ERROR : Somtic samples run

[ajain195]

Rscript clinCNV.R --normal /home/akkey/Akshay/wellytics/ClinCNV/samples/normal.cov --tumor /home/akkey/Akshay/wellytics/ClinCNV/samples/tumor.cov --out /home/akkey/Akshay/wellytics/ClinCNV/result --bed /home/akkey/Akshay/wellytics/ClinCNV/samples/bed_file.bed --pair /home/akkey/Akshay/wellytics/ClinCNV/samples/pairs.txt --folderWithScript /home/akkey/Akshay/wellytics/ClinCNV
Loading required package: iterators
Loading required package: parallel
Package 'mclust' version 6.1.1
Type 'citation("mclust")' for citing this R package in publications.
Loading required package: R.oo
Loading required package: R.methodsS3
R.methodsS3 v1.8.2 (2022-06-13 22:00:14 UTC) successfully loaded. See ?R.methodsS3 for help.
R.oo v1.26.0 (2024-01-24 05:12:50 UTC) successfully loaded. See ?R.oo for help.

Attaching package: ‘R.oo’

The following object is masked from ‘package:R.methodsS3’:

throw

The following objects are masked from ‘package:methods’:

getClasses, getMethods

The following objects are masked from ‘package:base’:

attach, detach, load, save

R.utils v2.12.3 (2023-11-18 01:00:02 UTC) successfully loaded. See ?R.utils for help.

Attaching package: ‘R.utils’

The following object is masked from ‘package:utils’:

timestamp

The following objects are masked from ‘package:base’:

cat, commandArgs, getOption, isOpen, nullfile, parse, warnings

Attaching package: ‘dbscan’

The following object is masked from ‘package:stats’:

as.dendrogram

[1] "We run script located in folder /home/akkey/Akshay/wellytics/ClinCNV . Please, specify ABSOLUTE paths, relative paths do not work for every machine. If everything crashes, please, check the correctness of this path first."
[1] "Tumor file was provided. Framework is switched to somatic."
[1] "START cluster allocation."
[1] "Cluster allocated."
[1] "END cluster allocation."
[1] "We are started with reading the coverage files and bed files 2024-08-11 23:03:06"
[1] "Started basic quality filtering. 2024-08-11 23:03:09"
[1] "Amount of regions after filtering of 0-covered regions 100"
[1] "Normalization with GC and length starts. 2024-08-11 23:03:24"
[1] "Percentage of regions remained after GC correction: 1"
[1] "Percentage of regions remained after GC correction: 1"
Error in { : task 1 failed - "dim(X) must have a positive length"
Calls: gc_and_sample_size_normalise -> %dopar% ->
Execution halted

[GermanDemidov]

Can you send the top-5 lines from tumor.cov and normal.cov lines?

[ajain195]

Sure ,

Hi german ,

i tried three different way

first

Data : coverages_normal.cov ( split into normal and tumor )
screenshot attached
bedfile : bed_file.bed

second

normal data : coverages_normal.cov
tumor data : NA06989_coverage.cov
bedfile : bed_file.bed

Third

annotate with hg19.chrom.sizes

Normal data : NA06986.coverage.cov
tumor data : NA06989_coverage.cov
bedfile : gcAnnotated.preparedBedHg19.bin1000.bed

For first and second facing same error

but for third error facing :

in above screenshot using screen, so result and the command i give shows like this to make it easy for uh to understand

[GermanDemidov]

Thanks @ajain195 - you need to merge the tumors into a cohort too =) ClinCNV estimates the variability of each "tumor/normal" value. If you have only one tumor sample, you can't esimate how variable the ratio between tumors and normals is. So - add more tumors to your analysis (more the merrier) and it should work. The error message was saying "something which was supposed to be a matrix is actually a vector".