-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_3/scaffold_3_1183811-1350000

-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_3-snap.309-T1
Valid prediction for snap_scaffold_3-snap.315-T1
Valid prediction for GlimmerHMM_glimmerT_6012-T1
Valid prediction for Augustus_model.g3913.t1
Valid prediction for Augustus_model.g3915.t1
Valid prediction for snap_scaffold_3-snap.322-T1
Valid prediction for GlimmerHMM_glimmerT_6000-T1
Couldn't classify 123542, 123670
Couldn't classify 129612, 129674
Sorry, prediction pasa_asmbl_39842.p1 fails validation.
(AGT)	 CC	123542-123670	GT	TGG
(GAC)	 AG	124437-124542	GT	AGG
(ACC)	 AG	126473-126609	GT	AGG
(ATC)	 AG	127109-127239	GT	AGG
(CAC)	 AG	128424-128511	GT	AGG
(CCA)	 AG	129612-129674	CT	GCC
-recovered pasa_asmbl_39842.p1, internal, 124437, 124542
-recovered pasa_asmbl_39842.p1, internal, 126473, 126609
-recovered pasa_asmbl_39842.p1, internal, 127109, 127239
-recovered pasa_asmbl_39842.p1, internal, 128424, 128511
Valid prediction for snap_scaffold_3-snap.311-T1
Valid prediction for snap_scaffold_3-snap.302-T1
Valid prediction for GlimmerHMM_glimmerT_6013-T1
Couldn't classify 79388, 79579
Couldn't classify 79852, 79965
Sorry, prediction pasa_asmbl_40887.p2 fails validation.
(ATT)	 AG	79388-79579	GT	TGG
(GAG)	 AG	79852-79965	TC	GGT
-recovered pasa_asmbl_40887.p2, internal, 79388, 79579
Couldn't classify 145598, 145708
Sorry, prediction pasa_asmbl_40781.p1 fails validation.
(GTG)	 CA	145598-145708	GT	ATG
(AGC)	 AG	146008-146145	GT	TGG
(CCC)	 AG	146390-146497	CA	AAC
-recovered pasa_asmbl_40781.p1, terminal, 146390, 146497
-recovered pasa_asmbl_40781.p1, internal, 146008, 146145
Valid prediction for GlimmerHMM_glimmerT_5999-T1
Valid prediction for snap_scaffold_3-snap.303-T1
Valid prediction for snap_scaffold_3-snap.324-T1
Valid prediction for snap_scaffold_3-snap.326-T1
Valid prediction for GlimmerHMM_glimmerT_6006-T1
Valid prediction for Augustus_model.g3921.t1
Valid prediction for snap_scaffold_3-snap.299-T1
Valid prediction for snap_scaffold_3-snap.310-T1
Valid prediction for GlimmerHMM_glimmerT_6007-T1
Valid prediction for GlimmerHMM_glimmerT_6002-T1
Couldn't classify 73837, 74031
Sorry, prediction pasa_asmbl_39841.p1 fails validation.
(ATG)	 CC	73392-73574	GT	AGG
(GAG)	 AG	73837-74031	GT	TAG
-recovered pasa_asmbl_39841.p1, initial, 73392, 73574
-recovered pasa_asmbl_39841.p1, internal, 73837, 74031
Valid prediction for snap_scaffold_3-snap.295-T1
Valid prediction for snap_scaffold_3-snap.297-T1
Couldn't classify 70672, 70752
Couldn't classify 71719, 71861
Sorry, prediction pasa_asmbl_40845.p1 fails validation.
(CTG)	 CC	70672-70752	GT	TGG
(GAG)	 AG	71024-71233	GT	AGG
(GGA)	 AG	71406-71508	GT	AGG
(AGC)	 AG	71719-71861	AT	ACA
-recovered pasa_asmbl_40845.p1, internal, 71024, 71233
-recovered pasa_asmbl_40845.p1, internal, 71406, 71508
Valid prediction for Augustus_model.g3922.t1
Valid prediction for GlimmerHMM_glimmerT_5996-T1
Valid prediction for Augustus_model.g3914.t1
Valid prediction for Augustus_model.g3911.t1
Valid prediction for GlimmerHMM_glimmerT_6004-T1
Valid prediction for snap_scaffold_3-snap.305-T1
Sorry, intron length (4) is less than minimum required (10)
Couldn't classify 44223, 44424
Sorry, prediction pasa_asmbl_40891.p1 fails validation.
(AGA)	 AC	44223-44424	GT	AGG
(GAT)	 AG	45142-45269	GT	AGG
(GGC)	 AG	45823-45932	GT	CAG
(CTA)	 AG	46121-46311	GT	AGG
(GTC)	 AG	46427-46669	GT	ATG
(TGT)	 AG	46778-47058	GT	TGG
(AAG)	 AG	47315-47524	GT	AGG
(GCA)	 AG	47697-47799	GT	AGG
(AGC)	 AG	48011-48204	GT	AGG
(GAG)	 AG	48457-48678	CA	AAC
-recovered pasa_asmbl_40891.p1, terminal, 48457, 48678
-recovered pasa_asmbl_40891.p1, internal, 45142, 45269
-recovered pasa_asmbl_40891.p1, internal, 45823, 45932
-recovered pasa_asmbl_40891.p1, internal, 46121, 46311
-recovered pasa_asmbl_40891.p1, internal, 46427, 46669
-recovered pasa_asmbl_40891.p1, internal, 46778, 47058
-recovered pasa_asmbl_40891.p1, internal, 47315, 47524
-recovered pasa_asmbl_40891.p1, internal, 47697, 47799
-recovered pasa_asmbl_40891.p1, internal, 48011, 48204
Valid prediction for GlimmerHMM_glimmerT_6010-T1
Valid prediction for snap_scaffold_3-snap.321-T1
Valid prediction for GlimmerHMM_glimmerT_6001-T1
Valid prediction for Augustus_model.g3916.t1
Valid prediction for snap_scaffold_3-snap.316-T1
Couldn't classify 5624, 5761
Couldn't classify 9517, 9684
Sorry, prediction pasa_asmbl_39835.p1 fails validation.
(GGC)	 CA	5624-5761	GT	AGG
(CCA)	 AG	7302-7403	GT	TGG
(CAA)	 AG	9517-9684	AC	AGA
-recovered pasa_asmbl_39835.p1, internal, 7302, 7403
Valid prediction for snap_scaffold_3-snap.301-T1
Valid prediction for GlimmerHMM_glimmerT_6005-T1
Valid prediction for snap_scaffold_3-snap.314-T1
Couldn't classify 67965, 68166
Couldn't classify 70120, 70313
Sorry, prediction pasa_asmbl_39838.p1 fails validation.
(AGA)	 GC	67965-68166	GT	AGG
(GAT)	 AG	68849-68976	GT	AGG
(GGC)	 AG	69531-69640	GT	CAG
(CTA)	 AG	69814-70004	GT	AGG
(GTC)	 AG	70120-70313	AA	CCA
-recovered pasa_asmbl_39838.p1, internal, 68849, 68976
-recovered pasa_asmbl_39838.p1, internal, 69531, 69640
-recovered pasa_asmbl_39838.p1, internal, 69814, 70004
Valid prediction for GlimmerHMM_glimmerT_5998-T1
Valid prediction for snap_scaffold_3-snap.313-T1
Valid prediction for snap_scaffold_3-snap.319-T1
Valid prediction for snap_scaffold_3-snap.304-T1
Valid prediction for Augustus_model.g3919.t1
Valid prediction for CodingQuarry_transcript_46071-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_3-snap.330-T1
Valid prediction for Augustus_model.g3912.t1
Valid prediction for snap_scaffold_3-snap.296-T1
Valid prediction for snap_scaffold_3-snap.323-T1
Valid prediction for snap_scaffold_3-snap.318-T1
Valid prediction for snap_scaffold_3-snap.306-T1
Valid prediction for snap_scaffold_3-snap.312-T1
Valid prediction for snap_scaffold_3-snap.328-T1
Valid prediction for GlimmerHMM_glimmerT_5997-T1
Valid prediction for GlimmerHMM_glimmerT_6008-T1
Valid prediction for Augustus_model.g3918.t1
Valid prediction for snap_scaffold_3-snap.325-T1
Valid prediction for CodingQuarry_transcript_46070-T1
Valid prediction for CodingQuarry_transcript_46072-T1
Couldn't classify 136654, 136746
Sorry, prediction pasa_asmbl_38700.p1 fails validation.
(GTG)	 GC	136654-136746	GT	AGG
(TTT)	 AG	136974-137103	GT	GAG
(TCA)	 AG	137220-137902	CC	AAC
add_exon() Sorry, pasa_asmbl_38700.p1 136974-137103-terminal-3 is invalid.
-recovered pasa_asmbl_38700.p1, terminal, 136974, 137103
-recovered pasa_asmbl_38700.p1, terminal, 137220, 137902
-recovered pasa_asmbl_38700.p1, internal, 136974, 137103
Valid prediction for Augustus_model.g3920.t1
Valid prediction for snap_scaffold_3-snap.320-T1
Valid prediction for snap_scaffold_3-snap.331-T1
Valid prediction for Augustus_model.g3917.t1
Valid prediction for GlimmerHMM_glimmerT_6011-T1
Valid prediction for snap_scaffold_3-snap.298-T1
Valid prediction for snap_scaffold_3-snap.332-T1
Valid prediction for GlimmerHMM_glimmerT_6009-T1
Valid prediction for snap_scaffold_3-snap.294-T1
Valid prediction for GlimmerHMM_glimmerT_6003-T1
Valid prediction for snap_scaffold_3-snap.317-T1
Valid prediction for snap_scaffold_3-snap.308-T1
Valid prediction for snap_scaffold_3-snap.329-T1
Valid prediction for HiQ_model.g3923.t1
Couldn't classify 134100, 134273
Sorry, prediction pasa_asmbl_39738.p1 fails validation.
(ATG)	 AG	131452-131579	GT	CCG
(GAA)	 AG	131907-132002	GT	GAG
(ACA)	 AG	132137-132215	GT	CGG
(GAT)	 AG	132639-132771	GT	AGG
(ACG)	 AG	133226-133370	GT	CAG
(GTC)	 AG	133799-133861	GT	AAG
(GGT)	 AG	133956-134013	GT	AGG
(GTG)	 AG	134100-134273	GT	AGG
-recovered pasa_asmbl_39738.p1, initial, 131452, 131579
add_exon() Sorry, pasa_asmbl_39738.p1 131907-132002-terminal-1 is invalid.
-recovered pasa_asmbl_39738.p1, terminal, 131907, 132002
-recovered pasa_asmbl_39738.p1, internal, 131452, 131579
-recovered pasa_asmbl_39738.p1, internal, 131907, 132002
-recovered pasa_asmbl_39738.p1, internal, 132137, 132215
-recovered pasa_asmbl_39738.p1, internal, 132639, 132771
-recovered pasa_asmbl_39738.p1, internal, 133226, 133370
-recovered pasa_asmbl_39738.p1, internal, 133799, 133861
-recovered pasa_asmbl_39738.p1, internal, 133956, 134013
-recovered pasa_asmbl_39738.p1, internal, 134100, 134273
Valid prediction for snap_scaffold_3-snap.327-T1
Valid prediction for pasa_asmbl_38701.p1
Valid prediction for GlimmerHMM_glimmerT_6014-T1
Valid prediction for pasa_asmbl_38704.p1
Valid prediction for snap_scaffold_3-snap.307-T1
Valid prediction for snap_scaffold_3-snap.300-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 6734, rend_intergenic: 3669  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24414, rend_intergenic: 9547  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31276, rend_intergenic: 28293  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32157, rend_intergenic: 31404  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60017, rend_intergenic: 49428  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62644, rend_intergenic: 61512  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83321, rend_intergenic: 82418  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92574, rend_intergenic: 91207  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111374, rend_intergenic: 101036  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116273, rend_intergenic: 113770  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124977, rend_intergenic: 116344  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149199, rend_intergenic: 126635  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 166190
-exon list size: 330


building trellis

0.3    
0.6    
0.9    
1.2    
1.5    
1.8    
2.1    
2.4    
2.7    
3.0    
3.3    
3.6    
3.9    
4.2    
4.5    
4.8    
5.1    
5.4    
5.7    
6.0    
6.3    
6.6    
6.9    
7.2    
7.5    
7.8    
8.1    
8.4    
8.7    
9.0    
9.3    
9.6    
9.9    
10.2    
10.5    
10.8    
11.1    
11.4    
11.7    
12.0    
12.3    
12.7    
13.0    
13.3    
13.6    
13.9    
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    
18.1    
18.4    
18.7    
19.0    
19.3    
19.6    
19.9    
20.2    
20.5    
20.8    
21.1    
21.4    
21.7    
22.0    
22.3    
22.6    
22.9    
23.2    
23.5    
23.8    
24.1    
24.4    
24.7    
25.0    
25.3    
25.6    
25.9    
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    
30.1    
30.4    
30.7    
31.0    
31.3    
31.6    
31.9    
32.2    
32.5    
32.8    
33.1    
33.4    
33.7    
34.0    
34.3    
34.6    
34.9    
35.2    
35.5    
35.8    
36.1    
36.4    
36.7    
37.0    
37.3    
37.7    
38.0    
38.3    
38.6    
38.9    
39.2    
39.5    
39.8    
40.1    
40.4    
40.7    
41.0    
41.3    
41.6    
41.9    
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    
46.1    
46.4    
46.7    
47.0    
47.3    
47.6    
47.9    
48.2    
48.5    
48.8    
49.1    
49.4    
49.7    
50.0    
50.3    
50.6    
50.9    
51.2    
51.5    
51.8    
52.1    
52.4    
52.7    
53.0    
53.3    
53.6    
53.9    
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    
58.1    
58.4    
58.7    
59.0    
59.3    
59.6    
59.9    
60.2    
60.5    
60.8    
61.1    
61.4    
61.7    
62.0    
62.3    
62.7    
63.0    
63.3    
63.6    
63.9    
64.2    
64.5    
64.8    
65.1    
65.4    
65.7    
66.0    
66.3    
66.6    
66.9    
67.2    
67.5    
67.8    
68.1    
68.4    
68.7    
69.0    
69.3    
69.6    
69.9    
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    
74.1    
74.4    
74.7    
75.0    
75.3    
75.6    
75.9    
76.2    
76.5    
76.8    
77.1    
77.4    
77.7    
78.0    
78.3    
78.6    
78.9    
79.2    
79.5    
79.8    
80.1    
80.4    
80.7    
81.0    
81.3    
81.6    
81.9    
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    
86.1    
86.4    
86.7    
87.0    
87.3    
87.7    
88.0    
88.3    
88.6    
88.9    
89.2    
89.5    
89.8    
90.1    
90.4    
90.7    
91.0    
91.3    
91.6    
91.9    
92.2    
92.5    
92.8    
93.1    
93.4    
93.7    
94.0    
94.3    
94.6    
94.9    
95.2    
95.5    
95.8    
96.1    
96.4    
96.7    
97.0    
97.3    
97.6    
97.9    
98.2    
98.5    
98.8    
99.1    
99.4    
99.7    
-found 20 predictions from path traversal
Error with prediction: snap lend_intergenic: 6734, rend_intergenic: 3669  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24414, rend_intergenic: 9547  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31276, rend_intergenic: 28293  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32157, rend_intergenic: 31404  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60017, rend_intergenic: 49428  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62644, rend_intergenic: 61512  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83321, rend_intergenic: 82418  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92574, rend_intergenic: 91207  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111374, rend_intergenic: 101036  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116273, rend_intergenic: 113770  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124977, rend_intergenic: 116344  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149199, rend_intergenic: 126635  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support