BRAKER1 fails: inappropriate ioctl for device

[Macspider]

Hi all, I'm having a problem which is more linux related than biology related. I'm running the BRAKER1 pipeline (which involves Augustus and Gene-mark ET) for a gene prediction, and I'm getting back a weird error which I wasn't able to solve using StackOverflow or other troubleshooting websites.
This is the STDERR:

NEXT STEP: check files and settings
NEXT STEP: check options
... options check complete.
NEXT STEP: check fasta headers
fasta headers check complete.
NEXT STEP: create SAM header file [...].
SAM file [...] complete.
NEXT STEP: check BAM headers
headers check for BAM file [...] complete.
NEXT STEP: make hints from BAM file [...]
failed to execute: Inappropriate ioctl for device

Inappropriate ioctl for device is something I never had the pleasure to solve. Can anybody help me?

Thank you very much,
Matteo

[Macspider]

I solved it trying the solutions suggested here.

https://gist.github.com/macmanes/bc5598e0d079ff6d71f2

[francicco]

I fix this compiling augustus with gcc/5.3.0

[Macspider]

Yep, exactly how I did.
I have other problems with BRAKER1, fancy take a look? Maybe you know:

http://seqanswers.com/forums/showthread.php?p=197504#post197504