run_BUSCO.py running problem
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2.2 years ago
ashaneev07 ▴ 20

I got the following error when I run run_BUSCO.py. i already have changed the augustus path in config.ini What should I do for solving this problem? Thank you

 python3.4 scripts/run_BUSCO.py --in sample_data/target.fa --lineage_path sample_data/example --mode genome --out TEST
INFO    ****************** Start a BUSCO 3.1.0 analysis, current time: 08/16/2019 17:39:10 ******************
INFO    Configuration loaded from /home/dcb/Documents/EV/Maker/busco-master/scripts/../config/config.ini
INFO    Init tools...
INFO    Check dependencies...
ERROR   Cannot write to Augustus config path, please make sure you have write permissions to /home/dcb/Documents/EV/Maker/maker/bin:/usr/local/bin:/usr/local/RepeatMasker:/home/dcb/miniconda3/bin:/home/dcb/miniconda3/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/usr/local/bin:/usr/local/bin/augustus:/usr/local/bin/
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
gene busco software error sequencing • 1.7k views
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Do you have writing permission for the augustus path you added in the config.ini file?

you can check it by running ls -l <path to augustus>

It will give you the permission for the "owner, group and all", you should check if you are not the owner of the path, you should check if the second before last character is an " w ", like here: -rw-rw-rw-

" r " stands for read " w " stands for write " x " stands for execute

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If you can change permission add writing right:

a_path=`which augustus`                         # path to augustus
a_path=${a_path::${#a_path}-12}            # remove last 12 digit
a_path="${a_path}config"                        # add config and you have the full path to config folder
chmod 755 $a_path                                 # add writing permission

either copy the folder add permisson and change path to AUGUSTUS_CONFIG_PATH:

a_path=`which augustus`                                                     # path to augustus
a_path=${a_path::${#a_path}-12}                                        # remove last 12 digit
a_path="${a_path}config"                                                    # add config and you have the full path to config folder
mkdir -p /tmp/augustus                                                        # create a folder where you will put the copy of the config folder
cp -r $a_path /tmp/augustus/                                               # copy the config folder to the new place created just before
chmod 755 /tmp/augustus/config                                         # add writing permission to the config folder
AUGUSTUS_CONFIG_PATH=/tmp/augustus/config          # change the AUGUSTUS_CONFIG_PATH  OS env to inform where to find the config file
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