Seq fault

[kspham]

Hi Bioturing team,

I tried as you suggested and used hera_build like this:

hera_build --gtf GRCh38_with vector.gtf --fasta GRCh38_with_vector.fa --outdir directory --fullindex 1

And indeed this helped to find reads mapping to the vector sequence. Before I always added the --grch38 1 parameter.
Still, I have two problems:

1. In one of my samples I get a “Segmentation fault” error. The rest of my samples run without problems. My hera was installed via Bioconda and there does not seem to be any update available (conda update hera). I read this article on biostars, so I thought it might have been corrected in the meantime: https://www.biostars.org/p/266226/
   The server I’m working on:
   $ cat /proc/version
   Linux version 3.10.0-327.36.3.el7.x86_64 (builder@kbuilder.dev.centos.org) (gcc version 4.8.5 20150623 (Red Hat 4.8.5-4) (GCC) ) Update README.md #1 SMP Mon Oct 24 16:09:20 UTC 2016

$ hera quant -i reference/index -o test25 -t 6 -f reference/GRCh38_739.fa -p test25_3_ raw/R1.fastq.gz raw/R2.fastq.gz
Hera is a program developed by BioTuring for RNA-Seq analysis.
Please contact info@bioturing.com if you need further support
Number of processed pairs : 1850000Segmentation fault

2. Although I get reads mapping the viral vector sequence, there are no fusions listed in the separate output file. I also found several pairs where one mate is within the vector and the other mate on a different chromosome. Therefore my question here is, does hera apply any additional filter or special requirements for these reads to be considered for fusions?

Thank you very much for your support.
Step by step I’m getting closer.

Best regards,
Tim Rath