| Back to Multiple platform build/check report for BioC 3.16: simplified long |
|
This page was generated on 2023-03-27 11:05:14 -0400 (Mon, 27 Mar 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4480 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4276 |
| lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4304 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the SpliceWiz package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SpliceWiz.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1945/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SpliceWiz 1.0.3 (landing page) Alex Chit Hei Wong
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK |  | ||||||||
| lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: SpliceWiz |
| Version: 1.0.3 |
| Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:SpliceWiz.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings SpliceWiz_1.0.3.tar.gz |
| StartedAt: 2023-03-25 00:11:43 -0400 (Sat, 25 Mar 2023) |
| EndedAt: 2023-03-25 00:22:25 -0400 (Sat, 25 Mar 2023) |
| EllapsedTime: 642.5 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: SpliceWiz.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:SpliceWiz.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings SpliceWiz_1.0.3.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/SpliceWiz.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘SpliceWiz/DESCRIPTION’ ... OK
* this is package ‘SpliceWiz’ version ‘1.0.3’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘SpliceWiz’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 14.8Mb
sub-directories of 1Mb or more:
R 1.9Mb
libs 11.9Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
NxtSE-class 49.032 0.556 49.659
ASE-methods 41.832 0.726 42.610
Build-Reference-methods 16.812 0.071 16.843
plotCoverage 8.490 0.119 8.290
Run_SpliceWiz_Filters 7.420 0.044 7.465
makeSE 5.301 0.040 5.336
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘SW_Cookbook.Rmd’ using ‘UTF-8’... OK
‘SW_QuickStart.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘SW_Cookbook.Rmd’ using rmarkdown
sh: 1: STAR: not found
sh: 1: STAR: not found
--- finished re-building ‘SW_Cookbook.Rmd’
--- re-building ‘SW_QuickStart.Rmd’ using rmarkdown
Quitting from lines 172-187 (SW_QuickStart.Rmd)
Error: processing vignette 'SW_QuickStart.Rmd' failed with diagnostics:
could not find function "SpliceWiz_example_NxtSE"
--- failed re-building ‘SW_QuickStart.Rmd’
SUMMARY: processing the following file failed:
‘SW_QuickStart.Rmd’
Error: Vignette re-building failed.
Execution halted
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 2 NOTEs
See
‘/home/biocbuild/bbs-3.16-bioc/meat/SpliceWiz.Rcheck/00check.log’
for details.
SpliceWiz.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL SpliceWiz ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-library’ * installing *source* package ‘SpliceWiz’ ... ** using staged installation ** libs g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/ompBAM/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/RcppProgress/include' -I/usr/local/include -fopenmp -DSPLICEWIZ -fpic -g -O2 -Wall -c BAM2blocks.cpp -o BAM2blocks.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/ompBAM/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/RcppProgress/include' -I/usr/local/include -fopenmp -DSPLICEWIZ -fpic -g -O2 -Wall -c FastaReader.cpp -o FastaReader.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/ompBAM/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/RcppProgress/include' -I/usr/local/include -fopenmp -DSPLICEWIZ -fpic -g -O2 -Wall -c FragmentBlocks.cpp -o FragmentBlocks.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/ompBAM/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/RcppProgress/include' -I/usr/local/include -fopenmp -DSPLICEWIZ -fpic -g -O2 -Wall -c GZTools.cpp -o GZTools.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/ompBAM/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/RcppProgress/include' -I/usr/local/include -fopenmp -DSPLICEWIZ -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/ompBAM/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/RcppProgress/include' -I/usr/local/include -fopenmp -DSPLICEWIZ -fpic -g -O2 -Wall -c ReadBlockProcessor.cpp -o ReadBlockProcessor.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/ompBAM/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/RcppProgress/include' -I/usr/local/include -fopenmp -DSPLICEWIZ -fpic -g -O2 -Wall -c ReadBlockProcessor_CoverageBlocks.cpp -o ReadBlockProcessor_CoverageBlocks.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/ompBAM/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/RcppProgress/include' -I/usr/local/include -fopenmp -DSPLICEWIZ -fpic -g -O2 -Wall -c ReadBlockProcessor_FragmentsMap.cpp -o ReadBlockProcessor_FragmentsMap.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/ompBAM/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/RcppProgress/include' -I/usr/local/include -fopenmp -DSPLICEWIZ -fpic -g -O2 -Wall -c ReadBlockProcessor_TandemJunctions.cpp -o ReadBlockProcessor_TandemJunctions.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/ompBAM/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/RcppProgress/include' -I/usr/local/include -fopenmp -DSPLICEWIZ -fpic -g -O2 -Wall -c covTools.cpp -o covTools.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/ompBAM/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/RcppProgress/include' -I/usr/local/include -fopenmp -DSPLICEWIZ -fpic -g -O2 -Wall -c main.cpp -o main.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/ompBAM/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/RcppProgress/include' -I/usr/local/include -fopenmp -DSPLICEWIZ -fpic -g -O2 -Wall -c swEngine.cpp -o swEngine.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/ompBAM/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/RcppProgress/include' -I/usr/local/include -fopenmp -DSPLICEWIZ -fpic -g -O2 -Wall -c synthReadGenerator.cpp -o synthReadGenerator.o g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.16-bioc/R/lib -L/usr/local/lib -o SpliceWiz.so BAM2blocks.o FastaReader.o FragmentBlocks.o GZTools.o RcppExports.o ReadBlockProcessor.o ReadBlockProcessor_CoverageBlocks.o ReadBlockProcessor_FragmentsMap.o ReadBlockProcessor_TandemJunctions.o covTools.o main.o swEngine.o synthReadGenerator.o -fopenmp -DSPLICEWIZ -L/home/biocbuild/bbs-3.16-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.16-bioc/R/site-library/00LOCK-SpliceWiz/00new/SpliceWiz/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (SpliceWiz)
SpliceWiz.Rcheck/tests/testthat.Rout
R version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(SpliceWiz)
Loading required package: NxtIRFdata
SpliceWiz package loaded with 2 threads
Use setSWthreads() to set the number of SpliceWiz threads
>
> test_check("SpliceWiz")
Loading required package: Rsubread
Mar 25 00:19:12 Converting FASTA to local TwoBitFile...done
Mar 25 00:19:13 Connecting to genome TwoBitFile...done
Mar 25 00:19:13 Making local copy of GTF file...done
Mar 25 00:19:13 Extracting temp genome FASTA from TwoBit file
Mar 25 00:19:13 Generating synthetic reads, saving to /tmp/Rtmp36EHI5/refWithMapExcl/Mappability/Reads.fa
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
10145 synthetic reads generated
Mar 25 00:19:13 Cleaning temp genome / gene annotation files
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
Rsubread 2.12.3
//================================= setting ==================================\\
|| ||
|| Index name : reference_index ||
|| Index space : base space ||
|| Index split : no-split ||
|| Repeat threshold : 100 repeats ||
|| Gapped index : no ||
|| ||
|| Free / total memory : 85.8GB / 125.4GB ||
|| ||
|| Input files : 1 file in total ||
|| o genome.fa ||
|| ||
\\============================================================================//
//================================= Running ==================================\\
|| ||
|| Check the integrity of provided reference sequences ... ||
|| No format issues were found ||
|| Scan uninformative subreads in reference sequences ... ||
|| Estimate the index size... ||
|| 8%, 0 mins elapsed, rate=43.7k bps/s ||
|| 16%, 0 mins elapsed, rate=86.0k bps/s ||
|| 24%, 0 mins elapsed, rate=127.2k bps/s ||
|| 33%, 0 mins elapsed, rate=167.3k bps/s ||
|| 41%, 0 mins elapsed, rate=206.4k bps/s ||
|| 49%, 0 mins elapsed, rate=244.6k bps/s ||
|| 58%, 0 mins elapsed, rate=281.7k bps/s ||
|| 66%, 0 mins elapsed, rate=318.0k bps/s ||
|| 74%, 0 mins elapsed, rate=353.7k bps/s ||
|| 83%, 0 mins elapsed, rate=388.7k bps/s ||
|| 91%, 0 mins elapsed, rate=422.7k bps/s ||
|| 3.0 GB of memory is needed for index building. ||
|| Build the index... ||
|| 8%, 0 mins elapsed, rate=4.6k bps/s ||
|| 16%, 0 mins elapsed, rate=9.1k bps/s ||
|| 24%, 0 mins elapsed, rate=13.7k bps/s ||
|| 33%, 0 mins elapsed, rate=18.2k bps/s ||
|| 41%, 0 mins elapsed, rate=22.7k bps/s ||
|| 49%, 0 mins elapsed, rate=27.2k bps/s ||
|| 58%, 0 mins elapsed, rate=31.6k bps/s ||
|| 66%, 0 mins elapsed, rate=36.0k bps/s ||
|| 74%, 0 mins elapsed, rate=40.4k bps/s ||
|| 83%, 0 mins elapsed, rate=44.8k bps/s ||
|| 91%, 0 mins elapsed, rate=49.2k bps/s ||
|| Save current index block... ||
|| [ 0.0% finished ] ||
|| [ 10.0% finished ] ||
|| [ 20.0% finished ] ||
|| [ 30.0% finished ] ||
|| [ 40.0% finished ] ||
|| [ 50.0% finished ] ||
|| [ 60.0% finished ] ||
|| [ 70.0% finished ] ||
|| [ 80.0% finished ] ||
|| [ 90.0% finished ] ||
|| [ 100.0% finished ] ||
|| ||
|| Total running time: 0.2 minutes. ||
|| Index ./reference_index was successfully built. ||
|| ||
\\============================================================================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
Rsubread 2.12.3
//================================= setting ==================================\\
|| ||
|| Function : Read alignment + Junction detection (RNA-Seq) ||
|| Input file : Reads.fa ||
|| Output file : AlignedReads.bam (BAM) ||
|| Index name : reference_index ||
|| ||
|| ------------------------------------ ||
|| ||
|| Threads : 1 ||
|| Phred offset : 33 ||
|| Min votes : 1 / 14 ||
|| Max mismatches : 3 ||
|| Max indel length : 5 ||
|| Report multi-mapping reads : yes ||
|| Max alignments per multi-mapping read : 1 ||
|| Annotations : transcripts.gtf (GTF) ||
|| ||
\\============================================================================//
//=============== Running (25-Mar-2023 00:19:22, pid=1714255) ================\\
|| ||
|| Check the input reads. ||
|| The input file contains base space reads. ||
|| Initialise the memory objects. ||
|| Estimate the mean read length. ||
|| Create the output BAM file. ||
|| Check the index. ||
|| Init the voting space. ||
|| Load the annotation file. ||
|| 538 annotation records were loaded. ||
|| Global environment is initialised. ||
|| Load the 1-th index block... ||
|| The index block has been loaded. ||
|| Start read mapping in chunk. ||
|| 65% completed, 0.5 mins elapsed, rate=24.6k reads per second ||
|| 83% completed, 0.5 mins elapsed, rate=0.3k reads per second ||
|| 99% completed, 0.5 mins elapsed, rate=0.3k reads per second ||
|| ||
|| Completed successfully. ||
|| ||
\\==================================== ====================================//
//================================ Summary =================================\\
|| ||
|| Total reads : 10,145 ||
|| Mapped : 10,145 (100.0%) ||
|| Uniquely mapped : 10,145 ||
|| Multi-mapping : 0 ||
|| ||
|| Unmapped : 0 ||
|| ||
|| Junctions : 0 ||
|| Indels : 1 ||
|| ||
|| Running time : 0.5 minutes ||
|| ||
\\============================================================================//
Mar 25 00:19:53 Calculating Mappability Exclusion regions from: /tmp/Rtmp36EHI5/refWithMapExcl/Mappability/AlignedReads.bam
Calculating Mappability Exclusions: /tmp/Rtmp36EHI5/refWithMapExcl/Mappability/AlignedReads.bam
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Performing final sort of fragment maps
Writing Mappability Exclusions
**************************************************|
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Mar 25 00:19:56 Reference generated without non-polyA reference
Mar 25 00:19:56 Reference generated without Mappability reference
Mar 25 00:19:56 Reference generated without Blacklist exclusion
Mar 25 00:19:56 Converting FASTA to local TwoBitFile...done
Mar 25 00:19:57 Connecting to genome TwoBitFile...done
Mar 25 00:19:57 Making local copy of GTF file...done
Mar 25 00:19:57 Reading source GTF file...done
Mar 25 00:19:58 Processing gtf file...
...genes
...transcripts
...CDS
...exons
done
Mar 25 00:20:00 Processing introns...
...data
...basic annotations
...splice motifs
...other info
...defining flanking exon clusters
done
Mar 25 00:20:04 Generating processBAM reference
...prepping data
...determining measurable introns (directional)
...determining measurable introns (non-directional)
...writing ref-cover.bed
...writing ref-ROI.bed
...writing ref-read-continues.ref
...writing ref-sj.ref
...writing ref-tj.ref
processBAM reference generated
Mar 25 00:20:11 Predicting NMD transcripts from genome sequence
...exonic transcripts
...retained introns
|
| | 0%
|
|======================================================================| 100%
done
Mar 25 00:20:13 Annotating Splice Events
Annotating Mutually-Exclusive-Exon Splice Events...done
Annotating Skipped-Exon Splice Events...done
Annotating Alternate 5' / 3' Splice Site Splice Events...done
Annotating Alternate First / Last Exon Splice Events...done
Annotating known retained introns...done
Mar 25 00:20:14 Splice Annotations Filtered
Mar 25 00:20:14 Translating Alternate Splice Peptides...done
Mar 25 00:20:14 Splice Annotations finished
Reference build finished
Mar 25 00:20:14 Running SpliceWiz processBAM
Reading reference file
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
Processing BAM file /tmp/Rtmp36EHI5/02H003.bam
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Performing final sort of fragment maps
Writing COV file
**************************************************|
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Writing output file
/tmp/Rtmp36EHI5/02H003.bam processed (519 milliseconds)
Mar 25 00:20:15 Running SpliceWiz processBAM
Reading reference file
Allocating memory to 2 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
Processing BAM file /tmp/Rtmp36EHI5/02H003.bam
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[----|----|----|----|----|----|----|----|----|----|
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Compiling data from threads
Performing final sort of fragment maps
Writing COV file
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Writing output file
/tmp/Rtmp36EHI5/02H003.bam processed (373 milliseconds)
Mar 25 00:20:16 SpliceWiz reference already exists in given directory
Mar 25 00:20:16 Running SpliceWiz processBAM
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/tmp/Rtmp36EHI5/02H003.bam processed (429 milliseconds)
/tmp/Rtmp36EHI5/02H025.bam processed (355 milliseconds)
/tmp/Rtmp36EHI5/02H026.bam processed (528 milliseconds)
/tmp/Rtmp36EHI5/02H033.bam processed (530 milliseconds)
/tmp/Rtmp36EHI5/02H043.bam processed (319 milliseconds)
/tmp/Rtmp36EHI5/02H046.bam processed (488 milliseconds)
Mar 25 00:20:18 Using MulticoreParam 1 threads
Mar 25 00:20:18 Validating Experiment; checking COV files...
Mar 25 00:20:18 Compiling Sample Stats
Mar 25 00:20:18 Compiling Junction List...merging...done
Mar 25 00:20:20 Compiling Junction Stats...merging...done
Mar 25 00:20:28 Compiling Intron Retention List...done
Mar 25 00:20:29 Compiling Tandem Junction List...merging...done
Mar 25 00:20:30 Tidying up splice junctions and intron retentions...
...annotating splice junctions
...looking for novel exons
Mar 25 00:20:34 Assembling novel splicing reference:
...loading reference FASTA/GTF
...injecting novel transcripts to GTF
...processing GTF
...processing introns from GTF
...annotating alternative splicing events
done
Mar 25 00:20:45 Tidying up splice junctions and intron retentions (part 2)...
...grouping splice junctions
...grouping introns
...loading splice events
...compiling rowEvents
done
Mar 25 00:20:52 Generating NxtSE assays
Mar 25 00:20:52 Using MulticoreParam 1 threads
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Mar 25 00:21:08 Building Final NxtSE Object
Mar 25 00:21:10 SpliceWiz (NxtSE) Collation Finished
Mar 25 00:21:10 Loading NxtSE object from file...done
Mar 25 00:21:10 Removing overlapping introns...
Mar 25 00:21:11 Iterating through IR events to determine introns of main isoforms
Mar 25 00:21:12 Iteration 1
Mar 25 00:21:13 Iteration 2
Mar 25 00:21:16 SpliceWiz reference already exists in given directory
Mar 25 00:21:16 processBAM has already been run on given BAM files
Mar 25 00:21:16 Using MulticoreParam 1 threads
Mar 25 00:21:16 Validating Experiment; checking COV files...
Mar 25 00:21:16 Compiling Sample Stats
Mar 25 00:21:16 Compiling Junction List...merging...done
Mar 25 00:21:17 Compiling Junction Stats...merging...done
Mar 25 00:21:24 Compiling Intron Retention List...done
Mar 25 00:21:25 Tidying up splice junctions and intron retentions...
...annotating splice junctions
...grouping splice junctions
...grouping introns
...loading splice events
...compiling rowEvents
done
Mar 25 00:21:34 Generating NxtSE assays
Mar 25 00:21:34 Using MulticoreParam 1 threads
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Mar 25 00:21:49 Building Final NxtSE Object
Mar 25 00:21:52 SpliceWiz (NxtSE) Collation Finished
Mar 25 00:21:52 Loading NxtSE object from file...done
Mar 25 00:21:52 Removing overlapping introns...
Mar 25 00:21:52 Iterating through IR events to determine introns of main isoforms
Mar 25 00:21:53 Iteration 1
Mar 25 00:21:55 Iteration 2
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 29 ]
>
> # bump to trigger r cmd check
>
> proc.time()
user system elapsed
163.594 16.550 179.971
SpliceWiz.Rcheck/SpliceWiz-Ex.timings
| name | user | system | elapsed | |
| ASE-methods | 41.832 | 0.726 | 42.610 | |
| ASEFilter-class | 0.049 | 0.000 | 0.050 | |
| Build-Reference-methods | 16.812 | 0.071 | 16.843 | |
| Coverage | 0.833 | 0.007 | 0.817 | |
| Graphics-User-Interface | 0.001 | 0.000 | 0.000 | |
| Mappability-methods | 1.077 | 0.008 | 1.086 | |
| NxtSE-class | 49.032 | 0.556 | 49.659 | |
| Run_SpliceWiz_Filters | 7.420 | 0.044 | 7.465 | |
| STAR-methods | 0.004 | 0.000 | 0.004 | |
| View-Reference-methods | 0.006 | 0.000 | 0.006 | |
| collateData | 0.094 | 0.010 | 0.115 | |
| coord2GR | 0.018 | 0.000 | 0.018 | |
| example-SpliceWiz-data | 0.007 | 0.000 | 0.007 | |
| findSamples | 0.005 | 0.000 | 0.005 | |
| isCOV | 0.006 | 0.000 | 0.008 | |
| makeSE | 5.301 | 0.040 | 5.336 | |
| make_plot_data | 4.318 | 0.000 | 4.318 | |
| plotCoverage | 8.490 | 0.119 | 8.290 | |
| processBAM | 2.594 | 0.151 | 1.577 | |
| setSWthreads | 0.007 | 0.004 | 0.028 | |
| theme_white | 0.188 | 0.000 | 0.188 | |