Re: Error in abundance profiling

[Célio Dias Santos Júnior]

Dear Amiteash,

I could not reproduce your error. However, it seems that something in the handling of temporary files in your system is not working as expected.

Supposedly, you are working on a server. It may have to do with the system used to handle files. Unfortunately, without further info, I cannot do much.

For while, I can suggest you use the "--tmp" option in Macrel and manually direct the temporary files for a location in your system that you can control

or have the rights to write.

Best,

Celio

On Wed, Oct 25, 2023 at 5:17 PM Amiteash Paul <ap6...@nyu.edu> wrote:

Hello everyone. I am trying to run macrel abundance to profile the abundance of AMPs predicted by macrel. However, I am running into the following error repeatedly, soon after the first step (translating protein sequence):

[command_index] Failed to open file '/tmpdata/tmp8bs2midc/paladin.faa' : No such file or directory
Traceback (most recent call last):
  File "/home/ap6444/miniconda3/envs/Jan23/bin/macrel", line 11, in <module>
    sys.exit(main())
  File "/home/ap6444/miniconda3/envs/Jan23/lib/python3.7/site-packages/macrel/main.py", line 358, in main
    do_abundance(args, tdir,logfile)
  File "/home/ap6444/miniconda3/envs/Jan23/lib/python3.7/site-packages/macrel/main.py", line 210, in do_abundance
    stdout=logfile)
  File "/home/ap6444/miniconda3/envs/Jan23/lib/python3.7/subprocess.py", line 363, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['paladin', 'index', '-r3', '/tmpdata/tmp8bs2midc/paladin.faa']' returned non-zero exit status 1

I have previously used macrel abundance without running into the above error. Any guidance regarding the same would be much appreciated.

Thanks and regards.

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