Running Pipeline with Patient_example Crashes

[baeckesebastian]

Hi,
running ./miracum_pipe.sh -p wes -d Patient_example crashes (see attached logfile report.log):

The following object is masked from 'package:gtools':

    logit

[1] "Load functions."
[1] "Preparations."
[1] "Filtering for Tumor."
Error in file(file, "rt") : cannot open the connection
Calls: filtering -> read.csv -> read.table -> file
In addition: Warning message:
In file(file, "rt") :
  cannot open file '/opt/MIRACUM-Pipe/assets/output/somaticGermline_Patient_example/WES/somaticGermline_Patient_example_vc.output.snp.Somatic.hc.TUMOR.avinput.hg19_multianno.csv': No such file or directory
Execution halted
Error in readChar(con, 5L, useBytes = TRUE) : cannot open the connection
Calls: load -> readChar
In addition: Warning message:
In readChar(con, 5L, useBytes = TRUE) :
  cannot open compressed file '/opt/MIRACUM-Pipe/assets/output/somaticGermline_Patient_example/Analyses/MTB.RData', probable reason 'No such file or directory'
Execution halted
mv: cannot stat '/opt/MIRACUM-Pipe/assets/output/somaticGermline_Patient_example/Analyses/Report.tex': No such file or directory
This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2019/dev/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
! I can't find file `/opt/MIRACUM-Pipe/assets/output/somaticGermline_Patient_ex
ample/Analyses/somaticGermline_Patient_example_Report.tex'.
<*> ...somaticGermline_Patient_example_Report.tex 
                                                  --output-directory=/opt/MI...

(Press Enter to retry, or Control-D to exit)
Please type another input file name
! Emergency stop.
<*> ...somaticGermline_Patient_example_Report.tex 
                                                  --output-directory=/opt/MI...

!  ==> Fatal error occurred, no output PDF file produced!
Transcript written on texput.log.
This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2019/dev/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
! I can't find file `/opt/MIRACUM-Pipe/assets/output/somaticGermline_Patient_ex
ample/Analyses/somaticGermline_Patient_example_Report.tex'.
<*> ...somaticGermline_Patient_example_Report.tex 
                                                  --output-directory=/opt/MI...

(Press Enter to retry, or Control-D to exit)
Please type another input file name
! Emergency stop.
<*> ...somaticGermline_Patient_example_Report.tex 
                                                  --output-directory=/opt/MI...

!  ==> Fatal error occurred, no output PDF file produced!
Transcript written on texput.log.