-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_1/scaffold_1_18983407-19189192

-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_1-snap.3531-T1
Valid prediction for Augustus_model.g1851.t1
Valid prediction for snap_scaffold_1-snap.3515-T1
Valid prediction for GlimmerHMM_glimmerT_2548-T1
Valid prediction for snap_scaffold_1-snap.3522-T1
Valid prediction for snap_scaffold_1-snap.3509-T1
Valid prediction for snap_scaffold_1-snap.3530-T1
Valid prediction for snap_scaffold_1-snap.3496-T1
Couldn't classify 55149, 55252
Sorry, prediction pasa_asmbl_2579.p1 fails validation.
(GCA)	 CT	55149-55252	GT	AAG
(CCA)	 AG	56216-56384	GT	CTG
(ATC)	 AG	57952-58041	GT	ACG
(ATC)	 AG	58656-58726	GT	AAG
(GAC)	 AG	58939-59041	GT	AAG
(GGC)	 AG	61204-61320	CA	GAC
-recovered pasa_asmbl_2579.p1, terminal, 61204, 61320
-recovered pasa_asmbl_2579.p1, internal, 56216, 56384
-recovered pasa_asmbl_2579.p1, internal, 57952, 58041
-recovered pasa_asmbl_2579.p1, internal, 58656, 58726
-recovered pasa_asmbl_2579.p1, internal, 58939, 59041
Valid prediction for GlimmerHMM_glimmerT_2570-T1
Valid prediction for GlimmerHMM_glimmerT_2571-T1
Valid prediction for snap_scaffold_1-snap.3504-T1
Couldn't classify 52978, 53145
Sorry, prediction CodingQuarry_transcript_3007-T1 fails validation.
(ATG)	 AG	52978-53145	TG	GAT
(GTG)	 AG	53274-53438	GT	AAG
-recovered CodingQuarry_transcript_3007-T1, terminal, 53274, 53438
-recovered CodingQuarry_transcript_3007-T1, internal, 53274, 53438
Valid prediction for snap_scaffold_1-snap.3507-T1
Valid prediction for snap_scaffold_1-snap.3513-T1
Valid prediction for GlimmerHMM_glimmerT_2552-T1
Valid prediction for Augustus_model.g1850.t1
Valid prediction for GlimmerHMM_glimmerT_2566-T1
Valid prediction for GlimmerHMM_glimmerT_2546-T1
Valid prediction for Augustus_model.g1848.t1
Valid prediction for GlimmerHMM_glimmerT_2569-T1
Valid prediction for snap_scaffold_1-snap.3529-T1
Valid prediction for snap_scaffold_1-snap.3521-T1
Valid prediction for snap_scaffold_1-snap.3501-T1
Valid prediction for snap_scaffold_1-snap.3498-T1
Valid prediction for HiQ_model.g1849.t1
Valid prediction for GlimmerHMM_glimmerT_2553-T1
Valid prediction for snap_scaffold_1-snap.3519-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_1-snap.3506-T1
Valid prediction for snap_scaffold_1-snap.3499-T1
Valid prediction for snap_scaffold_1-snap.3494-T1
Valid prediction for snap_scaffold_1-snap.3533-T1
Valid prediction for snap_scaffold_1-snap.3502-T1
Valid prediction for Augustus_model.g1859.t1
Valid prediction for GlimmerHMM_glimmerT_2561-T1
Valid prediction for GlimmerHMM_glimmerT_2558-T1
Valid prediction for pasa_asmbl_2576.p3
Valid prediction for GlimmerHMM_glimmerT_2550-T1
Valid prediction for snap_scaffold_1-snap.3528-T1
Valid prediction for GlimmerHMM_glimmerT_2551-T1
Valid prediction for Augustus_model.g1857.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 HiQ_model.g1845.t1
Valid prediction for snap_scaffold_1-snap.3514-T1
Couldn't classify 193134, 193234
Couldn't classify 193772, 193832
Sorry, prediction pasa_asmbl_1138.p1 fails validation.
(ATG)	 AT	184443-184608	GT	GGG
(AGT)	 AG	186765-186826	GT	AGG
(CTG)	 AG	189762-189848	GT	GGG
(GCC)	 AG	190433-190634	GT	AGG
(AGT)	 AG	191142-191230	GT	AGG
(GTC)	 AG	191579-191665	GT	AGG
(GGA)	 AG	192295-192414	GT	AGG
(GCA)	 AG	193134-193234	AT	TTA
(TTA)	 AC	193772-193832	AC	GTA
-recovered pasa_asmbl_1138.p1, initial, 184443, 184608
-recovered pasa_asmbl_1138.p1, internal, 186765, 186826
-recovered pasa_asmbl_1138.p1, internal, 189762, 189848
-recovered pasa_asmbl_1138.p1, internal, 190433, 190634
-recovered pasa_asmbl_1138.p1, internal, 191142, 191230
-recovered pasa_asmbl_1138.p1, internal, 191579, 191665
-recovered pasa_asmbl_1138.p1, internal, 192295, 192414
Valid prediction for snap_scaffold_1-snap.3508-T1
Couldn't classify 195197, 195298
Couldn't classify 200290, 200422
Sorry, prediction pasa_asmbl_1278.p1 fails validation.
(CAG)	 TG	195197-195298	GT	TGG
(GCG)	 AG	195544-195650	GT	TGG
(GTG)	 AG	195992-196131	GT	CGG
(CTG)	 AG	196603-196765	GT	GGG
(GTA)	 AG	197365-197591	GT	CGG
(ACC)	 AG	197959-198107	GT	CTG
(ACG)	 AG	198350-198478	GT	AGG
(AAT)	 AG	198870-199145	GT	AGG
(TCT)	 AG	199557-199723	GT	AGG
(CAC)	 AG	200290-200422	AG	AGA
-recovered pasa_asmbl_1278.p1, internal, 195544, 195650
-recovered pasa_asmbl_1278.p1, internal, 195992, 196131
-recovered pasa_asmbl_1278.p1, internal, 196603, 196765
-recovered pasa_asmbl_1278.p1, internal, 197365, 197591
-recovered pasa_asmbl_1278.p1, internal, 197959, 198107
-recovered pasa_asmbl_1278.p1, internal, 198350, 198478
-recovered pasa_asmbl_1278.p1, internal, 198870, 199145
-recovered pasa_asmbl_1278.p1, internal, 199557, 199723
Valid prediction for snap_scaffold_1-snap.3523-T1
Valid prediction for CodingQuarry_transcript_3009-T1
Valid prediction for GlimmerHMM_glimmerT_2568-T1
Valid prediction for snap_scaffold_1-snap.3503-T1
Valid prediction for snap_scaffold_1-snap.3520-T1
Valid prediction for snap_scaffold_1-snap.3510-T1
Valid prediction for snap_scaffold_1-snap.3500-T1
Valid prediction for Augustus_model.g1855.t1
Valid prediction for GlimmerHMM_glimmerT_2560-T1
Valid prediction for HiQ_model.g1846.t1
Valid prediction for snap_scaffold_1-snap.3505-T1
Valid prediction for GlimmerHMM_glimmerT_2554-T1
Valid prediction for snap_scaffold_1-snap.3495-T1
Valid prediction for Augustus_model.g1854.t1
Valid prediction for snap_scaffold_1-snap.3527-T1
Valid prediction for GlimmerHMM_glimmerT_2562-T1
Valid prediction for CodingQuarry_transcript_3006-T1
Valid prediction for Augustus_model.g1847.t1
Valid prediction for snap_scaffold_1-snap.3518-T1
Valid prediction for snap_scaffold_1-snap.3511-T1
Valid prediction for snap_scaffold_1-snap.3516-T1
Couldn't classify 91942, 92068
Sorry, prediction pasa_asmbl_1145.p1 fails validation.
(GAC)	 AG	91942-92068	GT	GTG
(TGC)	 AG	92203-92333	GT	AGG
(GAC)	 AG	92429-92572	GT	ATG
(AAC)	 AG	92838-93053	GT	AGG
-recovered pasa_asmbl_1145.p1, terminal, 92838, 93053
-recovered pasa_asmbl_1145.p1, internal, 91942, 92068
-recovered pasa_asmbl_1145.p1, internal, 92203, 92333
-recovered pasa_asmbl_1145.p1, internal, 92429, 92572
-recovered pasa_asmbl_1145.p1, internal, 92838, 93053
Couldn't classify 166742, 166834
Sorry, prediction pasa_asmbl_1141.p1 fails validation.
(ATG)	 AG	161824-161962	GT	AGG
(GAG)	 AG	164382-164454	GT	GAG
(GGA)	 AG	166076-166130	GT	AGG
(ACG)	 AG	166742-166834	AA	CCA
-recovered pasa_asmbl_1141.p1, initial, 161824, 161962
add_exon() Sorry, pasa_asmbl_1141.p1 161824-161962-terminal-3 is invalid.
-recovered pasa_asmbl_1141.p1, terminal, 161824, 161962
-recovered pasa_asmbl_1141.p1, internal, 161824, 161962
-recovered pasa_asmbl_1141.p1, internal, 164382, 164454
-recovered pasa_asmbl_1141.p1, internal, 166076, 166130
Valid prediction for snap_scaffold_1-snap.3526-T1
Valid prediction for GlimmerHMM_glimmerT_2545-T1
Valid prediction for GlimmerHMM_glimmerT_2567-T1
Couldn't classify 99903, 100041
Sorry, prediction pasa_asmbl_1143.p1 fails validation.
(ATG)	 CC	98442-98538	GT	AGG
(GCT)	 AG	98665-98837	GT	AGG
(AAA)	 AG	99004-99132	GT	CTG
(TAC)	 AG	99223-99408	GT	AGG
(GAA)	 AG	99524-99768	GT	ACG
(GTA)	 AG	99903-100041	AC	ATA
-recovered pasa_asmbl_1143.p1, initial, 98442, 98538
-recovered pasa_asmbl_1143.p1, internal, 98665, 98837
-recovered pasa_asmbl_1143.p1, internal, 99004, 99132
-recovered pasa_asmbl_1143.p1, internal, 99223, 99408
-recovered pasa_asmbl_1143.p1, internal, 99524, 99768
Valid prediction for snap_scaffold_1-snap.3512-T1
Valid prediction for GlimmerHMM_glimmerT_2547-T1
Valid prediction for HiQ_model.g1852.t1
Valid prediction for Augustus_model.g1853.t1
Valid prediction for snap_scaffold_1-snap.3497-T1
Valid prediction for GlimmerHMM_glimmerT_2563-T1
Valid prediction for snap_scaffold_1-snap.3525-T1
Valid prediction for GlimmerHMM_glimmerT_2557-T1
Valid prediction for CodingQuarry_transcript_3008-T1
Valid prediction for snap_scaffold_1-snap.3517-T1
Valid prediction for GlimmerHMM_glimmerT_2565-T1
Valid prediction for GlimmerHMM_glimmerT_2564-T1
Couldn't classify 175971, 175991
Sorry, prediction pasa_asmbl_1351.p1 fails validation.
(GAC)	 AT	175971-175991	GT	AGG
(GAC)	 AG	176092-176165	GT	CAG
(CAT)	 AG	176464-176522	GT	CGG
(ACG)	 AG	176969-177089	GT	AGG
(GTG)	 AG	177760-177890	GT	CGG
(CGA)	 AG	178576-178643	GT	TGG
(AGG)	 AG	179863-180009	TT	GAT
-recovered pasa_asmbl_1351.p1, terminal, 179863, 180009
-recovered pasa_asmbl_1351.p1, internal, 176092, 176165
-recovered pasa_asmbl_1351.p1, internal, 176464, 176522
-recovered pasa_asmbl_1351.p1, internal, 176969, 177089
-recovered pasa_asmbl_1351.p1, internal, 177760, 177890
-recovered pasa_asmbl_1351.p1, internal, 178576, 178643
Valid prediction for GlimmerHMM_glimmerT_2556-T1
Couldn't classify 100303, 100456
Sorry, prediction pasa_asmbl_1142.p1 fails validation.
(ATT)	 TC	100303-100456	GT	CCG
(AGA)	 AG	100666-100884	GT	GTG
(TGC)	 AG	101019-101149	GT	AGG
(GAC)	 AG	101245-101388	GT	ATG
(AAC)	 AG	101654-101869	GT	AGG
-recovered pasa_asmbl_1142.p1, terminal, 101654, 101869
-recovered pasa_asmbl_1142.p1, internal, 100666, 100884
-recovered pasa_asmbl_1142.p1, internal, 101019, 101149
-recovered pasa_asmbl_1142.p1, internal, 101245, 101388
-recovered pasa_asmbl_1142.p1, internal, 101654, 101869
Valid prediction for GlimmerHMM_glimmerT_2555-T1
Valid prediction for Augustus_model.g1856.t1
Valid prediction for GlimmerHMM_glimmerT_2549-T1
Valid prediction for snap_scaffold_1-snap.3524-T1
Valid prediction for GlimmerHMM_glimmerT_2559-T1
Valid prediction for Augustus_model.g1858.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 7386, rend_intergenic: 5350  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20527, rend_intergenic: 9639  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39030, rend_intergenic: 22872  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40855, rend_intergenic: 39636  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52845, rend_intergenic: 50196  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67638, rend_intergenic: 66903  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86536, rend_intergenic: 84094  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91236, rend_intergenic: 87006  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101512, rend_intergenic: 96835  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115257, rend_intergenic: 113165  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118050, rend_intergenic: 115452  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127222, rend_intergenic: 118342  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153927, rend_intergenic: 130845  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189956, rend_intergenic: 181300  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 205786
-exon list size: 323


building trellis

0.3    
0.6    
0.9    
1.2    
1.5    
1.8    
2.2    
2.5    
2.8    
3.1    
3.4    
3.7    
4.0    
4.3    
4.6    
4.9    
5.2    
5.5    
5.8    
6.2    
6.5    
6.8    
7.1    
7.4    
7.7    
8.0    
8.3    
8.6    
8.9    
9.2    
9.5    
9.8    
10.2    
10.5    
10.8    
11.1    
11.4    
11.7    
12.0    
12.3    
12.6    
12.9    
13.2    
13.5    
13.8    
14.2    
14.5    
14.8    
15.1    
15.4    
15.7    
16.0    
16.3    
16.6    
16.9    
17.2    
17.5    
17.8    
18.2    
18.5    
18.8    
19.1    
19.4    
19.7    
20.0    
20.3    
20.6    
20.9    
21.2    
21.5    
21.8    
22.2    
22.5    
22.8    
23.1    
23.4    
23.7    
24.0    
24.3    
24.6    
24.9    
25.2    
25.5    
25.8    
26.2    
26.5    
26.8    
27.1    
27.4    
27.7    
28.0    
28.3    
28.6    
28.9    
29.2    
29.5    
29.8    
30.2    
30.5    
30.8    
31.1    
31.4    
31.7    
32.0    
32.3    
32.6    
32.9    
33.2    
33.5    
33.8    
34.2    
34.5    
34.8    
35.1    
35.4    
35.7    
36.0    
36.3    
36.6    
36.9    
37.2    
37.5    
37.8    
38.2    
38.5    
38.8    
39.1    
39.4    
39.7    
40.0    
40.3    
40.6    
40.9    
41.2    
41.5    
41.8    
42.2    
42.5    
42.8    
43.1    
43.4    
43.7    
44.0    
44.3    
44.6    
44.9    
45.2    
45.5    
45.8    
46.2    
46.5    
46.8    
47.1    
47.4    
47.7    
48.0    
48.3    
48.6    
48.9    
49.2    
49.5    
49.8    
50.2    
50.5    
50.8    
51.1    
51.4    
51.7    
52.0    
52.3    
52.6    
52.9    
53.2    
53.5    
53.8    
54.2    
54.5    
54.8    
55.1    
55.4    
55.7    
56.0    
56.3    
56.6    
56.9    
57.2    
57.5    
57.8    
58.2    
58.5    
58.8    
59.1    
59.4    
59.7    
60.0    
60.3    
60.6    
60.9    
61.2    
61.5    
61.8    
62.2    
62.5    
62.8    
63.1    
63.4    
63.7    
64.0    
64.3    
64.6    
64.9    
65.2    
65.5    
65.8    
66.2    
66.5    
66.8    
67.1    
67.4    
67.7    
68.0    
68.3    
68.6    
68.9    
69.2    
69.5    
69.8    
70.2    
70.5    
70.8    
71.1    
71.4    
71.7    
72.0    
72.3    
72.6    
72.9    
73.2    
73.5    
73.8    
74.2    
74.5    
74.8    
75.1    
75.4    
75.7    
76.0    
76.3    
76.6    
76.9    
77.2    
77.5    
77.8    
78.2    
78.5    
78.8    
79.1    
79.4    
79.7    
80.0    
80.3    
80.6    
80.9    
81.2    
81.5    
81.8    
82.2    
82.5    
82.8    
83.1    
83.4    
83.7    
84.0    
84.3    
84.6    
84.9    
85.2    
85.5    
85.8    
86.2    
86.5    
86.8    
87.1    
87.4    
87.7    
88.0    
88.3    
88.6    
88.9    
89.2    
89.5    
89.8    
90.2    
90.5    
90.8    
91.1    
91.4    
91.7    
92.0    
92.3    
92.6    
92.9    
93.2    
93.5    
93.8    
94.2    
94.5    
94.8    
95.1    
95.4    
95.7    
96.0    
96.3    
96.6    
96.9    
97.2    
97.5    
97.8    
98.2    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 7386, rend_intergenic: 5350  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20527, rend_intergenic: 9639  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39030, rend_intergenic: 22872  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40855, rend_intergenic: 39636  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52845, rend_intergenic: 50196  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67638, rend_intergenic: 66903  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86536, rend_intergenic: 84094  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91236, rend_intergenic: 87006  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101512, rend_intergenic: 96835  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115257, rend_intergenic: 113165  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118050, rend_intergenic: 115452  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127222, rend_intergenic: 118342  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153927, rend_intergenic: 130845  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189956, rend_intergenic: 181300  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 25 predictions persist after filtering for low support