Chun Su

Hi. Thank you for quick reply. Here are the last 20 lines of bds.log. ``` $ tail -n 20 bds.log File "/mnt/isilon/sfgi/programs/atac_dnase_pipelines/ataqc/run_ataqc.py", line 1598, in main() File "/mnt/isilon/sfgi/programs/atac_dnase_pipelines/ataqc/run_ataqc.py", line 1454,...

Thank you! I think you are right about nonstandard character, since the name for the library is Naïve instead of naive.... But now, I have a new issue, which happened...

The error "Error in isVirtualExt(exti) :" comes from the attached library-conflict between snapATAC/ArchR and chromVAR. Starting new R session just loading chromVAR solved the problem.

@ctsa I tried to follow your suggestion [https://github.com/Illumina/strelka/issues/59](https://github.com/Illumina/strelka/issues/59) to use --forcedGT to re-genotyping tumor sample on merged calls. I check the log, it reports "Workflow successfully completed all tasks". However,...

It works for me now, by setting ~/.R/Makevars LDFLAGS=-L/path/to/your/gsl/lib -lgsl -lgslcblas CFLAGS=-I/path/to/your/gsl/include PKG_LIBS=-L/path/to/your/gsl/lib Then add following to ~/.bashrc export PATH=/path/to/your/gsl/bin:$PATH export LD_LIBRARY_PATH=/path/to/your/gsl/2.5/lib:/path/to/your/gsl/include:$LD_LIBRARY_PATH