database issue
wittney-m opened this issue · comments
Hi I ran the command below:
source activate super-focus
conda env config vars set SUPERFOCUS_DB=/home/wdmays/miniconda3/envs/super-focus/lib/python3.11/site-packages/superfocus_app/db/
superfocus --threads 8 -q /home/wdmays/SHASTA/fastq_files/zr12348_1_R1.fastq -q /home/wdmays/SHASTA/fastq_files/zr12348_2_R1.fastq -dir /home/wdmays/SHASTA/superfocus_output_diamond -o SHASTA_diamond -a diamond
This is the output error that I am receiving
WARNING: overwriting environment variables set in the machine
overwriting variable ['SUPERFOCUS_DB']
To make your changes take effect please reactivate your environment
[2023-10-10 08:47:31,281 - INFO] SUPER-FOCUS: A tool for agile functional analysis of shotgun metagenomic data
[2023-10-10 08:47:31,282 - INFO] Using /tmp/tmpmq4gqo0o as the temporary directory
Traceback (most recent call last):
File "/home/wdmays/miniconda3/envs/super-focus/bin/superfocus", line 8, in
sys.exit(main())
^^^^^^
File "/home/wdmays/miniconda3/envs/super-focus/lib/python3.11/site-packages/superfocus_app/superfocus.py", line 409, in main
subsystems_translation = get_subsystems(Path(WORK_DIRECTORY, "db/database_PKs.txt"))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/wdmays/miniconda3/envs/super-focus/lib/python3.11/site-packages/superfocus_app/superfocus.py", line 154, in get_subsystems
with open(translation_file) as database_file:
^^^^^^^^^^^^^^^^^^^^^^
FileNotFoundError: [Errno 2] No such file or directory: '/home/wdmays/miniconda3/envs/super-focus/lib/python3.11/site-packages/superfocus_app/db/db/database_PKs.txt'
Do I need to change the location of the databases? I am confused by this error.
Hi,
I have fixed the previous error but now still have issues with using the databases. This is the new error.
#CPU threads: 8
Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1)
Temporary directory: /tmp/tmpt_7akdam
Opening the database... No such file or directory
[0s]
Error: Error opening file /home/wdmays/miniconda3/envs/super-focus/lib/python3.11/site-packages/superfocus_app/db/db/static/diamond/90_clusters.db
Diamond blast was terminated by signal 1
Any other options for getting passed this issue? I have attempted to change the permissions of the files and directory but still no luck.
can you send me the listing (ls) of the files at /home/wdmays/miniconda3/envs/super-focus/lib/python3.11/site-packages/superfocus_app/db/db/static/diamond/?
Hi,
I have a folder with the following directories:
100_clusters
90_clusters
95_clusters
98_clusters
Within each directory is a database. For example in 100_clusters there is 100_clusters.db. file.
i see. the error you shared is expecting /home/wdmays/miniconda3/envs/super-focus/lib/python3.11/site-packages/superfocus_app/db/db/static/diamond/90_clusters.db, but I guess it is /home/wdmays/miniconda3/envs/super-focus/lib/python3.11/site-packages/superfocus_app/db/db/static/diamond/90_clusters /90_clusters.db in your directory