config.ini
Hi @matsepp, what is the significance of the ;
the precedes the lines in config.ini
# Path to the BUSCO dataset
;lineage_path = ./sample_data/example
In general, I'm having issues getting the lineage path to work:
export BUSCO_CONFIG_FILE="/mnt/lustre/macmaneslab/shared/BUSCODB/config.ini"
python $(which run_BUSCO.py) -i orthofuse/SRR3499127.10/SRR3499127.10.orthomerged.fasta -m transcriptome --cpu 12 -l eukaryota_odb9 -o SRR3499127.10
WARNING The dataset you provided does not contain the file dataset.cfg, likely because it is an old version. Default species (fly, eukaryota) will be used as augustus species
ERROR Impossible to read eukaryota_odb9/
head of config.ini to show that the lineage_path is set.
head /mnt/lustre/macmaneslab/shared/BUSCODB/config.ini
[busco]
lineage_path = /mnt/lustre/macmaneslab/shared/BUSCODB/
...
In fact, the eukaryote profile info is there.
ls /mnt/lustre/macmaneslab/shared/BUSCODB/
ls -lth /mnt/lustre/macmaneslab/shared/BUSCODB/eukaryota_odb9
total 1.1M
drwxr-xr-x 2 macmanes macmaneslab 28K Jun 9 11:54 prfl
-rw-r--r-- 1 macmanes macmaneslab 92K Jun 9 11:54 ancestral
-rw-r--r-- 1 macmanes macmaneslab 117 Jun 9 11:54 dataset.cfg
drwxr-xr-x 2 macmanes macmaneslab 28K Jun 9 11:54 hmms
drwxr-xr-x 2 macmanes macmaneslab 4.0K Jun 9 11:54 info
-rw-r--r-- 1 macmanes macmaneslab 11K Jun 9 11:54 lengths_cutoff
-rw-r--r-- 1 macmanes macmaneslab 919K Jun 9 11:54 ancestral_variants
-rw-r--r-- 1 macmanes macmaneslab 7.0K Jun 9 11:54 scores_cutoff
Version info
$(which run_BUSCO.py) --help
\usage: python BUSCO.py -i [SEQUENCE_FILE] -l [LINEAGE] -o [OUTPUT_NAME] -m [MODE] [OTHER OPTIONS]
Welcome to BUSCO 3.0.2: the Benchmarking Universal Single-Copy Ortholog assessment tool.