staramr in Galaxy error

[PHemarajata]

Hi, I installed staramr in Galaxy on a native Ubuntu, and got an error trying after using a Shovill-assembled configs (in a multi-fasta file). I was wondering what I did wrong and would appreciate any suggestion. Thank you!

Fatal error: Exit code 1 () 2018-06-10 14:51:10,922 INFO: No --pointfinder-organism specified. Will not search the PointFinder databases 2018-06-10 14:51:10,922 INFO: --output-dir not set. Files will be output to the respective --output-[type] setting 2018-06-10 14:51:10,931 INFO: Making BLAST databases for input files 2018-06-10 14:51:10,939 ERROR: Command '['makeblastdb', '-in', '/home/phemarajata/galaxy/database/tmp/tmpuuzos1zh/input-genomes/Shovill on data 11 and data 10: Contigs.fasta', '-dbtype', 'nucl', '-parse_seqids']' returned non-zero exit status 1. Traceback (most recent call last): File "/home/phemarajata/galaxy/database/dependencies/_conda/envs/__staramr@0.2.0/bin/staramr", line 68, in args.run_command(args) File "/home/phemarajata/galaxy/database/dependencies/_conda/envs/__staramr@0.2.0/lib/python3.6/site-packages/staramr/subcommand/Search.py", line 356, in run files=args.files) File "/home/phemarajata/galaxy/database/dependencies/_conda/envs/__staramr@0.2.0/lib/python3.6/site-packages/staramr/subcommand/Search.py", line 216, in _generate_results plength_threshold_pointfinder, report_all_blast) File "/home/phemarajata/galaxy/database/dependencies/_conda/envs/__staramr@0.2.0/lib/python3.6/site-packages/staramr/detection/AMRDetection.py", line 61, in run_amr_detection self._amr_detection_handler.run_blasts(files) File "/home/phemarajata/galaxy/database/dependencies/_conda/envs/__staramr@0.2.0/lib/python3.6/site-packages/staramr/blast/BlastHandler.py", line 96, in run_blasts db_files = self._make_db_from_input_files(self._input_genomes_tmp_dir, files) File "/home/phemarajata/galaxy/database/dependencies/_conda/envs/__staramr@0.2.0/lib/python3.6/site-packages/staramr/blast/BlastHandler.py", line 120, in _make_db_from_input_files future_blastdb.result() File "/home/phemarajata/galaxy/database/dependencies/_conda/envs/__staramr@0.2.0/lib/python3.6/concurrent/futures/_base.py", line 432, in result return self.__get_result() File "/home/phemarajata/galaxy/database/dependencies/_conda/envs/__staramr@0.2.0/lib/python3.6/concurrent/futures/_base.py", line 384, in __get_result raise self._exception File "/home/phemarajata/galaxy/database/dependencies/_conda/envs/__staramr@0.2.0/lib/python3.6/concurrent/futures/thread.py", line 56, in run result = self.fn(*self.args, **self.kwargs) File "/home/phemarajata/galaxy/database/dependencies/_conda/envs/__staramr@0.2.0/lib/python3.6/site-packages/staramr/blast/BlastHandler.py", line 196, in _make_blast_db subprocess.run(command, stdout=subprocess.PIPE, stderr=subprocess.PIPE).check_returncode() File "/home/phemarajata/galaxy/database/dependencies/_conda/envs/__staramr@0.2.0/lib/python3.6/subprocess.py", line 369, in check_returncode self.stderr) subprocess.CalledProcessError: Command '['makeblastdb', '-in', '/home/phemarajata/galaxy/database/tmp/tmpuuzos1zh/input-genomes/Shovill on data 11 and data 10: Contigs.fasta', '-dbtype', 'nucl', '-parse_seqids']' returned non-zero exit status 1.

[apetkau]

Woops, looks like I forgot to test the case where there's spaces in the input dataset filename in Galaxy. I've made an issue for this https://github.com/phac-nml/staramr/issues/19.

In the meantime, could you rename the dataset Shovill on data 11 and data 10: Contigs.fasta to remove the spaces in the name?

[PHemarajata]

It works! Thank you so much. I'm developing a Galaxy instance for my microbiologists and I love this all-in-one tool.

[apetkau]

No problem. I'm glad it's useful. If you have any other questions let me know.

[apetkau]

This should now be permanently fixed @PHemarajata. You will have to update the Galaxy tool to get the fix.