-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_4/scaffold_4_10873563-11019026

-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.2362-T1
Valid prediction for GeneMark_model.16943_t
Valid prediction for GlimmerHMM_glimmerT_10384-T1
Valid prediction for snap_scaffold_4-snap.2364-T1
Valid prediction for GlimmerHMM_glimmerT_10387-T1
Valid prediction for HiQ_model.g6809.t1
Valid prediction for Augustus_model.g6799.t1
Valid prediction for CodingQuarry_transcript_49023-T1
Valid prediction for GlimmerHMM_glimmerT_10390-T1
Valid prediction for HiQ_model.g6804.t1
Valid prediction for pasa_asmbl_43026.p1
Valid prediction for GeneMark_model.16916_t
Valid prediction for GlimmerHMM_glimmerT_10388-T1
Valid prediction for snap_scaffold_4-snap.2360-T1
Valid prediction for GlimmerHMM_glimmerT_10391-T1
Valid prediction for GeneMark_model.16923_t
Valid prediction for Augustus_model.g6811.t1
Valid prediction for snap_scaffold_4-snap.2339-T1
Couldn't classify 104459, 104492
Couldn't classify 106684, 106805
Sorry, prediction pasa_asmbl_43027.p1 fails validation.
(TAT)	 GG	104459-104492	GT	GAG
(GGA)	 AG	105514-105636	GT	CAG
(AGA)	 AG	105877-105999	GT	AAG
(GTC)	 AG	106684-106805	AG	AAA
-recovered pasa_asmbl_43027.p1, internal, 105514, 105636
-recovered pasa_asmbl_43027.p1, internal, 105877, 105999
Valid prediction for snap_scaffold_4-snap.2356-T1
Valid prediction for CodingQuarry_transcript_49022-T1
Valid prediction for pasa_asmbl_43016.p1
Valid prediction for GeneMark_model.16920_t
Valid prediction for GlimmerHMM_glimmerT_10383-T1
Valid prediction for snap_scaffold_4-snap.2342-T1
Valid prediction for GlimmerHMM_glimmerT_10379-T1
Couldn't classify 78118, 78152
Sorry, prediction pasa_asmbl_43022.p1 fails validation.
(GAG)	 GC	78118-78152	GT	AGG
(GCG)	 AG	78294-78527	GT	AGG
(AAA)	 AG	78703-78776	GT	GAG
(GCT)	 AG	79213-79385	GT	AGG
(CCC)	 AG	79557-79730	GT	AGG
(ATC)	 AG	80206-80423	GT	AGG
(ACC)	 AG	80667-80787	GT	CGG
(ATC)	 AG	80982-81327	GT	CAG
(ATC)	 AG	81646-81733	GT	AGG
(GGA)	 AG	81972-82116	GT	CGG
(GCG)	 AG	82313-82443	GT	AGG
(GGA)	 AG	82586-82646	GT	AAG
(CAA)	 AG	82763-82944	GT	AGG
(GAT)	 AG	83090-83174	GT	AGG
(GTG)	 AG	83280-83435	GT	AGG
(GTG)	 AG	83638-83751	GT	ATG
(GCA)	 AG	83889-84033	GT	TGG
(GGG)	 AG	84202-84287	GT	TGG
(GTG)	 AG	84390-84602	AG	AGA
-recovered pasa_asmbl_43022.p1, terminal, 84390, 84602
-recovered pasa_asmbl_43022.p1, internal, 78294, 78527
-recovered pasa_asmbl_43022.p1, internal, 78703, 78776
-recovered pasa_asmbl_43022.p1, internal, 79213, 79385
-recovered pasa_asmbl_43022.p1, internal, 79557, 79730
-recovered pasa_asmbl_43022.p1, internal, 80206, 80423
-recovered pasa_asmbl_43022.p1, internal, 80667, 80787
-recovered pasa_asmbl_43022.p1, internal, 80982, 81327
-recovered pasa_asmbl_43022.p1, internal, 81646, 81733
-recovered pasa_asmbl_43022.p1, internal, 81972, 82116
-recovered pasa_asmbl_43022.p1, internal, 82313, 82443
-recovered pasa_asmbl_43022.p1, internal, 82586, 82646
-recovered pasa_asmbl_43022.p1, internal, 82763, 82944
-recovered pasa_asmbl_43022.p1, internal, 83090, 83174
-recovered pasa_asmbl_43022.p1, internal, 83280, 83435
-recovered pasa_asmbl_43022.p1, internal, 83638, 83751
-recovered pasa_asmbl_43022.p1, internal, 83889, 84033
-recovered pasa_asmbl_43022.p1, internal, 84202, 84287
Valid prediction for snap_scaffold_4-snap.2335-T1
Valid prediction for GeneMark_model.16945_t
Valid prediction for snap_scaffold_4-snap.2340-T1
Valid prediction for GeneMark_model.16939_t
Valid prediction for Augustus_model.g6807.t1
Valid prediction for snap_scaffold_4-snap.2345-T1
Valid prediction for HiQ_model.g6808.t1
Valid prediction for snap_scaffold_4-snap.2352-T1
Valid prediction for snap_scaffold_4-snap.2337-T1
Valid prediction for GeneMark_model.16918_t
Valid prediction for snap_scaffold_4-snap.2341-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for pasa_asmbl_43021.p1
Valid prediction for GeneMark_model.16929_t
Valid prediction for GlimmerHMM_glimmerT_10373-T1
Valid prediction for snap_scaffold_4-snap.2366-T1
Valid prediction for GlimmerHMM_glimmerT_10380-T1
Valid prediction for Augustus_model.g6810.t1
Valid prediction for snap_scaffold_4-snap.2350-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GeneMark_model.16937_t
Valid prediction for GeneMark_model.16931_t
Valid prediction for Augustus_model.g6812.t1
Valid prediction for snap_scaffold_4-snap.2354-T1
Valid prediction for pasa_asmbl_43025.p1
Valid prediction for Augustus_model.g6814.t1
Valid prediction for GeneMark_model.16941_t
Valid prediction for GeneMark_model.16914_t
Valid prediction for snap_scaffold_4-snap.2347-T1
Couldn't classify 70406, 70508
Sorry, prediction pasa_asmbl_43018.p1 fails validation.
(ATG)	 GC	67645-67788	GT	AGG
(GTG)	 AG	68241-68384	GT	AGG
(GTT)	 AG	68607-68718	GT	AGG
(GAG)	 AG	68857-69011	GT	AGG
(GAG)	 AG	69221-69418	GT	AGG
(AAG)	 AG	69567-69777	GT	AGG
(CTG)	 AG	70136-70259	GT	GGG
(GCT)	 AG	70406-70508	CC	CCC
-recovered pasa_asmbl_43018.p1, initial, 67645, 67788
-recovered pasa_asmbl_43018.p1, internal, 68241, 68384
-recovered pasa_asmbl_43018.p1, internal, 68607, 68718
-recovered pasa_asmbl_43018.p1, internal, 68857, 69011
-recovered pasa_asmbl_43018.p1, internal, 69221, 69418
-recovered pasa_asmbl_43018.p1, internal, 69567, 69777
-recovered pasa_asmbl_43018.p1, internal, 70136, 70259
Couldn't classify 63672, 63765
Couldn't classify 66899, 67084
Sorry, prediction pasa_asmbl_43017.p1 fails validation.
(ATC)	 TC	63672-63765	GT	AGG
(AGC)	 AG	64867-65060	GT	AGG
(GAC)	 AG	65354-65470	GT	AGG
(AAT)	 AG	65577-65687	GT	AGG
(GTG)	 AG	65823-65977	GT	TGG
(GGG)	 AG	66499-66616	GT	AGG
(GTG)	 AG	66899-67084	TG	AGT
-recovered pasa_asmbl_43017.p1, internal, 64867, 65060
-recovered pasa_asmbl_43017.p1, internal, 65354, 65470
-recovered pasa_asmbl_43017.p1, internal, 65577, 65687
-recovered pasa_asmbl_43017.p1, internal, 65823, 65977
-recovered pasa_asmbl_43017.p1, internal, 66499, 66616
Valid prediction for GlimmerHMM_glimmerT_10386-T1
Valid prediction for GeneMark_model.16926_t
Valid prediction for GeneMark_model.16912_t
Valid prediction for GeneMark_model.16932_t
Couldn't classify 107260, 107395
Couldn't classify 108742, 108834
Couldn't classify 109103, 109158
Sorry, prediction pasa_asmbl_43028.p1 fails validation.
(CTC)	 CC	107260-107395	GC	TGG
(GCA)	 AG	107695-107847	GT	AGG
(ACA)	 AG	108742-108834	AT	TAA
(TTC)	 AC	109103-109158	AG	GAA
-recovered pasa_asmbl_43028.p1, internal, 107695, 107847
Valid prediction for snap_scaffold_4-snap.2369-T1
Valid prediction for CodingQuarry_transcript_49019-T1
Valid prediction for GlimmerHMM_glimmerT_10375-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GeneMark_model.16935_t
Valid prediction for GlimmerHMM_glimmerT_10385-T1
Valid prediction for GeneMark_model.16922_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.16933_t
Valid prediction for Augustus_model.g6806.t1
Valid prediction for Augustus_model.g6815.t1
Valid prediction for GeneMark_model.16930_t
Valid prediction for snap_scaffold_4-snap.2344-T1
Valid prediction for GeneMark_model.16915_t
Valid prediction for GeneMark_model.16936_t
Valid prediction for GlimmerHMM_glimmerT_10389-T1
Valid prediction for snap_scaffold_4-snap.2334-T1
Valid prediction for snap_scaffold_4-snap.2355-T1
Valid prediction for snap_scaffold_4-snap.2349-T1
Valid prediction for Augustus_model.g6798.t1
Valid prediction for pasa_asmbl_41617.p1
Couldn't classify 92739, 92740
Sorry, prediction CodingQuarry_transcript_49020-T1 fails validation.
(ATG)	 AC	92739-92740	GT	ATG
(GGA)	 AG	93253-93487	GT	TGG
(TGT)	 AG	93627-94461	GT	AGG
(GTG)	 AG	94713-94951	CT	AGC
-recovered CodingQuarry_transcript_49020-T1, terminal, 94713, 94951
-recovered CodingQuarry_transcript_49020-T1, internal, 93253, 93487
-recovered CodingQuarry_transcript_49020-T1, internal, 93627, 94461
Valid prediction for CodingQuarry_transcript_49025-T1
Valid prediction for GlimmerHMM_glimmerT_10392-T1
Valid prediction for GeneMark_model.16938_t
Valid prediction for GeneMark_model.16946_t
Valid prediction for GlimmerHMM_glimmerT_10377-T1
Valid prediction for snap_scaffold_4-snap.2343-T1
Valid prediction for GlimmerHMM_glimmerT_10376-T1
Valid prediction for GlimmerHMM_glimmerT_10372-T1
Valid prediction for GlimmerHMM_glimmerT_10393-T1
Valid prediction for GlimmerHMM_glimmerT_10381-T1
Valid prediction for Augustus_model.g6805.t1
Valid prediction for HiQ_model.g6803.t1
Valid prediction for GeneMark_model.16917_t
Valid prediction for snap_scaffold_4-snap.2363-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_4-snap.2348-T1
Valid prediction for snap_scaffold_4-snap.2353-T1
Valid prediction for snap_scaffold_4-snap.2358-T1
Valid prediction for CodingQuarry_transcript_49017-T1
Valid prediction for snap_scaffold_4-snap.2365-T1
Valid prediction for GeneMark_model.16925_t
Valid prediction for pasa_asmbl_41608.p1
Valid prediction for GeneMark_model.16934_t
Valid prediction for Augustus_model.g6800.t1
Valid prediction for snap_scaffold_4-snap.2368-T1
Valid prediction for GeneMark_model.16919_t
Valid prediction for snap_scaffold_4-snap.2346-T1
Valid prediction for pasa_asmbl_41610.p1
Valid prediction for GeneMark_model.16913_t
Couldn't classify 12517, 12562
Sorry, prediction pasa_asmbl_42382.p1 fails validation.
(AAG)	 GC	12517-12562	GT	GGG
(CCT)	 AG	12661-12796	GT	AAG
(GTT)	 AG	13183-13271	GT	AGG
(GAA)	 AG	13390-13453	GT	GGG
(CTG)	 AG	13666-13763	GT	AGG
(GGA)	 AG	14187-14281	CT	AAC
-recovered pasa_asmbl_42382.p1, terminal, 14187, 14281
-recovered pasa_asmbl_42382.p1, internal, 12661, 12796
-recovered pasa_asmbl_42382.p1, internal, 13183, 13271
-recovered pasa_asmbl_42382.p1, internal, 13390, 13453
-recovered pasa_asmbl_42382.p1, internal, 13666, 13763
Valid prediction for snap_scaffold_4-snap.2359-T1
Valid prediction for GlimmerHMM_glimmerT_10374-T1
Valid prediction for CodingQuarry_transcript_49018-T1
Valid prediction for GeneMark_model.16944_t
Valid prediction for Augustus_model.g6801.t1
Valid prediction for GeneMark_model.16928_t
Valid prediction for snap_scaffold_4-snap.2367-T1
Valid prediction for HiQ_model.g6813.t1
Valid prediction for GeneMark_model.16921_t
Valid prediction for snap_scaffold_4-snap.2338-T1
Valid prediction for snap_scaffold_4-snap.2370-T1
Valid prediction for snap_scaffold_4-snap.2336-T1
Valid prediction for Augustus_model.g6802.t1
Couldn't classify 92739, 92740
Sorry, prediction pasa_asmbl_41614.p1 fails validation.
(ATG)	 AC	92739-92740	GT	ATG
(GGA)	 AG	93253-93487	GT	TGG
(TGT)	 AG	93627-94461	GT	AGG
(GTG)	 AG	94713-94951	CT	AGC
-recovered pasa_asmbl_41614.p1, terminal, 94713, 94951
-recovered pasa_asmbl_41614.p1, internal, 93253, 93487
-recovered pasa_asmbl_41614.p1, internal, 93627, 94461
Valid prediction for snap_scaffold_4-snap.2361-T1
Valid prediction for GlimmerHMM_glimmerT_10382-T1
Valid prediction for GeneMark_model.16924_t
Valid prediction for GeneMark_model.16940_t
Valid prediction for GlimmerHMM_glimmerT_10378-T1
Valid prediction for snap_scaffold_4-snap.2351-T1
Valid prediction for GeneMark_model.16942_t
Valid prediction for GeneMark_model.16927_t
Valid prediction for snap_scaffold_4-snap.2357-T1
Couldn't classify 92739, 92740
Sorry, prediction CodingQuarry_transcript_49021-T1 fails validation.
(ATG)	 AC	92739-92740	GT	ATG
(GGA)	 AG	93253-93487	GT	TGG
(TGT)	 AG	93627-94604	GG	AAG
-recovered CodingQuarry_transcript_49021-T1, terminal, 93627, 94604
-recovered CodingQuarry_transcript_49021-T1, internal, 93253, 93487
Valid prediction for CodingQuarry_transcript_49024-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 5359, rend_intergenic: 4473  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 7610, rend_intergenic: 5387  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29894, rend_intergenic: 15066  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37867, rend_intergenic: 36524  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67200, rend_intergenic: 63776  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69408, rend_intergenic: 67536  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84602, rend_intergenic: 69552  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91497, rend_intergenic: 88298  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107246, rend_intergenic: 102443  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116031, rend_intergenic: 114986  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119943, rend_intergenic: 116049  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139854, rend_intergenic: 134210  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 145464
-exon list size: 580


building trellis

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68.7    
68.9    
69.1    
69.2    
69.4    
69.6    
69.8    
69.9    
70.1    
70.3    
70.4    
70.6    
70.8    
71.0    
71.1    
71.3    
71.5    
71.6    
71.8    
72.0    
72.2    
72.3    
72.5    
72.7    
72.9    
73.0    
73.2    
73.4    
73.5    
73.7    
73.9    
74.1    
74.2    
74.4    
74.6    
74.7    
74.9    
75.1    
75.3    
75.4    
75.6    
75.8    
75.9    
76.1    
76.3    
76.5    
76.6    
76.8    
77.0    
77.1    
77.3    
77.5    
77.7    
77.8    
78.0    
78.2    
78.4    
78.5    
78.7    
78.9    
79.0    
79.2    
79.4    
79.6    
79.7    
79.9    
80.1    
80.2    
80.4    
80.6    
80.8    
80.9    
81.1    
81.3    
81.4    
81.6    
81.8    
82.0    
82.1    
82.3    
82.5    
82.6    
82.8    
83.0    
83.2    
83.3    
83.5    
83.7    
83.8    
84.0    
84.2    
84.4    
84.5    
84.7    
84.9    
85.1    
85.2    
85.4    
85.6    
85.7    
85.9    
86.1    
86.3    
86.4    
86.6    
86.8    
86.9    
87.1    
87.3    
87.5    
87.6    
87.8    
88.0    
88.1    
88.3    
88.5    
88.7    
88.8    
89.0    
89.2    
89.3    
89.5    
89.7    
89.9    
90.0    
90.2    
90.4    
90.5    
90.7    
90.9    
91.1    
91.2    
91.4    
91.6    
91.8    
91.9    
92.1    
92.3    
92.4    
92.6    
92.8    
93.0    
93.1    
93.3    
93.5    
93.6    
93.8    
94.0    
94.2    
94.3    
94.5    
94.7    
94.8    
95.0    
95.2    
95.4    
95.5    
95.7    
95.9    
96.0    
96.2    
96.4    
96.6    
96.7    
96.9    
97.1    
97.3    
97.4    
97.6    
97.8    
97.9    
98.1    
98.3    
98.5    
98.6    
98.8    
99.0    
99.1    
99.3    
99.5    
99.7    
99.8    
-found 20 predictions from path traversal
Error with prediction: snap lend_intergenic: 5359, rend_intergenic: 4473  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 7610, rend_intergenic: 5387  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29894, rend_intergenic: 15066  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37867, rend_intergenic: 36524  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67200, rend_intergenic: 63776  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69408, rend_intergenic: 67536  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84602, rend_intergenic: 69552  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91497, rend_intergenic: 88298  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107246, rend_intergenic: 102443  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116031, rend_intergenic: 114986  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119943, rend_intergenic: 116049  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139854, rend_intergenic: 134210  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support