-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_2/scaffold_2_8180118-8582515

-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_2-snap.1668-T1
Valid prediction for GlimmerHMM_glimmerT_4173-T1
Valid prediction for Augustus_model.g2810.t1
Valid prediction for snap_scaffold_2-snap.1691-T1
Couldn't classify 133853, 133971
Sorry, prediction pasa_asmbl_24634.p1 fails validation.
(ATG)	 AG	129789-129875	GT	GGG
(GGC)	 AG	131224-131285	GT	GAG
(AAA)	 AG	131874-131984	GT	AGG
(ACC)	 AG	132357-132539	GT	AGG
(TTA)	 AG	132770-132909	GT	AGG
(TGA)	 AG	133119-133344	GT	TGG
(GTT)	 AG	133433-133533	GT	TGG
(CAA)	 AG	133696-133737	GT	ATG
(CTC)	 AG	133853-133971	CA	AGC
-recovered pasa_asmbl_24634.p1, initial, 129789, 129875
-recovered pasa_asmbl_24634.p1, internal, 129789, 129875
-recovered pasa_asmbl_24634.p1, internal, 131224, 131285
-recovered pasa_asmbl_24634.p1, internal, 131874, 131984
-recovered pasa_asmbl_24634.p1, internal, 132357, 132539
-recovered pasa_asmbl_24634.p1, internal, 132770, 132909
-recovered pasa_asmbl_24634.p1, internal, 133119, 133344
-recovered pasa_asmbl_24634.p1, internal, 133433, 133533
-recovered pasa_asmbl_24634.p1, internal, 133696, 133737
Valid prediction for pasa_asmbl_24642.p1
Valid prediction for snap_scaffold_2-snap.1674-T1
Valid prediction for snap_scaffold_2-snap.1696-T1
Valid prediction for snap_scaffold_2-snap.1697-T1
Valid prediction for snap_scaffold_2-snap.1688-T1
Valid prediction for snap_scaffold_2-snap.1677-T1
Valid prediction for GlimmerHMM_glimmerT_4179-T1
Valid prediction for snap_scaffold_2-snap.1694-T1
Valid prediction for snap_scaffold_2-snap.1680-T1
Valid prediction for Augustus_model.g2811.t1
Valid prediction for Augustus_model.g2819.t1
Valid prediction for Augustus_model.g2809.t1
Valid prediction for GlimmerHMM_glimmerT_4168-T1
Valid prediction for GlimmerHMM_glimmerT_4183-T1
Valid prediction for GlimmerHMM_glimmerT_4175-T1
Valid prediction for snap_scaffold_2-snap.1685-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_2-snap.1669-T1
Valid prediction for Augustus_model.g2815.t1
Valid prediction for GlimmerHMM_glimmerT_4169-T1
Valid prediction for HiQ_model.g2804.t1
Couldn't classify 95846, 95945
Sorry, prediction pasa_asmbl_24621.p1 fails validation.
(GGA)	 CA	95846-95945	GT	CAG
(GTC)	 AG	96043-96312	GT	AGG
(TGA)	 AG	96912-97076	GT	AGG
(GTA)	 AG	97300-97498	GT	GAG
(GAC)	 AG	98294-98429	GT	CAG
(AAT)	 AG	99062-99234	GT	CGG
(TAC)	 AG	99342-99406	GT	AGG
(GAT)	 AG	99711-100087	AT	AGA
add_exon() Sorry, pasa_asmbl_24621.p1 96912-97076-terminal-1 is invalid.
-recovered pasa_asmbl_24621.p1, terminal, 96912, 97076
add_exon() Sorry, pasa_asmbl_24621.p1 99342-99406-terminal-2 is invalid.
-recovered pasa_asmbl_24621.p1, terminal, 99342, 99406
-recovered pasa_asmbl_24621.p1, terminal, 99711, 100087
-recovered pasa_asmbl_24621.p1, internal, 96043, 96312
-recovered pasa_asmbl_24621.p1, internal, 96912, 97076
-recovered pasa_asmbl_24621.p1, internal, 97300, 97498
-recovered pasa_asmbl_24621.p1, internal, 98294, 98429
-recovered pasa_asmbl_24621.p1, internal, 99062, 99234
-recovered pasa_asmbl_24621.p1, internal, 99342, 99406
Valid prediction for pasa_asmbl_24637.p1
Valid prediction for GlimmerHMM_glimmerT_4182-T1
Valid prediction for HiQ_model.g2813.t1
Valid prediction for snap_scaffold_2-snap.1698-T1
Valid prediction for GlimmerHMM_glimmerT_4188-T1
Valid prediction for Augustus_model.g2820.t1
Valid prediction for snap_scaffold_2-snap.1671-T1
Valid prediction for snap_scaffold_2-snap.1670-T1
Valid prediction for Augustus_model.g2807.t1
Couldn't classify 6660, 6766
Sorry, prediction pasa_asmbl_24616.p1 fails validation.
(TCC)	 CG	6660-6766	GT	GGG
(GGA)	 AG	7444-7607	GT	TAG
(GTA)	 AG	9914-10155	GT	ATG
(ATT)	 AG	10977-11101	GT	AGG
(GAA)	 AG	12636-12750	GT	TGG
(AAA)	 AG	13075-13531	GT	TGG
(ACC)	 AG	13893-13956	GT	ATG
(AAA)	 AG	14371-14542	GT	AGG
(CTT)	 AG	14668-14712	GT	AGG
(AAG)	 AG	14835-14945	CT	AGC
-recovered pasa_asmbl_24616.p1, terminal, 14835, 14945
-recovered pasa_asmbl_24616.p1, internal, 7444, 7607
-recovered pasa_asmbl_24616.p1, internal, 9914, 10155
-recovered pasa_asmbl_24616.p1, internal, 10977, 11101
-recovered pasa_asmbl_24616.p1, internal, 12636, 12750
-recovered pasa_asmbl_24616.p1, internal, 13075, 13531
-recovered pasa_asmbl_24616.p1, internal, 13893, 13956
-recovered pasa_asmbl_24616.p1, internal, 14371, 14542
-recovered pasa_asmbl_24616.p1, internal, 14668, 14712
Couldn't classify 135734, 135769
Sorry, prediction pasa_asmbl_24636.p1 fails validation.
(GAG)	 AG	135734-135769	GT	AGG
(AAC)	 AG	135976-136128	GT	AGG
(CGC)	 AG	136629-136700	GT	AGG
(GAC)	 AG	137108-137257	GT	AGG
(GTG)	 AG	137360-137508	GT	AAG
(TTC)	 AG	137606-137702	GT	AGG
(GAA)	 AG	137797-137889	GT	AGG
(GTG)	 AG	137997-138170	GT	GGG
(GCG)	 AG	138684-138895	GT	AGG
(ACT)	 AG	138996-139135	GT	AGG
(CCA)	 AG	139209-139347	GT	AAG
(GTT)	 AG	139431-139581	GT	AAG
(ATC)	 AG	139685-139807	GC	AGG
(ACC)	 AG	139940-140062	GT	AGG
(GAT)	 AG	140193-140333	GT	AGG
(GTT)	 AG	140584-140697	GT	TAG
(TGC)	 AG	140910-141088	GT	CGG
(GAA)	 AG	141185-141284	GT	ACG
(AAG)	 AG	141406-141607	GT	TGG
(ATA)	 AG	141712-141961	GC	AGG
(GCA)	 AG	142310-142601	AG	GAA
-recovered pasa_asmbl_24636.p1, terminal, 142310, 142601
-recovered pasa_asmbl_24636.p1, internal, 135734, 135769
-recovered pasa_asmbl_24636.p1, internal, 135976, 136128
-recovered pasa_asmbl_24636.p1, internal, 136629, 136700
-recovered pasa_asmbl_24636.p1, internal, 137108, 137257
-recovered pasa_asmbl_24636.p1, internal, 137360, 137508
-recovered pasa_asmbl_24636.p1, internal, 137606, 137702
-recovered pasa_asmbl_24636.p1, internal, 137797, 137889
-recovered pasa_asmbl_24636.p1, internal, 137997, 138170
-recovered pasa_asmbl_24636.p1, internal, 138684, 138895
-recovered pasa_asmbl_24636.p1, internal, 138996, 139135
-recovered pasa_asmbl_24636.p1, internal, 139209, 139347
-recovered pasa_asmbl_24636.p1, internal, 139431, 139581
-recovered pasa_asmbl_24636.p1, internal, 139685, 139807
-recovered pasa_asmbl_24636.p1, internal, 139940, 140062
-recovered pasa_asmbl_24636.p1, internal, 140193, 140333
-recovered pasa_asmbl_24636.p1, internal, 140584, 140697
-recovered pasa_asmbl_24636.p1, internal, 140910, 141088
-recovered pasa_asmbl_24636.p1, internal, 141185, 141284
-recovered pasa_asmbl_24636.p1, internal, 141406, 141607
-recovered pasa_asmbl_24636.p1, internal, 141712, 141961
Couldn't classify 77714, 78109
Sorry, prediction pasa_asmbl_24620.p1 fails validation.
(GTG)	 AG	77714-78109	GG	TCG
Valid prediction for CodingQuarry_transcript_28625-T1
Valid prediction for snap_scaffold_2-snap.1673-T1
Valid prediction for Augustus_model.g2817.t1
Valid prediction for Augustus_model.g2808.t1
Valid prediction for GlimmerHMM_glimmerT_4165-T1
Couldn't classify 134230, 134291
Couldn't classify 135607, 135676
Sorry, prediction pasa_asmbl_24635.p1 fails validation.
(AAC)	 AG	134230-134291	GT	AGG
(GTG)	 AG	134467-134683	GT	CGG
(ATC)	 AG	134781-134870	GT	AGG
(GGG)	 AG	134985-135175	GT	AAG
(GTT)	 AG	135284-135472	GT	AAG
(GTG)	 AG	135607-135676	AT	ACA
-recovered pasa_asmbl_24635.p1, internal, 134230, 134291
-recovered pasa_asmbl_24635.p1, internal, 134467, 134683
-recovered pasa_asmbl_24635.p1, internal, 134781, 134870
-recovered pasa_asmbl_24635.p1, internal, 134985, 135175
-recovered pasa_asmbl_24635.p1, internal, 135284, 135472
Valid prediction for GlimmerHMM_glimmerT_4177-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_2-snap.1679-T1
Couldn't classify 105925, 106019
Couldn't classify 106113, 106320
Sorry, prediction pasa_asmbl_25372.p1 fails validation.
(GAT)	 AG	105925-106019	GT	AGG
(GAA)	 AG	106113-106320	CT	TGC
-recovered pasa_asmbl_25372.p1, internal, 105925, 106019
Valid prediction for snap_scaffold_2-snap.1683-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_2-snap.1676-T1
Valid prediction for snap_scaffold_2-snap.1678-T1
Valid prediction for CodingQuarry_transcript_28624-T1
Valid prediction for snap_scaffold_2-snap.1675-T1
Valid prediction for GlimmerHMM_glimmerT_4171-T1
Valid prediction for snap_scaffold_2-snap.1693-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 snap_scaffold_2-snap.1690-T1
Valid prediction for GlimmerHMM_glimmerT_4176-T1
Valid prediction for GlimmerHMM_glimmerT_4185-T1
Valid prediction for HiQ_model.g2805.t1
Valid prediction for snap_scaffold_2-snap.1687-T1
Valid prediction for snap_scaffold_2-snap.1672-T1
Valid prediction for GlimmerHMM_glimmerT_4180-T1
Valid prediction for GlimmerHMM_glimmerT_4172-T1
Valid prediction for CodingQuarry_transcript_28626-T1
Valid prediction for Augustus_model.g2806.t1
Valid prediction for snap_scaffold_2-snap.1695-T1
Valid prediction for snap_scaffold_2-snap.1682-T1
Valid prediction for GlimmerHMM_glimmerT_4187-T1
Valid prediction for snap_scaffold_2-snap.1689-T1
Valid prediction for GlimmerHMM_glimmerT_4178-T1
Valid prediction for GlimmerHMM_glimmerT_4167-T1
Valid prediction for GlimmerHMM_glimmerT_4186-T1
Valid prediction for GlimmerHMM_glimmerT_4170-T1
Valid prediction for HiQ_model.g2818.t1
Valid prediction for snap_scaffold_2-snap.1684-T1
Valid prediction for GlimmerHMM_glimmerT_4174-T1
Valid prediction for snap_scaffold_2-snap.1681-T1
Valid prediction for HiQ_model.g2812.t1
Valid prediction for Augustus_model.g2814.t1
Valid prediction for GlimmerHMM_glimmerT_4181-T1
Valid prediction for snap_scaffold_2-snap.1692-T1
Valid prediction for pasa_asmbl_23323.p2
Valid prediction for snap_scaffold_2-snap.1686-T1
Valid prediction for Augustus_model.g2816.t1
Valid prediction for GlimmerHMM_glimmerT_4166-T1
Valid prediction for GlimmerHMM_glimmerT_4164-T1
Valid prediction for GlimmerHMM_glimmerT_4184-T1
Valid prediction for pasa_asmbl_23329.p1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 69003, rend_intergenic: 67049  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 294948, rend_intergenic: 294314  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 402398
-exon list size: 307


building trellis

0.3    
0.6    
1.0    
1.3    
1.6    
1.9    
2.3    
2.6    
2.9    
3.2    
3.6    
3.9    
4.2    
4.5    
4.9    
5.2    
5.5    
5.8    
6.1    
6.5    
6.8    
7.1    
7.4    
7.8    
8.1    
8.4    
8.7    
9.1    
9.4    
9.7    
10.0    
10.4    
10.7    
11.0    
11.3    
11.7    
12.0    
12.3    
12.6    
12.9    
13.3    
13.6    
13.9    
14.2    
14.6    
14.9    
15.2    
15.5    
15.9    
16.2    
16.5    
16.8    
17.2    
17.5    
17.8    
18.1    
18.4    
18.8    
19.1    
19.4    
19.7    
20.1    
20.4    
20.7    
21.0    
21.4    
21.7    
22.0    
22.3    
22.7    
23.0    
23.3    
23.6    
23.9    
24.3    
24.6    
24.9    
25.2    
25.6    
25.9    
26.2    
26.5    
26.9    
27.2    
27.5    
27.8    
28.2    
28.5    
28.8    
29.1    
29.4    
29.8    
30.1    
30.4    
30.7    
31.1    
31.4    
31.7    
32.0    
32.4    
32.7    
33.0    
33.3    
33.7    
34.0    
34.3    
34.6    
35.0    
35.3    
35.6    
35.9    
36.2    
36.6    
36.9    
37.2    
37.5    
37.9    
38.2    
38.5    
38.8    
39.2    
39.5    
39.8    
40.1    
40.5    
40.8    
41.1    
41.4    
41.7    
42.1    
42.4    
42.7    
43.0    
43.4    
43.7    
44.0    
44.3    
44.7    
45.0    
45.3    
45.6    
46.0    
46.3    
46.6    
46.9    
47.2    
47.6    
47.9    
48.2    
48.5    
48.9    
49.2    
49.5    
49.8    
50.2    
50.5    
50.8    
51.1    
51.5    
51.8    
52.1    
52.4    
52.8    
53.1    
53.4    
53.7    
54.0    
54.4    
54.7    
55.0    
55.3    
55.7    
56.0    
56.3    
56.6    
57.0    
57.3    
57.6    
57.9    
58.3    
58.6    
58.9    
59.2    
59.5    
59.9    
60.2    
60.5    
60.8    
61.2    
61.5    
61.8    
62.1    
62.5    
62.8    
63.1    
63.4    
63.8    
64.1    
64.4    
64.7    
65.0    
65.4    
65.7    
66.0    
66.3    
66.7    
67.0    
67.3    
67.6    
68.0    
68.3    
68.6    
68.9    
69.3    
69.6    
69.9    
70.2    
70.6    
70.9    
71.2    
71.5    
71.8    
72.2    
72.5    
72.8    
73.1    
73.5    
73.8    
74.1    
74.4    
74.8    
75.1    
75.4    
75.7    
76.1    
76.4    
76.7    
77.0    
77.3    
77.7    
78.0    
78.3    
78.6    
79.0    
79.3    
79.6    
79.9    
80.3    
80.6    
80.9    
81.2    
81.6    
81.9    
82.2    
82.5    
82.8    
83.2    
83.5    
83.8    
84.1    
84.5    
84.8    
85.1    
85.4    
85.8    
86.1    
86.4    
86.7    
87.1    
87.4    
87.7    
88.0    
88.3    
88.7    
89.0    
89.3    
89.6    
90.0    
90.3    
90.6    
90.9    
91.3    
91.6    
91.9    
92.2    
92.6    
92.9    
93.2    
93.5    
93.9    
94.2    
94.5    
94.8    
95.1    
95.5    
95.8    
96.1    
96.4    
96.8    
97.1    
97.4    
97.7    
98.1    
98.4    
98.7    
99.0    
99.4    
99.7    
-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 69003, rend_intergenic: 67049  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 294948, rend_intergenic: 294314  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 22 predictions persist after filtering for low support