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yyoshiaki / VIRTUS

A bioinformatics pipeline for viral transcriptome detection and quantification considering splicing.
https://github.com/yyoshiaki/VIRTUS/wiki
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STAR --genomeSAindexNbases setting #18

Closed zhangzlab closed 3 years ago

zhangzlab commented 4 years ago

Dear,

I encountered the Segmentation fault (core dumped) at the STAR alignReads to the virus genome step. Then I checked the genomeSAindexNbases parameter in the virus index creation step and found the following warning.

'WARNING: --genomeSAindexNbases 14 is too large for the genome size=199753728, which may cause seg-fault at the mapping step. Re-run genome generation with recommended --genomeSAindexNbases 12'

Two questions:

  1. The recommended genomeSAindexNbases of STAR is min(14, log2(GenomeLength)/2 - 1). I noticed the GenomeLength of all virus genomes is just 198153, why 199753728 here.
  2. Should I change the genomeSAindexNbases in the virus index creation step?
zhangzlab commented 4 years ago

I recreated the index with genomeSAindexNbases = 12, and now it's ok.

yyoshiaki commented 4 years ago

Thank you for pointing it out, and sorry for my late reply. Actually, in createindex.cwl, we used the default --genomeSAindexNbases. In the next release, we consider specifying smaller --genomeSAindexNbases.

yyoshiaki commented 3 years ago

Fixed in #22 . Thank you!