I have a pipeline that was working with STAR and RSEM v1.2.28. I tried to update the genes used from Gencode vM4 to Gencode vM19 and I started getting a segmentation fault in rsem-calculate-credibility-intervals. I have tried using the latest release of RSEM 1.3.1 but get the same errors. I have tried running it with gdb and the segfault is in the sort in calcCI.cpp line 225. I don't see anything wrong with the gtf file, and had no errors when generating the indexes. I put notes and the indexes at
http://www.bx.psu.edu/~giardine/tests/tmp/rsemError/ The same RNA-seq data works when using Gencode vM4, so the difference isn't in the reads.
Thanks,
Belinda Giardine
I have a pipeline that was working with STAR and RSEM v1.2.28. I tried to update the genes used from Gencode vM4 to Gencode vM19 and I started getting a segmentation fault in rsem-calculate-credibility-intervals. I have tried using the latest release of RSEM 1.3.1 but get the same errors. I have tried running it with gdb and the segfault is in the sort in calcCI.cpp line 225. I don't see anything wrong with the gtf file, and had no errors when generating the indexes. I put notes and the indexes at http://www.bx.psu.edu/~giardine/tests/tmp/rsemError/ The same RNA-seq data works when using Gencode vM4, so the difference isn't in the reads. Thanks, Belinda Giardine