Issue mpwt with the --hf option

Hi,

I use Pathway Tools 25.5. and mpwt 0.7.0. on 12 bacteria gbk files generated with emapper2gbk and I use this command of mpwt:

mpwt -f ${path_directory_input} -o ${path_directory_output} --patho --hf --md --log ../output_job/mpwt/outpmpwt_logs --taxon-file ${path_directory_input}taxon_id.tsv --cpu 40  -v --flat --clean

There seems to be an error when using mpwt with the --hf option When I run my job on the cluster the .dat files are all created but when generating the log_error.txt and resume_inference.tsv files, there is an error and the files are not complete. In my .log it is written :

....
|Output Check| 12 on 12 builds have passed!
Traceback (most recent call last):
  File "/usr/local/bin/mpwt", line 8, in <module>
    sys.exit(run_mpwt())
  File "/usr/local/lib/python3.6/dist-packages/mpwt/__main__.py", line 376, in run_mpwt
    permission=permission)
  File "/usr/local/lib/python3.6/dist-packages/mpwt/mpwt_workflow.py", line 153, in multiprocess_pwt
    taxon_file, permission)
  File "/usr/local/lib/python3.6/dist-packages/mpwt/mpwt_workflow.py", line 393, in independent_mpwt
    check_mpwt_pathologic_runs(input_folders, patho_log)
  File "/usr/local/lib/python3.6/dist-packages/mpwt/results_check.py", line 199, in check_mpwt_pathologic_runs
    patho_resume_writer.writerow(*species_pathologic_informations[12])
TypeError: writerow() takes exactly one argument (0 given)
srun: error: zonda14: task 0: Exited with exit code 1

The files are not complete and since they are written from the pathologic.log file I have gone through it and there seems to be a recurring error which would explain why the log_error.txt and resume_inference.tsv files are not complete:

Normally to the end of one of my pathologic.log file after hole filler:(this file is resumed in the log_error.txt and resume_inference.tsv files)

Starting Hole Filler for ACUTALIBACTER_MURIS_STRAIN_KB18.
[Saving KB ACUTALIBACTER_MURIS_STRAIN_KB18BASE to V4-FASL file /beegfs/cmuller/pathwaystools/ptools-local/pgdbs/user/acutalibacter_muris_strain_kb18cyc/1.0/kb/acutalibacter_muris_strain_kb18base.ocelot
 17977 frames saved]
02-Mar-2022  03:05:21 Done

Crash to the end of one of my pathologic.log file after hole filler:(this file is not resumed in the log_error.txt and resume_inference.tsv files)

02-Mar-2022  00:38:14 Fatal error: mkdir of /programs/pathway-tools/aic-export/pgdbs/biocyc/ecocyc/25.5/data/priors/ failed: Read-only file system [errno=30].
Evaluation stack:

 ->(TPL::ZOOM-COMMAND :FROM-READ-EVAL-PRINT-LOOP NIL ...)
   (SYS::..RUNTIME-OPERATION "applyn" :UNKNOWN-ARGS)
   (TPL:DO-COMMAND "zoom" :FROM-READ-EVAL-PRINT-LOOP ...)

I think it might be a --hf problem because when I do the mpwt command without this option, it runs correctly. I found in pathwaystools/ptools-local/pgdbs/user/SPECIEScyc/1.0 that some species do not have the files: STRAIN_KB18_filled-holes_2022-03-07.html and the hole data.

And I suspect, from my data, that this might be because these specific gbk files are generated with multi-sequence FASTA files. I'm not sure about this but it seems that mpwt with the --hf option on each strain with a gbk file of this fasta type doesn't work in my data but work with others.

But it's weird because then why would it work without the --hf option?

I thank you in advance for your help

Best wishes,

Muller Coralie

AuReMe / mpwt

Issue mpwt with the --hf option #73