Error with blast n+ for STAR fusion

usegalaxy.org support
,
1

I’m trying to run a blastn of my fasta reference against itself to use in STAR fusion.

I’m been trying for a month now, it takes 4-5 days and always throws me this error:

Dataset Error Report

An error occurred while running the tool toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/2.10.1+galaxy0 .

Details

Execution resulted in the following messages:

Fatal error: Exit code 127 ()

Tool generated the following standard error:

blastn: error while loading shared libraries: libssl.so.1.0.0: cannot open shared object file: No such file or directory

I’m using two distinctly uploaded files as reference (even tough they are exact copies)

This is the tool preferences:

NCBI BLAST+ blastn

Dataset Information

Number: 454
Name: blastn GRCh38.p13.genome.fa.gz vs ‘Galaxy445-__ob__GRCh38.p13.genome.fa.gz__cb__V2.fasta.gz’
Created: Wed Dec 9 16:09:46 2020 (UTC)
Filesize: 0 bytes
Dbkey: ?
Format: tabular

Job Information

Galaxy Tool ID: toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/2.10.1+galaxy0
Galaxy Tool Version: 2.10.1+galaxy0
Tool Version: blastn: error while loading shared libraries: libssl.so.1.0.0: cannot open shared object file: No such file or directory
Tool Standard Output: stdout
Tool Standard Error: stderr
Tool Exit Code: 127
Job Messages * Fatal error: Exit code 127 ()
History Content API ID: bbd44e69cb8906b5117d0826a49decf7
Job API ID: bbd44e69cb8906b5824edc00a276a90e
History API ID: a7538c218afd56b8
UUID: 51ccd855-9cea-4d1e-8dd5-617bea9fc77a

Tool Parameters

Input Parameter Value
Nucleotide query sequence(s) * 91: GRCh38.p13.genome.fa.gz
Subject database/sequences file
database Empty.
histdb Empty.
Nucleotide FASTA subject file to use instead of a database * 453: Galaxy445-[GRCh38.p13.genome.fa.gz]V2.fasta.gz
Type of BLAST blastn - Traditional BLASTN requiring an exact match of 11, for somewhat similar sequences
Set expectation value cutoff 0.001
Output format 6
Advanced Options basic
Job Resource Parameters no

Inheritance Chain

blastn GRCh38.p13.genome.fa.gz vs ‘Galaxy445-__ob__GRCh38.p13.genome.fa.gz__cb__V2.fasta.gz’

Dataset peek

no peek

1 Like
2

Hello @GACG1

There is a known dependency issue with BLAST+ tools right now at usegalaxy.org, however, your job would fail for resources even if that issue was already fixed.

The computational resources required to BLAST the entire human reference genome against itself will exceed the resources available at any public Galaxy server, plus BLAST isn’t the best tool choice for that purpose.

If you are interested in same-genome and cross-genome comparative genomic alignments, the UCSC Genome Browser at http://genome.ucsc.edu/ hosts alignments for “Comparative Genomics” (many track choices) and “Repeat” (many choices, the track “Self Chain” would be “hg38 versus hg38”) for the Human Dec. 2013 (GRCh38/hg38) Assembly.

You can review the data within their Genome Browser, extract small portions of the alignments using their Table Browser, and find the entire alignments in their Downloads area.

Best :slight_smile: