ERROR: Hapo-G didn't finish successfully, exit code: -8

[JonEilers]

ERROR: Hapo-G didn't finish successfully, exit code: -8

[bistace]

Hello,

could you please paste the content of the /home/jon/Working_Files/hapo-g/round_3/logs/hapog_chunks_69.o and /home/jon/Working_Files/hapo-g/round_3/logs/hapog_chunks_69.e files?

[JonEilers]

both of those specific files are empty. It looks like only the hapog_chunks_#.o files have content. The hapog_chunks_#.e files are all empty

[bistace]

That's strange, could you try launching the faulty command? This should work:

cd /home/jon/Working_Files/hapo-g/round_3
/home/jon/miniconda3/envs/hapog/bin/build/hapog -b chunks_bam/chunks_69.bam -f chunks/chunks_69.fasta -o hapog_chunks/chunks_69.fasta -c hapog_chunks/chunks_69.changes

Also, is the fasta file chunks/chunks_69.fasta containing something or is it empty?

[JonEilers]

The fasta file chunks/chunks_69.fasta does have content. the `chunks_bam/chunks_69.bam also has some content. here is a link to the bam file and here is a link to the fasta file. Below is the terminal output from running the requested command.

(hapog) jon@jon-PowerEdge-R910:~/Working_Files/hapo-g/round_3$ /home/jon/miniconda3/envs/hapog/bin/build/hapog -b chunks_bam/chunks_69.bam -f chunks/chunks_69.fasta -o hapog_chunks/chunks_69.fasta -c hapog_chunks/chunks_69.changes
Floating point exception (core dumped)

[bistace]

Thanks a lot for providing the bam, we will look into this and will keep you informed.

[JonEilers]

Awesome, thanks! In case you want to try reproducing this - the genome can be found here and the pacbio is here

[bistace]

After inspecting the BAM file, it seems that it doesn't contain any alignment. It is not normal and something might have gone wrong during the alignment step, like a full disk. Could you please check that everything went as expected?

On our side, we're going to add checks for this situation.

[bistace]

We just pushed a version that improves the handling of empty BAM files on conda and on github. Could you please check if that solves your issue?

[JonEilers]

Well I am feeling a little silly. I totally forgot that I had renamed the fastq file so it'd work with dentist. So ya, no surprise the bam file is empty as there was no fastq file with that name. I'm running it with hapo-g version 1.1 at the moment. I'll run it with hapo-g version 1.2 after and will close this issue if all is working. Thanks for the assistance and sorry for wasting your time! One suggestion would be to add a check if file exists and error message if a file doesn't exist. Cheers!