GFA reports contig with length 0

[SMorrison42]

Hi, I'm using Unicycler in my pipeline and using the gfa python package to parse the .gfa file unicycler produces to assist with assessment of the final assembly. I've noticed in a few of my .gfa files it will report a contig length 0 with no sequence. What is the parameter I should use to remove contig length 0 from the gfa report?

[mikeyweigand]

Here's a specific example, output from assembly of Illumina NovaSeq reads from monkeypox virus. Note segment 12 has no sequence (length = 0 bp).

cat L*A13.assembly.gfa | grep ^S | cut -f1,2,4,5 | column -t
S  1   LN:i:151789  dp:f:1.0
S  2   LN:i:14767   dp:f:0.9675450839707439
S  3   LN:i:11567   dp:f:0.959489622964646
S  4   LN:i:5777    dp:f:0.9215721186123447
S  5   LN:i:4676    dp:f:1.9657676335501226
S  6   LN:i:1624    dp:f:2.023590772062553
S  7   LN:i:268     dp:f:2.1558008320217863
S  8   LN:i:24      dp:f:1.6570576416128175
S  9   LN:i:16      dp:f:20.642039801793622
S  10  LN:i:9       dp:f:27.790311595329598
S  11  LN:i:2       dp:f:0.6247140887830516
S  12  LN:i:0       dp:f:0.7382984685617883

Yet the graph includes linkages between 12 and other segments:

cat L*A13.assembly.gfa | grep ^L | grep 12
L       12      +       8       +       0M
L       12      +       11      +       0M
L       11      +       12      +       0M
L       12      -       8       +       0M