thread 'main' panicked at src/graph.rs:83:42:

[melisphdassociation]

Hi, I am trying to run prune_graph but I keep getting this error:

thread 'main' panicked at src/graph.rs:83:42:
cannot convert weight to float32: ParseFloatError { kind: Invalid }
note: run with `RUST_BACKTRACE=1` environment variable to display a backtrace

the command I used was

./target/release/prune_graph --header --in /home/mar/Documents/BonoboData/Inbreeding/Kokolopori_1x_downsampled_LD_newhead_bis.tsv --weight-field "r2" --weight-filter "dist <= 50000 && r2 >= 0.5" --out /home/mar/Documents/BonoboData/Inbreeding/Kokolopori_1x_downsampled_LD_unlinked.pos` and the input file is as seen below (lines 1-24).

site1	site2	dist	r2_ExpG	D	Dp	r2
chr21:13785523	chr21:13799870	14347	0	0	0	0
chr21:13785523	chr21:13799915	14392	0	0	0	0
chr21:13785523	chr21:13799945	14422	0	0	0	0
chr21:13785523	chr21:13799988	14465	0	0	0	0
chr21:13785523	chr21:13799992	14469	0	0	0	0
chr21:13785523	chr21:13799996	14473	0	0	0	0
chr21:13785523	chr21:13800009	14486	0	0	0	0
chr21:13785523	chr21:13800144	14621	0	0	0	0
chr21:13785523	chr21:13802726	17203	0.03762	0.105886	0.776129	0.223409
chr21:13785523	chr21:13802786	17263	0.20032	-0.186449	0.999537	0.865239
chr21:13785523	chr21:13802812	17289	0.022677	0.111929	0.76928	0.231784
chr21:13785523	chr21:13802852	17329	0.151713	0.138231	0.998166	0.439489
chr21:13785523	chr21:13802857	17334	0.024137	0.090714	0.780818	0.176644
chr21:13785523	chr21:13802866	17343	0.027376	0.072083	0.788954	0.134132
chr21:13785523	chr21:13802930	17407	0.200779	0.072818	0.999981	0.208974
chr21:13785523	chr21:13802944	17421	0.163352	0.078977	0.999959	0.228885
chr21:13785523	chr21:13802956	17433	0.174431	0.091935	0.999857	0.271932
chr21:13785523	chr21:13802979	17456	0.089505	0.096086	0.99903	0.284794
chr21:13785523	chr21:13803035	17512	0.033045	-0.10633	0.626227	0.199608
chr21:13785523	chr21:13803279	17756	0	0	0	0
chr21:13785523	chr21:13803280	17757	0	0	0	0
chr21:13785523	chr21:13803320	17797	0.000878	0.03711	0.270725	0.027265
chr21:13785523	chr21:13803337	17814	0,0007	0.028775	0.299227	0.021042

Would you be able to help me with this issue? I thought it might be the header but it doesn't seem to be the problem.
Thank you in advance

[fgvieira]

The error message means that there is a weight (r2) with a value that cannot be converted to a float32

Is that your full file? If not, are there any values on the column r2 that might be invalid?

[melisphdassociation]

Hello, in the end we managed to run the python script from ngsLD to do the pruning and it worked! Thanks anyway :)

[fgvieira]

If you have time, it would still be nice to know what was that could not be converted to a float32.
It is just so I can fix it and avoid future issues with other users.

[fgvieira]

@melisphdassociation did you manage to find the r2 value that was giving the error?