Can't Open Connection

[avrajit]

I used full path for the directory as below but there is problem of reading the files
/media/hp/DATa/tools/DriverML-master/run.driverml.sh -w /media/hp/DATa/tools/DriverML-master -i /media/hp/DATa/Pancreatic/WGS/Somatic_pairedSample/MAF_Somatic/driverInput.maf -f /media/hp/DATa/Ref/GRCh38.p14.genome.fa -r /media/hp/DATa/Ref/GRCh38.p14.genome.fa -o /media/hp/DATa/Pancreatic/WGS/Somatic_pairedSample/DriverMutation/SomaticDriver

The errors are
Can't open 'gene-characteristic-unix.txt' for reading: 'No such file or directory' at /media/hp/DATa/tools/DriverML-master/add-genes-to-characteristic.pl line 15
Can't open 'gene-characteristic-unix.txt' for reading: 'No such file or directory' at /media/hp/DATa/tools/DriverML-master/add-genes-to-characteristic.pl line 15
Final cluster number is 1
Error in file(file, "rt") : cannot open the connection
Calls: read.table -> file
In addition: Warning message:
In file(file, "rt") :
cannot open file '10_17_11_38_20_340645478_gene-characteristic.tmp': No such file or directory
Execution halted
Can't open '10_17_11_38_20_340645478_gene-class.tmp' for reading: 'No such file or directory' at /media/hp/DATa/tools/DriverML-master/pre-drgap.pl line 16
Error in file(file, "rt") : cannot open the connection
Calls: read.table -> file
In addition: Warning message:
In file(file, "rt") :
cannot open file 'pre_10_17_11_38_20_340645478_gene-characteristic.tmp': No such file or directory
Execution halted
Can't open 'pre_10_17_11_38_20_340645478_gene-class.tmp' for reading: 'No such file or directory' at /media/hp/DATa/tools/DriverML-master/pre-drgap.pl line 16
The file you sepcified does not exist at /media/hp/DATa/tools/DriverML-master/reduction.pl line 43.
The file you sepcified does not exist at /media/hp/DATa/tools/DriverML-master/reduction.pl line 43.
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 294435 15.8 692242 37 478378 25.6
Vcells 510708 3.9 8388608 64 1923835 14.7
Error in file(file, "rt") : cannot open the connection
Calls: read.table -> file
In addition: Warning message:
In file(file, "rt") :
cannot open file 'pre_10_17_11_38_20_340645478_subclass-1.tmp_exp.tmp': No such file or directory
Execution halted
There was an error opening the eta file.
Error in file(file, "rt") : cannot open the connection
Calls: read.table -> file
In addition: Warning message:
In file(file, "rt") :
cannot open file '10_17_11_38_20_340645478_out_file_1.tmp': No such file or directory
Execution halted
10_17_11_38_20_340645478

[kennethchow]

I'd like to add that I'm also getting a similar error to the one here. I am unsure of the cause of the problem, but I have tried debugging to no avail. I believe it has something to do with the creation of the .tmp files which can not be found by the script? But I have already chmod -R 755 to give full permissions to the folder. Not sure how to proceed, as I would wish to run this but might have to just go with MutSigCV