BS-seeker3
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2.1 years ago

Hi everyone, I would like to use the BS-seeker3 aligner to align human sequences, but I have problems when I try to do the indexing of the reference genome hg38. It seems that the indexing ended without errors but when I try to use the reference genome for the alignment it returns me an error:

BS-Seeker3 beta

Welcome to SNAP version 2.0.1.

Loading index from directory... Unable to open file 'reference_genome/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz_snap/W_C2T/GenomeIndex' for read. Index load failed, aborting. SNAP exited with exit code 1 from line 269 of file SNAPLib/AlignerContext.cpp Welcome to SNAP version 2.0.1.

Loading index from directory... Unable to open file 'reference_genome/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz_snap/W_C2T/GenomeIndex' for read. Index load failed, aborting. SNAP exited with exit code 1 from line 269 of file SNAPLib/AlignerContext.cpp Welcome to SNAP version 2.0.1.

I read that it could be a problem of memory in the indexing part. Did someone use bs-seeker3 on human sequences and succed in using it ?

BS-seeker3 • 305 views
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