oncoanalyser icon indicating copy to clipboard operation
oncoanalyser copied to clipboard
verified publisher icon nf-core

LINX error: java.lang.NullPointerException: Cannot read field "CopyNumber"

Open fevac opened this issue 2 months ago • 4 comments

Description of the bug

Hi,

I'm running into this error:

20:08:02.464 [ERROR] thread exception: java.lang.NullPointerException: Cannot read field "CopyNumber" because "cnStartPrevData" is null

I'm running oncoanalyser v2.2.0 with a single tumor sample. Using as parameters: mode: 'wgts' genome: 'GRCh37_hmf'

Any ideas of what could be wrong?

Thanks in advance for the help!

Command used and terminal output

nextflow \
  -log $workdir/nextflow_to_small_v2.2.0.log \
  -config $maindir/oncoanalyser/nextflow_config_v2.2.0_nextflow.yaml \
  run nf-core/oncoanalyser \
  -r 2.2.0 \
  -work-dir $workdir/work_small_nextflow \
  -resume \
  -profile singularity \
  -params-file  $workdir/params_file_v2.2.0_small.yaml

Relevant files

No response

System information

Nextflow version 25.04.8 build 5956 HPC Slurm Singularity Linux Oncoanalyser version 2.2.0

fevac avatar Oct 30 '25 13:10 fevac

Hi @fevac, thanks for reporting this. I've been able to run an oncoanalyser 2.2.0 'wgts' analysis with a tumour-only input, so I suspect this is error is related to your sample. Are you able to share your params file and .nextflow.log?

It would also be very useful to review your LINX inputs if you're able to send those across as well

scwatts avatar Nov 10 '25 06:11 scwatts

Hi @scwatts thanks for your reply. I tested a different sample and the most recent nextflow version and I get the same issue. We were able to successfully run Oncoanalyser on a previous version (-r 93ebe952d3a5db29676179d0c1087788ed4f7b46) for these same samples.

The params file used contains (some values replaced in capital letters):

mode: 'wgts'
genome: 'GRCh37_hmf'
input: /PATH2CASE/oncoanalyser_2.2.0/CASE/CASE_samplesheet_to_small.csv
outdir:  /PATH2CASE/oncoanalyser_2.2.0/CASE/results_to_small

The sample sheet contains:

group_id,subject_id,sample_id,sample_type,sequence_type,filetype,info,filepath
CASE,subjectID,SAMPLE,tumor,dna,fastq,library_id:SA_library;lane:L001,PATH2FASTQ1;PATH2FASTQ2

The full error for that process is:

Command error:
  22:45:28.000 [DEBUG] sample(SAMPLE) svID(46 type=SGL) unexpected JCN(est=0.0 unc=0.0)
  22:45:28.000 [DEBUG] sample(SAMPLE) svID(57 type=SGL) unexpected JCN(est=0.0 unc=0.0)
  22:45:28.000 [DEBUG] sample(SAMPLE) svID(59 type=SGL) unexpected JCN(est=0.0 unc=0.0)
  22:45:28.000 [DEBUG] sample(SAMPLE) svID(70 type=SGL) unexpected JCN(est=0.0 unc=0.0)
  22:45:28.001 [DEBUG] sample(SAMPLE) svID(88 type=SGL) unexpected JCN(est=0.0 unc=0.0)
  22:45:28.001 [DEBUG] sample(SAMPLE) svID(92 type=SGL) unexpected JCN(est=0.0 unc=0.0)
  22:45:28.001 [DEBUG] sample(SAMPLE) svID(93 type=SGL) unexpected JCN(est=0.0 unc=0.0)
  22:45:28.001 [DEBUG] sample(SAMPLE) svID(96 type=SGL) unexpected JCN(est=0.0 unc=0.0)
  22:45:28.001 [DEBUG] sample(SAMPLE) svID(98 type=BND) unexpected JCN(est=0.0 unc=0.0)
  22:45:28.001 [DEBUG] sample(SAMPLE) svID(112 type=SGL) unexpected JCN(est=0.0 unc=0.0)
  22:45:28.001 [DEBUG] sample(SAMPLE) svID(124 type=SGL) unexpected JCN(est=0.0 unc=0.0)
  22:45:28.002 [DEBUG] sample(SAMPLE) svID(127 type=SGL) unexpected JCN(est=0.0 unc=0.0)
  22:45:28.002 [DEBUG] sample(SAMPLE) svID(131 type=SGL) unexpected JCN(est=0.0 unc=0.0)
  22:45:28.002 [DEBUG] sample(SAMPLE) svID(134 type=SGL) unexpected JCN(est=0.0 unc=0.0)
  22:45:28.002 [DEBUG] sample(SAMPLE) svID(138 type=SGL) unexpected JCN(est=0.0 unc=0.0)
  22:45:28.002 [DEBUG] sample(SAMPLE) svID(139 type=SGL) unexpected JCN(est=0.0 unc=0.0)
  22:45:28.002 [DEBUG] sample(SAMPLE) svID(147 type=BND) unexpected JCN(est=0.0 unc=0.0)
  22:45:28.002 [DEBUG] sample(SAMPLE) svID(163 type=SGL) unexpected JCN(est=0.0 unc=0.0)
  22:45:28.003 [DEBUG] sample(SAMPLE) svID(187 type=INV) unexpected JCN(est=0.0 unc=0.0)
  22:45:28.003 [DEBUG] sample(SAMPLE) svID(190 type=SGL) unexpected JCN(est=0.0 unc=0.0)
  22:45:28.003 [DEBUG] sample(SAMPLE) svID(191 type=DEL) unexpected JCN(est=0.0 unc=0.0)
  22:45:28.003 [DEBUG] sample(SAMPLE) svID(197 type=BND) unexpected JCN(est=0.0 unc=0.0)
  22:45:28.003 [DEBUG] sample(SAMPLE) svID(198 type=SGL) unexpected JCN(est=0.0 unc=0.0)
  22:45:28.003 [DEBUG] sample(SAMPLE) svID(203 type=SGL) unexpected JCN(est=0.0 unc=0.0)
  22:45:28.003 [DEBUG] sample(SAMPLE) svID(220 type=SGL) unexpected JCN(est=0.0 unc=0.0)
  22:45:28.003 [DEBUG] sample(SAMPLE) svID(226 type=BND) unexpected JCN(est=0.0 unc=0.0)
  22:45:28.004 [DEBUG] sample(SAMPLE) svID(245 type=SGL) unexpected JCN(est=0.0 unc=0.0)
  22:45:28.004 [DEBUG] sample(SAMPLE) svID(253 type=SGL) unexpected JCN(est=0.0 unc=0.0)
  22:45:28.004 [DEBUG] sample(SAMPLE) svID(254 type=BND) unexpected JCN(est=0.0 unc=0.0)
  22:45:28.004 [DEBUG] sample(SAMPLE) svID(256 type=BND) unexpected JCN(est=0.0 unc=0.0)
  22:45:28.004 [DEBUG] sample(SAMPLE) svID(259 type=SGL) unexpected JCN(est=0.0 unc=0.0)
  22:45:28.004 [DEBUG] sample(SAMPLE) svID(267 type=SGL) unexpected JCN(est=0.0 unc=0.0)
  22:45:28.004 [DEBUG] sample(SAMPLE) svID(279 type=SGL) unexpected JCN(est=0.0 unc=0.0)
  22:45:28.004 [DEBUG] sample(SAMPLE) svID(285 type=BND) unexpected JCN(est=0.0 unc=0.0)
  22:45:28.005 [DEBUG] sample(SAMPLE) svID(286 type=BND) unexpected JCN(est=0.0 unc=0.0)
  22:45:28.005 [DEBUG] sample(SAMPLE) svID(310 type=SGL) unexpected JCN(est=0.0 unc=0.0)
  22:45:28.005 [DEBUG] sample(SAMPLE) svID(319 type=SGL) unexpected JCN(est=0.0 unc=0.0)
  22:45:28.005 [DEBUG] sample(SAMPLE) svID(333 type=SGL) unexpected JCN(est=0.0 unc=0.0)
  22:45:28.005 [DEBUG] sample(SAMPLE) svID(339 type=DEL) unexpected JCN(est=0.0 unc=0.0)
  22:45:28.005 [DEBUG] sample(SAMPLE) svID(346 type=BND) unexpected JCN(est=0.0 unc=0.0)
  22:45:28.006 [DEBUG] sample(SAMPLE) svID(356 type=BND) unexpected JCN(est=0.0 unc=0.0)
  22:45:28.006 [ERROR] thread exception: java.lang.NullPointerException: Cannot read field "CopyNumber" because "cnStartPrevData" is null
  java.lang.NullPointerException: Cannot read field "CopyNumber" because "cnStartPrevData" is null
  	at com.hartwig.hmftools.linx.cn.CnJcnCalcs.calculateAdjustedJcn(CnJcnCalcs.java:113)
  	at com.hartwig.hmftools.linx.cn.CnDataLoader.processSampleData(CnDataLoader.java:105)
  	at com.hartwig.hmftools.linx.cn.CnDataLoader.loadSampleData(CnDataLoader.java:91)
  	at com.hartwig.hmftools.linx.SampleAnalyser.processSample(SampleAnalyser.java:217)
  	at com.hartwig.hmftools.linx.SampleAnalyser.processSamples(SampleAnalyser.java:167)
  	at com.hartwig.hmftools.linx.LinxApplication.<init>(LinxApplication.java:145)
  	at com.hartwig.hmftools.linx.LinxApplication.main(LinxApplication.java:204)

I can send the log file to you by email or slack if that would help. Could you tell me where to send it?

Thanks a lot in advance! It would be great to get help with this as we feel a bit lost

fevac avatar Nov 25 '25 13:11 fevac

Thanks for the information, I'll get in contact with you on Slack to send the log file

scwatts avatar Nov 25 '25 22:11 scwatts

@scwatts I tested the same case on GRCh38 and completes without issues (everything else the same), so this seems related to the genome 37 version

fevac avatar Nov 28 '25 07:11 fevac