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Nextomics / nextsv

MIT License
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error [bwt_restore_sa] SA-BWT inconsistency: primary is not the same while running nextsv #7

Closed RatneshSingh closed 6 years ago

RatneshSingh commented 6 years ago

I received an error for [bwt_restore_sa] SA-BWT inconsistency: primary is not the same while running nextsv.

it is caused by bwa index and sawriter both creating index file with same name and overwriting each other. and then complaining about .sa file not being correct.

to solve the issue, create sawriter and bwa indexes in two different folders and provide the path in the config file.

fangli80 commented 6 years ago

Thank you for your comment. We also noticed this issue. As described in the README file, there are two parameters for reference FASTA file in the config file. The ref_fasta is the path to reference genome FASTA file used by BWA and NGMLR. The ref_blasr is the path to reference genome FASTA file used by BLASR. This two files should be in different folders. (You can link one file to another folder)