-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_3/scaffold_3_3837122-3932443

-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_3-snap.838-T1
Valid prediction for GeneMark_model.10611_t
Valid prediction for GlimmerHMM_glimmerT_6472-T1
Valid prediction for snap_scaffold_3-snap.839-T1
Valid prediction for GeneMark_model.10603_t
Valid prediction for GeneMark_model.10609_t
Valid prediction for Augustus_model.g4230.t1
Valid prediction for snap_scaffold_3-snap.829-T1
Valid prediction for snap_scaffold_3-snap.841-T1
Valid prediction for Augustus_model.g4229.t1
Valid prediction for GeneMark_model.10599_t
Valid prediction for CodingQuarry_transcript_46010-T1
Valid prediction for GeneMark_model.10607_t
Valid prediction for snap_scaffold_3-snap.825-T1
Valid prediction for GlimmerHMM_glimmerT_6463-T1
Valid prediction for GeneMark_model.10597_t
Valid prediction for GeneMark_model.10619_t
Valid prediction for snap_scaffold_3-snap.821-T1
Couldn't classify 47132, 47178
Couldn't classify 52308, 52423
Sorry, prediction pasa_asmbl_39938.p1 fails validation.
(ATC)	 TC	47132-47178	GT	AGG
(CAA)	 AG	47441-47513	GT	ACG
(TCT)	 AG	49846-49979	GT	GGG
(AGG)	 AG	50821-50861	GT	TGG
(GTT)	 AG	50976-51191	GT	TGG
(GCA)	 AG	51580-51704	GT	AGG
(GTC)	 AG	52009-52156	GT	AGG
(CGA)	 AG	52308-52423	CC	CCC
-recovered pasa_asmbl_39938.p1, internal, 47441, 47513
-recovered pasa_asmbl_39938.p1, internal, 49846, 49979
-recovered pasa_asmbl_39938.p1, internal, 50821, 50861
-recovered pasa_asmbl_39938.p1, internal, 50976, 51191
-recovered pasa_asmbl_39938.p1, internal, 51580, 51704
-recovered pasa_asmbl_39938.p1, internal, 52009, 52156
Valid prediction for GlimmerHMM_glimmerT_6471-T1
Valid prediction for GeneMark_model.10617_t
Valid prediction for snap_scaffold_3-snap.823-T1
Valid prediction for GeneMark_model.10604_t
Valid prediction for snap_scaffold_3-snap.835-T1
Valid prediction for snap_scaffold_3-snap.833-T1
Valid prediction for Augustus_model.g4226.t1
Valid prediction for GeneMark_model.10620_t
Valid prediction for snap_scaffold_3-snap.836-T1
Valid prediction for GeneMark_model.10601_t
Couldn't classify 52741, 52835
Sorry, prediction pasa_asmbl_39939.p1 fails validation.
(GAC)	 CA	52741-52835	GT	AGG
(GAA)	 AG	52954-53003	GT	AGG
(ACT)	 AG	53090-53224	GT	AGG
(AGT)	 AG	53320-53750	AC	GAA
-recovered pasa_asmbl_39939.p1, terminal, 53320, 53750
-recovered pasa_asmbl_39939.p1, internal, 52954, 53003
-recovered pasa_asmbl_39939.p1, internal, 53090, 53224
Valid prediction for GlimmerHMM_glimmerT_6468-T1
Valid prediction for GlimmerHMM_glimmerT_6470-T1
Valid prediction for GeneMark_model.10615_t
Couldn't classify 83909, 84033
Sorry, prediction pasa_asmbl_40779.p1 fails validation.
(ACA)	 AG	83909-84033	GT	AGG
(ACT)	 AG	85556-88379	AA	AAA
-recovered pasa_asmbl_40779.p1, terminal, 85556, 88379
-recovered pasa_asmbl_40779.p1, internal, 83909, 84033
Valid prediction for snap_scaffold_3-snap.819-T1
Valid prediction for snap_scaffold_3-snap.830-T1
Valid prediction for GlimmerHMM_glimmerT_6467-T1
Valid prediction for GeneMark_model.10613_t
Valid prediction for GlimmerHMM_glimmerT_6465-T1
Valid prediction for GeneMark_model.10596_t
Valid prediction for Augustus_model.g4231.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.10602_t
Valid prediction for GeneMark_model.10600_t
Valid prediction for GeneMark_model.10594_t
Valid prediction for GeneMark_model.10598_t
Valid prediction for GeneMark_model.10612_t
Valid prediction for GeneMark_model.10618_t
Valid prediction for GeneMark_model.10622_t
Valid prediction for snap_scaffold_3-snap.837-T1
Valid prediction for GlimmerHMM_glimmerT_6462-T1
Valid prediction for GeneMark_model.10608_t
Valid prediction for snap_scaffold_3-snap.827-T1
Valid prediction for GeneMark_model.10605_t
Valid prediction for snap_scaffold_3-snap.826-T1
Couldn't classify 31138, 31320
Sorry, prediction pasa_asmbl_39706.p1 fails validation.
(TTA)	 TT	31138-31320	GT	AGG
(AAA)	 AG	31397-31468	GT	GGG
(AAG)	 AG	31598-31733	GT	GGG
(ATT)	 AG	31990-32049	GT	GAG
(TTT)	 AG	32183-32285	GT	AAG
(GCA)	 AG	32400-32460	GT	AGG
(GTG)	 AG	33409-33496	GT	AGG
(AGG)	 AG	33715-33803	GT	AGG
(ATC)	 AG	33917-34000	CG	AAC
add_exon() Sorry, pasa_asmbl_39706.p1 32183-32285-terminal-3 is invalid.
-recovered pasa_asmbl_39706.p1, terminal, 32183, 32285
-recovered pasa_asmbl_39706.p1, terminal, 33917, 34000
-recovered pasa_asmbl_39706.p1, internal, 31397, 31468
-recovered pasa_asmbl_39706.p1, internal, 31598, 31733
-recovered pasa_asmbl_39706.p1, internal, 31990, 32049
-recovered pasa_asmbl_39706.p1, internal, 32183, 32285
-recovered pasa_asmbl_39706.p1, internal, 32400, 32460
-recovered pasa_asmbl_39706.p1, internal, 33409, 33496
-recovered pasa_asmbl_39706.p1, internal, 33715, 33803
Valid prediction for Augustus_model.g4224.t1
Valid prediction for GlimmerHMM_glimmerT_6469-T1
Valid prediction for GeneMark_model.10595_t
Valid prediction for snap_scaffold_3-snap.820-T1
Valid prediction for snap_scaffold_3-snap.840-T1
Valid prediction for snap_scaffold_3-snap.834-T1
Valid prediction for snap_scaffold_3-snap.824-T1
Valid prediction for snap_scaffold_3-snap.828-T1
Valid prediction for Augustus_model.g4227.t1
Couldn't classify 35624, 35770
Couldn't classify 37692, 37730
Sorry, prediction pasa_asmbl_39755.p1 fails validation.
(TCA)	 AC	35624-35770	GT	AGG
(CTG)	 AG	36647-36763	GT	AGG
(GGT)	 AG	37313-37420	GT	AGG
(GAC)	 AG	37692-37730	AA	AGA
-recovered pasa_asmbl_39755.p1, internal, 36647, 36763
-recovered pasa_asmbl_39755.p1, internal, 37313, 37420
Couldn't classify 38190, 38226
Sorry, prediction pasa_asmbl_38744.p2 fails validation.
(CAG)	 CG	38190-38226	GT	AGG
(GGA)	 AG	38407-38619	GT	CAG
(ACT)	 AG	38969-39156	AG	GAA
-recovered pasa_asmbl_38744.p2, terminal, 38969, 39156
-recovered pasa_asmbl_38744.p2, internal, 38407, 38619
Valid prediction for Augustus_model.g4225.t1
Valid prediction for GlimmerHMM_glimmerT_6464-T1
Valid prediction for CodingQuarry_transcript_46011-T1
Valid prediction for GeneMark_model.10614_t
Valid prediction for GeneMark_model.10616_t
Valid prediction for Augustus_model.g4228.t1
Valid prediction for snap_scaffold_3-snap.822-T1
Valid prediction for snap_scaffold_3-snap.831-T1
Valid prediction for snap_scaffold_3-snap.832-T1
Valid prediction for GlimmerHMM_glimmerT_6466-T1
Valid prediction for GeneMark_model.10610_t
Valid prediction for GeneMark_model.10606_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 5855, rend_intergenic: 3319  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 12468, rend_intergenic: 8127  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24288, rend_intergenic: 12919  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26580, rend_intergenic: 24723  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35925, rend_intergenic: 28191  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53750, rend_intergenic: 36920  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61120, rend_intergenic: 56645  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64749, rend_intergenic: 61126  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66526, rend_intergenic: 65250  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70180, rend_intergenic: 66583  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73120, rend_intergenic: 71995  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75759, rend_intergenic: 75043  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85820, rend_intergenic: 76316  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 95322
-exon list size: 474


building trellis

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1.1    
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18.9    
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20.8    
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24.8    
25.0    
25.2    
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25.8    
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27.7    
27.9    
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28.6    
28.8    
29.0    
29.2    
29.4    
29.6    
29.8    
30.0    
30.3    
30.5    
30.7    
30.9    
31.1    
31.3    
31.5    
31.7    
31.9    
32.1    
32.4    
32.6    
32.8    
33.0    
33.2    
33.4    
33.6    
33.8    
34.0    
34.2    
34.5    
34.7    
34.9    
35.1    
35.3    
35.5    
35.7    
35.9    
36.1    
36.3    
36.6    
36.8    
37.0    
37.2    
37.4    
37.6    
37.8    
38.0    
38.2    
38.4    
38.7    
38.9    
39.1    
39.3    
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39.7    
39.9    
40.1    
40.3    
40.5    
40.8    
41.0    
41.2    
41.4    
41.6    
41.8    
42.0    
42.2    
42.4    
42.6    
42.9    
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43.5    
43.7    
43.9    
44.1    
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44.7    
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45.4    
45.6    
45.8    
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46.6    
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48.1    
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48.5    
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49.6    
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50.4    
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52.7    
52.9    
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54.6    
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55.9    
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61.6    
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65.3    
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78.4    
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79.2    
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79.6    
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80.3    
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80.7    
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81.1    
81.3    
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82.1    
82.4    
82.6    
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83.0    
83.2    
83.4    
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83.8    
84.0    
84.2    
84.5    
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85.3    
85.5    
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86.1    
86.3    
86.6    
86.8    
87.0    
87.2    
87.4    
87.6    
87.8    
88.0    
88.2    
88.4    
88.7    
88.9    
89.1    
89.3    
89.5    
89.7    
89.9    
90.1    
90.3    
90.5    
90.8    
91.0    
91.2    
91.4    
91.6    
91.8    
92.0    
92.2    
92.4    
92.6    
92.9    
93.1    
93.3    
93.5    
93.7    
93.9    
94.1    
94.3    
94.5    
94.7    
95.0    
95.2    
95.4    
95.6    
95.8    
96.0    
96.2    
96.4    
96.6    
96.8    
97.1    
97.3    
97.5    
97.7    
97.9    
98.1    
98.3    
98.5    
98.7    
98.9    
99.2    
99.4    
99.6    
99.8    
-found 21 predictions from path traversal
Error with prediction: snap lend_intergenic: 5855, rend_intergenic: 3319  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 12468, rend_intergenic: 8127  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24288, rend_intergenic: 12919  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26580, rend_intergenic: 24723  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35925, rend_intergenic: 28191  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53750, rend_intergenic: 36920  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61120, rend_intergenic: 56645  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64749, rend_intergenic: 61126  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66526, rend_intergenic: 65250  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70180, rend_intergenic: 66583  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73120, rend_intergenic: 71995  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75759, rend_intergenic: 75043  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85820, rend_intergenic: 76316  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 14 predictions persist after filtering for low support