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freqQuad empty #81

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RhettRautsaw opened this issue Jan 20, 2022 · 1 comment
Open

freqQuad empty #81

RhettRautsaw opened this issue Jan 20, 2022 · 1 comment

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@RhettRautsaw
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Describe the bug & to reproduce
When running -t 16 or -t 32, ASTRAL appears to complete but freqQuad.csv is completely empty. The only error reported is:

Final quartet score is: won't report because of the existense of polytomies and to save time. To get the score run with -t 1 and you can score the tree below using -q. 
Final normalized quartet score is: won't report because of the existense of polytomies and to save time. To get the score run with -t 1 and you can score the tree below using -q. 

However -t 1 works perfectly in calculating the Final quartet score and normalized quartet score.

Log file

java  -Xmx62000M -D"java.library.path=/zfs/venom/Rhett/bin/ASTRAL-MP/lib/" -jar /zfs/venom/Rhett/bin/ASTRAL-MP/astral.5.15.4.jar -q astral-spp2_reroot_scored_t1.tre -t 16 -i ../../01_concat/genetrees/03_genetrees-pruned.tre -o astral-spp2_reroot_scored_t16.tre -C -T 16 -a astral-spp.mapfile2


================== ASTRAL ===================== 

This is ASTRAL version 5.15.4
Using native AVX batch computing.
Gene trees are treated as unrooted
Starting 16 threads ...
There are 16 threads used to run.
2241 trees read from ../../01_concat/genetrees/03_genetrees-pruned.tre
Scoring astral-spp2_reroot_scored_t1.tre
Scoring: 1 trees
Number of taxa: 1630 (237 species)
Taxa: {...removed for brevity...}
Taxon occupancy: {...removed for brevity...}
Using polytree-based weight calculation.
Number of gene trees: 2241
2241 trees have missing taxa
Polytree max score: 68316964818978
Polytree building time: 7.804 seconds.
Using native AVX batch computing method.
Counting unresolvable quartets ... 87151231408
Number of quartet trees in the gene trees: 68229813587570
Final quartet score is: won't report because of the existense of polytomies and to save time. To get the score run with -t 1 and you can score the tree below using -q. 
Final normalized quartet score is: won't report because of the existense of polytomies and to save time. To get the score run with -t 1 and you can score the tree below using -q. 
You may want to ignore posterior probabilities and other statistics related to the following branch branch because the effective number of genes impacting it is only 10:
	{Vipera_kaznakovi, Vipera_dinniki}
You may want to ignore posterior probabilities and other statistics related to the following branch branch because the effective number of genes impacting it is only 11:
	{Vipera_kaznakovi}
You may want to ignore posterior probabilities and other statistics related to the following branch branch because the effective number of genes impacting it is only 11:
	{Vipera_dinniki}
(Anolis_carolinensis,((Ascyt-I1310_SeqCap_unknown_h1,Ascyt-I1310_SeqCap_unknown_h0)N0'[pp1=1;pp2=0;pp3=0]':3.467881576164574,((Python_molurus,((Ecras-I7463_SeqCap_unknown_h1,Ecras-I7463_SeqCap_unknown_h0)N1'[pp1=1;pp2=0;pp3=0]':3.2756642127855957...remainder of tree removed for brevity...;
Scored tree with gene names:
(Anolis_carolinensis,((Ascyt-I1310_SeqCap_unknown_h1,Ascyt-I1310_SeqCap_unknown_h0)N0'[pp1=1;pp2=0;pp3=0]':3.467881576164574,((Python_molurus,((Ecras-I7463_SeqCap_unknown_h1,Ecras-I7463_SeqCap_unknown_h0)N1'[pp1=1;pp2=0;pp3=0]':3.2756642127855957...remainder of tree removed for brevity...;
ASTRAL finished in 74.831 secs
Shutting down threading

** This is ASTRAL version 5.15.4

@smirarab
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smirarab commented Apr 7, 2023

Can you try version 5.7.8? Or is that too slow?

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