output score is -1

[ShirleyLiu-BCH]

Dear Author,

thanks for the contribution on annotation of SVs, however I have exprericed a difficulty. when I run the test dataset with following command: ./svscore.pl -c whole_genome_SNVs.tsv.gz -e refGene.exons.bed.gz -f refGene.introns.bed.gz -i tests/stresstest.vcf -o sum -v span The annotation results are all -1. For example, 'SVSCORESUM=-1;SVSCORESUM_LEFT=-1;SVSCORESUM_RIGHT=-1 ' Could you help?

Shirley

[lganel]

Hi Shirley,

The first thing I notice is that -v should not take an argument. What happens if you remove span from the command you listed? There is no way to show only the SPAN scores, but if you run SVScore with -v, the SPAN scores will be retained and you can extract them with bcftools or similar.

Also, have you tried running the stress test using the testing script provided? That is, sh tests/test.sh path/to/whole_genome_SNVs.tsv.gz

Best,

Liron

[lganel]

I'm closing this issue since I haven't heard from you. Please feel free to reach out again if you have any other questions.

[gn5]

Hi, May I reopen this issue? I also get all -1 scores in the output vcf.
I have tried running the tests in tests/test.sh . The last 2 pass (I think) but the first one fails with a Segmentation fault:

Singularity>  $svscoredir/generateannotations.pl -c 1 -a 2 -b 3 -t 4 -s 5 -e 6 -f 7  -o $testdir $testdir/dummyannotations.bed 
# output bed `dummyannotations.exons.bed` and `dummyannotations.introns.bed` look ok, but then:

Singularity> $svscoredir/svscore.pl -f $testdir/dummyannotations.introns.bed -e $testdir/dummyannotations.exons.bed -o max,sum,top2,top2weighted,top3weighted,top4weighted,mean,meanweighted -dvc $testdir/dummyCADD.tsv.gz -i $testdir/stresstest.vcf > $testdir/stresstest.svscore.test.vcf

Writing config file
Preparing preprocessing command
Preprocessing command:
awk '$0~"^#" {print $0; next } { print $0 | "sort -k1,1V -k2,2n" }' /lustre/scratch119/humgen/projects/cnv_15x/svtools/results/svscore/gn5/tests/stresstest.vcf | bgzip -c > svscoretmp/stresstest1633958377.399.sort.vcf.gz; vcfanno -ends conf.toml svscoretmp/stresstest1633958377.399.sort.vcf.gz | perl /lustre/scratch119/realdata/mdt2/projects/cnv_15x/svtools/results/svscore/gn5/reorderheader.pl stdin /lustre/scratch119/humgen/projects/cnv_15x/svtools/results/svscore/gn5/tests/stresstest.vcf | svtools vcftobedpe > svscoretmp/stresstest1633958377.399.preprocess.bedpe

=============================================
vcfanno version 0.0.11-beta [built with devel +5ec87ba Thu Apr 28 15:36:34 2016 +0000]

see: https://github.com/brentp/vcfanno
=============================================
vcfanno.go:111: found 3 sources from 2 files
vcfanno.go:208: annotated 21 variants in 0.00 seconds (6639.0 / second)
Reading transcript list
Entering loop
Segmentation fault (core dumped)

This is using

vcfanno version 0.0.11-beta [built with devel +5ec87ba Thu Apr 28 15:36:34 2016 +0000]
SVScore version 0.6
svtools 0.5.1
bgzip (htslib) 1.13
perl 5, version 26, subversion 2 (v5.26.2) built for x86_64-linux-thread-multi

Running from a container I prepared: https://github.com/wtsi-hgi/svscore_container/blob/main/Dockerfile https://hub.docker.com/repository/docker/wtsihgi/svscore

Do you know what I could try to get rid of this error and -1 scores? Thank you,

Guillaume

[lganel]

Hi Guillaume,

Please open a separate issue. Getting scores of -1 is a somewhat general error, so your problem is probably separate from that in this issue.

Thanks,

Liron