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metageni / SUPER-FOCUS

A tool for agile functional analysis of shotgun metagenomic data
GNU General Public License v3.0
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database issue #84

Closed wittney-m closed 1 year ago

wittney-m commented 1 year ago

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.

wittney-m commented 1 year ago

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.

metageni-twist commented 1 year ago

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/?

wittney-m commented 1 year ago

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.

metageni-twist commented 1 year ago

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