Wrong setting of POA, but it still finish without error

[baozg]

Hi,

I wrong set -P with an empty variable and it was passed with -O. The command was -P $POA -O 0.001, but the $POA is en empty variable. It could finish without any errors. What does this take into the pggb? Is still using the asm5?

smoothxg:
  version:            v0.7.0-18-g4ff4cf2
  skip-normalization: false
  n-haps:             61
  path-jump-max:      0
  edge-jump-max:      0
  poa-length-target:  700,900,1100
  poa-params:         -O
  poa_padding:        0.001
  run_abpoa:          false
  run_global_poa:     false
  pad-max-depth:      100
  write-maf:          false
  consensus-spec:     false
  consensus-prefix:   Consensus_
  block-id-min:       .9000
  block-ratio-min:    0

[AndreaGuarracino]

Can you provide the your.log file of such a run?

[baozg]

smoothxg -t 128 -T 128 -g /data/chr2_p90.s10000.n61.k47.G700-900-1100.DM/chr2.fa.gz.47c7dfd.e34d4cd.seqwish.gfa -r 61 --base /data/chr2_p90.s10000.n61.k47.G700-900-1100.DM --chop-to 100 -I .9000 -R 0 -j 0 -e 0 -l 700,900,1100 -P -O -O 0.001 -Y 6100 -d 0 -D 0 -Q Consensus_ -V -o /data/chr2_p90.s10000.n61.k47.G700-900-1100.DM/chr2.fa.gz.47c7dfd.e34d4cd.98ebc75.smooth.gfa

[AndreaGuarracino]

smoothxg would go with the following parameters for the POA:

poa_m 1
poa_n 4
poa_g 6
poa_e 2
poa_q 26
poa_c 1

equivalent to -P asm20.

[baozg]

Thanks a lot. It exactly meet with my dataset.