Back to Workflows build report for BioC 3.7

BUILD WEB VIG report for TCGAWorkflow on malbec2

This page was generated on 2018-05-18 12:48:10 -0400 (Fri, 18 May 2018).

Package 20/21HostnameOS / ArchINSTALLBUILDBUILD WEB VIG
TCGAWorkflow 1.2.0
Tiago Chedraoui Silva
Snapshot Date: 2018-05-18 07:35:08 -0400 (Fri, 18 May 2018)
URL: https://git.bioconductor.org/packages/TCGAWorkflow
Branch: RELEASE_3_7
Last Commit: f07f804
Last Changed Date: 2018-04-30 10:07:09 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: TCGAWorkflow
Version: 1.2.0
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R -q -e 'rmarkdown::render(".buildwebvig/TCGAWorkflow/TCGAWorkflow.Rmd", output_format="BiocStyle:::html_fragment")' && /home/biocbuild/bbs-3.7-bioc/R/bin/R -q -e 'knitr::purl(".buildwebvig/TCGAWorkflow/TCGAWorkflow.Rmd", ".buildwebvig/TCGAWorkflow/TCGAWorkflow.R")'
StartedAt: 2018-05-18 08:52:23 -0400 (Fri, 18 May 2018)
EndedAt: 2018-05-18 09:13:38 -0400 (Fri, 18 May 2018)
EllapsedTime: 1274.8 seconds
RetCode: 0
Status:  OK 

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R -q -e 'rmarkdown::render(".buildwebvig/TCGAWorkflow/TCGAWorkflow.Rmd", output_format="BiocStyle:::html_fragment")' && /home/biocbuild/bbs-3.7-bioc/R/bin/R -q -e 'knitr::purl(".buildwebvig/TCGAWorkflow/TCGAWorkflow.Rmd", ".buildwebvig/TCGAWorkflow/TCGAWorkflow.R")'
###
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> rmarkdown::render(".buildwebvig/TCGAWorkflow/TCGAWorkflow.Rmd", output_format="BiocStyle:::html_fragment")


processing file: TCGAWorkflow.Rmd

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Loading required package: GenomicRanges
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--------------------------------------
o GDCquery: Searching in GDC database
--------------------------------------
Genome of reference: hg38
--------------------------------------------
oo Accessing GDC. This might take a while...
--------------------------------------------
ooo Project: TCGA-GBM
--------------------
oo Filtering results
--------------------
ooo By barcode
----------------
oo Checking data
----------------
ooo Check if there are duplicated cases
ooo Check if there results for the query
-------------------
o Preparing output
-------------------
Downloading data for project TCGA-GBM
GDCdownload will download 2 files. A total of 60.227 KB
Downloading as: Fri_May_18_08_53_28_2018.tar.gz
To get the following information please change the clinical.info argument
=> new_tumor_events: new_tumor_event 
=> drugs: drug 
=> follow_ups: follow_up 
=> radiations: radiation
Parsing follow up version: follow_up_v1.0

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gbm subtype information from:doi:10.1016/j.cell.2015.12.028

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Starting GBM
trying URL 'ftp://ftp.broadinstitute.org/pub/GISTIC2.0/hg19_support/CNV.hg19.bypos.111213.txt'
Content type 'unknown' length 358469 bytes (350 KB)
==================================================
Parsed with column specification:
cols(
  ID = col_character(),
  Chromosome = col_integer(),
  Start = col_integer(),
  End = col_integer(),
  Flankingstart = col_integer(),
  Flankingend = col_integer()
)
Loading Marker Informations
........................
Done
Loading Copy Number Data
................................................
Done

Performing Data Preprocessing

Done

Computing Discontinuity Matrix
.
Done
Computing Probability Distribution
....
Done
Assessing the Significance of Observed Data
..
Done
Writing GAIA_GBM_flt.txt.igv.gistic File for Integrative Genomics Viewer (IGV) Tool
..
Done
Running Homogeneous peel-off Algorithm With Significance Threshold of 0.25 and Homogenous Threshold of 0.12
..
Done

Writing Output File 'GAIA_GBM_flt.txt' Containing the Significant Regions

File 'GAIA_GBM_flt.txt' Saved


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silent variants: 38433
Summarizing..
Gene Summary..
NOTE: Possible FLAGS among top ten genes:
Checking clinical data..
Annotation missing for below samples in MAF
Done !

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gbm subtype information from:doi:10.1016/j.cell.2015.12.028
lgg subtype information from:doi:10.1016/j.cell.2015.12.028

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Looking for clinical data in annoatation slot of MAF..
Number of mutated samples for given genes: 
Median survival..

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========================================
circlize version 0.4.3
CRAN page: https://cran.r-project.org/package=circlize
Github page: https://github.com/jokergoo/circlize
Documentation: http://jokergoo.github.io/circlize_book/book/

If you use it in published research, please cite:
Gu, Z. circlize implements and enhances circular visualization 
  in R. Bioinformatics 2014.
========================================

Note: 2 points are out of plotting region in sector 'chr17', track '4'.


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Note: 1 point is out of plotting region in sector 'chr17', track '5'.


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I Need about  11 seconds for this Complete Normalization Upper Quantile  [Processing 80k elements /s]  
Step 1 of 4: newSeqExpressionSet ...
Step 2 of 4: withinLaneNormalization ...
Step 3 of 4: betweenLaneNormalization ...
Step 4 of 4: .quantileNormalization ...
Batch correction skipped since no factors provided
----------------------- DEA -------------------------------
there are Cond1 type LGG in  20 samples
there are Cond2 type GBM in  20 samples
there are  14477 features as miRNA or genes 
I Need about  19 seconds for this DEA. [Processing 30k elements /s]  
----------------------- END DEA -------------------------------

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clusterProfiler v3.8.1  For help: https://guangchuangyu.github.io/software/clusterProfiler

If you use clusterProfiler in published research, please cite:
Guangchuang Yu, Li-Gen Wang, Yanyan Han, Qing-Yu He. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS: A Journal of Integrative Biology. 2012, 16(5):284-287.

Attaching package: 'clusterProfiler'

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Loading required package: org.Hs.eg.db
Loading required package: AnnotationDbi

'select()' returned 1:many mapping between keys and columns
Info: Downloading xml files for hsa05214, 1/1 pathways..
Info: Downloading png files for hsa05214, 1/1 pathways..
'select()' returned 1:1 mapping between keys and columns
Info: Working in directory /home/biocbuild/bbs-3.7-workflows/meat/.buildwebvig/TCGAWorkflow
Info: Writing image file hsa05214.pathview.png
Info: some node width is different from others, and hence adjusted!

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==================== DATA Summary ====================
==================== END DATA Summary ====================
==================== T test results ====================
==================== END T test results ====================

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Group1:TCGA-GBM
Group2:TCGA-LGG
Calculating the diference between the mean methylation of the groups...
Calculating the p-values of each probe...

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Loading required package: grid
========================================
ComplexHeatmap version 1.18.0
Bioconductor page: http://bioconductor.org/packages/ComplexHeatmap/
Github page: https://github.com/jokergoo/ComplexHeatmap
Documentation: http://bioconductor.org/packages/ComplexHeatmap/

If you use it in published research, please cite:
Gu, Z. Complex heatmaps reveal patterns and correlations in multidimensional 
  genomic data. Bioinformatics 2016.
========================================


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Found more than one class "textConnection" in cache; using the first, from namespace 'BiocGenerics'
Also defined by 'RJSONIO'
Found more than one class "textConnection" in cache; using the first, from namespace 'BiocGenerics'
Also defined by 'RJSONIO'
Found more than one class "textConnection" in cache; using the first, from namespace 'BiocGenerics'
Also defined by 'RJSONIO'
Downloading genome information (try:0) Using: Homo sapiens genes (GRCh37.p13)
o Fetching auxiliary information
oo Fetching probes genomic information
http://zwdzwd.io/InfiniumAnnotation/current/hm450/hm450.hg19.manifest.rds
trying URL 'http://zwdzwd.io/InfiniumAnnotation/current/hm450/hm450.hg19.manifest.rds'
Content type 'unknown' length 18546360 bytes (17.7 MB)
==================================================
downloaded 17.7 MB

oo Fetching TSS information
Downloading transcripts information. Using: Homo sapiens genes (GRCh37.p13)
o Mapping probes to nearest TSS
o Mapping results information
o Plotting figure
oo Adding names to genes
o Saving results
oo Saving significant results as: starburst_results.csv
oo It contains pair with changes both in the expression level of the nearest gene and  in the DNA methylation level

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ChIPseeker v1.16.0  For help: https://guangchuangyu.github.io/ChIPseeker

If you use ChIPseeker in published research, please cite:
Guangchuang Yu, Li-Gen Wang, Qing-Yu He. ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization. Bioinformatics 2015, 31(14):2382-2383

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Scale for 'x' is already present. Adding another scale for 'x', which will
replace the existing scale.
Scale for 'colour' is already present. Adding another scale for 'colour',
which will replace the existing scale.

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Loading required package: ELMER.data
Downloading transcripts information. Using: Homo sapiens genes (GRCh37.p13)
Returning distal probes: 163576
Downloading genome information (try:0) Using: Homo sapiens genes (GRCh37.p13)
Loading from disk
Checking samples have both DNA methylation and Gene expression and they are in the same order...
Starting to add information to samples
 => Add clinical information to samples
Add FFPE information. More information at: 
=> https://cancergenome.nih.gov/cancersselected/biospeccriteria 
=> http://gdac.broadinstitute.org/runs/sampleReports/latest/FPPP_FFPE_Cases.html
 => Adding subtype information to samples
gbm subtype information from:doi:10.1016/j.cell.2015.12.028
 => Adding subtype information to samples
lgg subtype information from:doi:10.1016/j.cell.2015.12.028
Creating MultiAssayExperiment
MAE saved as: mae.rda

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Get diff methylated probes
ELMER will search for probes hypomethylated in group TCGA-GBM (n:10) compared to TCGA-LGG (n:10)
Number of probes: 2936
Saving results
Number of relevant probes found: 289

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Get nearby genes
Searching for the 4 near genes
Get anti correlated probes-genes
Using pre-defined groups. U (unmethylated): TCGA-GBM, M (methylated): TCGA-LGG
-------------------
* Filtering probes
-------------------
For more information see function preAssociationProbeFiltering
Making sure we have at least 5% of beta values lesser than 0.3 and 5% of beta values greater 0.3.
Removing 2287 probes out of 2936
Calculating Pp (probe - gene) for all nearby genes
File created: elmer/hypo/getPair.hypo.all.pairs.statistic.csv
Downloading transcripts information. Using: Homo sapiens genes (GRCh37.p13)
Update the distance to gene to distance to the nearest TSS of the gene

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Loading object: Probes.motif.hg19.450K
Retrieving TFClass family classification from ELMER.data.
Retrieving TFClass subfamily classification from ELMER.data.
------------------------------------
** Filtering motifs based on quality
------------------------------------
Number of enriched motifs with quality:
-----------
 => A: 15
 => B: 5
 => C: 6
 => D: 5
 => S: 0
-----------
Considering only motifs with quality from A up to DS: 31 motifs are enriched.

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Using pre-defined groups. U (unmethylated): TCGA-GBM, M (methylated): TCGA-LGG
-------------------------------------------------------------------------------------------------------------------
** Downloading TF list from Lambert, Samuel A., et al. The human transcription factors. Cell 172.4 (2018): 650-665.
-------------------------------------------------------------------------------------------------------------------
Accessing TF families from TFClass database to indentify known potential TF
Retrieving TFClass family classification from ELMER.data.
Retrieving TFClass subfamily classification from ELMER.data.
Calculating the average methylation at all motif-adjacent probes 
Performing Mann-Whitney U test
Finding potential TF and known potential TF
-----------------
** Creating plots
-----------------
TF rank plot highlighting TF in the same family (folder: elmer/hypo/TFrankPlot)
Retrieving TFClass family classification from ELMER.data.
Retrieving TFClass subfamily classification from ELMER.data.
Saving plot as: elmer/hypo/TFrankPlot/ETS1_HUMAN.H11MO.0.A.TFrankPlot.pdf
Saving plot as: elmer/hypo/TFrankPlot/KLF6_HUMAN.H11MO.0.A.TFrankPlot.pdf
Saving plot as: elmer/hypo/TFrankPlot/ELF5_HUMAN.H11MO.0.A.TFrankPlot.pdf
Saving plot as: elmer/hypo/TFrankPlot/ZN524_HUMAN.H11MO.0.D.TFrankPlot.pdf
Saving plot as: elmer/hypo/TFrankPlot/FLI1_HUMAN.H11MO.1.A.TFrankPlot.pdf
Saving plot as: elmer/hypo/TFrankPlot/EGR2_HUMAN.H11MO.1.A.TFrankPlot.pdf
Saving plot as: elmer/hypo/TFrankPlot/FLI1_HUMAN.H11MO.0.A.TFrankPlot.pdf
Saving plot as: elmer/hypo/TFrankPlot/E2F4_HUMAN.H11MO.0.A.TFrankPlot.pdf
Saving plot as: elmer/hypo/TFrankPlot/ELF2_HUMAN.H11MO.0.C.TFrankPlot.pdf
Saving plot as: elmer/hypo/TFrankPlot/E2F4_HUMAN.H11MO.1.A.TFrankPlot.pdf
Saving plot as: elmer/hypo/TFrankPlot/PLAG1_HUMAN.H11MO.0.D.TFrankPlot.pdf
Saving plot as: elmer/hypo/TFrankPlot/ZFP82_HUMAN.H11MO.0.C.TFrankPlot.pdf
Saving plot as: elmer/hypo/TFrankPlot/GRHL1_HUMAN.H11MO.0.D.TFrankPlot.pdf
Saving plot as: elmer/hypo/TFrankPlot/SP2_HUMAN.H11MO.1.B.TFrankPlot.pdf
Saving plot as: elmer/hypo/TFrankPlot/PLAL1_HUMAN.H11MO.0.D.TFrankPlot.pdf
Saving plot as: elmer/hypo/TFrankPlot/ERG_HUMAN.H11MO.0.A.TFrankPlot.pdf
Saving plot as: elmer/hypo/TFrankPlot/ZN341_HUMAN.H11MO.0.C.TFrankPlot.pdf
Saving plot as: elmer/hypo/TFrankPlot/SP4_HUMAN.H11MO.1.A.TFrankPlot.pdf
Saving plot as: elmer/hypo/TFrankPlot/ELK4_HUMAN.H11MO.0.A.TFrankPlot.pdf
Saving plot as: elmer/hypo/TFrankPlot/ZN467_HUMAN.H11MO.0.C.TFrankPlot.pdf
Saving plot as: elmer/hypo/TFrankPlot/KLF14_HUMAN.H11MO.0.D.TFrankPlot.pdf
Saving plot as: elmer/hypo/TFrankPlot/E2F3_HUMAN.H11MO.0.A.TFrankPlot.pdf
Saving plot as: elmer/hypo/TFrankPlot/ZN331_HUMAN.H11MO.0.C.TFrankPlot.pdf
Saving plot as: elmer/hypo/TFrankPlot/FEV_HUMAN.H11MO.0.B.TFrankPlot.pdf
Saving plot as: elmer/hypo/TFrankPlot/KLF15_HUMAN.H11MO.0.A.TFrankPlot.pdf
Saving plot as: elmer/hypo/TFrankPlot/KLF12_HUMAN.H11MO.0.C.TFrankPlot.pdf
Saving plot as: elmer/hypo/TFrankPlot/MBD2_HUMAN.H11MO.0.B.TFrankPlot.pdf
Saving plot as: elmer/hypo/TFrankPlot/EHF_HUMAN.H11MO.0.B.TFrankPlot.pdf
Saving plot as: elmer/hypo/TFrankPlot/E2F1_HUMAN.H11MO.0.A.TFrankPlot.pdf
Saving plot as: elmer/hypo/TFrankPlot/ELF1_HUMAN.H11MO.0.A.TFrankPlot.pdf
Saving plot as: elmer/hypo/TFrankPlot/E2F7_HUMAN.H11MO.0.B.TFrankPlot.pdf

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Retrieving TFClass family classification from ELMER.data.
Retrieving TFClass subfamily classification from ELMER.data.

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output file: TCGAWorkflow.knit.md

/usr/bin/pandoc +RTS -K512m -RTS TCGAWorkflow.utf8.md --to html4 --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash+smart --output TCGAWorkflow.html --email-obfuscation none --self-contained --wrap preserve --standalone --section-divs --table-of-contents --toc-depth 3 --template /home/biocbuild/bbs-3.7-bioc/R/library/BiocStyle/resources/fragment.html --no-highlight --number-sections --include-in-header /tmp/Rtmp12XWgf/rmarkdown-str440910792d7f.html --mathjax --variable 'mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --filter /usr/bin/pandoc-citeproc 
pandoc-citeproc: reference sham2014statistical not found

Output created: TCGAWorkflow.html
There were 50 or more warnings (use warnings() to see the first 50)
> 
> 
> knitr::purl(".buildwebvig/TCGAWorkflow/TCGAWorkflow.Rmd", ".buildwebvig/TCGAWorkflow/TCGAWorkflow.R")


processing file: .buildwebvig/TCGAWorkflow/TCGAWorkflow.Rmd

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output file: .buildwebvig/TCGAWorkflow/TCGAWorkflow.R

[1] ".buildwebvig/TCGAWorkflow/TCGAWorkflow.R"
> 
>