Hi,
I’m writing as I’m attempting to import a reference genome into my Galaxy server, which has previously been successful, however, when reaching the step where Picard Indexing has to occur I’m running into an error. Specifically, I see the Fatal error: Exit code 1. It to me seems like it thinks I do not have a correct version of the tool Picard index, but I’ve attempted to download all varients without luck. I’m not sure what I’m missing? I hope someone can help.
Asta
Hi @asta
This post has the best way to run these: Indexing reference genomes with Data Managers: Resources, tutorials, troubleshooting
Few questions to start with:
- You are running Data Managers on a local install of Galaxy? Or is this a docker or cloud Galaxy?
- What version of Galaxy? Where was it sourced? The URL would be helpful or explain.
- What version of the fasta index DM did you run?
- Did you create a new database key or use one that was already available?
- Did you provide a fasta file from the history or did you look one up (and from which source)?
- Did you allow that to completely finish successfully before running the Picard index DM?
- What version of the Picard index DM did you run?
Let’s start there.
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Yes, the link is in fact from one of my own previous posts, where you of were of great help However, this is exactly why I’m confused; I got it to run previously with your instructions but now it appears to not work. To answer the questions:
- It is a university server so there should be plenty of space.
- galaxy.pharm.nottingham.ac.uk
- The successful SAM FASTA index I ran was 0.0.1 (toolshed.g2.bx.psu.edu/repos/devteam/data_manager_sam_fasta_index_builder/sam_fasta_index_builder/0.0.1)
- I’m not sure what you mean by database key, but since I’m using a university server nothing was there previously, I’ve downloaded all tools and data managers myself
- I used Create DBKey and Reference Genome first (toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_dbkeys_all_fasta/data_manager_fetch_genome_all_fasta_dbkey/0.0.3) with Mouse Dec. 2011 (GRCm38/mm10) (mm10) from UCSC
- Yes the SAM FASTA tool had finished successfully before I tried Picard index
- The Picard version that’s currently failing for me is 0.0.1 (toolshed.g2.bx.psu.edu/repos/devteam/data_manager_picard_index_builder/picard_index_builder_data_manager/0.0.1), I have tried to download all available versions to me in the toolbox.
Thank you!