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pirovc / ganon

ganon2 classifies genomic sequences against large sets of references efficiently, with integrated download and update of databases (refseq/genbank), taxonomic profiling (ncbi/gtdb), binning and hierarchical classification, customized reporting and more
https://pirovc.github.io/ganon/
MIT License
86 stars 13 forks source link

System exit when trying to build index with raptor #275

Closed ksavhughes closed 7 months ago

ksavhughes commented 8 months ago

Hi ganon team,

I'm not really sure what is going on here. Can you help me?

error message: Parse finished - skipping Building index (raptor) Traceback (most recent call last): File "/home/karsav1511/.conda/envs/ganon/bin/ganon", line 33, in sys.exit(load_entry_point('ganon==2.0.0', 'console_scripts', 'ganon')()) File "/home/karsav1511/.conda/envs/ganon/lib/python3.10/site-packages/ganon/ganon.py", line 53, in main_cli sys.exit(0 if main() else 1) File "/home/karsav1511/.conda/envs/ganon/lib/python3.10/site-packages/ganon/ganon.py", line 36, in main ret = build_custom(cfg) File "/home/karsav1511/.conda/envs/ganon/lib/python3.10/site-packages/ganon/build_update.py", line 365, in build_custom Path(build_output_folder + new_target + exts).symlink_to(first_file) File "/home/karsav1511/.conda/envs/ganon/lib/python3.10/pathlib.py", line 1255, in symlink_to self._accessor.symlink(target, self, target_is_directory) FileExistsError: [Errno 17] File exists: '/ourdisk/hpc/hofmanlmamr/karsav1511/auto_archive_notyet/tape_2copies/RefSeq/ganonRefSeqLim3/refs/bacteria3/GCF_006777585.1_ASM677758v1_genomic.fna.gz' -> 'bacteria3_files/build/2078.fna.gz'

pirovc commented 8 months ago

Hi, thanks for reporting. To avoid this issue, delete the build folder inside of bacteria3_files and try again. There are some temporary files created from previous attempts generating this error. This is a bug and will be fixed soon.

ksavhughes commented 7 months ago

Thank you!

pirovc commented 7 months ago

Fixed in v2.0.1 #281