*ks.svg figure is empty

[shiyi-pan]

hi, I run the WGD using format.SoyC09.CDS.fasta and ormat.SoyC09.gff as my input file,here is my code:

wgd mcl -n 8 --cds --mcl -s format.SoyC09.CDS.fasta -o SoyC09.CDS.out
wgd ksd --n_threads 8 --pairwise SoyC09.CDS.out/format.SoyC09.CDS.fasta.blast.tsv.mcl format.SoyC09.CDS.fasta
wgd syn format.SoyC09.gff format.SoyC09.CDS.fasta
wgd kde wgd_ksd/format.SoyC09.CDS.fasta.ks.tsv
wgd mix wgd_ksd/format.SoyC09.CDS.fasta.ks.tsv

I don't find errors in log but the output figures like ks.svg and dotplot.svg are empty. coud't you help me fix this problem？
here is my input file and log file.
cds.zip
format.SoyC09.CDS.fasta.ks.zip
gff.zip
log.txt

[arzwa]

Does the tsv output file with the Ks distribution look fine? If so I would guess it's something with the plotting libraries in your python installation or so. You can always make a plot yourself using R or python or whatever you are familiar with. You can also try wgd viz to further debug what's going wrong.

[shiyi-pan]

thank you for your reply.
first, I have run WGD with the test data named Sspon.v20190103 and it works well,so I don't think it's the plotting libraries problem.
second , I couldn't find any abnormal in tsv output file and here is my tsv output file:
format.SoyC09.CDS.fasta.ks.tsv.zip
thank you again.

[arzwa]

I can't tell what went wrong for you. If I run

wgd viz -ks format.SoyC09.CDS.fasta.ks.tsv

I get a perfectly fine histogram (wgd_hist.svg).

[shiyi-pan]

thank you very much. This is so weird. when I run wgd with the test data,it works well ,here is the commoda and log:

wgd viz -ks ./wgd_syn/Sspon.v20190103.cds.fasta.blast.tsv.mcl.ks_anchors.tsv

2021-03-22 15:08:47: INFO Plotting Ks distributions overlay
2021-03-22 15:08:47: INFO Will plot node-averaged histograms

but when using my data, I got an error, here is the commoda and log:

wgd viz -ks /ds3512/home/panyp/NN1138-2/04.WGD_data/wgd_ksd/format.final.cds.fa.ks.tsv

2021-03-22 15:06:50: INFO Not a Ks distribution: /ds3512/home/panyp/NN1138-2/04.WGD_data/wgd_ksd/format.final.cds.fa.ks.tsv
2021-03-22 15:06:50: INFO Plotting Ks distributions overlay
Traceback (most recent call last):
File "/ds3512/home/panyp/ruanjian/python3/bin/wgd", line 11, in
load_entry_point('wgd==1.2', 'console_scripts', 'wgd')()
File "/ds3512/home/panyp/ruanjian/python3/lib/python3.6/site-packages/click/core.py", line 764, in call
return self.main(*args, **kwargs)
File "/ds3512/home/panyp/ruanjian/python3/lib/python3.6/site-packages/click/core.py", line 717, in main
rv = self.invoke(ctx)
File "/ds3512/home/panyp/ruanjian/python3/lib/python3.6/site-packages/click/core.py", line 1137, in invoke
return process_result(sub_ctx.command.invoke(sub_ctx))
File "/ds3512/home/panyp/ruanjian/python3/lib/python3.6/site-packages/click/core.py", line 956, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/ds3512/home/panyp/ruanjian/python3/lib/python3.6/site-packages/click/core.py", line 555, in invoke
return callback(*args, **kwargs)
File "/ds3512/home/panyp/ruanjian/python3/lib/python3.6/site-packages/wgd-1.2-py3.6.egg/wgd_cli.py", line 1286, in viz
File "/ds3512/home/panyp/ruanjian/python3/lib/python3.6/site-packages/wgd-1.2-py3.6.egg/wgd_cli.py", line 1378, in viz
File "/ds3512/home/panyp/ruanjian/python3/lib/python3.6/site-packages/wgd-1.2-py3.6.egg/wgd/viz.py", line 136, in plot_selection
File "/ds3512/home/panyp/ruanjian/python3/lib/python3.6/site-packages/wgd-1.2-py3.6.egg/wgd/viz.py", line 69, in plot_dists
File "/ds3512/home/panyp/ruanjian/python3/lib/python3.6/site-packages/numpy/core/shape_base.py", line 340, in hstack
return _nx.concatenate(arrs, 1)

could you give me some advise to fix it? thank you again .

[arzwa]

You did not send me the Sspon.v20190103.cds.fasta.blast.tsv.mcl.ks_anchors.tsv file. Are you sure the file looks as expected? You might have some issues in your wgd syn command leading to a failure to detect synteny... make sure to set the -a and -f options correctly to mark the correspondence between your cds and gff files.

[shiyi-pan]

I'm sorry I didn't notice this answer early. When I run the WGD using Sspon.v20190103 CDS and GFF file, it works well. But when I run it in my gff file and CDS file , it run wrong, So i didn't upload the Sspon.v20190103.cds.fasta.blast.tsv.mcl.ks_anchors.tsv file. I upload my CDS and GFF data and ks file and log file , I couldn't find any problem, could you help me check these files ? thank you very much.