Segmentation fault error

[lilinzhou]

Hi,

I have just successfully installed the latest version of augustus from source code, the installation went smoothly and I can see the help messages correctly when run augustus alone. But when I run augustus or etraining with a fasta, I get a Segmentation fault error, I am sorry I have no other error message to provide, as there is no log file either, the command I am running is the following: augustus --species=arabidopsis example.fa etraining --species=test example.gb the example.fa used comes from the examples folder.

Any solutions for this?

[MarioStanke]

Are both commands crashing? I suspect it has something to do with your compute setting or files.

Can you please check whether the parameter files are like in the repository?

ls -la $AUGUSTUS_CONFIG_PATH/species/arabidopsis/

testis no valid species. Perhaps you have previously interrupted a training of arabidopsis and have corrupted parameter files.

[QianChwnLyn]

Are both commands crashing? I suspect it has something to do with your compute setting or files.

Can you please check whether the parameter files are like in the repository?

ls -la $AUGUSTUS_CONFIG_PATH/species/arabidopsis/

testis no valid species. Perhaps you have previously interrupted a training of arabidopsis and have corrupted parameter files.

Hi, I also met this problem. this is my code. augustus --species=human --gff3=off --outfile=Bow.gtf step03_cd-hit-est.fa

And this is error info.

Can you help me to solve it? Thanks

[MarioStanke]

If I can reproduce the problem, I can probably fix it. For this I would need the example input and the content of the species subfolder that is specified in the augustus command line. Can either of you share these files?