-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_10/scaffold_10_3411358-3571365

-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: +)Couldn't classify 69607, 69719
Couldn't classify 73697, 73823
Sorry, prediction pasa_asmbl_4324.p1 fails validation.
(AGT)	 GC	69607-69719	GT	AGG
(GTG)	 AG	70227-70293	GT	TGG
(GAG)	 AG	70605-70707	GT	AGG
(ATA)	 AG	70809-70978	GT	AGG
(ATG)	 AG	71333-71495	GT	AGG
(ACA)	 AG	72098-72191	GT	TGG
(GCA)	 AG	73697-73823	GA	AGG
-recovered pasa_asmbl_4324.p1, initial, 71333, 71495
-recovered pasa_asmbl_4324.p1, internal, 70227, 70293
-recovered pasa_asmbl_4324.p1, internal, 70605, 70707
-recovered pasa_asmbl_4324.p1, internal, 70809, 70978
-recovered pasa_asmbl_4324.p1, internal, 71333, 71495
-recovered pasa_asmbl_4324.p1, internal, 72098, 72191
Valid prediction for Augustus_model.g16739.t1
Valid prediction for GlimmerHMM_glimmerT_24965-T1
Valid prediction for GeneMark_model.42650_t
Valid prediction for GeneMark_model.42645_t
Valid prediction for GeneMark_model.42661_t
Valid prediction for snap_scaffold_10-snap.742-T1
Valid prediction for GeneMark_model.42642_t
Valid prediction for snap_scaffold_10-snap.732-T1
Valid prediction for GeneMark_model.42635_t
Valid prediction for snap_scaffold_10-snap.751-T1
Valid prediction for GeneMark_model.42668_t
Valid prediction for snap_scaffold_10-snap.759-T1
Valid prediction for snap_scaffold_10-snap.740-T1
Valid prediction for GeneMark_model.42629_t
Valid prediction for snap_scaffold_10-snap.734-T1
Valid prediction for GeneMark_model.42659_t
Valid prediction for snap_scaffold_10-snap.755-T1
Valid prediction for GeneMark_model.42648_t
Valid prediction for GlimmerHMM_glimmerT_24966-T1
Valid prediction for CodingQuarry_transcript_5326-T1
Valid prediction for snap_scaffold_10-snap.761-T1
Valid prediction for GeneMark_model.42626_t
Valid prediction for GeneMark_model.42620_t
Valid prediction for HiQ_model.g16727.t1
Valid prediction for GeneMark_model.42666_t
Valid prediction for snap_scaffold_10-snap.764-T1
Valid prediction for snap_scaffold_10-snap.739-T1
Valid prediction for GeneMark_model.42637_t
Valid prediction for snap_scaffold_10-snap.736-T1
Valid prediction for GeneMark_model.42664_t
Valid prediction for GeneMark_model.42655_t
Valid prediction for GlimmerHMM_glimmerT_24953-T1
Couldn't classify 27369, 27827
Sorry, prediction pasa_asmbl_3124.p1 fails validation.
(GTA)	 GG	27369-27827	GT	GAG
Valid prediction for snap_scaffold_10-snap.738-T1
Couldn't classify 61097, 61309
Couldn't classify 65473, 65621
Sorry, prediction pasa_asmbl_4323.p1 fails validation.
(GTG)	 AG	61097-61309	GT	AGG
(GTG)	 AG	64253-64282	GT	AGG
(ATC)	 AG	65083-65410	GT	AGG
(GAG)	 AG	65473-65621	GG	GGG
-recovered pasa_asmbl_4323.p1, internal, 61097, 61309
-recovered pasa_asmbl_4323.p1, internal, 64253, 64282
-recovered pasa_asmbl_4323.p1, internal, 65083, 65410
Valid prediction for Augustus_model.g16736.t1
Valid prediction for pasa_asmbl_4317.p1
Couldn't classify 81514, 81819
Sorry, prediction pasa_asmbl_4325.p2 fails validation.
(AGC)	 CC	81514-81819	TC	AGT
Valid prediction for snap_scaffold_10-snap.754-T1
Valid prediction for snap_scaffold_10-snap.745-T1
Valid prediction for GeneMark_model.42662_t
Valid prediction for snap_scaffold_10-snap.746-T1
Valid prediction for HiQ_model.g16729.t1
Valid prediction for Augustus_model.g16738.t1
Couldn't classify 95548, 95634
Sorry, prediction pasa_asmbl_4330.p2 fails validation.
(CAG)	 CA	95548-95634	GC	AGG
(ATC)	 AG	96523-96594	GT	GGG
(CTG)	 AG	97315-97512	GT	AGG
(GAT)	 AG	97610-97732	GC	AAG
-recovered pasa_asmbl_4330.p2, terminal, 97610, 97732
-recovered pasa_asmbl_4330.p2, internal, 96523, 96594
-recovered pasa_asmbl_4330.p2, internal, 97315, 97512
-recovered pasa_asmbl_4330.p2, internal, 97610, 97732
Valid prediction for GlimmerHMM_glimmerT_24956-T1
Valid prediction for GlimmerHMM_glimmerT_24954-T1
Valid prediction for GeneMark_model.42640_t
Couldn't classify 10696, 10709
Sorry, prediction pasa_asmbl_4319.p1 fails validation.
(CGA)	 CG	10696-10709	GT	GGG
(GTC)	 AG	10999-11204	GT	CGG
(GTG)	 AG	11330-11516	GT	AGG
(GTT)	 AG	11637-11724	GT	AGG
(TGT)	 AG	11878-11957	GT	AGG
(AGC)	 AG	12084-12177	GT	GAG
(AAC)	 AG	12294-12388	GT	TGG
(GAG)	 AG	12515-12573	GT	AGG
(GTC)	 AG	12770-12893	GT	AGG
(TGA)	 AG	13469-13558	GT	TGG
(CTA)	 AG	13657-13779	GT	GGG
(AGG)	 AG	14306-14413	GT	GGG
(GTT)	 AG	14536-14654	GT	GCG
(CGA)	 AG	15059-15252	GG	GAG
-recovered pasa_asmbl_4319.p1, terminal, 15059, 15252
-recovered pasa_asmbl_4319.p1, internal, 10999, 11204
-recovered pasa_asmbl_4319.p1, internal, 11330, 11516
-recovered pasa_asmbl_4319.p1, internal, 11637, 11724
-recovered pasa_asmbl_4319.p1, internal, 11878, 11957
-recovered pasa_asmbl_4319.p1, internal, 12084, 12177
-recovered pasa_asmbl_4319.p1, internal, 12294, 12388
-recovered pasa_asmbl_4319.p1, internal, 12515, 12573
-recovered pasa_asmbl_4319.p1, internal, 12770, 12893
-recovered pasa_asmbl_4319.p1, internal, 13469, 13558
-recovered pasa_asmbl_4319.p1, internal, 13657, 13779
-recovered pasa_asmbl_4319.p1, internal, 14306, 14413
-recovered pasa_asmbl_4319.p1, internal, 14536, 14654
Valid prediction for GeneMark_model.42647_t
Valid prediction for Augustus_model.g16737.t1
Valid prediction for snap_scaffold_10-snap.760-T1
Valid prediction for GeneMark_model.42638_t
Valid prediction for GeneMark_model.42652_t
Valid prediction for GeneMark_model.42624_t
Couldn't classify 89056, 89169
Couldn't classify 94626, 94736
Sorry, prediction pasa_asmbl_4329.p1 fails validation.
(GAG)	 AG	89056-89169	GT	AGG
(GCC)	 AG	90055-90129	GT	ATG
(ATG)	 AG	90299-90424	GT	AGG
(GAG)	 AG	90660-90803	GT	AGG
(GGC)	 AG	90917-90958	GT	GGG
(ACC)	 AG	91234-91362	GT	AGG
(ATC)	 AG	94100-94192	GT	AGG
(AGG)	 AG	94626-94736	GT	ACG
-recovered pasa_asmbl_4329.p1, initial, 90299, 90424
-recovered pasa_asmbl_4329.p1, internal, 89056, 89169
-recovered pasa_asmbl_4329.p1, internal, 90055, 90129
-recovered pasa_asmbl_4329.p1, internal, 90299, 90424
-recovered pasa_asmbl_4329.p1, internal, 90660, 90803
-recovered pasa_asmbl_4329.p1, internal, 90917, 90958
-recovered pasa_asmbl_4329.p1, internal, 91234, 91362
-recovered pasa_asmbl_4329.p1, internal, 94100, 94192
-recovered pasa_asmbl_4329.p1, internal, 94626, 94736
Valid prediction for snap_scaffold_10-snap.757-T1
Valid prediction for GeneMark_model.42670_t
Valid prediction for GeneMark_model.42622_t
Valid prediction for GlimmerHMM_glimmerT_24968-T1
Valid prediction for GeneMark_model.42632_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 GlimmerHMM_glimmerT_24962-T1
Valid prediction for GeneMark_model.42643_t
Valid prediction for snap_scaffold_10-snap.741-T1
Valid prediction for GeneMark_model.42658_t
Valid prediction for GeneMark_model.42623_t
Valid prediction for GeneMark_model.42649_t
Valid prediction for GeneMark_model.42641_t
Valid prediction for Augustus_model.g16733.t1
Valid prediction for Augustus_model.g16740.t1
Valid prediction for GlimmerHMM_glimmerT_24973-T1
Valid prediction for GeneMark_model.42660_t
Valid prediction for GeneMark_model.42646_t
Valid prediction for Augustus_model.g16730.t1
Valid prediction for GlimmerHMM_glimmerT_24969-T1
Valid prediction for snap_scaffold_10-snap.737-T1
Valid prediction for GlimmerHMM_glimmerT_24970-T1
Valid prediction for GlimmerHMM_glimmerT_24971-T1
Valid prediction for snap_scaffold_10-snap.748-T1
Valid prediction for GlimmerHMM_glimmerT_24961-T1
Valid prediction for GeneMark_model.42663_t
Valid prediction for snap_scaffold_10-snap.733-T1
Valid prediction for GeneMark_model.42631_t
Valid prediction for GeneMark_model.42651_t
Valid prediction for GeneMark_model.42628_t
Valid prediction for snap_scaffold_10-snap.750-T1
Valid prediction for GlimmerHMM_glimmerT_24975-T1
Valid prediction for GeneMark_model.42639_t
Valid prediction for GlimmerHMM_glimmerT_24957-T1
Valid prediction for GlimmerHMM_glimmerT_24960-T1
Valid prediction for GeneMark_model.42630_t
Valid prediction for Augustus_model.g16732.t1
Valid prediction for GlimmerHMM_glimmerT_24955-T1
Valid prediction for GlimmerHMM_glimmerT_24967-T1
Couldn't classify 43999, 44010
Couldn't classify 45742, 45767
Sorry, prediction pasa_asmbl_3130.p1 fails validation.
(CTC)	 CC	43999-44010	GT	GGG
(CCC)	 AG	44172-44283	GT	AGG
(GAG)	 AG	44453-44550	GT	AGG
(CAC)	 AG	45548-45653	GT	AGG
(GCT)	 AG	45742-45767	GA	AGG
-recovered pasa_asmbl_3130.p1, internal, 44172, 44283
-recovered pasa_asmbl_3130.p1, internal, 44453, 44550
-recovered pasa_asmbl_3130.p1, internal, 45548, 45653
Valid prediction for Augustus_model.g16734.t1
Valid prediction for GlimmerHMM_glimmerT_24959-T1
Valid prediction for snap_scaffold_10-snap.762-T1
Valid prediction for GlimmerHMM_glimmerT_24974-T1
Couldn't classify 128645, 128743
Couldn't classify 129510, 129649
Sorry, prediction pasa_asmbl_3126.p1 fails validation.
(GCG)	 AG	128645-128743	GT	TGG
(ATC)	 AG	128973-129114	GT	AAG
(ACG)	 AG	129510-129649	CA	GCC
-recovered pasa_asmbl_3126.p1, internal, 128645, 128743
-recovered pasa_asmbl_3126.p1, internal, 128973, 129114
Valid prediction for snap_scaffold_10-snap.744-T1
Valid prediction for Augustus_model.g16735.t1
Valid prediction for GeneMark_model.42621_t
Valid prediction for GeneMark_model.42627_t
Valid prediction for GeneMark_model.42625_t
Valid prediction for GeneMark_model.42656_t
Valid prediction for snap_scaffold_10-snap.735-T1
Valid prediction for snap_scaffold_10-snap.758-T1
Valid prediction for snap_scaffold_10-snap.747-T1
Valid prediction for GlimmerHMM_glimmerT_24964-T1
Valid prediction for GeneMark_model.42654_t
Valid prediction for GeneMark_model.42669_t
Valid prediction for GlimmerHMM_glimmerT_24958-T1
Valid prediction for GeneMark_model.42653_t
Valid prediction for GeneMark_model.42657_t
Valid prediction for snap_scaffold_10-snap.752-T1
Valid prediction for snap_scaffold_10-snap.753-T1
Valid prediction for HiQ_model.g16728.t1
Valid prediction for GeneMark_model.42667_t
Valid prediction for GlimmerHMM_glimmerT_24972-T1
Valid prediction for GeneMark_model.42634_t
Valid prediction for GeneMark_model.42644_t
Valid prediction for Augustus_model.g16731.t1
Valid prediction for GeneMark_model.42636_t
Valid prediction for CodingQuarry_transcript_5327-T1
Valid prediction for pasa_asmbl_3129.p1
Valid prediction for snap_scaffold_10-snap.756-T1
Valid prediction for GlimmerHMM_glimmerT_24963-T1
Valid prediction for snap_scaffold_10-snap.749-T1
Valid prediction for Augustus_model.g16741.t1
Valid prediction for snap_scaffold_10-snap.763-T1
Valid prediction for GeneMark_model.42665_t
Valid prediction for snap_scaffold_10-snap.743-T1
Valid prediction for GeneMark_model.42633_t
Couldn't classify 35284, 35540
Couldn't classify 35747, 35861
Sorry, prediction pasa_asmbl_3131.p2 fails validation.
(AGG)	 AG	35284-35540	GT	AGG
(GGA)	 AG	35747-35861	CC	AGC
-recovered pasa_asmbl_3131.p2, internal, 35284, 35540
Valid prediction for GlimmerHMM_glimmerT_24952-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 21695, rend_intergenic: 12210  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23647, rend_intergenic: 22011  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38573, rend_intergenic: 29221  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40948, rend_intergenic: 39888  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45406, rend_intergenic: 42767  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81819, rend_intergenic: 65283  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84302, rend_intergenic: 83073  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97732, rend_intergenic: 84319  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105949, rend_intergenic: 103287  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111892, rend_intergenic: 109385  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129255, rend_intergenic: 114099  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141289, rend_intergenic: 129766  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151850, rend_intergenic: 141748  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 160008
-exon list size: 624


building trellis

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74.0    
74.1    
74.3    
74.4    
74.6    
74.8    
74.9    
75.1    
75.2    
75.4    
75.6    
75.7    
75.9    
76.0    
76.2    
76.4    
76.5    
76.7    
76.8    
77.0    
77.2    
77.3    
77.5    
77.6    
77.8    
78.0    
78.1    
78.3    
78.4    
78.6    
78.8    
78.9    
79.1    
79.2    
79.4    
79.6    
79.7    
79.9    
80.0    
80.2    
80.4    
80.5    
80.7    
80.8    
81.0    
81.2    
81.3    
81.5    
81.6    
81.8    
81.9    
82.1    
82.3    
82.4    
82.6    
82.7    
82.9    
83.1    
83.2    
83.4    
83.5    
83.7    
83.9    
84.0    
84.2    
84.3    
84.5    
84.7    
84.8    
85.0    
85.1    
85.3    
85.5    
85.6    
85.8    
85.9    
86.1    
86.3    
86.4    
86.6    
86.7    
86.9    
87.1    
87.2    
87.4    
87.5    
87.7    
87.9    
88.0    
88.2    
88.3    
88.5    
88.7    
88.8    
89.0    
89.1    
89.3    
89.5    
89.6    
89.8    
89.9    
90.1    
90.3    
90.4    
90.6    
90.7    
90.9    
91.1    
91.2    
91.4    
91.5    
91.7    
91.9    
92.0    
92.2    
92.3    
92.5    
92.7    
92.8    
93.0    
93.1    
93.3    
93.5    
93.6    
93.8    
93.9    
94.1    
94.2    
94.4    
94.6    
94.7    
94.9    
95.0    
95.2    
95.4    
95.5    
95.7    
95.8    
96.0    
96.2    
96.3    
96.5    
96.6    
96.8    
97.0    
97.1    
97.3    
97.4    
97.6    
97.8    
97.9    
98.1    
98.2    
98.4    
98.6    
98.7    
98.9    
99.0    
99.2    
99.4    
99.5    
99.7    
99.8    
-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 21695, rend_intergenic: 12210  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23647, rend_intergenic: 22011  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38573, rend_intergenic: 29221  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40948, rend_intergenic: 39888  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45406, rend_intergenic: 42767  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81819, rend_intergenic: 65283  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84302, rend_intergenic: 83073  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97732, rend_intergenic: 84319  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105949, rend_intergenic: 103287  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111892, rend_intergenic: 109385  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129255, rend_intergenic: 114099  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141289, rend_intergenic: 129766  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151850, rend_intergenic: 141748  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support