DecodeGenome

I got the same error message " OSError: libopenslide.so.0: cannot open shared object file: No such file or directory " after run "python3 -m stnet prepare spatial" command at virtual...

Hi Riederd, please see the attachment. Thanks. [c5_vcf_contents.tar.gz](https://github.com/icbi-lab/nextNEOpi/files/15167117/c5_vcf_contents.tar.gz)

Hi Riederd, Thank you very much. For installVEPplugins process, I did not see any error messages. I now copies these two files, and hopefully everything is ok. Best Regards!

Dear Dr. Dietmar, Thanks you very much for your prompt response. Please find files you need which could help you identify the problems. Beste Regards, Wei ________________________________ From: Dietmar Rieder...

Hi Riederd, The files are attached here now, please let me know whether you can see them. Thanks, Wei [contents.tar.gz](https://github.com/icbi-lab/nextNEOpi/files/15111893/contents.tar.gz) [nextflow.log](https://github.com/icbi-lab/nextNEOpi/files/15111896/nextflow.log)

Hi, Riederd, here is the contents in /wynton/group/bivona/Analytic_tools/NextNeoPi/nextNEOpi/work/9e/57ee15ac58f72351d24ddb25b46813/ Thanks, [9e_contents.tar.gz](https://github.com/icbi-lab/nextNEOpi/files/15112606/9e_contents.tar.gz)

Hi Riederd, We defined "tmpDir: /wynton/scratch/wwu888/nextNEOpi" (see in nextflow.log, line="Apr-24 21:11:40.257 [main] INFO nextflow.script.BaseScript") , why the nextNeopi is trying to create temporay file to "/scratch/wwu888/" here. Even using this...

Hi Riederd, I tried your suggestion, it is the same error. yara_mapper still reads the ENV as /scratch/wwu888. I checked /scratch/wwu888, it does contain singularity. Any other sugguestions? Thanks, Wei

Hi, The problem was solved with setting: "export SINGULARITYENV_TMPDIR=/wynton/scratch/wwu888/nextNEOpi". However, when running the command:  a new error occured, see #17. Thanks, Wei