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fritzsedlazeck / SURVIVOR_ant

A framework to annotate SVs with previous known SVs (vcf file) and or with genomic features (gff and or bed files)
MIT License
13 stars 2 forks source link

unknown error #11

Closed TendoLiu closed 4 years ago

TendoLiu commented 5 years ago

Code:

vcf1=Lumpy.vcf vcf2=Delly.vcf vcf3=Manta.vcf

$SurvivorPath/survivor_ant \

-o combined.vcf \ -l 20 \ -v $vcf3 $vcf2 $vcf1 \ -i $vcf1 \ -b $hg19_geneANT

Output: PARSE ERROR: Argument: Delly.vcf Couldn't find match for argument

The error info is two ambiguous to understand.

Thanks

TendoLiu commented 5 years ago

Use only required options $SurvivorPath/survivor_ant \

-i $vcf1

Running: INITIALIZE VCF: Parse VCF: 0 Parse BED: 0 Parse GFF: 0 PRint: start printing print entries

Error: Segmentation fault (core dumped)

fritzsedlazeck commented 5 years ago

can you open and read the delly.vcf or is it a compressed file?

fritzsedlazeck commented 5 years ago

and are these files in the directory you are executing it from ?

TendoLiu commented 5 years ago

`cd /bgfs/soesterreich/pan_data/soesterreich/Tendo/Projects/Project2_cfDNA_fusion_capture/Jobtest/SVcompare/VCFs hg19_geneANT=/bgfs/soesterreich/pan_data/soesterreich/Tendo/Projects/Project2_cfDNA_fusion_capture/module/RefenceFiles/hg19/UCSC_hg19_geneAnnotation SurvivorPath=/bgfs/soesterreich/pan_data/soesterreich/Tendo/Projects/Project2_cfDNA_fusion_capture/module/SVcompare/SURVIVOR_ant/bin/survivor_ant-core-0.1.0

vcf1=Lumpy.vcf vcf2=Delly.vcf vcf3=Manta.vcf

$SurvivorPath/survivor_ant \ -o combined.vcf \ -l 20 \ -v $vcf3 $vcf2 $vcf1 \ -i $vcf1 ` Yes. The vcf files are not compressed and they are in the working directory. I am executing survivor_ant from a different path.

Thanks, Tendo

TendoLiu commented 5 years ago

bash-4.2$ cd /bgfs/soesterreich/pan_data/soesterreich/Tendo/Projects/Project2_cfDNA_fusion_capture/Jobtest/SVcompare/VCFs bash-4.2$ ls Delly.vcf Lumpy.vcf Manta.vcf

Pretty sure the vcf files looks good. They are outputs from other well-known SV callers. Not even one of them could work. Any clues what could be the mistake?

Best wishes, Tendo