Troubleshooting

Below are some common errors that we could encounter

1. No such file or directory

If you get the error below:

/usr/bin/time: cannot run augustus: No such file or directory
Command exited with non-zero status 127

The same is applicable if you get an error with:

optimize_augustus.pl
classify_transcripts

We get this error because augustus (for example) was not in the PATH. To add augustus to the PATH, please execute the below command.

source activate_reat

If you still get the error, please make sure that you are in the right working directory. You can check if you are in the right working directory by looking at the start of the wiki commands you are following. If you are not sure or have difficulties, please ask us.

2. command not found

If you get the error below:

seqkit: command not found

The same is applicable if you get an error with:

gff2gbSmallDNA.pl
randomSplit.pl
new_species.pl
etraining
augustus
reat

Please execute the below command:

source activate_reat