parameter.ctrl not found

[Alex-Nesta]

Hi, this is a silly issue, but I've hit a roadblock.

I did a fresh git clone of LIONS within the hour 9:50 EST Jan 22, 2018.

I am running it on my institution's cluster.

I modified input.list, parameter.ctrl, and system.sysctrl appropriately.

Then I ran bash lions.sh from my root LIONS directory.

I have also tried specifying parameters with

[nestaa@helix LIONS]$ bash lions.sh ./controls/parameter.ctrl 

I get the following error:

 Import parameter file.
    Project Parameters: ./controls/parameter.ctrl

 running initializeLIONS.sh

 ./LIONS/scripts/initilizeLIONS.sh ...
 ==============================================================
     Project Name: MCF7vsMCF10A 
     Run Identification Number: 190122_1006
     Library List: /projects/beck-lab/alex/bin/LIONS/controls/input.list
     Genome: hg38 
     System: glitch
             cores: 1
             qsub:  (if applicable)
     LIONS base dir: /projects/beck-lab/alex/bin/LIONS
     Call Settings: oncoexaptation

 ------ Run LIONS self-check procedures ------ 

 Initialize/initializeScripts.sh found.
 ... checking scripts
     Check that LIONS scripts exist and are read/executable

... /projects/beck-lab/alex/bin/LIONS/controls/input.list found.
 ./controls/parameter.ctrl not found (empty or non-readable).
 ===== ERROR 2: MISSING REQUISITE FILE ===== 

here is what the file structure looks like:

[nestaa@helix LIONS]$ pwd
/projects/beck-lab/alex/bin/LIONS

[nestaa@helix LIONS]$ ls -lha controls/
total 368K
drwxr-sr-x  5 nestaa beck-lab  363 Jan 22 09:24 .
drwxr-sr-x 11 nestaa beck-lab  424 Jan 22 09:28 ..
-rwxr-xr-x  1 nestaa beck-lab 1.6K Jan 22 09:24 docker.sysctrl
-rwxr-xr-x  1 nestaa beck-lab 6.7K Jan 22 09:24 docker_test.ctrl
-rwxr-xr-x  1 nestaa beck-lab 1.6K Jan 22 09:24 glitch.sysctrl
drwxr-sr-x  2 nestaa beck-lab  600 Jan 22 09:24 inactive
-rw-r--r--  1 nestaa beck-lab  496 Jan 22 09:29 input.list
drwxr-sr-x  2 nestaa beck-lab  302 Jan 22 09:24 old
-rwxr-xr-x  1 nestaa beck-lab 7.0K Jan 22 09:40 parameter.ctrl
-rwxr-xr-x  1 nestaa beck-lab 6.7K Jan 22 09:24 sandbox.ctrl
-rwxr-xr-x  1 nestaa beck-lab 6.7K Jan 22 09:24 synTALL_test.ctrl
-rw-r--r--  1 nestaa beck-lab   84 Jan 22 09:24 synTALL_test.list
-rwxr-xr-x  1 nestaa beck-lab 1.7K Jan 22 09:29 system.sysctrl
drwxr-sr-x  2 nestaa beck-lab   92 Jan 22 09:24 template

parameter.ctrl is definitely there and readable. I'm at a loss here.

Thanks for the help, Alex

[biscuit13161]

Hi Alex,

It seems that you need to specify the full path to the parameter.ctrl for Lions to find it at this point.

Hth, Richard

On Tue, 22 Jan 2019, 18:00 Alex Nesta <notifications@github.com wrote:

Hi, this is a silly issue, but I've hit a roadblock.

I did a fresh git clone of LIONS within the hour 9:50 EST Jan 22, 2018.

I am running it on my institution's cluster.

I modified input.list, parameter.ctrl, and system.sysctrl appropriately.

Then I wen to run bash lions.sh from my root LIONS directory.

I get the following error:

------ Run LIONS self-check procedures ------

Initialize/initializeScripts.sh found. ... checking scripts Check that LIONS scripts exist and are read/executable

... /projects/beck-lab/alex/bin/LIONS/controls/input.list found. ./controls/parameter.ctrl not found (empty or non-readable). ===== ERROR 2: MISSING REQUISITE FILE =====

here is what the file structure looks like:

[nestaa@helix LIONS]$ pwd /projects/beck-lab/alex/bin/LIONS

[nestaa@helix LIONS]$ ls -lha controls/ total 368K drwxr-sr-x 5 nestaa beck-lab 363 Jan 22 09:24 . drwxr-sr-x 11 nestaa beck-lab 424 Jan 22 09:28 .. -rwxr-xr-x 1 nestaa beck-lab 1.6K Jan 22 09:24 docker.sysctrl -rwxr-xr-x 1 nestaa beck-lab 6.7K Jan 22 09:24 docker_test.ctrl -rwxr-xr-x 1 nestaa beck-lab 1.6K Jan 22 09:24 glitch.sysctrl drwxr-sr-x 2 nestaa beck-lab 600 Jan 22 09:24 inactive -rw-r--r-- 1 nestaa beck-lab 496 Jan 22 09:29 input.list drwxr-sr-x 2 nestaa beck-lab 302 Jan 22 09:24 old -rwxr-xr-x 1 nestaa beck-lab 7.0K Jan 22 09:40 parameter.ctrl -rwxr-xr-x 1 nestaa beck-lab 6.7K Jan 22 09:24 sandbox.ctrl -rwxr-xr-x 1 nestaa beck-lab 6.7K Jan 22 09:24 synTALL_test.ctrl -rw-r--r-- 1 nestaa beck-lab 84 Jan 22 09:24 synTALL_test.list -rwxr-xr-x 1 nestaa beck-lab 1.7K Jan 22 09:29 system.sysctrl drwxr-sr-x 2 nestaa beck-lab 92 Jan 22 09:24 template

parameter.ctrl is definitely there and readable. I'm at a loss here.

Thanks for the help, Alex

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[Alex-Nesta]

bash lions.sh /projects/beck-lab/alex/bin/LIONS/controls/parameter.ctrl

This works. Strange that all of the other files are found without issue using relative path.