-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_17/scaffold_17_12971660-13074001

-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 GeneMark_model.73013_t
Valid prediction for GeneMark_model.73032_t
Valid prediction for snap_scaffold_17-snap.2688-T1
Valid prediction for CodingQuarry_transcript_22178-T1
Couldn't classify 71446, 71530
Sorry, prediction pasa_asmbl_18428.p2 fails validation.
(GAT)	 TA	71446-71530	GT	AGG
(CTT)	 AG	71688-71772	GT	AGG
(TCA)	 AG	72076-72130	GT	TTG
(GTG)	 AG	72404-72547	AG	AGA
-recovered pasa_asmbl_18428.p2, terminal, 72404, 72547
-recovered pasa_asmbl_18428.p2, internal, 71688, 71772
-recovered pasa_asmbl_18428.p2, internal, 72076, 72130
Valid prediction for snap_scaffold_17-snap.2691-T1
Valid prediction for pasa_asmbl_18430.p2
Valid prediction for GlimmerHMM_glimmerT_42250-T1
Valid prediction for HiQ_model.g28286.t1
Couldn't classify 22742, 22853
Sorry, prediction pasa_asmbl_18420.p1 fails validation.
(TCA)	 AT	22742-22853	GT	AGG
(ATG)	 AG	23243-23335	GT	AGG
(TCT)	 AG	23827-24230	GT	GAG
add_exon() Sorry, pasa_asmbl_18420.p1 23243-23335-initial-1 is invalid.
-recovered pasa_asmbl_18420.p1, initial, 23243, 23335
-recovered pasa_asmbl_18420.p1, terminal, 23827, 24230
-recovered pasa_asmbl_18420.p1, internal, 23243, 23335
-recovered pasa_asmbl_18420.p1, internal, 23827, 24230
Couldn't classify 46549, 47775
Sorry, prediction pasa_asmbl_18422.p1 fails validation.
(CTT)	 AG	46549-47775	GA	GAG
Valid prediction for CodingQuarry_transcript_22177-T1
Valid prediction for snap_scaffold_17-snap.2670-T1
Valid prediction for GeneMark_model.73010_t
Valid prediction for snap_scaffold_17-snap.2678-T1
Valid prediction for GeneMark_model.73031_t
Valid prediction for CodingQuarry_transcript_22179-T1
Valid prediction for Augustus_model.g28297.t1
Valid prediction for Augustus_model.g28293.t1
Valid prediction for snap_scaffold_17-snap.2682-T1
Valid prediction for HiQ_model.g28289.t1
Couldn't classify 17946, 18011
Sorry, prediction pasa_asmbl_18586.p1 fails validation.
(AGC)	 CC	17946-18011	GT	GGG
(GAT)	 AG	18201-18302	GT	TGG
(GGT)	 AG	18515-18609	GT	TGG
(CTC)	 AG	18738-18903	GT	TGG
(CTC)	 AG	19326-19396	GT	AGG
(ACT)	 AG	20436-20559	GT	AGG
(GTG)	 AG	20979-21134	GT	AGG
(ACG)	 AG	21290-21394	AA	GAA
-recovered pasa_asmbl_18586.p1, terminal, 21290, 21394
-recovered pasa_asmbl_18586.p1, internal, 18201, 18302
-recovered pasa_asmbl_18586.p1, internal, 18515, 18609
-recovered pasa_asmbl_18586.p1, internal, 18738, 18903
-recovered pasa_asmbl_18586.p1, internal, 19326, 19396
-recovered pasa_asmbl_18586.p1, internal, 20436, 20559
-recovered pasa_asmbl_18586.p1, internal, 20979, 21134
Valid prediction for HiQ_model.g28288.t1
Valid prediction for GlimmerHMM_glimmerT_42245-T1
Valid prediction for GeneMark_model.73029_t
Valid prediction for GeneMark_model.73023_t
Valid prediction for GeneMark_model.73034_t
Valid prediction for Augustus_model.g28292.t1
Valid prediction for GeneMark_model.73024_t
Valid prediction for GeneMark_model.73021_t
Couldn't classify 58125, 58176
Sorry, prediction pasa_asmbl_18424.p1 fails validation.
(ATG)	 AG	56485-56535	GT	GGG
(GGG)	 AG	56716-56940	GT	GGG
(ATA)	 AG	57279-57397	GT	GTG
(GTT)	 AG	58125-58176	AA	ATA
-recovered pasa_asmbl_18424.p1, initial, 56485, 56535
-recovered pasa_asmbl_18424.p1, internal, 56485, 56535
-recovered pasa_asmbl_18424.p1, internal, 56716, 56940
-recovered pasa_asmbl_18424.p1, internal, 57279, 57397
Valid prediction for GeneMark_model.73027_t
Valid prediction for snap_scaffold_17-snap.2687-T1
Valid prediction for CodingQuarry_transcript_22176-T1
Valid prediction for GeneMark_model.73019_t
Valid prediction for GeneMark_model.73017_t
Valid prediction for Augustus_model.g28294.t1
Couldn't classify 60014, 60105
Sorry, prediction pasa_asmbl_18425.p1 fails validation.
(GAA)	 CA	60014-60105	GT	AGG
(GTA)	 AG	61057-61144	GT	AGG
(TTT)	 AG	61748-61848	GT	TGG
(TCA)	 AG	62149-62268	GT	ATG
(TCT)	 AG	63235-63357	GT	AGG
(AGT)	 AG	63646-63781	GT	CGG
(ACG)	 AG	64155-64217	GT	AGG
(GCA)	 AG	64400-64537	GT	AGG
(GTT)	 AG	65031-65234	AG	AGA
-recovered pasa_asmbl_18425.p1, terminal, 65031, 65234
-recovered pasa_asmbl_18425.p1, internal, 61057, 61144
-recovered pasa_asmbl_18425.p1, internal, 61748, 61848
-recovered pasa_asmbl_18425.p1, internal, 62149, 62268
-recovered pasa_asmbl_18425.p1, internal, 63235, 63357
-recovered pasa_asmbl_18425.p1, internal, 63646, 63781
-recovered pasa_asmbl_18425.p1, internal, 64155, 64217
-recovered pasa_asmbl_18425.p1, internal, 64400, 64537
Valid prediction for snap_scaffold_17-snap.2693-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_17-snap.2668-T1
Valid prediction for Augustus_model.g28298.t1
Valid prediction for GlimmerHMM_glimmerT_42252-T1
Valid prediction for snap_scaffold_17-snap.2685-T1
Valid prediction for pasa_asmbl_18421.p1
Valid prediction for snap_scaffold_17-snap.2675-T1
Valid prediction for GeneMark_model.73009_t
Valid prediction for Augustus_model.g28291.t1
Valid prediction for GlimmerHMM_glimmerT_42256-T1
Valid prediction for snap_scaffold_17-snap.2694-T1
Valid prediction for CodingQuarry_transcript_22175-T1
Valid prediction for Augustus_model.g28295.t1
Valid prediction for GlimmerHMM_glimmerT_42243-T1
Valid prediction for GeneMark_model.73036_t
Valid prediction for GlimmerHMM_glimmerT_42255-T1
Valid prediction for snap_scaffold_17-snap.2671-T1
Valid prediction for GeneMark_model.73038_t
Valid prediction for GlimmerHMM_glimmerT_42254-T1
Valid prediction for GlimmerHMM_glimmerT_42261-T1
Valid prediction for GlimmerHMM_glimmerT_42260-T1
Valid prediction for snap_scaffold_17-snap.2683-T1
Valid prediction for GlimmerHMM_glimmerT_42247-T1
Valid prediction for snap_scaffold_17-snap.2677-T1
Valid prediction for GlimmerHMM_glimmerT_42249-T1
Valid prediction for GeneMark_model.73040_t
Valid prediction for snap_scaffold_17-snap.2690-T1
Valid prediction for GeneMark_model.73042_t
Valid prediction for GeneMark_model.73015_t
Couldn't classify 88496, 88616
Couldn't classify 91455, 91657
Sorry, prediction pasa_asmbl_18567.p1 fails validation.
(AGA)	 TA	88496-88616	GT	AGG
(CTG)	 AG	89976-90095	GT	AGG
(GCG)	 AG	91455-91657	CT	TGC
-recovered pasa_asmbl_18567.p1, internal, 89976, 90095
Valid prediction for GeneMark_model.73012_t

-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.73035_t
Valid prediction for snap_scaffold_17-snap.2692-T1
Valid prediction for snap_scaffold_17-snap.2680-T1
Valid prediction for snap_scaffold_17-snap.2686-T1
Valid prediction for GeneMark_model.73011_t
Valid prediction for GlimmerHMM_glimmerT_42253-T1
Valid prediction for snap_scaffold_17-snap.2689-T1
Valid prediction for GeneMark_model.73016_t
Valid prediction for snap_scaffold_17-snap.2679-T1
Valid prediction for snap_scaffold_17-snap.2681-T1
Valid prediction for snap_scaffold_17-snap.2669-T1
Valid prediction for GeneMark_model.73028_t
Valid prediction for GeneMark_model.73014_t
Valid prediction for GeneMark_model.73033_t
Valid prediction for snap_scaffold_17-snap.2695-T1
Valid prediction for pasa_asmbl_19395.p1
Valid prediction for GlimmerHMM_glimmerT_42248-T1
Valid prediction for GlimmerHMM_glimmerT_42246-T1
Valid prediction for CodingQuarry_transcript_22180-T1
Valid prediction for Augustus_model.g28287.t1
Valid prediction for GeneMark_model.73022_t
Valid prediction for GeneMark_model.73041_t
Valid prediction for GeneMark_model.73025_t
Valid prediction for GlimmerHMM_glimmerT_42251-T1
Valid prediction for HiQ_model.g28296.t1
Valid prediction for snap_scaffold_17-snap.2674-T1
Couldn't classify 18515, 18997
Sorry, prediction pasa_asmbl_19392.p1 fails validation.
(ACA)	 CA	18515-18997	GT	AGG
(GCG)	 AG	19272-19460	GT	AGG
(GAC)	 AG	21803-21922	GT	ACG
(ATG)	 AG	23244-23387	GT	CCG
(GCC)	 AG	23737-23853	CC	GAC
-recovered pasa_asmbl_19392.p1, initial, 23244, 23387
-recovered pasa_asmbl_19392.p1, terminal, 23737, 23853
-recovered pasa_asmbl_19392.p1, internal, 19272, 19460
-recovered pasa_asmbl_19392.p1, internal, 21803, 21922
-recovered pasa_asmbl_19392.p1, internal, 23244, 23387
Valid prediction for GeneMark_model.73039_t
Valid prediction for GlimmerHMM_glimmerT_42242-T1
Valid prediction for GeneMark_model.73037_t
Valid prediction for GlimmerHMM_glimmerT_42257-T1
Valid prediction for HiQ_model.g28299.t1
Valid prediction for GeneMark_model.73018_t
Valid prediction for snap_scaffold_17-snap.2684-T1
Valid prediction for Augustus_model.g28290.t1
Valid prediction for snap_scaffold_17-snap.2673-T1
Valid prediction for GeneMark_model.73026_t
Valid prediction for GlimmerHMM_glimmerT_42259-T1
Valid prediction for GeneMark_model.73008_t
Valid prediction for GeneMark_model.73030_t
Valid prediction for GlimmerHMM_glimmerT_42258-T1
Valid prediction for GlimmerHMM_glimmerT_42244-T1
Valid prediction for GeneMark_model.73020_t
Valid prediction for snap_scaffold_17-snap.2672-T1
Valid prediction for snap_scaffold_17-snap.2676-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 15871, rend_intergenic: 11134  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22461, rend_intergenic: 19796  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38564, rend_intergenic: 36874  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47802, rend_intergenic: 43473  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50957, rend_intergenic: 50354  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59005, rend_intergenic: 56680  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59560, rend_intergenic: 59170  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65234, rend_intergenic: 61625  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84001, rend_intergenic: 78512  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93909, rend_intergenic: 89497  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98352, rend_intergenic: 96620  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 102342
-exon list size: 392


building trellis

0.3    
0.5    
0.8    
1.0    
1.3    
1.5    
1.8    
2.0    
2.3    
2.5    
2.8    
3.0    
3.3    
3.6    
3.8    
4.1    
4.3    
4.6    
4.8    
5.1    
5.3    
5.6    
5.8    
6.1    
6.3    
6.6    
6.9    
7.1    
7.4    
7.6    
7.9    
8.1    
8.4    
8.6    
8.9    
9.1    
9.4    
9.6    
9.9    
10.2    
10.4    
10.7    
10.9    
11.2    
11.4    
11.7    
11.9    
12.2    
12.4    
12.7    
12.9    
13.2    
13.5    
13.7    
14.0    
14.2    
14.5    
14.7    
15.0    
15.2    
15.5    
15.7    
16.0    
16.2    
16.5    
16.8    
17.0    
17.3    
17.5    
17.8    
18.0    
18.3    
18.5    
18.8    
19.0    
19.3    
19.5    
19.8    
20.1    
20.3    
20.6    
20.8    
21.1    
21.3    
21.6    
21.8    
22.1    
22.3    
22.6    
22.8    
23.1    
23.4    
23.6    
23.9    
24.1    
24.4    
24.6    
24.9    
25.1    
25.4    
25.6    
25.9    
26.1    
26.4    
26.6    
26.9    
27.2    
27.4    
27.7    
27.9    
28.2    
28.4    
28.7    
28.9    
29.2    
29.4    
29.7    
29.9    
30.2    
30.5    
30.7    
31.0    
31.2    
31.5    
31.7    
32.0    
32.2    
32.5    
32.7    
33.0    
33.2    
33.5    
33.8    
34.0    
34.3    
34.5    
34.8    
35.0    
35.3    
35.5    
35.8    
36.0    
36.3    
36.5    
36.8    
37.1    
37.3    
37.6    
37.8    
38.1    
38.3    
38.6    
38.8    
39.1    
39.3    
39.6    
39.8    
40.1    
40.4    
40.6    
40.9    
41.1    
41.4    
41.6    
41.9    
42.1    
42.4    
42.6    
42.9    
43.1    
43.4    
43.7    
43.9    
44.2    
44.4    
44.7    
44.9    
45.2    
45.4    
45.7    
45.9    
46.2    
46.4    
46.7    
47.0    
47.2    
47.5    
47.7    
48.0    
48.2    
48.5    
48.7    
49.0    
49.2    
49.5    
49.7    
50.0    
50.3    
50.5    
50.8    
51.0    
51.3    
51.5    
51.8    
52.0    
52.3    
52.5    
52.8    
53.0    
53.3    
53.6    
53.8    
54.1    
54.3    
54.6    
54.8    
55.1    
55.3    
55.6    
55.8    
56.1    
56.3    
56.6    
56.9    
57.1    
57.4    
57.6    
57.9    
58.1    
58.4    
58.6    
58.9    
59.1    
59.4    
59.6    
59.9    
60.2    
60.4    
60.7    
60.9    
61.2    
61.4    
61.7    
61.9    
62.2    
62.4    
62.7    
62.9    
63.2    
63.5    
63.7    
64.0    
64.2    
64.5    
64.7    
65.0    
65.2    
65.5    
65.7    
66.0    
66.2    
66.5    
66.8    
67.0    
67.3    
67.5    
67.8    
68.0    
68.3    
68.5    
68.8    
69.0    
69.3    
69.5    
69.8    
70.1    
70.3    
70.6    
70.8    
71.1    
71.3    
71.6    
71.8    
72.1    
72.3    
72.6    
72.8    
73.1    
73.4    
73.6    
73.9    
74.1    
74.4    
74.6    
74.9    
75.1    
75.4    
75.6    
75.9    
76.1    
76.4    
76.6    
76.9    
77.2    
77.4    
77.7    
77.9    
78.2    
78.4    
78.7    
78.9    
79.2    
79.4    
79.7    
79.9    
80.2    
80.5    
80.7    
81.0    
81.2    
81.5    
81.7    
82.0    
82.2    
82.5    
82.7    
83.0    
83.2    
83.5    
83.8    
84.0    
84.3    
84.5    
84.8    
85.0    
85.3    
85.5    
85.8    
86.0    
86.3    
86.5    
86.8    
87.1    
87.3    
87.6    
87.8    
88.1    
88.3    
88.6    
88.8    
89.1    
89.3    
89.6    
89.8    
90.1    
90.4    
90.6    
90.9    
91.1    
91.4    
91.6    
91.9    
92.1    
92.4    
92.6    
92.9    
93.1    
93.4    
93.7    
93.9    
94.2    
94.4    
94.7    
94.9    
95.2    
95.4    
95.7    
95.9    
96.2    
96.4    
96.7    
97.0    
97.2    
97.5    
97.7    
98.0    
98.2    
98.5    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 21 predictions from path traversal
Error with prediction: snap lend_intergenic: 15871, rend_intergenic: 11134  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22461, rend_intergenic: 19796  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38564, rend_intergenic: 36874  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47802, rend_intergenic: 43473  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50957, rend_intergenic: 50354  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59005, rend_intergenic: 56680  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59560, rend_intergenic: 59170  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65234, rend_intergenic: 61625  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84001, rend_intergenic: 78512  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93909, rend_intergenic: 89497  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98352, rend_intergenic: 96620  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 18 predictions persist after filtering for low support