DriverML icon indicating copy to clipboard operation
DriverML copied to clipboard

Error: cannot open the connection

Open Rohit-Satyam opened this issue 2 years ago • 0 comments

When Running DriverML, I get the following error even after using the absolute path. combined_mak.txt

Please help

./run.driverml.sh -w /mnt/d/2046llc/CancerPipe/test/mskcc-vcf2maf-754d68a/DriverML -i /mnt/d/2046llc/CancerPipe/test/mskcc-vcf2maf-754d68a/DriverML/combined_mak.txt -f /mnt/d/2046llc/CancerPipe/resources/chrM.fasta -r /mnt/d/2046llc/CancerPipe/resources/resources_broad_hg38_v0_Homo_sapiens_assembly38.fasta -o rohit
Final cluster number is 1

interpolation number is 100 
./run.driverml.sh: line 208:  1396 Killed                  $path/cluster.r $interpolation_number $cluster_final ${date}
Can't open '02_08_16_22_49_387393511_gene-class.tmp' for reading: 'No such file or directory' at /mnt/d/2046llc/CancerPipe/test/mskcc-vcf2maf-754d68a/DriverML/pre-drgap.pl line 16
./run.driverml.sh: line 213:  1413 Killed                  $path/cluster.r $interpolation_number 1 ${date_pre}
Can't open 'pre_02_08_16_22_49_387393511_gene-class.tmp' for reading: 'No such file or directory' at /mnt/d/2046llc/CancerPipe/test/mskcc-vcf2maf-754d68a/DriverML/pre-drgap.pl line 16
The file you sepcified does not exist at /mnt/d/2046llc/CancerPipe/test/mskcc-vcf2maf-754d68a/DriverML/reduction.pl line 43.
The file you sepcified does not exist at /mnt/d/2046llc/CancerPipe/test/mskcc-vcf2maf-754d68a/DriverML/reduction.pl line 43.
         used (Mb) gc trigger (Mb) max used (Mb)
Ncells 262390 14.1     641325 34.3   431169 23.1
Vcells 442862  3.4    8388608 64.0  1753648 13.4
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_02_08_16_22_49_387393511_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 '02_08_16_22_49_387393511_out_file_1.tmp': No such file or directory
Execution halted
02_08_16_22_49_387393511

Rohit-Satyam avatar Feb 08 '23 11:02 Rohit-Satyam