COHCAP / Discussion / General Discussion: Can't seem to get the program working error

Anonymous - 2013-10-24

I am trying to get it to work with the sample data
The program stops here is the log file
[2013-10-24 17:20:42] Running COHCAP....

No expression file("Expression File") specified. Pipeline will run without data integration

[2013-10-24 17:20:42] Annotating Report....

485512 annotated probes
No detection p-values found in beta file!

[2013-10-24 17:20:56] Creating QC Figures....

[1] "Group: mutant" "Group: parental"
null device
1
null device
1
NULL

[2013-10-24 17:21:38] Calculating CpG Site Statistics....

[1] "Reading Sample Description File...."
[1] 6 2
[1] "Reading Beta Table...."
[1] 485513 15
[1] "Group: mutant" "Group: parental"
[1] "Differential Methylation Stats for 2 Groups with Reference"

[2013-10-24 17:22:42] Creating .wig files....

Error in colnames<-(*tmp*, value = c("IlmnID", "Chr", "Location", :
'names' attribute [18] must be the same length as the vector [14]
Execution halted
Uncaught exception from user code:
Could not open C:\Users\luciej\Desktop\cohcap-v-1.2.4\bin\output\Test_CpG_stats.txt! at cohcap.pl line 1689.
main::create_wig_files('C:\Users\luciej\Desktop\cohcap-v-1.2.4\bin\output\Test_CpG_st...', 'C:\Users\luciej\Desktop\cohcap-v-1.2.4\bin\output', 'PC') called at cohcap.pl line 509
main::run_cohcap('C:\Users\luciej\Desktop\cohcap-v-1.2.4\bin\output\Test_param.txt', 'PC', 'C:\Users\luciej\Desktop\cohcap-v-1.2.4\bin\', 1, 1, 1, 1, 1, 1, ...) called at cohcap.pl line 122

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Anonymous - 2013-10-24

Here is the param file

Test_param.txt

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Anonymous - 2013-10-24

It says the number of groups is 1 but it produces the same error for 2

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Charles Warden - 2013-10-25

It looks like you probably have Perl and R configured correctly, but just to confirm:

Can you see the .pdf files created by the QC step? If so, do they look reasonable (e.g. do they match screenshosts on the main page) or are they just blank files?

Yes - the number of groups should be 2. Also, the reference should be "parental" (or "mutant" - it doesn't really matter, but the reference needs to be one of the group IDs). The other parameters seem correct. Can you please delete all of the current output files and try re-running the program with these settings?

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Anonymous - 2013-10-25

It worked. Thanks!

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Charles Warden - 2013-10-25

Great - thank you for using COHCAP!

Please let me know if you have any other problems.

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Anonymous - 2013-12-05

Unable to solve the error !!!
Can u pleas help us to solve the error ??

[2013-12-04 17:20:06] Running COHCAP....

No expression file("Expression File") specified. Pipeline will run without data integration

[2013-12-04 17:20:06] Annotating Report....

485512 annotated probes
No detection p-values found in beta file!

[2013-12-04 17:20:47] Creating QC Figures....

[1] "Group: normal" "Group: tumor"
null device
1
null device
1
NULL

[2013-12-04 17:22:16] Calculating CpG Site Statistics....

[1] "Reading Sample Description File...."
[1] 22 2
[1] "Reading Beta Table...."
[1] 485513 31
[1] "Group: normal" "Group: tumor"
[1] "Differential Methylation Stats for 2 Groups with Reference"

[2013-12-04 17:24:21] Creating .wig files....

Error in colnames<-(*tmp*, value = c("IlmnID", "Chr", "Location", :
'names' attribute [18] must be the same length as the vector [14]
Execution halted
Uncaught exception from user code:
Could not open D:\cohcap-v-1.2.4\cohcap-v-1.2.4\Demo\Demo_CpG_stats.txt! at cohcap.pl line 1689.
main::create_wig_files('D:\cohcap-v-1.2.4\cohcap-v-1.2.4\Demo\Demo_CpG_stats.txt', 'D:\cohcap-v-1.2.4\cohcap-v-1.2.4\Demo', 'PC') called at cohcap.pl line 509
main::run_cohcap('D:\cohcap-v-1.2.4\cohcap-v-1.2.4\Demo\Demo_param.txt', 'PC', 'D:\COHCAP~1.4\COHCAP~1.4\bin\', 1, 1, 1, 1, 1, 1, ...) called at cohcap.pl line 122

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Anonymous - 2013-12-05

Another error in CpG Island finding !!!

[2013-12-04 18:48:52] Running COHCAP....

No expression file("Expression File") specified. Pipeline will run without data integration

[2013-12-04 18:48:52] Annotating Report....

485512 annotated probes
No detection p-values found in beta file!

[2013-12-04 18:49:28] Creating QC Figures....

[1] "Group: normal" "Group: tumor"
null device
1
null device
1
NULL

[2013-12-04 18:50:57] Calculating CpG Site Statistics....

[1] "Reading Sample Description File...."
[1] 22 2
[1] "Reading Beta Table...."
[1] 485513 31
[1] "Group: normal" "Group: tumor"
[1] "Differential Methylation Stats for 2 Groups with Reference"
NULL

[2013-12-04 18:56:47] Creating .wig files....

[2013-12-04 18:56:53] Finished creating normal.avg.beta.wig....
[2013-12-04 18:56:59] Finished creating tumor.avg.beta.wig....
[2013-12-04 18:57:06] Finished creating tumor.vs.normal.delta.beta.wig....

[2013-12-04 18:57:06] Filtering for Differentially Methylated CpG Sites....

[2013-12-04 18:57:13] Differentially Methylated Region (CpG Island) Analysis....

[2013-12-04 18:57:13] Methylation Analysis Complete!....

Error in matrix(unlist(value, recursive = FALSE, use.names = FALSE), nrow = nr, :
negative extents to matrix
Calls: [ -> [.data.frame -> Ops.data.frame -> matrix
Execution halted

DDD_param.txt

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Anonymous - 2013-12-05

[2013-12-04 18:48:52] Running COHCAP....

No expression file("Expression File") specified. Pipeline will run without data integration

[2013-12-04 18:48:52] Annotating Report....

485512 annotated probes
No detection p-values found in beta file!

[2013-12-04 18:49:28] Creating QC Figures....

[1] "Group: normal" "Group: tumor"
null device
1
null device
1
NULL

[2013-12-04 18:50:57] Calculating CpG Site Statistics....

[1] "Reading Sample Description File...."
[1] 22 2
[1] "Reading Beta Table...."
[1] 485513 31
[1] "Group: normal" "Group: tumor"
[1] "Differential Methylation Stats for 2 Groups with Reference"
NULL

[2013-12-04 18:56:47] Creating .wig files....

[2013-12-04 18:56:53] Finished creating normal.avg.beta.wig....
[2013-12-04 18:56:59] Finished creating tumor.avg.beta.wig....
[2013-12-04 18:57:06] Finished creating tumor.vs.normal.delta.beta.wig....

[2013-12-04 18:57:06] Filtering for Differentially Methylated CpG Sites....

[2013-12-04 18:57:13] Differentially Methylated Region (CpG Island) Analysis....

[2013-12-04 18:57:13] Methylation Analysis Complete!....

Error in matrix(unlist(value, recursive = FALSE, use.names = FALSE), nrow = nr, :
negative extents to matrix
Calls: [ -> [.data.frame -> Ops.data.frame -> matrix
Execution halted

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Charles Warden - 2013-12-05

It looks to me like you are running COHCAP with default parameters (based upon the _param.txt file that was provided). It also looks like you are working with patient data and everything is working up until the CpG island analysis.

It is hard to say for certain at this point, but I think you may need to use more liberal criteria. Patient data is more heterogeneous than cell line data - I would probably recommend at least changing the methyl cutoff to 0.3 (that is what I did for the TCGA breast cancer data).

The best way to check is to see how many CpG sites are in the file with the word "filtered" in it. If that file is empty, no CpG sites remain for CpG island analysis. Even if the file has some data, you currently need 4 CpG sites within a CpG island to get a result. If this is not the case for any CpG islands, then the CpG island code can't run.

Can you please take a look at that file and let me know how many CpG sites are being used for the CpG island analysis?

Last edit: Charles Warden 2013-12-05

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Can't seem to get the program working error

City of Hope CpG Island Analysis Pipeline

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Can't seem to get the program working error

Can't seem to get the program working error

City of Hope CpG Island Analysis Pipeline

Forums

Help

Can't seem to get the program working error document.SUBSCRIPTION_OPTIONS = { "thing": "topic", "subscribed": false, "url": "subscribe", "icon": { "css": "fa fa-envelope-o" } };

Can't seem to get the program working error