-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_6954483-7181341

-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.1448-T1
Valid prediction for Augustus_model.g4406.t1
Valid prediction for snap_scaffold_3-snap.1443-T1
Valid prediction for GlimmerHMM_glimmerT_6763-T1
Valid prediction for GlimmerHMM_glimmerT_6765-T1
Valid prediction for snap_scaffold_3-snap.1408-T1
Valid prediction for Augustus_model.g4412.t1
Valid prediction for Augustus_model.g4413.t1
Valid prediction for Augustus_model.g4415.t1
Valid prediction for Augustus_model.g4411.t1
Valid prediction for snap_scaffold_3-snap.1435-T1
Valid prediction for snap_scaffold_3-snap.1452-T1
Valid prediction for Augustus_model.g4405.t1
Valid prediction for GlimmerHMM_glimmerT_6768-T1
Valid prediction for snap_scaffold_3-snap.1413-T1
Valid prediction for snap_scaffold_3-snap.1437-T1
Valid prediction for GlimmerHMM_glimmerT_6762-T1
Valid prediction for Augustus_model.g4414.t1
Valid prediction for Augustus_model.g4410.t1
Valid prediction for Augustus_model.g4409.t1
Valid prediction for snap_scaffold_3-snap.1441-T1
Valid prediction for GlimmerHMM_glimmerT_6764-T1
Valid prediction for GlimmerHMM_glimmerT_6767-T1
Valid prediction for snap_scaffold_3-snap.1431-T1
Valid prediction for snap_scaffold_3-snap.1425-T1
Valid prediction for Augustus_model.g4407.t1
Valid prediction for snap_scaffold_3-snap.1433-T1
Valid prediction for snap_scaffold_3-snap.1440-T1
Valid prediction for snap_scaffold_3-snap.1429-T1
Valid prediction for GlimmerHMM_glimmerT_6756-T1
Valid prediction for GlimmerHMM_glimmerT_6758-T1
Valid prediction for GlimmerHMM_glimmerT_6773-T1
Valid prediction for Augustus_model.g4404.t1
Couldn't classify 142387, 142472
Couldn't classify 143310, 143315
Sorry, prediction pasa_asmbl_40148.p1 fails validation.
(GAG)	 TA	142387-142472	GT	GAG
(TTT)	 AG	142604-142673	GT	ACG
(GAG)	 AG	142782-142868	GT	TGG
(GGC)	 AG	142958-143050	GT	AGG
(GAC)	 AG	143149-143199	GT	AGG
(AAA)	 AG	143310-143315	GT	CGG
-recovered pasa_asmbl_40148.p1, internal, 142604, 142673
-recovered pasa_asmbl_40148.p1, internal, 142782, 142868
-recovered pasa_asmbl_40148.p1, internal, 142958, 143050
-recovered pasa_asmbl_40148.p1, internal, 143149, 143199
-recovered pasa_asmbl_40148.p1, internal, 143310, 143315
Valid prediction for snap_scaffold_3-snap.1424-T1
Valid prediction for snap_scaffold_3-snap.1438-T1
Valid prediction for Augustus_model.g4416.t1
Valid prediction for snap_scaffold_3-snap.1417-T1
Valid prediction for snap_scaffold_3-snap.1439-T1
Valid prediction for GlimmerHMM_glimmerT_6754-T1
Valid prediction for GlimmerHMM_glimmerT_6766-T1
Valid prediction for Augustus_model.g4408.t1
Valid prediction for GlimmerHMM_glimmerT_6761-T1
Valid prediction for snap_scaffold_3-snap.1445-T1
Valid prediction for snap_scaffold_3-snap.1409-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 GlimmerHMM_glimmerT_6750-T1
Valid prediction for GlimmerHMM_glimmerT_6760-T1
Valid prediction for snap_scaffold_3-snap.1423-T1
Valid prediction for GlimmerHMM_glimmerT_6770-T1
Valid prediction for GlimmerHMM_glimmerT_6759-T1
Valid prediction for GlimmerHMM_glimmerT_6755-T1
Valid prediction for Augustus_model.g4403.t1
Valid prediction for Augustus_model.g4402.t1
Valid prediction for snap_scaffold_3-snap.1444-T1
Valid prediction for snap_scaffold_3-snap.1430-T1
Valid prediction for snap_scaffold_3-snap.1449-T1
Valid prediction for snap_scaffold_3-snap.1428-T1
Valid prediction for snap_scaffold_3-snap.1420-T1
Valid prediction for snap_scaffold_3-snap.1422-T1
Valid prediction for snap_scaffold_3-snap.1412-T1
Valid prediction for snap_scaffold_3-snap.1432-T1
Valid prediction for snap_scaffold_3-snap.1434-T1
Valid prediction for snap_scaffold_3-snap.1415-T1
Valid prediction for snap_scaffold_3-snap.1447-T1
Valid prediction for GlimmerHMM_glimmerT_6772-T1
Couldn't classify 215627, 215672
Sorry, prediction pasa_asmbl_38952.p1 fails validation.
(GAG)	 GT	215627-215672	GT	AGG
(GCG)	 AG	216622-216749	GT	CTG
(ATC)	 AG	216832-216988	GT	TGG
(ACA)	 AG	218631-218930	GT	GGG
(AGA)	 AG	219203-219235	GT	TGG
(ACG)	 AG	219349-219439	GT	ACG
(AGG)	 AG	219578-219781	GT	ATG
(GAT)	 AG	219922-220139	GT	AGG
(AAA)	 AG	220250-220373	GT	TTG
(GGT)	 AG	220511-220663	GT	AAG
(GGC)	 AG	220886-221009	GT	AGG
(AAA)	 AG	221103-221193	GT	AGG
(AAG)	 AG	221312-221440	GT	AGG
(GTT)	 AG	221614-221858	GT	GAG
add_exon() Sorry, pasa_asmbl_38952.p1 219922-220139-terminal-2 is invalid.
-recovered pasa_asmbl_38952.p1, terminal, 219922, 220139
-recovered pasa_asmbl_38952.p1, terminal, 221614, 221858
-recovered pasa_asmbl_38952.p1, internal, 216622, 216749
-recovered pasa_asmbl_38952.p1, internal, 216832, 216988
-recovered pasa_asmbl_38952.p1, internal, 218631, 218930
-recovered pasa_asmbl_38952.p1, internal, 219203, 219235
-recovered pasa_asmbl_38952.p1, internal, 219349, 219439
-recovered pasa_asmbl_38952.p1, internal, 219578, 219781
-recovered pasa_asmbl_38952.p1, internal, 219922, 220139
-recovered pasa_asmbl_38952.p1, internal, 220250, 220373
-recovered pasa_asmbl_38952.p1, internal, 220511, 220663
-recovered pasa_asmbl_38952.p1, internal, 220886, 221009
-recovered pasa_asmbl_38952.p1, internal, 221103, 221193
-recovered pasa_asmbl_38952.p1, internal, 221312, 221440
-recovered pasa_asmbl_38952.p1, internal, 221614, 221858
Valid prediction for snap_scaffold_3-snap.1410-T1
Valid prediction for HiQ_model.g4399.t1
Valid prediction for GlimmerHMM_glimmerT_6757-T1
Valid prediction for snap_scaffold_3-snap.1416-T1
Valid prediction for snap_scaffold_3-snap.1411-T1
Valid prediction for snap_scaffold_3-snap.1450-T1
Valid prediction for GlimmerHMM_glimmerT_6752-T1
Valid prediction for snap_scaffold_3-snap.1446-T1
Valid prediction for snap_scaffold_3-snap.1436-T1
Valid prediction for snap_scaffold_3-snap.1407-T1
Valid prediction for snap_scaffold_3-snap.1427-T1
Valid prediction for Augustus_model.g4418.t1
Valid prediction for GlimmerHMM_glimmerT_6749-T1
Valid prediction for snap_scaffold_3-snap.1418-T1
Valid prediction for GlimmerHMM_glimmerT_6769-T1
Valid prediction for GlimmerHMM_glimmerT_6751-T1
Valid prediction for snap_scaffold_3-snap.1451-T1
Valid prediction for snap_scaffold_3-snap.1453-T1
Valid prediction for Augustus_model.g4400.t1
Couldn't classify 208585, 209425
Couldn't classify 211199, 211272
Sorry, prediction pasa_asmbl_38953.p1 fails validation.
(GGA)	 GA	208585-209425	GT	CGG
(ACG)	 AG	210582-210698	GT	CGG
(ATC)	 AG	211199-211272	TT	AGT
-recovered pasa_asmbl_38953.p1, internal, 210582, 210698
Valid prediction for GlimmerHMM_glimmerT_6771-T1
Valid prediction for Augustus_model.g4417.t1
Valid prediction for GlimmerHMM_glimmerT_6753-T1
Valid prediction for snap_scaffold_3-snap.1426-T1
Valid prediction for GlimmerHMM_glimmerT_6775-T1
Valid prediction for snap_scaffold_3-snap.1414-T1
Valid prediction for snap_scaffold_3-snap.1421-T1
Valid prediction for Augustus_model.g4401.t1
Valid prediction for snap_scaffold_3-snap.1419-T1
Valid prediction for snap_scaffold_3-snap.1442-T1
Valid prediction for GlimmerHMM_glimmerT_6774-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 34112, rend_intergenic: 9251  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60979, rend_intergenic: 49623  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64641, rend_intergenic: 62141  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87881, rend_intergenic: 66769  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98877, rend_intergenic: 93930  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104098, rend_intergenic: 99600  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110871, rend_intergenic: 109173  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116515, rend_intergenic: 111107  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124293, rend_intergenic: 117743  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130018, rend_intergenic: 126224  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145803, rend_intergenic: 133912  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184916, rend_intergenic: 179744  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 224250, rend_intergenic: 220629  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 226859
-exon list size: 429


building trellis

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23.4    
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23.9    
24.1    
24.4    
24.6    
24.8    
25.1    
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25.5    
25.8    
26.0    
26.2    
26.5    
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27.6    
27.8    
28.1    
28.3    
28.5    
28.8    
29.0    
29.2    
29.5    
29.7    
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30.2    
30.4    
30.6    
30.9    
31.1    
31.3    
31.6    
31.8    
32.0    
32.3    
32.5    
32.7    
32.9    
33.2    
33.4    
33.6    
33.9    
34.1    
34.3    
34.6    
34.8    
35.0    
35.3    
35.5    
35.7    
36.0    
36.2    
36.4    
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36.9    
37.1    
37.4    
37.6    
37.8    
38.1    
38.3    
38.5    
38.7    
39.0    
39.2    
39.4    
39.7    
39.9    
40.1    
40.4    
40.6    
40.8    
41.1    
41.3    
41.5    
41.8    
42.0    
42.2    
42.5    
42.7    
42.9    
43.2    
43.4    
43.6    
43.9    
44.1    
44.3    
44.5    
44.8    
45.0    
45.2    
45.5    
45.7    
45.9    
46.2    
46.4    
46.6    
46.9    
47.1    
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47.6    
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48.3    
48.5    
48.7    
49.0    
49.2    
49.4    
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49.9    
50.1    
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50.6    
50.8    
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51.3    
51.5    
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53.8    
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60.6    
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75.4    
75.6    
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76.1    
76.3    
76.6    
76.8    
77.0    
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78.0    
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78.4    
78.7    
78.9    
79.1    
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79.6    
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80.0    
80.3    
80.5    
80.7    
81.0    
81.2    
81.4    
81.7    
81.9    
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82.4    
82.6    
82.8    
83.1    
83.3    
83.5    
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84.0    
84.2    
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84.9    
85.2    
85.4    
85.6    
85.8    
86.1    
86.3    
86.5    
86.8    
87.0    
87.2    
87.5    
87.7    
87.9    
88.2    
88.4    
88.6    
88.9    
89.1    
89.3    
89.6    
89.8    
90.0    
90.3    
90.5    
90.7    
91.0    
91.2    
91.4    
91.6    
91.9    
92.1    
92.3    
92.6    
92.8    
93.0    
93.3    
93.5    
93.7    
94.0    
94.2    
94.4    
94.7    
94.9    
95.1    
95.4    
95.6    
95.8    
96.1    
96.3    
96.5    
96.8    
97.0    
97.2    
97.4    
97.7    
97.9    
98.1    
98.4    
98.6    
98.8    
99.1    
99.3    
99.5    
99.8    
-found 37 predictions from path traversal
Error with prediction: snap lend_intergenic: 34112, rend_intergenic: 9251  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60979, rend_intergenic: 49623  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64641, rend_intergenic: 62141  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87881, rend_intergenic: 66769  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98877, rend_intergenic: 93930  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104098, rend_intergenic: 99600  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110871, rend_intergenic: 109173  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116515, rend_intergenic: 111107  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124293, rend_intergenic: 117743  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130018, rend_intergenic: 126224  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145803, rend_intergenic: 133912  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184916, rend_intergenic: 179744  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 224250, rend_intergenic: 220629  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support