bam2hints error - libbamtools.so.2.5.2

[desmodus1984]

Hi,
I am working with a marine mammals and I am interested in annotating its genome.
I tried Augustus once, without training, and then I did BUSCO assessment with the protein data.
BUSCO score with the genome itself is about 97%, but with Augustus proteins is 45.3%.
I don't have RNA data from my species, but I have RNA from its sister species.
I read that one can generate hints from RNA data and I wanted to try it.
I mapped the RNA-seq reads and I wanted to use the bam file to generate the hints.
I tried running bam2hints it and I got an error:
bam2hints: error while loading shared libraries: libbamtools.so.2.5.2: cannot open shared object file: No such file or directory
I looked at the directory and the script is supposed to be compiled there, as mentioned elsewhere.

Any reason why bam2hints is not working?
I tried installing bamtools in conda and it didn't work either.

Any way how to fix this problem?

[KatharinaHoff]

The easiest is probably to pull e.g. the singularity container of BRAKER. bam2hints is included there. The other option is to install the development dependencies and compile on your machine. I annotated several wales with GALBA, btw. Worked reasonably well, no RNAseq required. You find details in the GALBA paper. Works well for vertebrates. Tiberius may be another great option. desmodus1984 ***@***.***> schrieb am Mo. 14. Juli 2025 um 16:52:

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*desmodus1984* created an issue (Gaius-Augustus/Augustus#437) <#437> Hi, I am working with a marine mammals and I am interested in annotating its genome. I tried Augustus once, without training, and then I did BUSCO assessment with the protein data. BUSCO score with the genome itself is about 97%, but with Augustus proteins is 45.3%. I don't have RNA data from my species, but I have RNA from its sister species. I read that one can generate hints from RNA data and I wanted to try it. I mapped the RNA-seq reads and I wanted to use the bam file to generate the hints. I tried running bam2hints it and I got an error: bam2hints: error while loading shared libraries: libbamtools.so.2.5.2: cannot open shared object file: No such file or directory I looked at the directory and the script is supposed to be compiled there, as mentioned elsewhere. Any reason why bam2hints is not working? I tried installing bamtools in conda and it didn't work either. Any way how to fix this problem? — Reply to this email directly, view it on GitHub <#437>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AJMC6JBNR7577QFPPKVK73T3IO74VAVCNFSM6AAAAACBPJKFG6VHI2DSMVQWIX3LMV43ASLTON2WKOZTGIZDSMBVGE2DCMI> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>