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geronimp / enrichM

Toolbox for comparative genomics of MAGs
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Error opening file /home/databases/enrichm_database_v10/databases/uniref100.dmnd #108

Open zyyalice opened 4 years ago

zyyalice commented 4 years ago

Hi

I get this error when i use the following commond:

enrichm annotate --genome_directory all_cat/ --ko --threads 40 --output 1 [2020-06-28 09:21:07 AM] INFO: Running command: /home/emma/anaconda2/envs/enrichm_0.5.0/bin/enrichm annotate --genome_directory all_cat/ --ko --threads 40 --output 1 [2020-06-28 09:21:07 AM] INFO: Loading databases [2020-06-28 09:21:07 AM] INFO: Loading reference db paths [2020-06-28 09:21:08 AM] INFO: Running pipeline: annotate [2020-06-28 09:21:08 AM] INFO: Setting up for genome annotation [2020-06-28 09:21:08 AM] INFO: Calling proteins for annotation [2020-06-28 09:21:08 AM] INFO: - Calling proteins for 4 genomes [2020-06-28 09:22:34 AM] INFO: Starting annotation: [2020-06-28 09:22:34 AM] INFO: - Annotating genomes with ko ids [2020-06-28 09:22:34 AM] INFO: - BLASTing genomes No such file or directory Error: Error opening file /home/emma/databases/enrichm_database_v10/databases/uniref100.dmnd Traceback (most recent call last): File "/home/emma/anaconda2/envs/enrichm_0.5.0/bin/enrichm", line 357, in r.main(args, sys.argv) File "/home/emma/anaconda2/envs/enrichm_0.5.0/lib/python3.7/site-packages/enrichm/run.py", line 323, in main args.protein_files) File "/home/emma/anaconda2/envs/enrichm_0.5.0/lib/python3.7/site-packages/enrichm/annotate.py", line 661, in do self.annotate_ko(genomes_list) File "/home/emma/anaconda2/envs/enrichm_0.5.0/lib/python3.7/site-packages/enrichm/annotate.py", line 230, in annotate_ko for genome_name, batch in self.get_batches(output_annotation_path): File "/home/emma/anaconda2/envs/enrichm_0.5.0/lib/python3.7/site-packages/enrichm/annotate.py", line 242, in get_batches input_file_io = open(input_file) FileNotFoundError: [Errno 2] No such file or directory: '1/annotations_ko/DIAMOND_search.tsv'

Could you help me? Thank you! Looking forward to your reply.

SvenTobias-Hunefeldt commented 3 years ago

Hi.

How did you download enrichM? Because if you do it over conda then you end up downloading version 0.4.3, which did not have the option of hmm/diamond within the python script, while the uniref100 database file "home/emma/databases/enrichm_database_v10/databases/uniref100.dmnd" had already been split into hmmer and diamond compatible versions.

You should be able to check what version you have by calling conda list inside your enrvironment.

The way I fixed it is by downloading the 0.5.0 from "https://anaconda.org/bioconda/enrichm/files" and used that to install enrichM into a conda environment.