ctg_cns.py fails

[Christian Dreischer]

Hi,

I run NextDenovo v2.4.0 on a diploid genome with ~ 100x PacBio CLR data.
Everything seems to run fine until /NextDenovo/lib/ctg_cns.py is executed.
The log file says "ctg_cns done", but folder "03.ctg_graph" contains no nd.asm.f.part*.fasta files and file "nd.asm.fasta" is empty.
When I execute NextDenovo/lib/ctg_cns.py -p 15 -g /01_run/03.ctg_graph/01.ctg_graph.sh.work/ctg_graph0/nd.asm.p.fasta -b /01_run/03.ctg_graph/01.ctg_graph.sh.work/ctg_graph0/nd.asm.p.fasta.blc -i 0 -r clr -l /01_run/03.ctg_graph/03.ctg_cns.input.bams -o nd.asm.f.part000.fasta manually, I get

Start a corrected worker in 611849 from parent 611848
Start a corrected worker in 611850 from parent 611848
Start a corrected worker in 611851 from parent 611848
Start a corrected worker in 611852 from parent 611848

and an empty "nd.asm.f.part000.fasta" file. The process ends immediately.
I was wondering about the "genome file" "01_run/03.ctg_graph/01.ctg_graph.sh.work/ctg_graph0/nd.asm.p.fasta " as it is no fasta file but rather graphml. I run NextDenvo with nextgraph_options = -a 2

?xml version="1.0" encoding="UTF-8"?>
graphml xmlns="http://graphml.graphdrawing.org/xmlns">
key attr.name="l" attr.type="int" for="edge" id="e0"/>
key attr.name="ide" attr.type="int" for="edge" id="e1"/>
key attr.name="len" attr.type="int" for="edge" id="e4"/>
key attr.name="sco" attr.type="int" for="edge" id="e5"/>
key attr.name="nodeid" attr.type="int" for="node" id="n0"/>
key attr.name="revnodeid" attr.type="int" for="node" id="n1"/>
graph edgedefault="directed">
node id="7127384.b">
data key="n0">3
data key="n1">4
/node>

File "nd.asm.p.fasta" in folder "01.ctg_graph.sh.work/ctg_graph0" also seems to be a graphml file. File nd.asm.p.fasta.blc is empty.

Can you make sense of this?

Thanks
Chris