I am trying to run inferCNV and have successfully up until step 18. I tried a suggestion in a issue response to set output_format = NA but I got the same error message as before. Can someone please help with this error? Thank you in advance.
Input command:
perform infercnv operations to reveal cnv signal
infercnv_obj = infercnv::run(infercnv_obj,
cutoff=0.1, # use 1 for smart-seq, 0.1 for 10x-genomics
out_dir="output_dir", # dir is auto-created for storing outputs
cluster_by_groups=T, # cluster
denoise=T,
HMM=T,
output_format = NA
)
Output where error begins:
STEP 18: Run Bayesian Network Model on HMM predicted CNVs
INFO [2021-10-25 17:48:26] Creating the following Directory: output_dir/BayesNetOutput.HMMi6.hmm_mode-samples
INFO [2021-10-25 17:48:26] Initializing new MCM InferCNV Object.
INFO [2021-10-25 17:48:26] validating infercnv_obj
INFO [2021-10-25 17:48:26] Total CNV's: 64
INFO [2021-10-25 17:48:26] Loading BUGS Model.
INFO [2021-10-25 17:48:26] Running Sampling Using Parallel with 4 Cores
INFO [2021-10-25 18:10:43] Obtaining probabilities post-sampling
INFO [2021-10-25 18:11:24] Gibbs sampling time: 22.9711995999018 Minutes
INFO [2021-10-25 18:11:56] ::plot_cnv:Start
INFO [2021-10-25 18:11:56] ::plot_cnv:Current data dimensions (r,c)=6101,6071 Total=388132.636222287 Min=0 Max=0.930717604594164.
INFO [2021-10-25 18:11:56] ::plot_cnv:Depending on the size of the matrix this may take a moment.
Error in png(paste(out_dir, paste(output_filename, ".png", sep = ""), :
unable to start png() device
In addition: Warning messages:
1: In png(paste(out_dir, paste(output_filename, ".png", sep = ""), :
unable to open file 'output_dir/BayesNetOutput.HMMi6.hmm_mode-samples/infercnv.NormalProbabilities.PreFiltering.png' for writing
2: In png(paste(out_dir, paste(output_filename, ".png", sep = ""), :
opening device failed
Hello,
I am trying to run inferCNV and have successfully up until step 18. I tried a suggestion in a issue response to set output_format = NA but I got the same error message as before. Can someone please help with this error? Thank you in advance.
Input command:
perform infercnv operations to reveal cnv signal
infercnv_obj = infercnv::run(infercnv_obj, cutoff=0.1, # use 1 for smart-seq, 0.1 for 10x-genomics out_dir="output_dir", # dir is auto-created for storing outputs cluster_by_groups=T, # cluster denoise=T, HMM=T, output_format = NA )
Output where error begins:
STEP 18: Run Bayesian Network Model on HMM predicted CNVs
INFO [2021-10-25 17:48:26] Creating the following Directory: output_dir/BayesNetOutput.HMMi6.hmm_mode-samples INFO [2021-10-25 17:48:26] Initializing new MCM InferCNV Object. INFO [2021-10-25 17:48:26] validating infercnv_obj INFO [2021-10-25 17:48:26] Total CNV's: 64 INFO [2021-10-25 17:48:26] Loading BUGS Model. INFO [2021-10-25 17:48:26] Running Sampling Using Parallel with 4 Cores INFO [2021-10-25 18:10:43] Obtaining probabilities post-sampling INFO [2021-10-25 18:11:24] Gibbs sampling time: 22.9711995999018 Minutes INFO [2021-10-25 18:11:56] ::plot_cnv:Start INFO [2021-10-25 18:11:56] ::plot_cnv:Current data dimensions (r,c)=6101,6071 Total=388132.636222287 Min=0 Max=0.930717604594164. INFO [2021-10-25 18:11:56] ::plot_cnv:Depending on the size of the matrix this may take a moment.
Error in png(paste(out_dir, paste(output_filename, ".png", sep = ""), : unable to start png() device In addition: Warning messages: 1: In png(paste(out_dir, paste(output_filename, ".png", sep = ""), : unable to open file 'output_dir/BayesNetOutput.HMMi6.hmm_mode-samples/infercnv.NormalProbabilities.PreFiltering.png' for writing 2: In png(paste(out_dir, paste(output_filename, ".png", sep = ""), : opening device failed