Comments (3)
AndreaGuarracino
commented on August 11, 2024
@ld9866, see #256, it could be related. Check the first lines of the DRB1-3123.fa.gz.f38ac34.alignments.wfmash.paf file and please let me know.
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ld9866
commented on August 11, 2024
Hello, l upload the first line here:
Look forward to receiving your reply!
gi|568815529:3998044-4011446 13403 0 13403 + gi|568815567:3779003-3792415 13413 0 13413 13402 13413 31 gi:f:99.9851 bi:f:99.918 md:f:99.9926 wt:i:13 pt:i:8 aa:i:1 ap:i:1 cg:Z:4896=10D6889=1X1617=
DRB1-3123.fa.gz.f38ac34.alignments.wfmash.zip
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AndreaGuarracino
commented on August 11, 2024
Hi @ld9866, the problem is that you are using the output of wfmash without adding -m as indicated in the tutorial here. However, I have just updated the paf2net script to support also this kind of PAF file, to avoid other users getting the same problem in the future. Therefore, you can either follow carefully the tutorial or update your paf2net script!
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Related Issues (20)
- empty VCF after running PanGenIe on the pggb assembly HOT 1
- GFA with no P lines HOT 5
- DRB1-3123 example not producing a nice graph anymore after `biwflambda` update. HOT 5
- PGGB use case with hexaploidy genomes HOT 1
- force reference output in VCF HOT 2
- Three chromosome take too long time HOT 16
- High heterogeneity in sequences identity HOT 2
- extracting node path-coverage information HOT 3
- wfmash -Y option HOT 3
- About the result study HOT 4
- Question about the example "scerevisiae7.fasta.gz " HOT 1
- Annotating the 1D pangenome graph visualisation with centromere coordinates
- Get the fasta file of non reference sequence
- [W::vcf_parse] Contig '2' is not defined in the header. (Quick workaround: index the file with tabix.) HOT 4
- PGGB get the fasta file of non reference sequence
- Building a graph from fragmented assemblies
- interoperability with vg - error:[vg::SmallSnarlSimplifier] Invalid graph on iteration 0 HOT 14
- Current Bioconda release does not find python scripts HOT 7
- Possible community detection bug HOT 5
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