-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_17/scaffold_17_11905013-12085858

-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 GlimmerHMM_glimmerT_42101-T1
Valid prediction for GeneMark_model.72665_t
Valid prediction for GlimmerHMM_glimmerT_42108-T1
Valid prediction for snap_scaffold_17-snap.2447-T1
Valid prediction for snap_scaffold_17-snap.2425-T1
Valid prediction for GeneMark_model.72649_t
Couldn't classify 101334, 101378
Couldn't classify 104712, 104720
Sorry, prediction pasa_asmbl_18374.p1 fails validation.
(CCT)	 AG	101334-101378	GT	AGG
(GTA)	 AG	101978-102037	GT	GGG
(GAG)	 AG	102871-103014	GT	AGG
(CTG)	 AG	103714-103869	GT	AGG
(CTT)	 AG	104186-104383	GT	TGG
(CTT)	 AG	104712-104720	AG	GGA
-recovered pasa_asmbl_18374.p1, internal, 101334, 101378
-recovered pasa_asmbl_18374.p1, internal, 101978, 102037
-recovered pasa_asmbl_18374.p1, internal, 102871, 103014
-recovered pasa_asmbl_18374.p1, internal, 103714, 103869
-recovered pasa_asmbl_18374.p1, internal, 104186, 104383
Valid prediction for GeneMark_model.72642_t
Valid prediction for GeneMark_model.72675_t
Valid prediction for GeneMark_model.72670_t
Valid prediction for GlimmerHMM_glimmerT_42103-T1
Valid prediction for snap_scaffold_17-snap.2429-T1
Valid prediction for GeneMark_model.72683_t
Valid prediction for GeneMark_model.72658_t
Valid prediction for snap_scaffold_17-snap.2433-T1
Valid prediction for Augustus_model.g28216.t1
Couldn't classify 139936, 139992
Sorry, prediction pasa_asmbl_18634.p1 fails validation.
(TTT)	 GC	139936-139992	GT	AGG
(GCA)	 AG	140161-140871	GT	AGG
(GCT)	 AG	141333-141393	GT	CGG
(ACA)	 AG	141766-141887	GT	AGG
(TCT)	 AG	142148-142333	GT	AGG
(ACT)	 AG	142593-142760	GT	AGG
(GAC)	 AG	142981-143137	GT	AGG
(GTG)	 AG	143301-143487	GT	AGG
(GGC)	 AG	143844-143994	GT	AGG
(GAC)	 AG	144110-144427	GT	AGG
(GTG)	 AG	144645-144941	GT	GTG
(CAG)	 AG	145333-145565	GT	AGG
(GGT)	 AG	145655-145760	GT	AGG
(GGC)	 AG	145887-146063	GT	GCG
(TCC)	 AG	146427-146630	GT	AGG
(AGA)	 AG	146898-147124	GT	AGG
(GAT)	 AG	147334-147422	GT	AGG
(GGA)	 AG	147694-147826	GT	AGG
(GTT)	 AG	147973-148103	GT	AGG
(GAT)	 AG	148541-148584	AA	AGA
-recovered pasa_asmbl_18634.p1, terminal, 148541, 148584
-recovered pasa_asmbl_18634.p1, internal, 140161, 140871
-recovered pasa_asmbl_18634.p1, internal, 141333, 141393
-recovered pasa_asmbl_18634.p1, internal, 141766, 141887
-recovered pasa_asmbl_18634.p1, internal, 142148, 142333
-recovered pasa_asmbl_18634.p1, internal, 142593, 142760
-recovered pasa_asmbl_18634.p1, internal, 142981, 143137
-recovered pasa_asmbl_18634.p1, internal, 143301, 143487
-recovered pasa_asmbl_18634.p1, internal, 143844, 143994
-recovered pasa_asmbl_18634.p1, internal, 144110, 144427
-recovered pasa_asmbl_18634.p1, internal, 144645, 144941
-recovered pasa_asmbl_18634.p1, internal, 145333, 145565
-recovered pasa_asmbl_18634.p1, internal, 145655, 145760
-recovered pasa_asmbl_18634.p1, internal, 145887, 146063
-recovered pasa_asmbl_18634.p1, internal, 146427, 146630
-recovered pasa_asmbl_18634.p1, internal, 146898, 147124
-recovered pasa_asmbl_18634.p1, internal, 147334, 147422
-recovered pasa_asmbl_18634.p1, internal, 147694, 147826
-recovered pasa_asmbl_18634.p1, internal, 147973, 148103
Valid prediction for GeneMark_model.72659_t
Valid prediction for snap_scaffold_17-snap.2448-T1
Valid prediction for GlimmerHMM_glimmerT_42105-T1
Valid prediction for Augustus_model.g28218.t1
Valid prediction for GlimmerHMM_glimmerT_42117-T1
Valid prediction for GeneMark_model.72677_t
Valid prediction for snap_scaffold_17-snap.2445-T1
Valid prediction for GlimmerHMM_glimmerT_42109-T1
Valid prediction for snap_scaffold_17-snap.2430-T1
Valid prediction for GeneMark_model.72655_t
Valid prediction for snap_scaffold_17-snap.2441-T1
Valid prediction for Augustus_model.g28214.t1
Valid prediction for GeneMark_model.72646_t
Valid prediction for GlimmerHMM_glimmerT_42111-T1
Valid prediction for snap_scaffold_17-snap.2450-T1
Valid prediction for snap_scaffold_17-snap.2454-T1
Valid prediction for GeneMark_model.72651_t
Valid prediction for GlimmerHMM_glimmerT_42112-T1
Valid prediction for GeneMark_model.72673_t
Valid prediction for snap_scaffold_17-snap.2443-T1
Couldn't classify 106812, 107912
Couldn't classify 109669, 109749
Sorry, prediction pasa_asmbl_18378.p1 fails validation.
(GAA)	 AC	106812-107912	GT	AGG
(GAG)	 AG	109669-109749	CA	AGC
Valid prediction for GeneMark_model.72662_t
Valid prediction for GeneMark_model.72657_t
Valid prediction for snap_scaffold_17-snap.2453-T1
Valid prediction for snap_scaffold_17-snap.2456-T1
Valid prediction for GeneMark_model.72661_t
Valid prediction for GeneMark_model.72667_t
Couldn't classify 105930, 106667
Sorry, prediction pasa_asmbl_18377.p2 fails validation.
(GAG)	 CC	105930-106667	GA	AGG
Valid prediction for snap_scaffold_17-snap.2431-T1
Valid prediction for snap_scaffold_17-snap.2427-T1
Valid prediction for snap_scaffold_17-snap.2436-T1
Valid prediction for pasa_asmbl_18373.p1
Valid prediction for snap_scaffold_17-snap.2463-T1
Valid prediction for snap_scaffold_17-snap.2426-T1
Valid prediction for GeneMark_model.72664_t
Valid prediction for Augustus_model.g28217.t1
Valid prediction for GeneMark_model.72678_t
Couldn't classify 115185, 115520
Couldn't classify 120534, 120733
Sorry, prediction pasa_asmbl_18379.p1 fails validation.
(AAG)	 TC	115185-115520	GT	AGG
(GTT)	 AG	116288-116635	GT	AGG
(AAG)	 AG	117446-117567	GT	AGG
(AAA)	 AG	118514-118713	GT	AGG
(ACG)	 AG	120534-120733	AC	CGA
-recovered pasa_asmbl_18379.p1, internal, 116288, 116635
-recovered pasa_asmbl_18379.p1, internal, 117446, 117567
-recovered pasa_asmbl_18379.p1, internal, 118514, 118713
Valid prediction for GeneMark_model.72648_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 snap_scaffold_17-snap.2423-T1
Valid prediction for pasa_asmbl_19355.p1
Valid prediction for snap_scaffold_17-snap.2446-T1
Valid prediction for HiQ_model.g28210.t1
Valid prediction for Augustus_model.g28212.t1
Valid prediction for GeneMark_model.72684_t
Valid prediction for snap_scaffold_17-snap.2457-T1
Valid prediction for GeneMark_model.72666_t
Valid prediction for snap_scaffold_17-snap.2438-T1
Valid prediction for GeneMark_model.72652_t
Valid prediction for snap_scaffold_17-snap.2451-T1
Valid prediction for Augustus_model.g28209.t1
Couldn't classify 21095, 21205
Sorry, prediction pasa_asmbl_19514.p1 fails validation.
(ATG)	 CA	15900-16001	GT	AGG
(ATC)	 AG	16254-16410	GT	AGG
(GGA)	 AG	16496-16588	GT	AGG
(ACA)	 AG	16703-16832	GT	AAG
(ATG)	 AG	16924-17155	GT	GGG
(GTG)	 AG	17625-17740	GT	AAG
(GGA)	 AG	18032-18175	GT	TGG
(GCA)	 AG	18418-18574	GT	GGG
(CAC)	 AG	18887-18994	GT	CTG
(TAT)	 AG	19255-19411	GT	CAG
(ACT)	 AG	19725-19876	GT	AGG
(GTG)	 AG	20344-20510	GT	AAG
(CGA)	 AG	20658-20745	GT	AAG
(AGC)	 AG	21095-21205	GG	AGG
-recovered pasa_asmbl_19514.p1, initial, 15900, 16001
add_exon() Sorry, pasa_asmbl_19514.p1 16924-17155-initial-1 is invalid.
-recovered pasa_asmbl_19514.p1, initial, 16924, 17155
add_exon() Sorry, pasa_asmbl_19514.p1 16254-16410-terminal-3 is invalid.
-recovered pasa_asmbl_19514.p1, terminal, 16254, 16410
-recovered pasa_asmbl_19514.p1, internal, 16254, 16410
-recovered pasa_asmbl_19514.p1, internal, 16496, 16588
-recovered pasa_asmbl_19514.p1, internal, 16703, 16832
-recovered pasa_asmbl_19514.p1, internal, 16924, 17155
-recovered pasa_asmbl_19514.p1, internal, 17625, 17740
-recovered pasa_asmbl_19514.p1, internal, 18032, 18175
-recovered pasa_asmbl_19514.p1, internal, 18418, 18574
-recovered pasa_asmbl_19514.p1, internal, 18887, 18994
-recovered pasa_asmbl_19514.p1, internal, 19255, 19411
-recovered pasa_asmbl_19514.p1, internal, 19725, 19876
-recovered pasa_asmbl_19514.p1, internal, 20344, 20510
-recovered pasa_asmbl_19514.p1, internal, 20658, 20745
Valid prediction for snap_scaffold_17-snap.2440-T1
Valid prediction for GeneMark_model.72672_t
Valid prediction for GeneMark_model.72668_t
Valid prediction for snap_scaffold_17-snap.2459-T1
Valid prediction for snap_scaffold_17-snap.2432-T1
Valid prediction for snap_scaffold_17-snap.2455-T1
Valid prediction for snap_scaffold_17-snap.2464-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for CodingQuarry_transcript_22144-T1
Valid prediction for snap_scaffold_17-snap.2442-T1
Valid prediction for GeneMark_model.72643_t
Valid prediction for snap_scaffold_17-snap.2444-T1
Valid prediction for snap_scaffold_17-snap.2449-T1
Valid prediction for snap_scaffold_17-snap.2460-T1
Valid prediction for Augustus_model.g28211.t1
Valid prediction for GeneMark_model.72674_t
Valid prediction for GeneMark_model.72653_t
Valid prediction for GlimmerHMM_glimmerT_42115-T1
Couldn't classify 94264, 95304
Sorry, prediction pasa_asmbl_19356.p1 fails validation.
(ACC)	 GC	94264-95304	CC	GAC
Valid prediction for GlimmerHMM_glimmerT_42113-T1
Valid prediction for snap_scaffold_17-snap.2439-T1
Valid prediction for GeneMark_model.72671_t
Valid prediction for GlimmerHMM_glimmerT_42110-T1
Valid prediction for GeneMark_model.72656_t
Valid prediction for GlimmerHMM_glimmerT_42118-T1
Valid prediction for snap_scaffold_17-snap.2428-T1
Valid prediction for GeneMark_model.72645_t
Valid prediction for CodingQuarry_transcript_22145-T1
Valid prediction for snap_scaffold_17-snap.2452-T1
Valid prediction for GeneMark_model.72669_t
Valid prediction for CodingQuarry_transcript_22149-T1
Valid prediction for HiQ_model.g28221.t1
Valid prediction for snap_scaffold_17-snap.2422-T1
Valid prediction for snap_scaffold_17-snap.2437-T1
Valid prediction for pasa_asmbl_19351.p1
Valid prediction for HiQ_model.g28220.t1
Valid prediction for GlimmerHMM_glimmerT_42102-T1
Valid prediction for GlimmerHMM_glimmerT_42104-T1
Valid prediction for snap_scaffold_17-snap.2461-T1
Valid prediction for GeneMark_model.72681_t
Valid prediction for Augustus_model.g28222.t1
Valid prediction for GlimmerHMM_glimmerT_42107-T1
Couldn't classify 116062, 116084
Sorry, prediction pasa_asmbl_19354.p1 fails validation.
(ATC)	 CA	116062-116084	GT	AGG
(GTT)	 AG	116194-116336	GT	AGG
(ACG)	 AG	116520-116697	GT	GGG
(GTG)	 AG	116823-116958	GT	AGG
(ATC)	 AG	117132-117206	GT	TGG
(ACT)	 AG	117288-117308	GG	GAG
-recovered pasa_asmbl_19354.p1, terminal, 117288, 117308
-recovered pasa_asmbl_19354.p1, internal, 116194, 116336
-recovered pasa_asmbl_19354.p1, internal, 116520, 116697
-recovered pasa_asmbl_19354.p1, internal, 116823, 116958
-recovered pasa_asmbl_19354.p1, internal, 117132, 117206
Valid prediction for snap_scaffold_17-snap.2458-T1
Valid prediction for snap_scaffold_17-snap.2462-T1
Valid prediction for GlimmerHMM_glimmerT_42106-T1
Valid prediction for GeneMark_model.72644_t
Valid prediction for HiQ_model.g28213.t1
Valid prediction for GeneMark_model.72654_t
Valid prediction for GlimmerHMM_glimmerT_42114-T1
Valid prediction for Augustus_model.g28223.t1
Valid prediction for CodingQuarry_transcript_22146-T1
Valid prediction for snap_scaffold_17-snap.2424-T1
Valid prediction for GeneMark_model.72679_t
Valid prediction for GeneMark_model.72660_t
Valid prediction for GeneMark_model.72647_t
Couldn't classify 25893, 26044
Sorry, prediction pasa_asmbl_19358.p1 fails validation.
(TGC)	 CC	25893-26044	GT	CAG
(AAT)	 AG	26237-26417	AG	GAA
-recovered pasa_asmbl_19358.p1, terminal, 26237, 26417
Valid prediction for Augustus_model.g28215.t1
Valid prediction for snap_scaffold_17-snap.2434-T1
Valid prediction for GeneMark_model.72650_t
Valid prediction for Augustus_model.g28219.t1
Valid prediction for GeneMark_model.72663_t
Valid prediction for GeneMark_model.72676_t
Valid prediction for snap_scaffold_17-snap.2435-T1
Valid prediction for GlimmerHMM_glimmerT_42116-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 19087, rend_intergenic: 13702  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26992, rend_intergenic: 23917  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28482, rend_intergenic: 27473  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34013, rend_intergenic: 32236  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54187, rend_intergenic: 47586  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73554, rend_intergenic: 69837  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110699, rend_intergenic: 102447  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115612, rend_intergenic: 113093  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122670, rend_intergenic: 116380  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127656, rend_intergenic: 124946  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139565, rend_intergenic: 133912  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148584, rend_intergenic: 140167  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 180846
-exon list size: 585


building trellis

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69.5    
69.7    
69.8    
70.0    
70.2    
70.4    
70.5    
70.7    
70.9    
71.0    
71.2    
71.4    
71.6    
71.7    
71.9    
72.1    
72.2    
72.4    
72.6    
72.7    
72.9    
73.1    
73.3    
73.4    
73.6    
73.8    
73.9    
74.1    
74.3    
74.4    
74.6    
74.8    
75.0    
75.1    
75.3    
75.5    
75.6    
75.8    
76.0    
76.1    
76.3    
76.5    
76.7    
76.8    
77.0    
77.2    
77.3    
77.5    
77.7    
77.9    
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    
80.7    
80.9    
81.1    
81.3    
81.4    
81.6    
81.8    
81.9    
82.1    
82.3    
82.5    
82.6    
82.8    
83.0    
83.1    
83.3    
83.5    
83.6    
83.8    
84.0    
84.2    
84.3    
84.5    
84.7    
84.8    
85.0    
85.2    
85.3    
85.5    
85.7    
85.9    
86.0    
86.2    
86.4    
86.5    
86.7    
86.9    
87.1    
87.2    
87.4    
87.6    
87.7    
87.9    
88.1    
88.2    
88.4    
88.6    
88.8    
88.9    
89.1    
89.3    
89.4    
89.6    
89.8    
89.9    
90.1    
90.3    
90.5    
90.6    
90.8    
91.0    
91.1    
91.3    
91.5    
91.7    
91.8    
92.0    
92.2    
92.3    
92.5    
92.7    
92.8    
93.0    
93.2    
93.4    
93.5    
93.7    
93.9    
94.0    
94.2    
94.4    
94.5    
94.7    
94.9    
95.1    
95.2    
95.4    
95.6    
95.7    
95.9    
96.1    
96.3    
96.4    
96.6    
96.8    
96.9    
97.1    
97.3    
97.4    
97.6    
97.8    
98.0    
98.1    
98.3    
98.5    
98.6    
98.8    
99.0    
99.1    
99.3    
99.5    
99.7    
99.8    
-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 19087, rend_intergenic: 13702  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26992, rend_intergenic: 23917  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28482, rend_intergenic: 27473  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34013, rend_intergenic: 32236  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54187, rend_intergenic: 47586  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73554, rend_intergenic: 69837  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110699, rend_intergenic: 102447  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115612, rend_intergenic: 113093  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122670, rend_intergenic: 116380  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127656, rend_intergenic: 124946  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139565, rend_intergenic: 133912  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148584, rend_intergenic: 140167  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support