MitoScape
GitHub: https://github.com/CHOP-CMEM/MitoScape
GitHub
This follows similar steps as before.
git clone https://github.com/CHOP-CMEM/MitoScape
cd MitoScape
java -version
sbt assembly
java -Xmx16G -jar target/scala-2.12/MitoScapeClassify.jar \
--threads 4 \
--prob 0.9 \
--ld mitomap.ld \
--numt NUMTs_hg38.txt \
--classifier MTClassifierModel.RF \
--prefix sample123 \
--out sample123_output
We have
$ java -version
openjdk version "1.8.0_462"
OpenJDK Runtime Environment (build 1.8.0_462-b08)
OpenJDK 64-Bit Server VM (build 25.462-b08, mixed mode)
$ sbt assembly
[info] Loading settings for project mitoscape-build from plugins.sbt ...
[info] Loading project definition from /home/jhz22/work/MitoScape/project
[info] Loading settings for project mitoscape from build.sbt ...
[info] Set current project to MitoScape (in build file:/home/jhz22/work/MitoScape/)
[info] Updating ...
[info] Done updating.
[warn] There may be incompatibilities among your library dependencies.
[warn] Run 'evicted' to see detailed eviction warnings
[info] Compiling 6 Scala sources to /home/jhz22/work/MitoScape/target/scala-2.12/classes ...
[info] Done compiling.
[info] Packaging /home/jhz22/work/MitoScape/target/scala-2.12/mitoscape_2.12-0.1.jar ...
[info] Done packaging.
[info] Strategy 'concat' was applied to 12 files (Run the task at debug level to see details)
[info] Strategy 'deduplicate' was applied to 9 files (Run the task at debug level to see details)
[info] Strategy 'discard' was applied to 377 files (Run the task at debug level to see details)
[info] Strategy 'first' was applied to 201 files (Run the task at debug level to see details)
[info] Strategy 'last' was applied to 3 files (Run the task at debug level to see details)
[info] Strategy 'rename' was applied to 19 files (Run the task at debug level to see details)
[info] Packaging /home/jhz22/work/MitoScape/target/scala-2.12/MitoScapeClassify.jar ...
[info] Done packaging.
[success] Total time: 325 s, completed Sep 11, 2025 10:16:02 AM
1.0
wget -qO- https://github.com/CHOP-CMEM/MitoScape/archive/refs/tags/v1.0.tar.gz | tar xvfz -
cd MitoScape-1.0/
mv build.sbt build.sbt.save
module load ceuadmin/Scala
cs install --dir ~/bin sbt
module load openjdk/11.0.12_7/gcc/czpuqhmv
assembly
Several changes are necessary:
Only the first file is generated on the fly below and the other two provided directly for legibility here.
As documented, Scale build tool (sbt) is invoked.
echo $JAVA_HOME
cat << 'EOF' > project/plugins.sbt
addSbtPlugin("com.typesafe.sbt" % "sbt-native-packager" % "1.8.1")
addSbtPlugin("com.eed3si9n" % "sbt-assembly" % "1.1.0")
EOF
~/bin/sbt assembly
ll target/scala-2.12/
which gives
$ ~/bin/sbt assembly
[info] welcome to sbt 1.11.6 (Eclipse Foundation Java 11.0.12)
[info] loading settings for project mitoscape-1-0-build from plugins.sbt...
[info] loading project definition from /home/jhz22/MitoScape-1.0/project
[info] compiling 1 Scala source to /home/jhz22/MitoScape-1.0/project/target/scala-2.12/sbt-1.0/classes ...
[info] loading settings for project mitoscape-1-0 from build.sbt...
[info] set current project to MitoScape (in build file:/home/jhz22/MitoScape-1.0/)
[success] Total time: 223 s (0:03:43.0), completed Sep 10, 2025, 5:00:36 PM
[info] compiling 6 Scala sources to /home/jhz22/MitoScape-1.0/target/scala-2.12/classes ...
[info] Strategy 'discard' was applied to 5 files (Run the task at debug level to see details)
[info] Strategy 'first' was applied to 1134 files (Run the task at debug level to see details)
[success] Total time: 294 s (0:04:54.0), completed Sep 10, 2025, 5:05:29 PM
$ ll target/scala-2.12/
total 210128
-rw-rw-r-- 1 jhz22 jhz22 185703796 Sep 10 17:05 MitoScapeClassify.jar
Additional details
~/bin/sbt clean compile
~/bin/sbt test:compile
~/bin/sbt package
ls target/scala-2.12/
ls target/scala-2.12/classes/MitoScape/
jar tf target/scala-2.12/mitoscape_2.12-0.1.jar | grep MitoScape
~/bin/sbt run
which shows
$ ls target/scala-2.12/
classes/ mitoscape_2.12-0.1.jar mitoscape_2.12-0.1-tests.jar sync/ test-sync/ update/ zinc/
$ ls target/scala-2.12/classes/MitoScape/
BamReader.class MDParser.class 'MTClassify$$typecreator4$1.class' 'MTReader$$typecreator4$1.class'
Feature.class 'MTClassifierModel$$typecreator4$1.class' 'MTClassify$.class' MTReader.class
'LD$$typecreator4$1.class' 'MTClassifierModel$.class' MTClassify.class NucFeature.class
LD.class MTClassifierModel.class MTFeature.class NucReader.class
$ jar tf target/scala-2.12/mitoscape_2.12-0.1.jar | grep MitoScape
MitoScape/
MitoScape/BamReader.class
MitoScape/Feature.class
MitoScape/LD$$typecreator4$1.class
MitoScape/LD.class
MitoScape/MDParser.class
MitoScape/MTClassifierModel$$typecreator4$1.class
MitoScape/MTClassifierModel$.class
MitoScape/MTClassifierModel.class
MitoScape/MTClassify$$typecreator4$1.class
MitoScape/MTClassify$.class
MitoScape/MTClassify.class
MitoScape/MTFeature.class
MitoScape/MTReader$$typecreator4$1.class
MitoScape/MTReader.class
MitoScape/NucFeature.class
MitoScape/NucReader.class
$ /home/jhz22/.local/share/coursier/bin/sbt run
[info] welcome to sbt 1.11.6 (Eclipse Foundation Java 11.0.12)
[info] loading settings for project mitoscape-1-0-build from plugins.sbt...
[info] loading project definition from /rds/project/rds-4o5vpvAowP0/software/MitoScape-1.0/project
[info] loading settings for project mitoscape-1-0 from build.sbt...
[info] set current project to MitoScape (in build file:/rds/project/rds-4o5vpvAowP0/software/MitoScape-1.0/)
[info] running MitoScape.MTClassify
Usage: mtclassify
--prefix <prefix of bam file>
--out <output file>
--prob <probability threshold>
--threads <number of threads>
References
Saunders, M. A., T. A. Schwarz, L. E. Colleoni, A. L. Drong, D. D. A. MacArthur, C. E. T. Halldorsson, D. I. Chanda, et al. 2021. "MitoScape: A Big-Data, Machine-Learning Platform for Obtaining Mitochondrial DNA from Next-Generation Sequencing Data." PLoS Computational Biology 17 (11): e1009594. https://doi.org/10.1371/journal.pcbi.1009594.