-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_5/scaffold_5_4920450-5088887

-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 GlimmerHMM_glimmerT_12152-T1
Valid prediction for GlimmerHMM_glimmerT_12129-T1
Couldn't classify 130197, 130298
Sorry, prediction pasa_asmbl_43999.p1 fails validation.
(GCT)	 TA	130197-130298	GT	AGG
(GTG)	 AG	130654-130802	GT	GCG
(CTA)	 AG	131340-131399	GT	TTG
(ATA)	 AG	133543-133590	GT	GCG
(GTA)	 AG	135142-135243	GT	AGG
(AAA)	 AG	137085-137133	GT	AGG
(GTG)	 AG	137560-137640	AG	GAA
-recovered pasa_asmbl_43999.p1, terminal, 137560, 137640
-recovered pasa_asmbl_43999.p1, internal, 130654, 130802
-recovered pasa_asmbl_43999.p1, internal, 131340, 131399
-recovered pasa_asmbl_43999.p1, internal, 133543, 133590
-recovered pasa_asmbl_43999.p1, internal, 135142, 135243
-recovered pasa_asmbl_43999.p1, internal, 137085, 137133
Valid prediction for Augustus_model.g7995.t1
Valid prediction for GeneMark_model.20539_t
Valid prediction for CodingQuarry_transcript_51930-T1
Couldn't classify 28314, 28329
Sorry, prediction pasa_asmbl_43984.p1 fails validation.
(CCA)	 GG	28314-28329	GT	CGG
(ATC)	 AG	28672-28756	GT	TGG
(CTC)	 AG	28899-28962	GT	AGG
(GTT)	 AG	29164-29235	GT	TGG
(GGC)	 AG	29447-29502	GT	AAG
(GAC)	 AG	30024-30033	AG	AAA
-recovered pasa_asmbl_43984.p1, terminal, 30024, 30033
-recovered pasa_asmbl_43984.p1, internal, 28672, 28756
-recovered pasa_asmbl_43984.p1, internal, 28899, 28962
-recovered pasa_asmbl_43984.p1, internal, 29164, 29235
-recovered pasa_asmbl_43984.p1, internal, 29447, 29502
Valid prediction for Augustus_model.g8003.t1
Valid prediction for GlimmerHMM_glimmerT_12149-T1
Valid prediction for HiQ_model.g8004.t1
Valid prediction for snap_scaffold_5-snap.1007-T1
Valid prediction for GeneMark_model.20517_t
Valid prediction for GlimmerHMM_glimmerT_12142-T1
Valid prediction for GlimmerHMM_glimmerT_12140-T1
Valid prediction for Augustus_model.g7998.t1
Valid prediction for Augustus_model.g7997.t1
Valid prediction for GeneMark_model.20540_t
Valid prediction for snap_scaffold_5-snap.986-T1
Valid prediction for snap_scaffold_5-snap.990-T1
Valid prediction for snap_scaffold_5-snap.1005-T1
Valid prediction for CodingQuarry_transcript_51925-T1
Valid prediction for GeneMark_model.20527_t
Valid prediction for snap_scaffold_5-snap.1018-T1
Valid prediction for Augustus_model.g7999.t1
Valid prediction for GlimmerHMM_glimmerT_12128-T1
Valid prediction for GlimmerHMM_glimmerT_12145-T1
Valid prediction for GlimmerHMM_glimmerT_12139-T1
Valid prediction for snap_scaffold_5-snap.1009-T1
Valid prediction for snap_scaffold_5-snap.995-T1
Valid prediction for CodingQuarry_transcript_51928-T1
Valid prediction for snap_scaffold_5-snap.1011-T1
Valid prediction for CodingQuarry_transcript_51927-T1
Valid prediction for GlimmerHMM_glimmerT_12148-T1
Valid prediction for CodingQuarry_transcript_51931-T1
Valid prediction for Augustus_model.g8007.t1
Valid prediction for pasa_asmbl_43991.p1
Valid prediction for HiQ_model.g8002.t1
Valid prediction for GlimmerHMM_glimmerT_12133-T1
Valid prediction for GlimmerHMM_glimmerT_12143-T1
Valid prediction for GlimmerHMM_glimmerT_12137-T1
Valid prediction for GlimmerHMM_glimmerT_12146-T1
Valid prediction for GeneMark_model.20523_t
Valid prediction for snap_scaffold_5-snap.993-T1
Valid prediction for CodingQuarry_transcript_51932-T1
Valid prediction for GlimmerHMM_glimmerT_12134-T1
Valid prediction for GlimmerHMM_glimmerT_12138-T1
Valid prediction for Augustus_model.g7996.t1
Valid prediction for GeneMark_model.20544_t
Valid prediction for GeneMark_model.20513_t
Valid prediction for snap_scaffold_5-snap.984-T1
Valid prediction for GeneMark_model.20532_t
Valid prediction for GeneMark_model.20501_t
Valid prediction for snap_scaffold_5-snap.992-T1
Valid prediction for CodingQuarry_transcript_51924-T1
Couldn't classify 102602, 102824
Couldn't classify 103058, 103167
Sorry, prediction pasa_asmbl_45088.p2 fails validation.
(GAG)	 AC	102602-102824	GT	AGG
(TTG)	 AG	103058-103167	GG	GGG
Valid prediction for GeneMark_model.20541_t
Valid prediction for GlimmerHMM_glimmerT_12147-T1
Valid prediction for GlimmerHMM_glimmerT_12144-T1
Valid prediction for GeneMark_model.20493_t
Valid prediction for snap_scaffold_5-snap.1012-T1
Valid prediction for pasa_asmbl_44006.p1
Valid prediction for GeneMark_model.20511_t
Valid prediction for GeneMark_model.20506_t
Couldn't classify 124318, 124565
Sorry, prediction CodingQuarry_transcript_51929-T1 fails validation.
(ATG)	 GG	120155-120328	GT	AGG
(CCT)	 AG	122566-122720	GT	GGG
(CTT)	 AG	122910-123084	GT	AGG
(TCG)	 AG	123225-123320	GT	AGG
(GAG)	 AG	123432-123665	GT	AGG
(AGT)	 AG	123904-123926	GT	AAG
(GGT)	 AG	124058-124179	GT	AGG
(TTG)	 AG	124318-124565	GA	TAG
(GAG)	 AG	124602-124691	GT	AGG
(GCA)	 AG	126012-126098	CG	AAC
-recovered CodingQuarry_transcript_51929-T1, initial, 120155, 120328
-recovered CodingQuarry_transcript_51929-T1, terminal, 126012, 126098
-recovered CodingQuarry_transcript_51929-T1, internal, 122566, 122720
-recovered CodingQuarry_transcript_51929-T1, internal, 122910, 123084
-recovered CodingQuarry_transcript_51929-T1, internal, 123225, 123320
-recovered CodingQuarry_transcript_51929-T1, internal, 123432, 123665
-recovered CodingQuarry_transcript_51929-T1, internal, 123904, 123926
-recovered CodingQuarry_transcript_51929-T1, internal, 124058, 124179
-recovered CodingQuarry_transcript_51929-T1, internal, 124602, 124691
Valid prediction for snap_scaffold_5-snap.989-T1
Valid prediction for GeneMark_model.20536_t
Valid prediction for GeneMark_model.20504_t
Valid prediction for GeneMark_model.20490_t
Valid prediction for GeneMark_model.20499_t
Valid prediction for pasa_asmbl_43989.p1
Valid prediction for Augustus_model.g7992.t1
Valid prediction for GeneMark_model.20525_t
Valid prediction for GlimmerHMM_glimmerT_12130-T1
Valid prediction for GeneMark_model.20498_t
Valid prediction for GeneMark_model.20529_t
Couldn't classify 115884, 116054
Couldn't classify 116249, 116347
Sorry, prediction CodingQuarry_transcript_51926-T1 fails validation.
(ATG)	 TC	114248-114354	GT	AGG
(GAA)	 AG	115495-115708	GT	AGG
(GCC)	 AG	115884-116054	GG	GAG
(GGT)	 AT	116249-116347	AC	AGA
-recovered CodingQuarry_transcript_51926-T1, initial, 114248, 114354
-recovered CodingQuarry_transcript_51926-T1, internal, 115495, 115708
Valid prediction for snap_scaffold_5-snap.1014-T1
Valid prediction for snap_scaffold_5-snap.1022-T1
Valid prediction for GeneMark_model.20534_t
Valid prediction for snap_scaffold_5-snap.1020-T1
Valid prediction for Augustus_model.g7994.t1
Valid prediction for Augustus_model.g8005.t1
Valid prediction for GeneMark_model.20521_t
Valid prediction for snap_scaffold_5-snap.1008-T1
Valid prediction for GeneMark_model.20515_t
Valid prediction for GeneMark_model.20508_t
Valid prediction for GeneMark_model.20519_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.20510_t
Valid prediction for Augustus_model.g8009.t1
Valid prediction for snap_scaffold_5-snap.1016-T1
Valid prediction for GeneMark_model.20492_t
Valid prediction for snap_scaffold_5-snap.1001-T1
Valid prediction for GeneMark_model.20496_t
Valid prediction for snap_scaffold_5-snap.1003-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_5-snap.994-T1
Valid prediction for GeneMark_model.20516_t
Valid prediction for snap_scaffold_5-snap.1021-T1
Valid prediction for GeneMark_model.20542_t
Valid prediction for GlimmerHMM_glimmerT_12131-T1
Valid prediction for GeneMark_model.20528_t
Valid prediction for GeneMark_model.20514_t
Valid prediction for GeneMark_model.20520_t
Valid prediction for snap_scaffold_5-snap.1010-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GeneMark_model.20509_t
Valid prediction for GeneMark_model.20502_t
Valid prediction for GlimmerHMM_glimmerT_12153-T1
Valid prediction for GlimmerHMM_glimmerT_12135-T1
Valid prediction for GlimmerHMM_glimmerT_12136-T1
Valid prediction for pasa_asmbl_45409.p2
Valid prediction for GlimmerHMM_glimmerT_12132-T1
Valid prediction for GeneMark_model.20533_t
Valid prediction for GeneMark_model.20507_t
Valid prediction for pasa_asmbl_45408.p1
Valid prediction for GeneMark_model.20546_t
Valid prediction for snap_scaffold_5-snap.983-T1
Valid prediction for Augustus_model.g7993.t1
Valid prediction for GeneMark_model.20495_t
Valid prediction for snap_scaffold_5-snap.1006-T1
Valid prediction for pasa_asmbl_45414.p1
Valid prediction for GeneMark_model.20543_t
Valid prediction for CodingQuarry_transcript_51934-T1
Valid prediction for GeneMark_model.20524_t
Valid prediction for GeneMark_model.20497_t
Valid prediction for snap_scaffold_5-snap.1013-T1
Valid prediction for GeneMark_model.20537_t
Valid prediction for GeneMark_model.20500_t
Valid prediction for GlimmerHMM_glimmerT_12154-T1
Valid prediction for GeneMark_model.20530_t
Valid prediction for snap_scaffold_5-snap.988-T1
Valid prediction for snap_scaffold_5-snap.1004-T1
Valid prediction for snap_scaffold_5-snap.987-T1
Valid prediction for GeneMark_model.20518_t
Valid prediction for snap_scaffold_5-snap.996-T1
Valid prediction for GlimmerHMM_glimmerT_12151-T1
Valid prediction for CodingQuarry_transcript_51933-T1
Valid prediction for GeneMark_model.20491_t
Valid prediction for snap_scaffold_5-snap.1017-T1
Valid prediction for GeneMark_model.20535_t
Valid prediction for GeneMark_model.20505_t
Valid prediction for GeneMark_model.20531_t
Valid prediction for HiQ_model.g8000.t1
Valid prediction for snap_scaffold_5-snap.997-T1
Valid prediction for Augustus_model.g8008.t1
Valid prediction for snap_scaffold_5-snap.999-T1
Valid prediction for GeneMark_model.20538_t
Valid prediction for snap_scaffold_5-snap.1019-T1
Valid prediction for HiQ_model.g8006.t1
Valid prediction for GeneMark_model.20512_t
Valid prediction for GeneMark_model.20526_t
Valid prediction for snap_scaffold_5-snap.985-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for snap_scaffold_5-snap.1002-T1
Valid prediction for Augustus_model.g8001.t1
Valid prediction for snap_scaffold_5-snap.1015-T1
Valid prediction for GeneMark_model.20503_t
Valid prediction for GeneMark_model.20494_t
Valid prediction for snap_scaffold_5-snap.991-T1
Valid prediction for GlimmerHMM_glimmerT_12150-T1
Valid prediction for GeneMark_model.20522_t
Valid prediction for GlimmerHMM_glimmerT_12141-T1
Valid prediction for snap_scaffold_5-snap.1000-T1
Valid prediction for snap_scaffold_5-snap.998-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 8196, rend_intergenic: 4799  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18086, rend_intergenic: 13506  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35289, rend_intergenic: 31472  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47073, rend_intergenic: 38280  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47712, rend_intergenic: 47397  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54130, rend_intergenic: 48146  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103544, rend_intergenic: 54143  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107765, rend_intergenic: 105204  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117079, rend_intergenic: 110428  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135856, rend_intergenic: 132901  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153992, rend_intergenic: 150131  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156917, rend_intergenic: 155259  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163333, rend_intergenic: 160401  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166201, rend_intergenic: 164086  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 168438
-exon list size: 876


building trellis

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60.7    
60.8    
60.9    
61.0    
61.2    
61.3    
61.4    
61.5    
61.6    
61.7    
61.8    
62.0    
62.1    
62.2    
62.3    
62.4    
62.5    
62.6    
62.8    
62.9    
63.0    
63.1    
63.2    
63.3    
63.4    
63.6    
63.7    
63.8    
63.9    
64.0    
64.1    
64.2    
64.4    
64.5    
64.6    
64.7    
64.8    
64.9    
65.0    
65.1    
65.3    
65.4    
65.5    
65.6    
65.7    
65.8    
65.9    
66.1    
66.2    
66.3    
66.4    
66.5    
66.6    
66.7    
66.9    
67.0    
67.1    
67.2    
67.3    
67.4    
67.5    
67.7    
67.8    
67.9    
68.0    
68.1    
68.2    
68.3    
68.5    
68.6    
68.7    
68.8    
68.9    
69.0    
69.1    
69.2    
69.4    
69.5    
69.6    
69.7    
69.8    
69.9    
70.0    
70.2    
70.3    
70.4    
70.5    
70.6    
70.7    
70.8    
71.0    
71.1    
71.2    
71.3    
71.4    
71.5    
71.6    
71.8    
71.9    
72.0    
72.1    
72.2    
72.3    
72.4    
72.6    
72.7    
72.8    
72.9    
73.0    
73.1    
73.2    
73.3    
73.5    
73.6    
73.7    
73.8    
73.9    
74.0    
74.1    
74.3    
74.4    
74.5    
74.6    
74.7    
74.8    
74.9    
75.1    
75.2    
75.3    
75.4    
75.5    
75.6    
75.7    
75.9    
76.0    
76.1    
76.2    
76.3    
76.4    
76.5    
76.7    
76.8    
76.9    
77.0    
77.1    
77.2    
77.3    
77.4    
77.6    
77.7    
77.8    
77.9    
78.0    
78.1    
78.2    
78.4    
78.5    
78.6    
78.7    
78.8    
78.9    
79.0    
79.2    
79.3    
79.4    
79.5    
79.6    
79.7    
79.8    
80.0    
80.1    
80.2    
80.3    
80.4    
80.5    
80.6    
80.8    
80.9    
81.0    
81.1    
81.2    
81.3    
81.4    
81.5    
81.7    
81.8    
81.9    
82.0    
82.1    
82.2    
82.3    
82.5    
82.6    
82.7    
82.8    
82.9    
83.0    
83.1    
83.3    
83.4    
83.5    
83.6    
83.7    
83.8    
83.9    
84.1    
84.2    
84.3    
84.4    
84.5    
84.6    
84.7    
84.9    
85.0    
85.1    
85.2    
85.3    
85.4    
85.5    
85.6    
85.8    
85.9    
86.0    
86.1    
86.2    
86.3    
86.4    
86.6    
86.7    
86.8    
86.9    
87.0    
87.1    
87.2    
87.4    
87.5    
87.6    
87.7    
87.8    
87.9    
88.0    
88.2    
88.3    
88.4    
88.5    
88.6    
88.7    
88.8    
89.0    
89.1    
89.2    
89.3    
89.4    
89.5    
89.6    
89.7    
89.9    
90.0    
90.1    
90.2    
90.3    
90.4    
90.5    
90.7    
90.8    
90.9    
91.0    
91.1    
91.2    
91.3    
91.5    
91.6    
91.7    
91.8    
91.9    
92.0    
92.1    
92.3    
92.4    
92.5    
92.6    
92.7    
92.8    
92.9    
93.1    
93.2    
93.3    
93.4    
93.5    
93.6    
93.7    
93.8    
94.0    
94.1    
94.2    
94.3    
94.4    
94.5    
94.6    
94.8    
94.9    
95.0    
95.1    
95.2    
95.3    
95.4    
95.6    
95.7    
95.8    
95.9    
96.0    
96.1    
96.2    
96.4    
96.5    
96.6    
96.7    
96.8    
96.9    
97.0    
97.2    
97.3    
97.4    
97.5    
97.6    
97.7    
97.8    
97.9    
98.1    
98.2    
98.3    
98.4    
98.5    
98.6    
98.7    
98.9    
99.0    
99.1    
99.2    
99.3    
99.4    
99.5    
99.7    
99.8    
99.9    
-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 8196, rend_intergenic: 4799  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18086, rend_intergenic: 13506  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35289, rend_intergenic: 31472  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47073, rend_intergenic: 38280  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47712, rend_intergenic: 47397  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54130, rend_intergenic: 48146  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103544, rend_intergenic: 54143  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107765, rend_intergenic: 105204  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117079, rend_intergenic: 110428  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135856, rend_intergenic: 132901  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153992, rend_intergenic: 150131  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156917, rend_intergenic: 155259  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163333, rend_intergenic: 160401  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166201, rend_intergenic: 164086  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 18 predictions persist after filtering for low support