-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_19/scaffold_19_6124844-6337060

-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.g30181.t1
Valid prediction for GlimmerHMM_glimmerT_45257-T1
Valid prediction for CodingQuarry_transcript_25623-T1
Valid prediction for GlimmerHMM_glimmerT_45251-T1
Valid prediction for snap_scaffold_19-snap.1308-T1
Valid prediction for CodingQuarry_transcript_25628-T1
Valid prediction for GlimmerHMM_glimmerT_45242-T1
Valid prediction for snap_scaffold_19-snap.1305-T1
Valid prediction for pasa_asmbl_22203.p1
Valid prediction for GlimmerHMM_glimmerT_45248-T1
Valid prediction for Augustus_model.g30167.t1
Valid prediction for GlimmerHMM_glimmerT_45260-T1
Couldn't classify 93252, 93294
Couldn't classify 96637, 96821
Sorry, prediction pasa_asmbl_22205.p2 fails validation.
(CTG)	 CC	93252-93294	GT	AGG
(GGG)	 AG	96071-96286	GT	AGG
(GGG)	 AG	96637-96821	CT	CAC
-recovered pasa_asmbl_22205.p2, internal, 96071, 96286
Valid prediction for GeneMark_model.79133_t
Valid prediction for CodingQuarry_transcript_25626-T1
Valid prediction for snap_scaffold_19-snap.1312-T1
Valid prediction for HiQ_model.g30179.t1
Valid prediction for snap_scaffold_19-snap.1293-T1
Valid prediction for HiQ_model.g30175.t1
Valid prediction for snap_scaffold_19-snap.1314-T1
Valid prediction for snap_scaffold_19-snap.1315-T1
Valid prediction for GeneMark_model.79118_t
Valid prediction for GeneMark_model.79127_t
Couldn't classify 98821, 98898
Sorry, prediction pasa_asmbl_22727.p1 fails validation.
(CCT)	 CA	98821-98898	GT	GGG
(AGT)	 AG	99190-99264	GT	GGG
(GGG)	 AG	99400-99444	GT	CTG
(GGT)	 AG	99535-99588	GT	TGG
(GGC)	 AG	99890-99943	GT	ATG
(GGA)	 AG	100101-100154	GT	AGG
(GGA)	 AG	100345-100398	GT	AGG
(GGT)	 AG	100591-100644	GT	AGG
(GGT)	 AG	100750-100794	GT	CGG
(GGT)	 AG	100890-100943	GT	TGG
(GGA)	 AG	101041-101085	GT	TGG
(GGT)	 AG	101286-101339	GT	AGG
(GGC)	 AG	101461-101559	GT	GGG
(GGT)	 AG	101704-101748	GT	TGG
(GGA)	 AG	102172-102270	GT	TGG
(GGA)	 AG	102375-102428	GT	TAG
(GGT)	 AG	102709-102816	GT	TGG
(GGT)	 AG	102940-102993	GT	AGG
(GGA)	 AG	103165-103263	GT	GGG
(GGC)	 AG	103442-103495	GT	TGG
(GGA)	 AG	103607-103705	GT	CTG
(GGA)	 AG	103855-103908	GT	AGG
(GGA)	 AG	104045-104098	GT	CAG
(GGA)	 AG	104312-104365	GT	AGG
(GGT)	 AG	104528-104581	GT	AGG
(GGT)	 AG	104888-104932	GT	GGG
(GGT)	 AG	105088-105186	GT	AGG
(GGA)	 AG	105435-105542	GT	TAG
(GGG)	 AG	105680-105733	GT	GGG
(GGA)	 AG	105956-106009	GT	AGG
(GGA)	 AG	106273-106326	GT	CTG
(GGA)	 AG	106412-106465	GT	CTG
(GGT)	 AG	106712-106819	GT	AGG
(GGG)	 AG	106976-107029	GT	CAG
(GGG)	 AG	107121-107174	GT	CTG
(GGT)	 AG	107379-107540	GT	GGG
(GGT)	 AG	107743-107850	GT	CTG
(GGT)	 AG	108002-108109	GT	AGG
(GGA)	 AG	108220-108273	GT	GGG
(GGA)	 AG	108347-108454	GT	ATG
(GGT)	 AG	108563-108616	GT	TGG
(GGG)	 AG	108772-108879	GT	CCG
(GGA)	 AG	109909-109962	GT	GAG
(GGG)	 AG	110048-110155	GT	AGG
(GGA)	 AG	110305-110650	GT	TGG
(GTG)	 AG	110814-111004	GT	GAG
(TTC)	 AG	111084-111326	GT	CGG
(GAA)	 AG	111530-111676	AC	AAA
-recovered pasa_asmbl_22727.p1, terminal, 111530, 111676
-recovered pasa_asmbl_22727.p1, internal, 99190, 99264
-recovered pasa_asmbl_22727.p1, internal, 99400, 99444
-recovered pasa_asmbl_22727.p1, internal, 99535, 99588
-recovered pasa_asmbl_22727.p1, internal, 99890, 99943
-recovered pasa_asmbl_22727.p1, internal, 100101, 100154
-recovered pasa_asmbl_22727.p1, internal, 100345, 100398
-recovered pasa_asmbl_22727.p1, internal, 100591, 100644
-recovered pasa_asmbl_22727.p1, internal, 100750, 100794
-recovered pasa_asmbl_22727.p1, internal, 100890, 100943
-recovered pasa_asmbl_22727.p1, internal, 101041, 101085
-recovered pasa_asmbl_22727.p1, internal, 101286, 101339
-recovered pasa_asmbl_22727.p1, internal, 101461, 101559
-recovered pasa_asmbl_22727.p1, internal, 101704, 101748
-recovered pasa_asmbl_22727.p1, internal, 102172, 102270
-recovered pasa_asmbl_22727.p1, internal, 102375, 102428
-recovered pasa_asmbl_22727.p1, internal, 102709, 102816
-recovered pasa_asmbl_22727.p1, internal, 102940, 102993
-recovered pasa_asmbl_22727.p1, internal, 103165, 103263
-recovered pasa_asmbl_22727.p1, internal, 103442, 103495
-recovered pasa_asmbl_22727.p1, internal, 103607, 103705
-recovered pasa_asmbl_22727.p1, internal, 103855, 103908
-recovered pasa_asmbl_22727.p1, internal, 104045, 104098
-recovered pasa_asmbl_22727.p1, internal, 104312, 104365
-recovered pasa_asmbl_22727.p1, internal, 104528, 104581
-recovered pasa_asmbl_22727.p1, internal, 104888, 104932
-recovered pasa_asmbl_22727.p1, internal, 105088, 105186
-recovered pasa_asmbl_22727.p1, internal, 105435, 105542
-recovered pasa_asmbl_22727.p1, internal, 105680, 105733
-recovered pasa_asmbl_22727.p1, internal, 105956, 106009
-recovered pasa_asmbl_22727.p1, internal, 106273, 106326
-recovered pasa_asmbl_22727.p1, internal, 106412, 106465
-recovered pasa_asmbl_22727.p1, internal, 106712, 106819
-recovered pasa_asmbl_22727.p1, internal, 106976, 107029
-recovered pasa_asmbl_22727.p1, internal, 107121, 107174
-recovered pasa_asmbl_22727.p1, internal, 107379, 107540
-recovered pasa_asmbl_22727.p1, internal, 107743, 107850
-recovered pasa_asmbl_22727.p1, internal, 108002, 108109
-recovered pasa_asmbl_22727.p1, internal, 108220, 108273
-recovered pasa_asmbl_22727.p1, internal, 108347, 108454
-recovered pasa_asmbl_22727.p1, internal, 108563, 108616
-recovered pasa_asmbl_22727.p1, internal, 108772, 108879
-recovered pasa_asmbl_22727.p1, internal, 109909, 109962
-recovered pasa_asmbl_22727.p1, internal, 110048, 110155
-recovered pasa_asmbl_22727.p1, internal, 110305, 110650
-recovered pasa_asmbl_22727.p1, internal, 110814, 111004
-recovered pasa_asmbl_22727.p1, internal, 111084, 111326
Couldn't classify 44425, 44997
Sorry, prediction pasa_asmbl_22192.p1 fails validation.
(TTC)	 CC	44425-44997	CT	AAC
Valid prediction for GeneMark_model.79137_t
Valid prediction for GeneMark_model.79117_t
Valid prediction for pasa_asmbl_22206.p1
Valid prediction for CodingQuarry_transcript_25624-T1
Valid prediction for GeneMark_model.79139_t
Valid prediction for snap_scaffold_19-snap.1313-T1
Valid prediction for snap_scaffold_19-snap.1294-T1
Valid prediction for HiQ_model.g30178.t1
Valid prediction for CodingQuarry_transcript_25625-T1
Valid prediction for Augustus_model.g30174.t1
Valid prediction for snap_scaffold_19-snap.1310-T1
Valid prediction for GlimmerHMM_glimmerT_45245-T1
Valid prediction for GeneMark_model.79110_t
Valid prediction for GeneMark_model.79125_t
Valid prediction for GeneMark_model.79113_t
Valid prediction for GeneMark_model.79122_t
Valid prediction for GeneMark_model.79119_t
Valid prediction for snap_scaffold_19-snap.1302-T1
Valid prediction for snap_scaffold_19-snap.1323-T1
Valid prediction for GeneMark_model.79123_t
Valid prediction for snap_scaffold_19-snap.1309-T1
Valid prediction for snap_scaffold_19-snap.1311-T1
Valid prediction for GeneMark_model.79121_t
Valid prediction for snap_scaffold_19-snap.1322-T1
Valid prediction for HiQ_model.g30173.t1
Valid prediction for GeneMark_model.79124_t
Valid prediction for GlimmerHMM_glimmerT_45256-T1
Couldn't classify 58902, 59078
Sorry, prediction pasa_asmbl_22702.p1 fails validation.
(ATG)	 AG	57376-57684	GT	AGG
(GCC)	 AG	58647-58820	GT	AGG
(CTG)	 AG	58902-59078	AG	AGA
-recovered pasa_asmbl_22702.p1, initial, 57376, 57684
-recovered pasa_asmbl_22702.p1, internal, 57376, 57684
-recovered pasa_asmbl_22702.p1, internal, 58647, 58820
Valid prediction for Augustus_model.g30182.t1
Valid prediction for Augustus_model.g30177.t1
Valid prediction for GlimmerHMM_glimmerT_45249-T1
Valid prediction for GlimmerHMM_glimmerT_45247-T1
Valid prediction for GeneMark_model.79141_t
Valid prediction for GlimmerHMM_glimmerT_45253-T1
Valid prediction for snap_scaffold_19-snap.1306-T1
Valid prediction for GlimmerHMM_glimmerT_45254-T1
Valid prediction for GlimmerHMM_glimmerT_45263-T1
Valid prediction for GeneMark_model.79116_t
Valid prediction for GeneMark_model.79130_t
Valid prediction for GlimmerHMM_glimmerT_45239-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 GeneMark_model.79126_t
Valid prediction for GeneMark_model.79134_t
Valid prediction for GeneMark_model.79114_t
Valid prediction for snap_scaffold_19-snap.1295-T1
Valid prediction for CodingQuarry_transcript_25620-T1
Valid prediction for snap_scaffold_19-snap.1298-T1
Valid prediction for GlimmerHMM_glimmerT_45238-T1
Valid prediction for Augustus_model.g30185.t1
Valid prediction for GlimmerHMM_glimmerT_45246-T1
Valid prediction for GlimmerHMM_glimmerT_45244-T1
Couldn't classify 121441, 121584
Sorry, prediction pasa_asmbl_21406.p1 fails validation.
(AGG)	 TC	121441-121584	GT	GGG
(TTT)	 AG	121706-121823	GT	AGG
(ACA)	 AG	121964-122107	GT	AGG
(ATG)	 AG	122293-122594	AG	GAA
add_exon() Sorry, pasa_asmbl_21406.p1 121706-121823-terminal-3 is invalid.
-recovered pasa_asmbl_21406.p1, terminal, 121706, 121823
-recovered pasa_asmbl_21406.p1, terminal, 122293, 122594
-recovered pasa_asmbl_21406.p1, internal, 121706, 121823
-recovered pasa_asmbl_21406.p1, internal, 121964, 122107
Valid prediction for GeneMark_model.79135_t
Valid prediction for GlimmerHMM_glimmerT_45240-T1
Valid prediction for GlimmerHMM_glimmerT_45262-T1
Valid prediction for GeneMark_model.79120_t
Valid prediction for Augustus_model.g30172.t1
Valid prediction for snap_scaffold_19-snap.1320-T1
Valid prediction for GlimmerHMM_glimmerT_45250-T1
Valid prediction for CodingQuarry_transcript_25629-T1
Valid prediction for Augustus_model.g30183.t1
Valid prediction for GeneMark_model.79112_t
Valid prediction for snap_scaffold_19-snap.1319-T1
Valid prediction for GlimmerHMM_glimmerT_45261-T1
Valid prediction for snap_scaffold_19-snap.1297-T1
Sorry, intron length (5) is less than minimum required (10)
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for GeneMark_model.79128_t
Valid prediction for GeneMark_model.79109_t
Valid prediction for Augustus_model.g30187.t1
Couldn't classify 173835, 174260
Sorry, prediction pasa_asmbl_21402.p1 fails validation.
(CAG)	 CA	173835-174260	AC	GAA
Valid prediction for snap_scaffold_19-snap.1300-T1
Valid prediction for CodingQuarry_transcript_25627-T1
Couldn't classify 195961, 196656
Sorry, prediction pasa_asmbl_21400.p1 fails validation.
(GGT)	 TT	195961-196656	AC	AAA
Valid prediction for snap_scaffold_19-snap.1299-T1
Valid prediction for GlimmerHMM_glimmerT_45259-T1
Valid prediction for GlimmerHMM_glimmerT_45255-T1
Couldn't classify 194344, 194515
Couldn't classify 194726, 195834
Sorry, prediction pasa_asmbl_21401.p1 fails validation.
(CAG)	 CA	194344-194515	GT	AGG
(GTG)	 AG	194726-195834	GG	AAG
Valid prediction for snap_scaffold_19-snap.1321-T1
Valid prediction for GlimmerHMM_glimmerT_45252-T1
Valid prediction for HiQ_model.g30186.t1
Valid prediction for HiQ_model.g30169.t1
Valid prediction for GlimmerHMM_glimmerT_45258-T1
Valid prediction for GlimmerHMM_glimmerT_45241-T1
Valid prediction for snap_scaffold_19-snap.1304-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_19-snap.1303-T1
Valid prediction for snap_scaffold_19-snap.1317-T1
Valid prediction for Augustus_model.g30184.t1
Valid prediction for snap_scaffold_19-snap.1316-T1
Valid prediction for pasa_asmbl_21399.p1
Valid prediction for HiQ_model.g30180.t1
Valid prediction for Augustus_model.g30170.t1
Valid prediction for GeneMark_model.79111_t
Valid prediction for Augustus_model.g30176.t1
Valid prediction for snap_scaffold_19-snap.1301-T1
Valid prediction for GeneMark_model.79136_t
Valid prediction for GeneMark_model.79138_t
Valid prediction for snap_scaffold_19-snap.1296-T1
Valid prediction for GeneMark_model.79140_t
Valid prediction for Augustus_model.g30168.t1
Valid prediction for snap_scaffold_19-snap.1318-T1
Valid prediction for GeneMark_model.79132_t
Valid prediction for GeneMark_model.79131_t
Valid prediction for Augustus_model.g30171.t1
Valid prediction for GlimmerHMM_glimmerT_45243-T1
Valid prediction for Augustus_model.g30166.t1
Valid prediction for snap_scaffold_19-snap.1307-T1
Couldn't classify 95610, 95672
Sorry, prediction pasa_asmbl_21408.p1 fails validation.
(GAT)	 CA	95610-95672	GT	AGG
(TTC)	 AG	96032-96103	GT	AGG
(TTT)	 AG	96212-96310	GT	AAG
(GAC)	 AG	96458-96595	GT	GTG
(GCT)	 AG	96819-96935	GT	GAG
(ATT)	 AG	97145-97222	GT	CGG
(GCA)	 AG	98040-98190	GT	AGG
(ACG)	 AG	98277-98371	GT	AGG
(GAG)	 AG	98920-98991	TA	GAT
-recovered pasa_asmbl_21408.p1, terminal, 98920, 98991
-recovered pasa_asmbl_21408.p1, internal, 96032, 96103
-recovered pasa_asmbl_21408.p1, internal, 96212, 96310
-recovered pasa_asmbl_21408.p1, internal, 96458, 96595
-recovered pasa_asmbl_21408.p1, internal, 96819, 96935
-recovered pasa_asmbl_21408.p1, internal, 97145, 97222
-recovered pasa_asmbl_21408.p1, internal, 98040, 98190
-recovered pasa_asmbl_21408.p1, internal, 98277, 98371
Valid prediction for GeneMark_model.79115_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 44945, rend_intergenic: 43841  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 210714, rend_intergenic: 197181  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 212217
-exon list size: 543


building trellis

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70.6    
70.8    
71.0    
71.2    
71.4    
71.6    
71.7    
71.9    
72.1    
72.3    
72.5    
72.7    
72.8    
73.0    
73.2    
73.4    
73.6    
73.8    
73.9    
74.1    
74.3    
74.5    
74.7    
74.9    
75.0    
75.2    
75.4    
75.6    
75.8    
76.0    
76.1    
76.3    
76.5    
76.7    
76.9    
77.1    
77.2    
77.4    
77.6    
77.8    
78.0    
78.2    
78.3    
78.5    
78.7    
78.9    
79.1    
79.3    
79.4    
79.6    
79.8    
80.0    
80.2    
80.4    
80.6    
80.7    
80.9    
81.1    
81.3    
81.5    
81.7    
81.8    
82.0    
82.2    
82.4    
82.6    
82.8    
82.9    
83.1    
83.3    
83.5    
83.7    
83.9    
84.0    
84.2    
84.4    
84.6    
84.8    
85.0    
85.1    
85.3    
85.5    
85.7    
85.9    
86.1    
86.2    
86.4    
86.6    
86.8    
87.0    
87.2    
87.3    
87.5    
87.7    
87.9    
88.1    
88.3    
88.4    
88.6    
88.8    
89.0    
89.2    
89.4    
89.5    
89.7    
89.9    
90.1    
90.3    
90.5    
90.6    
90.8    
91.0    
91.2    
91.4    
91.6    
91.7    
91.9    
92.1    
92.3    
92.5    
92.7    
92.8    
93.0    
93.2    
93.4    
93.6    
93.8    
93.9    
94.1    
94.3    
94.5    
94.7    
94.9    
95.0    
95.2    
95.4    
95.6    
95.8    
96.0    
96.1    
96.3    
96.5    
96.7    
96.9    
97.1    
97.2    
97.4    
97.6    
97.8    
98.0    
98.2    
98.3    
98.5    
98.7    
98.9    
99.1    
99.3    
99.4    
99.6    
99.8    
-found 25 predictions from path traversal
Error with prediction: snap lend_intergenic: 44945, rend_intergenic: 43841  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 210714, rend_intergenic: 197181  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

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