I have personal Galaxy instance running on centOS 7. I am having issue with Bowtie2 and HISAT2. It's the same error on both.
I think it is an issue with Genome index.
Steps for getting Genome into local Galaxy instance.
1. Fetch Genome into local galaxy using "Get data USCS Main table".
2. Build index using Bowtie2 index builder (Galaxy Version 18.104.22.168+galaxy1).
3. Upload FASTQ files into Galaxy.
4. FastQC Read Quality reports (Galaxy Version 0.72+galaxy1).
5. FASTQ Masker by quality score (Galaxy Version 1.1.5)
6. Bowtie2 - map reads against reference genome (Galaxy Version 22.214.171.124+galaxy0).
Input: FASTQ Masker file from Step 5, Use a built-in index and select reference genome built in Step 2.
This is where I get the following error and this is same with HISAT2.
[E::idx_find_and_load] Could not retrieve index file for '/home/webuser/galaxy/database/objects/6/7/d/dataset_67dde163-6ec6-4f51-afa6-f8aa2aee66b0.dat'
Any input is greatly appreciated.