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dbeisser / Natrix2

Open-source bioinformatics pipeline for the preprocessing of raw amplicon sequencing / metabarcoding data.
MIT License
10 stars 2 forks source link

custom_database #20

Closed dmgr90 closed 1 month ago

dmgr90 commented 2 months ago

Hi!

I have a question regarding the use of a custom database to blast on? Are there any files that need to accompany the database? Any specific format. I want to have everything ready to avoid the pipeline to try to connect to NCBI since I often get connection problems.

Thank you in advance for any information :)

dmgr90 commented 2 months ago

--2024-08-09 10:17:27-- ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/new_taxdump/new_taxdump.tar.gz => ‘/lustre/groups/hpc/urban_lab/datasets/ncbi/natrix/.listing’ --2024-08-09 10:17:27-- ftp://ftp.ncbi.nlm.nih.gov/blast/db/ => ‘.listing’ Resolving ftp.ncbi.nlm.nih.gov (ftp.ncbi.nlm.nih.gov)... Resolving ftp.ncbi.nlm.nih.gov (ftp.ncbi.nlm.nih.gov)... 130.14.250.11130.14.250.7, , 130.14.250.10130.14.250.31, , 130.14.250.31130.14.250.12, ..., ...

Connecting to ftp.ncbi.nlm.nih.gov (ftp.ncbi.nlm.nih.gov)|130.14.250.11|:21... Connecting to ftp.ncbi.nlm.nih.gov (ftp.ncbi.nlm.nih.gov)|130.14.250.7|:21... failed: Connection timed out. failed: Connection timed out. I cant seem to get past this, no matter the quality of the connection

dusti1n commented 2 months ago

Thank you for providing the details of your issue. You can try manually downloading the required database files for BLAST and placing them in the appropriate directory (e.g., database/ncbi/). As long as all the necessary files are in place, Snakemake should utilize the local files without any issues. However, please note that Snakemake might still attempt to establish a brief connection to synchronize or validate the files.

If this approach doesn't resolve the issue, there could be other factors at play, such as a firewall blocking the connection. Unfortunately, an offline mode isn't currently configurable within the Snakemake settings. If you could share your configuration file with me, I'd be happy to take a closer look and help you troubleshoot further.

If you have any additional questions, feel free to reach out at any time.

Best regards, Dustin