Error while searching proteins against Swissprot

[Aluminio-visto]

Hi everyone, I'm using Microbeannotator to re-annotate some plasmid proteins I've got in a Prokka.faa file. As I built the database with diamond method, I launch microbeannotator with the same method but I keep getting the same error (see below). When I try to run it with sword metod everything goes fine (although pretty slowly), with blast method the program is not able to run the swissprot, refseq or trembl sections. I'm running on a 132Gb, 36 threads machine with enough disk space. Ubuntu 20.04, Conda with microbeannotator virtual environment. I tried to solve this by downloading a properly functioning diamond binary and using --method_bin, but it doesn't work neither. Any help would be greatly appreciated. Thank you in advance.

microbeannotator -i ./ref/PROKKA_05122022.faa -d /home/usuario/Databases/microbeannotator/ --method diamond -o ./microannotb --threads 30

2022-05-20 14:49:34,893 [INFO]: ---- This is MicrobeAnnotator v2.0.5 ---- 2022-05-20 14:49:34,893 [INFO]: Validating user inputs 2022-05-20 14:49:34,893 [INFO]: Passed 2022-05-20 14:49:34,893 [INFO]: Processing 1 files. I will run 1 files in parallel with 30 threads per file. 2022-05-20 14:49:34,894 [INFO]: Searching proteins against KOfam profiles 2022-05-20 14:49:34,894 [INFO]: Parsing HMM profile metadata 2022-05-20 14:49:42,431 [INFO]: Filtering and saving results... 2022-05-20 14:49:42,436 [INFO]: Search against KOfam done! 2022-05-20 14:49:42,483 [INFO]: Searching proteins against Swissprot No such file or directory Error: Error calling stat on file /home/usuario/Databases/microbeannotator/protein_db/uniprot_sprot.dmnd multiprocessing.pool.RemoteTraceback: """ Traceback (most recent call last): File "/home/usuario/miniconda3/envs/microbeannotator/lib/python3.7/multiprocessing/pool.py", line 121, in worker result = (True, func(*args, *kwds)) File "/home/usuario/miniconda3/envs/microbeannotator/lib/python3.7/multiprocessing/pool.py", line 44, in mapstar return list(map(args)) File "/home/usuario/miniconda3/envs/microbeannotator/lib/python3.7/site-packages/microbeannotator/pipeline/protein_search.py", line 232, in similarity_search blast_filter_slow(method_output_file, filtered_file, id_perc, bitscore, evalue, aln_percent) File "/home/usuario/miniconda3/envs/microbeannotator/lib/python3.7/site-packages/microbeannotator/pipeline/protein_search.py", line 138, in blast_filter_slow with open(input_tab) as blast_input: FileNotFoundError: [Errno 2] No such file or directory: 'microannotb/swissprot_results/PROKKA_05122022.faa.step_2.diamond' """

The above exception was the direct cause of the following exception:

Traceback (most recent call last): File "/home/usuario/miniconda3/envs/microbeannotator/bin/microbeannotator", line 981, in main() File "/home/usuario/miniconda3/envs/microbeannotator/bin/microbeannotator", line 429, in main multiple_arguments=arguments_to_pass), input_proteins) File "/home/usuario/miniconda3/envs/microbeannotator/lib/python3.7/multiprocessing/pool.py", line 268, in map return self._map_async(func, iterable, mapstar, chunksize).get() File "/home/usuario/miniconda3/envs/microbeannotator/lib/python3.7/multiprocessing/pool.py", line 657, in get raise self._value FileNotFoundError: [Errno 2] No such file or directory: 'microannotb/swissprot_results/PROKKA_05122022.faa.step_2.diamond'

[nlmjacquemin]

Hi @Aluminio-visto,

I have the same error, may you have some updates on this?

Thanks

[NataliHB]

Hi,

I've got this error, has anyone managed to get it to work?

Thanks

[luciagrami]

There is a similar issue and apparently the problem is diamond, if you change to method blast it works fine