A bug apper， when log files in

[deyuanyang]

Hi,

When I used BUSCO output files, an error was reported. If I remove log files, it is ok. Can you solve it？
(BUSCO_phylogenomics) cody@cody:/media/cody/de1ca27e-ece1-4202-86f5-b63ed873ebe9/Tere_results/tere/test$ BUSCO_phylogenomics.py -i ./ -o sss -t 40 --supermatrix_only
08-02-2025 03:54:11 Starting BUSCO Phylogenomics Pipeline
08-02-2025 03:54:11 User provided arguments: ['/home/cody/miniforge3/envs/BUSCO_phylogenomics/bin/BUSCO_phylogenomics.py', '-i', './', '-o', 'sss', '-t', '40', '--supermatrix_only']
08-02-2025 03:54:11 Parsed arguments: {'input': './', 'output': 'sss', 'threads': 40, 'supermatrix_only': True, 'gene_trees_only': False, 'nt': False, 'psc': 100.0, 'trimal_strategy': 'automated1', 'missing_character': '?', 'gene_tree_program': 'fasttree', 'busco_version_3': False}
fasttree
08-02-2025 03:54:11 Looking for BUSCO runs in /media/cody/de1ca27e-ece1-4202-86f5-b63ed873ebe9/Tere_results/tere/test
08-02-2025 03:54:11 Found 8 BUSCO directories:
run_SRR26312818_trinity_SRR26312818_trinity.Trinity.fasta /media/cody/de1ca27e-ece1-4202-86f5-b63ed873ebe9/Tere_results/tere/test/run_SRR26312818_trinity_SRR26312818_trinity.Trinity.fasta/run_metazoa_odb10
run_SRR26312818_trinity_SRR26312818_trinity.Trinity.fasta /media/cody/de1ca27e-ece1-4202-86f5-b63ed873ebe9/Tere_results/tere/test/run_SRR26312818_trinity_SRR26312818_trinity.Trinity.fasta/logs
run_SRR26316595_trinity_SRR26316595_trinity.Trinity.fasta /media/cody/de1ca27e-ece1-4202-86f5-b63ed873ebe9/Tere_results/tere/test/run_SRR26316595_trinity_SRR26316595_trinity.Trinity.fasta/run_metazoa_odb10
run_SRR26316595_trinity_SRR26316595_trinity.Trinity.fasta /media/cody/de1ca27e-ece1-4202-86f5-b63ed873ebe9/Tere_results/tere/test/run_SRR26316595_trinity_SRR26316595_trinity.Trinity.fasta/logs
run_SRR19644659_trinity_SRR19644659_trinity.Trinity.fasta /media/cody/de1ca27e-ece1-4202-86f5-b63ed873ebe9/Tere_results/tere/test/run_SRR19644659_trinity_SRR19644659_trinity.Trinity.fasta/run_metazoa_odb10
run_SRR19644659_trinity_SRR19644659_trinity.Trinity.fasta /media/cody/de1ca27e-ece1-4202-86f5-b63ed873ebe9/Tere_results/tere/test/run_SRR19644659_trinity_SRR19644659_trinity.Trinity.fasta/logs
run_SRR26312819_trinity_SRR26312819_trinity.Trinity.fasta /media/cody/de1ca27e-ece1-4202-86f5-b63ed873ebe9/Tere_results/tere/test/run_SRR26312819_trinity_SRR26312819_trinity.Trinity.fasta/run_metazoa_odb10
run_SRR26312819_trinity_SRR26312819_trinity.Trinity.fasta /media/cody/de1ca27e-ece1-4202-86f5-b63ed873ebe9/Tere_results/tere/test/run_SRR26312819_trinity_SRR26312819_trinity.Trinity.fasta/logs

08-02-2025 03:54:11 Identifying complete and single-copy BUSCO sequences
Traceback (most recent call last):
File "/home/cody/miniforge3/envs/BUSCO_phylogenomics/bin/BUSCO_phylogenomics.py", line 410, in
main()
~~~~^^
File "/home/cody/miniforge3/envs/BUSCO_phylogenomics/bin/BUSCO_phylogenomics.py", line 138, in main
chdir(join(busco_sample, "busco_sequences", "single_copy_busco_sequences"))
~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
FileNotFoundError: [Errno 2] No such file or directory: '/media/cody/de1ca27e-ece1-4202-86f5-b63ed873ebe9/Tere_results/tere/test/run_SRR26312818_trinity_SRR26312818_trinity.Trinity.fasta/logs/busco_sequences/single_copy_busco_sequences'

[jamiemcg]

Hi @deyuanyang,

This might be a simple issue related to #12
Having "run_" in your output directory names causes issues.

Try renaming your output directories, e.g.,

run_SRR26312818_trinity_SRR26312818_trinity --> SRR26312818_trinity_SRR26312818_trinity