DoAbsolute ABSOLUTE.RData does not exist, drop it ERROR

[tanayb001]

I have copy number segment file generated using DNACopy package and maf file generated using Mutect2 file. Now I want to use DoAbsolute to infer copy number calls and here is my command which is generating these errors:

> DoAbsolute("p1_seg.txt", Maf = "IITK-P01.maf", sigma.p = 0, max.sigma.h = 0.2, min.ploidy = 0.5,
+   max.ploidy = 10, primary.disease = "PRAD", platform = "Illumina_WES",
+   temp.dir = ("/home/iit/Documents/ABSOLUTE/tmp"), clean.temp = FALSE,
+   results.dir = getwd(), max.as.seg.count = 1500,  max.non.clonal = 0.05,  max.neg.genome = 0.005,  
+   copy.num.type = "total",  min.mut.af = 0.1,  min.no.mut = 5,
+   verbose = FALSE,  nThread = 1L,  keepAllResult = TRUE,  recover = FALSE)
-> Setting results directory as /home/iit/Documents/ABSOLUTE 
-> Setting temp directory as /home/iit/Documents/ABSOLUTE/tmp 
Directory /home/iit/Documents/ABSOLUTE/tmp/cache does not exists.
----> Error detected, see log for more details.
--> Files in cache directory:
[1] "tmp"
Warning in DoAbsolute("p1_seg.txt", Maf = "IITK-P01.maf", sigma.p = 0, max.sigma.h = 0.2,  :
  --> Result file /home/iit/Documents/ABSOLUTE/tmp/cache/IITK-P01-TD.ABSOLUTE.RData does not exist, drop it.
Error in DoAbsolute("p1_seg.txt", Maf = "IITK-P01.maf", sigma.p = 0, max.sigma.h = 0.2,  : 
  No result file to proceed.
>

Please let me know how to solve it.

[ShixiangWang]

There should have a error.log in your result directory, what's the output?

[tanayb001]

No output is generating. The error log file contains this:

Detected error in sample IITK-P01-TD Error message: the condition has length > 1 Where: if !is.na(res) { mode.tab[(i - 1) * n.d + j, ] <- c(res[[1]], res[[2]], res[[3]]) } Skipping this sample.

The tmp directory has a cache folder and new maf and .seg file.

The segment input file looks like this: Sample Chromosome Start End Num_Probes Segment_Mean IITK-P01-TD chr1 16739 13392417 8527 0.3464 IITK-P01-TD chr1 13392517 13395697 5 -1.04 IITK-P01-TD chr1 13416259 68375421 28515 0.2675

Please let me know what can I do to run the tool.

[ShixiangWang]

Are you using the modified ABSOLUTE?

path_to_file = system.file("extdata", "ABSOLUTE_1.0.6.tar.gz", package = "DoAbsolute", mustWork = T)
install.packages(path_to_file, repos = NULL, type="source")

If yes, you could send me the file and code to run DoAbsolute, debugging may be required.

[tanayb001]

I installed both ABSOLUTE and DoAbsolute package. I Absolute I'm not understanding all the step by step process. Also I got error while running CreateReviewObject command. So I move to use DoAbsolute. Yes I installed using

path_to_file = system.file("extdata", "ABSOLUTE_1.0.6.tar.gz", package = "DoAbsolute", mustWork = T) install.packages(path_to_file, repos = NULL, type="source")

from https://github.com/ShixiangWang/DoAbsolute#example

How I'll send you the files? I ran the above code mentioned in the issue.

[ShixiangWang]

Ok, send it to w_shixiang@163.com . I will test it at my spare time.

[tanayb001]

Fine. I'll share the segmented file and its respective maf file.