Incompatibility between --outSAMattributes --outSAMtype BAM SortedByCoordinate and --quantMode?

[Alexander Stoddard]

I seem to have found a combinatorial bug with the following three options  using STAR_2.4.0j_modified (Linux_x86_64_static binary).

If I specify all three of the following options I get an immediate segfault upon getting to "Started mapping" in the Log (all aligned output files are empty).

--outSAMtype BAM SortedByCoordinate

--outSAMattributes All

--quantMode TranscriptomeSAM

Any two of the above three run fine. The segfault appears only with all three together. (Or I am just going crazy at this point).

Thank you,

Alexander Stoddard

[Alexander Dobin]

Hi Alexander, 

I cannot reproduce this behavior on my test dataset. What happens if you list all the necessary parameters on --outSAMattributes, instead of using "All"?

Cheers

Alex