Failure in creating an index

kingsfordgroup / sailfish

Rapid Mapping-based Isoform Quantification from RNA-Seq Reads

http://www.cs.cmu.edu/~ckingsf/software/sailfish

GNU General Public License v3.0

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Failure in creating an index #112

Closed LucilaT closed 5 years ago

LucilaT commented 5 years ago

UPDATE: I have solved it. It was a problem with the assembly.fasta file.

Hi, I am trying to create an index of my assembly and I obtained this error:

FAILURE: return code from libdivsufsort() was -1

The command I used is the following: salmon index -t assembly.fasta -i assembly_index --type quasi -k 31

Any ideas of what can be happening? Any help is welcome. Thank you in advance, Lucila

rob-p commented 5 years ago

Hi @lucilaT,

Thanks for reporting the issue and the fix. I'd just like to point you at our Salmon tool, which is the successor to sailfish. It is much more actively maintained and frequently updated, and has many new features not available in Sailfish.

Best, Rob