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dnanexus-rnd / GLnexus

Scalable gVCF merging and joint variant calling for population sequencing projects
Apache License 2.0
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Invalid: BCFKeyValueData::import_gvcf:invalid data set name #272

Open aguygarner opened 3 years ago

aguygarner commented 3 years ago

I am running into an error whet trying to merge my .g.vcf.gz files outpiut from PEPPER for long read data. I am running the command as follows but get the resulting error for my run. Just wondering if you have any advice.

singularity exec --bind /usr/lib/locale/ glnexus_v1.4.1.sif glnexus_cli \ --config DeepVariant \ --threads 10 \ --bed contig_81883.coord.bed \ *.g.vcf.gz > Test.contig81883.PEPPER.joint.bcf

[8781] [2021-11-15 21:58:40.154] [GLnexus] [error] Samplix.678_03_01.R2R3Myb.Guppyv.5.0.1.NF_L500_Q10.minimap2.mapont.noMD.phlox_flye.curated.medaka.v1.sorted.pepper_contig_81883.rename.g.vcf.gz Invalid: BCFKeyValueData::import_gvcf: invalid data set name (Samplix.678_03_01.R2R3Myb.Guppyv.5.0.1.NF_L500_Q10.minimap2.mapont.noMD.phlox_flye.curated.medaka.v1.sorted.pepper_contig_81883.rename) [8781] [2021-11-15 21:58:40.154] [GLnexus] [error] Samplix.678_08_07.R2R3Myb.Guppyv.5.0.1.NF_L500_Q10.minimap2.mapont.noMD.phlox_flye.curated.medaka.v1.sorted.pepper_contig_81883.rename.g.vcf.gz Invalid: BCFKeyValueData::import_gvcf: invalid data set name (Samplix.678_08_07.R2R3Myb.Guppyv.5.0.1.NF_L500_Q10.minimap2.mapont.noMD.phlox_flye.curated.medaka.v1.sorted.pepper_contig_81883.rename)