I have local Galaxy installed. Also I used Data Manager for creating indexes.
- Galaxy - 19.05
- HISAT2 - 2.1.0+galaxy5
I have just tried to run Hisat2 on usegalaxy.org with one of my files and it run successfully.
I uploaded this file to galaxy:
Then I run HISAT2 using this file as input (single end) fastq and hg38 as index , that’s all, very simple
In usegalaxy.org it works, in local galaxy it runs forever…
I don’t have any error, just eternal job. This only one thing that I can found this message:
Could not display BAM file, error was:
file has no sequences defined (mode=‘rb’) - is it SAM/BAM format? Consider opening with check_sq=False
Also I try the same run in console and notice the same behavior.