-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_21/scaffold_21_11541737-11729415

-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_21-snap.2495-T1
Valid prediction for HiQ_model.g33474.t1
Valid prediction for snap_scaffold_21-snap.2513-T1
Valid prediction for snap_scaffold_21-snap.2512-T1
Valid prediction for Augustus_model.g33465.t1
Valid prediction for snap_scaffold_21-snap.2496-T1
Valid prediction for GeneMark_model.86454_t
Valid prediction for snap_scaffold_21-snap.2501-T1
Valid prediction for GlimmerHMM_glimmerT_49878-T1
Valid prediction for GlimmerHMM_glimmerT_49892-T1
Valid prediction for GeneMark_model.86432_t
Valid prediction for GeneMark_model.86437_t
Valid prediction for snap_scaffold_21-snap.2506-T1
Couldn't classify 173438, 173529
Couldn't classify 178914, 178993
Sorry, prediction pasa_asmbl_28944.p1 fails validation.
(GGG)	 CA	173438-173529	GT	AGG
(GGC)	 AG	174248-174440	GT	AGG
(GAG)	 AG	175309-175395	GT	TGG
(GTG)	 AG	177054-177192	GT	AGG
(GTC)	 AG	177750-177909	GT	AAG
(GAA)	 AG	178035-178221	GT	TGG
(GAT)	 AG	178476-178698	GT	AGG
(GTT)	 AG	178914-178993	CG	GAC
-recovered pasa_asmbl_28944.p1, internal, 174248, 174440
-recovered pasa_asmbl_28944.p1, internal, 175309, 175395
-recovered pasa_asmbl_28944.p1, internal, 177054, 177192
-recovered pasa_asmbl_28944.p1, internal, 177750, 177909
-recovered pasa_asmbl_28944.p1, internal, 178035, 178221
-recovered pasa_asmbl_28944.p1, internal, 178476, 178698
Valid prediction for GlimmerHMM_glimmerT_49879-T1
Valid prediction for snap_scaffold_21-snap.2515-T1
Valid prediction for GeneMark_model.86434_t
Valid prediction for snap_scaffold_21-snap.2504-T1
Valid prediction for snap_scaffold_21-snap.2499-T1
Valid prediction for snap_scaffold_21-snap.2505-T1
Valid prediction for GeneMark_model.86443_t
Valid prediction for GeneMark_model.86440_t
Valid prediction for GeneMark_model.86447_t
Valid prediction for snap_scaffold_21-snap.2502-T1
Valid prediction for GeneMark_model.86470_t
Valid prediction for snap_scaffold_21-snap.2528-T1
Valid prediction for GeneMark_model.86419_t
Valid prediction for snap_scaffold_21-snap.2524-T1
Valid prediction for GlimmerHMM_glimmerT_49891-T1
Valid prediction for GlimmerHMM_glimmerT_49875-T1
Valid prediction for GeneMark_model.86415_t
Valid prediction for GlimmerHMM_glimmerT_49895-T1
Valid prediction for GeneMark_model.86422_t
Valid prediction for GeneMark_model.86436_t
Valid prediction for GlimmerHMM_glimmerT_49873-T1
Valid prediction for GeneMark_model.86472_t
Valid prediction for GeneMark_model.86427_t
Valid prediction for GeneMark_model.86449_t
Valid prediction for snap_scaffold_21-snap.2526-T1
Valid prediction for Augustus_model.g33475.t1
Valid prediction for Augustus_model.g33473.t1
Valid prediction for GeneMark_model.86452_t
Valid prediction for snap_scaffold_21-snap.2525-T1
Valid prediction for snap_scaffold_21-snap.2522-T1
Valid prediction for GlimmerHMM_glimmerT_49871-T1
Valid prediction for GeneMark_model.86455_t
Valid prediction for snap_scaffold_21-snap.2494-T1
Valid prediction for GeneMark_model.86468_t
Valid prediction for GeneMark_model.86458_t
Valid prediction for GeneMark_model.86417_t
Valid prediction for GeneMark_model.86425_t
Valid prediction for Augustus_model.g33461.t1
Valid prediction for GeneMark_model.86423_t
Valid prediction for snap_scaffold_21-snap.2517-T1
Valid prediction for snap_scaffold_21-snap.2533-T1
Couldn't classify 163808, 163873
Couldn't classify 172661, 172773
Sorry, prediction pasa_asmbl_29016.p1 fails validation.
(GTC)	 AG	163808-163873	GT	AGG
(GTT)	 AG	163987-164058	GT	CTG
(ACT)	 AG	164713-164778	GT	AGG
(GTG)	 AG	166134-166221	GT	GGG
(CTA)	 AG	166359-166465	GT	AGG
(GCG)	 AG	166563-166739	GT	AGG
(GTG)	 AG	167051-167261	GT	TGG
(CGG)	 AG	167380-167522	GT	AGG
(ACC)	 AG	168975-169075	GT	AGG
(GAC)	 AG	169355-169418	GT	AGG
(TCA)	 AG	169544-169688	GT	GGG
(GTG)	 AG	172661-172773	CT	CGC
-recovered pasa_asmbl_29016.p1, internal, 163808, 163873
-recovered pasa_asmbl_29016.p1, internal, 163987, 164058
-recovered pasa_asmbl_29016.p1, internal, 164713, 164778
-recovered pasa_asmbl_29016.p1, internal, 166134, 166221
-recovered pasa_asmbl_29016.p1, internal, 166359, 166465
-recovered pasa_asmbl_29016.p1, internal, 166563, 166739
-recovered pasa_asmbl_29016.p1, internal, 167051, 167261
-recovered pasa_asmbl_29016.p1, internal, 167380, 167522
-recovered pasa_asmbl_29016.p1, internal, 168975, 169075
-recovered pasa_asmbl_29016.p1, internal, 169355, 169418
-recovered pasa_asmbl_29016.p1, internal, 169544, 169688
Couldn't classify 162832, 163245
Sorry, prediction pasa_asmbl_28943.p2 fails validation.
(ATG)	 TC	162832-163245	AG	CCA
Valid prediction for GeneMark_model.86445_t
Valid prediction for snap_scaffold_21-snap.2508-T1
Valid prediction for snap_scaffold_21-snap.2514-T1
Valid prediction for GeneMark_model.86465_t
Valid prediction for GlimmerHMM_glimmerT_49888-T1
Valid prediction for GeneMark_model.86461_t
Valid prediction for Augustus_model.g33472.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 GeneMark_model.86424_t
Valid prediction for GeneMark_model.86466_t
Valid prediction for snap_scaffold_21-snap.2518-T1
Valid prediction for Augustus_model.g33471.t1
Valid prediction for GeneMark_model.86414_t
Valid prediction for GeneMark_model.86426_t
Valid prediction for CodingQuarry_transcript_32690-T1
Valid prediction for GeneMark_model.86459_t
Valid prediction for snap_scaffold_21-snap.2523-T1
Couldn't classify 95960, 96108
Couldn't classify 98370, 98448
Sorry, prediction pasa_asmbl_28160.p1 fails validation.
(ATC)	 CC	95960-96108	GT	AGG
(TTT)	 AG	96453-96549	GT	AGG
(GGG)	 AG	96631-96764	GT	AGG
(ACG)	 AG	97952-98083	GT	GGG
(CAC)	 AG	98370-98448	AG	GGA
-recovered pasa_asmbl_28160.p1, internal, 96453, 96549
-recovered pasa_asmbl_28160.p1, internal, 96631, 96764
-recovered pasa_asmbl_28160.p1, internal, 97952, 98083
Valid prediction for GlimmerHMM_glimmerT_49894-T1
Valid prediction for GlimmerHMM_glimmerT_49883-T1
Valid prediction for snap_scaffold_21-snap.2511-T1
Valid prediction for snap_scaffold_21-snap.2534-T1
Valid prediction for snap_scaffold_21-snap.2529-T1
Valid prediction for GeneMark_model.86444_t
Valid prediction for snap_scaffold_21-snap.2527-T1
Valid prediction for GlimmerHMM_glimmerT_49877-T1
Valid prediction for GeneMark_model.86462_t
Valid prediction for GeneMark_model.86430_t
Valid prediction for snap_scaffold_21-snap.2532-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GeneMark_model.86457_t
Valid prediction for GeneMark_model.86442_t
Valid prediction for GlimmerHMM_glimmerT_49893-T1
Valid prediction for GeneMark_model.86438_t
Valid prediction for GlimmerHMM_glimmerT_49885-T1
Valid prediction for snap_scaffold_21-snap.2507-T1
Valid prediction for GeneMark_model.86446_t
Valid prediction for GlimmerHMM_glimmerT_49876-T1
Valid prediction for pasa_asmbl_28157.p1
Valid prediction for Augustus_model.g33464.t1
Valid prediction for GeneMark_model.86463_t
Valid prediction for GeneMark_model.86431_t
Valid prediction for GlimmerHMM_glimmerT_49881-T1
Valid prediction for GeneMark_model.86453_t
Valid prediction for Augustus_model.g33476.t1
Valid prediction for GlimmerHMM_glimmerT_49887-T1
Valid prediction for GlimmerHMM_glimmerT_49872-T1
Valid prediction for Augustus_model.g33470.t1
Valid prediction for snap_scaffold_21-snap.2521-T1
Valid prediction for GeneMark_model.86433_t
Valid prediction for snap_scaffold_21-snap.2500-T1
Valid prediction for Augustus_model.g33462.t1
Valid prediction for GeneMark_model.86420_t
Valid prediction for GeneMark_model.86469_t
Valid prediction for snap_scaffold_21-snap.2530-T1
Valid prediction for snap_scaffold_21-snap.2510-T1
Valid prediction for Augustus_model.g33468.t1
Valid prediction for Augustus_model.g33463.t1
Valid prediction for Augustus_model.g33466.t1
Valid prediction for snap_scaffold_21-snap.2497-T1
Valid prediction for CodingQuarry_transcript_32689-T1
Valid prediction for GeneMark_model.86441_t
Valid prediction for GlimmerHMM_glimmerT_49890-T1
Valid prediction for GlimmerHMM_glimmerT_49882-T1
Valid prediction for GlimmerHMM_glimmerT_49886-T1
Valid prediction for GlimmerHMM_glimmerT_49880-T1
Valid prediction for Augustus_model.g33467.t1
Valid prediction for GeneMark_model.86456_t
Valid prediction for snap_scaffold_21-snap.2516-T1
Valid prediction for snap_scaffold_21-snap.2503-T1
Valid prediction for GeneMark_model.86429_t
Valid prediction for snap_scaffold_21-snap.2493-T1
Valid prediction for GeneMark_model.86448_t
Valid prediction for GlimmerHMM_glimmerT_49884-T1
Valid prediction for GeneMark_model.86471_t
Valid prediction for Augustus_model.g33469.t1
Couldn't classify 54231, 54361
Sorry, prediction pasa_asmbl_28162.p1 fails validation.
(AAG)	 AG	54231-54361	GT	AGG
(GCC)	 AG	56134-56203	GT	CGG
(GCC)	 AG	56431-56593	GT	AGG
(ACA)	 AG	58707-59056	AC	AAA
-recovered pasa_asmbl_28162.p1, terminal, 58707, 59056
-recovered pasa_asmbl_28162.p1, internal, 54231, 54361
-recovered pasa_asmbl_28162.p1, internal, 56134, 56203
-recovered pasa_asmbl_28162.p1, internal, 56431, 56593
Couldn't classify 53622, 54062
Sorry, prediction pasa_asmbl_28164.p1 fails validation.
(AAT)	 CT	53622-54062	TC	CCT
Valid prediction for GlimmerHMM_glimmerT_49874-T1
Valid prediction for snap_scaffold_21-snap.2520-T1
Valid prediction for GeneMark_model.86416_t
Valid prediction for GeneMark_model.86450_t
Valid prediction for GeneMark_model.86439_t
Valid prediction for GeneMark_model.86421_t
Valid prediction for snap_scaffold_21-snap.2498-T1
Valid prediction for snap_scaffold_21-snap.2509-T1
Valid prediction for snap_scaffold_21-snap.2531-T1
Valid prediction for GeneMark_model.86435_t
Valid prediction for GeneMark_model.86451_t
Valid prediction for snap_scaffold_21-snap.2519-T1
Valid prediction for GlimmerHMM_glimmerT_49889-T1
Valid prediction for GeneMark_model.86464_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 12774, rend_intergenic: 3025  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18281, rend_intergenic: 16141  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29914, rend_intergenic: 25450  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50600, rend_intergenic: 34345  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55792, rend_intergenic: 51193  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70536, rend_intergenic: 56956  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75483, rend_intergenic: 70769  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79401, rend_intergenic: 76389  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109758, rend_intergenic: 87885  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112966, rend_intergenic: 111793  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120861, rend_intergenic: 118202  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129946, rend_intergenic: 128715  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133669, rend_intergenic: 130916  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140698, rend_intergenic: 137668  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153642, rend_intergenic: 151706  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164950, rend_intergenic: 153833  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180002, rend_intergenic: 165314  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184135, rend_intergenic: 180059  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 187679
-exon list size: 836


building trellis

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62.4    
62.5    
62.6    
62.8    
62.9    
63.0    
63.1    
63.2    
63.4    
63.5    
63.6    
63.7    
63.8    
64.0    
64.1    
64.2    
64.3    
64.4    
64.6    
64.7    
64.8    
64.9    
65.0    
65.2    
65.3    
65.4    
65.5    
65.6    
65.8    
65.9    
66.0    
66.1    
66.2    
66.3    
66.5    
66.6    
66.7    
66.8    
66.9    
67.1    
67.2    
67.3    
67.4    
67.5    
67.7    
67.8    
67.9    
68.0    
68.1    
68.3    
68.4    
68.5    
68.6    
68.7    
68.9    
69.0    
69.1    
69.2    
69.3    
69.5    
69.6    
69.7    
69.8    
69.9    
70.0    
70.2    
70.3    
70.4    
70.5    
70.6    
70.8    
70.9    
71.0    
71.1    
71.2    
71.4    
71.5    
71.6    
71.7    
71.8    
72.0    
72.1    
72.2    
72.3    
72.4    
72.6    
72.7    
72.8    
72.9    
73.0    
73.2    
73.3    
73.4    
73.5    
73.6    
73.7    
73.9    
74.0    
74.1    
74.2    
74.3    
74.5    
74.6    
74.7    
74.8    
74.9    
75.1    
75.2    
75.3    
75.4    
75.5    
75.7    
75.8    
75.9    
76.0    
76.1    
76.3    
76.4    
76.5    
76.6    
76.7    
76.8    
77.0    
77.1    
77.2    
77.3    
77.4    
77.6    
77.7    
77.8    
77.9    
78.0    
78.2    
78.3    
78.4    
78.5    
78.6    
78.8    
78.9    
79.0    
79.1    
79.2    
79.4    
79.5    
79.6    
79.7    
79.8    
80.0    
80.1    
80.2    
80.3    
80.4    
80.5    
80.7    
80.8    
80.9    
81.0    
81.1    
81.3    
81.4    
81.5    
81.6    
81.7    
81.9    
82.0    
82.1    
82.2    
82.3    
82.5    
82.6    
82.7    
82.8    
82.9    
83.1    
83.2    
83.3    
83.4    
83.5    
83.7    
83.8    
83.9    
84.0    
84.1    
84.2    
84.4    
84.5    
84.6    
84.7    
84.8    
85.0    
85.1    
85.2    
85.3    
85.4    
85.6    
85.7    
85.8    
85.9    
86.0    
86.2    
86.3    
86.4    
86.5    
86.6    
86.8    
86.9    
87.0    
87.1    
87.2    
87.4    
87.5    
87.6    
87.7    
87.8    
87.9    
88.1    
88.2    
88.3    
88.4    
88.5    
88.7    
88.8    
88.9    
89.0    
89.1    
89.3    
89.4    
89.5    
89.6    
89.7    
89.9    
90.0    
90.1    
90.2    
90.3    
90.5    
90.6    
90.7    
90.8    
90.9    
91.1    
91.2    
91.3    
91.4    
91.5    
91.6    
91.8    
91.9    
92.0    
92.1    
92.2    
92.4    
92.5    
92.6    
92.7    
92.8    
93.0    
93.1    
93.2    
93.3    
93.4    
93.6    
93.7    
93.8    
93.9    
94.0    
94.2    
94.3    
94.4    
94.5    
94.6    
94.7    
94.9    
95.0    
95.1    
95.2    
95.3    
95.5    
95.6    
95.7    
95.8    
95.9    
96.1    
96.2    
96.3    
96.4    
96.5    
96.7    
96.8    
96.9    
97.0    
97.1    
97.3    
97.4    
97.5    
97.6    
97.7    
97.9    
98.0    
98.1    
98.2    
98.3    
98.4    
98.6    
98.7    
98.8    
98.9    
99.0    
99.2    
99.3    
99.4    
99.5    
99.6    
99.8    
99.9    
-found 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 12774, rend_intergenic: 3025  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18281, rend_intergenic: 16141  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29914, rend_intergenic: 25450  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50600, rend_intergenic: 34345  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55792, rend_intergenic: 51193  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70536, rend_intergenic: 56956  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75483, rend_intergenic: 70769  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79401, rend_intergenic: 76389  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109758, rend_intergenic: 87885  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112966, rend_intergenic: 111793  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120861, rend_intergenic: 118202  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129946, rend_intergenic: 128715  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133669, rend_intergenic: 130916  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140698, rend_intergenic: 137668  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153642, rend_intergenic: 151706  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164950, rend_intergenic: 153833  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180002, rend_intergenic: 165314  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184135, rend_intergenic: 180059  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support