Question: VisCap 'mat.cov' not found error in R
0
gravatar for ceruleanivy
16 months ago by
ceruleanivy30
ceruleanivy30 wrote:

I am using VisCap (https://github.com/pughlab/VisCap/wiki) in order to conclude copy number variations by reading BAM files created from Ion Torrent next-generation sequencing on FFPE tumor samples. After successfully creating the required output from the GATK DepthOfCoverage tool and running VisCap using RTerm.exe I get the following error;

Error in make_matrix_from_cov_files(lane_dir, cov_file_pattern, cov_field) : object 'mat.cov' not found
Execution halted

I've nearly tried everything from re-generating the reference genome index files (FAI, DICT) to re-running every individual analysis for each BAM going through the DepthOfCoverage tool, including the necessary update for the required R packages and sub-dependencies to make it run normally. I've contacted the corresponding author in the published paper, but never got an official reply, while the whole project seems abandoned (despite being published in a highly reputable journal). Therefore, I'm counting to anyone that might have used the software in the past or suspects anything that could solve the problem.

next-gen R software error • 515 views
ADD COMMENTlink modified 3 months ago by nkausthu20 • written 16 months ago by ceruleanivy30
0
gravatar for hns
12 months ago by
hns140
USA/Boston
hns140 wrote:

Hi Ceruleanivy,

You just need to change the cov_file_pattern to reflect the cov file pattern that you have.

Thank you.

ADD COMMENTlink written 12 months ago by hns140
0
gravatar for nkausthu
3 months ago by
nkausthu20
nkausthu20 wrote:

I have the same issue. It would be really great if someone can comment on this

Attaching package: ‘gplots’

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

lowess

Attaching package: ‘zoo’

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

as.Date, as.Date.numeric

character(0) Error in make_matrix_from_cov_files(lane_dir, cov_file_pattern, cov_field) : object 'mat.cov' not found Execution halted

ADD COMMENTlink written 3 months ago by nkausthu20
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