Issue with Bowtie2 and HISAT2

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
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
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.

Thank you.

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It seems that your input BAM files has no index. Can you check your Galaxy logs during the upload of a BAM file and see if you find some errors?

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Hi @smahavadi

If you didn’t find the problem yet, it may be that the genome is missing an index. Likely the samtools index.

Please see this prior Q&A and the one it links to for more details:

Best, Jen

Sorry but I am still having issues. I am also confused about uploading BAM files because Bowtie2 is what is supposed to output BAM file and I can’t get it working.

I see a lot of discussion about indexes such as Picard but it’s not clear as how is BOWTIE2 tied to all these tools. Is there a detailed steps of fetching and building indexes for a reference genome like below:

  1. Fetch Genome into local galaxy using “Get data USCS Main table”.
  2. Build index using Bowtie2 index builder.