Daan Speth

HMMER 3.2.1 anvio v7 was installed following the conda/pip instructions on the installation page, roughly 2 weeks ago

thanks @ivagljiva & @meren!

Hi @ivagljiva & @meren, I'm sad to report that I encountered this issue again yesterday, both in the master branch and version 7.1. I was alerted to it when using...

Hi @meren, I've emailed you the contigs dbs where this issue occurred for me. They are generated from this genome: https://www.ncbi.nlm.nih.gov/nuccore/LR794158 Oddly, this is the genome that @ivagljiva tested the...

To test that last statement I just freshly generated the contigs db from the genome fasta (with simplified name), and get the defective behaviour in both the master branch and...

ah, rereading the issue thread: my HMMER version is 3.3.2 in both conda envs, so a different version than was installed when I encountered this issue first

Here it is @meren : v7.1: HMMER version: # HMMER 3.3.2 (Nov 2020); http://hmmer.org/ Number of genes Prodigal found in the genome: 311 Number of Bacteria_71 HMM hits found in...

what I had noticed (at the time I first reported this), is that the number of genes reported does not seem to be fixed for a given number of threads,...

@meren Here's an example showing this behaviour, with number of threads set to 30: ``` (anvi_dev) dspeth@bigmem-7:/scratch/dspeth/workdir_temp/anvi_hmm_test$ ./test_issue_1748.sh HMMER version: # HMMER 3.3.2 (Nov 2020); http://hmmer.org/ Number of genes Prodigal...

aiaiai, sorry to hear this. I agree that the library must work on linux, otherwise there would be many very noisy errors. Also, I might do some googling, but unfortunately...