41:38. Copy failed: No such file or directory at /usr/local/share/perl/5.26.1/Tephra/Command/findtirs.pm line 73. INFO - Command - 'tephra findtirs' completed at: 10-06-2020 05:41:39. Use of uninitialized value $tirc_fas in -e at /usr/local/share/perl/5.26.1/Tephra/Command/all.pm line 282. INFO - Command - 'tephra findnonltrs' started at: 10-06-2020 05:41:39. `

Any ideas?

[sestaton]

What OS are you trying to use Singularity on? This is one thing I've not been able to test thoroughly on different systems.

I can see the image is also not up to date, so I will try to rebuild that today.

[jguhlin]

Ubuntu. But let me try the updated image and see if it is still an issue.

[sestaton]

Ubuntu. But let me try the updated image and see if it is still an issue.

Sorry, I meant I need to update the Singularity image in the repository. There's nothing you can really do on that front for now

[sestaton]

Thank you for the patience. I am making a new release today with large-scale changes to the build system. These changes may not directly fix this issue but they will make it easier to debug problems with the Docker and Singularity.

I will update when a new release is made.

[sestaton]

Could you try again with the latest container version (v0.13.0)?

Also, please show the full commands you use to pull and interact with the container.