Error!

[AteeqMKhaliq]

Hi,

When we are trying to execute DriverML with the Example dataset its throwing the error please have a look,

sh DriverML-master/run.driverml.sh -w DriverML-master -i DriverML-master/example/UVM.txt -f hg38.fa -r hg19.fa -o UVM-summary1.txt
Can't open 'gene-characteristic-unix.txt' for reading: 'No such file or directory' at DriverML-master/add-genes-to-characteristic.pl line 15
Can't open 'gene-characteristic-unix.txt' for reading: 'No such file or directory' at 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 '02_19_13_29_21_065276949_gene-characteristic.tmp': No such file or directory
Execution halted
Can't open '02_19_13_29_21_065276949_gene-class.tmp' for reading: 'No such file or directory' at DriverML-master/pre-drgap.pl line 16
DriverML-master/monte_carlo_sim.cpp: In function ‘int main(int, char**)’:
DriverML-master/monte_carlo_sim.cpp:221:37: error: expected ‘+’, ‘*’, ‘-’, ‘&’, ‘^’, ‘|’, ‘&&’, ‘||’, ‘min’ or ‘max’ before ‘vec_plus’
#pragma omp parallel for reduction(vec_plus:p2sides_noN)
^
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_19_13_29_21_065276949_gene-characteristic.tmp': No such file or directory
Execution halted
Can't open 'pre_02_19_13_29_21_065276949_gene-class.tmp' for reading: 'No such file or directory' at DriverML-master/pre-drgap.pl line 16
The file you sepcified does not exist at DriverML-master/reduction.pl line 43.
The file you sepcified does not exist at DriverML-master/reduction.pl line 43.
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 262704 14.1 641817 34.3 431538 23.1
Vcells 442934 3.4 8388608 64.0 1753383 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_19_13_29_21_065276949_subclass-1.tmp_exp.tmp': No such file or directory
Execution halted
DriverML-master/run.driverml.sh: line 232: ./02_19_13_29_21_065276949_monte_carlo.out.tmp: No such file or directory
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_19_13_29_21_065276949_out_file_1.tmp': No such file or directory
Execution halted
02_19_13_29_21_065276949

Please let us know if we are doing it correctly.
Regards
Khaliq

[yasirniazi]

hi .
same issue facing .
kindly guide regarding this issue

[HelloYiHan]

Hi,
Sorry for the late reply. The Coronavirus disease 2019 is spreading in our country and we are restricted at home. So there are delays in our work.
I suggest using an absolute path in the command line like that:

nohup /AbsolutePath/DriverML-master/run.driverml.sh -w /AbsolutePath/DriverML-master -i example/UVM.txt -f /AbsolutePath/GRCh38.fa -r /AbsolutePath/hg19.fa -m 10 -o UVM-summary.txt > UVM-nohup.out

We are developing the second version of this software in order to make it more easily to use.
Let me know if you have any questions or concerns.

[yasirniazi]

Thanks for Reply Sir. May your country get rid of said virus soon. I have run this tool using this command but lots of directory error occurs(posted in githup issues section) . I try my best to resolve but failed to find solutions. Kindly help me regarding this issue

…

On Thu, Feb 27, 2020, 7:05 PM YiHan ***@***.***> wrote: Hi, Sorry for the late reply. The Coronavirus disease 2019 is spreading in our country and we are restricted at home. So there are delays in our work. I suggest using an absolute path in the command line like that: nohup /AbsolutePath/DriverML-master/run.driverml.sh -w /AbsolutePath/DriverML-master -i example/UVM.txt -f /AbsolutePath/GRCh38.fa -r /AbsolutePath/hg19.fa -m 10 -o UVM-summary.txt > UVM-nohup.out We are developing the second version of this software in order to make it more easily to use. Let me know if you have any questions or concerns. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#7?email_source=notifications&email_token=AGYILSY3PV2ERD7TTXZULO3RE7CC3A5CNFSM4KYAFLS2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOENEQK5I#issuecomment-591988085>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AGYILS2YVM5WQPU7DUJB25DRE7CC3ANCNFSM4KYAFLSQ> .

[complexgenome]

I run into the same error.
Also, when I run the script throws loads of warnings:

Use of uninitialized value $flank1bp in reverse at /data1/users/sanjeev/drivers/DriverML/DriverML/reduction.pl line 261.
substr outside of string at /data1/users/sanjeev/drivers/DriverML/DriverML/reduction.pl line 252.

@HelloYiHan can you help?

I provide full/absolute path of the input files.