-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_12/scaffold_12_7479845-7680128

-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 Augustus_model.g20110.t1
Valid prediction for GlimmerHMM_glimmerT_30211-T1
Valid prediction for snap_scaffold_12-snap.1421-T1
Valid prediction for Augustus_model.g20118.t1
Valid prediction for GeneMark_model.52125_t
Valid prediction for snap_scaffold_12-snap.1414-T1
Valid prediction for GeneMark_model.52154_t
Valid prediction for GlimmerHMM_glimmerT_30197-T1
Valid prediction for GlimmerHMM_glimmerT_30193-T1
Valid prediction for snap_scaffold_12-snap.1396-T1
Valid prediction for GlimmerHMM_glimmerT_30200-T1
Valid prediction for pasa_asmbl_8725.p1
Valid prediction for GeneMark_model.52130_t
Valid prediction for GeneMark_model.52146_t
Valid prediction for GlimmerHMM_glimmerT_30208-T1
Couldn't classify 136108, 136452
Sorry, prediction pasa_asmbl_7729.p1 fails validation.
(GCT)	 GA	136108-136452	AC	GAA
Valid prediction for HiQ_model.g20112.t1
Valid prediction for snap_scaffold_12-snap.1406-T1
Valid prediction for snap_scaffold_12-snap.1411-T1
Valid prediction for snap_scaffold_12-snap.1429-T1
Valid prediction for GeneMark_model.52133_t
Valid prediction for GlimmerHMM_glimmerT_30206-T1
Valid prediction for snap_scaffold_12-snap.1401-T1
Valid prediction for GeneMark_model.52142_t
Valid prediction for GlimmerHMM_glimmerT_30195-T1
Valid prediction for GeneMark_model.52140_t
Valid prediction for Augustus_model.g20108.t1
Valid prediction for GeneMark_model.52165_t
Valid prediction for GlimmerHMM_glimmerT_30190-T1
Couldn't classify 118177, 118234
Sorry, prediction pasa_asmbl_8730.p1 fails validation.
(ATG)	 CA	117066-117227	GT	TGG
(GAG)	 AG	117583-117715	GT	AGG
(ATA)	 AG	117843-117999	GT	AGG
(GCT)	 AG	118177-118234	TT	TGT
-recovered pasa_asmbl_8730.p1, initial, 117066, 117227
add_exon() Sorry, pasa_asmbl_8730.p1 117583-117715-terminal-3 is invalid.
-recovered pasa_asmbl_8730.p1, terminal, 117583, 117715
-recovered pasa_asmbl_8730.p1, internal, 117583, 117715
-recovered pasa_asmbl_8730.p1, internal, 117843, 117999
Valid prediction for GeneMark_model.52129_t
Valid prediction for CodingQuarry_transcript_10259-T1
Valid prediction for GeneMark_model.52144_t
Valid prediction for HiQ_model.g20101.t1
Valid prediction for CodingQuarry_transcript_10265-T1
Valid prediction for CodingQuarry_transcript_10270-T1
Valid prediction for GeneMark_model.52138_t
Valid prediction for GlimmerHMM_glimmerT_30191-T1
Valid prediction for Augustus_model.g20115.t1
Valid prediction for snap_scaffold_12-snap.1428-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_12-snap.1417-T1
Valid prediction for Augustus_model.g20121.t1
Valid prediction for snap_scaffold_12-snap.1413-T1
Valid prediction for CodingQuarry_transcript_10277-T1
Valid prediction for snap_scaffold_12-snap.1419-T1
Valid prediction for snap_scaffold_12-snap.1418-T1
Valid prediction for CodingQuarry_transcript_10269-T1
Valid prediction for pasa_asmbl_8733.p1
Valid prediction for GlimmerHMM_glimmerT_30186-T1
Valid prediction for Augustus_model.g20113.t1
Valid prediction for GlimmerHMM_glimmerT_30194-T1
Valid prediction for snap_scaffold_12-snap.1423-T1
Valid prediction for GeneMark_model.52148_t
Valid prediction for GeneMark_model.52156_t
Valid prediction for snap_scaffold_12-snap.1435-T1
Valid prediction for pasa_asmbl_8735.p1
Valid prediction for GeneMark_model.52128_t
Valid prediction for snap_scaffold_12-snap.1426-T1
Couldn't classify 195710, 195844
Couldn't classify 197271, 197647
Sorry, prediction pasa_asmbl_8753.p1 fails validation.
(CAT)	 GT	195710-195844	GT	ACG
(GGC)	 AG	196706-196741	GT	CAG
(ACT)	 AG	196835-196939	GT	ATG
(GAG)	 AG	197053-197170	GT	AGG
(ACT)	 AG	197271-197647	GG	GGG
-recovered pasa_asmbl_8753.p1, internal, 196706, 196741
-recovered pasa_asmbl_8753.p1, internal, 196835, 196939
-recovered pasa_asmbl_8753.p1, internal, 197053, 197170
Valid prediction for Augustus_model.g20102.t1
Valid prediction for HiQ_model.g20117.t1
Valid prediction for CodingQuarry_transcript_10275-T1
Valid prediction for pasa_asmbl_8739.p1
Valid prediction for GeneMark_model.52157_t
Valid prediction for GlimmerHMM_glimmerT_30202-T1
Valid prediction for GeneMark_model.52122_t
Valid prediction for snap_scaffold_12-snap.1409-T1
Valid prediction for CodingQuarry_transcript_10276-T1
Valid prediction for GeneMark_model.52152_t
Couldn't classify 118495, 118600
Sorry, prediction pasa_asmbl_8731.p1 fails validation.
(GGG)	 CC	118495-118600	GT	AGG
(TCT)	 AG	119018-119194	GT	CGG
(GTA)	 AG	119295-119388	GT	AGG
(TCC)	 AG	119623-119696	GT	GGG
(GGT)	 AG	119922-120071	GT	TGG
(GCT)	 AG	120265-120567	GT	TGG
(GAT)	 AG	120680-121053	CA	GAC
-recovered pasa_asmbl_8731.p1, terminal, 120680, 121053
-recovered pasa_asmbl_8731.p1, internal, 119018, 119194
-recovered pasa_asmbl_8731.p1, internal, 119295, 119388
-recovered pasa_asmbl_8731.p1, internal, 119623, 119696
-recovered pasa_asmbl_8731.p1, internal, 119922, 120071
-recovered pasa_asmbl_8731.p1, internal, 120265, 120567
Valid prediction for snap_scaffold_12-snap.1424-T1
Valid prediction for HiQ_model.g20109.t1
Valid prediction for Augustus_model.g20106.t1
Valid prediction for CodingQuarry_transcript_10264-T1
Valid prediction for CodingQuarry_transcript_10266-T1
Valid prediction for CodingQuarry_transcript_10274-T1
Valid prediction for GeneMark_model.52159_t
Valid prediction for Augustus_model.g20119.t1
Valid prediction for pasa_asmbl_8747.p1
Valid prediction for GeneMark_model.52121_t
Valid prediction for snap_scaffold_12-snap.1402-T1
Valid prediction for snap_scaffold_12-snap.1395-T1
Valid prediction for HiQ_model.g20103.t1
Valid prediction for GeneMark_model.52162_t
Valid prediction for snap_scaffold_12-snap.1412-T1
Valid prediction for GeneMark_model.52126_t
Valid prediction for GlimmerHMM_glimmerT_30205-T1
Couldn't classify 172470, 172830
Couldn't classify 175682, 175767
Sorry, prediction pasa_asmbl_8744.p2 fails validation.
(GTT)	 CA	172470-172830	GT	TGG
(TGG)	 AG	175682-175767	GA	AAG
Valid prediction for GeneMark_model.52161_t
Valid prediction for Augustus_model.g20097.t1
Valid prediction for Augustus_model.g20123.t1
Valid prediction for GlimmerHMM_glimmerT_30203-T1
Valid prediction for snap_scaffold_12-snap.1430-T1
Valid prediction for GeneMark_model.52135_t
Valid prediction for GlimmerHMM_glimmerT_30189-T1
Valid prediction for snap_scaffold_12-snap.1431-T1
Valid prediction for GeneMark_model.52151_t
Valid prediction for GeneMark_model.52132_t
Valid prediction for snap_scaffold_12-snap.1432-T1
Valid prediction for GeneMark_model.52163_t
Valid prediction for GeneMark_model.52150_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 GeneMark_model.52123_t
Valid prediction for snap_scaffold_12-snap.1416-T1
Valid prediction for snap_scaffold_12-snap.1422-T1
Valid prediction for CodingQuarry_transcript_10272-T1
Valid prediction for GlimmerHMM_glimmerT_30196-T1
Valid prediction for snap_scaffold_12-snap.1405-T1
Valid prediction for GeneMark_model.52147_t
Valid prediction for pasa_asmbl_7737.p1
Valid prediction for Augustus_model.g20111.t1
Valid prediction for GeneMark_model.52141_t
Valid prediction for GeneMark_model.52134_t
Valid prediction for GlimmerHMM_glimmerT_30207-T1
Valid prediction for GeneMark_model.52155_t
Valid prediction for CodingQuarry_transcript_10262-T1
Valid prediction for snap_scaffold_12-snap.1407-T1
Valid prediction for HiQ_model.g20104.t1
Valid prediction for pasa_asmbl_7719.p1
Valid prediction for HiQ_model.g20100.t1
Valid prediction for snap_scaffold_12-snap.1425-T1
Valid prediction for Augustus_model.g20099.t1
Valid prediction for CodingQuarry_transcript_10267-T1
Valid prediction for pasa_asmbl_7739.p1
Valid prediction for snap_scaffold_12-snap.1398-T1
Valid prediction for CodingQuarry_transcript_10258-T1
Valid prediction for CodingQuarry_transcript_10261-T1
Valid prediction for GeneMark_model.52131_t
Valid prediction for CodingQuarry_transcript_10271-T1
Valid prediction for snap_scaffold_12-snap.1433-T1
Couldn't classify 41367, 41533
Sorry, prediction CodingQuarry_transcript_10273-T1 fails validation.
(ATG)	 GA	37751-37804	GT	TGG
(AGA)	 AG	38974-39058	GT	AGG
(AGA)	 AG	39196-39300	GT	CTG
(GCT)	 AG	39647-39804	GT	GGG
(GAG)	 AG	39902-40036	GT	AGG
(ACG)	 AG	40213-40366	GT	AGG
(GAG)	 AG	40531-40650	GT	AGG
(GGA)	 AG	40817-40912	GT	GGG
(GTG)	 AG	40994-41100	GT	AGG
(GTG)	 AG	41195-41267	GT	TGG
(ATG)	 TG	41367-41533	GT	AGG
(CAT)	 AG	41835-41987	GT	GGG
(GAG)	 AG	42098-42226	GT	GGG
(CAT)	 AG	42433-42646	GT	CGG
(AGA)	 AG	42873-43066	GT	AGG
(GTG)	 AG	43229-43337	GT	AGG
(AGA)	 AG	43447-43545	GT	AGG
(TGT)	 AG	43867-44010	GT	TGG
(CTG)	 AG	44099-44196	GT	AGG
(ATC)	 AG	44299-44505	GG	GAG
-recovered CodingQuarry_transcript_10273-T1, initial, 37751, 37804
add_exon() Sorry, CodingQuarry_transcript_10273-T1 41367-41533-initial-1 is invalid.
-recovered CodingQuarry_transcript_10273-T1, initial, 41367, 41533
-recovered CodingQuarry_transcript_10273-T1, terminal, 44299, 44505
-recovered CodingQuarry_transcript_10273-T1, internal, 38974, 39058
-recovered CodingQuarry_transcript_10273-T1, internal, 39196, 39300
-recovered CodingQuarry_transcript_10273-T1, internal, 39647, 39804
-recovered CodingQuarry_transcript_10273-T1, internal, 39902, 40036
-recovered CodingQuarry_transcript_10273-T1, internal, 40213, 40366
-recovered CodingQuarry_transcript_10273-T1, internal, 40531, 40650
-recovered CodingQuarry_transcript_10273-T1, internal, 40817, 40912
-recovered CodingQuarry_transcript_10273-T1, internal, 40994, 41100
-recovered CodingQuarry_transcript_10273-T1, internal, 41195, 41267
-recovered CodingQuarry_transcript_10273-T1, internal, 41835, 41987
-recovered CodingQuarry_transcript_10273-T1, internal, 42098, 42226
-recovered CodingQuarry_transcript_10273-T1, internal, 42433, 42646
-recovered CodingQuarry_transcript_10273-T1, internal, 42873, 43066
-recovered CodingQuarry_transcript_10273-T1, internal, 43229, 43337
-recovered CodingQuarry_transcript_10273-T1, internal, 43447, 43545
-recovered CodingQuarry_transcript_10273-T1, internal, 43867, 44010
-recovered CodingQuarry_transcript_10273-T1, internal, 44099, 44196
Valid prediction for Augustus_model.g20122.t1
Valid prediction for GlimmerHMM_glimmerT_30201-T1
Valid prediction for CodingQuarry_transcript_10268-T1
Valid prediction for HiQ_model.g20107.t1
Valid prediction for GeneMark_model.52149_t
Valid prediction for Augustus_model.g20120.t1
Valid prediction for GlimmerHMM_glimmerT_30198-T1
Valid prediction for GlimmerHMM_glimmerT_30204-T1
Valid prediction for snap_scaffold_12-snap.1394-T1
Valid prediction for snap_scaffold_12-snap.1404-T1
Valid prediction for GlimmerHMM_glimmerT_30210-T1
Valid prediction for snap_scaffold_12-snap.1397-T1
Valid prediction for GeneMark_model.52127_t
Valid prediction for GeneMark_model.52145_t
Valid prediction for snap_scaffold_12-snap.1399-T1
Valid prediction for GeneMark_model.52137_t
Valid prediction for GeneMark_model.52153_t
Valid prediction for GlimmerHMM_glimmerT_30187-T1
Valid prediction for snap_scaffold_12-snap.1400-T1
Valid prediction for Augustus_model.g20098.t1
Valid prediction for GeneMark_model.52164_t
Valid prediction for CodingQuarry_transcript_10263-T1
Valid prediction for snap_scaffold_12-snap.1434-T1
Valid prediction for Augustus_model.g20105.t1
Valid prediction for GlimmerHMM_glimmerT_30192-T1
Valid prediction for GlimmerHMM_glimmerT_30188-T1
Valid prediction for pasa_asmbl_7724.p1
Valid prediction for snap_scaffold_12-snap.1403-T1
Valid prediction for snap_scaffold_12-snap.1420-T1
Valid prediction for GlimmerHMM_glimmerT_30199-T1
Valid prediction for HiQ_model.g20116.t1
Valid prediction for GeneMark_model.52139_t
Valid prediction for GeneMark_model.52160_t
Valid prediction for snap_scaffold_12-snap.1427-T1
Valid prediction for GeneMark_model.52158_t
Valid prediction for GlimmerHMM_glimmerT_30209-T1
Valid prediction for GeneMark_model.52136_t
Valid prediction for GeneMark_model.52143_t
Valid prediction for GeneMark_model.52124_t
Valid prediction for snap_scaffold_12-snap.1408-T1
Valid prediction for snap_scaffold_12-snap.1410-T1
Valid prediction for HiQ_model.g20114.t1
Valid prediction for snap_scaffold_12-snap.1415-T1
Valid prediction for pasa_asmbl_7727.p1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 15914, rend_intergenic: 12515  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20031, rend_intergenic: 16734  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38412, rend_intergenic: 33639  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47151, rend_intergenic: 39822  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54303, rend_intergenic: 49969  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70673, rend_intergenic: 65297  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77998, rend_intergenic: 71555  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97782, rend_intergenic: 80264  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132038, rend_intergenic: 127729  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135310, rend_intergenic: 132572  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162534, rend_intergenic: 156093  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 89402, rend_intergenic: 89399  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 200284
-exon list size: 665


building trellis

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62.8    
63.0    
63.1    
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    
68.7    
68.8    
69.0    
69.1    
69.3    
69.4    
69.6    
69.7    
69.9    
70.0    
70.2    
70.3    
70.5    
70.6    
70.8    
70.9    
71.1    
71.2    
71.4    
71.5    
71.7    
71.8    
72.0    
72.1    
72.3    
72.4    
72.6    
72.7    
72.9    
73.0    
73.2    
73.3    
73.5    
73.6    
73.8    
73.9    
74.1    
74.2    
74.4    
74.5    
74.7    
74.8    
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    
77.1    
77.2    
77.4    
77.5    
77.7    
77.8    
78.0    
78.1    
78.3    
78.4    
78.6    
78.7    
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    
84.3    
84.4    
84.6    
84.7    
84.9    
85.0    
85.2    
85.3    
85.5    
85.6    
85.8    
85.9    
86.1    
86.2    
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    
88.8    
88.9    
89.1    
89.2    
89.4    
89.5    
89.7    
89.8    
90.0    
90.1    
90.3    
90.4    
90.6    
90.7    
90.9    
91.0    
91.2    
91.3    
91.5    
91.6    
91.8    
91.9    
92.1    
92.2    
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    
94.5    
94.6    
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 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 15914, rend_intergenic: 12515  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20031, rend_intergenic: 16734  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38412, rend_intergenic: 33639  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47151, rend_intergenic: 39822  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54303, rend_intergenic: 49969  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70673, rend_intergenic: 65297  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77998, rend_intergenic: 71555  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97782, rend_intergenic: 80264  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132038, rend_intergenic: 127729  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135310, rend_intergenic: 132572  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162534, rend_intergenic: 156093  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 89402, rend_intergenic: 89399  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 29 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 12514
-exon list size: 3


building trellis

20.0    
40.0    
60.0    
80.0    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 11828
-exon list size: 1


building trellis

33.3    
66.7    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support
	-no exons in range 1273 - 11828