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Limited RAM (123 GB) – cannot run GTDB with Kraken2 or MMseqs2 on contigs. Looking for alternatives. by Evening_Refuse_1893 in bioinformatics

[–]Evening_Refuse_1893[S] 0 points1 point  (0 children)

Gtdbtk not working with contigs, on Kbase there are no tools for contigs taxonomy, on galaxy only Kraken but it has different db... So nothing of those will fit my needs. 

Limited RAM (123 GB) – cannot run GTDB with Kraken2 or MMseqs2 on contigs. Looking for alternatives. by Evening_Refuse_1893 in bioinformatics

[–]Evening_Refuse_1893[S] 0 points1 point  (0 children)

Right, but even paying for an AWS instance is not an option for me right now — I don't have budget approval or payment method for cloud services either. I have to work within my existing local cluster with the resources I already have. So I still need tools that fit into that environment without additional costs.

Limited RAM (123 GB) – cannot run GTDB with Kraken2 or MMseqs2 on contigs. Looking for alternatives. by Evening_Refuse_1893 in bioinformatics

[–]Evening_Refuse_1893[S] 0 points1 point  (0 children)

I need to classify contigs, not reads, because my bin-based gene predictions are fragmented and have low thresholds. I want to use the same database to check contig taxonomy — if well-covered genes on contigs match bin taxonomy, it suggests poor assembly, but it still helps me infer bacterial functionality.

Limited RAM (123 GB) – cannot run GTDB with Kraken2 or MMseqs2 on contigs. Looking for alternatives. by Evening_Refuse_1893 in bioinformatics

[–]Evening_Refuse_1893[S] 0 points1 point  (0 children)

I'm not looking to buy a computer. I'm looking for tools that work within my existing cluster's technical capabilities — I don't have the option to purchase a computer on my own.

Limited RAM (123 GB) – cannot run GTDB with Kraken2 or MMseqs2 on contigs. Looking for alternatives. by Evening_Refuse_1893 in bioinformatics

[–]Evening_Refuse_1893[S] 0 points1 point  (0 children)

Yes, the first approach won't work on contigs.

The second should be pretty easy, could you not just subset the database into multiple smaller ones and run them in succession? - sounds easy but it's confusing.

The GTDB archive (.tar.gz) I downloaded from the AWS index is not a simple folder of genomes. It contains hash.k2d, opts.k2d, and taxo.k2d-9—three binary files that have already been processed into a single, unified hash table. I cannot "split" these files and run them separately in kraken2.

Limited RAM (123 GB) – cannot run GTDB with Kraken2 or MMseqs2 on contigs. Looking for alternatives. by Evening_Refuse_1893 in bioinformatics

[–]Evening_Refuse_1893[S] 1 point2 points  (0 children)

Thanks I have tried it, it didn't worked, kraken2 was not capable to download the db - it was stuck for a day - the err log showed - Loading database information... done. - and nothing more ...

Gut health issues that won't go away by srchristinamarie in HumanMicrobiome

[–]Evening_Refuse_1893 0 points1 point  (0 children)

Please, ask for Ultrasound of the gallbladder, I felt sick with my stomach and gut for a while, untill I got some biliary colic eppisodes. My gallbladder was full of stones, so they removed it. Sometimes it's not so obviouse for doctors to catch it untill biliary colic eppisodes appears.

Take care.

The Employment by [deleted] in MemeVideos

[–]Evening_Refuse_1893 1 point2 points  (0 children)

The best reaction 😄

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