When I submitted my FASTQSANGER.GZ file to HISAT2 updated version (Galaxy Version 2.1.0+galaxy4), I received following error.
“file has no sequences defined (mode=‘rb’) - is it SAM/BAM format? Consider opening with check_sq=False”
I Changed the version to HISAT2 (Galaxy Version 2.1.0+galaxy3), and there were no errors. Please check the updated version for any bugs that prevents HISAT2 to recognize FASTQSANGER as one. instead it is searching for a SAM/BAM format input?