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GenSpectrum / LAPIS-SILO

Sequence Indexing engine for Large Order of genomic data
GNU Affero General Public License v3.0
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Preprocessing error is unclear which file has error #361

Open corneliusroemer opened 7 months ago

corneliusroemer commented 7 months ago

I'm getting the following silo preprocessing error, but I'd like the error message to say which file is a directory:

[2024-03-25 16:45:49.497] [logger] [error] [api.cpp:297] basic_filebuf::xsgetn error reading the file: Is a directory

Full context:

[2024-03-25 16:45:49.484] [logger] [info] [api.cpp:329] Starting SILO
[2024-03-25 16:45:49.484] [logger] [info] [api.cpp:289] Starting SILO preprocessing
[2024-03-25 16:45:49.484] [logger] [info] [preprocessing_config_reader.cpp:54] Reading preprocessing config from ./default_preprocessing_config.yaml
[2024-03-25 16:45:49.484] [logger] [info] [preprocessing_config_reader.cpp:54] Reading preprocessing config from ./preprocessing_config.yaml
[2024-03-25 16:45:49.497] [logger] [error] [api.cpp:297] basic_filebuf::xsgetn error reading the file: Is a directory
[2024-03-25 16:45:49.497] [logger] [info] [api.cpp:334] Stopping SILO
std::exception
SiloApi command failed with exit code 70, cleaning up and exiting.
fengelniederhammer commented 7 months ago

Should be done as part of #129

Taepper commented 3 weeks ago

Cannot reproduce, maybe fixed by earlier preprocessing refactorings.