-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_21/scaffold_21_7117789-7294311

-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 GeneMark_model.85249_t
Valid prediction for GeneMark_model.85229_t
Valid prediction for snap_scaffold_21-snap.1492-T1
Valid prediction for GeneMark_model.85273_t
Valid prediction for Augustus_model.g32986.t1
Valid prediction for Augustus_model.g32993.t1
Valid prediction for GeneMark_model.85264_t
Valid prediction for snap_scaffold_21-snap.1501-T1
Valid prediction for GeneMark_model.85253_t
Valid prediction for Augustus_model.g32987.t1
Valid prediction for GlimmerHMM_glimmerT_49214-T1
Valid prediction for GlimmerHMM_glimmerT_49202-T1
Valid prediction for snap_scaffold_21-snap.1497-T1
Valid prediction for GeneMark_model.85245_t
Valid prediction for Augustus_model.g32976.t1
Valid prediction for Augustus_model.g32988.t1
Valid prediction for snap_scaffold_21-snap.1515-T1
Valid prediction for GeneMark_model.85251_t
Valid prediction for GeneMark_model.85260_t
Valid prediction for snap_scaffold_21-snap.1519-T1
Valid prediction for GlimmerHMM_glimmerT_49209-T1
Valid prediction for snap_scaffold_21-snap.1512-T1
Valid prediction for GeneMark_model.85226_t
Valid prediction for snap_scaffold_21-snap.1483-T1
Valid prediction for GeneMark_model.85239_t
Valid prediction for GlimmerHMM_glimmerT_49204-T1
Valid prediction for GeneMark_model.85236_t
Valid prediction for snap_scaffold_21-snap.1482-T1
Couldn't classify 150417, 150474
Sorry, prediction pasa_asmbl_28733.p1 fails validation.
(CAG)	 CC	150417-150474	GT	TGG
(TGC)	 AG	150708-150832	GT	AGG
(GAG)	 AG	151070-151238	GT	TGG
(AGG)	 AG	151356-151455	GT	CGG
(GAG)	 AG	153075-153139	GT	AGG
(GGG)	 AG	153341-153454	GT	AGG
(GTG)	 AG	153612-153859	GT	GGG
(CTG)	 AG	154024-154239	GT	TGG
(GGC)	 AG	154501-154650	GT	ATG
(GTG)	 AG	154830-155023	GT	GGG
(GCC)	 AG	155534-155692	GT	GAG
(GGA)	 AG	156195-156306	CC	GAC
add_exon() Sorry, pasa_asmbl_28733.p1 155534-155692-terminal-1 is invalid.
-recovered pasa_asmbl_28733.p1, terminal, 155534, 155692
-recovered pasa_asmbl_28733.p1, terminal, 156195, 156306
-recovered pasa_asmbl_28733.p1, internal, 150708, 150832
-recovered pasa_asmbl_28733.p1, internal, 151070, 151238
-recovered pasa_asmbl_28733.p1, internal, 151356, 151455
-recovered pasa_asmbl_28733.p1, internal, 153075, 153139
-recovered pasa_asmbl_28733.p1, internal, 153341, 153454
-recovered pasa_asmbl_28733.p1, internal, 153612, 153859
-recovered pasa_asmbl_28733.p1, internal, 154024, 154239
-recovered pasa_asmbl_28733.p1, internal, 154501, 154650
-recovered pasa_asmbl_28733.p1, internal, 154830, 155023
-recovered pasa_asmbl_28733.p1, internal, 155534, 155692
Valid prediction for GlimmerHMM_glimmerT_49220-T1
Valid prediction for snap_scaffold_21-snap.1499-T1
Valid prediction for Augustus_model.g32991.t1
Valid prediction for GlimmerHMM_glimmerT_49211-T1
Valid prediction for snap_scaffold_21-snap.1484-T1
Valid prediction for GlimmerHMM_glimmerT_49218-T1
Valid prediction for snap_scaffold_21-snap.1500-T1
Valid prediction for GlimmerHMM_glimmerT_49213-T1
Valid prediction for GlimmerHMM_glimmerT_49215-T1
Valid prediction for Augustus_model.g32992.t1
Valid prediction for GeneMark_model.85269_t
Valid prediction for GeneMark_model.85272_t
Valid prediction for GlimmerHMM_glimmerT_49192-T1
Valid prediction for Augustus_model.g32982.t1
Valid prediction for GeneMark_model.85228_t
Valid prediction for snap_scaffold_21-snap.1505-T1
Valid prediction for snap_scaffold_21-snap.1508-T1
Valid prediction for snap_scaffold_21-snap.1521-T1
Valid prediction for GlimmerHMM_glimmerT_49219-T1
Valid prediction for Augustus_model.g32980.t1
Valid prediction for snap_scaffold_21-snap.1491-T1
Valid prediction for snap_scaffold_21-snap.1510-T1
Valid prediction for GeneMark_model.85258_t
Valid prediction for snap_scaffold_21-snap.1513-T1
Valid prediction for snap_scaffold_21-snap.1487-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_49205-T1
Valid prediction for GlimmerHMM_glimmerT_49206-T1
Valid prediction for snap_scaffold_21-snap.1523-T1
Valid prediction for snap_scaffold_21-snap.1506-T1
Valid prediction for snap_scaffold_21-snap.1486-T1
Valid prediction for snap_scaffold_21-snap.1507-T1
Valid prediction for snap_scaffold_21-snap.1524-T1
Valid prediction for GlimmerHMM_glimmerT_49217-T1
Valid prediction for GeneMark_model.85247_t
Valid prediction for GeneMark_model.85262_t
Valid prediction for Augustus_model.g32990.t1
Valid prediction for snap_scaffold_21-snap.1496-T1
Valid prediction for GeneMark_model.85234_t
Valid prediction for GlimmerHMM_glimmerT_49193-T1
Valid prediction for Augustus_model.g32995.t1
Valid prediction for GlimmerHMM_glimmerT_49221-T1
Valid prediction for GeneMark_model.85240_t
Valid prediction for Augustus_model.g32994.t1
Valid prediction for GeneMark_model.85267_t
Valid prediction for GlimmerHMM_glimmerT_49199-T1
Valid prediction for Augustus_model.g32975.t1
Valid prediction for snap_scaffold_21-snap.1516-T1
Valid prediction for GeneMark_model.85232_t

-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 GeneMark_model.85235_t
Valid prediction for GlimmerHMM_glimmerT_49201-T1
Valid prediction for snap_scaffold_21-snap.1511-T1
Valid prediction for snap_scaffold_21-snap.1527-T1
Valid prediction for GeneMark_model.85259_t
Valid prediction for snap_scaffold_21-snap.1525-T1
Valid prediction for Augustus_model.g32997.t1
Valid prediction for snap_scaffold_21-snap.1502-T1
Valid prediction for GeneMark_model.85266_t
Valid prediction for GlimmerHMM_glimmerT_49194-T1
Valid prediction for GeneMark_model.85271_t
Valid prediction for Augustus_model.g32981.t1
Valid prediction for snap_scaffold_21-snap.1488-T1
Valid prediction for snap_scaffold_21-snap.1498-T1
Valid prediction for GlimmerHMM_glimmerT_49198-T1
Valid prediction for GlimmerHMM_glimmerT_49210-T1
Valid prediction for GeneMark_model.85248_t
Valid prediction for snap_scaffold_21-snap.1514-T1
Valid prediction for GlimmerHMM_glimmerT_49195-T1
Valid prediction for GlimmerHMM_glimmerT_49207-T1
Valid prediction for GlimmerHMM_glimmerT_49196-T1
Valid prediction for Augustus_model.g32985.t1
Valid prediction for snap_scaffold_21-snap.1489-T1
Valid prediction for GlimmerHMM_glimmerT_49222-T1
Valid prediction for snap_scaffold_21-snap.1493-T1
Valid prediction for GeneMark_model.85263_t
Valid prediction for snap_scaffold_21-snap.1517-T1
Valid prediction for Augustus_model.g32979.t1
Valid prediction for snap_scaffold_21-snap.1509-T1
Valid prediction for snap_scaffold_21-snap.1520-T1
Valid prediction for GlimmerHMM_glimmerT_49212-T1
Valid prediction for GeneMark_model.85227_t
Valid prediction for GeneMark_model.85276_t
Couldn't classify 154895, 155035
Sorry, prediction pasa_asmbl_27810.p1 fails validation.
(ATG)	 AG	150262-150433	GT	AAG
(CAA)	 AG	150781-150881	GT	CTG
(GGC)	 AG	150986-151139	GT	AGG
(ACA)	 AG	151332-151369	GT	TGG
(AAC)	 AG	152992-153054	GT	AGG
(GGT)	 AG	154895-155035	AA	CGA
-recovered pasa_asmbl_27810.p1, initial, 150262, 150433
-recovered pasa_asmbl_27810.p1, internal, 150262, 150433
-recovered pasa_asmbl_27810.p1, internal, 150781, 150881
-recovered pasa_asmbl_27810.p1, internal, 150986, 151139
-recovered pasa_asmbl_27810.p1, internal, 151332, 151369
-recovered pasa_asmbl_27810.p1, internal, 152992, 153054
Valid prediction for GeneMark_model.85231_t
Valid prediction for GeneMark_model.85246_t
Valid prediction for GeneMark_model.85257_t
Couldn't classify 160323, 160457
Sorry, prediction pasa_asmbl_27808.p1 fails validation.
(ACG)	 GA	160323-160457	GT	GGG
(GCT)	 AG	160569-160706	GT	AGG
(CAT)	 AG	160827-160916	GG	AGG
-recovered pasa_asmbl_27808.p1, terminal, 160827, 160916
-recovered pasa_asmbl_27808.p1, internal, 160569, 160706
Valid prediction for snap_scaffold_21-snap.1494-T1
Valid prediction for Augustus_model.g32977.t1
Valid prediction for GlimmerHMM_glimmerT_49216-T1
Valid prediction for GeneMark_model.85237_t
Couldn't classify 155176, 155335
Couldn't classify 160037, 160123
Sorry, prediction pasa_asmbl_27809.p1 fails validation.
(GTC)	 CC	155176-155335	GT	GAG
(GGA)	 AG	155908-155971	GT	GGG
(AGC)	 AG	158090-158138	GT	AGG
(GTG)	 AG	158318-158430	GT	AGG
(TTA)	 AG	159772-159889	GT	AGG
(TGT)	 AG	160037-160123	TC	GCT
-recovered pasa_asmbl_27809.p1, internal, 155908, 155971
-recovered pasa_asmbl_27809.p1, internal, 158090, 158138
-recovered pasa_asmbl_27809.p1, internal, 158318, 158430
-recovered pasa_asmbl_27809.p1, internal, 159772, 159889
Valid prediction for Augustus_model.g32978.t1
Valid prediction for GeneMark_model.85244_t
Valid prediction for GlimmerHMM_glimmerT_49200-T1
Valid prediction for GeneMark_model.85261_t
Valid prediction for snap_scaffold_21-snap.1495-T1
Valid prediction for CodingQuarry_transcript_32552-T1
Valid prediction for GeneMark_model.85255_t
Valid prediction for snap_scaffold_21-snap.1504-T1
Valid prediction for Augustus_model.g32984.t1
Valid prediction for GeneMark_model.85238_t
Valid prediction for GeneMark_model.85256_t
Valid prediction for GeneMark_model.85243_t
Valid prediction for snap_scaffold_21-snap.1485-T1
Valid prediction for Augustus_model.g32996.t1
Valid prediction for GeneMark_model.85274_t
Valid prediction for snap_scaffold_21-snap.1518-T1
Valid prediction for GeneMark_model.85230_t
Valid prediction for Augustus_model.g32983.t1
Valid prediction for snap_scaffold_21-snap.1522-T1
Valid prediction for snap_scaffold_21-snap.1490-T1
Valid prediction for snap_scaffold_21-snap.1503-T1
Valid prediction for GeneMark_model.85241_t
Valid prediction for CodingQuarry_transcript_32551-T1
Couldn't classify 2042, 2152
Sorry, prediction pasa_asmbl_27815.p1 fails validation.
(GAA)	 AA	2042-2152	GT	GGG
(ACA)	 AG	2410-2477	GT	GGG
(GGC)	 AG	2577-2708	GT	AGG
(TAT)	 AG	2914-3043	GT	AGG
(GTC)	 AG	3142-3286	GT	GGG
(CTC)	 AG	3500-3627	AG	AAA
-recovered pasa_asmbl_27815.p1, terminal, 3500, 3627
-recovered pasa_asmbl_27815.p1, internal, 2410, 2477
-recovered pasa_asmbl_27815.p1, internal, 2577, 2708
-recovered pasa_asmbl_27815.p1, internal, 2914, 3043
-recovered pasa_asmbl_27815.p1, internal, 3142, 3286
Valid prediction for GeneMark_model.85250_t
Valid prediction for GlimmerHMM_glimmerT_49203-T1
Valid prediction for GeneMark_model.85254_t
Valid prediction for Augustus_model.g32989.t1
Valid prediction for HiQ_model.g32998.t1
Valid prediction for GlimmerHMM_glimmerT_49197-T1
Valid prediction for GeneMark_model.85275_t
Valid prediction for GeneMark_model.85268_t
Valid prediction for GlimmerHMM_glimmerT_49223-T1
Valid prediction for GlimmerHMM_glimmerT_49208-T1
Valid prediction for GeneMark_model.85265_t
Valid prediction for GeneMark_model.85233_t
Valid prediction for snap_scaffold_21-snap.1526-T1
Valid prediction for GeneMark_model.85242_t
Valid prediction for GeneMark_model.85270_t
Valid prediction for GeneMark_model.85252_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 22739, rend_intergenic: 12842  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33226, rend_intergenic: 29881  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55637, rend_intergenic: 52761  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88898, rend_intergenic: 77950  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91264, rend_intergenic: 89397  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110316, rend_intergenic: 108578  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114517, rend_intergenic: 111996  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128293, rend_intergenic: 114986  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132178, rend_intergenic: 129366  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141950, rend_intergenic: 135774  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147058, rend_intergenic: 142492  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156306, rend_intergenic: 150075  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159565, rend_intergenic: 159466  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164377, rend_intergenic: 160085  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 176523
-exon list size: 780


building trellis

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62.3    
62.4    
62.5    
62.7    
62.8    
62.9    
63.0    
63.2    
63.3    
63.4    
63.6    
63.7    
63.8    
63.9    
64.1    
64.2    
64.3    
64.5    
64.6    
64.7    
64.8    
65.0    
65.1    
65.2    
65.3    
65.5    
65.6    
65.7    
65.9    
66.0    
66.1    
66.2    
66.4    
66.5    
66.6    
66.8    
66.9    
67.0    
67.1    
67.3    
67.4    
67.5    
67.6    
67.8    
67.9    
68.0    
68.2    
68.3    
68.4    
68.5    
68.7    
68.8    
68.9    
69.1    
69.2    
69.3    
69.4    
69.6    
69.7    
69.8    
69.9    
70.1    
70.2    
70.3    
70.5    
70.6    
70.7    
70.8    
71.0    
71.1    
71.2    
71.4    
71.5    
71.6    
71.7    
71.9    
72.0    
72.1    
72.3    
72.4    
72.5    
72.6    
72.8    
72.9    
73.0    
73.1    
73.3    
73.4    
73.5    
73.7    
73.8    
73.9    
74.0    
74.2    
74.3    
74.4    
74.6    
74.7    
74.8    
74.9    
75.1    
75.2    
75.3    
75.4    
75.6    
75.7    
75.8    
76.0    
76.1    
76.2    
76.3    
76.5    
76.6    
76.7    
76.9    
77.0    
77.1    
77.2    
77.4    
77.5    
77.6    
77.7    
77.9    
78.0    
78.1    
78.3    
78.4    
78.5    
78.6    
78.8    
78.9    
79.0    
79.2    
79.3    
79.4    
79.5    
79.7    
79.8    
79.9    
80.1    
80.2    
80.3    
80.4    
80.6    
80.7    
80.8    
80.9    
81.1    
81.2    
81.3    
81.5    
81.6    
81.7    
81.8    
82.0    
82.1    
82.2    
82.4    
82.5    
82.6    
82.7    
82.9    
83.0    
83.1    
83.2    
83.4    
83.5    
83.6    
83.8    
83.9    
84.0    
84.1    
84.3    
84.4    
84.5    
84.7    
84.8    
84.9    
85.0    
85.2    
85.3    
85.4    
85.5    
85.7    
85.8    
85.9    
86.1    
86.2    
86.3    
86.4    
86.6    
86.7    
86.8    
87.0    
87.1    
87.2    
87.3    
87.5    
87.6    
87.7    
87.9    
88.0    
88.1    
88.2    
88.4    
88.5    
88.6    
88.7    
88.9    
89.0    
89.1    
89.3    
89.4    
89.5    
89.6    
89.8    
89.9    
90.0    
90.2    
90.3    
90.4    
90.5    
90.7    
90.8    
90.9    
91.0    
91.2    
91.3    
91.4    
91.6    
91.7    
91.8    
91.9    
92.1    
92.2    
92.3    
92.5    
92.6    
92.7    
92.8    
93.0    
93.1    
93.2    
93.4    
93.5    
93.6    
93.7    
93.9    
94.0    
94.1    
94.2    
94.4    
94.5    
94.6    
94.8    
94.9    
95.0    
95.1    
95.3    
95.4    
95.5    
95.7    
95.8    
95.9    
96.0    
96.2    
96.3    
96.4    
96.5    
96.7    
96.8    
96.9    
97.1    
97.2    
97.3    
97.4    
97.6    
97.7    
97.8    
98.0    
98.1    
98.2    
98.3    
98.5    
98.6    
98.7    
98.8    
99.0    
99.1    
99.2    
99.4    
99.5    
99.6    
99.7    
99.9    
-found 37 predictions from path traversal
Error with prediction: snap lend_intergenic: 22739, rend_intergenic: 12842  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33226, rend_intergenic: 29881  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55637, rend_intergenic: 52761  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88898, rend_intergenic: 77950  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91264, rend_intergenic: 89397  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110316, rend_intergenic: 108578  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114517, rend_intergenic: 111996  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128293, rend_intergenic: 114986  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132178, rend_intergenic: 129366  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141950, rend_intergenic: 135774  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147058, rend_intergenic: 142492  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156306, rend_intergenic: 150075  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159565, rend_intergenic: 159466  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164377, rend_intergenic: 160085  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 24 predictions persist after filtering for low support