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HobnobMancer / cazomevolve

`cazomevolve` ('cazome-evolve') investigates the evolution of CAZomes, and identifies CAZy families that co-occur within the genomes of candidate species, more frequently than would be expected by lineage.
https://hobnobmancer.github.io/cazomevolve/
MIT License
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Connectivity issue with connection to NCBI when using get_dbcan_cazymes #23

Closed PeterMBlack closed 3 months ago

PeterMBlack commented 5 months ago

Error occurs when trying to retrieve the tax ids from NCBI for adding taxonomic information to the 2 output tab delimited lists when running the get_dbcan_cazymes command on the St Andrews Kennedy Supercluster.

Output slurm log file (timed out after 24hrs): slurm-232789.out.txt

Slurm script used to run this analysis: AnnotateCazomesLargerGroup250224.sh.txt

(Also included is the output for cazomevolve run_dbcan, which has a code future proofing warning for extracting the values from the dbcan overview.txt file for each of the tools which may cause a future issue)

HobnobMancer commented 3 months ago

Issue should be fixed with cazy_webscraper >= 2.3.0.3