R3.1.1

[OskarSchnappauf]

Dear Ted,

Thank you very much for developing this tool. I tried to run Atlas-CNV on our cluster here at the NIH, but unfortunately, R3.1.1 is not supported anymore on our HPC. Just wondered, are you planning to update your tool to run with a more recent R version or is there any other way to run it with a newer version of R? Thank you very much for your help. Best, Oskar

[theodorc]

Hi Oskar,

Thank you for your interest in Atlas-CNV.

Although, I haven't tested I think the R code should still work with newer versions of R as long as the 3 required packages are included and loaded. R3.1.1 was used at the time of publication. Most of the R calls are routine and basic routines which should not have change dramatically.

Have you encountered an error using a more recent R version? Please post error messages if you can.

Thanks, Ted

[OskarSchnappauf]

Hi Ted,

Thank you so much for your reply. The message I get when I try to run Atlas-CNV with another R version is the following:

$ perl atlas_cnv.pl --config config_R_3.4.3 --panel Panel_final.txt --sample Sample_2.txt

No user defined cnv threshold_del provided, so defaults will be used. No user defined cnv threshold_dup provided, so defaults will be used. cp: cannot stat ‘/data/schnappaufog/2019_07_25_MiSeq_FirstRun/DepthData/5092.DATA.sample_interval_summary’: 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 '5092/5092.DATA.sample_interval_summary': No such file or directory Execution halted cp: cannot stat ‘/data/schnappaufog/2019_07_25_MiSeq_FirstRun/DepthData/5094.DATA.sample_interval_summary’: 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 '5094/5094.DATA.sample_interval_summary': No such file or directory Execution halted cp: cannot stat ‘/data/schnappaufog/2019_07_25_MiSeq_FirstRun/DepthData/4600.DATA.sample_interval_summary’: 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 '4600/4600.DATA.sample_interval_summary': No such file or directory Execution halted Warning message: package ‘reshape2’ was built under R version 3.4.4 Warning message: package ‘optparse’ was built under R version 3.4.4 Warning message: package ‘plotrix’ was built under R version 3.4.4 Error in [<-.data.frame(*tmp*, a, i, value = NA) : replacement has 1 row, data has 0 Calls: remove_5pc_outliers -> [<- -> [<-.data.frame Execution halted Warning message: package ‘reshape2’ was built under R version 3.4.4 Warning message: package ‘optparse’ was built under R version 3.4.4 Warning message: package ‘plotrix’ was built under R version 3.4.4 Error in [<-.data.frame(*tmp*, a, i, value = NA) : replacement has 1 row, data has 0 Calls: remove_5pc_outliers -> [<- -> [<-.data.frame Execution halted Warning message: package ‘reshape2’ was built under R version 3.4.4 Warning message: package ‘optparse’ was built under R version 3.4.4 Warning message: package ‘plotrix’ was built under R version 3.4.4 Error in [<-.data.frame(*tmp*, a, i, value = NA) : replacement has 1 row, data has 0 Calls: remove_5pc_outliers -> [<- -> [<-.data.frame Execution halted cp: cannot stat ‘5092/5092.cnv*’: No such file or directory cp: cannot stat ‘5092/5092.pdf’: No such file or directory cp: cannot stat ‘5094/5094.cnv*’: No such file or directory cp: cannot stat ‘5094/5094.pdf’: No such file or directory cp: cannot stat ‘4600/4600.cnv*’: No such file or directory cp: cannot stat ‘4600/4600.pdf’: No such file or directory

I managed to run Atlas-CNV by installing R\3.1.1. I wondered, can I run it also on fewer than 47 samples? I run it on 10 patients and did only get “NA” in the ExonQC file.

Thank you so much for your help. Oskar

From: Ted Chiang [email protected] Reply-To: theodorc/Atlas-CNV [email protected] Date: Tuesday, December 3, 2019 at 11:00 PM To: theodorc/Atlas-CNV [email protected] Cc: "Schnappauf, Oskar (NIH/NHGRI) [F]" [email protected], Author [email protected] Subject: Re: [theodorc/Atlas-CNV] R3.1.1 (#7)

Hi Oskar,

Thank you for your interest in Atlas-CNV.

Although, I haven't tested I think the R code should still work with newer versions of R as long as the 3 required packages are included and loaded. R3.1.1 was used at the time of publication. Most of the R calls are routine and basic routines which should not have change dramatically.

Have you encountered an error using a more recent R version? Please post error messages if you can.

Thanks, Ted

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/theodorc/Atlas-CNV/issues/7?email_source=notifications&email_token=AIBMSWNE2WYB65TWUHUSJMDQW4TKFA5CNFSM4JU25YN2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEF3UW7Y#issuecomment-561466239, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AIBMSWNJ2CBEPNGHI4YB7V3QW4TKFANCNFSM4JU25YNQ.

[theodorc]

Hi Oskar,

Ah yes, it looks like some of the newer versions of those R packages are problematic. If you manage to get it to work in 3.1.1., then that will do. Anything over 25 samples would be good enough in my opinion. 10 samples is a bit on the lower side. I've seen it work well with 20+ samples. With fewer samples, you may need to calibrate and get a feel for how 'tight' the exon StDevs are. Of course every capture design (or panel of genes) will differ slightly.

Best, Ted

[OskarSchnappauf]

Dear Ted,

thank you so much for your reply. I managed to run Atlas-CNV using 3.1.1 and I run it on the DepthData for 46 samples (I got several output files as well as pdfs for each sample). However, somehow I don't get any CNVs called. I get values for the rpkm, however, the Cscore_matrix only shows NA for each of the genomic coordinates:

Samples 1:948954-948956 1:949364-949858 1:22964110-22964272 4817 NA NA NA

The exon_treshold_dup, the exon_treshold_del, and the ExonQC look like this: x 1 NA 2 NA 3 NA 4 NA 5 NA 6 NA 7 NA 8 NA 9 NA 10 NA 11 NA

Do you have any idea what the reason could be? Please see below what error messages I received during the run. I so much appreciate your help. Best, Oskar

[OskarSchnappauf]

perl atlas_cnv.pl --config config --panel Panel_final.txt --sample Samples_MiSeq_2.txt No user defined cnv threshold_del provided, so defaults will be used. No user defined cnv threshold_dup provided, so defaults will be used. Error in contrasts<-(*tmp*, value = contr.funs[1 + isOF[nn]]) : contrasts can be applied only to factors with 2 or more levels Calls: anova ... model.matrix -> model.matrix.default -> contrasts<- Execution halted Error in contrasts<-(*tmp*, value = contr.funs[1 + isOF[nn]]) : contrasts can be applied only to factors with 2 or more levels Calls: anova ... model.matrix -> model.matrix.default -> contrasts<- Execution halted Error in contrasts<-(*tmp*, value = contr.funs[1 + isOF[nn]]) : contrasts can be applied only to factors with 2 or more levels Calls: anova ... model.matrix -> model.matrix.default -> contrasts<- Execution halted Error in contrasts<-(*tmp*, value = contr.funs[1 + isOF[nn]]) : contrasts can be applied only to factors with 2 or more levels Calls: anova ... model.matrix -> model.matrix.default -> contrasts<- Execution halted

[theodorc]

Hi Oskar,

I'm sorry for being slow to respond.

Could you post a few lines of your input files? [--config config --panel Panel_final.txt --sample Samples_MiSeq_2.txt], so I can help debug? Usually it may be some slight file formatting issues.

Thanks, Ted

[OskarSchnappauf]

Hi Ted,

Thank you so much for your reply and the time you spent on helping the users of your tool. I finally managed to get Atlas-CNV running. The reason for my issue was the sample file. When I opened it with a text editor or excel to enter my sample names and then saved it, I received an error message running your tool. I then downloaded your example files and tried those and it worked. I figured, I had to use command line to generate the sample file and then it worked. The results so far look very promising and hopefully it will help our lab to make more diagnoses for our patients. I will keep you updated. Thank you again! Best, Oskar

From: Ted Chiang [email protected] Reply-To: theodorc/Atlas-CNV [email protected] Date: Thursday, December 12, 2019 at 1:22 AM To: theodorc/Atlas-CNV [email protected] Cc: "Schnappauf, Oskar (NIH/NHGRI) [F]" [email protected], Author [email protected] Subject: Re: [theodorc/Atlas-CNV] R3.1.1 (#7)

Hi Oskar,

I'm sorry for being slow to respond.

Could you post a few lines of your input files? [--config config --panel Panel_final.txt --sample Samples_MiSeq_2.txt], so I can help debug? Usually it may be some slight file formatting issues.

Thanks, Ted

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/theodorc/Atlas-CNV/issues/7?email_source=notifications&email_token=AIBMSWP74WQOCMBXXJYG3YDQYHIULA5CNFSM4JU25YN2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEGVSQPI#issuecomment-564865085, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AIBMSWLQDCU2SAOV3W7ENM3QYHIULANCNFSM4JU25YNQ.