mismatched line lengths at line 3 within sequence

[Ahmad-40]

[vg autoindex] Executing command: vg autoindex --workflow giraffe -r /public/home/ahmad/outdir/in.fa.gz.bf3285f.11fba48.11fe66b.smooth.final.gfa -v /public/home/ahmad/outdir/in.fa.gz.bf3285f.11fba48.11fe66b.smooth.final.RAlphonso.vcf -p pangenome
[IndexRegistry]: Checking for phasing in VCF(s).
[IndexRegistry]: Chunking inputs for parallelism.
index file /public/home/ahmad//outdir/in.fa.gz.bf3285f.11fba48.11fe66b.smooth.final.gfa.fai not found, generating...
ERROR: mismatched line lengths at line 3 within sequence
File not suitable for fasta index generation. Note the GFA file was obtained as a result of pggb run ( partition-before-pggb -i /public/home/ahmad/pangen/in.fa.gz
-o /public/home/ahmad/outdir
-n 5
-t 15
-p 90
-s 5k
-V 'R:1000'). Here are more details of the file for consideration awk '{print length($0)}' /public/home/ahmad/outdir/in.fa.gz.bf3285f.11fba48.11fe66b.smooth.final.gfa
9
20
196
20
20
9
20
9
20
179
20
20
9
20
9
20
17
20
20
9
20
9
20
130
How to fix this issue?

[AndreaGuarracino]

@Ahmad-40, you are giving to vg autoindex -r a GFA file instead of a FASTA file!

vg autoindex
usage: vg autoindex [options]
options:
  output:
    -p, --prefix PREFIX    prefix to use for all output (default: index)
    -w, --workflow NAME    workflow to produce indexes for, can be provided multiple
                           times. options: map, mpmap, rpvg, giraffe (default: map)
  input data:
    -r, --ref-fasta FILE   FASTA file containing the reference sequence (may repeat)
...