Step 9 - Merging proteins files

[ntromas]

Hi!

I am trying to download the full db using Aspera and I got an error at step 9 :

Completed: 392708K bytes transferred in 58 seconds (54553K bits/sec), in 14 files, 1 directory. 2022-02-15 13:32:43,211 [INFO]: Merging protein files Traceback (most recent call last): File "/home/nico/miniconda3/envs/microbeannotator/bin/microbeannotator_db_builder", line 445, in main() File "/home/nico/miniconda3/envs/microbeannotator/bin/microbeannotator_db_builder", line 437, in main single_step, aspera, keep_temp, bin_path) File "/home/nico/miniconda3/envs/microbeannotator/bin/microbeannotator_db_builder", line 175, in database_duilder refseq_prot = refseq.refseq_fasta_downloader(database_directory) File "/home/nico/miniconda3/envs/microbeannotator/lib/python3.7/site-packages/microbeannotator/database/refseq_data_downloader.py", line 104, in refseq_fasta_downloader rmtree(temp_fasta_files) File "/home/nico/miniconda3/envs/microbeannotator/lib/python3.7/shutil.py", line 498, in rmtree onerror(os.rmdir, path, sys.exc_info()) File "/home/nico/miniconda3/envs/microbeannotator/lib/python3.7/shutil.py", line 496, in rmtree os.rmdir(path) OSError: [Errno 39] Directory not empty: 'MicrobeAnnotator_full/temp_refseq_proteins'

The funny part is tat the folder temp_refseq_proteins is empty...

Thanks for your help,

Nico

[silvtal]

You could try out my branch, which helped me with similar database-building problems. I list the changes I made here

[justinmaire]

Hello,

I'm having a similar issue and the database builder stops at step 9, has there been an update to fix it, or is there something else I should do that will fix it?

(microbeannotator) ubuntu@metagenomics:/data$ microbeannotator_db_builder -d MicrobeAnnotator_DB -m diamond --step 9 2022-05-24 00:30:59,574 [INFO]: This is MicrobeAnnotator v2.0.5 2022-05-24 00:30:59,575 [INFO]: I will download and format the databases I use. 2022-05-24 00:30:59,575 [INFO]: Creating database folders 2022-05-24 00:30:59,575 [INFO]: Step 9 2022-05-24 00:30:59,575 [INFO]: Downloading protein fasta files using Aspera Connect. Traceback (most recent call last): File "/data/miniconda3/envs/microbeannotator/bin/microbeannotator_db_builder", line 445, in main() File "/data/miniconda3/envs/microbeannotator/bin/microbeannotator_db_builder", line 437, in main single_step, aspera, keep_temp, bin_path) File "/data/miniconda3/envs/microbeannotator/bin/microbeannotator_db_builder", line 175, in database_duilder refseq_prot = refseq.refseq_fasta_downloader(database_directory) File "/data/miniconda3/envs/microbeannotator/lib/python3.7/site-packages/microbeannotator/database/refseq_data_downloader.py", line 61, in refseq_fasta_downloader ascp_key = get_aspera_key() File "/data/miniconda3/envs/microbeannotator/lib/python3.7/site-packages/microbeannotator/database/refseq_data_downloader.py", line 277, in get_aspera_key install_folder = Path(path_to_ascp).parents[1] File "/data/miniconda3/envs/microbeannotator/lib/python3.7/pathlib.py", line 1027, in new self = cls._from_parts(args, init=False) File "/data/miniconda3/envs/microbeannotator/lib/python3.7/pathlib.py", line 674, in _from_parts drv, root, parts = self._parse_args(args) File "/data/miniconda3/envs/microbeannotator/lib/python3.7/pathlib.py", line 658, in _parse_args a = os.fspath(a) TypeError: expected str, bytes or os.PathLike object, not NoneType

Thanks! Justin

[NataliHB]

Hi,

I am having the same issue in this step:

2022-10-10 09:22:32,724 [INFO]: Step 9 2022-10-10 09:22:32,724 [INFO]: Downloading protein fasta files using Aspera Connect. Traceback (most recent call last): File "/mnt/iusers01/fatpou01/sees01/mbexrnh4/.conda/envs/microbeannotator/bin/microbeannotator_db_builder", line 445, in main() File "/mnt/iusers01/fatpou01/sees01/mbexrnh4/.conda/envs/microbeannotator/bin/microbeannotator_db_builder", line 437, in main single_step, aspera, keep_temp, bin_path) File "/mnt/iusers01/fatpou01/sees01/mbexrnh4/.conda/envs/microbeannotator/bin/microbeannotator_db_builder", line 175, in database_duilder refseq_prot = refseq.refseq_fasta_downloader(database_directory) File "/mnt/iusers01/fatpou01/sees01/mbexrnh4/.conda/envs/microbeannotator/lib/python3.7/site-packages/microbeannotator/database/refseq_data_downloader.py", line 61, in refseq_fasta_downloader ascp_key = get_aspera_key() File "/mnt/iusers01/fatpou01/sees01/mbexrnh4/.conda/envs/microbeannotator/lib/python3.7/site-packages/microbeannotator/database/refseq_data_downloader.py", line 277, in get_aspera_key install_folder = Path(path_to_ascp).parents[1] File "/mnt/iusers01/fatpou01/sees01/mbexrnh4/.conda/envs/microbeannotator/lib/python3.7/pathlib.py", line 1027, in new self = cls._from_parts(args, init=False) File "/mnt/iusers01/fatpou01/sees01/mbexrnh4/.conda/envs/microbeannotator/lib/python3.7/pathlib.py", line 674, in _from_parts drv, root, parts = self._parse_args(args) File "/mnt/iusers01/fatpou01/sees01/mbexrnh4/.conda/envs/microbeannotator/lib/python3.7/pathlib.py", line 658, in _parse_args a = os.fspath(a) TypeError: expected str, bytes or os.PathLike object, not NoneType

Does anyone has managed to solve this?

Cheers, Natali