-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_13/scaffold_13_12008503-12166594

-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 HiQ_model.g22334.t1
Valid prediction for Augustus_model.g22323.t1
Valid prediction for snap_scaffold_13-snap.2277-T1
Couldn't classify 78264, 78344
Sorry, prediction pasa_asmbl_11310.p1 fails validation.
(ATG)	 TC	77616-77722	GT	CAG
(GGA)	 AG	77871-78093	GT	GGG
(AGA)	 AG	78264-78344	CC	ACC
-recovered pasa_asmbl_11310.p1, initial, 77616, 77722
-recovered pasa_asmbl_11310.p1, internal, 77871, 78093
Valid prediction for GeneMark_model.56683_t
Valid prediction for GeneMark_model.56669_t
Valid prediction for snap_scaffold_13-snap.2274-T1
Valid prediction for snap_scaffold_13-snap.2244-T1
Valid prediction for GeneMark_model.56698_t
Valid prediction for snap_scaffold_13-snap.2276-T1
Valid prediction for Augustus_model.g22326.t1
Valid prediction for GeneMark_model.56689_t
Valid prediction for snap_scaffold_13-snap.2254-T1
Valid prediction for snap_scaffold_13-snap.2252-T1
Valid prediction for GeneMark_model.56665_t
Valid prediction for Augustus_model.g22333.t1
Valid prediction for GlimmerHMM_glimmerT_33207-T1
Valid prediction for GlimmerHMM_glimmerT_33226-T1
Couldn't classify 135760, 135927
Sorry, prediction pasa_asmbl_11320.p1 fails validation.
(AAC)	 AT	135760-135927	GT	AGG
(GAC)	 AG	136330-136497	GT	CAG
(CTG)	 AG	136754-136804	GT	AAG
(GTC)	 AG	136975-137065	GT	CGG
(TGG)	 AG	137182-137345	GT	AGG
(GCC)	 AG	137550-137712	GT	GGG
(ACC)	 AG	138229-138359	GT	ACG
(GAT)	 AG	138592-138699	GT	AGG
(GCG)	 AG	139329-139435	GT	AGG
(CTC)	 AG	139566-139614	GT	TGG
(ATG)	 AG	139912-140043	GT	AGG
(CAA)	 AG	140206-140323	GT	CTG
(TGG)	 AG	140437-140513	GT	AGG
(TTG)	 AG	140784-140915	GT	AGG
(GCG)	 AG	141114-141206	GT	TAG
(GAT)	 AG	141364-141411	GT	TGG
(GTG)	 AG	141641-141723	GT	AAG
(CAA)	 AG	141930-142035	GT	AGG
(GCT)	 AG	142261-142374	GT	AGG
(AAA)	 AG	143070-143150	AA	AAA
-recovered pasa_asmbl_11320.p1, initial, 139912, 140043
-recovered pasa_asmbl_11320.p1, terminal, 143070, 143150
-recovered pasa_asmbl_11320.p1, internal, 136330, 136497
-recovered pasa_asmbl_11320.p1, internal, 136754, 136804
-recovered pasa_asmbl_11320.p1, internal, 136975, 137065
-recovered pasa_asmbl_11320.p1, internal, 137182, 137345
-recovered pasa_asmbl_11320.p1, internal, 137550, 137712
-recovered pasa_asmbl_11320.p1, internal, 138229, 138359
-recovered pasa_asmbl_11320.p1, internal, 138592, 138699
-recovered pasa_asmbl_11320.p1, internal, 139329, 139435
-recovered pasa_asmbl_11320.p1, internal, 139566, 139614
-recovered pasa_asmbl_11320.p1, internal, 139912, 140043
-recovered pasa_asmbl_11320.p1, internal, 140206, 140323
-recovered pasa_asmbl_11320.p1, internal, 140437, 140513
-recovered pasa_asmbl_11320.p1, internal, 140784, 140915
-recovered pasa_asmbl_11320.p1, internal, 141114, 141206
-recovered pasa_asmbl_11320.p1, internal, 141364, 141411
-recovered pasa_asmbl_11320.p1, internal, 141641, 141723
-recovered pasa_asmbl_11320.p1, internal, 141930, 142035
-recovered pasa_asmbl_11320.p1, internal, 142261, 142374
Valid prediction for snap_scaffold_13-snap.2278-T1
Valid prediction for snap_scaffold_13-snap.2264-T1
Valid prediction for snap_scaffold_13-snap.2248-T1
Valid prediction for GeneMark_model.56695_t
Valid prediction for GeneMark_model.56710_t
Valid prediction for snap_scaffold_13-snap.2259-T1
Valid prediction for HiQ_model.g22329.t1
Valid prediction for GeneMark_model.56711_t
Valid prediction for snap_scaffold_13-snap.2256-T1
Valid prediction for snap_scaffold_13-snap.2269-T1
Valid prediction for GeneMark_model.56700_t
Valid prediction for GlimmerHMM_glimmerT_33221-T1
Valid prediction for snap_scaffold_13-snap.2271-T1
Valid prediction for GeneMark_model.56676_t
Valid prediction for GeneMark_model.56712_t
Valid prediction for GlimmerHMM_glimmerT_33228-T1
Valid prediction for Augustus_model.g22324.t1
Valid prediction for Augustus_model.g22331.t1
Valid prediction for GlimmerHMM_glimmerT_33225-T1
Valid prediction for GlimmerHMM_glimmerT_33224-T1
Valid prediction for GlimmerHMM_glimmerT_33229-T1
Valid prediction for GlimmerHMM_glimmerT_33223-T1
Valid prediction for GeneMark_model.56672_t
Valid prediction for GeneMark_model.56667_t
Valid prediction for GeneMark_model.56693_t
Valid prediction for snap_scaffold_13-snap.2270-T1
Valid prediction for GlimmerHMM_glimmerT_33213-T1
Couldn't classify 79056, 79254
Couldn't classify 86797, 87013
Couldn't classify 87421, 87499
Sorry, prediction pasa_asmbl_11311.p1 fails validation.
(ACG)	 AG	79056-79254	GT	AGG
(ATT)	 AG	80241-80376	GT	AGG
(CCA)	 AG	80613-80699	GT	AGG
(GTT)	 AG	80807-80984	GT	AGG
(GTG)	 AG	83401-83785	GT	AGG
(GAG)	 AG	83984-84148	GT	CGG
(AGG)	 AG	85993-86136	GT	AGG
(TGC)	 AG	86797-87013	AT	GGA
(GTT)	 AC	87421-87499	GT	AGG
(ATT)	 AG	87828-87938	CA	AGC
-recovered pasa_asmbl_11311.p1, terminal, 87828, 87938
-recovered pasa_asmbl_11311.p1, internal, 79056, 79254
-recovered pasa_asmbl_11311.p1, internal, 80241, 80376
-recovered pasa_asmbl_11311.p1, internal, 80613, 80699
-recovered pasa_asmbl_11311.p1, internal, 80807, 80984
-recovered pasa_asmbl_11311.p1, internal, 83401, 83785
-recovered pasa_asmbl_11311.p1, internal, 83984, 84148
-recovered pasa_asmbl_11311.p1, internal, 85993, 86136
Valid prediction for Augustus_model.g22325.t1
Valid prediction for Augustus_model.g22335.t1
Valid prediction for GeneMark_model.56706_t
Valid prediction for snap_scaffold_13-snap.2243-T1
Valid prediction for GeneMark_model.56681_t
Couldn't classify 25541, 25747
Sorry, prediction pasa_asmbl_11305.p1 fails validation.
(ATG)	 GG	20125-20322	GT	AGG
(GTC)	 AG	20544-20690	GT	AGG
(GGA)	 AG	20937-21092	GT	AGG
(GAA)	 AG	21270-21326	GT	AGG
(GGG)	 AG	21888-22065	GT	CGG
(TTA)	 AG	22423-22585	GT	AGG
(TTC)	 AG	23263-23405	GT	TGG
(AGT)	 AG	23598-23770	GT	AGG
(TGG)	 AG	24053-24286	GT	GGG
(GAT)	 AG	24501-24827	GT	AGG
(GTG)	 AG	25029-25214	GT	AGG
(CGT)	 AG	25541-25747	GT	AGG
-recovered pasa_asmbl_11305.p1, initial, 20125, 20322
-recovered pasa_asmbl_11305.p1, internal, 20544, 20690
-recovered pasa_asmbl_11305.p1, internal, 20937, 21092
-recovered pasa_asmbl_11305.p1, internal, 21270, 21326
-recovered pasa_asmbl_11305.p1, internal, 21888, 22065
-recovered pasa_asmbl_11305.p1, internal, 22423, 22585
-recovered pasa_asmbl_11305.p1, internal, 23263, 23405
-recovered pasa_asmbl_11305.p1, internal, 23598, 23770
-recovered pasa_asmbl_11305.p1, internal, 24053, 24286
-recovered pasa_asmbl_11305.p1, internal, 24501, 24827
-recovered pasa_asmbl_11305.p1, internal, 25029, 25214
-recovered pasa_asmbl_11305.p1, internal, 25541, 25747
Valid prediction for Augustus_model.g22319.t1
Valid prediction for GlimmerHMM_glimmerT_33217-T1
Valid prediction for GeneMark_model.56708_t
Valid prediction for CodingQuarry_transcript_13237-T1
Valid prediction for GeneMark_model.56674_t
Valid prediction for snap_scaffold_13-snap.2261-T1
Valid prediction for GeneMark_model.56678_t
Valid prediction for GeneMark_model.56704_t
Valid prediction for GlimmerHMM_glimmerT_33227-T1
Valid prediction for GeneMark_model.56696_t
Valid prediction for GlimmerHMM_glimmerT_33220-T1
Valid prediction for GlimmerHMM_glimmerT_33211-T1
Valid prediction for GeneMark_model.56686_t
Valid prediction for HiQ_model.g22332.t1
Valid prediction for snap_scaffold_13-snap.2268-T1
Couldn't classify 27298, 27399
Sorry, prediction pasa_asmbl_11306.p1 fails validation.
(CAG)	 CA	27298-27399	GT	ATG
(TGC)	 AG	27622-27711	GT	CTG
(TGG)	 AG	27831-27945	GT	TAG
(CGT)	 AG	28137-28249	GT	CCG
(ACG)	 AG	28747-28857	GT	TGG
(AAC)	 AG	29170-29218	GT	AGG
(GGC)	 AG	29522-29618	GT	GAG
(GAA)	 AG	29755-29920	GT	AGG
(AAG)	 AG	30179-30229	CA	GAC
-recovered pasa_asmbl_11306.p1, terminal, 30179, 30229
-recovered pasa_asmbl_11306.p1, internal, 27622, 27711
-recovered pasa_asmbl_11306.p1, internal, 27831, 27945
-recovered pasa_asmbl_11306.p1, internal, 28137, 28249
-recovered pasa_asmbl_11306.p1, internal, 28747, 28857
-recovered pasa_asmbl_11306.p1, internal, 29170, 29218
-recovered pasa_asmbl_11306.p1, internal, 29522, 29618
-recovered pasa_asmbl_11306.p1, internal, 29755, 29920
Valid prediction for GeneMark_model.56702_t
Valid prediction for GlimmerHMM_glimmerT_33215-T1
Valid prediction for GeneMark_model.56691_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_13-snap.2249-T1
Valid prediction for GeneMark_model.56684_t
Valid prediction for snap_scaffold_13-snap.2263-T1
Valid prediction for Augustus_model.g22320.t1
Valid prediction for GeneMark_model.56699_t
Valid prediction for GeneMark_model.56703_t
Valid prediction for CodingQuarry_transcript_13236-T1
Valid prediction for GeneMark_model.56687_t
Valid prediction for GeneMark_model.56668_t
Valid prediction for Augustus_model.g22321.t1
Valid prediction for GeneMark_model.56697_t
Valid prediction for Augustus_model.g22322.t1
Valid prediction for snap_scaffold_13-snap.2250-T1
Valid prediction for GeneMark_model.56682_t
Valid prediction for GlimmerHMM_glimmerT_33218-T1
Valid prediction for GlimmerHMM_glimmerT_33219-T1
Valid prediction for GlimmerHMM_glimmerT_33216-T1
Valid prediction for snap_scaffold_13-snap.2247-T1
Valid prediction for snap_scaffold_13-snap.2253-T1
Valid prediction for GeneMark_model.56692_t
Valid prediction for Augustus_model.g22327.t1
Valid prediction for GeneMark_model.56673_t
Valid prediction for snap_scaffold_13-snap.2273-T1
Valid prediction for snap_scaffold_13-snap.2262-T1
Valid prediction for GeneMark_model.56666_t
Valid prediction for snap_scaffold_13-snap.2275-T1
Valid prediction for GeneMark_model.56680_t
Valid prediction for GlimmerHMM_glimmerT_33214-T1
Valid prediction for snap_scaffold_13-snap.2267-T1
Valid prediction for GlimmerHMM_glimmerT_33222-T1
Valid prediction for GeneMark_model.56671_t
Valid prediction for GlimmerHMM_glimmerT_33212-T1
Valid prediction for snap_scaffold_13-snap.2272-T1
Valid prediction for GeneMark_model.56690_t
Valid prediction for GeneMark_model.56677_t
Valid prediction for GeneMark_model.56675_t
Valid prediction for GeneMark_model.56694_t
Valid prediction for GeneMark_model.56688_t
Valid prediction for Augustus_model.g22330.t1
Valid prediction for snap_scaffold_13-snap.2257-T1
Valid prediction for GeneMark_model.56707_t
Valid prediction for snap_scaffold_13-snap.2245-T1
Valid prediction for GeneMark_model.56701_t
Couldn't classify 83274, 83328
Sorry, prediction pasa_asmbl_10087.p1 fails validation.
(ATT)	 TA	83274-83328	GT	GAG
(AGT)	 AG	83604-83743	GC	AGG
(GTG)	 AG	83975-84079	CC	GAC
-recovered pasa_asmbl_10087.p1, terminal, 83975, 84079
-recovered pasa_asmbl_10087.p1, internal, 83604, 83743
Valid prediction for GeneMark_model.56679_t
Valid prediction for snap_scaffold_13-snap.2251-T1
Valid prediction for Augustus_model.g22328.t1
Valid prediction for pasa_asmbl_10086.p1
Valid prediction for GeneMark_model.56709_t
Valid prediction for snap_scaffold_13-snap.2258-T1
Valid prediction for snap_scaffold_13-snap.2265-T1
Valid prediction for GlimmerHMM_glimmerT_33210-T1
Couldn't classify 141696, 141715
Couldn't classify 141794, 141905
Sorry, prediction CodingQuarry_transcript_13235-T1 fails validation.
(ATG)	 CA	141696-141715	AA	GTA
(CCA)	 GT	141794-141905	CA	GAC
Valid prediction for GeneMark_model.56670_t
Valid prediction for snap_scaffold_13-snap.2246-T1
Valid prediction for snap_scaffold_13-snap.2255-T1
Valid prediction for snap_scaffold_13-snap.2260-T1
Valid prediction for snap_scaffold_13-snap.2266-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_33208-T1
Valid prediction for GlimmerHMM_glimmerT_33209-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 30675, rend_intergenic: 24082  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46852, rend_intergenic: 41111  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50285, rend_intergenic: 46944  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60044, rend_intergenic: 51579  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61489, rend_intergenic: 60093  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66384, rend_intergenic: 61919  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67199, rend_intergenic: 66388  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87053, rend_intergenic: 77906  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118169, rend_intergenic: 112641  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120113, rend_intergenic: 118603  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130804, rend_intergenic: 121827  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 158092
-exon list size: 671


building trellis

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62.1    
62.3    
62.4    
62.6    
62.7    
62.9    
63.0    
63.2    
63.3    
63.4    
63.6    
63.7    
63.9    
64.0    
64.2    
64.3    
64.5    
64.6    
64.8    
64.9    
65.1    
65.2    
65.4    
65.5    
65.7    
65.8    
66.0    
66.1    
66.3    
66.4    
66.6    
66.7    
66.9    
67.0    
67.2    
67.3    
67.5    
67.6    
67.8    
67.9    
68.1    
68.2    
68.4    
68.5    
68.6    
68.8    
68.9    
69.1    
69.2    
69.4    
69.5    
69.7    
69.8    
70.0    
70.1    
70.3    
70.4    
70.6    
70.7    
70.9    
71.0    
71.2    
71.3    
71.5    
71.6    
71.8    
71.9    
72.1    
72.2    
72.4    
72.5    
72.7    
72.8    
73.0    
73.1    
73.3    
73.4    
73.6    
73.7    
73.8    
74.0    
74.1    
74.3    
74.4    
74.6    
74.7    
74.9    
75.0    
75.2    
75.3    
75.5    
75.6    
75.8    
75.9    
76.1    
76.2    
76.4    
76.5    
76.7    
76.8    
77.0    
77.1    
77.3    
77.4    
77.6    
77.7    
77.9    
78.0    
78.2    
78.3    
78.5    
78.6    
78.8    
78.9    
79.0    
79.2    
79.3    
79.5    
79.6    
79.8    
79.9    
80.1    
80.2    
80.4    
80.5    
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    
82.8    
82.9    
83.1    
83.2    
83.4    
83.5    
83.7    
83.8    
84.0    
84.1    
84.2    
84.4    
84.5    
84.7    
84.8    
85.0    
85.1    
85.3    
85.4    
85.6    
85.7    
85.9    
86.0    
86.2    
86.3    
86.5    
86.6    
86.8    
86.9    
87.1    
87.2    
87.4    
87.5    
87.7    
87.8    
88.0    
88.1    
88.3    
88.4    
88.6    
88.7    
88.9    
89.0    
89.2    
89.3    
89.5    
89.6    
89.7    
89.9    
90.0    
90.2    
90.3    
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    
92.6    
92.7    
92.9    
93.0    
93.2    
93.3    
93.5    
93.6    
93.8    
93.9    
94.1    
94.2    
94.4    
94.5    
94.7    
94.8    
94.9    
95.1    
95.2    
95.4    
95.5    
95.7    
95.8    
96.0    
96.1    
96.3    
96.4    
96.6    
96.7    
96.9    
97.0    
97.2    
97.3    
97.5    
97.6    
97.8    
97.9    
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 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 30675, rend_intergenic: 24082  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46852, rend_intergenic: 41111  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50285, rend_intergenic: 46944  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60044, rend_intergenic: 51579  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61489, rend_intergenic: 60093  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66384, rend_intergenic: 61919  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67199, rend_intergenic: 66388  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87053, rend_intergenic: 77906  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118169, rend_intergenic: 112641  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120113, rend_intergenic: 118603  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130804, rend_intergenic: 121827  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