-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_16/scaffold_16_2253965-2442977

-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 GeneMark_model.66252_t
Valid prediction for GlimmerHMM_glimmerT_38774-T1
Valid prediction for snap_scaffold_16-snap.414-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_38759-T1
Valid prediction for GeneMark_model.66273_t
Valid prediction for GeneMark_model.66267_t
Valid prediction for GeneMark_model.66284_t
Valid prediction for GeneMark_model.66275_t
Valid prediction for Augustus_model.g26002.t1
Valid prediction for snap_scaffold_16-snap.404-T1
Valid prediction for GeneMark_model.66255_t
Valid prediction for GeneMark_model.66290_t
Valid prediction for snap_scaffold_16-snap.400-T1
Valid prediction for GeneMark_model.66292_t
Valid prediction for snap_scaffold_16-snap.402-T1
Valid prediction for GeneMark_model.66286_t
Valid prediction for GlimmerHMM_glimmerT_38752-T1
Valid prediction for GeneMark_model.66258_t
Valid prediction for snap_scaffold_16-snap.384-T1
Valid prediction for GlimmerHMM_glimmerT_38767-T1
Valid prediction for GlimmerHMM_glimmerT_38758-T1
Valid prediction for GeneMark_model.66271_t
Valid prediction for Augustus_model.g26007.t1
Valid prediction for GlimmerHMM_glimmerT_38764-T1
Valid prediction for snap_scaffold_16-snap.391-T1
Valid prediction for snap_scaffold_16-snap.403-T1
Valid prediction for snap_scaffold_16-snap.381-T1
Valid prediction for snap_scaffold_16-snap.405-T1
Valid prediction for GeneMark_model.66288_t
Valid prediction for snap_scaffold_16-snap.416-T1
Valid prediction for Augustus_model.g26010.t1
Valid prediction for snap_scaffold_16-snap.385-T1
Valid prediction for GeneMark_model.66263_t
Valid prediction for snap_scaffold_16-snap.389-T1
Valid prediction for snap_scaffold_16-snap.396-T1
Valid prediction for GlimmerHMM_glimmerT_38762-T1
Valid prediction for GeneMark_model.66269_t
Valid prediction for GlimmerHMM_glimmerT_38772-T1
Valid prediction for GeneMark_model.66293_t
Valid prediction for GlimmerHMM_glimmerT_38765-T1
Valid prediction for GlimmerHMM_glimmerT_38748-T1
Valid prediction for GeneMark_model.66259_t
Valid prediction for GlimmerHMM_glimmerT_38775-T1
Valid prediction for GeneMark_model.66281_t
Valid prediction for Augustus_model.g26005.t1
Valid prediction for Augustus_model.g26013.t1
Valid prediction for CodingQuarry_transcript_19872-T1
Valid prediction for GeneMark_model.66279_t
Valid prediction for snap_scaffold_16-snap.378-T1
Valid prediction for GlimmerHMM_glimmerT_38755-T1
Valid prediction for Augustus_model.g26018.t1
Valid prediction for Augustus_model.g26015.t1
Couldn't classify 185728, 185880
Sorry, prediction pasa_asmbl_16917.p1 fails validation.
(ATG)	 AA	181844-182161	GT	AGG
(AAG)	 AG	182345-182515	GT	TGG
(ATC)	 AG	183273-183534	GT	ACG
(CCA)	 AG	184889-184995	GT	AGG
(ATG)	 AG	185728-185880	GT	TAG
-recovered pasa_asmbl_16917.p1, initial, 181844, 182161
-recovered pasa_asmbl_16917.p1, initial, 185728, 185880
-recovered pasa_asmbl_16917.p1, internal, 182345, 182515
-recovered pasa_asmbl_16917.p1, internal, 183273, 183534
-recovered pasa_asmbl_16917.p1, internal, 184889, 184995
-recovered pasa_asmbl_16917.p1, internal, 185728, 185880
Valid prediction for GlimmerHMM_glimmerT_38763-T1
Valid prediction for snap_scaffold_16-snap.383-T1
Valid prediction for GlimmerHMM_glimmerT_38754-T1
Valid prediction for snap_scaffold_16-snap.397-T1
Valid prediction for GeneMark_model.66278_t
Valid prediction for snap_scaffold_16-snap.392-T1
Valid prediction for Augustus_model.g26004.t1
Valid prediction for snap_scaffold_16-snap.399-T1
Valid prediction for pasa_asmbl_16915.p1
Valid prediction for snap_scaffold_16-snap.408-T1
Valid prediction for GlimmerHMM_glimmerT_38768-T1
Valid prediction for GlimmerHMM_glimmerT_38766-T1
Valid prediction for snap_scaffold_16-snap.415-T1
Valid prediction for GlimmerHMM_glimmerT_38773-T1
Valid prediction for GeneMark_model.66265_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 Augustus_model.g26003.t1
Valid prediction for snap_scaffold_16-snap.409-T1
Valid prediction for GeneMark_model.66272_t
Valid prediction for GeneMark_model.66257_t
Valid prediction for Augustus_model.g26012.t1
Valid prediction for GeneMark_model.66270_t
Couldn't classify 54664, 55830
Sorry, prediction pasa_asmbl_16138.p1 fails validation.
(AAA)	 CC	54664-55830	AA	AGA
Valid prediction for snap_scaffold_16-snap.387-T1
Valid prediction for snap_scaffold_16-snap.395-T1
Valid prediction for GeneMark_model.66289_t
Valid prediction for Augustus_model.g26016.t1
Valid prediction for GeneMark_model.66262_t
Valid prediction for GlimmerHMM_glimmerT_38776-T1
Couldn't classify 163434, 163478
Couldn't classify 170926, 171065
Sorry, prediction pasa_asmbl_16132.p1 fails validation.
(GTC)	 AC	163434-163478	GT	TGG
(CAC)	 AG	164818-164918	GT	AGG
(GTC)	 AG	165285-165413	GT	AGG
(GGA)	 AG	165761-165862	GT	GCG
(GAT)	 AG	166140-166260	GT	AGG
(GGG)	 AG	167915-167996	GT	AGG
(GCT)	 AG	168372-168492	GT	AGG
(TTT)	 AG	170331-170506	GT	AGG
(ACC)	 AG	170926-171065	GC	AGG
-recovered pasa_asmbl_16132.p1, terminal, 167915, 167996
-recovered pasa_asmbl_16132.p1, internal, 164818, 164918
-recovered pasa_asmbl_16132.p1, internal, 165285, 165413
-recovered pasa_asmbl_16132.p1, internal, 165761, 165862
-recovered pasa_asmbl_16132.p1, internal, 166140, 166260
-recovered pasa_asmbl_16132.p1, internal, 167915, 167996
-recovered pasa_asmbl_16132.p1, internal, 168372, 168492
-recovered pasa_asmbl_16132.p1, internal, 170331, 170506
-recovered pasa_asmbl_16132.p1, internal, 170926, 171065
Valid prediction for snap_scaffold_16-snap.377-T1
Valid prediction for GlimmerHMM_glimmerT_38756-T1
Valid prediction for snap_scaffold_16-snap.380-T1
Valid prediction for GeneMark_model.66282_t
Valid prediction for GlimmerHMM_glimmerT_38770-T1
Valid prediction for snap_scaffold_16-snap.382-T1
Valid prediction for GeneMark_model.66291_t
Valid prediction for pasa_asmbl_16133.p1
Valid prediction for snap_scaffold_16-snap.390-T1
Valid prediction for GlimmerHMM_glimmerT_38753-T1
Valid prediction for Augustus_model.g26011.t1
Valid prediction for GlimmerHMM_glimmerT_38751-T1
Valid prediction for snap_scaffold_16-snap.398-T1
Couldn't classify 8186, 8357
Couldn't classify 9633, 9680
Sorry, prediction pasa_asmbl_16140.p1 fails validation.
(AAC)	 CC	8186-8357	GT	TGG
(AAC)	 AG	8652-8818	GT	ATG
(GGT)	 AG	8977-9210	GT	GCG
(ATA)	 AG	9633-9680	GA	AGG
-recovered pasa_asmbl_16140.p1, internal, 8652, 8818
-recovered pasa_asmbl_16140.p1, internal, 8977, 9210
Valid prediction for snap_scaffold_16-snap.406-T1
Valid prediction for GeneMark_model.66274_t
Valid prediction for GlimmerHMM_glimmerT_38749-T1
Valid prediction for snap_scaffold_16-snap.411-T1
Valid prediction for GeneMark_model.66280_t
Valid prediction for GeneMark_model.66268_t
Valid prediction for snap_scaffold_16-snap.379-T1
Valid prediction for GeneMark_model.66254_t
Valid prediction for GeneMark_model.66276_t
Couldn't classify 13316, 13412
Sorry, prediction pasa_asmbl_16139.p1 fails validation.
(GTC)	 GG	13316-13412	GT	AGG
(GCC)	 AG	14596-14688	GT	AGG
(CGA)	 AG	14832-14905	GT	AGG
(GGT)	 AG	16164-16508	GA	AGG
-recovered pasa_asmbl_16139.p1, terminal, 14596, 14688
-recovered pasa_asmbl_16139.p1, terminal, 16164, 16508
-recovered pasa_asmbl_16139.p1, internal, 14596, 14688
-recovered pasa_asmbl_16139.p1, internal, 14832, 14905
Valid prediction for CodingQuarry_transcript_19870-T1
Valid prediction for snap_scaffold_16-snap.388-T1
Valid prediction for GeneMark_model.66264_t
Couldn't classify 157814, 157911
Sorry, prediction pasa_asmbl_16741.p1 fails validation.
(AAA)	 TG	157814-157911	GT	AGG
(GCG)	 AG	158689-158871	GT	AGG
(GAT)	 AG	159685-159750	GT	AGG
(CAC)	 AG	162631-162667	AC	GAA
-recovered pasa_asmbl_16741.p1, terminal, 162631, 162667
-recovered pasa_asmbl_16741.p1, internal, 158689, 158871
-recovered pasa_asmbl_16741.p1, internal, 159685, 159750
Valid prediction for GlimmerHMM_glimmerT_38769-T1
Valid prediction for GeneMark_model.66266_t
Valid prediction for GlimmerHMM_glimmerT_38771-T1
Valid prediction for Augustus_model.g26014.t1
Valid prediction for GeneMark_model.66256_t
Valid prediction for snap_scaffold_16-snap.393-T1
Valid prediction for GeneMark_model.66285_t
Valid prediction for GeneMark_model.66287_t
Valid prediction for GeneMark_model.66260_t
Valid prediction for snap_scaffold_16-snap.376-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for Augustus_model.g26006.t1
Valid prediction for snap_scaffold_16-snap.412-T1
Valid prediction for GlimmerHMM_glimmerT_38757-T1
Valid prediction for snap_scaffold_16-snap.386-T1
Valid prediction for snap_scaffold_16-snap.394-T1
Couldn't classify 56083, 56595
Sorry, prediction pasa_asmbl_16136.p1 fails validation.
(GGG)	 AA	56083-56595	GT	AGG
(GTA)	 AG	56674-57049	GT	AGG
(ACT)	 AG	57173-57207	CC	AGC
-recovered pasa_asmbl_16136.p1, terminal, 57173, 57207
-recovered pasa_asmbl_16136.p1, internal, 56674, 57049
Valid prediction for GlimmerHMM_glimmerT_38761-T1
Valid prediction for GeneMark_model.66261_t
Valid prediction for GeneMark_model.66251_t
Valid prediction for CodingQuarry_transcript_19871-T1
Valid prediction for Augustus_model.g26017.t1
Valid prediction for GeneMark_model.66253_t
Valid prediction for GlimmerHMM_glimmerT_38760-T1
Valid prediction for HiQ_model.g26009.t1
Valid prediction for snap_scaffold_16-snap.410-T1
Valid prediction for GlimmerHMM_glimmerT_38750-T1
Valid prediction for snap_scaffold_16-snap.401-T1
Valid prediction for snap_scaffold_16-snap.407-T1
Valid prediction for snap_scaffold_16-snap.413-T1
Sorry, intron length (7) is less than minimum required (10)
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for Augustus_model.g26008.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 26374, rend_intergenic: 17823  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38308, rend_intergenic: 27276  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41421, rend_intergenic: 38333  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54124, rend_intergenic: 52152  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57141, rend_intergenic: 54791  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60392, rend_intergenic: 57676  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64426, rend_intergenic: 61920  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70208, rend_intergenic: 67907  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77486, rend_intergenic: 75614  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89215, rend_intergenic: 83576  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123172, rend_intergenic: 100527  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180103, rend_intergenic: 155141  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 189013
-exon list size: 718


building trellis

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80.0    
80.1    
80.3    
80.4    
80.6    
80.7    
80.8    
81.0    
81.1    
81.2    
81.4    
81.5    
81.7    
81.8    
81.9    
82.1    
82.2    
82.4    
82.5    
82.6    
82.8    
82.9    
83.1    
83.2    
83.3    
83.5    
83.6    
83.8    
83.9    
84.0    
84.2    
84.3    
84.4    
84.6    
84.7    
84.9    
85.0    
85.1    
85.3    
85.4    
85.6    
85.7    
85.8    
86.0    
86.1    
86.2    
86.4    
86.5    
86.7    
86.8    
86.9    
87.1    
87.2    
87.4    
87.5    
87.6    
87.8    
87.9    
88.1    
88.2    
88.3    
88.5    
88.6    
88.8    
88.9    
89.0    
89.2    
89.3    
89.4    
89.6    
89.7    
89.9    
90.0    
90.1    
90.3    
90.4    
90.6    
90.7    
90.8    
91.0    
91.1    
91.2    
91.4    
91.5    
91.7    
91.8    
91.9    
92.1    
92.2    
92.4    
92.5    
92.6    
92.8    
92.9    
93.1    
93.2    
93.3    
93.5    
93.6    
93.8    
93.9    
94.0    
94.2    
94.3    
94.4    
94.6    
94.7    
94.9    
95.0    
95.1    
95.3    
95.4    
95.6    
95.7    
95.8    
96.0    
96.1    
96.2    
96.4    
96.5    
96.7    
96.8    
96.9    
97.1    
97.2    
97.4    
97.5    
97.6    
97.8    
97.9    
98.1    
98.2    
98.3    
98.5    
98.6    
98.8    
98.9    
99.0    
99.2    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 26374, rend_intergenic: 17823  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38308, rend_intergenic: 27276  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41421, rend_intergenic: 38333  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54124, rend_intergenic: 52152  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57141, rend_intergenic: 54791  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60392, rend_intergenic: 57676  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64426, rend_intergenic: 61920  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70208, rend_intergenic: 67907  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77486, rend_intergenic: 75614  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89215, rend_intergenic: 83576  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123172, rend_intergenic: 100527  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180103, rend_intergenic: 155141  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