My lab has just installed HISAT2 on our instance of Galaxy. Unfortunately I am having some trouble. When I run HISAT2 (input was fastq files with metadata as fastqsanger), the job completes however the resulting BAM file is only ~ 2 kB and when viewed in Tablet there are not reads. HISAT2 did not give any error messages either. Does anyone know what is going on, and what are possible solutions?
Edit: Some runs show this message
gzip: input_f.fastq.gz: not in gzip format gzip: input_r.fastq.gz: not in gzip format 0 reads 0.00% overall alignment rate
while others show
Building DifferenceCoverSample Building sPrime Building sPrimeOrder V-Sorting samples V-Sorting samples time: 00:02:06 Allocating rank array Ranking v-sort output Ranking v-sort output time: 00:00:26 Invoking Larsson-Sadakane on ranks I