-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_25/scaffold_25_6748010-6907251

-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 GlimmerHMM_glimmerT_54389-T1
Valid prediction for snap_scaffold_25-snap.1433-T1
Valid prediction for GlimmerHMM_glimmerT_54380-T1
Valid prediction for Augustus_model.g36083.t1
Valid prediction for CodingQuarry_transcript_38768-T1
Valid prediction for GlimmerHMM_glimmerT_54377-T1
Valid prediction for snap_scaffold_25-snap.1461-T1
Valid prediction for snap_scaffold_25-snap.1446-T1
Valid prediction for snap_scaffold_25-snap.1454-T1
Valid prediction for snap_scaffold_25-snap.1427-T1
Valid prediction for snap_scaffold_25-snap.1432-T1
Valid prediction for snap_scaffold_25-snap.1440-T1
Valid prediction for Augustus_model.g36082.t1
Valid prediction for GlimmerHMM_glimmerT_54374-T1
Valid prediction for snap_scaffold_25-snap.1460-T1
Valid prediction for GlimmerHMM_glimmerT_54387-T1
Valid prediction for snap_scaffold_25-snap.1436-T1
Valid prediction for GlimmerHMM_glimmerT_54367-T1
Valid prediction for GlimmerHMM_glimmerT_54368-T1
Valid prediction for snap_scaffold_25-snap.1445-T1
Valid prediction for snap_scaffold_25-snap.1447-T1
Valid prediction for snap_scaffold_25-snap.1430-T1
Valid prediction for snap_scaffold_25-snap.1449-T1
Valid prediction for snap_scaffold_25-snap.1428-T1
Valid prediction for Augustus_model.g36087.t1
Valid prediction for Augustus_model.g36081.t1
Valid prediction for Augustus_model.g36080.t1
Valid prediction for snap_scaffold_25-snap.1456-T1
Valid prediction for GlimmerHMM_glimmerT_54375-T1
Valid prediction for snap_scaffold_25-snap.1443-T1
Valid prediction for GlimmerHMM_glimmerT_54362-T1
Valid prediction for snap_scaffold_25-snap.1437-T1
Valid prediction for GlimmerHMM_glimmerT_54363-T1
Valid prediction for Augustus_model.g36091.t1
Valid prediction for Augustus_model.g36085.t1
Valid prediction for snap_scaffold_25-snap.1431-T1
Valid prediction for snap_scaffold_25-snap.1459-T1
Couldn't classify 21525, 21671
Sorry, prediction pasa_asmbl_33647.p3 fails validation.
(CGG)	 AG	21525-21671	GT	GGG
(AAT)	 AG	23330-23476	GT	AGG
(TCG)	 AG	25816-25920	TC	GAT
-recovered pasa_asmbl_33647.p3, terminal, 25816, 25920
-recovered pasa_asmbl_33647.p3, internal, 21525, 21671
-recovered pasa_asmbl_33647.p3, internal, 23330, 23476
Valid prediction for snap_scaffold_25-snap.1426-T1
Valid prediction for snap_scaffold_25-snap.1425-T1
Valid prediction for GlimmerHMM_glimmerT_54370-T1
Valid prediction for GlimmerHMM_glimmerT_54364-T1
Valid prediction for snap_scaffold_25-snap.1438-T1
Valid prediction for pasa_asmbl_33650.p1
Valid prediction for pasa_asmbl_33649.p1
Valid prediction for snap_scaffold_25-snap.1451-T1
Couldn't classify 13771, 13864
Couldn't classify 16143, 16329
Sorry, prediction pasa_asmbl_33645.p2 fails validation.
(TTC)	 GG	13771-13864	GT	AGG
(AAA)	 AG	15203-15266	GT	AGG
(CCT)	 AG	15926-16021	GT	AGG
(GCT)	 AG	16143-16329	GT	TGG
-recovered pasa_asmbl_33645.p2, internal, 15203, 15266
-recovered pasa_asmbl_33645.p2, internal, 15926, 16021
-recovered pasa_asmbl_33645.p2, internal, 16143, 16329
Valid prediction for GlimmerHMM_glimmerT_54390-T1
Valid prediction for Augustus_model.g36098.t1
Valid prediction for snap_scaffold_25-snap.1424-T1
Valid prediction for Augustus_model.g36092.t1
Valid prediction for snap_scaffold_25-snap.1422-T1
Valid prediction for snap_scaffold_25-snap.1453-T1
Valid prediction for GlimmerHMM_glimmerT_54385-T1
Valid prediction for Augustus_model.g36090.t1
Valid prediction for snap_scaffold_25-snap.1429-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_25-snap.1435-T1
Valid prediction for GlimmerHMM_glimmerT_54388-T1
Valid prediction for GlimmerHMM_glimmerT_54383-T1
Valid prediction for Augustus_model.g36088.t1
Valid prediction for snap_scaffold_25-snap.1434-T1
Couldn't classify 40974, 41150
Sorry, prediction pasa_asmbl_34376.p1 fails validation.
(ATG)	 AG	35574-35715	GT	CGG
(GGG)	 AG	36203-36436	GT	GGG
(TCA)	 AG	36753-36892	GT	AGG
(GAC)	 AG	39427-39588	GT	AGG
(GGA)	 AG	40974-41150	GC	TGG
-recovered pasa_asmbl_34376.p1, initial, 35574, 35715
-recovered pasa_asmbl_34376.p1, internal, 35574, 35715
-recovered pasa_asmbl_34376.p1, internal, 36203, 36436
-recovered pasa_asmbl_34376.p1, internal, 36753, 36892
-recovered pasa_asmbl_34376.p1, internal, 39427, 39588
-recovered pasa_asmbl_34376.p1, internal, 40974, 41150
Valid prediction for Augustus_model.g36099.t1
Couldn't classify 94244, 94382
Couldn't classify 94931, 95455
Sorry, prediction pasa_asmbl_34370.p1 fails validation.
(GAA)	 TT	94244-94382	GT	TGG
(ACC)	 AG	94512-94598	GT	AGG
(GAA)	 AG	94702-94766	GT	AAG
(CTG)	 AG	94931-95455	GA	AGG
-recovered pasa_asmbl_34370.p1, internal, 94512, 94598
-recovered pasa_asmbl_34370.p1, internal, 94702, 94766
Valid prediction for snap_scaffold_25-snap.1423-T1
Valid prediction for GlimmerHMM_glimmerT_54361-T1
Couldn't classify 96226, 96367
Couldn't classify 97103, 97316
Sorry, prediction pasa_asmbl_34368.p1 fails validation.
(GTG)	 CT	96226-96367	GT	AGG
(AGT)	 AG	96484-96582	GT	AGG
(AAC)	 AG	96704-96832	GT	GGG
(CCA)	 AG	96923-96995	GT	AGG
(TTC)	 AG	97103-97316	AT	ACA
-recovered pasa_asmbl_34368.p1, internal, 96484, 96582
-recovered pasa_asmbl_34368.p1, internal, 96704, 96832
-recovered pasa_asmbl_34368.p1, internal, 96923, 96995
Valid prediction for GlimmerHMM_glimmerT_54382-T1
Valid prediction for Augustus_model.g36097.t1
Valid prediction for snap_scaffold_25-snap.1442-T1
Valid prediction for pasa_asmbl_34372.p2
Valid prediction for snap_scaffold_25-snap.1448-T1
Valid prediction for GlimmerHMM_glimmerT_54373-T1
Valid prediction for Augustus_model.g36094.t1
Valid prediction for GlimmerHMM_glimmerT_54384-T1
Valid prediction for Augustus_model.g36093.t1
Valid prediction for GlimmerHMM_glimmerT_54386-T1
Valid prediction for Augustus_model.g36086.t1
Valid prediction for snap_scaffold_25-snap.1452-T1
Valid prediction for GlimmerHMM_glimmerT_54366-T1
Valid prediction for Augustus_model.g36084.t1
Valid prediction for GlimmerHMM_glimmerT_54365-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_54379-T1
Valid prediction for snap_scaffold_25-snap.1444-T1
Valid prediction for GlimmerHMM_glimmerT_54372-T1
Valid prediction for Augustus_model.g36100.t1
Valid prediction for snap_scaffold_25-snap.1455-T1
Valid prediction for Augustus_model.g36096.t1
Valid prediction for GlimmerHMM_glimmerT_54369-T1
Valid prediction for GlimmerHMM_glimmerT_54376-T1
Valid prediction for Augustus_model.g36095.t1
Valid prediction for snap_scaffold_25-snap.1458-T1
Valid prediction for Augustus_model.g36089.t1
Valid prediction for snap_scaffold_25-snap.1441-T1
Valid prediction for snap_scaffold_25-snap.1439-T1
Valid prediction for GlimmerHMM_glimmerT_54378-T1
Valid prediction for snap_scaffold_25-snap.1457-T1
Valid prediction for snap_scaffold_25-snap.1450-T1
Couldn't classify 95531, 95723
Couldn't classify 95870, 95976
Sorry, prediction pasa_asmbl_34369.p1 fails validation.
(CAA)	 AC	95531-95723	GT	AAG
(AGA)	 AG	95870-95976	AT	ACA
Valid prediction for GlimmerHMM_glimmerT_54381-T1
Valid prediction for GlimmerHMM_glimmerT_54371-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 12004, rend_intergenic: 10512  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81620, rend_intergenic: 76456  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94260, rend_intergenic: 94003  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98630, rend_intergenic: 94289  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107593, rend_intergenic: 99053  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126878, rend_intergenic: 121273  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134279, rend_intergenic: 128747  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136472, rend_intergenic: 134279  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139781, rend_intergenic: 139215  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145014, rend_intergenic: 140227  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 159242
-exon list size: 406


building trellis

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2.9    
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3.4    
3.7    
3.9    
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4.9    
5.1    
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5.9    
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9.1    
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10.5    
10.8    
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14.5    
14.7    
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15.4    
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15.9    
16.2    
16.4    
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16.9    
17.2    
17.4    
17.6    
17.9    
18.1    
18.4    
18.6    
18.9    
19.1    
19.4    
19.6    
19.9    
20.1    
20.3    
20.6    
20.8    
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21.6    
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24.3    
24.5    
24.8    
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25.2    
25.5    
25.7    
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26.2    
26.5    
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27.5    
27.7    
27.9    
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28.7    
28.9    
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29.7    
29.9    
30.1    
30.4    
30.6    
30.9    
31.1    
31.4    
31.6    
31.9    
32.1    
32.4    
32.6    
32.8    
33.1    
33.3    
33.6    
33.8    
34.1    
34.3    
34.6    
34.8    
35.0    
35.3    
35.5    
35.8    
36.0    
36.3    
36.5    
36.8    
37.0    
37.3    
37.5    
37.7    
38.0    
38.2    
38.5    
38.7    
39.0    
39.2    
39.5    
39.7    
40.0    
40.2    
40.4    
40.7    
40.9    
41.2    
41.4    
41.7    
41.9    
42.2    
42.4    
42.6    
42.9    
43.1    
43.4    
43.6    
43.9    
44.1    
44.4    
44.6    
44.9    
45.1    
45.3    
45.6    
45.8    
46.1    
46.3    
46.6    
46.8    
47.1    
47.3    
47.5    
47.8    
48.0    
48.3    
48.5    
48.8    
49.0    
49.3    
49.5    
49.8    
50.0    
50.2    
50.5    
50.7    
51.0    
51.2    
51.5    
51.7    
52.0    
52.2    
52.5    
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52.9    
53.2    
53.4    
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53.9    
54.2    
54.4    
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54.9    
55.1    
55.4    
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55.9    
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56.4    
56.6    
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58.1    
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58.6    
58.8    
59.1    
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59.6    
59.8    
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60.3    
60.5    
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61.3    
61.5    
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62.0    
62.3    
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63.0    
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71.6    
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73.0    
73.3    
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74.0    
74.3    
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75.2    
75.5    
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76.0    
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77.0    
77.2    
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77.9    
78.2    
78.4    
78.7    
78.9    
79.2    
79.4    
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79.9    
80.1    
80.4    
80.6    
80.9    
81.1    
81.4    
81.6    
81.9    
82.1    
82.4    
82.6    
82.8    
83.1    
83.3    
83.6    
83.8    
84.1    
84.3    
84.6    
84.8    
85.0    
85.3    
85.5    
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86.0    
86.3    
86.5    
86.8    
87.0    
87.3    
87.5    
87.7    
88.0    
88.2    
88.5    
88.7    
89.0    
89.2    
89.5    
89.7    
90.0    
90.2    
90.4    
90.7    
90.9    
91.2    
91.4    
91.7    
91.9    
92.2    
92.4    
92.6    
92.9    
93.1    
93.4    
93.6    
93.9    
94.1    
94.4    
94.6    
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95.1    
95.3    
95.6    
95.8    
96.1    
96.3    
96.6    
96.8    
97.1    
97.3    
97.5    
97.8    
98.0    
98.3    
98.5    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 32 predictions from path traversal
Error with prediction: snap lend_intergenic: 12004, rend_intergenic: 10512  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81620, rend_intergenic: 76456  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94260, rend_intergenic: 94003  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98630, rend_intergenic: 94289  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107593, rend_intergenic: 99053  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126878, rend_intergenic: 121273  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134279, rend_intergenic: 128747  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136472, rend_intergenic: 134279  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139781, rend_intergenic: 139215  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145014, rend_intergenic: 140227  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