Error running Macrel on Wormbase genome

[Javier Calvelo]

Hello all. I ran with the following error trying to run Macrel on the Hymenolepis microstoma genome availabl on the genebank. The test files and other assemblies work perfectly. What's is the issue?  Thanks

Genome: 
https://parasite.wormbase.org/Hymenolepis_microstoma_prjeb124/Info/Index/

Comand line:
macrel contigs -t 25 --fasta hymenolepis_microstoma.PRJEB124.WBPS16.genomic.fa --output TEST

Error message:
Traceback (most recent call last):
 File "/home/amanda/miniconda3/envs/macrel/bin/macrel", line 11, in <module>
   sys.exit(main())
 File "/home/amanda/miniconda3/envs/macrel/lib/python3.9/site-packages/macrel/main.py", line 349, in m
ain
   do_smorfs(args, tdir,logfile)
 File "/home/amanda/miniconda3/envs/macrel/lib/python3.9/site-packages/macrel/main.py", line 147, in d
o_smorfs
   subprocess.check_call(
 File "/home/amanda/miniconda3/envs/macrel/lib/python3.9/subprocess.py", line 373, in check_call
   raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['prodigal_sm', '-c', '-m', '-n', '-p', 'meta', '-f', 'sco', '-
a', 'TEST/macrel.out.all_orfs.faa', '-i', '/tmp/tmprjvl0rq4/contigs.fna']' returned non-zero exit statu
s 56.

[Luis Pedro Coelho]

Dear Javier,

The immediate issue is that the genome is too large for prodigal (which was developed for prokaryotes):

Sequence too long (max 32000000 permitted).

*

There is another UX issues in that macrel is not printing the error from prodigal to allow the user to diagnose it. I will open an issue (@Celio Dias: can you have a look and see if we can fix it for the next release?)

Best

Luis

Luis Pedro Coelho | Fudan University | http://luispedro.org

https://orcid.org/0000-0002-9280-7885

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[Javier Calvelo]

I see, thanks Luis

[Luis Pedro Coelho]

As a workaround, you can split the genome into chunks. That should work
Luis