-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_2/scaffold_2_2855651-3018566

-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.5690_t
Valid prediction for snap_scaffold_2-snap.695-T1
Valid prediction for snap_scaffold_2-snap.684-T1
Valid prediction for snap_scaffold_2-snap.686-T1
Valid prediction for GeneMark_model.5705_t
Couldn't classify 139643, 139797
Couldn't classify 139861, 140014
Sorry, prediction CodingQuarry_transcript_28425-T1 fails validation.
(ATG)	 CG	139643-139797	CT	GCC
(CTC)	 GC	139861-140014	GG	AAG
Valid prediction for GlimmerHMM_glimmerT_3523-T1
Valid prediction for Augustus_model.g2345.t1
Valid prediction for snap_scaffold_2-snap.687-T1
Valid prediction for GlimmerHMM_glimmerT_3527-T1
Valid prediction for GeneMark_model.5703_t
Couldn't classify 133748, 134062
Sorry, prediction pasa_asmbl_24290.p1 fails validation.
(GAG)	 AG	133748-134062	GT	AGG
(GTC)	 AG	134348-134449	GT	AGG
(GCA)	 AG	134605-134799	GC	AGG
(ACC)	 AG	134924-135106	GT	AGG
(ACG)	 AG	135370-135555	GT	AGG
(GGC)	 AG	135916-136047	GT	AGG
(GAG)	 AG	136207-136392	GT	TGG
(GTC)	 AG	136613-136851	GT	CGG
(GTG)	 AG	137313-137433	GT	AGG
(ATA)	 AG	137523-137621	GT	AGG
(CAC)	 AG	138090-138212	TC	GAT
-recovered pasa_asmbl_24290.p1, terminal, 138090, 138212
-recovered pasa_asmbl_24290.p1, internal, 133748, 134062
-recovered pasa_asmbl_24290.p1, internal, 134348, 134449
-recovered pasa_asmbl_24290.p1, internal, 134605, 134799
-recovered pasa_asmbl_24290.p1, internal, 134924, 135106
-recovered pasa_asmbl_24290.p1, internal, 135370, 135555
-recovered pasa_asmbl_24290.p1, internal, 135916, 136047
-recovered pasa_asmbl_24290.p1, internal, 136207, 136392
-recovered pasa_asmbl_24290.p1, internal, 136613, 136851
-recovered pasa_asmbl_24290.p1, internal, 137313, 137433
-recovered pasa_asmbl_24290.p1, internal, 137523, 137621
Valid prediction for GlimmerHMM_glimmerT_3509-T1
Valid prediction for snap_scaffold_2-snap.689-T1
Valid prediction for GeneMark_model.5725_t
Valid prediction for Augustus_model.g2347.t1
Valid prediction for snap_scaffold_2-snap.664-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for snap_scaffold_2-snap.681-T1
Valid prediction for GeneMark_model.5707_t
Valid prediction for GlimmerHMM_glimmerT_3514-T1
Valid prediction for Augustus_model.g2352.t1
Couldn't classify 139643, 139692
Couldn't classify 139714, 139818
Couldn't classify 139840, 140014
Sorry, prediction CodingQuarry_transcript_28427-T1 fails validation.
(ATG)	 CG	139643-139692	CT	GCC
(CTC)	 GC	139714-139818	CT	GCC
(CTC)	 GC	139840-140014	GG	AAG
Valid prediction for GeneMark_model.5698_t
Valid prediction for Augustus_model.g2350.t1
Valid prediction for snap_scaffold_2-snap.665-T1
Valid prediction for snap_scaffold_2-snap.659-T1
Valid prediction for GeneMark_model.5708_t
Valid prediction for GlimmerHMM_glimmerT_3516-T1
Valid prediction for Augustus_model.g2346.t1
Couldn't classify 139643, 139818
Couldn't classify 139861, 140014
Sorry, prediction CodingQuarry_transcript_28426-T1 fails validation.
(ATG)	 CG	139643-139818	CT	GCC
(CTC)	 GC	139861-140014	GG	AAG
Valid prediction for GeneMark_model.5712_t
Valid prediction for snap_scaffold_2-snap.677-T1
Valid prediction for GlimmerHMM_glimmerT_3519-T1
Valid prediction for snap_scaffold_2-snap.675-T1
Valid prediction for GeneMark_model.5721_t
Valid prediction for GeneMark_model.5693_t
Valid prediction for GeneMark_model.5730_t
Valid prediction for GlimmerHMM_glimmerT_3520-T1
Valid prediction for GeneMark_model.5711_t
Valid prediction for GlimmerHMM_glimmerT_3513-T1
Valid prediction for GlimmerHMM_glimmerT_3518-T1
Valid prediction for GeneMark_model.5723_t
Valid prediction for GeneMark_model.5719_t
Valid prediction for GeneMark_model.5727_t
Valid prediction for GeneMark_model.5696_t
Valid prediction for GeneMark_model.5713_t
Valid prediction for GlimmerHMM_glimmerT_3512-T1
Valid prediction for GeneMark_model.5716_t
Valid prediction for GeneMark_model.5732_t
Valid prediction for snap_scaffold_2-snap.658-T1
Valid prediction for snap_scaffold_2-snap.663-T1
Valid prediction for GlimmerHMM_glimmerT_3517-T1
Valid prediction for GlimmerHMM_glimmerT_3524-T1
Valid prediction for HiQ_model.g2351.t1
Valid prediction for snap_scaffold_2-snap.673-T1
Valid prediction for GeneMark_model.5729_t
Valid prediction for GeneMark_model.5700_t
Couldn't classify 109708, 109869
Sorry, prediction pasa_asmbl_24285.p1 fails validation.
(TTT)	 AG	109708-109869	GT	CTG
(GTC)	 AG	110068-110178	GT	AGG
(GCT)	 AG	112335-112379	GT	AGG
(CAC)	 AG	112793-112880	GT	CGG
(GTC)	 AG	115408-115619	GA	AGG
-recovered pasa_asmbl_24285.p1, terminal, 115408, 115619
-recovered pasa_asmbl_24285.p1, internal, 109708, 109869
-recovered pasa_asmbl_24285.p1, internal, 110068, 110178
-recovered pasa_asmbl_24285.p1, internal, 112335, 112379
-recovered pasa_asmbl_24285.p1, internal, 112793, 112880
Valid prediction for snap_scaffold_2-snap.679-T1
Couldn't classify 126402, 126503
Couldn't classify 132603, 132719
Sorry, prediction pasa_asmbl_24289.p1 fails validation.
(GTG)	 AG	126402-126503	GT	AGG
(ACG)	 AG	127078-127194	GT	AGG
(ACC)	 AG	128872-129210	GT	AGG
(CTC)	 AG	129785-129934	GT	TGG
(CTG)	 AG	130181-130300	GT	AGG
(AAT)	 AG	130443-130646	GC	AGG
(GTG)	 AG	130862-131062	GT	AGG
(CTG)	 AG	132056-132169	GT	AGG
(GAG)	 AG	132283-132438	GT	AGG
(AAC)	 AG	132603-132719	CT	GCC
-recovered pasa_asmbl_24289.p1, internal, 126402, 126503
-recovered pasa_asmbl_24289.p1, internal, 127078, 127194
-recovered pasa_asmbl_24289.p1, internal, 128872, 129210
-recovered pasa_asmbl_24289.p1, internal, 129785, 129934
-recovered pasa_asmbl_24289.p1, internal, 130181, 130300
-recovered pasa_asmbl_24289.p1, internal, 130443, 130646
-recovered pasa_asmbl_24289.p1, internal, 130862, 131062
-recovered pasa_asmbl_24289.p1, internal, 132056, 132169
-recovered pasa_asmbl_24289.p1, internal, 132283, 132438
Valid prediction for snap_scaffold_2-snap.667-T1
Valid prediction for snap_scaffold_2-snap.671-T1
Valid prediction for GeneMark_model.5718_t
Couldn't classify 101205, 101451
Sorry, prediction pasa_asmbl_24282.p1 fails validation.
(GAG)	 AG	101205-101451	GT	AGG
(ATA)	 AG	101761-101901	GT	AGG
(CGC)	 AG	102408-102454	AC	AGA
-recovered pasa_asmbl_24282.p1, terminal, 102408, 102454
-recovered pasa_asmbl_24282.p1, internal, 101205, 101451
-recovered pasa_asmbl_24282.p1, internal, 101761, 101901
Valid prediction for Augustus_model.g2348.t1
Valid prediction for GlimmerHMM_glimmerT_3522-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 GlimmerHMM_glimmerT_3508-T1
Valid prediction for GeneMark_model.5706_t
Valid prediction for snap_scaffold_2-snap.662-T1
Valid prediction for Augustus_model.g2356.t1
Valid prediction for GeneMark_model.5701_t
Valid prediction for GlimmerHMM_glimmerT_3521-T1
Valid prediction for GeneMark_model.5695_t
Valid prediction for GlimmerHMM_glimmerT_3506-T1
Valid prediction for GlimmerHMM_glimmerT_3511-T1
Valid prediction for GlimmerHMM_glimmerT_3505-T1
Valid prediction for snap_scaffold_2-snap.672-T1
Valid prediction for snap_scaffold_2-snap.674-T1
Valid prediction for Augustus_model.g2344.t1
Valid prediction for GeneMark_model.5734_t
Valid prediction for snap_scaffold_2-snap.693-T1
Valid prediction for GeneMark_model.5724_t
Valid prediction for snap_scaffold_2-snap.688-T1
Valid prediction for GeneMark_model.5702_t
Valid prediction for snap_scaffold_2-snap.690-T1
Valid prediction for pasa_asmbl_22954.p2
Valid prediction for pasa_asmbl_22967.p1
Valid prediction for GeneMark_model.5722_t
Valid prediction for GeneMark_model.5704_t
Valid prediction for snap_scaffold_2-snap.696-T1
Valid prediction for GeneMark_model.5691_t
Valid prediction for snap_scaffold_2-snap.683-T1
Valid prediction for GeneMark_model.5697_t
Valid prediction for snap_scaffold_2-snap.680-T1
Valid prediction for Augustus_model.g2354.t1
Valid prediction for CodingQuarry_transcript_28423-T1
Valid prediction for snap_scaffold_2-snap.691-T1
Valid prediction for GeneMark_model.5733_t
Valid prediction for HiQ_model.g2341.t1
Valid prediction for GeneMark_model.5728_t
Valid prediction for snap_scaffold_2-snap.682-T1
Valid prediction for snap_scaffold_2-snap.685-T1
Valid prediction for snap_scaffold_2-snap.669-T1
Valid prediction for GeneMark_model.5731_t
Valid prediction for Augustus_model.g2343.t1
Valid prediction for snap_scaffold_2-snap.676-T1
Valid prediction for GeneMark_model.5692_t
Valid prediction for GlimmerHMM_glimmerT_3515-T1
Couldn't classify 120517, 120591
Couldn't classify 122163, 122179
Sorry, prediction pasa_asmbl_24063.p1 fails validation.
(TTC)	 AC	120517-120591	GT	GGG
(GAC)	 AG	121220-121369	GT	AGG
(GCA)	 AG	121912-122017	GT	CGG
(CCA)	 AG	122163-122179	GA	AGG
-recovered pasa_asmbl_24063.p1, internal, 121220, 121369
-recovered pasa_asmbl_24063.p1, internal, 121912, 122017
Valid prediction for snap_scaffold_2-snap.670-T1
Valid prediction for GeneMark_model.5694_t
Valid prediction for GeneMark_model.5689_t
Valid prediction for snap_scaffold_2-snap.661-T1
Valid prediction for snap_scaffold_2-snap.666-T1
Valid prediction for GlimmerHMM_glimmerT_3528-T1
Valid prediction for snap_scaffold_2-snap.692-T1
Valid prediction for GlimmerHMM_glimmerT_3525-T1
Valid prediction for GeneMark_model.5717_t
Valid prediction for GlimmerHMM_glimmerT_3526-T1
Valid prediction for GlimmerHMM_glimmerT_3529-T1
Valid prediction for HiQ_model.g2342.t1
Valid prediction for GeneMark_model.5720_t
Valid prediction for GeneMark_model.5710_t
Valid prediction for snap_scaffold_2-snap.697-T1
Valid prediction for GeneMark_model.5715_t
Valid prediction for GeneMark_model.5699_t
Valid prediction for GlimmerHMM_glimmerT_3510-T1
Valid prediction for snap_scaffold_2-snap.694-T1
Couldn't classify 115966, 116292
Sorry, prediction pasa_asmbl_22972.p2 fails validation.
(ATG)	 AC	115966-116292	GG	GGG
Valid prediction for Augustus_model.g2353.t1
Valid prediction for GeneMark_model.5726_t
Valid prediction for snap_scaffold_2-snap.660-T1
Valid prediction for snap_scaffold_2-snap.678-T1
Valid prediction for CodingQuarry_transcript_28428-T1
Valid prediction for GlimmerHMM_glimmerT_3530-T1
Valid prediction for GlimmerHMM_glimmerT_3507-T1
Valid prediction for Augustus_model.g2349.t1
Valid prediction for snap_scaffold_2-snap.668-T1
Couldn't classify 20715, 20868
Sorry, prediction pasa_asmbl_22977.p2 fails validation.
(AAG)	 AG	20715-20868	GT	TGG
(CGA)	 AG	21319-21416	GT	AGG
(AGG)	 AG	21984-22082	TT	GAT
-recovered pasa_asmbl_22977.p2, terminal, 21984, 22082
-recovered pasa_asmbl_22977.p2, internal, 20715, 20868
-recovered pasa_asmbl_22977.p2, internal, 21319, 21416
Valid prediction for Augustus_model.g2355.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 34800, rend_intergenic: 22185  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56747, rend_intergenic: 51137  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73526, rend_intergenic: 62805  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81230, rend_intergenic: 75620  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83790, rend_intergenic: 81786  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90247, rend_intergenic: 87201  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102454, rend_intergenic: 100053  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113395, rend_intergenic: 110025  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120492, rend_intergenic: 118779  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143051, rend_intergenic: 121838  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152325, rend_intergenic: 146171  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 162916
-exon list size: 682


building trellis

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74.4    
74.6    
74.7    
74.9    
75.0    
75.1    
75.3    
75.4    
75.6    
75.7    
75.9    
76.0    
76.2    
76.3    
76.5    
76.6    
76.8    
76.9    
77.0    
77.2    
77.3    
77.5    
77.6    
77.8    
77.9    
78.1    
78.2    
78.4    
78.5    
78.7    
78.8    
78.9    
79.1    
79.2    
79.4    
79.5    
79.7    
79.8    
80.0    
80.1    
80.3    
80.4    
80.6    
80.7    
80.8    
81.0    
81.1    
81.3    
81.4    
81.6    
81.7    
81.9    
82.0    
82.2    
82.3    
82.5    
82.6    
82.7    
82.9    
83.0    
83.2    
83.3    
83.5    
83.6    
83.8    
83.9    
84.1    
84.2    
84.4    
84.5    
84.6    
84.8    
84.9    
85.1    
85.2    
85.4    
85.5    
85.7    
85.8    
86.0    
86.1    
86.3    
86.4    
86.5    
86.7    
86.8    
87.0    
87.1    
87.3    
87.4    
87.6    
87.7    
87.9    
88.0    
88.2    
88.3    
88.5    
88.6    
88.7    
88.9    
89.0    
89.2    
89.3    
89.5    
89.6    
89.8    
89.9    
90.1    
90.2    
90.4    
90.5    
90.6    
90.8    
90.9    
91.1    
91.2    
91.4    
91.5    
91.7    
91.8    
92.0    
92.1    
92.3    
92.4    
92.5    
92.7    
92.8    
93.0    
93.1    
93.3    
93.4    
93.6    
93.7    
93.9    
94.0    
94.2    
94.3    
94.4    
94.6    
94.7    
94.9    
95.0    
95.2    
95.3    
95.5    
95.6    
95.8    
95.9    
96.1    
96.2    
96.3    
96.5    
96.6    
96.8    
96.9    
97.1    
97.2    
97.4    
97.5    
97.7    
97.8    
98.0    
98.1    
98.2    
98.4    
98.5    
98.7    
98.8    
99.0    
99.1    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 24 predictions from path traversal
Error with prediction: snap lend_intergenic: 34800, rend_intergenic: 22185  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56747, rend_intergenic: 51137  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73526, rend_intergenic: 62805  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81230, rend_intergenic: 75620  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83790, rend_intergenic: 81786  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90247, rend_intergenic: 87201  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102454, rend_intergenic: 100053  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113395, rend_intergenic: 110025  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120492, rend_intergenic: 118779  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143051, rend_intergenic: 121838  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152325, rend_intergenic: 146171  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