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hartwigmedical / hmftools

Various algorithms for analysing genomics data
GNU General Public License v3.0
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cobalt targeted mode null pointer exception #512

Open briankegerreis opened 5 months ago

briankegerreis commented 5 months ago

Hello,

I tried to follow the instructions for targeted NGS here using amber 3.9.1 and cobalt 1.15.2. Unfortunately I'm getting a null pointer exception from the Normalisation step with little explanation. Would appreciate help diagnosing the issue.

Command:

java -cp /hmftools/cobalt_v1.15.2.jar com.hartwig.hmftools.cobalt.norm.NormalisationFileBuilder -sample_id_file sample_ids.csv -cobalt_dir cobalt/ -amber_dir amber/ -ref_genome_version V38 -gc_profile GC_profile.1000bp.38.cnp -target_regions_bed targets.bed -output_file norm_file.tsv

Stderr:

17:11:14.100 [main] [INFO ] - loaded 8 samples from file
17:11:14.102 [main] [INFO ] - loading GC profile: GC_profile.1000bp.38.cnp
17:11:16.086 [main] [INFO ] - running Cobalt normalisation file generation from 8 samples
17:11:16.551 [main] [INFO ] - loaded 226228 target regions from file(targets.bed)
Exception in thread "main" java.lang.NullPointerException
        at com.hartwig.hmftools.cobalt.norm.GcProfileCache.findGcProfile(GcProfileCache.java:51)
        at com.hartwig.hmftools.cobalt.norm.NormalisationFileBuilder.setGcProfileData(NormalisationFileBuilder.java:138)
        at com.hartwig.hmftools.cobalt.norm.NormalisationFileBuilder.run(NormalisationFileBuilder.java:60)
        at com.hartwig.hmftools.cobalt.norm.NormalisationFileBuilder.main(NormalisationFileBuilder.java:177)

There is nothing special about my target BED:

chr1    12080   12251
chr1    12595   12802
chr1    13163   13658
chr1    14620   15015
chr1    15795   15914
chr1    16743   17098
chr1    17247   18121
chr1    18216   18411
chr1    18963   19169
chr1    24260   24532
charlesshale commented 4 months ago

Could you repeat this routine using the latest Cobalt and Amber versions: https://github.com/hartwigmedical/hmftools/releases/tag/amber-v4.0 https://github.com/hartwigmedical/hmftools/releases/tag/cobalt-v1.16

and see if the issue persists. Thanks.

briankegerreis commented 4 months ago

I tried updating the tools but I'm still seeing the same error message. I also noticed -target_regions_bed has been added to the list of amber's options in the latest release and wasn't sure if that needed to be part of the process? But when I tried to pass it, it immediately failed: 10:28:29.569 [INFO ] Amber version 4.0 10:28:39.814 [ERROR] failed to load target regions file(): targets.bed