# BAQLaVa **URL:** https://forum.biobakery.org/c/microbial-community-profiling/baqlava/76.md [Latest](https://forum.biobakery.org/latest.md) · [Categories](https://forum.biobakery.org/categories.md) --- ## [About the BAQLaVa category](https://forum.biobakery.org/t/about-the-baqlava-category/8161)
**Author:** [@sagunmaharjann](https://forum.biobakery.org/u/sagunmaharjann)\ **Replies:** 0\ **Last updated:** [June 20, 2025, 7:52pm UTC](https://forum.biobakery.org/t/about-the-baqlava-category/8161 "2025-06-20T19:52:22Z")
Name: BAQLaVa User manual || Tutorial Description: BAQLaVa, Bioinformatic Application of Quantification and Labeling of Viral Taxonomy, is a tool designed to perform viral community profiling on metagenomic, metatr… --- ## [Issue with baqlava-db download](https://forum.biobakery.org/t/issue-with-baqlava-db-download/9026)
**Author:** [@eodonne3](https://forum.biobakery.org/u/eodonne3)\ **Replies:** 1\ **Last updated:** [August 6, 2026, 9:22pm UTC](https://forum.biobakery.org/t/issue-with-baqlava-db-download/9026 "2026-08-06T21:22:15Z")
Hi, I am attempting to download the BAQLaVa reference database from: https://huttenhower.sph.harvard.edu/baqlava-db/databases.V0.5.tar.gz The URL redirects to: https://g-227ca.190ebd.75bc.data.globus.org/baqlava-db/d… --- ## [Clarifying "BAQLaVa ORFs" used for the manuscript's trait annotation](https://forum.biobakery.org/t/clarifying-baqlava-orfs-used-for-the-manuscripts-trait-annotation/9019)
**Author:** [@dsh82](https://forum.biobakery.org/u/dsh82)\ **Replies:** 0\ **Last updated:** [July 31, 2026, 4:16pm UTC](https://forum.biobakery.org/t/clarifying-baqlava-orfs-used-for-the-manuscripts-trait-annotation/9019 "2026-07-31T16:16:26Z")
Hi BAQLaVa team, Thanks for developing BAQLaVa. I’m working through the viral trait enrichment analysis from the manuscript (Fig. 4) and would like to confirm an implementation detail. Which ORF set was used for the Pf… --- ## [Possible to merge markers and proteins files?](https://forum.biobakery.org/t/possible-to-merge-markers-and-proteins-files/9009)
**Author:** [@young\_doktor](https://forum.biobakery.org/u/young_doktor)\ **Replies:** 0\ **Last updated:** [July 27, 2026, 12:25am UTC](https://forum.biobakery.org/t/possible-to-merge-markers-and-proteins-files/9009 "2026-07-27T00:25:52Z")
Hi! Thank you for creating BAQLaVa. I was able to get through and merge my profile files into a single VBG table. I tried the same code (adapted for that used for the VBG table) for the markers and proteins files: \*\_tem… --- ## [About sequence IDs in BAQLaVa Full Length Genomes](https://forum.biobakery.org/t/about-sequence-ids-in-baqlava-full-length-genomes/8942)
**Author:** [@Tiezhu](https://forum.biobakery.org/u/Tiezhu)\ **Replies:** 2\ **Last updated:** [June 29, 2026, 10:01am UTC](https://forum.biobakery.org/t/about-sequence-ids-in-baqlava-full-length-genomes/8942 "2026-06-29T10:01:32Z")
First of all, I’d like to thank you for developing BAQLaVa. I have one question regarding the sequence IDs in BAQLaVa Full Length Genomes and VGB IDs. In the BAQLaVa Full Length Genomes database, each viral genome has… --- ## [Installing Baqlava](https://forum.biobakery.org/t/installing-baqlava/8768)
**Author:** [@Faeze\_Darbaniyan](https://forum.biobakery.org/u/Faeze_Darbaniyan)\ **Replies:** 20\ **Last updated:** [June 22, 2026, 7:16pm UTC](https://forum.biobakery.org/t/installing-baqlava/8768 "2026-06-22T19:16:53Z")
Hi, I have been trying to install baqlava. First I installed humann v4.0.0.alpha.1. However, I am unable to install anadama2 (as a pre-requiry) properly –\> doesn’t give any error but doesn’t show any output when hitting… --- ## [BAQLaVA VGB lifestyle prediction](https://forum.biobakery.org/t/baqlava-vgb-lifestyle-prediction/8836)
**Author:** [@alsdnr2295](https://forum.biobakery.org/u/alsdnr2295)\ **Replies:** 1\ **Last updated:** [June 17, 2026, 8:10pm UTC](https://forum.biobakery.org/t/baqlava-vgb-lifestyle-prediction/8836 "2026-06-17T20:10:09Z")
Hello, and thank you for developing and maintaining BAQLaVa. I am currently working on phage lifestyle classification (temperate, virulent, or unclassified) using BAQLaVa-derived VGBs, and I would be very grateful for y… --- ## [Inquiry regarding the identification and removal of false-positive plasmids in non-iHMP datasets](https://forum.biobakery.org/t/inquiry-regarding-the-identification-and-removal-of-false-positive-plasmids-in-non-ihmp-datasets/8797)
**Author:** [@alsdnr2295](https://forum.biobakery.org/u/alsdnr2295)\ **Replies:** 1\ **Last updated:** [March 6, 2026, 12:17am UTC](https://forum.biobakery.org/t/inquiry-regarding-the-identification-and-removal-of-false-positive-plasmids-in-non-ihmp-datasets/8797 "2026-03-06T00:17:51Z")
Inquiry on reproducing the method for identifying false-positive plasmids (re: remove\_plasmid.py) Hello BAQLaVa team, my name is min-uk, Park Thank you for developing this great pipeline. While reviewing the scripts, … --- ## [Inquiry regarding MetaPhlAn and HUMAnN versions used in the BAQLaVa preprint](https://forum.biobakery.org/t/inquiry-regarding-metaphlan-and-humann-versions-used-in-the-baqlava-preprint/8795)
**Author:** [@alsdnr2295](https://forum.biobakery.org/u/alsdnr2295)\ **Replies:** 1\ **Last updated:** [March 5, 2026, 11:48pm UTC](https://forum.biobakery.org/t/inquiry-regarding-metaphlan-and-humann-versions-used-in-the-baqlava-preprint/8795 "2026-03-05T23:48:34Z")
hello, my name is Min-uk Park. I recently read your bioRxiv preprint on BAQLaVa with great interest. I am currently planning to set up the BAQLaVa pipeline for my virome research, and I have a quick question regarding t… --- ## [Using BAQLaVa Full-Length Genomes and Marker/Protein ID Formats](https://forum.biobakery.org/t/using-baqlava-full-length-genomes-and-marker-protein-id-formats/8794)
**Author:** [@alsdnr2295](https://forum.biobakery.org/u/alsdnr2295)\ **Replies:** 1\ **Last updated:** [March 5, 2026, 11:21pm UTC](https://forum.biobakery.org/t/using-baqlava-full-length-genomes-and-marker-protein-id-formats/8794 "2026-03-05T23:21:15Z")
Inquiry: Using BAQLaVa Full-Length Genomes and Marker/Protein ID Formats Dear BAQLaVa Team, Hello, my name is Min-uk Park, a researcher at Seoul National University. I am currently conducting virome profiling research … --- ## [Baqlava failing at depletion step due to misnamed file?](https://forum.biobakery.org/t/baqlava-failing-at-depletion-step-due-to-misnamed-file/8745)
**Author:** [@scottdaniel\_at\_chop](https://forum.biobakery.org/u/scottdaniel_at_chop)\ **Replies:** 3\ **Last updated:** [February 5, 2026, 3:36pm UTC](https://forum.biobakery.org/t/baqlava-failing-at-depletion-step-due-to-misnamed-file/8745 "2026-02-05T15:36:02Z")
Hi again, Hopefully this boils down to a simple user error but I’m running Baqlava again on some metagenomic samples and I’m getting a repeating error where it’s not finding the bowtie2\_unaligned.fa file. The exact erro… --- ## [Question about ICTV taxonomy version and naming in BaqLaVa](https://forum.biobakery.org/t/question-about-ictv-taxonomy-version-and-naming-in-baqlava/8683)
**Author:** [@alsdnr2295](https://forum.biobakery.org/u/alsdnr2295)\ **Replies:** 1\ **Last updated:** [December 17, 2025, 5:59pm UTC](https://forum.biobakery.org/t/question-about-ictv-taxonomy-version-and-naming-in-baqlava/8683 "2025-12-17T17:59:35Z")
Subject: Question about ICTV taxonomy version and naming in BaqLaVa Dear BaqLaVa team, I hope this message finds you well. I am currently working on a project where I need to standardize viral annotations from NCBI to… --- ## [Feature request: Include taxonomy columns for baqlava\_join\_table utility script](https://forum.biobakery.org/t/feature-request-include-taxonomy-columns-for-baqlava-join-table-utility-script/8666)
**Author:** [@scottdaniel\_at\_chop](https://forum.biobakery.org/u/scottdaniel_at_chop)\ **Replies:** 1\ **Last updated:** [December 11, 2025, 9:05pm UTC](https://forum.biobakery.org/t/feature-request-include-taxonomy-columns-for-baqlava-join-table-utility-script/8666 "2025-12-11T21:05:24Z")
Hi, Thank you for creating the baqlava\_join\_table utility function. Unfortunately, it was not was I was expecting. What I get is just the VGB column and then all the samples’ RPKs. Is there a reason the the taxonomy col… --- ## [How to parallelize baqlava over many samples?](https://forum.biobakery.org/t/how-to-parallelize-baqlava-over-many-samples/8656)
**Author:** [@scottdaniel\_at\_chop](https://forum.biobakery.org/u/scottdaniel_at_chop)\ **Replies:** 2\ **Last updated:** [December 4, 2025, 8:24pm UTC](https://forum.biobakery.org/t/how-to-parallelize-baqlava-over-many-samples/8656 "2025-12-04T20:24:26Z")
When I want to quickly parallelize a bioinformatic tool I write one batch script that loops through my samples and one batch script that launches a slurm job for each sample. Unfortunately, I run into an anadama error wh… --- ## [Adding a --metaphlan-options and/or bowtie2db flag to baqlava](https://forum.biobakery.org/t/adding-a-metaphlan-options-and-or-bowtie2db-flag-to-baqlava/8455)
**Author:** [@jawah003](https://forum.biobakery.org/u/jawah003)\ **Replies:** 2\ **Last updated:** [December 4, 2025, 8:10pm UTC](https://forum.biobakery.org/t/adding-a-metaphlan-options-and-or-bowtie2db-flag-to-baqlava/8455 "2025-12-04T20:10:04Z")
Hi! When running baqlava with bacterial read depletion, would it be possible to include the --metaphlan-options flag from humann3.9? This might make it easier to get around issues with the humann config file, as well as … --- ## [MinPath error with baqlava 0.5 metaphlan 3.1.0 and humann 3.9](https://forum.biobakery.org/t/minpath-error-with-baqlava-0-5-metaphlan-3-1-0-and-humann-3-9/8653)
**Author:** [@scottdaniel\_at\_chop](https://forum.biobakery.org/u/scottdaniel_at_chop)\ **Replies:** 2\ **Last updated:** [December 4, 2025, 7:58pm UTC](https://forum.biobakery.org/t/minpath-error-with-baqlava-0-5-metaphlan-3-1-0-and-humann-3-9/8653 "2025-12-04T19:58:42Z")
Hi, After numerous tries getting the exact software version to play nicely (along with the correct database) I thought I was getting close until I got a weird MinPath error trying to run the demo.fq with baqlava 0.5: (… --- ## [Error with file naming](https://forum.biobakery.org/t/error-with-file-naming/8328)
**Author:** [@Che](https://forum.biobakery.org/u/Che)\ **Replies:** 1\ **Last updated:** [August 1, 2025, 8:39pm UTC](https://forum.biobakery.org/t/error-with-file-naming/8328 "2025-08-01T20:39:31Z")
If baqlava is analyzing a file with a “.” character in the name it fails to create the intermediate/paths with the correct name and truncates the name at the period. The assumption is that the “.” signifies a file extens… --- ## [Baqlava marker file has markers not seen in the profile](https://forum.biobakery.org/t/baqlava-marker-file-has-markers-not-seen-in-the-profile/8101)
**Author:** [@Che](https://forum.biobakery.org/u/Che)\ **Replies:** 1\ **Last updated:** [June 20, 2025, 6:49pm UTC](https://forum.biobakery.org/t/baqlava-marker-file-has-markers-not-seen-in-the-profile/8101 "2025-06-20T18:49:39Z")
I have made run several metagenomic samples through Baqlava and keep seeing VGBs in the tempfile\_markers.txt file that don’t show up in the profile files. Shouldn’t every marker that has a hit show up in the profile file…