Error while processing 54 genomes

[aaronmussig]

I am also getting similar error while processing 54 genomes:
ERROR: Input file does not exist: /tmp/tmpl4th9zaugtdbtk_prodigal_tmp_/4/Ensifer_psoraleae_CCBAU 65732_GCF_013283645.1.gff
Process Process-3:1:1:
Traceback (most recent call last):
File "/home/dnd/miniconda3/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
self.run()
File "/home/dnd/miniconda3/lib/python3.8/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
File "/home/dnd/miniconda3/lib/python3.8/site-packages/gtdbtk/biolib_lite/parallel.py", line 107, in __producer
rtn = producer_callback(dataItem)
File "/home/dnd/miniconda3/lib/python3.8/site-packages/gtdbtk/biolib_lite/prodigal_biolib.py", line 147, in producer
prodigalParser = ProdigalGeneFeatureParser(gff_file_tmp)
File "/home/dnd/miniconda3/lib/python3.8/site-packages/gtdbtk/biolib_lite/prodigal_biolib.py", line 313, in init
check_file_exists(filename)
File "/home/dnd/miniconda3/lib/python3.8/site-packages/gtdbtk/biolib_lite/common.py", line 96, in check_file_exists
raise BioLibFileNotFound('Input file does not exist: ' + input_file)
gtdbtk.biolib_lite.exceptions.BioLibFileNotFound: Input file does not exist: /tmp/tmpl4th9zaugtdbtk_prodigal_tmp/4/Ensifer_psoraleae_CCBAU 65732_GCF_013283645.1.gff

gtdbtk.biolib_lite.exceptions.BioLibFileNotFound: Input file does not exist: /tmp/tmpu5ref0kbgtdbtk_prodigal_tmp_/4/Ensifer_psoraleae_CCBAU 65732_G283645.1.gff
Process Process-3:
Traceback (most recent call last):
File "/home/dnd/miniconda3/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
self.run()
File "/home/dnd/miniconda3/lib/python3.8/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
File "/home/dnd/miniconda3/lib/python3.8/site-packages/gtdbtk/external/prodigal.py", line 141, in _worker
rtn_files = self._run_prodigal(genome_id, file_path, usr_tln_table)
File "/home/dnd/miniconda3/lib/python3.8/site-packages/gtdbtk/external/prodigal.py", line 107, in _run_prodigal
raise Exception("An error was encountered while running Prodigal.")
Exception: An error was encountered while running Prodigal.
==> Processed 52/54 genomes (96%) |██████████████▍| [87.36genome/s, ETA 00:00][2021-06-19 17:22:08] ERROR: Controlled exit resulting from an unrecoe error or warning.

================================================================================
EXCEPTION: ProdigalException
MESSAGE: An exception was caught while running Prodigal.

Originally posted by @RahiPraveen in #325 (comment)

[aaronmussig]

Hi @RahiPraveen this issue is caused by having a space in the name of the input file, if you replace the spaces with underscores it will work.

In version 1.5.1 this will be fixed.

[RahiPraveen]

Hi @RahiPraveen this issue is caused by having a space in the name of the input file, if you replace the spaces with underscores it will work.

In version 1.5.1 this will be fixed.
@aaronmussig
Oh, yes I found those sequences with spaces in their labels, it worked. Thanks