I am using cn.mops package to identify CNVs.
If I run:
read.counts = getSegmentReadCountsFromBAM(BAMFiles=bam.files, sampleNames=sam.names, GR=gr, parallel=30)
The output looks fine, but I get warnings:
There were 30 warnings (use warnings() to see them)
> warnings()
Warning messages:
1: closing unused connection 32 (<-localhost:11112)
2: closing unused connection 31 (<-localhost:11112)
3: closing unused connection 30 (<-localhost:11112)
............
What do the warnings mean? Should I take care for these warnings?
> sessionInfo()
R version 3.3.3 (2017-03-06)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: openSUSE 13.1 (Bottle) (x86_64)
locale:
[1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8
[5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8
[7] LC_PAPER=en_GB.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] cn.mops_1.20.1
[2] pracma_2.0.4
[3] reshape_0.8.6
[4] ggplot2_2.2.1
[5] BSgenome.Hsapiens.1000genomes.hs37d5_0.99.1
[6] BSgenome_1.42.0
[7] rtracklayer_1.34.2
[8] ggdendro_0.1-20
[9] SomaticSignatures_2.10.0
[10] VariantAnnotation_1.20.3
[11] Rsamtools_1.26.2
[12] Biostrings_2.42.1
[13] XVector_0.14.1
[14] SummarizedExperiment_1.4.0
[15] Biobase_2.34.0
[16] GenomicRanges_1.26.4
[17] GenomeInfoDb_1.10.3
[18] IRanges_2.8.2
[19] S4Vectors_0.12.2
[20] BiocGenerics_0.20.0
