vg chunk failed: GBWT::load(): Invalid heade

[gaochenx]

hi

When I apply the web version of sequenceTubeMap, I get the following error

Unexpected token '<', "<!DOCTYPE "... is not valid JSON

This is my process for building xg files

vg construct -t 40 -a -f -S -v ndex.recode.vcf.gz -r index.fa > index.vg vg index -t 20 -L -x index.xg index.vg

thank

[gaochenx]

https://github.com/vgteam/sequenceTubeMap/issues/277#issuecomment-1662576956 The problems we are facing now are the same as those in 227#.

I tried to process my file using the example process to get x.vg.xg, x.vg.gbwt.

But there is still an error. I checked the VCF file. I found that my file was not phased.

The reason is that some individuals are in a state of deletion of some SNPs. Will phasing affect the results? If it is necessary to phase, how to represent the missing part of this section?

vg chunk failed: GBWT::load(): Invalid header: GBWT v5: 1136 sequences of total length 3911026, alphabet size 55546 with offset 1 terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc ERROR: Signal 6 occurred. VG has crashed. Visit https://github.com/vgteam/vg/issues/new/choose to report a bug. Stack trace path: /tmp/vg_crash_gqziDA/stacktrace.txt Please include the stack trace file in your bug report

thank

[gaochenx]

I tried it and uploading only XG file is normal. That is, there is a problem with the GBWT file.

So I tried to determine if it was a problem with the phasing, I removed all rows with missing values.

There was still an error.

Then I compared the x.vcf.gz file with my file and changed 0 to 0|0, but there is still an error.

I'm considering whether there might be a problem with the scripts provided in the pipeline. vg index "${1}" -v "${1%.vg}.vcf.gz" -x "${1}.xg" --gbwt-name "${1}.gbwt"

So I changed the command to the following: vg construct -a -r 68M.fa -v 11.recode.vcf.gz >x.vg vg index x.vg -x x.vg.xg vg autoindex --workflow giraffe --prefix x --ref-fasta 68M.fa --vcf 11.recode.vcf.gz --threads 20 vg gbwt -o x.gbwt -g x.gg -Z x.giraffe.gbz

There was still an error.

I'm now unsure of the cause of the issue. Would you mind helping me?