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mtisza1 / Cenote-Taker2

Cenote-Taker2: Discover and Annotate Divergent Viral Contigs (Please use Cenote-Taker 3 instead)
MIT License
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conda install of bowtie fails? #23

Closed DarrenObbard closed 1 year ago

DarrenObbard commented 2 years ago

Hi!

I just tried a new clean set up of cenote-taker2, and I get this error:

Aligning provided reads to contigs over cutoff to determine coverage.
time update: making bowtie2 indices  01-25-22---17:26:07
Aligning reads to BowTie2 index.
time update: aligning reads to bowtie2 indices  01-25-22---17:26:07
/data/home/dobbard/miniconda3/envs/cenote-taker2_env/bin/bowtie2-align-s: symbol lookup error: /data/home/dobbard/miniconda3/envs/cenote-taker2_env/bin/bowtie2-align-s: undefined symbol: _ZN3tbb10interface78internal15task_arena_base19internal_
initializeEv
(ERR): Description of arguments failed!
Exiting now ...

It may be related to this conda / bowtie2 problem: https://github.com/BenLangmead/bowtie2/issues/336

Blindly following the instruction I found there:

conda install tbb=2020.2

seems to work.

mtisza1 commented 2 years ago

Darren,

Thanks as always for bringing up the issue.

First, let me apologize for the delay in replying. I've been extremely busy lately, and I've had to decide to not reply to Cenote-Taker 2 issues temporarily. I will be "back" to quick responses and updates(!) at the end of February.

Looks like you figured this out, and I expect it will help folks trying to install this tool. I'm going to update the install scripts to specify tbb=2020.2 in the conda environment as soon as I'm able.

Best,

Mike