unknown error in wgscoverageplotter

[dcopetti]

Java version: openjdk 20-internal 2023-03-21 OpenJDK Runtime Environment (build 20-internal-adhoc..src) OpenJDK 64-Bit Server VM (build 20-internal-adhoc..src, mixed mode, sharing

Subject of the issue

per base <=0 with drawing-width

jvarkit version: 300623ffe java version: openjdk 20-internal 2023-03-21

• the value of ${JAVA_HOME}
• which OS

Steps to reproduce

the command is: java -jar /wing2/users/dcopetti/bin/jvarkit.jar wgscoverageplotter --dimension 5000x500 -C -1 --clip --percentile median -o primary_covplot_100k.svg --min-contig-length 100k -R assembly.primary_racon_2.2.2024.fa raw_reads_to_primarys.bam

Expected behaviour

Run without problems?

Actual behaviour

the error I get is this: [SEVERE][WGSCoveragePlotter]pixel per base <=0 with drawing-width:4890.0 distance-between-contigs:1.0 n-chromosomes:5676 genome-length:2688438887 java.lang.IllegalStateException: pixel per base <=0 with drawing-width:4890.0 distance-between-contigs:1.0 n-chromosomes:5676 genome-length:2688438887 at com.github.lindenb.jvarkit.tools.bam2graphics.WGSCoveragePlotter.doWork(WGSCoveragePlotter.java:358) at com.github.lindenb.jvarkit.util.jcommander.Launcher.instanceMain(Launcher.java:819) at com.github.lindenb.jvarkit.util.jcommander.Launcher.instanceMainWithExit(Launcher.java:982) at com.github.lindenb.jvarkit.tools.bam2graphics.WGSCoveragePlotter.main(WGSCoveragePlotter.java:650) at java.base/jdk.internal.reflect.DirectMethodHandleAccessor.invoke(DirectMethodHandleAccessor.java:104) at java.base/java.lang.reflect.Method.invoke(Method.java:578) at com.github.lindenb.jvarkit.tools.jvarkit.JvarkitCentral$Command.execute(JvarkitCentral.java:256) at com.github.lindenb.jvarkit.tools.jvarkit.JvarkitCentral.run(JvarkitCentral.java:708) at com.github.lindenb.jvarkit.tools.jvarkit.JvarkitCentral.main(JvarkitCentral.java:719) [INFO][Launcher]wgscoverageplotter Exited with failure (-1)

I was able to use this script and these options before with other files, now I can't understand what the error message means. Are there contigs with coverage = 0? Thanks, Dario

[lindenb]

one contig cannot be displayed because the resulting width will be just too small. Try with a wider dimension.

[dcopetti]

thanks! increasing to 150 or 200 kb resolved the issue