Alex Chit Hei Wong
| Snapshot Date: 2025-01-03 13:40 -0500 (Fri, 03 Jan 2025) |
| git_url: https://git.bioconductor.org/packages/SpliceWiz |
| git_branch: devel |
| git_last_commit: 8784449 |
| git_last_commit_date: 2024-10-29 11:12:40 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-01-04 11:44 -0500 (Sat, 04 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4756 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4475 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4435 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4390 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4383 |
| 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 | ||||
| Package 2024/2275 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SpliceWiz 1.9.0 (landing page) Alex Chit Hei Wong
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
To the developers/maintainers of the SpliceWiz package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: SpliceWiz |
| Version: 1.9.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SpliceWiz.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SpliceWiz_1.9.0.tar.gz |
| StartedAt: 2025-01-03 23:29:47 -0500 (Fri, 03 Jan 2025) |
| EndedAt: 2025-01-03 23:49:53 -0500 (Fri, 03 Jan 2025) |
| EllapsedTime: 1206.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SpliceWiz.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SpliceWiz.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SpliceWiz_1.9.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/SpliceWiz.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SpliceWiz/DESCRIPTION’ ... OK
* this is package ‘SpliceWiz’ version ‘1.9.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 43 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.
* 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
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code 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 whether startup messages can be suppressed ... 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
NxtSE-class.Rd: SummarizedExperiment-class
SpliceWiz-package.Rd: SummarizedExperiment-class, rowData, colData
makeSE.Rd: colData
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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
Build-Reference-methods 54.697 1.497 57.178
NxtSE-class 53.676 1.261 55.312
ASE-methods 30.772 0.339 31.273
covPlotObject-class 22.439 0.516 23.123
plotCoverage 15.818 0.186 16.105
Run_SpliceWiz_Filters 7.516 0.042 7.589
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 4 NOTEs
See
‘/Users/biocbuild/bbs-3.21-bioc/meat/SpliceWiz.Rcheck/00check.log’
for details.
SpliceWiz.Rcheck/00install.out
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SpliceWiz
###
##############################################################################
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘SpliceWiz’ ...
** using staged installation
Configuring without OpenMP for MacOS
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++11
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppProgress/include' -I/opt/R/x86_64/include -DSPLICEWIZ -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c BAM2blocks.cpp -o BAM2blocks.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppProgress/include' -I/opt/R/x86_64/include -DSPLICEWIZ -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c FastaReader.cpp -o FastaReader.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppProgress/include' -I/opt/R/x86_64/include -DSPLICEWIZ -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c FragmentBlocks.cpp -o FragmentBlocks.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppProgress/include' -I/opt/R/x86_64/include -DSPLICEWIZ -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c GZTools.cpp -o GZTools.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppProgress/include' -I/opt/R/x86_64/include -DSPLICEWIZ -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppProgress/include' -I/opt/R/x86_64/include -DSPLICEWIZ -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c ReadBlockProcessor.cpp -o ReadBlockProcessor.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppProgress/include' -I/opt/R/x86_64/include -DSPLICEWIZ -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c ReadBlockProcessor_CoverageBlocks.cpp -o ReadBlockProcessor_CoverageBlocks.o
ReadBlockProcessor_CoverageBlocks.cpp:251:16: warning: variable 'len' set but not used [-Wunused-but-set-variable]
unsigned int len=0;
^
1 warning generated.
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppProgress/include' -I/opt/R/x86_64/include -DSPLICEWIZ -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c ReadBlockProcessor_FragmentsMap.cpp -o ReadBlockProcessor_FragmentsMap.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppProgress/include' -I/opt/R/x86_64/include -DSPLICEWIZ -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c ReadBlockProcessor_TandemJunctions.cpp -o ReadBlockProcessor_TandemJunctions.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppProgress/include' -I/opt/R/x86_64/include -DSPLICEWIZ -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c covTools.cpp -o covTools.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppProgress/include' -I/opt/R/x86_64/include -DSPLICEWIZ -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c main.cpp -o main.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppProgress/include' -I/opt/R/x86_64/include -DSPLICEWIZ -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c swEngine.cpp -o swEngine.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppProgress/include' -I/opt/R/x86_64/include -DSPLICEWIZ -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c synthReadGenerator.cpp -o synthReadGenerator.o
clang++ -arch x86_64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/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 -DSPLICEWIZ -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/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 Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
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 1 threads
Use setSWthreads() to set the number of SpliceWiz threads
>
> test_check("SpliceWiz")
Loading required package: Rsubread
Jan 03 23:39:45 Converting FASTA to local TwoBitFile...done
Jan 03 23:39:46 Connecting to genome TwoBitFile...done
Jan 03 23:39:46 Making local copy of GTF file...done
Jan 03 23:39:47 Extracting temp genome FASTA from TwoBit file
Jan 03 23:39:48 Generating synthetic reads, saving to /private/tmp/RtmprqhPsY/refWithMapExcl/Mappability/Reads.fa
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
10145 synthetic reads generated
Jan 03 23:39:48 Cleaning temp genome / gene annotation files
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
Rsubread 2.21.1
//================================= setting ==================================\\
|| ||
|| Index name : reference_index ||
|| Index space : base space ||
|| Index split : no-split ||
|| Repeat threshold : 100 repeats ||
|| Gapped index : no ||
|| ||
|| Free / total memory : 53.8GB / 96.0GB ||
|| ||
|| 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=41.1k bps/s ||
|| 16%, 0 mins elapsed, rate=80.9k bps/s ||
|| 24%, 0 mins elapsed, rate=119.4k bps/s ||
|| 33%, 0 mins elapsed, rate=156.8k bps/s ||
|| 41%, 0 mins elapsed, rate=193.4k bps/s ||
|| 49%, 0 mins elapsed, rate=229.0k bps/s ||
|| 58%, 0 mins elapsed, rate=263.9k bps/s ||
|| 66%, 0 mins elapsed, rate=298.0k bps/s ||
|| 74%, 0 mins elapsed, rate=331.7k bps/s ||
|| 83%, 0 mins elapsed, rate=363.8k bps/s ||
|| 91%, 0 mins elapsed, rate=394.9k bps/s ||
|| 3.0 GB of memory is needed for index building. ||
|| Build the index... ||
|| 8%, 0 mins elapsed, rate=4.4k bps/s ||
|| 16%, 0 mins elapsed, rate=8.7k bps/s ||
|| 24%, 0 mins elapsed, rate=13.1k bps/s ||
|| 33%, 0 mins elapsed, rate=17.4k bps/s ||
|| 41%, 0 mins elapsed, rate=21.7k bps/s ||
|| 49%, 0 mins elapsed, rate=26.0k bps/s ||
|| 58%, 0 mins elapsed, rate=30.3k bps/s ||
|| 66%, 0 mins elapsed, rate=34.6k bps/s ||
|| 74%, 0 mins elapsed, rate=38.8k bps/s ||
|| 83%, 0 mins elapsed, rate=43.1k bps/s ||
|| 91%, 0 mins elapsed, rate=47.3k 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: 0.3 minutes. ||
|| Index ./reference_index was successfully built. ||
|| ||
\\============================================================================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
Rsubread 2.21.1
//================================= 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 (03-Jan-2025 23:40:07, pid=65952) =================\\
|| ||
|| 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, 5.7 mins elapsed, rate=31.4k reads per second ||
|| 83% completed, 5.7 mins elapsed, rate=0.0k reads per second ||
|| 99% completed, 5.7 mins elapsed, rate=0.0k 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 : 5.7 minutes ||
|| ||
\\============================================================================//
Jan 03 23:45:50 Calculating Mappability Exclusion regions from: /tmp/RtmprqhPsY/refWithMapExcl/Mappability/AlignedReads.bam
Calculating Mappability Exclusions: /private/tmp/RtmprqhPsY/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%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
SpliceWiz was compiled without OpenMP
Jan 03 23:45:54 Reference generated without non-polyA reference
Jan 03 23:45:54 Reference generated without Mappability reference
Jan 03 23:45:54 Reference generated without Blacklist exclusion
Jan 03 23:45:54 Converting FASTA to local TwoBitFile...done
Jan 03 23:45:55 Connecting to genome TwoBitFile...done
Jan 03 23:45:55 Making local copy of GTF file...done
Jan 03 23:45:55 Reading source GTF file...done
Jan 03 23:45:56 Processing gtf file...
...genes
...transcripts
...CDS
...exons
done
Jan 03 23:45:57 Gene ontology not prepared for this reference
Jan 03 23:45:59 Processing introns...
...data
...basic annotations
...splice motifs
...other info
...defining flanking exon clusters
done
Jan 03 23:46:03 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
Jan 03 23:46:11 Predicting NMD transcripts from genome sequence
...exonic transcripts
...retained introns
|
| | 0%
|
|======================================================================| 100%
done
Jan 03 23:46:13 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
Jan 03 23:46:14 Splice Annotations Filtered
Jan 03 23:46:15 Translating Alternate Splice Peptides...done
Jan 03 23:46:16 Splice Annotations finished
Reference build finished
Jan 03 23:46:17 Running SpliceWiz processBAM
Jan 03 23:46:18 Using MulticoreParam 1 threads
Reading reference file
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
Processing BAM file /private/tmp/RtmprqhPsY/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
/private/tmp/RtmprqhPsY/02H003.bam processed (419 milliseconds)
Jan 03 23:46:18 SpliceWiz processBAM processed RtmprqhPsY/02H003.bam
Jan 03 23:46:18 Running SpliceWiz processBAM
Jan 03 23:46:19 Using MulticoreParam 1 threads
Reading reference file
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
Processing BAM file /private/tmp/RtmprqhPsY/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
/private/tmp/RtmprqhPsY/02H003.bam processed (439 milliseconds)
Jan 03 23:46:20 SpliceWiz processBAM processed RtmprqhPsY/02H003.bam
Jan 03 23:46:20 Reference generated without non-polyA reference
Jan 03 23:46:20 Reference generated without Mappability reference
Jan 03 23:46:20 Reference generated without Blacklist exclusion
Jan 03 23:46:20 Converting FASTA to local TwoBitFile...done
Jan 03 23:46:21 Connecting to genome TwoBitFile...done
Jan 03 23:46:21 Making local copy of GTF file...done
Jan 03 23:46:21 Reading source GTF file...done
Jan 03 23:46:22 Processing gtf file...
...genes
...transcripts
...CDS
Jan 03 23:46:22 No protein information detected in reference! For full functionality, ensure there are valid entries with type == `CDS` in the gtf file. Protein reference and NMD annotation is skipped.
...exons
done
Jan 03 23:46:23 Gene ontology not prepared for this reference
Jan 03 23:46:25 Processing introns...
...data
...basic annotations
...splice motifs
...other info
...defining flanking exon clusters
done
Jan 03 23:46:29 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
Jan 03 23:46:35 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
Jan 03 23:46:37 Splice Annotations Filtered
Reference build finished
Jan 03 23:46:39 Running SpliceWiz processBAM
Jan 03 23:46:40 Using MulticoreParam 1 threads
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
/private/tmp/RtmprqhPsY/02H003.bam processed (425 milliseconds)
Jan 03 23:46:40 SpliceWiz processBAM processed RtmprqhPsY/02H003.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
/private/tmp/RtmprqhPsY/02H025.bam processed (318 milliseconds)
Jan 03 23:46:41 SpliceWiz processBAM processed RtmprqhPsY/02H025.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/private/tmp/RtmprqhPsY/02H026.bam processed (514 milliseconds)
Jan 03 23:46:41 SpliceWiz processBAM processed RtmprqhPsY/02H026.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/private/tmp/RtmprqhPsY/02H033.bam processed (549 milliseconds)
Jan 03 23:46:42 SpliceWiz processBAM processed RtmprqhPsY/02H033.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/private/tmp/RtmprqhPsY/02H043.bam processed (356 milliseconds)
Jan 03 23:46:42 SpliceWiz processBAM processed RtmprqhPsY/02H043.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/private/tmp/RtmprqhPsY/02H046.bam processed (488 milliseconds)
Jan 03 23:46:43 SpliceWiz processBAM processed RtmprqhPsY/02H046.bam
Jan 03 23:46:44 Using MulticoreParam 1 threads
Jan 03 23:46:44 Validating Experiment; checking COV files...
Jan 03 23:46:44 Compiling Sample Stats
Jan 03 23:46:44 Compiling Junction List...merging...done
Jan 03 23:46:45 Compiling Junction Stats...merging...done
Jan 03 23:46:53 Compiling Intron Retention List...done
Jan 03 23:46:54 Tidying up splice junctions and intron retentions...
...annotating splice junctions
...copying splicing reference
...grouping splice junctions
...grouping introns
...loading splice events
...compiling rowEvents
done
Jan 03 23:47:05 Generating NxtSE assays
Jan 03 23:47:06 Using MulticoreParam 1 threads
|
| | 0%
|
|============ | 17%
|
|======================= | 33%
|
|=================================== | 50%
|
|=============================================== | 67%
|
|========================================================== | 83%
|
|======================================================================| 100%
Jan 03 23:47:21 Building Final NxtSE Object
Jan 03 23:47:21 ...consolidating assays to H5 file
Jan 03 23:47:23 ...packaging reference
Jan 03 23:47:23 ...synthesising NxtSE
Jan 03 23:47:23 ...determining how overlapping introns should be removed
Jan 03 23:47:26 SpliceWiz (NxtSE) Collation Finished
Jan 03 23:47:26 Loading NxtSE object from file...
Jan 03 23:47:26 ...loading reference (NxtSE)
Jan 03 23:47:26 ...linking assays
Jan 03 23:47:26 ...linking COV files
Jan 03 23:47:26 ...loading rowData
Jan 03 23:47:26 ...removing overlapping introns...
Jan 03 23:47:26 NxtSE loaded
Jan 03 23:47:27 SpliceWiz reference already exists in given directory
Jan 03 23:47:27 Running SpliceWiz processBAM
Jan 03 23:47:28 Using MulticoreParam 1 threads
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
/private/tmp/RtmprqhPsY/02H003.bam processed (399 milliseconds)
Jan 03 23:47:28 SpliceWiz processBAM processed RtmprqhPsY/02H003.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/private/tmp/RtmprqhPsY/02H025.bam processed (331 milliseconds)
Jan 03 23:47:28 SpliceWiz processBAM processed RtmprqhPsY/02H025.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
/private/tmp/RtmprqhPsY/02H026.bam processed (497 milliseconds)
Jan 03 23:47:29 SpliceWiz processBAM processed RtmprqhPsY/02H026.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/private/tmp/RtmprqhPsY/02H033.bam processed (510 milliseconds)
Jan 03 23:47:30 SpliceWiz processBAM processed RtmprqhPsY/02H033.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/private/tmp/RtmprqhPsY/02H043.bam processed (299 milliseconds)
Jan 03 23:47:30 SpliceWiz processBAM processed RtmprqhPsY/02H043.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/private/tmp/RtmprqhPsY/02H046.bam processed (482 milliseconds)
Jan 03 23:47:30 SpliceWiz processBAM processed RtmprqhPsY/02H046.bam
Jan 03 23:47:31 Using MulticoreParam 1 threads
Jan 03 23:47:31 Validating Experiment; checking COV files...
Jan 03 23:47:32 Compiling Sample Stats
Jan 03 23:47:32 Compiling Junction List...merging...done
Jan 03 23:47:33 Compiling Junction Stats...merging...done
Jan 03 23:47:40 Compiling Intron Retention List...done
Jan 03 23:47:41 Compiling Tandem Junction List...merging...done
Jan 03 23:47:43 Tidying up splice junctions and intron retentions...
...annotating splice junctions
...looking for novel exons
Jan 03 23:47:46 Assembling novel splicing reference:
...loading reference FASTA/GTF
...injecting novel transcripts to GTF
...processing GTF
...processing introns from GTF
...annotating alternative splicing events
done
Jan 03 23:47:56 Tidying up splice junctions and intron retentions (part 2)...
...grouping splice junctions
...grouping introns
...loading splice events
...compiling rowEvents
done
Jan 03 23:48:05 Generating NxtSE assays
Jan 03 23:48:06 Using MulticoreParam 1 threads
|
| | 0%
|
|============ | 17%
|
|======================= | 33%
|
|=================================== | 50%
|
|=============================================== | 67%
|
|========================================================== | 83%
|
|======================================================================| 100%
Jan 03 23:48:21 Building Final NxtSE Object
Jan 03 23:48:21 ...consolidating assays to H5 file
Jan 03 23:48:23 ...packaging reference
Jan 03 23:48:23 ...synthesising NxtSE
Jan 03 23:48:23 ...determining how overlapping introns should be removed
Jan 03 23:48:26 SpliceWiz (NxtSE) Collation Finished
Jan 03 23:48:26 Loading NxtSE object from file...
Jan 03 23:48:26 ...loading reference (NxtSE)
Jan 03 23:48:26 ...linking assays
Jan 03 23:48:26 ...linking COV files
Jan 03 23:48:26 ...loading rowData
Jan 03 23:48:26 ...removing overlapping introns...
Jan 03 23:48:26 NxtSE loaded
Jan 03 23:48:27 SpliceWiz reference already exists in given directory
Jan 03 23:48:27 Running SpliceWiz processBAM
Jan 03 23:48:28 Using MulticoreParam 1 threads
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
/private/tmp/RtmprqhPsY/02H003.bam processed (408 milliseconds)
Jan 03 23:48:28 SpliceWiz processBAM processed RtmprqhPsY/02H003.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/private/tmp/RtmprqhPsY/02H025.bam processed (305 milliseconds)
Jan 03 23:48:29 SpliceWiz processBAM processed RtmprqhPsY/02H025.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/private/tmp/RtmprqhPsY/02H026.bam processed (458 milliseconds)
Jan 03 23:48:29 SpliceWiz processBAM processed RtmprqhPsY/02H026.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/private/tmp/RtmprqhPsY/02H033.bam processed (461 milliseconds)
Jan 03 23:48:29 SpliceWiz processBAM processed RtmprqhPsY/02H033.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/private/tmp/RtmprqhPsY/02H043.bam processed (297 milliseconds)
Jan 03 23:48:30 SpliceWiz processBAM processed RtmprqhPsY/02H043.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/private/tmp/RtmprqhPsY/02H046.bam processed (421 milliseconds)
Jan 03 23:48:30 SpliceWiz processBAM processed RtmprqhPsY/02H046.bam
Jan 03 23:48:31 Using MulticoreParam 1 threads
Jan 03 23:48:31 Validating Experiment; checking COV files...
Jan 03 23:48:31 Compiling Sample Stats
Jan 03 23:48:31 Compiling Junction List...merging...done
Jan 03 23:48:33 Compiling Junction Stats...merging...done
Jan 03 23:48:40 Compiling Intron Retention List...done
Jan 03 23:48:41 Tidying up splice junctions and intron retentions...
...annotating splice junctions
...copying splicing reference
...grouping splice junctions
...grouping introns
...loading splice events
...compiling rowEvents
done
Jan 03 23:48:52 Generating NxtSE assays
Jan 03 23:48:54 Using MulticoreParam 1 threads
|
| | 0%
|
|============ | 17%
|
|======================= | 33%
|
|=================================== | 50%
|
|=============================================== | 67%
|
|========================================================== | 83%
|
|======================================================================| 100%
Jan 03 23:49:09 Building Final NxtSE Object
Jan 03 23:49:09 ...consolidating assays to H5 file
Jan 03 23:49:11 ...packaging reference
Jan 03 23:49:11 ...synthesising NxtSE
Jan 03 23:49:11 ...determining how overlapping introns should be removed
Jan 03 23:49:14 SpliceWiz (NxtSE) Collation Finished
Jan 03 23:49:14 Loading NxtSE object from file...
Jan 03 23:49:14 ...loading reference (NxtSE)
Jan 03 23:49:14 ...linking assays
Jan 03 23:49:14 ...linking COV files
Jan 03 23:49:14 ...loading rowData
Jan 03 23:49:14 ...removing overlapping introns...
Jan 03 23:49:14 NxtSE loaded
path paired strand depth mean_frag_size
02H003 ../SpliceWiz_Output/02H003.txt.gz TRUE -1 106256 149.3108
02H025 ../SpliceWiz_Output/02H025.txt.gz TRUE -1 84872 151.5914
02H026 ../SpliceWiz_Output/02H026.txt.gz TRUE -1 131514 150.3238
02H033 ../SpliceWiz_Output/02H033.txt.gz TRUE -1 129013 153.9754
02H043 ../SpliceWiz_Output/02H043.txt.gz TRUE -1 80254 155.4004
02H046 ../SpliceWiz_Output/02H046.txt.gz TRUE -1 120174 151.2840
directionality_strength Intergenic_Fraction rRNA_Fraction
02H003 9850 0 0
02H025 9848 0 0
02H026 9848 0 0
02H033 9855 0 0
02H043 9841 0 0
02H046 9857 0 0
NonPolyA_Fraction Mitochondrial_Fraction Unanno_Jn_Fraction
02H003 0 0 0.013449472
02H025 0 0 0.011203515
02H026 0 0 0.007282382
02H033 0 0 0.006310241
02H043 0 0 0.005871040
02H046 0 0 0.009819533
NMD_Jn_Fraction Fraction_Splice_Reads Fraction_Span_Reads IRBurden_clean
02H003 0.019509970 0.3506908 0.1735243 0.05796583
02H025 0.019360162 0.3712414 0.1591691 0.03963531
02H026 0.004298323 0.3980261 0.1615037 0.02576549
02H033 0.007705562 0.4003550 0.1734089 0.03090263
02H043 0.028069104 0.3671219 0.1807511 0.03762138
02H046 0.010542303 0.3725598 0.1603508 0.05099352
IRBurden_exitrons IRBurden_clean_unstranded IRBurden_exitrons_unstranded
02H003 0.1291810 0.03844293 0.1296020
02H025 0.1192351 0.02730399 0.1194005
02H026 0.1231055 0.02010410 0.1231939
02H033 0.1378958 0.02300500 0.1380215
02H043 0.1392935 0.02286515 0.1397365
02H046 0.1132136 0.03359077 0.1133852
IRBurden_antisense
02H003 0.021393335
02H025 0.013191532
02H026 0.006007119
02H033 0.008453742
02H043 0.015837096
02H046 0.019043703
MD5 is fcdc53e0f7fbd843529077ebd26dd058
Jan 03 23:49:17 Reference generated without non-polyA reference
Jan 03 23:49:17 Reference generated without Mappability reference
Jan 03 23:49:17 Reference generated without Blacklist exclusion
Jan 03 23:49:17 Converting FASTA to local TwoBitFile...done
Jan 03 23:49:18 Connecting to genome TwoBitFile...done
Jan 03 23:49:18 Making local copy of GTF file...done
Jan 03 23:49:19 Reading source GTF file...done
Jan 03 23:49:19 Processing gtf file...
...genes
...transcripts
...CDS
...exons
done
Jan 03 23:49:20 Gene ontology not prepared for this reference
Jan 03 23:49:22 Processing introns...
...data
...basic annotations
...splice motifs
...other info
...defining flanking exon clusters
done
Jan 03 23:49:26 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
Jan 03 23:49:33 Predicting NMD transcripts from genome sequence
...exonic transcripts
...retained introns
|
| | 0%
|
|======================================================================| 100%
done
Jan 03 23:49:35 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
Jan 03 23:49:37 Splice Annotations Filtered
Jan 03 23:49:38 Translating Alternate Splice Peptides...done
Jan 03 23:49:38 Splice Annotations finished
Reference build finished
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 47 ]
>
> # bump to trigger r cmd check
>
> proc.time()
user system elapsed
399.051 198.282 611.410
SpliceWiz.Rcheck/SpliceWiz-Ex.timings
| name | user | system | elapsed | |
| ASE-GLM-edgeR | 2.299 | 0.133 | 2.451 | |
| ASE-methods | 30.772 | 0.339 | 31.273 | |
| ASEFilter-class | 0.053 | 0.005 | 0.060 | |
| Build-Reference-methods | 54.697 | 1.497 | 57.178 | |
| Coverage | 0.866 | 0.027 | 0.899 | |
| Gene-ontology-methods | 2.201 | 0.083 | 2.305 | |
| Graphics-User-Interface | 0.000 | 0.001 | 0.000 | |
| Mappability-methods | 2.554 | 0.051 | 2.621 | |
| NxtSE-class | 53.676 | 1.261 | 55.312 | |
| Run_SpliceWiz_Filters | 7.516 | 0.042 | 7.589 | |
| STAR-methods | 0.003 | 0.008 | 0.031 | |
| View-Reference-methods | 0.205 | 0.024 | 0.231 | |
| collateData | 2.531 | 0.072 | 2.643 | |
| coord2GR | 0.025 | 0.003 | 0.028 | |
| covDataObject-class | 1.652 | 0.031 | 1.702 | |
| covPlotObject-class | 22.439 | 0.516 | 23.123 | |
| covPlotly-class | 1.116 | 0.019 | 1.139 | |
| example-SpliceWiz-data | 0.012 | 0.002 | 0.014 | |
| findSamples | 0.005 | 0.005 | 0.010 | |
| isCOV | 0.014 | 0.004 | 0.017 | |
| makeSE | 1.945 | 0.153 | 2.125 | |
| make_plot_data | 0.055 | 0.003 | 0.058 | |
| plotCoverage | 15.818 | 0.186 | 16.105 | |
| processBAM | 2.922 | 0.486 | 3.174 | |
| setSWthreads | 0.003 | 0.008 | 0.025 | |
| theme_white | 0.176 | 0.069 | 0.247 | |