Entering edit mode
3.3 years ago
evafinegan
•
0
Hello All,
I am using pangenome graph builder
to align multiple genomes and create make a graph genome using:
pggb -i input.fasta.gz -w 100000 -s 20000 -p 120 -a 70 -n 5 -t 16 -v -l output
It runs the alignment step and generates corresponding PAF
output file. However, in the seqwish
step, it gives this error:
Passed in argument, but no positional arguments were ready to receive it: 8
seqwish {OPTIONS}
seqwish: a variation graph inducer
OPTIONS:
-h, --help display this help menu
-a[FILE], --sxs-alns=[FILE] induce the graph from these .sxs
formatted alignments
-p[FILE], --paf-alns=[FILE] induce the graph from these PAF
formatted alignments
-s[FILE], --seqs=[FILE] the sequences used to generate the
alignments (FASTA, FASTQ, .seq)
-b[BASE], --base=[BASE] build graph using this basename
-g[FILE], --gfa=[FILE] write the graph in GFA to FILE
-m[FILE], --match-list=[FILE] use the sequence match list in FILE to
subset the input alignments
-o[BASE], --vgp-out=[BASE] write the graph in VGP format with
basename FILE
-t[N], --threads=[N] use this many threads during parallel
steps
-r[N], --repeat-max=[N] limit transitive closure to include no
more than N copies of a given input base
-k, --keep-temp keep intermediate files generated during
graph induction
-d, --debug enable debugging
seqwish -t 16 -s input.fasta.gz -p input.paf -k 8 -g input.gfa -B 1000000 -P
It is not recognizing options -k -B -P
and I did give these options in the command line. I think it is automatically coming with some other parameter. I am not sure how to avoid these parameters. Thank you for any help!