-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_4/scaffold_4_12232055-12451850

-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_4-snap.2646-T1
Valid prediction for CodingQuarry_transcript_49146-T1
Valid prediction for GlimmerHMM_glimmerT_10361-T1
Valid prediction for GlimmerHMM_glimmerT_10379-T1
Valid prediction for snap_scaffold_4-snap.2629-T1
Valid prediction for Augustus_model.g6730.t1
Valid prediction for GlimmerHMM_glimmerT_10382-T1
Valid prediction for snap_scaffold_4-snap.2628-T1
Valid prediction for snap_scaffold_4-snap.2623-T1
Valid prediction for GlimmerHMM_glimmerT_10387-T1
Valid prediction for CodingQuarry_transcript_49144-T1
Valid prediction for snap_scaffold_4-snap.2630-T1
Valid prediction for Augustus_model.g6747.t1
Valid prediction for GlimmerHMM_glimmerT_10389-T1
Valid prediction for snap_scaffold_4-snap.2614-T1
Valid prediction for Augustus_model.g6751.t1
Valid prediction for Augustus_model.g6744.t1
Valid prediction for snap_scaffold_4-snap.2618-T1
Valid prediction for GlimmerHMM_glimmerT_10383-T1
Couldn't classify 203957, 204118
Sorry, prediction pasa_asmbl_41721.p1 fails validation.
(CCC)	 AG	203957-204118	GT	AGG
(AAA)	 AG	204314-204565	GT	AGG
(TTC)	 AG	204743-204811	GT	AGG
(TTC)	 AG	204919-205092	GT	TGG
(GTC)	 AG	205224-205355	GT	AGG
(GAG)	 AG	205482-205573	GT	AGG
(TTT)	 AG	206539-206646	GT	AGG
(CCA)	 AG	206965-207046	GC	AAG
-recovered pasa_asmbl_41721.p1, terminal, 206965, 207046
-recovered pasa_asmbl_41721.p1, internal, 203957, 204118
-recovered pasa_asmbl_41721.p1, internal, 204314, 204565
-recovered pasa_asmbl_41721.p1, internal, 204743, 204811
-recovered pasa_asmbl_41721.p1, internal, 204919, 205092
-recovered pasa_asmbl_41721.p1, internal, 205224, 205355
-recovered pasa_asmbl_41721.p1, internal, 205482, 205573
-recovered pasa_asmbl_41721.p1, internal, 206539, 206646
-recovered pasa_asmbl_41721.p1, internal, 206965, 207046
Valid prediction for GlimmerHMM_glimmerT_10386-T1
Valid prediction for GlimmerHMM_glimmerT_10370-T1
Valid prediction for snap_scaffold_4-snap.2643-T1
Valid prediction for Augustus_model.g6750.t1
Couldn't classify 182052, 182142
Sorry, prediction pasa_asmbl_41719.p1 fails validation.
(TCA)	 CC	182052-182142	GT	AGG
(GTG)	 AG	182239-182386	GT	AGG
(AGT)	 AG	182691-182799	GC	AAG
(ATC)	 AG	182947-183078	AC	AAA
-recovered pasa_asmbl_41719.p1, terminal, 182947, 183078
-recovered pasa_asmbl_41719.p1, internal, 182239, 182386
-recovered pasa_asmbl_41719.p1, internal, 182691, 182799
Valid prediction for Augustus_model.g6741.t1
Valid prediction for snap_scaffold_4-snap.2645-T1
Valid prediction for Augustus_model.g6752.t1
Valid prediction for GlimmerHMM_glimmerT_10373-T1
Valid prediction for snap_scaffold_4-snap.2607-T1
Valid prediction for Augustus_model.g6732.t1
Valid prediction for Augustus_model.g6727.t1
Valid prediction for Augustus_model.g6746.t1
Valid prediction for Augustus_model.g6738.t1
Valid prediction for snap_scaffold_4-snap.2650-T1
Valid prediction for GlimmerHMM_glimmerT_10385-T1
Couldn't classify 158320, 158352
Couldn't classify 159312, 159467
Sorry, prediction pasa_asmbl_42233.p1 fails validation.
(ATC)	 CC	158320-158352	GT	AGG
(GAG)	 AG	158673-158734	GT	TGG
(TGT)	 AG	159104-159212	GT	AGG
(GCC)	 AG	159312-159467	GT	AGG
-recovered pasa_asmbl_42233.p1, internal, 158673, 158734
-recovered pasa_asmbl_42233.p1, internal, 159104, 159212
-recovered pasa_asmbl_42233.p1, internal, 159312, 159467
Valid prediction for snap_scaffold_4-snap.2640-T1
Valid prediction for Augustus_model.g6749.t1
Valid prediction for pasa_asmbl_41715.p1
Valid prediction for GlimmerHMM_glimmerT_10377-T1
Couldn't classify 160579, 160658
Sorry, prediction pasa_asmbl_42178.p1 fails validation.
(ATG)	 AG	159638-159655	GT	AGG
(GCT)	 AG	159754-159829	GT	AGG
(GGG)	 AG	159939-160005	GT	AGG
(CCT)	 AG	160252-160376	GT	AGG
(GCT)	 AG	160579-160658	GA	CGG
-recovered pasa_asmbl_42178.p1, initial, 159638, 159655
add_exon() Sorry, pasa_asmbl_42178.p1 159754-159829-terminal-3 is invalid.
-recovered pasa_asmbl_42178.p1, terminal, 159754, 159829
add_exon() Sorry, pasa_asmbl_42178.p1 160252-160376-terminal-2 is invalid.
-recovered pasa_asmbl_42178.p1, terminal, 160252, 160376
-recovered pasa_asmbl_42178.p1, internal, 159638, 159655
-recovered pasa_asmbl_42178.p1, internal, 159754, 159829
-recovered pasa_asmbl_42178.p1, internal, 159939, 160005
-recovered pasa_asmbl_42178.p1, internal, 160252, 160376
Valid prediction for Augustus_model.g6755.t1
Valid prediction for snap_scaffold_4-snap.2644-T1
Valid prediction for GlimmerHMM_glimmerT_10357-T1
Valid prediction for Augustus_model.g6733.t1
Couldn't classify 163742, 163766
Couldn't classify 166402, 166451
Sorry, prediction pasa_asmbl_41716.p1 fails validation.
(TCC)	 AC	163742-163766	GT	AGG
(CCA)	 AG	163975-164072	GT	GGG
(ATA)	 AG	164268-164318	GT	AGG
(TCT)	 AG	164570-164736	GT	ATG
(GTC)	 AG	164837-164905	GT	ACG
(GAG)	 AG	165265-165381	GT	AGG
(TTT)	 AG	165545-165692	GT	AGG
(CTC)	 AG	165862-165957	GT	AGG
(ACT)	 AG	166114-166255	GT	GGG
(ACC)	 AG	166402-166451	GC	AGG
-recovered pasa_asmbl_41716.p1, internal, 163975, 164072
-recovered pasa_asmbl_41716.p1, internal, 164268, 164318
-recovered pasa_asmbl_41716.p1, internal, 164570, 164736
-recovered pasa_asmbl_41716.p1, internal, 164837, 164905
-recovered pasa_asmbl_41716.p1, internal, 165265, 165381
-recovered pasa_asmbl_41716.p1, internal, 165545, 165692
-recovered pasa_asmbl_41716.p1, internal, 165862, 165957
-recovered pasa_asmbl_41716.p1, internal, 166114, 166255
-recovered pasa_asmbl_41716.p1, internal, 166402, 166451
Valid prediction for snap_scaffold_4-snap.2626-T1
Valid prediction for HiQ_model.g6748.t1
Valid prediction for GlimmerHMM_glimmerT_10371-T1
Valid prediction for snap_scaffold_4-snap.2615-T1
Valid prediction for snap_scaffold_4-snap.2637-T1
Valid prediction for Augustus_model.g6753.t1
Valid prediction for snap_scaffold_4-snap.2624-T1
Valid prediction for GlimmerHMM_glimmerT_10372-T1
Couldn't classify 202917, 203008
Couldn't classify 203749, 203832
Sorry, prediction pasa_asmbl_42208.p1 fails validation.
(TTT)	 TC	202917-203008	GT	ACG
(GTG)	 AG	203173-203281	GT	AGG
(GAG)	 AG	203430-203591	GT	AGG
(GTG)	 AG	203749-203832	CC	CAC
-recovered pasa_asmbl_42208.p1, internal, 203173, 203281
-recovered pasa_asmbl_42208.p1, internal, 203430, 203591
Valid prediction for snap_scaffold_4-snap.2611-T1
Valid prediction for GlimmerHMM_glimmerT_10362-T1
Valid prediction for GlimmerHMM_glimmerT_10380-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_4-snap.2639-T1
Valid prediction for snap_scaffold_4-snap.2609-T1
Valid prediction for snap_scaffold_4-snap.2648-T1
Valid prediction for GlimmerHMM_glimmerT_10365-T1
Couldn't classify 106930, 107124
Couldn't classify 107276, 107740
Sorry, prediction pasa_asmbl_43547.p1 fails validation.
(AAA)	 AA	106930-107124	GT	GGG
(GAG)	 AG	107276-107740	GA	AAG
Valid prediction for GlimmerHMM_glimmerT_10375-T1
Valid prediction for GlimmerHMM_glimmerT_10359-T1
Valid prediction for Augustus_model.g6734.t1
Valid prediction for snap_scaffold_4-snap.2636-T1
Valid prediction for GlimmerHMM_glimmerT_10360-T1
Valid prediction for GlimmerHMM_glimmerT_10388-T1
Valid prediction for GlimmerHMM_glimmerT_10364-T1
Valid prediction for pasa_asmbl_42912.p1
Valid prediction for Augustus_model.g6736.t1
Valid prediction for Augustus_model.g6729.t1
Valid prediction for GlimmerHMM_glimmerT_10376-T1
Valid prediction for GlimmerHMM_glimmerT_10369-T1
Valid prediction for snap_scaffold_4-snap.2616-T1
Valid prediction for GlimmerHMM_glimmerT_10384-T1
Valid prediction for snap_scaffold_4-snap.2647-T1
Valid prediction for HiQ_model.g6742.t1
Valid prediction for GlimmerHMM_glimmerT_10358-T1
Valid prediction for snap_scaffold_4-snap.2649-T1
Valid prediction for pasa_asmbl_42894.p1
Valid prediction for GlimmerHMM_glimmerT_10363-T1
Valid prediction for Augustus_model.g6728.t1
Valid prediction for snap_scaffold_4-snap.2612-T1
Valid prediction for GlimmerHMM_glimmerT_10367-T1
Valid prediction for snap_scaffold_4-snap.2620-T1
Valid prediction for snap_scaffold_4-snap.2638-T1
Valid prediction for snap_scaffold_4-snap.2634-T1
Valid prediction for Augustus_model.g6743.t1
Valid prediction for snap_scaffold_4-snap.2613-T1
Valid prediction for snap_scaffold_4-snap.2621-T1
Valid prediction for GlimmerHMM_glimmerT_10368-T1
Valid prediction for GlimmerHMM_glimmerT_10378-T1
Valid prediction for GlimmerHMM_glimmerT_10381-T1
Couldn't classify 104728, 104780
Couldn't classify 106076, 106110
Sorry, prediction pasa_asmbl_42904.p1 fails validation.
(ACT)	 TG	104728-104780	GT	GAG
(CAA)	 AG	104994-105096	GT	GGG
(GTC)	 AG	105207-105283	GT	TTG
(AAA)	 AG	105375-105412	GT	GGG
(AAA)	 AG	105522-105604	GT	AGG
(GCG)	 AG	105730-105806	GT	ATG
(AAA)	 AG	105913-105950	GT	AGG
(AGT)	 AG	106076-106110	TT	AGT
-recovered pasa_asmbl_42904.p1, internal, 104994, 105096
-recovered pasa_asmbl_42904.p1, internal, 105207, 105283
-recovered pasa_asmbl_42904.p1, internal, 105375, 105412
-recovered pasa_asmbl_42904.p1, internal, 105522, 105604
-recovered pasa_asmbl_42904.p1, internal, 105730, 105806
-recovered pasa_asmbl_42904.p1, internal, 105913, 105950
Valid prediction for snap_scaffold_4-snap.2619-T1
Couldn't classify 109337, 109723
Sorry, prediction pasa_asmbl_42899.p1 fails validation.
(AAC)	 TC	109337-109723	GT	AGG
(CAG)	 AG	109935-110103	GT	AAG
(ATT)	 AG	110222-110382	GT	AGG
(AAC)	 AG	110561-110751	GT	AGG
(TAA)	 AG	110920-111020	GT	CGG
(GTC)	 AG	111159-111257	GT	AGG
(GAG)	 AG	111543-111724	GA	GAG
-recovered pasa_asmbl_42899.p1, terminal, 111543, 111724
-recovered pasa_asmbl_42899.p1, internal, 109935, 110103
-recovered pasa_asmbl_42899.p1, internal, 110222, 110382
-recovered pasa_asmbl_42899.p1, internal, 110561, 110751
-recovered pasa_asmbl_42899.p1, internal, 110920, 111020
-recovered pasa_asmbl_42899.p1, internal, 111159, 111257
Valid prediction for snap_scaffold_4-snap.2622-T1
Valid prediction for pasa_asmbl_42906.p1
Valid prediction for snap_scaffold_4-snap.2625-T1
Valid prediction for HiQ_model.g6745.t1
Valid prediction for Augustus_model.g6739.t1
Valid prediction for snap_scaffold_4-snap.2608-T1
Valid prediction for snap_scaffold_4-snap.2635-T1
Valid prediction for snap_scaffold_4-snap.2633-T1
Valid prediction for GlimmerHMM_glimmerT_10374-T1
Valid prediction for Augustus_model.g6740.t1
Valid prediction for Augustus_model.g6737.t1
Valid prediction for snap_scaffold_4-snap.2631-T1
Valid prediction for snap_scaffold_4-snap.2642-T1
Valid prediction for snap_scaffold_4-snap.2606-T1
Valid prediction for snap_scaffold_4-snap.2632-T1
Valid prediction for Augustus_model.g6754.t1
Valid prediction for snap_scaffold_4-snap.2610-T1
Valid prediction for Augustus_model.g6731.t1
Valid prediction for GlimmerHMM_glimmerT_10366-T1
Valid prediction for snap_scaffold_4-snap.2617-T1
Couldn't classify 108032, 108892
Sorry, prediction pasa_asmbl_42903.p1 fails validation.
(GAT)	 CG	108032-108892	CC	CCC
Valid prediction for snap_scaffold_4-snap.2627-T1
Couldn't classify 72639, 72974
Sorry, prediction pasa_asmbl_42909.p1 fails validation.
(ATG)	 CT	71460-72177	GT	AGG
(GTT)	 AG	72416-72549	GT	TGG
(GTG)	 AG	72639-72974	AC	AGA
-recovered pasa_asmbl_42909.p1, initial, 71460, 72177
-recovered pasa_asmbl_42909.p1, internal, 72416, 72549
Valid prediction for Augustus_model.g6735.t1
Valid prediction for snap_scaffold_4-snap.2641-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 13231, rend_intergenic: 11729  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23723, rend_intergenic: 19968  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26719, rend_intergenic: 23867  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29450, rend_intergenic: 27731  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43456, rend_intergenic: 39373  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72926, rend_intergenic: 58055  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86976, rend_intergenic: 77424  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100598, rend_intergenic: 95472  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138690, rend_intergenic: 131088  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166526, rend_intergenic: 154120  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 207046, rend_intergenic: 192152  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 219796
-exon list size: 655


building trellis

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62.6    
62.7    
62.9    
63.0    
63.2    
63.3    
63.5    
63.6    
63.8    
63.9    
64.1    
64.2    
64.4    
64.5    
64.7    
64.8    
65.0    
65.1    
65.3    
65.4    
65.6    
65.8    
65.9    
66.1    
66.2    
66.4    
66.5    
66.7    
66.8    
67.0    
67.1    
67.3    
67.4    
67.6    
67.7    
67.9    
68.0    
68.2    
68.3    
68.5    
68.6    
68.8    
68.9    
69.1    
69.3    
69.4    
69.6    
69.7    
69.9    
70.0    
70.2    
70.3    
70.5    
70.6    
70.8    
70.9    
71.1    
71.2    
71.4    
71.5    
71.7    
71.8    
72.0    
72.1    
72.3    
72.5    
72.6    
72.8    
72.9    
73.1    
73.2    
73.4    
73.5    
73.7    
73.8    
74.0    
74.1    
74.3    
74.4    
74.6    
74.7    
74.9    
75.0    
75.2    
75.3    
75.5    
75.6    
75.8    
76.0    
76.1    
76.3    
76.4    
76.6    
76.7    
76.9    
77.0    
77.2    
77.3    
77.5    
77.6    
77.8    
77.9    
78.1    
78.2    
78.4    
78.5    
78.7    
78.8    
79.0    
79.1    
79.3    
79.5    
79.6    
79.8    
79.9    
80.1    
80.2    
80.4    
80.5    
80.7    
80.8    
81.0    
81.1    
81.3    
81.4    
81.6    
81.7    
81.9    
82.0    
82.2    
82.3    
82.5    
82.6    
82.8    
83.0    
83.1    
83.3    
83.4    
83.6    
83.7    
83.9    
84.0    
84.2    
84.3    
84.5    
84.6    
84.8    
84.9    
85.1    
85.2    
85.4    
85.5    
85.7    
85.8    
86.0    
86.1    
86.3    
86.5    
86.6    
86.8    
86.9    
87.1    
87.2    
87.4    
87.5    
87.7    
87.8    
88.0    
88.1    
88.3    
88.4    
88.6    
88.7    
88.9    
89.0    
89.2    
89.3    
89.5    
89.6    
89.8    
90.0    
90.1    
90.3    
90.4    
90.6    
90.7    
90.9    
91.0    
91.2    
91.3    
91.5    
91.6    
91.8    
91.9    
92.1    
92.2    
92.4    
92.5    
92.7    
92.8    
93.0    
93.2    
93.3    
93.5    
93.6    
93.8    
93.9    
94.1    
94.2    
94.4    
94.5    
94.7    
94.8    
95.0    
95.1    
95.3    
95.4    
95.6    
95.7    
95.9    
96.0    
96.2    
96.3    
96.5    
96.7    
96.8    
97.0    
97.1    
97.3    
97.4    
97.6    
97.7    
97.9    
98.0    
98.2    
98.3    
98.5    
98.6    
98.8    
98.9    
99.1    
99.2    
99.4    
99.5    
99.7    
99.8    
-found 37 predictions from path traversal
Error with prediction: snap lend_intergenic: 13231, rend_intergenic: 11729  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23723, rend_intergenic: 19968  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26719, rend_intergenic: 23867  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29450, rend_intergenic: 27731  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43456, rend_intergenic: 39373  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72926, rend_intergenic: 58055  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86976, rend_intergenic: 77424  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100598, rend_intergenic: 95472  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138690, rend_intergenic: 131088  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166526, rend_intergenic: 154120  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 207046, rend_intergenic: 192152  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 31 predictions persist after filtering for low support