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.
- Fetch Genome into local galaxy using "Get data USCS Main table".
- Build index using Bowtie2 index builder (Galaxy Version 126.96.36.199+galaxy1).
- Upload FASTQ files into Galaxy.
- FastQC Read Quality reports (Galaxy Version 0.72+galaxy1).
- FASTQ Masker by quality score (Galaxy Version 1.1.5)
- Bowtie2 - map reads against reference genome (Galaxy Version 188.8.131.52+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.