-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_22/scaffold_22_1629774-1855292

-reading genomic sequence.

** Processing features (+)

-finding all potential splice sites, looking for GT/GC donors and AG acceptors.
-finding all potential starts and stops. (strand: +)
-loading gene prediction evidence. (strand: +)Valid prediction for snap_scaffold_22-snap.310-T1
Valid prediction for CodingQuarry_transcript_34049-T1
Valid prediction for Augustus_model.g33668.t1
Valid prediction for snap_scaffold_22-snap.306-T1
Valid prediction for GlimmerHMM_glimmerT_50194-T1
Valid prediction for snap_scaffold_22-snap.290-T1
Valid prediction for CodingQuarry_transcript_34051-T1
Valid prediction for GlimmerHMM_glimmerT_50197-T1
Valid prediction for snap_scaffold_22-snap.285-T1
Valid prediction for snap_scaffold_22-snap.288-T1
Valid prediction for snap_scaffold_22-snap.299-T1
Valid prediction for Augustus_model.g33673.t1
Valid prediction for Augustus_model.g33672.t1
Valid prediction for GlimmerHMM_glimmerT_50196-T1
Valid prediction for GeneMark_model.86857_t
Valid prediction for GlimmerHMM_glimmerT_50198-T1
Couldn't classify 58937, 59032
Couldn't classify 60615, 60716
Sorry, prediction pasa_asmbl_29795.p1 fails validation.
(CTC)	 CA	58937-59032	GT	AGG
(GTC)	 AG	59761-59865	GT	AGG
(TTG)	 AG	60615-60716	GT	AGG
-recovered pasa_asmbl_29795.p1, internal, 59761, 59865
-recovered pasa_asmbl_29795.p1, internal, 60615, 60716
Valid prediction for pasa_asmbl_29220.p1
Valid prediction for snap_scaffold_22-snap.292-T1
Couldn't classify 24058, 24157
Couldn't classify 24588, 24687
Sorry, prediction pasa_asmbl_29218.p1 fails validation.
(TAC)	 AC	24058-24157	GT	CAG
(ATG)	 AG	24303-24450	GT	AGG
(CTA)	 AG	24588-24687	AA	ACA
add_exon() Sorry, pasa_asmbl_29218.p1 24303-24450-initial-1 is invalid.
-recovered pasa_asmbl_29218.p1, initial, 24303, 24450
-recovered pasa_asmbl_29218.p1, internal, 24303, 24450
Valid prediction for snap_scaffold_22-snap.291-T1
Valid prediction for GlimmerHMM_glimmerT_50187-T1
Valid prediction for snap_scaffold_22-snap.302-T1
Valid prediction for Augustus_model.g33666.t1
Valid prediction for Augustus_model.g33674.t1
Valid prediction for snap_scaffold_22-snap.298-T1
Couldn't classify 69258, 69287
Sorry, prediction pasa_asmbl_29221.p1 fails validation.
(CTG)	 CA	69258-69287	GT	AGG
(ATG)	 AG	70177-70248	GT	AGG
(ATT)	 AG	70358-70460	GT	AGG
(TTC)	 AG	70825-70905	GT	AGG
(GAC)	 AG	71062-71190	GT	TGG
(GTG)	 AG	71376-71491	GT	CGG
(TCT)	 AG	71626-71886	GT	AGG
(GAC)	 AG	72005-72094	GT	AGG
(ACT)	 AG	72391-72568	GT	AGG
(ATG)	 AG	73099-73196	GT	AGG
(GCA)	 AG	73848-74096	GT	AGG
(TTT)	 AG	74430-74505	GT	AGG
(CTG)	 AG	74866-74939	CA	AGC
-recovered pasa_asmbl_29221.p1, initial, 70177, 70248
add_exon() Sorry, pasa_asmbl_29221.p1 73099-73196-initial-1 is invalid.
-recovered pasa_asmbl_29221.p1, initial, 73099, 73196
-recovered pasa_asmbl_29221.p1, terminal, 70358, 70460
-recovered pasa_asmbl_29221.p1, terminal, 74866, 74939
-recovered pasa_asmbl_29221.p1, internal, 70177, 70248
-recovered pasa_asmbl_29221.p1, internal, 70358, 70460
-recovered pasa_asmbl_29221.p1, internal, 70825, 70905
-recovered pasa_asmbl_29221.p1, internal, 71062, 71190
-recovered pasa_asmbl_29221.p1, internal, 71376, 71491
-recovered pasa_asmbl_29221.p1, internal, 71626, 71886
-recovered pasa_asmbl_29221.p1, internal, 72005, 72094
-recovered pasa_asmbl_29221.p1, internal, 72391, 72568
-recovered pasa_asmbl_29221.p1, internal, 73099, 73196
-recovered pasa_asmbl_29221.p1, internal, 73848, 74096
-recovered pasa_asmbl_29221.p1, internal, 74430, 74505
Valid prediction for GeneMark_model.86881_t
Valid prediction for GeneMark_model.86880_t
Valid prediction for GeneMark_model.86871_t
Valid prediction for snap_scaffold_22-snap.293-T1
Valid prediction for Augustus_model.g33662.t1
Valid prediction for GlimmerHMM_glimmerT_50186-T1
Valid prediction for GlimmerHMM_glimmerT_50200-T1
Valid prediction for GlimmerHMM_glimmerT_50195-T1
Valid prediction for GeneMark_model.86876_t
Couldn't classify 109256, 109333
Sorry, prediction pasa_asmbl_29226.p1 fails validation.
(GTT)	 AG	109256-109333	GT	AGG
(GGC)	 AG	110044-110082	GT	AGG
(CCG)	 AG	112502-112564	GT	ACG
(GGG)	 AG	114991-115141	GT	ATG
(ATG)	 AG	116793-116920	GT	AGG
(ATT)	 AG	118080-118142	AG	GAA
-recovered pasa_asmbl_29226.p1, initial, 116793, 116920
-recovered pasa_asmbl_29226.p1, terminal, 118080, 118142
-recovered pasa_asmbl_29226.p1, internal, 109256, 109333
-recovered pasa_asmbl_29226.p1, internal, 110044, 110082
-recovered pasa_asmbl_29226.p1, internal, 112502, 112564
-recovered pasa_asmbl_29226.p1, internal, 114991, 115141
-recovered pasa_asmbl_29226.p1, internal, 116793, 116920
Valid prediction for snap_scaffold_22-snap.305-T1
Valid prediction for snap_scaffold_22-snap.294-T1
Valid prediction for pasa_asmbl_29758.p1
Couldn't classify 90349, 90407
Sorry, prediction pasa_asmbl_29224.p1 fails validation.
(TCT)	 TG	90349-90407	GT	AGG
(TGC)	 AG	90689-90753	GT	TGG
(GTG)	 AG	90881-90986	GT	AGG
(TTA)	 AG	91066-91154	GT	TGG
(TTT)	 AG	91342-91389	GT	AGG
(CGG)	 AG	91524-91666	GT	AGG
(CCC)	 AG	91877-91975	TG	GAT
-recovered pasa_asmbl_29224.p1, terminal, 91877, 91975
-recovered pasa_asmbl_29224.p1, internal, 90689, 90753
-recovered pasa_asmbl_29224.p1, internal, 90881, 90986
-recovered pasa_asmbl_29224.p1, internal, 91066, 91154
-recovered pasa_asmbl_29224.p1, internal, 91342, 91389
-recovered pasa_asmbl_29224.p1, internal, 91524, 91666
Valid prediction for GeneMark_model.86873_t
Valid prediction for HiQ_model.g33669.t1
Valid prediction for snap_scaffold_22-snap.308-T1
Valid prediction for snap_scaffold_22-snap.315-T1
Valid prediction for GeneMark_model.86878_t
Valid prediction for Augustus_model.g33671.t1
Valid prediction for snap_scaffold_22-snap.297-T1
Valid prediction for GlimmerHMM_glimmerT_50189-T1
Valid prediction for snap_scaffold_22-snap.312-T1
Valid prediction for Augustus_model.g33676.t1
Valid prediction for Augustus_model.g33661.t1
Valid prediction for snap_scaffold_22-snap.289-T1
Valid prediction for HiQ_model.g33667.t1
Valid prediction for GlimmerHMM_glimmerT_50188-T1
Valid prediction for GlimmerHMM_glimmerT_50199-T1
Valid prediction for GeneMark_model.86860_t
Valid prediction for GlimmerHMM_glimmerT_50184-T1
Valid prediction for snap_scaffold_22-snap.301-T1
Valid prediction for GeneMark_model.86856_t
Valid prediction for Augustus_model.g33664.t1
Valid prediction for Augustus_model.g33675.t1
Valid prediction for CodingQuarry_transcript_34048-T1
Valid prediction for GeneMark_model.86866_t
Valid prediction for snap_scaffold_22-snap.307-T1
Valid prediction for GeneMark_model.86868_t
Valid prediction for GlimmerHMM_glimmerT_50191-T1
Valid prediction for snap_scaffold_22-snap.314-T1
Valid prediction for GeneMark_model.86864_t
Couldn't classify 159620, 159678
Couldn't classify 163300, 163431
Sorry, prediction pasa_asmbl_29228.p1 fails validation.
(GAC)	 CA	159620-159678	GT	AGG
(GAG)	 AG	160789-160906	GT	AGG
(GCT)	 AG	163300-163431	GA	GTG
-recovered pasa_asmbl_29228.p1, internal, 160789, 160906
Valid prediction for CodingQuarry_transcript_34050-T1
Valid prediction for snap_scaffold_22-snap.304-T1

-loading the search evidence (protein and EST search results, strand: +)
-scoring exons (strand: +)

** Processing features (-)

-finding all potential splice sites, looking for GT/GC donors and AG acceptors.
-finding all potential starts and stops. (strand: -)
-loading gene prediction evidence. (strand: -)Valid prediction for GeneMark_model.86863_t
Valid prediction for snap_scaffold_22-snap.286-T1
Valid prediction for GeneMark_model.86879_t
Valid prediction for Augustus_model.g33663.t1
Valid prediction for GeneMark_model.86872_t
Valid prediction for snap_scaffold_22-snap.300-T1
Valid prediction for snap_scaffold_22-snap.309-T1
Valid prediction for GeneMark_model.86874_t
Valid prediction for GeneMark_model.86875_t
Valid prediction for HiQ_model.g33665.t1
Valid prediction for snap_scaffold_22-snap.296-T1
Valid prediction for GeneMark_model.86862_t
Valid prediction for GeneMark_model.86882_t
Valid prediction for GlimmerHMM_glimmerT_50192-T1
Valid prediction for GeneMark_model.86870_t
Valid prediction for HiQ_model.g33670.t1
Valid prediction for snap_scaffold_22-snap.282-T1
Valid prediction for GeneMark_model.86869_t
Valid prediction for GeneMark_model.86877_t
Valid prediction for snap_scaffold_22-snap.311-T1
Valid prediction for GeneMark_model.86867_t
Valid prediction for snap_scaffold_22-snap.284-T1
Valid prediction for GlimmerHMM_glimmerT_50185-T1
Valid prediction for snap_scaffold_22-snap.303-T1
Valid prediction for snap_scaffold_22-snap.287-T1
Valid prediction for snap_scaffold_22-snap.295-T1
Valid prediction for snap_scaffold_22-snap.283-T1
Valid prediction for GeneMark_model.86858_t
Couldn't classify 92649, 92838
Sorry, prediction pasa_asmbl_29915.p1 fails validation.
(GGA)	 AG	92649-92838	GT	GGG
(GCA)	 AG	93408-93580	GT	CTG
(GGC)	 AG	94041-94148	GT	AGG
(AGC)	 AG	94919-94969	CA	AAC
-recovered pasa_asmbl_29915.p1, terminal, 94919, 94969
-recovered pasa_asmbl_29915.p1, internal, 92649, 92838
-recovered pasa_asmbl_29915.p1, internal, 93408, 93580
-recovered pasa_asmbl_29915.p1, internal, 94041, 94148
Valid prediction for GlimmerHMM_glimmerT_50190-T1
Valid prediction for snap_scaffold_22-snap.313-T1
Valid prediction for GeneMark_model.86855_t
Valid prediction for GeneMark_model.86861_t
Valid prediction for pasa_asmbl_29910.p1
Valid prediction for GeneMark_model.86865_t
Valid prediction for GlimmerHMM_glimmerT_50193-T1
Valid prediction for GlimmerHMM_glimmerT_50201-T1
Valid prediction for GlimmerHMM_glimmerT_50202-T1
Valid prediction for GeneMark_model.86854_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 198014, rend_intergenic: 195889  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 204816, rend_intergenic: 203399  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 225519
-exon list size: 465


building trellis

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24.0    
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26.6    
26.8    
27.0    
27.2    
27.4    
27.6    
27.8    
28.1    
28.3    
28.5    
28.7    
28.9    
29.1    
29.3    
29.6    
29.8    
30.0    
30.2    
30.4    
30.6    
30.8    
31.0    
31.3    
31.5    
31.7    
31.9    
32.1    
32.3    
32.5    
32.8    
33.0    
33.2    
33.4    
33.6    
33.8    
34.0    
34.3    
34.5    
34.7    
34.9    
35.1    
35.3    
35.5    
35.8    
36.0    
36.2    
36.4    
36.6    
36.8    
37.0    
37.3    
37.5    
37.7    
37.9    
38.1    
38.3    
38.5    
38.8    
39.0    
39.2    
39.4    
39.6    
39.8    
40.0    
40.3    
40.5    
40.7    
40.9    
41.1    
41.3    
41.5    
41.8    
42.0    
42.2    
42.4    
42.6    
42.8    
43.0    
43.3    
43.5    
43.7    
43.9    
44.1    
44.3    
44.5    
44.8    
45.0    
45.2    
45.4    
45.6    
45.8    
46.0    
46.3    
46.5    
46.7    
46.9    
47.1    
47.3    
47.5    
47.8    
48.0    
48.2    
48.4    
48.6    
48.8    
49.0    
49.3    
49.5    
49.7    
49.9    
50.1    
50.3    
50.5    
50.7    
51.0    
51.2    
51.4    
51.6    
51.8    
52.0    
52.2    
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52.7    
52.9    
53.1    
53.3    
53.5    
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54.2    
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54.6    
54.8    
55.0    
55.2    
55.5    
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55.9    
56.1    
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57.0    
57.2    
57.4    
57.6    
57.8    
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58.9    
59.1    
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59.5    
59.7    
60.0    
60.2    
60.4    
60.6    
60.8    
61.0    
61.2    
61.5    
61.7    
61.9    
62.1    
62.3    
62.5    
62.7    
63.0    
63.2    
63.4    
63.6    
63.8    
64.0    
64.2    
64.5    
64.7    
64.9    
65.1    
65.3    
65.5    
65.7    
66.0    
66.2    
66.4    
66.6    
66.8    
67.0    
67.2    
67.5    
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67.9    
68.1    
68.3    
68.5    
68.7    
69.0    
69.2    
69.4    
69.6    
69.8    
70.0    
70.2    
70.4    
70.7    
70.9    
71.1    
71.3    
71.5    
71.7    
71.9    
72.2    
72.4    
72.6    
72.8    
73.0    
73.2    
73.4    
73.7    
73.9    
74.1    
74.3    
74.5    
74.7    
74.9    
75.2    
75.4    
75.6    
75.8    
76.0    
76.2    
76.4    
76.7    
76.9    
77.1    
77.3    
77.5    
77.7    
77.9    
78.2    
78.4    
78.6    
78.8    
79.0    
79.2    
79.4    
79.7    
79.9    
80.1    
80.3    
80.5    
80.7    
80.9    
81.2    
81.4    
81.6    
81.8    
82.0    
82.2    
82.4    
82.7    
82.9    
83.1    
83.3    
83.5    
83.7    
83.9    
84.2    
84.4    
84.6    
84.8    
85.0    
85.2    
85.4    
85.7    
85.9    
86.1    
86.3    
86.5    
86.7    
86.9    
87.2    
87.4    
87.6    
87.8    
88.0    
88.2    
88.4    
88.7    
88.9    
89.1    
89.3    
89.5    
89.7    
89.9    
90.1    
90.4    
90.6    
90.8    
91.0    
91.2    
91.4    
91.6    
91.9    
92.1    
92.3    
92.5    
92.7    
92.9    
93.1    
93.4    
93.6    
93.8    
94.0    
94.2    
94.4    
94.6    
94.9    
95.1    
95.3    
95.5    
95.7    
95.9    
96.1    
96.4    
96.6    
96.8    
97.0    
97.2    
97.4    
97.6    
97.9    
98.1    
98.3    
98.5    
98.7    
98.9    
99.1    
99.4    
99.6    
99.8    
-found 23 predictions from path traversal
Error with prediction: snap lend_intergenic: 198014, rend_intergenic: 195889  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 204816, rend_intergenic: 203399  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support