Beginning analysis... ##------ Thu Oct 7 09:36:35 2021 ------## report: /tmp/efe676b1-2a6f-4535-826f-acf2c1f4a210/report.html index: /tmp/efe676b1-2a6f-4535-826f-acf2c1f4a210/index.html log: /tmp/efe676b1-2a6f-4535-826f-acf2c1f4a210/log.txt rlranges: /tmp/efe676b1-2a6f-4535-826f-acf2c1f4a210/rlranges.rds logdebug: /tmp/efe676b1-2a6f-4535-826f-acf2c1f4a210/log.debug.txt runID: efe676b1-2a6f-4535-826f-acf2c1f4a210 userSample: SRX1070676 userGenome: hg38 userMode: DRIP userLabel: POS userPeaks: SRX1070676_hg38.broadPeak5352750/tmp/Rtmp3LPRss/9fe631b5a2295d5b1d6cc86c/0.broadPeak USERDATA_S3: s3://rlbase-userdata tmpHTML1: /tmp/Rtmp3LPRss/file139fe73da212ba.html [[1]] Building RLRanges Loading required package: BiocGenerics Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:stats’: IQR, mad, sd, var, xtabs The following objects are masked from ‘package:base’: anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which.max, which.min Loading required package: S4Vectors Loading required package: stats4 Attaching package: ‘S4Vectors’ The following objects are masked from ‘package:base’: expand.grid, I, unname [[2]] Running RLSeq [1/6] RLFS Perm Test [2/6] Predict Condition snapshotDate(): 2021-10-06 see ?RLHub and browseVignettes('RLHub') for documentation see ?RLHub and browseVignettes('RLHub') for documentation [3/6] Feature Enrichment Test see ?RLHub and browseVignettes('RLHub') for documentation [4/6] Correlation Analysis No coverage provided... skipping. [5/6] Gene Annotation snapshotDate(): 2021-10-07 Loading required package: GenomicFeatures Loading required package: GenomicRanges Loading required package: AnnotationDbi Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. 228 genes were dropped because they have exons located on both strands of the same reference sequence or on more than one reference sequence, so cannot be represented by a single genomic range. Use 'single.strand.genes.only=FALSE' to get all the genes in a GRangesList object, or use suppressMessages() to suppress this message. [6/6] R-loop Region Analysis see ?RLHub and browseVignettes('RLHub') for documentation [[3]] Building Report processing file: report.Rmd | | | 0% | |........ | 11% inline R code fragments | |................ | 22% label: setup (with options) List of 2 $ include: logi FALSE $ echo : logi FALSE | |....................... | 33% inline R code fragments | |............................... | 44% label: unnamed-chunk-1 | |....................................... | 56% ordinary text without R code | |............................................... | 67% label: childRMD (with options) List of 1 $ results: chr "asis" snapshotDate(): 2021-10-06 see ?RLHub and browseVignettes('RLHub') for documentation see ?RLHub and browseVignettes('RLHub') for documentation see ?RLHub and browseVignettes('RLHub') for documentation | |...................................................... | 78% ordinary text without R code | |.............................................................. | 89% label: unnamed-chunk-2 | |......................................................................| 100% inline R code fragments output file: report.knit.md /usr/lib/rstudio-server/bin/pandoc/pandoc +RTS -K512m -RTS report.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output /tmp/efe676b1-2a6f-4535-826f-acf2c1f4a210/report.html --lua-filter /home/millerh1/R/x86_64-pc-linux-gnu-library/4.1/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /home/millerh1/R/x86_64-pc-linux-gnu-library/4.1/rmarkdown/rmarkdown/lua/latex-div.lua --self-contained --variable bs3=TRUE --standalone --section-divs --table-of-contents --toc-depth 2 --variable toc_float=1 --variable toc_selectors=h1,h2 --variable toc_print=1 --template /home/millerh1/R/x86_64-pc-linux-gnu-library/4.1/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable theme=flatly --css report_style.css --include-in-header /tmp/RtmpUgTcyP/rmarkdown-str13a0f440726df4.html --mathjax --variable 'mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --variable source_embed=report.Rmd --include-after-body /tmp/RtmpUgTcyP/file13a0f4119d8ef8.html --variable code_menu=1 --include-in-header header.html Output created: /tmp/efe676b1-2a6f-4535-826f-acf2c1f4a210/report.html [[4]] Uploading to AWS Saving RDS to AWS... Locating credentials Checking for credentials in user-supplied values Checking for credentials in Environment Variables Searching for credentials file(s) Attempting to read credentials from '.aws/credentials' Attempting to read credentials from '/home/millerh1/.aws/credentials' Attempting to find profile 'default' Using profile 'default' from credentials files from '/home/millerh1/.aws/credentials' Using value in credentials file for AWS Access Key ID Using value in credentials file for AWS Secret Access Key Using default value for AWS Region ('us-east-1') S3 Request URL: https://s3.amazonaws.com/rlbase-userdata/efe676b1-2a6f-4535-826f-acf2c1f4a210/rlranges.rds Executing request with AWS credentials Locating credentials Checking for credentials in user-supplied values Using user-supplied value for AWS Access Key ID Using user-supplied value for AWS Secret Access Key Using user-supplied value for AWS Region ('us-east-1') | | | 0% | |====== | 9% | |============ | 18% | |=================== | 27% | |========================= | 36% | |=============================== | 44% | |===================================== | 53% | |============================================ | 62% | |================================================== | 71% | |======================================================== | 80% | |============================================================== | 89% | |==================================================================== | 98% | |======================================================================| 100% Parsing AWS API response Success: (200) OK Saving report to AWS... Locating credentials Checking for credentials in user-supplied values Checking for credentials in Environment Variables Searching for credentials file(s) Attempting to read credentials from '.aws/credentials' Attempting to read credentials from '/home/millerh1/.aws/credentials' Attempting to find profile 'default' Using profile 'default' from credentials files from '/home/millerh1/.aws/credentials' Using value in credentials file for AWS Access Key ID Using value in credentials file for AWS Secret Access Key Using default value for AWS Region ('us-east-1') S3 Request URL: https://s3.amazonaws.com/rlbase-userdata/efe676b1-2a6f-4535-826f-acf2c1f4a210/report.html Executing request with AWS credentials Locating credentials Checking for credentials in user-supplied values Using user-supplied value for AWS Access Key ID Using user-supplied value for AWS Secret Access Key Using user-supplied value for AWS Region ('us-east-1') | | | 0% | |= | 2% | |== | 3% | |=== | 5% | |==== | 6% | |===== | 8% | |====== | 9% | |======= | 11% | |======== | 12% | |========== | 14% | |=========== | 15% | |============ | 17% | |============= | 18% | |============== | 20% | |=============== | 21% | |================ | 23% | |================= | 24% | |================== | 26% | |=================== | 27% | |==================== | 29% | |===================== | 30% | |====================== | 32% | |======================= | 33% | |======================== | 35% | |========================= | 36% | |========================== | 38% | |=========================== | 39% | |============================= | 41% | |============================== | 42% | |=============================== | 44% | |================================ | 45% | |================================= | 47% | |================================== | 48% | |=================================== | 50% | |==================================== | 51% | |===================================== | 53% | |====================================== | 54% | |======================================= | 56% | |======================================== | 57% | |========================================= | 59% | |========================================== | 60% | |=========================================== | 62% | |============================================ | 63% | |============================================= | 65% | |============================================== | 66% | |================================================ | 68% | |================================================= | 69% | |================================================== | 71% | |=================================================== | 72% | |==================================================== | 74% | |===================================================== | 75% | |====================================================== | 77% | |======================================================= | 78% | |======================================================== | 80% | |========================================================= | 81% | |========================================================== | 83% | |=========================================================== | 85% | |============================================================ | 86% | |============================================================= | 88% | |============================================================== | 89% | |=============================================================== | 91% | |================================================================ | 92% | |================================================================= | 94% | |=================================================================== | 95% | |==================================================================== | 97% | |===================================================================== | 98% | |======================================================================| 100% Parsing AWS API response Success: (200) OK Done! ##------ Thu Oct 7 09:38:36 2021 ------## There were 50 or more warnings (use warnings() to see the first 50)