-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_18/scaffold_18_5450915-5610032

-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.74810_t
Valid prediction for snap_scaffold_18-snap.1146-T1
Valid prediction for GlimmerHMM_glimmerT_43358-T1
Valid prediction for GeneMark_model.74812_t
Valid prediction for snap_scaffold_18-snap.1152-T1
Valid prediction for GeneMark_model.74840_t
Valid prediction for GlimmerHMM_glimmerT_43369-T1
Valid prediction for snap_scaffold_18-snap.1145-T1
Valid prediction for GlimmerHMM_glimmerT_43353-T1
Valid prediction for Augustus_model.g29009.t1
Valid prediction for snap_scaffold_18-snap.1166-T1
Valid prediction for snap_scaffold_18-snap.1154-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for Augustus_model.g29011.t1
Valid prediction for snap_scaffold_18-snap.1149-T1
Valid prediction for GeneMark_model.74814_t
Valid prediction for GeneMark_model.74832_t
Valid prediction for GlimmerHMM_glimmerT_43351-T1
Valid prediction for GlimmerHMM_glimmerT_43372-T1
Valid prediction for snap_scaffold_18-snap.1150-T1
Valid prediction for HiQ_model.g29027.t1
Valid prediction for GlimmerHMM_glimmerT_43360-T1
Valid prediction for Augustus_model.g29013.t1
Valid prediction for GlimmerHMM_glimmerT_43356-T1
Valid prediction for Augustus_model.g29006.t1
Valid prediction for GeneMark_model.74826_t
Valid prediction for GeneMark_model.74834_t
Valid prediction for GeneMark_model.74831_t
Valid prediction for GlimmerHMM_glimmerT_43362-T1
Valid prediction for GeneMark_model.74820_t
Valid prediction for snap_scaffold_18-snap.1147-T1
Valid prediction for CodingQuarry_transcript_23719-T1
Valid prediction for pasa_asmbl_20623.p1
Valid prediction for snap_scaffold_18-snap.1151-T1
Valid prediction for GeneMark_model.74829_t
Valid prediction for Augustus_model.g29024.t1
Valid prediction for GeneMark_model.74824_t
Valid prediction for snap_scaffold_18-snap.1156-T1
Valid prediction for GeneMark_model.74816_t
Valid prediction for Augustus_model.g29007.t1
Valid prediction for pasa_asmbl_20618.p1
Valid prediction for CodingQuarry_transcript_23716-T1
Valid prediction for snap_scaffold_18-snap.1168-T1
Valid prediction for snap_scaffold_18-snap.1172-T1
Valid prediction for HiQ_model.g29014.t1
Valid prediction for GeneMark_model.74848_t
Valid prediction for HiQ_model.g29029.t1
Valid prediction for GeneMark_model.74828_t
Valid prediction for GeneMark_model.74836_t
Valid prediction for GeneMark_model.74822_t
Valid prediction for snap_scaffold_18-snap.1141-T1
Valid prediction for snap_scaffold_18-snap.1153-T1
Valid prediction for CodingQuarry_transcript_23713-T1
Valid prediction for GeneMark_model.74846_t
Valid prediction for snap_scaffold_18-snap.1173-T1
Valid prediction for GeneMark_model.74844_t
Valid prediction for snap_scaffold_18-snap.1170-T1
Valid prediction for GeneMark_model.74808_t
Valid prediction for snap_scaffold_18-snap.1158-T1
Valid prediction for Augustus_model.g29016.t1
Valid prediction for GeneMark_model.74817_t
Couldn't classify 153803, 153838
Sorry, prediction pasa_asmbl_20627.p2 fails validation.
(CAG)	 GG	153803-153838	GT	CAG
(CTT)	 AG	154587-154766	GT	TGG
(GTG)	 AG	154976-155105	GT	CTG
(ACC)	 AG	155449-155558	GT	ACG
(GAC)	 AG	155935-156027	AG	AAA
-recovered pasa_asmbl_20627.p2, terminal, 155935, 156027
-recovered pasa_asmbl_20627.p2, internal, 154587, 154766
-recovered pasa_asmbl_20627.p2, internal, 154976, 155105
-recovered pasa_asmbl_20627.p2, internal, 155449, 155558
Valid prediction for GlimmerHMM_glimmerT_43375-T1
Valid prediction for Augustus_model.g29017.t1
Valid prediction for GlimmerHMM_glimmerT_43354-T1
Valid prediction for GlimmerHMM_glimmerT_43364-T1
Valid prediction for snap_scaffold_18-snap.1143-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_43352-T1
Valid prediction for snap_scaffold_18-snap.1142-T1
Valid prediction for Augustus_model.g29015.t1
Valid prediction for Augustus_model.g29008.t1
Valid prediction for GlimmerHMM_glimmerT_43368-T1
Valid prediction for snap_scaffold_18-snap.1140-T1
Valid prediction for CodingQuarry_transcript_23714-T1
Valid prediction for HiQ_model.g29026.t1
Valid prediction for GlimmerHMM_glimmerT_43349-T1
Valid prediction for GeneMark_model.74842_t
Valid prediction for GlimmerHMM_glimmerT_43355-T1
Couldn't classify 68010, 68135
Sorry, prediction pasa_asmbl_19882.p1 fails validation.
(TAT)	 AC	68010-68135	GT	AGG
(CTG)	 AG	68453-68530	GT	AGG
(CAA)	 AG	68654-68755	GT	AGG
(GTG)	 AG	69143-69283	GT	GCG
(GTG)	 AG	69463-69651	GT	GGG
(GTG)	 AG	70658-70817	GT	AGG
(ACC)	 AG	71036-71191	GT	AGG
(ACA)	 AG	71869-71909	CA	AGC
-recovered pasa_asmbl_19882.p1, terminal, 71869, 71909
-recovered pasa_asmbl_19882.p1, internal, 68453, 68530
-recovered pasa_asmbl_19882.p1, internal, 68654, 68755
-recovered pasa_asmbl_19882.p1, internal, 69143, 69283
-recovered pasa_asmbl_19882.p1, internal, 69463, 69651
-recovered pasa_asmbl_19882.p1, internal, 70658, 70817
-recovered pasa_asmbl_19882.p1, internal, 71036, 71191
Valid prediction for snap_scaffold_18-snap.1144-T1
Valid prediction for Augustus_model.g29018.t1
Valid prediction for GlimmerHMM_glimmerT_43363-T1
Valid prediction for snap_scaffold_18-snap.1159-T1
Valid prediction for snap_scaffold_18-snap.1160-T1
Valid prediction for Augustus_model.g29021.t1
Valid prediction for GlimmerHMM_glimmerT_43370-T1
Valid prediction for GeneMark_model.74807_t
Valid prediction for GlimmerHMM_glimmerT_43350-T1
Valid prediction for GlimmerHMM_glimmerT_43374-T1
Valid prediction for GlimmerHMM_glimmerT_43357-T1
Valid prediction for GlimmerHMM_glimmerT_43361-T1
Valid prediction for GeneMark_model.74833_t
Valid prediction for snap_scaffold_18-snap.1167-T1
Valid prediction for GeneMark_model.74839_t
Valid prediction for GlimmerHMM_glimmerT_43359-T1
Valid prediction for GlimmerHMM_glimmerT_43365-T1
Valid prediction for CodingQuarry_transcript_23718-T1
Valid prediction for GeneMark_model.74815_t
Valid prediction for GeneMark_model.74835_t
Valid prediction for GlimmerHMM_glimmerT_43366-T1
Valid prediction for pasa_asmbl_19902.p1
Valid prediction for snap_scaffold_18-snap.1155-T1
Valid prediction for snap_scaffold_18-snap.1139-T1
Valid prediction for HiQ_model.g29025.t1
Couldn't classify 27175, 27553
Sorry, prediction pasa_asmbl_19898.p1 fails validation.
(CAC)	 GT	27175-27553	GT	TGG
(GCT)	 AG	29969-30117	GT	AGG
(ATC)	 AG	31457-31477	AT	GAA
-recovered pasa_asmbl_19898.p1, terminal, 31457, 31477
-recovered pasa_asmbl_19898.p1, internal, 29969, 30117
Valid prediction for GeneMark_model.74830_t
Valid prediction for Augustus_model.g29005.t1
Valid prediction for GlimmerHMM_glimmerT_43371-T1
Valid prediction for GeneMark_model.74823_t
Valid prediction for snap_scaffold_18-snap.1165-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_18-snap.1169-T1
Valid prediction for GlimmerHMM_glimmerT_43348-T1
Valid prediction for GeneMark_model.74843_t
Couldn't classify 33806, 34360
Sorry, prediction pasa_asmbl_19896.p1 fails validation.
(ACT)	 GG	33806-34360	AT	AGA
Valid prediction for GeneMark_model.74819_t
Valid prediction for GeneMark_model.74845_t
Valid prediction for Augustus_model.g29022.t1
Valid prediction for GeneMark_model.74821_t
Valid prediction for Augustus_model.g29028.t1
Valid prediction for GeneMark_model.74809_t
Valid prediction for snap_scaffold_18-snap.1164-T1
Valid prediction for snap_scaffold_18-snap.1148-T1
Valid prediction for GeneMark_model.74837_t
Valid prediction for GeneMark_model.74838_t
Valid prediction for GeneMark_model.74827_t
Couldn't classify 74322, 74621
Sorry, prediction pasa_asmbl_19879.p1 fails validation.
(ATG)	 TA	74322-74621	AC	ACA
Valid prediction for CodingQuarry_transcript_23717-T1
Couldn't classify 33170, 33484
Sorry, prediction pasa_asmbl_19897.p1 fails validation.
(GAG)	 AC	33170-33484	AT	GCA
Valid prediction for GeneMark_model.74818_t
Valid prediction for snap_scaffold_18-snap.1157-T1
Valid prediction for snap_scaffold_18-snap.1171-T1
Valid prediction for CodingQuarry_transcript_23715-T1
Valid prediction for GeneMark_model.74813_t
Valid prediction for GeneMark_model.74806_t
Valid prediction for GeneMark_model.74825_t
Valid prediction for Augustus_model.g29003.t1
Valid prediction for GlimmerHMM_glimmerT_43373-T1
Couldn't classify 10046, 10211
Sorry, prediction pasa_asmbl_19908.p1 fails validation.
(ATG)	 CG	8622-8701	GT	AGG
(TGA)	 AG	8959-9015	GT	AGG
(ACA)	 AG	9135-9204	GT	AGG
(CTG)	 AG	9345-9563	GT	AGG
(GAG)	 AG	9757-9941	GT	AGG
(GTT)	 AG	10046-10211	CA	AGC
-recovered pasa_asmbl_19908.p1, initial, 8622, 8701
-recovered pasa_asmbl_19908.p1, internal, 8959, 9015
-recovered pasa_asmbl_19908.p1, internal, 9135, 9204
-recovered pasa_asmbl_19908.p1, internal, 9345, 9563
-recovered pasa_asmbl_19908.p1, internal, 9757, 9941
Couldn't classify 14352, 14439
Sorry, prediction pasa_asmbl_19907.p1 fails validation.
(CTG)	 CC	14352-14439	GT	GGG
(GGG)	 AG	14620-14736	GT	GGG
(GAG)	 AG	14838-14953	GT	TGG
(ACG)	 AG	15076-15123	GT	GGG
(GGT)	 AG	15229-15300	GT	AGG
(GAA)	 AG	15414-15470	GT	AGG
(GCA)	 AG	15606-15632	AA	AAA
-recovered pasa_asmbl_19907.p1, terminal, 15606, 15632
-recovered pasa_asmbl_19907.p1, internal, 14620, 14736
-recovered pasa_asmbl_19907.p1, internal, 14838, 14953
-recovered pasa_asmbl_19907.p1, internal, 15076, 15123
-recovered pasa_asmbl_19907.p1, internal, 15229, 15300
-recovered pasa_asmbl_19907.p1, internal, 15414, 15470
Valid prediction for snap_scaffold_18-snap.1162-T1
Valid prediction for snap_scaffold_18-snap.1161-T1
Valid prediction for Augustus_model.g29012.t1
Valid prediction for GeneMark_model.74847_t
Valid prediction for Augustus_model.g29004.t1
Couldn't classify 44012, 44171
Sorry, prediction pasa_asmbl_19890.p2 fails validation.
(GTG)	 AG	44012-44171	GT	AGG
(ACC)	 AG	44433-44588	GT	AGG
(GAT)	 AG	45057-45091	TT	GAT
-recovered pasa_asmbl_19890.p2, terminal, 45057, 45091
-recovered pasa_asmbl_19890.p2, internal, 44012, 44171
-recovered pasa_asmbl_19890.p2, internal, 44433, 44588
Valid prediction for Augustus_model.g29010.t1
Valid prediction for HiQ_model.g29019.t1
Valid prediction for GeneMark_model.74841_t
Valid prediction for GeneMark_model.74811_t
Valid prediction for snap_scaffold_18-snap.1163-T1
Valid prediction for Augustus_model.g29020.t1
Valid prediction for Augustus_model.g29023.t1
Valid prediction for CodingQuarry_transcript_23720-T1
Valid prediction for GlimmerHMM_glimmerT_43367-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 17172, rend_intergenic: 7984  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25773, rend_intergenic: 24130  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32549, rend_intergenic: 26025  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41600, rend_intergenic: 40597  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102735, rend_intergenic: 100270  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131710, rend_intergenic: 129063  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151207, rend_intergenic: 145613  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 159118
-exon list size: 647


building trellis

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87.4    
87.5    
87.7    
87.8    
88.0    
88.1    
88.3    
88.4    
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    
90.8    
90.9    
91.1    
91.2    
91.4    
91.5    
91.7    
91.8    
92.0    
92.1    
92.3    
92.4    
92.6    
92.8    
92.9    
93.1    
93.2    
93.4    
93.5    
93.7    
93.8    
94.0    
94.1    
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    
96.5    
96.6    
96.8    
96.9    
97.1    
97.2    
97.4    
97.5    
97.7    
97.8    
98.0    
98.2    
98.3    
98.5    
98.6    
98.8    
98.9    
99.1    
99.2    
99.4    
99.5    
99.7    
99.8    
-found 35 predictions from path traversal
Error with prediction: snap lend_intergenic: 17172, rend_intergenic: 7984  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25773, rend_intergenic: 24130  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32549, rend_intergenic: 26025  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41600, rend_intergenic: 40597  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102735, rend_intergenic: 100270  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131710, rend_intergenic: 129063  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151207, rend_intergenic: 145613  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 24 predictions persist after filtering for low support