Linx plotting error - Githubissues

jaesvi commented 5 months ago

Hi, I'm running Linx (v1.24.1, through Oncoanalyser) and for some samples I get a plotting error. The SvVisualiser command is:

java \
    -Xmx16g \
    -cp /opt/linx/linx.jar \
    com.hartwig.hmftools.linx.visualiser.SvVisualiser \
    -sample ACH-000012 \
    -vis_file_dir linx_somatic \
    -ref_genome_version 38 \
    -ensembl_data_dir ensembl_data \
    -circos /opt/conda/bin/circos \
    -threads 4 \
    -plot_out plots/all/ \
    -data_out reportable/all_data/

This will plot some clusters properly until reaching cluster-39:

10:02:10 - [INFO ] - Generating ACH-000012.cluster-39.sv2.003.png via command: /opt/conda/bin/circos -nosvg -conf /nfs/research/icortes/DATA/broad.wgs/oncoanalyser/work/7f/c7976a321bce556e06e290072d6e8a/data/all_data/ACH-000012.cluster-39.sv2.circos.003.conf -outputdir /nfs/research/icortes/DATA/broad.wgs/oncoanalyser/work/7f/c7976a321bce556e06e290072d6e8a/plots/all -outputfile ACH-000012.cluster-39.sv2.003.png
10:02:13 - [INFO ] - Executing R script via command: Rscript /tmp/script14616716124940271539.R data/all_data//ACH-000012.cluster-39.sv2.chromosome.circos data/all_data//ACH-000012.cluster-39.sv2.cytoBand.txt plots/all//ACH-000012.cluster-39.sv2.003.png 48.0 150 6
10:02:33 - [FATAL] - Error executing R script. Examine error file /tmp/chromosomeRangePlot.R3869294969340833157.error for details.
10:02:33 - [WARN ] - error adding chromosomal context
java.util.concurrent.ExecutionException: java.lang.Exception: plotting error
    at java.base/java.util.concurrent.FutureTask.report(FutureTask.java:122)
    at java.base/java.util.concurrent.FutureTask.get(FutureTask.java:191)
    at com.hartwig.hmftools.linx.visualiser.SvVisualiser.run(SvVisualiser.java:131)
    at com.hartwig.hmftools.linx.visualiser.SvVisualiser.main(SvVisualiser.java:374)
Caused by: java.lang.Exception: plotting error
    at com.hartwig.hmftools.linx.visualiser.SvVisualiser.createImageFrame(SvVisualiser.java:354)
    at com.hartwig.hmftools.linx.visualiser.SvVisualiser.lambda$submitFrame$29(SvVisualiser.java:323)
    at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
    at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
    at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
    at java.base/java.lang.Thread.run(Thread.java:834)

I can confirm that data/all_data//ACH-000012.cluster-39.sv2.chromosome.circos is empty, which prompts the R error:

Error in read.table(chromosomeRangePath, h = F, sep = "\t", comment = "!",  : 
  no lines available in input
Execution halted

I am not sure as to where to start debugging this one, so any help is appreciated.

Thanks!

charlesshale commented 4 months ago

Would it be possible for you to share the Linx VIS files so I can debug this? If so, email me directly: c.shale@hartwigmedicalfoundation.nl

Alternatively you could try running the latest Linx release to see the issue has already been addressed: https://github.com/hartwigmedical/hmftools/releases/tag/linx-v1.25

jaesvi commented 4 months ago

Sent via email. I can also confirm that error remains in linx-v1.25

charlesshale commented 4 months ago

The cause of this is:

the sample has SVs on chrY but Purple determines the gender/sex as female
no Purple copy number records are written for chrY
when Linx attempts to generate a plot for a pair of clustered SGLs on chrY it fails to find copy number data and the R-script throws an error

This has been addressed in Purple as per this minor release: https://github.com/hartwigmedical/hmftools/releases/tag/purple-v4.0.2

hartwigmedical / hmftools

Linx plotting error #514