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get_organelle_from_reads.py can not find the embplant_nr db in SGE #336

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xiefumin1 opened this issue Jun 7, 2024 · 0 comments
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@xiefumin1
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On a local computer, the program runs fine, but when using the SGEsystem, the get_organelle_config.py script is unable to run regardless of whether the default path or a manually specified path is used for building the databases.
like this,
ERROR: default embplant_nr database not added yet!

Install it by: get_organelle_config.py -a embplant_nr
or
Install all types by: get_organelle_config.py -a all
But in fact, these libraries have already been installed
(GetOrganelle) [xx@bogon raw]$get_organelle_config.py --update

Python 3.10.14 | packaged by conda-forge | (main, Mar 20 2024, 12:45:18) [GCC 12.3.0]
DEPENDENCIES: Bowtie2 failed.; Blast 2.15.0
WORKING DIR: /data/backup/gxl/2.data/plastid/raw
/data/backup/xx/3.software/miniconda3/envs/GetOrganelle/bin/get_organelle_config.py --update

Existing databases(s):
embplant_nr Seed Database: 0.0.1
embplant_nr Label Database: 0.0.1

bowtie2-build embplant_nr.fasta ... skipped
makeblastdb embplant_nr.fasta ... skipped

Total cost: 1.77 s

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