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vg chunk failed: GBWT::load(): Invalid heade #347
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#277 (comment) 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 |
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. So I changed the command to the following: There was still an error. I'm now unsure of the cause of the issue. Would you mind helping me? |
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
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