Caro-Ca
commented
4 years ago Hi, I still get an error while running Busco. This is the error message:
(base) edgar@pathos:~/BUSCO/scripts$ python run_BUSCO.py -i /home/edgar/BUSCO/scripts/R18_CRRNF_fungap_out_prot.fasta -l ascomycota_odb9 -o R18_CRRNF_busco -m prot
INFO ****************** Start a BUSCO 3.1.0 analysis, current time: 10/14/2019 15:21:17 ******************
INFO Configuration loaded from /home/edgar/BUSCO/scripts/../config/config.ini
INFO Init tools...
INFO Check dependencies...
ERROR "hmmsearch" is not accessible, add or modify its path in the config file. Do not include the command in the path !
ERROR BUSCO analysis failed !
ERROR Check the logs, read the user guide, if you still need technical support, then please contact mailto:support@orthodb.org
(base) edgar@pathos:~/BUSCO/scripts$ cd ../config/
(base) edgar@pathos:~/BUSCO/config$ ls
config.ini config.ini.default
(base) edgar@pathos:~/BUSCO/config$ ll
total 16
drwxrwxr-x 2 edgar edgar 4096 sep 27 11:27 ./
drwxrwxr-x 8 edgar edgar 4096 sep 27 11:19 ../
-rw-rw-r-- 1 edgar edgar 2199 okt 11 17:42 config.ini
-rwxrwxr-x 1 edgar edgar 2199 sep 27 11:17 config.ini.default*
(base) edgar@pathos:~/BUSCO/config$ echo $BUSCO_CONFIG_FILE /home/edgar/hmmer-3.2.1/bin/hmmsearch:/home/edgar/anaconda2/bin/python:/home/edgar/Augustus/bin:/home/edgar/ncbi-blast-2.9.0+/bin:/home/edgar/BUSCO/config/config.ini:/home/edgar/hmmer-3.2.1/bin:
(base) edgar@pathos:~/BUSCO/config$Hope you can help me out, Thank you
Hi! This is a silly question for you, but I am not familiar with the command export. While I was looking at the installing manual you mentioned
What I did is: BUSCO_CONFIG_PATH=/home/edgar/BUSCO/config/config.ini NCBI_CONFIG_PATH=/home/edgar/BUSCO/config/config.ini HMMER_CONFIG_PATH=/home/edgar/BUSCO/config/config.ini
Is this correct? The problem is that I got an error while running BUSCO. I couldn't get a log file and the config.ini is empty even though I copied the config.ini.default to config.ini
Thank you in advance for your help.