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runBP.log
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nohup: ignoring input
Loading required package: snowfall
Loading required package: snow
Warning message:
replacing previous import ‘gplots::lowess’ by ‘stats::lowess’ when loading ‘TED’
Read 900 items
[1] "EMSEMBLE IDs detected. Cleaning up genes based on EMSEMBLE IDs."
A total of 44 genes from RB chrM chrX chrY have been excluded
A total of 0 lowly expressed genes have been excluded
[1] "removing non-numeric genes..."
[1] "removing outlier genes..."
Number of outlier genes filtered= 7
[1] "aligning reference and mixture..."
[1] "run first sampling"
Start run... This may take a while
R Version: R version 4.1.3 (2022-03-10)
snowfall 1.84-6.1 initialized (using snow 0.4-4): parallel execution on 20 CPUs.
Stopping cluster
[1] "merge subtypes"
Fibroblast tumor B cell myocyte Macrophage Endothelial T cell
Min. 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
1st Qu. 0.016 0.738 0.000 0.000 0.000 0.006 0.001 0.000
Median 0.060 0.872 0.000 0.000 0.000 0.018 0.005 0.000
Mean 0.100 0.809 0.001 0.023 0.014 0.035 0.011 0.003
3rd Qu. 0.143 0.949 0.000 0.007 0.000 0.046 0.013 0.000
Max. 0.966 1.000 0.030 0.810 0.860 0.402 0.125 0.096
Dendritic Mast
Min. 0.000 0.000
1st Qu. 0.000 0.000
Median 0.000 0.001
Mean 0.002 0.001
3rd Qu. 0.000 0.002
Max. 0.154 0.022
[1] "pooling information across samples"
Start optimization... This may take a while
snowfall 1.84-6.1 initialized (using snow 0.4-4): parallel execution on 20 CPUs.
Stopping cluster
[1] "run final sampling"
Start run... This may take a while
snowfall 1.84-6.1 initialized (using snow 0.4-4): parallel execution on 20 CPUs.
Stopping cluster
tumor Fibroblast B cell myocyte Macrophage Endothelial T cell
Min. 0.010 0.000 0.000 0.000 0.000 0.000 0.000 0.000
1st Qu. 0.790 0.011 0.000 0.000 0.000 0.005 0.002 0.000
Median 0.897 0.046 0.000 0.000 0.000 0.016 0.006 0.000
Mean 0.845 0.078 0.001 0.021 0.010 0.029 0.010 0.004
3rd Qu. 0.957 0.104 0.001 0.006 0.000 0.039 0.012 0.002
Max. 0.999 0.857 0.036 0.821 0.915 0.232 0.101 0.099
Dendritic Mast
Min. 0.000 0.000
1st Qu. 0.000 0.000
Median 0.000 0.001
Mean 0.003 0.001
3rd Qu. 0.000 0.002
Max. 0.164 0.015
[1] "vst transformation is feasible"
converting counts to integer mode
Warning messages:
1: In searchCommandline(parallel, cpus = cpus, type = type, socketHosts = socketHosts, :
Unknown option on commandline: --file
2: In searchCommandline(parallel, cpus = cpus, type = type, socketHosts = socketHosts, :
Unknown option on commandline: --file
3: In searchCommandline(parallel, cpus = cpus, type = type, socketHosts = socketHosts, :
Unknown option on commandline: --file