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VCF file empty when calling SV on ONT data #4279
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I'd suggest not using Others have had issues where GraphAligner does not write mapping qualities (you can check your GAM with
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after running this code for over 4 hours it is still an empty file. the first couple steps took only a fraction, but the vcf file stays empty |
I was also wondering how the vcf file is generated. Does the entire vcf have to be loaded into memory and is then pasted into the output file, or is it procedurally generated in the output? |
It outputs the VCF all at once at the end. |
Do you know what would be a good cutoff value be when looking in a mammalian genome? |
And what timeframe should I keep in mind for producing the VCF file, my gam file is 27.7 GB, the reads are 38.3 GB, my VG graph is 6.06 GB and contains 52.4 million nodes, 71.9 million edges and a total length of 2.7 billion. Thank! |
There's a |
Unfortunately the --progress option is not available for me in vg call, but I will try to run with gbz and see how that goes |
When trying to run with a gbz file, I encounter the following error, what could cause this? I am running the following code now: vg gbwt -G /minigraph_cactus/output_WG/output_WG.gfa -o output_WG.gbwt -d temp -p vg snarls -t 32 output_WG.gbz > mapped_LW.snarls vg call output_WG.gbz -z -t 32 -r mapped_LW.snarls -k mapped_LW.pack -C 100000 > mapped_C100000_LW_snarls_git.vcf vg: /private/groups/patenlab/jeizenga/GitHub/vg/include/sdsl/int_vector.hpp:1391: sdsl::int_vector< >::reference sdsl::int_vector< >::operator[](const size_type&) [with unsigned char t_width = 0; sdsl::int_vector< >::reference = sdsl::int_vector_reference<sdsl::int_vector<0> >; sdsl::int_vector< >::size_type = long unsigned int]: Assertion `idx < this->size()' failed. |
1. What were you trying to do?
calling structural variation after mapping long-read data on whole genome pangenome graph
2. What did you want to happen?
create a VCF file which contained the variants based on the reads
3. What actually happened?
The VCF file stays empty
4. If you got a line like
Stack trace path: /somewhere/on/your/computer/stacktrace.txt
, please copy-paste the contents of that file here:5. What data and command can the vg dev team use to make the problem happen?
reads were aligned with GraphAligner:
GraphAligner -t 32 -g whole_genome.gfa -f reads/LW1.fastq.gz -a mapped_LW.gam -x vg
And I wanted to call variants following the tutorial on https://github.com/vgteam/vg/wiki/SV-Genotyping-and-variant-calling
6. What does running
vg version
say?Hopefully you can assist me!
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