I ran "wgd dmd" and "wgd ksd" before and everything worked fine, but running "wgd syn" failed,
wgd syn -o PeniCBMAcds.syn -ks PeniCBMAcds.ksd/PeniCBMAcds.fasta.ks.tsv -f mRNA -a ID PeniCBMAcds.gff PeniCBMAcds.dmd/PeniCBMAcds.fasta.mcl
this is the error content：
(wgd) yu123@yu123-PC:~/Desktop/T7wgd/ceshi$ wgd syn -o PeniCBMAcds.syn -ks PeniCBMAcds.ksd/PeniCBMAcds.fasta.ks.tsv -f mRNA -a ID PeniCBMAcds.gff PeniCBMAcds.dmd/PeniCBMAcds.fasta.mcl
2024-10-17 20:47:57: INFO i-adhore stdout: This is i-ADHoRe v3.0.
Copyright (c) 2002-2010, Flanders Interuniversity Institute for Biotechnology, VIB.
Algorithm designed by Klaas Vandepoele, Cedric Simillion, Jan Fostier, Dieter De Witte,
Koen Janssens, Sebastian Proost, Yvan Saeys and Yves Van de Peer.
Process 1/1 is alive on yu123-PC.
2024-10-17 20:47:57: INFO i-adhore stderr: Error opening the settings file: -version
2024-10-17 20:47:57: INFO Made output directory PeniCBMAcds.syn
2024-10-17 20:47:57: INFO Parsing GFF file
2024-10-17 20:47:58: INFO Writing gene lists
2024-10-17 20:47:58: INFO Writing families file
2024-10-17 20:47:58: INFO Writing configuration file
2024-10-17 20:47:58: INFO Running I-ADHoRe 3.0
2024-10-17 20:48:01: WARNING WARNING: Maximum allowed number of gaps in the alignment not specified. Setting to cluster_gap.
WARNING: Tandem gap size not correct in settings file. Using default (gap_size / 2)
2024-10-17 20:48:01: INFO
This is i-ADHoRe v3.0.
Copyright (c) 2002-2010, Flanders Interuniversity Institute for Biotechnology, VIB.
Algorithm designed by Klaas Vandepoele, Cedric Simillion, Jan Fostier, Dieter De Witte,
Koen Janssens, Sebastian Proost, Yvan Saeys and Yves Van de Peer.
Process 1/1 is alive on yu123-PC.
i-ADHoRe parameters
Number of genelists = 749
Blast table = PeniCBMAcds.syn/families.tsv
Output path = PeniCBMAcds.syn/i-adhore-out/
Gap size = 30
Cluster gap size = 35
Cloud gap size = 0
Cloud cluster gap size = 0
Max gaps in alignment = 35
Tandem gap = 15
Flush output = 1000
Q-value = 0.75
Anchorpoints = 3
Probability cutoff = 0.01
Cloud filtering method = Binomial
Level 2 only = false
Use family = true
Write statistics = false
Alignment method = GreedyGraphbased4
Multiple hypothesis correction = FDR
Number of threads = 1
Compare aligners = false
Collinear searches only
Visualize GHM.png = false
Visualize Alignment = true
Verbose output = true
**** END i-AdDHoRe parameters *****
Creating dataset... done. (time: 0.00943708s)
Mapping gene families... done. (time: 0.010159s)
Remapping tandem duplicates... done. (time: 0.006392s)
Writing genelists file... done. (time: 0.042654s)
Collinear Search
Level 2 multiplicon detection... done. (time: 2.20706s)
Profile detection...
140 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found.
139 multiplicons to evaluate - evaluating level 2 multiplicon... 3 new multiplicons found.
141 multiplicons to evaluate - evaluating level 3 multiplicon... 0 new multiplicons found.
140 multiplicons to evaluate - evaluating level 3 multiplicon... 0 new multiplicons found.
139 multiplicons to evaluate - evaluating level 3 multiplicon... 0 new multiplicons found.
138 multiplicons to evaluate - evaluating level 2 multiplicon... 5 new multiplicons found.
142 multiplicons to evaluate - evaluating level 3 multiplicon... 5 new multiplicons found.
146 multiplicons to evaluate - evaluating level 4 multiplicon... 1 new multiplicons found.
146 multiplicons to evaluate - evaluating level 5 multiplicon... too few aligned homologs
145 multiplicons to evaluate - evaluating level 4 multiplicon... 3 new multiplicons found.
147 multiplicons to evaluate - evaluating level 5 multiplicon... 0 new multiplicons found.
146 multiplicons to evaluate - evaluating level 5 multiplicon... 0 new multiplicons found.
145 multiplicons to evaluate - evaluating level 5 multiplicon... 0 new multiplicons found.
144 multiplicons to evaluate - evaluating level 4 multiplicon... all elements masked
143 multiplicons to evaluate - evaluating level 4 multiplicon... all elements masked
142 multiplicons to evaluate - evaluating level 4 multiplicon... all elements masked
141 multiplicons to evaluate - evaluating level 3 multiplicon... all elements masked
140 multiplicons to evaluate - evaluating level 3 multiplicon... all elements masked
139 multiplicons to evaluate - evaluating level 3 multiplicon... all elements masked
138 multiplicons to evaluate - evaluating level 3 multiplicon... all elements masked
137 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant
136 multiplicons to evaluate - evaluating level 2 multiplicon... 5 new multiplicons found.
140 multiplicons to evaluate - evaluating level 3 multiplicon... 1 new multiplicons found.
140 multiplicons to evaluate - evaluating level 4 multiplicon... 3 new multiplicons found.
142 multiplicons to evaluate - evaluating level 5 multiplicon... 2 new multiplicons found.
143 multiplicons to evaluate - evaluating level 6 multiplicon... 2 new multiplicons found.
144 multiplicons to evaluate - evaluating level 7 multiplicon... 1 new multiplicons found.
144 multiplicons to evaluate - evaluating level 8 multiplicon... 0 new multiplicons found.
143 multiplicons to evaluate - evaluating level 7 multiplicon... all elements masked
142 multiplicons to evaluate - evaluating level 6 multiplicon... all elements masked
141 multiplicons to evaluate - evaluating level 5 multiplicon... all elements masked
140 multiplicons to evaluate - evaluating level 5 multiplicon... all elements masked
139 multiplicons to evaluate - evaluating level 3 multiplicon... 0 new multiplicons found.
138 multiplicons to evaluate - evaluating level 3 multiplicon... all elements masked
137 multiplicons to evaluate - evaluating level 3 multiplicon... all elements masked
136 multiplicons to evaluate - evaluating level 3 multiplicon... all elements masked
135 multiplicons to evaluate - evaluating level 2 multiplicon... 1 new multiplicons found.
135 multiplicons to evaluate - evaluating level 3 multiplicon... 0 new multiplicons found.
134 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant
133 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant
132 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found.
131 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found.
130 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant
129 multiplicons to evaluate - evaluating level 2 multiplicon... 2 new multiplicons found.
130 multiplicons to evaluate - evaluating level 3 multiplicon... 1 new multiplicons found.
130 multiplicons to evaluate - evaluating level 4 multiplicon... 0 new multiplicons found.
129 multiplicons to evaluate - evaluating level 3 multiplicon... all elements masked
128 multiplicons to evaluate - evaluating level 2 multiplicon... 1 new multiplicons found.
128 multiplicons to evaluate - evaluating level 3 multiplicon... 0 new multiplicons found.
127 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant
126 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found.
125 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found.
124 multiplicons to evaluate - evaluating level 2 multiplicon... 1 new multiplicons found.
124 multiplicons to evaluate - evaluating level 3 multiplicon... 0 new multiplicons found.
123 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant
122 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant
121 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant
120 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found.
119 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant
118 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant
117 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant
116 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant
115 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found.
114 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant
113 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant
112 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant
111 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant
110 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant
109 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found.
108 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found.
107 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant
106 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found.
105 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found.
104 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant
103 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant
102 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant
101 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found.
100 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant
99 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant
98 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant
97 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant
96 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found.
95 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found.
94 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found.
93 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found.
92 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant
91 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant
90 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant
89 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant
88 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant
87 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant
86 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant
85 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant
84 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found.
83 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found.
82 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant
81 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found.
80 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found.
79 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant
78 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant
77 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found.
76 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant
75 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant
74 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant
73 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found.
72 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant
71 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found.
70 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant
69 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found.
68 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant
67 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found.
66 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found.
65 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found.
64 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found.
63 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found.
62 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant
61 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found.
60 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found.
59 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found.
58 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant
57 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant
56 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant
55 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant
54 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found.
53 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant
52 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found.
51 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant
50 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant
49 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant
48 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found.
47 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant
46 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant
45 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant
44 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant
43 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found.
42 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant
41 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found.
40 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant
39 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant
38 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant
37 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant
36 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant
35 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant
34 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant
33 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant
32 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant
31 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant
30 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant
29 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant
28 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant
27 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant
26 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found.
25 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found.
24 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found.
23 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant
22 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found.
21 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant
20 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found.
19 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant
18 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant
17 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant
16 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found.
15 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant
14 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant
13 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant
12 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found.
11 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found.
10 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant
9 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant
8 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant
7 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found.
6 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found.
5 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant
4 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found.
3 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found.
2 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found.
1 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found.
Flushing output files...Visualize AlignedProfiles
done.
Time for Higher Level Detection: 0.261017s.
All Done! Bye...
2024-10-17 20:48:01: INFO Drawing co-linearity dotplot
/home/yu123/.local/lib/python3.6/site-packages/wgd/viz.py:223: UserWarning: Attempting to set identical left == right == 0 results in singular transformations; automatically expanding.
ax.set_xlim(0, max(x))
/home/yu123/.local/lib/python3.6/site-packages/wgd/viz.py:224: UserWarning: Attempting to set identical bottom == top == 0 results in singular transformations; automatically expanding.
ax.set_ylim(0, max(x))
Traceback (most recent call last):
File "/home/yu123/.local/bin/wgd", line 8, in
sys.exit(cli())
File "/home/yu123/.local/lib/python3.6/site-packages/click/core.py", line 1128, in call
return self.main(args, kwargs)
File "/home/yu123/.local/lib/python3.6/site-packages/click/core.py", line 1053, in main
rv = self.invoke(ctx)
File "/home/yu123/.local/lib/python3.6/site-packages/click/core.py", line 1659, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/yu123/.local/lib/python3.6/site-packages/click/core.py", line 1395, in invoke
return ctx.invoke(self.callback, ctx.params)
File "/home/yu123/.local/lib/python3.6/site-packages/click/core.py", line 754, in invoke
return __callback(args, kwargs)
File "/home/yu123/.local/lib/python3.6/site-packages/wgd_cli.py", line 857, in syn
gene_attribute, min_length, ks_range, iadhore_opts
File "/home/yu123/.local/lib/python3.6/site-packages/wgdcli.py", line 949, in syn
'{}.dotplot.svg'.format(os.path.basename(families)))
File "/home/yu123/.local/lib/python3.6/site-packages/wgd/viz.py", line 244, in syntenic_dotplot
[row['begin_x'], row['end_x']]]
File "/home/yu123/.local/lib/python3.6/site-packages/wgd/viz.py", line 243, in
x = [genomic_elements[curr_list_x] + x for x in
KeyError: 94.0
arzwa
commented
2 hours ago
I ran "wgd dmd" and "wgd ksd" before and everything worked fine, but running "wgd syn" failed, wgd syn -o PeniCBMAcds.syn -ks PeniCBMAcds.ksd/PeniCBMAcds.fasta.ks.tsv -f mRNA -a ID PeniCBMAcds.gff PeniCBMAcds.dmd/PeniCBMAcds.fasta.mcl this is the error content： (wgd) yu123@yu123-PC:~/Desktop/T7wgd/ceshi$ wgd syn -o PeniCBMAcds.syn -ks PeniCBMAcds.ksd/PeniCBMAcds.fasta.ks.tsv -f mRNA -a ID PeniCBMAcds.gff PeniCBMAcds.dmd/PeniCBMAcds.fasta.mcl
2024-10-17 20:47:57: INFO i-adhore stdout: This is i-ADHoRe v3.0. Copyright (c) 2002-2010, Flanders Interuniversity Institute for Biotechnology, VIB. Algorithm designed by Klaas Vandepoele, Cedric Simillion, Jan Fostier, Dieter De Witte, Koen Janssens, Sebastian Proost, Yvan Saeys and Yves Van de Peer.
Process 1/1 is alive on yu123-PC. 2024-10-17 20:47:57: INFO i-adhore stderr: Error opening the settings file: -version 2024-10-17 20:47:57: INFO Made output directory PeniCBMAcds.syn 2024-10-17 20:47:57: INFO Parsing GFF file 2024-10-17 20:47:58: INFO Writing gene lists 2024-10-17 20:47:58: INFO Writing families file 2024-10-17 20:47:58: INFO Writing configuration file 2024-10-17 20:47:58: INFO Running I-ADHoRe 3.0 2024-10-17 20:48:01: WARNING WARNING: Maximum allowed number of gaps in the alignment not specified. Setting to cluster_gap.
WARNING: Tandem gap size not correct in settings file. Using default (gap_size / 2)
2024-10-17 20:48:01: INFO This is i-ADHoRe v3.0. Copyright (c) 2002-2010, Flanders Interuniversity Institute for Biotechnology, VIB. Algorithm designed by Klaas Vandepoele, Cedric Simillion, Jan Fostier, Dieter De Witte, Koen Janssens, Sebastian Proost, Yvan Saeys and Yves Van de Peer.
Process 1/1 is alive on yu123-PC.
i-ADHoRe parameters Number of genelists = 749 Blast table = PeniCBMAcds.syn/families.tsv Output path = PeniCBMAcds.syn/i-adhore-out/ Gap size = 30 Cluster gap size = 35 Cloud gap size = 0 Cloud cluster gap size = 0 Max gaps in alignment = 35 Tandem gap = 15 Flush output = 1000 Q-value = 0.75 Anchorpoints = 3 Probability cutoff = 0.01 Cloud filtering method = Binomial Level 2 only = false Use family = true Write statistics = false Alignment method = GreedyGraphbased4 Multiple hypothesis correction = FDR Number of threads = 1 Compare aligners = false Collinear searches only Visualize GHM.png = false Visualize Alignment = true Verbose output = true **** END i-AdDHoRe parameters *****
Creating dataset... done. (time: 0.00943708s) Mapping gene families... done. (time: 0.010159s) Remapping tandem duplicates... done. (time: 0.006392s) Writing genelists file... done. (time: 0.042654s) Collinear Search Level 2 multiplicon detection... done. (time: 2.20706s) Profile detection... 140 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found. 139 multiplicons to evaluate - evaluating level 2 multiplicon... 3 new multiplicons found. 141 multiplicons to evaluate - evaluating level 3 multiplicon... 0 new multiplicons found. 140 multiplicons to evaluate - evaluating level 3 multiplicon... 0 new multiplicons found. 139 multiplicons to evaluate - evaluating level 3 multiplicon... 0 new multiplicons found. 138 multiplicons to evaluate - evaluating level 2 multiplicon... 5 new multiplicons found. 142 multiplicons to evaluate - evaluating level 3 multiplicon... 5 new multiplicons found. 146 multiplicons to evaluate - evaluating level 4 multiplicon... 1 new multiplicons found. 146 multiplicons to evaluate - evaluating level 5 multiplicon... too few aligned homologs 145 multiplicons to evaluate - evaluating level 4 multiplicon... 3 new multiplicons found. 147 multiplicons to evaluate - evaluating level 5 multiplicon... 0 new multiplicons found. 146 multiplicons to evaluate - evaluating level 5 multiplicon... 0 new multiplicons found. 145 multiplicons to evaluate - evaluating level 5 multiplicon... 0 new multiplicons found. 144 multiplicons to evaluate - evaluating level 4 multiplicon... all elements masked 143 multiplicons to evaluate - evaluating level 4 multiplicon... all elements masked 142 multiplicons to evaluate - evaluating level 4 multiplicon... all elements masked 141 multiplicons to evaluate - evaluating level 3 multiplicon... all elements masked 140 multiplicons to evaluate - evaluating level 3 multiplicon... all elements masked 139 multiplicons to evaluate - evaluating level 3 multiplicon... all elements masked 138 multiplicons to evaluate - evaluating level 3 multiplicon... all elements masked 137 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant 136 multiplicons to evaluate - evaluating level 2 multiplicon... 5 new multiplicons found. 140 multiplicons to evaluate - evaluating level 3 multiplicon... 1 new multiplicons found. 140 multiplicons to evaluate - evaluating level 4 multiplicon... 3 new multiplicons found. 142 multiplicons to evaluate - evaluating level 5 multiplicon... 2 new multiplicons found. 143 multiplicons to evaluate - evaluating level 6 multiplicon... 2 new multiplicons found. 144 multiplicons to evaluate - evaluating level 7 multiplicon... 1 new multiplicons found. 144 multiplicons to evaluate - evaluating level 8 multiplicon... 0 new multiplicons found. 143 multiplicons to evaluate - evaluating level 7 multiplicon... all elements masked 142 multiplicons to evaluate - evaluating level 6 multiplicon... all elements masked 141 multiplicons to evaluate - evaluating level 5 multiplicon... all elements masked 140 multiplicons to evaluate - evaluating level 5 multiplicon... all elements masked 139 multiplicons to evaluate - evaluating level 3 multiplicon... 0 new multiplicons found. 138 multiplicons to evaluate - evaluating level 3 multiplicon... all elements masked 137 multiplicons to evaluate - evaluating level 3 multiplicon... all elements masked 136 multiplicons to evaluate - evaluating level 3 multiplicon... all elements masked 135 multiplicons to evaluate - evaluating level 2 multiplicon... 1 new multiplicons found. 135 multiplicons to evaluate - evaluating level 3 multiplicon... 0 new multiplicons found. 134 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant 133 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant 132 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found. 131 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found. 130 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant 129 multiplicons to evaluate - evaluating level 2 multiplicon... 2 new multiplicons found. 130 multiplicons to evaluate - evaluating level 3 multiplicon... 1 new multiplicons found. 130 multiplicons to evaluate - evaluating level 4 multiplicon... 0 new multiplicons found. 129 multiplicons to evaluate - evaluating level 3 multiplicon... all elements masked 128 multiplicons to evaluate - evaluating level 2 multiplicon... 1 new multiplicons found. 128 multiplicons to evaluate - evaluating level 3 multiplicon... 0 new multiplicons found. 127 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant 126 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found. 125 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found. 124 multiplicons to evaluate - evaluating level 2 multiplicon... 1 new multiplicons found. 124 multiplicons to evaluate - evaluating level 3 multiplicon... 0 new multiplicons found. 123 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant 122 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant 121 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant 120 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found. 119 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant 118 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant 117 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant 116 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant 115 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found. 114 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant 113 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant 112 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant 111 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant 110 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant 109 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found. 108 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found. 107 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant 106 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found. 105 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found. 104 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant 103 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant 102 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant 101 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found. 100 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant 99 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant 98 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant 97 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant 96 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found. 95 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found. 94 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found. 93 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found. 92 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant 91 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant 90 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant 89 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant 88 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant 87 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant 86 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant 85 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant 84 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found. 83 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found. 82 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant 81 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found. 80 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found. 79 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant 78 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant 77 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found. 76 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant 75 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant 74 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant 73 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found. 72 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant 71 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found. 70 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant 69 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found. 68 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant 67 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found. 66 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found. 65 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found. 64 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found. 63 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found. 62 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant 61 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found. 60 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found. 59 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found. 58 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant 57 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant 56 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant 55 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant 54 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found. 53 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant 52 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found. 51 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant 50 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant 49 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant 48 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found. 47 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant 46 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant 45 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant 44 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant 43 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found. 42 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant 41 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found. 40 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant 39 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant 38 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant 37 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant 36 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant 35 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant 34 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant 33 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant 32 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant 31 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant 30 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant 29 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant 28 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant 27 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant 26 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found. 25 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found. 24 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found. 23 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant 22 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found. 21 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant 20 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found. 19 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant 18 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant 17 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant 16 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found. 15 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant 14 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant 13 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant 12 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found. 11 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found. 10 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant 9 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant 8 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant 7 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found. 6 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found. 5 multiplicons to evaluate - evaluating level 2 multiplicon... level-2 multiplicon is redundant 4 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found. 3 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found. 2 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found. 1 multiplicons to evaluate - evaluating level 2 multiplicon... 0 new multiplicons found. Flushing output files...Visualize AlignedProfiles done. Time for Higher Level Detection: 0.261017s.
All Done! Bye...
2024-10-17 20:48:01: INFO Drawing co-linearity dotplot /home/yu123/.local/lib/python3.6/site-packages/wgd/viz.py:223: UserWarning: Attempting to set identical left == right == 0 results in singular transformations; automatically expanding. ax.set_xlim(0, max(x)) /home/yu123/.local/lib/python3.6/site-packages/wgd/viz.py:224: UserWarning: Attempting to set identical bottom == top == 0 results in singular transformations; automatically expanding. ax.set_ylim(0, max(x)) Traceback (most recent call last): File "/home/yu123/.local/bin/wgd", line 8, in
sys.exit(cli())
File "/home/yu123/.local/lib/python3.6/site-packages/click/core.py", line 1128, in call
return self.main(args, kwargs)
File "/home/yu123/.local/lib/python3.6/site-packages/click/core.py", line 1053, in main
rv = self.invoke(ctx)
File "/home/yu123/.local/lib/python3.6/site-packages/click/core.py", line 1659, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/yu123/.local/lib/python3.6/site-packages/click/core.py", line 1395, in invoke
return ctx.invoke(self.callback, ctx.params)
File "/home/yu123/.local/lib/python3.6/site-packages/click/core.py", line 754, in invoke
return __callback(args, kwargs)
File "/home/yu123/.local/lib/python3.6/site-packages/wgd_cli.py", line 857, in syn
gene_attribute, min_length, ks_range, iadhore_opts
File "/home/yu123/.local/lib/python3.6/site-packages/wgdcli.py", line 949, in syn
'{}.dotplot.svg'.format(os.path.basename(families)))
File "/home/yu123/.local/lib/python3.6/site-packages/wgd/viz.py", line 244, in syntenic_dotplot
[row['begin_x'], row['end_x']]]
File "/home/yu123/.local/lib/python3.6/site-packages/wgd/viz.py", line 243, in
x = [genomic_elements[curr_list_x] + x for x in
KeyError: 94.0
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