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No output file - cygwin #1

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rjsicko opened this Issue Nov 21, 2014 · 9 comments

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@rjsicko

rjsicko commented Nov 21, 2014

Ran in cygwin and it says it completed successfully, but no files are output.

"$ ./geneSCF -i=./141120-Eb_publication_cnvs-Entrez.txt -t=gid -db=REACTOME -o=eb_publication_cnvs

processing started....Fri, Nov 21, 2014 11:57:55 AM

Run successful. Check your output directory eb_publication_cnvs

Parameters used:

background genes: 30000
Identitiy: Entrez GeneID
Database used: REACTOME
Output file: eb_publication_cnvs141120-Eb_publication_cnvs-Entrez.txt_REACTOME_functional_classification.tsv
WARNING: Your output is not sorted with P-val/FDR.


Author: Santhilal Subhash
santhilal.subhash@gu.se
Last Updated: 2014 June 14
Fri, Nov 21, 2014 11:57:58 AM finished processing

rsicko@HR17423 ~/geneSCF-master
$ which eb_publication_cnvs141120-Eb_publication_cnvs-Entrez.txt_REACTOME_functional_classification.tsv
which: no eb_publication_cnvs141120-Eb_publication_cnvs-Entrez.txt_REACTOME_functional_classification.tsv in (/usr/local/bin:/usr/bin:/cygdrive/c/Program Files/ImageMagick-6.8.9-Q16:/cygdrive/c/Perl/site/bin:/cygdrive/c/Perl/bin:/cygdrive/c/Windows/system32:/cygdrive/c/Windows:/cygdrive/c/Windows/System32/Wbem:/cygdrive/c/Program Files (x86)/Common Files/Roxio Shared/DLLShared:/cygdrive/c/Program Files (x86)/Common Files/Roxio Shared/10.0/DLLShared:/cygdrive/c/Windows/System32/WindowsPowerShell/v1.0:/cygdrive/c/Program Files (x86)/Lotus/Notes:/cygdrive/c/Windows/System32/WindowsPowerShell/v1.0:/cygdrive/c/Program Files (x86)/MATLAB/MATLAB Compiler Runtime/v714/runtime/win32:/cygdrive/c/Program Files/SlikSvn/bin:/cygdrive/c/Applied Biosystems/PeakScanner)"

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decodebiology Nov 21, 2014

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please try by providing the whole path of input (-i=) and the output directory (-o=). Let me know if it stills does not gives any output.

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decodebiology commented Nov 21, 2014

please try by providing the whole path of input (-i=) and the output directory (-o=). Let me know if it stills does not gives any output.

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decodebiology Nov 21, 2014

Owner

And for your information, this tool has been tested on Linux and Mac machines. I am sorry to say that this will not work on windows environments.

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decodebiology commented Nov 21, 2014

And for your information, this tool has been tested on Linux and Mac machines. I am sorry to say that this will not work on windows environments.

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rjsicko Nov 21, 2014

just tried on ubuntu and still no output...
"rsicko@rsicko-ngs-box:~/Programs/geneSCF-master$ ./geneSCF -i=./141120-Eb_publication_cnvs-Entrez.txt -t=gid -db=REACTOME -o=./test/eb_publication_cnvs

processing started....Fri Nov 21 12:31:44 EST 2014

Run successful. Check your output directory ./test/eb_publication_cnvs

Parameters used:

background genes: 30000
Identitiy: Entrez GeneID
Database used: REACTOME
Output file: ./test/eb_publication_cnvs141120-Eb_publication_cnvs-Entrez.txt_REACTOME_functional_classification.tsv
WARNING: Your output is not sorted with P-val/FDR.


Author: Santhilal Subhash
santhilal.subhash@gu.se
Last Updated: 2014 June 14
Fri Nov 21 12:31:46 EST 2014 finished processing
rsicko@rsicko-ngs-box:/Programs/geneSCF-master$ cd test
rsicko@rsicko-ngs-box:
/Programs/geneSCF-master/test$ ls
output sample_gene_list_id sample_gene_list_sym
rsicko@rsicko-ngs-box:~/Programs/geneSCF-master/test$ "

rjsicko commented Nov 21, 2014

just tried on ubuntu and still no output...
"rsicko@rsicko-ngs-box:~/Programs/geneSCF-master$ ./geneSCF -i=./141120-Eb_publication_cnvs-Entrez.txt -t=gid -db=REACTOME -o=./test/eb_publication_cnvs

processing started....Fri Nov 21 12:31:44 EST 2014

Run successful. Check your output directory ./test/eb_publication_cnvs

Parameters used:

background genes: 30000
Identitiy: Entrez GeneID
Database used: REACTOME
Output file: ./test/eb_publication_cnvs141120-Eb_publication_cnvs-Entrez.txt_REACTOME_functional_classification.tsv
WARNING: Your output is not sorted with P-val/FDR.


Author: Santhilal Subhash
santhilal.subhash@gu.se
Last Updated: 2014 June 14
Fri Nov 21 12:31:46 EST 2014 finished processing
rsicko@rsicko-ngs-box:/Programs/geneSCF-master$ cd test
rsicko@rsicko-ngs-box:
/Programs/geneSCF-master/test$ ls
output sample_gene_list_id sample_gene_list_sym
rsicko@rsicko-ngs-box:~/Programs/geneSCF-master/test$ "

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decodebiology Nov 21, 2014

Owner

Please try by providing the whole path for input and output.

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decodebiology commented Nov 21, 2014

Please try by providing the whole path for input and output.

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rjsicko Nov 21, 2014

Still nothing
"rsicko@rsicko-ngs-box:~/Programs/geneSCF-master$ ./geneSCF -i=/home/rsicko/Programs/geneSCF-master/141120-Eb_publication_cnvs-Entrez.txt -t=gid -db=REACTOME -o=/home/rsicko/Programs/geneSCF-master/test/eb_publication_cnvs

processing started....Fri Nov 21 12:40:57 EST 2014

Run successful. Check your output directory /home/rsicko/Programs/geneSCF-master/test/eb_publication_cnvs

Parameters used:

background genes: 30000
Identitiy: Entrez GeneID
Database used: REACTOME
Output file: /home/rsicko/Programs/geneSCF-master/test/eb_publication_cnvs141120-Eb_publication_cnvs-Entrez.txt_REACTOME_functional_classification.tsv
WARNING: Your output is not sorted with P-val/FDR.


Author: Santhilal Subhash
santhilal.subhash@gu.se
Last Updated: 2014 June 14
Fri Nov 21 12:40:59 EST 2014 finished processing
rsicko@rsicko-ngs-box:/Programs/geneSCF-master$ cd test
rsicko@rsicko-ngs-box:
/Programs/geneSCF-master/test$ ls
output sample_gene_list_id sample_gene_list_sym"

rjsicko commented Nov 21, 2014

Still nothing
"rsicko@rsicko-ngs-box:~/Programs/geneSCF-master$ ./geneSCF -i=/home/rsicko/Programs/geneSCF-master/141120-Eb_publication_cnvs-Entrez.txt -t=gid -db=REACTOME -o=/home/rsicko/Programs/geneSCF-master/test/eb_publication_cnvs

processing started....Fri Nov 21 12:40:57 EST 2014

Run successful. Check your output directory /home/rsicko/Programs/geneSCF-master/test/eb_publication_cnvs

Parameters used:

background genes: 30000
Identitiy: Entrez GeneID
Database used: REACTOME
Output file: /home/rsicko/Programs/geneSCF-master/test/eb_publication_cnvs141120-Eb_publication_cnvs-Entrez.txt_REACTOME_functional_classification.tsv
WARNING: Your output is not sorted with P-val/FDR.


Author: Santhilal Subhash
santhilal.subhash@gu.se
Last Updated: 2014 June 14
Fri Nov 21 12:40:59 EST 2014 finished processing
rsicko@rsicko-ngs-box:/Programs/geneSCF-master$ cd test
rsicko@rsicko-ngs-box:
/Programs/geneSCF-master/test$ ls
output sample_gene_list_id sample_gene_list_sym"

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decodebiology Nov 21, 2014

Owner

Are you sure whether you are using it in proper installation of Ubuntu rather than any virtual-box?

Owner

decodebiology commented Nov 21, 2014

Are you sure whether you are using it in proper installation of Ubuntu rather than any virtual-box?

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rjsicko Nov 21, 2014

It is Ubuntu ran through virtual box... not sure that should matter; the file system in virtual box behaves as if Ubuntu was installed on the disk, no? I ran the command you suggested and still no output

rjsicko commented Nov 21, 2014

It is Ubuntu ran through virtual box... not sure that should matter; the file system in virtual box behaves as if Ubuntu was installed on the disk, no? I ran the command you suggested and still no output

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rjsicko Nov 21, 2014

got it. I changed the output to an existing directory and it worked... it appears geneSCF can't make a new directory for output

rjsicko commented Nov 21, 2014

got it. I changed the output to an existing directory and it worked... it appears geneSCF can't make a new directory for output

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decodebiology Nov 21, 2014

Owner

Yes I am working on it to improve the usage of this tool. And let me know if there is any other questions regarding the output or any technical information. Soon I will be also updating with other databases, more organisms support with detailed user manual. And I will be closing this issue for now.

Owner

decodebiology commented Nov 21, 2014

Yes I am working on it to improve the usage of this tool. And let me know if there is any other questions regarding the output or any technical information. Soon I will be also updating with other databases, more organisms support with detailed user manual. And I will be closing this issue for now.

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