| Back to Multiple platform build/check report for BioC 3.17 |
|
This page was generated on 2023-04-12 10:55:32 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | 4.3.0 alpha (2023-04-03 r84154) | 4547 |
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" | 4333 |
| 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: - 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. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 1972/2207 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SpliceWiz 1.1.7 (landing page) Alex Chit Hei Wong
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | ERROR | ||||||||||
| Package: SpliceWiz |
| Version: 1.1.7 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:SpliceWiz.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings SpliceWiz_1.1.7.tar.gz |
| StartedAt: 2023-04-11 23:50:13 -0400 (Tue, 11 Apr 2023) |
| EndedAt: 2023-04-12 00:05:24 -0400 (Wed, 12 Apr 2023) |
| EllapsedTime: 911.0 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: SpliceWiz.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:SpliceWiz.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings SpliceWiz_1.1.7.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/SpliceWiz.Rcheck’
* using R version 4.3.0 alpha (2023-04-03 r84154)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘SpliceWiz/DESCRIPTION’ ... OK
* this is package ‘SpliceWiz’ version ‘1.1.7’
* 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
* used C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
installed size is 8.1Mb
sub-directories of 1Mb or more:
R 2.0Mb
libs 4.9Mb
* 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 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 ... 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 ... ERROR
Running examples in ‘SpliceWiz-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getAvailableGO
> ### Title: Builds reference files used by SpliceWiz
> ### Aliases: getAvailableGO Build-Reference-methods getResources buildRef
> ### buildFullRef getNonPolyARef
>
> ### ** Examples
>
> # Quick runnable example: generate a reference using SpliceWiz's example genome
>
> example_ref <- file.path(tempdir(), "Reference")
> getResources(
+ reference_path = example_ref,
+ fasta = chrZ_genome(),
+ gtf = chrZ_gtf()
+ )
Apr 11 23:56:35 Converting FASTA to local TwoBitFile...done
Apr 11 23:56:36 Connecting to genome TwoBitFile...done
Apr 11 23:56:36 Making local copy of GTF file...done
> buildRef(
+ reference_path = example_ref
+ )
Apr 11 23:56:37 Reference generated without non-polyA reference
Apr 11 23:56:37 Reference generated without Mappability reference
Apr 11 23:56:37 Reference generated without Blacklist exclusion
Apr 11 23:56:37 Connecting to genome TwoBitFile...done
Apr 11 23:56:37 Reading source GTF file...done
Apr 11 23:56:37 Processing gtf file...
...genes
...transcripts
...CDS
...exons
done
Apr 11 23:56:38 Gene ontology not prepared for this reference
Apr 11 23:56:40 Processing introns...
...data
...basic annotations
...splice motifs
...other info
...defining flanking exon clusters
done
Apr 11 23:56:45 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
Apr 11 23:56:53 Predicting NMD transcripts from genome sequence
...exonic transcripts
...retained introns
|
| | 0%
|
|======================================================================| 100%
done
Apr 11 23:56:55 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
Apr 11 23:56:56 Splice Annotations Filtered
Apr 11 23:56:57 Translating Alternate Splice Peptides...done
Apr 11 23:56:58 Splice Annotations finished
Reference build finished
>
> # NB: the above is equivalent to:
>
> example_ref <- file.path(tempdir(), "Reference")
> buildRef(
+ reference_path = example_ref,
+ fasta = chrZ_genome(),
+ gtf = chrZ_gtf()
+ )
Apr 11 23:56:59 SpliceWiz reference already exists in given directory
NULL
>
> # Get the path to the Non-PolyA BED file for hg19
>
> getNonPolyARef("hg19")
[1] "/home/biocbuild/bbs-3.17-bioc/R/site-library/SpliceWiz/extra-input-files/Human_hg19_nonPolyA_ROI.bed"
>
> # View available species for AnnotationHub's Ensembl/orgDB-based GO resources
>
> availSpecies <- getAvailableGO()
>
> # Build example reference with `Homo sapiens` Ens/orgDB gene ontology
>
> ont_ref <- file.path(tempdir(), "Reference_withGO")
> buildRef(
+ reference_path = ont_ref,
+ fasta = chrZ_genome(),
+ gtf = chrZ_gtf(),
+ ontologySpecies = "Homo sapiens"
+ )
Apr 11 23:57:02 Reference generated without non-polyA reference
Apr 11 23:57:02 Reference generated without Mappability reference
Apr 11 23:57:02 Reference generated without Blacklist exclusion
Apr 11 23:57:02 Converting FASTA to local TwoBitFile...done
Apr 11 23:57:04 Connecting to genome TwoBitFile...done
Apr 11 23:57:04 Making local copy of GTF file...done
Apr 11 23:57:04 Reading source GTF file...done
Apr 11 23:57:04 Processing gtf file...
...genes
...transcripts
...CDS
...exons
done
Apr 11 23:57:08 Retrieving gene GO-term pairings
Error in if (any(bad)) stop("invalid subscripts: ", paste(sQuote(S4Vectors:::selectSome(bad)), :
missing value where TRUE/FALSE needed
Calls: buildRef ... .fetch_orgDB -> subset -> subset.default -> [ -> [ -> .db_uid<-
Execution halted
* 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 ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 3 NOTEs
See
‘/home/biocbuild/bbs-3.17-bioc/meat/SpliceWiz.Rcheck/00check.log’
for details.
SpliceWiz.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL SpliceWiz ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’ * installing *source* package ‘SpliceWiz’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’ using C++11 g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/ompBAM/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.17-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-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/ompBAM/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.17-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-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/ompBAM/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.17-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-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/ompBAM/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.17-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-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/ompBAM/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.17-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-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/ompBAM/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.17-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-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/ompBAM/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.17-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-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/ompBAM/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.17-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-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/ompBAM/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.17-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-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/ompBAM/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.17-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-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/ompBAM/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.17-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-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/ompBAM/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.17-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-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/ompBAM/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.17-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-3.17-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-3.17-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.17-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 4.3.0 alpha (2023-04-03 r84154)
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
Apr 11 23:57:25 Converting FASTA to local TwoBitFile...done
Apr 11 23:57:26 Connecting to genome TwoBitFile...done
Apr 11 23:57:26 Making local copy of GTF file...done
Apr 11 23:57:27 Extracting temp genome FASTA from TwoBit file
Apr 11 23:57:28 Generating synthetic reads, saving to /tmp/Rtmp6VYJyW/refWithMapExcl/Mappability/Reads.fa
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
10145 synthetic reads generated
Apr 11 23:57:28 Cleaning temp genome / gene annotation files
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
Rsubread 2.13.5
//================================= setting ==================================\\
|| ||
|| Index name : reference_index ||
|| Index space : base space ||
|| Index split : no-split ||
|| Repeat threshold : 100 repeats ||
|| Gapped index : no ||
|| ||
|| Free / total memory : 70.4GB / 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=43.4k bps/s ||
|| 16%, 0 mins elapsed, rate=85.6k bps/s ||
|| 24%, 0 mins elapsed, rate=126.9k bps/s ||
|| 33%, 0 mins elapsed, rate=167.7k bps/s ||
|| 41%, 0 mins elapsed, rate=208.0k bps/s ||
|| 49%, 0 mins elapsed, rate=247.7k bps/s ||
|| 58%, 0 mins elapsed, rate=286.7k bps/s ||
|| 66%, 0 mins elapsed, rate=325.1k bps/s ||
|| 74%, 0 mins elapsed, rate=363.2k bps/s ||
|| 83%, 0 mins elapsed, rate=400.7k bps/s ||
|| 91%, 0 mins elapsed, rate=437.6k bps/s ||
|| 3.0 GB of memory is needed for index building. ||
|| Build the index... ||
|| 8%, 0 mins elapsed, rate=4.3k bps/s ||
|| 16%, 0 mins elapsed, rate=8.5k bps/s ||
|| 24%, 0 mins elapsed, rate=12.7k bps/s ||
|| 33%, 0 mins elapsed, rate=17.0k bps/s ||
|| 41%, 0 mins elapsed, rate=21.2k bps/s ||
|| 49%, 0 mins elapsed, rate=25.3k bps/s ||
|| 58%, 0 mins elapsed, rate=29.5k bps/s ||
|| 66%, 0 mins elapsed, rate=33.7k bps/s ||
|| 74%, 0 mins elapsed, rate=37.8k bps/s ||
|| 83%, 0 mins elapsed, rate=41.9k bps/s ||
|| 91%, 0 mins elapsed, rate=46.0k 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 2.13.5
//================================= 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 (11-Apr-2023 23:57:38, pid=1465651) ================\\
|| ||
|| 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=29.1k 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 ||
|| ||
\\============================================================================//
Apr 11 23:58:10 Calculating Mappability Exclusion regions from: /tmp/Rtmp6VYJyW/refWithMapExcl/Mappability/AlignedReads.bam
Calculating Mappability Exclusions: /tmp/Rtmp6VYJyW/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%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Apr 11 23:58:14 Reference generated without non-polyA reference
Apr 11 23:58:14 Reference generated without Mappability reference
Apr 11 23:58:14 Reference generated without Blacklist exclusion
Apr 11 23:58:14 Converting FASTA to local TwoBitFile...done
Apr 11 23:58:16 Connecting to genome TwoBitFile...done
Apr 11 23:58:16 Making local copy of GTF file...done
Apr 11 23:58:16 Reading source GTF file...done
Apr 11 23:58:16 Processing gtf file...
...genes
...transcripts
...CDS
...exons
done
Apr 11 23:58:17 Gene ontology not prepared for this reference
Apr 11 23:58:20 Processing introns...
...data
...basic annotations
...splice motifs
...other info
...defining flanking exon clusters
done
Apr 11 23:58:25 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
Apr 11 23:58:33 Predicting NMD transcripts from genome sequence
...exonic transcripts
...retained introns
|
| | 0%
|
|======================================================================| 100%
done
Apr 11 23:58:35 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
Apr 11 23:58:37 Splice Annotations Filtered
Apr 11 23:58:38 Translating Alternate Splice Peptides...done
Apr 11 23:58:38 Splice Annotations finished
Reference build finished
Apr 11 23:58:40 Running SpliceWiz processBAM
Reading reference file
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
Processing BAM file /tmp/Rtmp6VYJyW/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/Rtmp6VYJyW/02H003.bam processed (414 milliseconds)
Apr 11 23:58:40 Running SpliceWiz processBAM
Reading reference file
Allocating memory to 2 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
Processing BAM file /tmp/Rtmp6VYJyW/02H003.bam
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Compiling data from threads
Performing final sort of fragment maps
Writing COV file
**************************************************|
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Writing output file
/tmp/Rtmp6VYJyW/02H003.bam processed (256 milliseconds)
Apr 11 23:58:41 SpliceWiz reference already exists in given directory
Apr 11 23:58:41 Running SpliceWiz processBAM
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/tmp/Rtmp6VYJyW/02H003.bam processed (414 milliseconds)
/tmp/Rtmp6VYJyW/02H025.bam processed (327 milliseconds)
/tmp/Rtmp6VYJyW/02H026.bam processed (518 milliseconds)
/tmp/Rtmp6VYJyW/02H033.bam processed (507 milliseconds)
/tmp/Rtmp6VYJyW/02H043.bam processed (319 milliseconds)
/tmp/Rtmp6VYJyW/02H046.bam processed (453 milliseconds)
Apr 11 23:58:45 Using MulticoreParam 1 threads
Apr 11 23:58:45 Validating Experiment; checking COV files...
Apr 11 23:58:45 Compiling Sample Stats
Apr 11 23:58:45 Compiling Junction List...merging...done
Apr 11 23:58:46 Compiling Junction Stats...merging...done
Apr 11 23:58:54 Compiling Intron Retention List...done
Apr 11 23:58:55 Compiling Tandem Junction List...merging...done
Apr 11 23:58:56 Tidying up splice junctions and intron retentions...
...annotating splice junctions
...looking for novel exons
Apr 11 23:59:00 Assembling novel splicing reference:
...loading reference FASTA/GTF
...injecting novel transcripts to GTF
...processing GTF
...processing introns from GTF
...annotating alternative splicing events
done
Apr 11 23:59:11 Tidying up splice junctions and intron retentions (part 2)...
...grouping splice junctions
...grouping introns
...loading splice events
...compiling rowEvents
done
Apr 11 23:59:19 Generating NxtSE assays
Apr 11 23:59:20 Using MulticoreParam 1 threads
|
| | 0%
|
|============ | 17%
|
|======================= | 33%
|
|=================================== | 50%
|
|=============================================== | 67%
|
|========================================================== | 83%
|
|======================================================================| 100%
Apr 11 23:59:36 Building Final NxtSE Object
Apr 11 23:59:36 ...consolidating assays to H5 file
Apr 11 23:59:38 ...packaging reference
Apr 11 23:59:38 ...synthesising NxtSE
Apr 11 23:59:38 ...determining how overlapping introns should be removed
Apr 11 23:59:44 SpliceWiz (NxtSE) Collation Finished
Apr 11 23:59:44 Loading NxtSE object from file...
Apr 11 23:59:44 ...loading reference (NxtSE)
Apr 11 23:59:44 ...linking assays
Apr 11 23:59:44 ...linking COV files
Apr 11 23:59:44 ...loading rowData
Apr 11 23:59:44 ...removing overlapping introns...
Apr 11 23:59:44 NxtSE loaded
Apr 11 23:59:45 SpliceWiz reference already exists in given directory
Apr 11 23:59:45 Running SpliceWiz processBAM
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/tmp/Rtmp6VYJyW/02H003.bam processed (393 milliseconds)
/tmp/Rtmp6VYJyW/02H025.bam processed (313 milliseconds)
/tmp/Rtmp6VYJyW/02H026.bam processed (493 milliseconds)
/tmp/Rtmp6VYJyW/02H033.bam processed (507 milliseconds)
/tmp/Rtmp6VYJyW/02H043.bam processed (307 milliseconds)
/tmp/Rtmp6VYJyW/02H046.bam processed (441 milliseconds)
Apr 11 23:59:48 Using MulticoreParam 1 threads
Apr 11 23:59:48 Validating Experiment; checking COV files...
Apr 11 23:59:48 Compiling Sample Stats
Apr 11 23:59:48 Compiling Junction List...merging...done
Apr 11 23:59:49 Compiling Junction Stats...merging...done
Apr 11 23:59:57 Compiling Intron Retention List...done
Apr 11 23:59:58 Tidying up splice junctions and intron retentions...
...annotating splice junctions
...copying splicing reference
...grouping splice junctions
...grouping introns
...loading splice events
...compiling rowEvents
done
Apr 12 00:00:09 Generating NxtSE assays
Apr 12 00:00:10 Using MulticoreParam 1 threads
|
| | 0%
|
|============ | 17%
|
|======================= | 33%
|
|=================================== | 50%
|
|=============================================== | 67%
|
|========================================================== | 83%
|
|======================================================================| 100%
Apr 12 00:00:26 Building Final NxtSE Object
Apr 12 00:00:26 ...consolidating assays to H5 file
Apr 12 00:00:27 ...packaging reference
Apr 12 00:00:27 ...synthesising NxtSE
Apr 12 00:00:27 ...determining how overlapping introns should be removed
Apr 12 00:00:33 SpliceWiz (NxtSE) Collation Finished
Apr 12 00:00:33 Loading NxtSE object from file...
Apr 12 00:00:33 ...loading reference (NxtSE)
Apr 12 00:00:33 ...linking assays
Apr 12 00:00:33 ...linking COV files
Apr 12 00:00:33 ...loading rowData
Apr 12 00:00:33 ...removing overlapping introns...
Apr 12 00:00:33 NxtSE loaded
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 29 ]
>
> # bump to trigger r cmd check
>
> proc.time()
user system elapsed
182.228 20.645 202.950
SpliceWiz.Rcheck/SpliceWiz-Ex.timings
| name | user | system | elapsed | |
| ASE-GLM-edgeR | 3.729 | 0.163 | 3.893 | |
| ASE-methods | 36.368 | 1.240 | 37.665 | |
| ASEFilter-class | 0.039 | 0.004 | 0.043 | |