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sanger-pathogens / seroba

k-mer based Pipeline to identify the Serotype from Illumina NGS reads
https://sanger-pathogens.github.io/seroba/
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Dependencies issues when using seroba through conda #61

Open AleSR13 opened 3 years ago

AleSR13 commented 3 years ago

Hello! I have encountered few issues while trying to run seroba through a conda environment. One is the same reported in issue #59 with biopython and the other one is with bowtie2. In the later one, seroba runs properly at the beginning but then it stops with an error about not being able to get the bowtie2 --version. The specific error that bowtie2 throws is this:

error while loading shared libraries: libtbb.so.2: cannot open shared object file: No such file or directory

I tracked down both errors and it turns out that in order to use seroba, you need to list as dependencies biopython=1.74 (see this forum) and tbb=2020.3 (see this other forum). I made few tests and it seems to work fine for me (with seroba 1.0.0 and 1.0.2).

It would be really helpful to have these dependencies properly documented (I assume the error is not unique from the conda version but I did not test it) or simply have them included in the installation.

bhclement commented 3 years ago

Thanks. My installation issues have been resolved with biopython=1.74 and tbb=2020.3 too. But did you encounter issue #60 and #37 ? seroba summary did not work properly. I have pred.tsv only.

eppinglen commented 3 years ago

@bhclement

Which serotypes are reported in the pred.tsv ? The detailed_serogroup_info.txt is not created for all serotypes, due the construction of the PneumoCaT database. This file will only be printed if there is information available on presence/absence of allelic variants or SNPs for a specific serotype. If SeroBA predicts a serotype only based on the sequence identity this file is not created.

bhclement commented 3 years ago

Thanks. its serotype 13.

bhclement commented 3 years ago

@eppinglen I have another question on serotype. Do you have an email address?

eppinglen commented 3 years ago

@bhclement if you have any further question, feel free to contact me at eppingl@rki.de

CarmenSheppard commented 2 years ago

I'm getting the Bio.Alphabet issue still with conda installation, I have already downgraded to Biopython 1.74 and then tried 1.73 and downgraded tbb as above as well. @eppinglen . I have updated in conda and am running seroba 1.0.2. The error suggests that the library can be removed from scripts?

AleSR13 commented 2 years ago

I don't think I have the same error than you @CarmenSheppard but I did encounter a new dependecy error with Seroba (now with kmc). I used this file to create a new conda environment that solves my issue:

name: seroba
channels:
  - defaults
  - bioconda
dependencies:
  - seroba=1.0.2
  - biopython=1.74
  - tbb=2020.3
  - kmc=3.1.2rc1