-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_9/scaffold_9_4770979-4917008

-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 Augustus_model.g14657.t1
Valid prediction for GlimmerHMM_glimmerT_22059-T1
Valid prediction for Augustus_model.g14670.t1
Valid prediction for GlimmerHMM_glimmerT_22065-T1
Valid prediction for snap_scaffold_9-snap.1011-T1
Valid prediction for snap_scaffold_9-snap.1017-T1
Couldn't classify 112437, 112506
Couldn't classify 116256, 116320
Sorry, prediction pasa_asmbl_53965.p2 fails validation.
(CAC)	 TA	112437-112506	GT	AGG
(ATT)	 AG	113279-113398	GT	CGG
(TGG)	 AG	113614-113727	GT	CCG
(CGG)	 AG	116256-116320	TA	GCT
-recovered pasa_asmbl_53965.p2, internal, 113279, 113398
-recovered pasa_asmbl_53965.p2, internal, 113614, 113727
Couldn't classify 129064, 129275
Sorry, prediction pasa_asmbl_53971.p1 fails validation.
(TCT)	 AC	129064-129275	GT	CGG
(GTC)	 AG	129482-129667	GT	AAG
(GCC)	 AG	130104-130143	GT	AAG
(CCC)	 AG	132649-132709	GT	GTG
(CCA)	 AG	133013-133071	GT	AGG
(GAG)	 AG	133237-133283	GT	AAG
(GGA)	 AG	133374-133465	GT	CAG
(GCC)	 AG	133887-133911	GT	AGG
(GAG)	 AG	134384-134426	GA	AGG
-recovered pasa_asmbl_53971.p1, terminal, 134384, 134426
-recovered pasa_asmbl_53971.p1, internal, 129482, 129667
-recovered pasa_asmbl_53971.p1, internal, 130104, 130143
-recovered pasa_asmbl_53971.p1, internal, 132649, 132709
-recovered pasa_asmbl_53971.p1, internal, 133013, 133071
-recovered pasa_asmbl_53971.p1, internal, 133237, 133283
-recovered pasa_asmbl_53971.p1, internal, 133374, 133465
-recovered pasa_asmbl_53971.p1, internal, 133887, 133911
Valid prediction for CodingQuarry_transcript_62160-T1
Valid prediction for snap_scaffold_9-snap.995-T1
Valid prediction for GlimmerHMM_glimmerT_22062-T1
Valid prediction for pasa_asmbl_53962.p1
Valid prediction for GlimmerHMM_glimmerT_22067-T1
Valid prediction for Augustus_model.g14671.t1
Valid prediction for GlimmerHMM_glimmerT_22057-T1
Valid prediction for GlimmerHMM_glimmerT_22068-T1
Couldn't classify 125290, 125387
Sorry, prediction pasa_asmbl_53969.p1 fails validation.
(AAA)	 AG	125290-125387	GT	ATG
(GAT)	 AG	125854-125955	GT	GTG
(CAC)	 AG	126091-126170	GT	CAG
(TCT)	 AG	126313-126397	GT	AAG
(GCT)	 AG	126489-126628	GT	CGG
(ATG)	 AG	126718-126814	GT	AGG
(GAT)	 AG	126911-126989	GT	CTG
(GGG)	 AG	127123-127196	GT	AGG
(CTA)	 AG	127481-127522	GT	AGG
(ACC)	 AG	128265-128580	TT	AGT
add_exon() Sorry, pasa_asmbl_53969.p1 126718-126814-initial-1 is invalid.
-recovered pasa_asmbl_53969.p1, initial, 126718, 126814
-recovered pasa_asmbl_53969.p1, terminal, 128265, 128580
-recovered pasa_asmbl_53969.p1, internal, 125290, 125387
-recovered pasa_asmbl_53969.p1, internal, 125854, 125955
-recovered pasa_asmbl_53969.p1, internal, 126091, 126170
-recovered pasa_asmbl_53969.p1, internal, 126313, 126397
-recovered pasa_asmbl_53969.p1, internal, 126489, 126628
-recovered pasa_asmbl_53969.p1, internal, 126718, 126814
-recovered pasa_asmbl_53969.p1, internal, 126911, 126989
-recovered pasa_asmbl_53969.p1, internal, 127123, 127196
-recovered pasa_asmbl_53969.p1, internal, 127481, 127522
Valid prediction for CodingQuarry_transcript_62158-T1
Valid prediction for snap_scaffold_9-snap.1012-T1
Valid prediction for Augustus_model.g14672.t1
Valid prediction for snap_scaffold_9-snap.1004-T1
Valid prediction for snap_scaffold_9-snap.1001-T1
Valid prediction for Augustus_model.g14673.t1
Valid prediction for GlimmerHMM_glimmerT_22072-T1
Valid prediction for CodingQuarry_transcript_62161-T1
Valid prediction for snap_scaffold_9-snap.1019-T1
Valid prediction for snap_scaffold_9-snap.1024-T1
Valid prediction for Augustus_model.g14664.t1
Valid prediction for snap_scaffold_9-snap.1007-T1
Valid prediction for Augustus_model.g14669.t1
Valid prediction for HiQ_model.g14667.t1
Couldn't classify 55650, 55680
Sorry, prediction pasa_asmbl_53958.p1 fails validation.
(TTT)	 AT	55650-55680	GT	AGG
(ATG)	 AG	55800-56005	GT	CAG
(GTT)	 AG	56160-56308	GT	AGG
(GAG)	 AG	56813-56945	CC	GAC
add_exon() Sorry, pasa_asmbl_53958.p1 55800-56005-initial-1 is invalid.
-recovered pasa_asmbl_53958.p1, initial, 55800, 56005
-recovered pasa_asmbl_53958.p1, terminal, 56813, 56945
-recovered pasa_asmbl_53958.p1, internal, 55800, 56005
-recovered pasa_asmbl_53958.p1, internal, 56160, 56308
Valid prediction for Augustus_model.g14655.t1
Valid prediction for Augustus_model.g14659.t1
Couldn't classify 63137, 64261
Sorry, prediction pasa_asmbl_53959.p1 fails validation.
(CTC)	 GC	63137-64261	GT	GGG
Valid prediction for snap_scaffold_9-snap.1006-T1
Valid prediction for GlimmerHMM_glimmerT_22064-T1
Valid prediction for snap_scaffold_9-snap.1015-T1
Couldn't classify 17672, 17756
Sorry, prediction pasa_asmbl_53956.p1 fails validation.
(ATG)	 GC	15982-16098	GT	AGG
(AAG)	 AG	16383-16489	GT	GTG
(GTA)	 AG	17672-17756	CT	CCC
-recovered pasa_asmbl_53956.p1, initial, 15982, 16098
-recovered pasa_asmbl_53956.p1, internal, 16383, 16489
Valid prediction for pasa_asmbl_53970.p1
Couldn't classify 71008, 71107
Couldn't classify 73434, 73505
Sorry, prediction pasa_asmbl_54780.p1 fails validation.
(CAG)	 TC	71008-71107	GT	CGG
(GTA)	 AG	71328-71541	GT	AGG
(GAC)	 AG	71686-71890	GT	AGG
(AAA)	 AG	72941-73042	GT	TGG
(AAA)	 AG	73147-73218	GT	AGG
(GTG)	 AG	73434-73505	AA	GGA
-recovered pasa_asmbl_54780.p1, internal, 71328, 71541
-recovered pasa_asmbl_54780.p1, internal, 71686, 71890
-recovered pasa_asmbl_54780.p1, internal, 72941, 73042
-recovered pasa_asmbl_54780.p1, internal, 73147, 73218
Valid prediction for Augustus_model.g14665.t1
Valid prediction for Augustus_model.g14662.t1
Valid prediction for GlimmerHMM_glimmerT_22055-T1
Valid prediction for GlimmerHMM_glimmerT_22073-T1
Valid prediction for snap_scaffold_9-snap.1009-T1
Valid prediction for snap_scaffold_9-snap.999-T1
Valid prediction for snap_scaffold_9-snap.1022-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 CodingQuarry_transcript_62157-T1
Valid prediction for snap_scaffold_9-snap.1018-T1
Valid prediction for pasa_asmbl_54972.p1
Valid prediction for GlimmerHMM_glimmerT_22061-T1
Valid prediction for GlimmerHMM_glimmerT_22066-T1
Valid prediction for GlimmerHMM_glimmerT_22056-T1
Valid prediction for snap_scaffold_9-snap.1023-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g14668.t1
Valid prediction for snap_scaffold_9-snap.1002-T1
Valid prediction for snap_scaffold_9-snap.1016-T1
Valid prediction for Augustus_model.g14661.t1
Valid prediction for snap_scaffold_9-snap.997-T1
Valid prediction for GlimmerHMM_glimmerT_22060-T1
Valid prediction for snap_scaffold_9-snap.1008-T1
Valid prediction for snap_scaffold_9-snap.1000-T1
Valid prediction for snap_scaffold_9-snap.1020-T1
Valid prediction for snap_scaffold_9-snap.1013-T1
Valid prediction for snap_scaffold_9-snap.1014-T1
Valid prediction for GlimmerHMM_glimmerT_22058-T1
Valid prediction for snap_scaffold_9-snap.1010-T1
Valid prediction for GlimmerHMM_glimmerT_22070-T1
Valid prediction for snap_scaffold_9-snap.1025-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for snap_scaffold_9-snap.998-T1
Valid prediction for snap_scaffold_9-snap.1021-T1
Sorry, intron length (3) is less than minimum required (10)
Couldn't classify 78930, 79244
Sorry, prediction pasa_asmbl_53960.p1 fails validation.
(CCT)	 AT	78930-79244	AC	TCA
Valid prediction for GlimmerHMM_glimmerT_22063-T1
Valid prediction for snap_scaffold_9-snap.1003-T1
Valid prediction for HiQ_model.g14660.t1
Valid prediction for snap_scaffold_9-snap.996-T1
Valid prediction for GlimmerHMM_glimmerT_22071-T1
Valid prediction for Augustus_model.g14656.t1
Valid prediction for pasa_asmbl_54976.p1
Valid prediction for HiQ_model.g14666.t1
Valid prediction for CodingQuarry_transcript_62159-T1
Valid prediction for HiQ_model.g14663.t1
Valid prediction for Augustus_model.g14658.t1
Valid prediction for GlimmerHMM_glimmerT_22069-T1
Couldn't classify 68476, 68546
Sorry, prediction pasa_asmbl_54978.p1 fails validation.
(GCA)	 TC	68476-68546	GT	AGG
(CTT)	 AG	68630-68698	GT	CAG
(GTG)	 AG	68893-69017	GT	AGG
(CCC)	 AG	69126-69255	GC	CCG
(ATA)	 AG	69444-69514	GT	AGG
(GTG)	 AG	69603-69934	GG	GAG
-recovered pasa_asmbl_54978.p1, terminal, 69603, 69934
-recovered pasa_asmbl_54978.p1, internal, 68630, 68698
-recovered pasa_asmbl_54978.p1, internal, 68893, 69017
-recovered pasa_asmbl_54978.p1, internal, 69126, 69255
-recovered pasa_asmbl_54978.p1, internal, 69444, 69514
Valid prediction for snap_scaffold_9-snap.1005-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 7531, rend_intergenic: 3935  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28730, rend_intergenic: 15136  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33013, rend_intergenic: 31569  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38629, rend_intergenic: 33710  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44660, rend_intergenic: 40861  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52913, rend_intergenic: 47049  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73649, rend_intergenic: 64048  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92164, rend_intergenic: 86341  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97856, rend_intergenic: 92454  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106692, rend_intergenic: 102206  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122715, rend_intergenic: 112341  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127703, rend_intergenic: 124879  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134525, rend_intergenic: 128877  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144271, rend_intergenic: 137534  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 146030
-exon list size: 375


building trellis

0.3    
0.5    
0.8    
1.1    
1.3    
1.6    
1.9    
2.1    
2.4    
2.7    
2.9    
3.2    
3.4    
3.7    
4.0    
4.2    
4.5    
4.8    
5.0    
5.3    
5.6    
5.8    
6.1    
6.4    
6.6    
6.9    
7.2    
7.4    
7.7    
8.0    
8.2    
8.5    
8.8    
9.0    
9.3    
9.5    
9.8    
10.1    
10.3    
10.6    
10.9    
11.1    
11.4    
11.7    
11.9    
12.2    
12.5    
12.7    
13.0    
13.3    
13.5    
13.8    
14.1    
14.3    
14.6    
14.9    
15.1    
15.4    
15.6    
15.9    
16.2    
16.4    
16.7    
17.0    
17.2    
17.5    
17.8    
18.0    
18.3    
18.6    
18.8    
19.1    
19.4    
19.6    
19.9    
20.2    
20.4    
20.7    
21.0    
21.2    
21.5    
21.8    
22.0    
22.3    
22.5    
22.8    
23.1    
23.3    
23.6    
23.9    
24.1    
24.4    
24.7    
24.9    
25.2    
25.5    
25.7    
26.0    
26.3    
26.5    
26.8    
27.1    
27.3    
27.6    
27.9    
28.1    
28.4    
28.6    
28.9    
29.2    
29.4    
29.7    
30.0    
30.2    
30.5    
30.8    
31.0    
31.3    
31.6    
31.8    
32.1    
32.4    
32.6    
32.9    
33.2    
33.4    
33.7    
34.0    
34.2    
34.5    
34.7    
35.0    
35.3    
35.5    
35.8    
36.1    
36.3    
36.6    
36.9    
37.1    
37.4    
37.7    
37.9    
38.2    
38.5    
38.7    
39.0    
39.3    
39.5    
39.8    
40.1    
40.3    
40.6    
40.8    
41.1    
41.4    
41.6    
41.9    
42.2    
42.4    
42.7    
43.0    
43.2    
43.5    
43.8    
44.0    
44.3    
44.6    
44.8    
45.1    
45.4    
45.6    
45.9    
46.2    
46.4    
46.7    
46.9    
47.2    
47.5    
47.7    
48.0    
48.3    
48.5    
48.8    
49.1    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
50.9    
51.2    
51.5    
51.7    
52.0    
52.3    
52.5    
52.8    
53.1    
53.3    
53.6    
53.8    
54.1    
54.4    
54.6    
54.9    
55.2    
55.4    
55.7    
56.0    
56.2    
56.5    
56.8    
57.0    
57.3    
57.6    
57.8    
58.1    
58.4    
58.6    
58.9    
59.2    
59.4    
59.7    
59.9    
60.2    
60.5    
60.7    
61.0    
61.3    
61.5    
61.8    
62.1    
62.3    
62.6    
62.9    
63.1    
63.4    
63.7    
63.9    
64.2    
64.5    
64.7    
65.0    
65.3    
65.5    
65.8    
66.0    
66.3    
66.6    
66.8    
67.1    
67.4    
67.6    
67.9    
68.2    
68.4    
68.7    
69.0    
69.2    
69.5    
69.8    
70.0    
70.3    
70.6    
70.8    
71.1    
71.4    
71.6    
71.9    
72.1    
72.4    
72.7    
72.9    
73.2    
73.5    
73.7    
74.0    
74.3    
74.5    
74.8    
75.1    
75.3    
75.6    
75.9    
76.1    
76.4    
76.7    
76.9    
77.2    
77.5    
77.7    
78.0    
78.2    
78.5    
78.8    
79.0    
79.3    
79.6    
79.8    
80.1    
80.4    
80.6    
80.9    
81.2    
81.4    
81.7    
82.0    
82.2    
82.5    
82.8    
83.0    
83.3    
83.6    
83.8    
84.1    
84.4    
84.6    
84.9    
85.1    
85.4    
85.7    
85.9    
86.2    
86.5    
86.7    
87.0    
87.3    
87.5    
87.8    
88.1    
88.3    
88.6    
88.9    
89.1    
89.4    
89.7    
89.9    
90.2    
90.5    
90.7    
91.0    
91.2    
91.5    
91.8    
92.0    
92.3    
92.6    
92.8    
93.1    
93.4    
93.6    
93.9    
94.2    
94.4    
94.7    
95.0    
95.2    
95.5    
95.8    
96.0    
96.3    
96.6    
96.8    
97.1    
97.3    
97.6    
97.9    
98.1    
98.4    
98.7    
98.9    
99.2    
99.5    
99.7    
-found 22 predictions from path traversal
Error with prediction: snap lend_intergenic: 7531, rend_intergenic: 3935  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28730, rend_intergenic: 15136  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33013, rend_intergenic: 31569  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38629, rend_intergenic: 33710  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44660, rend_intergenic: 40861  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52913, rend_intergenic: 47049  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73649, rend_intergenic: 64048  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92164, rend_intergenic: 86341  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97856, rend_intergenic: 92454  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106692, rend_intergenic: 102206  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122715, rend_intergenic: 112341  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127703, rend_intergenic: 124879  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134525, rend_intergenic: 128877  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144271, rend_intergenic: 137534  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support