-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_27/scaffold_27_4067454-4281990

-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 pasa_asmbl_36263.p1
Valid prediction for snap_scaffold_27-snap.975-T1
Valid prediction for GlimmerHMM_glimmerT_57148-T1
Valid prediction for snap_scaffold_27-snap.970-T1
Valid prediction for snap_scaffold_27-snap.968-T1
Valid prediction for GlimmerHMM_glimmerT_57151-T1
Valid prediction for snap_scaffold_27-snap.973-T1
Valid prediction for snap_scaffold_27-snap.990-T1
Valid prediction for GlimmerHMM_glimmerT_57152-T1
Valid prediction for HiQ_model.g37898.t1
Valid prediction for snap_scaffold_27-snap.1002-T1
Couldn't classify 156764, 156802
Couldn't classify 157685, 157742
Sorry, prediction pasa_asmbl_36261.p1 fails validation.
(GTC)	 CG	156764-156802	GT	GGG
(ACA)	 AG	156897-156980	GT	AGG
(AGA)	 AG	157193-157354	GT	AGG
(GAA)	 AG	157489-157568	GT	AAG
(GTA)	 AG	157685-157742	AT	CCA
-recovered pasa_asmbl_36261.p1, internal, 156897, 156980
-recovered pasa_asmbl_36261.p1, internal, 157193, 157354
-recovered pasa_asmbl_36261.p1, internal, 157489, 157568
Valid prediction for Augustus_model.g37892.t1
Couldn't classify 60650, 60680
Sorry, prediction pasa_asmbl_36257.p1 fails validation.
(CTG)	 CC	60650-60680	GT	AGG
(AGA)	 AG	60810-60937	GT	AGG
(AAT)	 AG	61023-61130	GT	AGG
(CAT)	 AG	61484-61657	GT	AGG
(ATG)	 AG	61891-62064	GT	GAG
(AAA)	 AG	62238-62342	GT	AGG
(GCT)	 AG	62687-62887	GT	AGG
(GTG)	 AG	62988-63129	GT	AGG
(GGA)	 AG	63726-63856	GT	AGG
(GAC)	 AG	63960-64040	GT	AGG
(GTC)	 AG	64159-64308	GT	AGG
(GAT)	 AG	65008-65127	GT	AGG
(ATC)	 AG	65205-65380	GT	AAG
(GGT)	 AG	65554-65786	GT	CTG
(CCA)	 AG	66073-66280	GT	ATG
(CAG)	 AG	66606-66777	GT	AAG
(CTG)	 AG	67055-67266	GT	AGG
(TGC)	 AG	67557-67665	GT	ACG
(AGG)	 AG	67758-67856	GT	ATG
(ACC)	 AG	68198-68375	GT	CGG
(GGG)	 AG	68505-68572	GT	AGG
(AAG)	 AG	69836-69958	GT	ATG
(TCA)	 AG	70115-70207	GT	AGG
(AAC)	 AG	70318-70402	GT	CGG
(GTA)	 AG	70523-70590	GT	AGG
(TAC)	 AG	70712-70828	GT	AGG
(GGT)	 AG	72489-72584	GT	CTG
(GCG)	 AG	72805-73036	GT	CTG
(CAA)	 AG	73152-73326	GT	AGG
(CTA)	 AG	73642-73870	TA	AGT
-recovered pasa_asmbl_36257.p1, initial, 61891, 62064
-recovered pasa_asmbl_36257.p1, terminal, 73642, 73870
-recovered pasa_asmbl_36257.p1, internal, 60810, 60937
-recovered pasa_asmbl_36257.p1, internal, 61023, 61130
-recovered pasa_asmbl_36257.p1, internal, 61484, 61657
-recovered pasa_asmbl_36257.p1, internal, 61891, 62064
-recovered pasa_asmbl_36257.p1, internal, 62238, 62342
-recovered pasa_asmbl_36257.p1, internal, 62687, 62887
-recovered pasa_asmbl_36257.p1, internal, 62988, 63129
-recovered pasa_asmbl_36257.p1, internal, 63726, 63856
-recovered pasa_asmbl_36257.p1, internal, 63960, 64040
-recovered pasa_asmbl_36257.p1, internal, 64159, 64308
-recovered pasa_asmbl_36257.p1, internal, 65008, 65127
-recovered pasa_asmbl_36257.p1, internal, 65205, 65380
-recovered pasa_asmbl_36257.p1, internal, 65554, 65786
-recovered pasa_asmbl_36257.p1, internal, 66073, 66280
-recovered pasa_asmbl_36257.p1, internal, 66606, 66777
-recovered pasa_asmbl_36257.p1, internal, 67055, 67266
-recovered pasa_asmbl_36257.p1, internal, 67557, 67665
-recovered pasa_asmbl_36257.p1, internal, 67758, 67856
-recovered pasa_asmbl_36257.p1, internal, 68198, 68375
-recovered pasa_asmbl_36257.p1, internal, 68505, 68572
-recovered pasa_asmbl_36257.p1, internal, 69836, 69958
-recovered pasa_asmbl_36257.p1, internal, 70115, 70207
-recovered pasa_asmbl_36257.p1, internal, 70318, 70402
-recovered pasa_asmbl_36257.p1, internal, 70523, 70590
-recovered pasa_asmbl_36257.p1, internal, 70712, 70828
-recovered pasa_asmbl_36257.p1, internal, 72489, 72584
-recovered pasa_asmbl_36257.p1, internal, 72805, 73036
-recovered pasa_asmbl_36257.p1, internal, 73152, 73326
Valid prediction for HiQ_model.g37899.t1
Valid prediction for GlimmerHMM_glimmerT_57170-T1
Valid prediction for HiQ_model.g37895.t1
Valid prediction for snap_scaffold_27-snap.967-T1
Valid prediction for snap_scaffold_27-snap.966-T1
Valid prediction for Augustus_model.g37883.t1
Valid prediction for snap_scaffold_27-snap.964-T1
Valid prediction for snap_scaffold_27-snap.999-T1
Valid prediction for snap_scaffold_27-snap.969-T1
Valid prediction for snap_scaffold_27-snap.972-T1
Valid prediction for snap_scaffold_27-snap.1003-T1
Valid prediction for snap_scaffold_27-snap.993-T1
Valid prediction for GlimmerHMM_glimmerT_57144-T1
Valid prediction for snap_scaffold_27-snap.983-T1
Valid prediction for GlimmerHMM_glimmerT_57171-T1
Valid prediction for snap_scaffold_27-snap.996-T1
Valid prediction for Augustus_model.g37878.t1
Valid prediction for pasa_asmbl_36259.p1
Valid prediction for snap_scaffold_27-snap.1000-T1
Valid prediction for HiQ_model.g37889.t1
Valid prediction for pasa_asmbl_36254.p1
Valid prediction for GlimmerHMM_glimmerT_57147-T1
Valid prediction for pasa_asmbl_36258.p1
Valid prediction for GlimmerHMM_glimmerT_57149-T1
Valid prediction for snap_scaffold_27-snap.1007-T1
Couldn't classify 175850, 175883
Sorry, prediction pasa_asmbl_36265.p1 fails validation.
(GGA)	 AA	175850-175883	GT	AGG
(ATT)	 AG	176201-176266	GT	AGG
(GTA)	 AG	176429-176555	GT	GAG
(GTC)	 AG	176788-176914	GT	TGG
(AGG)	 AG	177137-177217	AA	GAA
-recovered pasa_asmbl_36265.p1, terminal, 176201, 176266
-recovered pasa_asmbl_36265.p1, terminal, 177137, 177217
-recovered pasa_asmbl_36265.p1, internal, 176201, 176266
-recovered pasa_asmbl_36265.p1, internal, 176429, 176555
-recovered pasa_asmbl_36265.p1, internal, 176788, 176914
Valid prediction for pasa_asmbl_36262.p1
Valid prediction for GlimmerHMM_glimmerT_57166-T1
Valid prediction for Augustus_model.g37881.t1
Couldn't classify 58395, 58501
Sorry, prediction pasa_asmbl_36598.p1 fails validation.
(ATG)	 GG	57633-57746	GT	CTG
(GAG)	 AG	57915-58038	GT	GGG
(GCT)	 AG	58135-58251	GT	AGG
(ACG)	 AG	58395-58501	CT	CCC
-recovered pasa_asmbl_36598.p1, initial, 57633, 57746
-recovered pasa_asmbl_36598.p1, internal, 57915, 58038
-recovered pasa_asmbl_36598.p1, internal, 58135, 58251
Valid prediction for Augustus_model.g37884.t1
Valid prediction for snap_scaffold_27-snap.991-T1
Valid prediction for snap_scaffold_27-snap.1005-T1
Valid prediction for snap_scaffold_27-snap.977-T1
Valid prediction for GlimmerHMM_glimmerT_57158-T1
Valid prediction for snap_scaffold_27-snap.974-T1
Valid prediction for HiQ_model.g37879.t1
Valid prediction for snap_scaffold_27-snap.987-T1
Valid prediction for Augustus_model.g37901.t1
Valid prediction for GlimmerHMM_glimmerT_57146-T1
Valid prediction for CodingQuarry_transcript_41866-T1
Valid prediction for GlimmerHMM_glimmerT_57157-T1
Valid prediction for GlimmerHMM_glimmerT_57168-T1
Valid prediction for Augustus_model.g37882.t1
Valid prediction for GlimmerHMM_glimmerT_57162-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 snap_scaffold_27-snap.979-T1
Valid prediction for snap_scaffold_27-snap.1004-T1
Valid prediction for Augustus_model.g37902.t1
Valid prediction for GlimmerHMM_glimmerT_57145-T1
Valid prediction for snap_scaffold_27-snap.986-T1
Couldn't classify 34868, 35598
Sorry, prediction pasa_asmbl_37221.p1 fails validation.
(ATG)	 AG	32691-32890	GT	CGG
(GCA)	 AG	33429-33536	GT	AAG
(GGT)	 AG	33746-33823	GT	AAG
(GGA)	 AG	33983-34094	GT	AGG
(GCC)	 AG	34355-34595	GT	AAG
(ATG)	 AG	34868-35598	GA	AGG
-recovered pasa_asmbl_37221.p1, initial, 32691, 32890
-recovered pasa_asmbl_37221.p1, internal, 32691, 32890
-recovered pasa_asmbl_37221.p1, internal, 33429, 33536
-recovered pasa_asmbl_37221.p1, internal, 33746, 33823
-recovered pasa_asmbl_37221.p1, internal, 33983, 34094
-recovered pasa_asmbl_37221.p1, internal, 34355, 34595
Valid prediction for snap_scaffold_27-snap.989-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for Augustus_model.g37888.t1
Valid prediction for snap_scaffold_27-snap.992-T1
Valid prediction for CodingQuarry_transcript_41870-T1
Valid prediction for Augustus_model.g37897.t1
Valid prediction for GlimmerHMM_glimmerT_57153-T1
Valid prediction for snap_scaffold_27-snap.984-T1
Valid prediction for GlimmerHMM_glimmerT_57164-T1
Valid prediction for HiQ_model.g37885.t1
Valid prediction for pasa_asmbl_36947.p1
Valid prediction for snap_scaffold_27-snap.1008-T1
Valid prediction for snap_scaffold_27-snap.1006-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_27-snap.971-T1
Valid prediction for GlimmerHMM_glimmerT_57159-T1
Valid prediction for snap_scaffold_27-snap.981-T1
Valid prediction for GlimmerHMM_glimmerT_57156-T1
Valid prediction for snap_scaffold_27-snap.988-T1
Valid prediction for snap_scaffold_27-snap.998-T1
Valid prediction for Augustus_model.g37891.t1
Valid prediction for CodingQuarry_transcript_41868-T1
Couldn't classify 205281, 205323
Couldn't classify 206424, 206444
Sorry, prediction pasa_asmbl_36943.p1 fails validation.
(CTC)	 AG	205281-205323	GT	AGG
(CGC)	 AG	205798-205887	GT	AGG
(TCG)	 AG	206057-206208	GT	TGG
(GCC)	 AG	206424-206444	CT	GTC
-recovered pasa_asmbl_36943.p1, internal, 205281, 205323
-recovered pasa_asmbl_36943.p1, internal, 205798, 205887
-recovered pasa_asmbl_36943.p1, internal, 206057, 206208
Valid prediction for Augustus_model.g37900.t1
Valid prediction for snap_scaffold_27-snap.995-T1
Valid prediction for GlimmerHMM_glimmerT_57154-T1
Valid prediction for Augustus_model.g37877.t1
Valid prediction for snap_scaffold_27-snap.1001-T1
Couldn't classify 84873, 84989
Sorry, prediction pasa_asmbl_36950.p1 fails validation.
(GTG)	 AG	84873-84989	GT	AGG
(TTG)	 AG	85616-85720	GT	AGG
(ACG)	 AG	85847-85960	GT	GGG
(CCT)	 AG	86075-86223	GT	AGG
(GAT)	 AG	86387-86417	GT	GGG
(ACC)	 AG	86528-86670	GT	AGG
(CAA)	 AG	86807-86853	GT	GAG
(GTT)	 AG	87016-87080	AT	AGA
add_exon() Sorry, pasa_asmbl_36950.p1 86807-86853-terminal-2 is invalid.
-recovered pasa_asmbl_36950.p1, terminal, 86807, 86853
-recovered pasa_asmbl_36950.p1, terminal, 87016, 87080
-recovered pasa_asmbl_36950.p1, internal, 84873, 84989
-recovered pasa_asmbl_36950.p1, internal, 85616, 85720
-recovered pasa_asmbl_36950.p1, internal, 85847, 85960
-recovered pasa_asmbl_36950.p1, internal, 86075, 86223
-recovered pasa_asmbl_36950.p1, internal, 86387, 86417
-recovered pasa_asmbl_36950.p1, internal, 86528, 86670
-recovered pasa_asmbl_36950.p1, internal, 86807, 86853
Valid prediction for Augustus_model.g37896.t1
Valid prediction for Augustus_model.g37890.t1
Valid prediction for GlimmerHMM_glimmerT_57150-T1
Valid prediction for snap_scaffold_27-snap.997-T1
Valid prediction for Augustus_model.g37894.t1
Valid prediction for GlimmerHMM_glimmerT_57163-T1
Valid prediction for GlimmerHMM_glimmerT_57160-T1
Valid prediction for GlimmerHMM_glimmerT_57155-T1
Valid prediction for GlimmerHMM_glimmerT_57161-T1
Valid prediction for snap_scaffold_27-snap.982-T1
Valid prediction for HiQ_model.g37887.t1
Valid prediction for Augustus_model.g37886.t1
Valid prediction for snap_scaffold_27-snap.978-T1
Valid prediction for GlimmerHMM_glimmerT_57169-T1
Valid prediction for snap_scaffold_27-snap.1009-T1
Valid prediction for snap_scaffold_27-snap.985-T1
Valid prediction for GlimmerHMM_glimmerT_57172-T1
Valid prediction for snap_scaffold_27-snap.980-T1
Valid prediction for GlimmerHMM_glimmerT_57167-T1
Couldn't classify 202099, 202122
Couldn't classify 203310, 203330
Sorry, prediction pasa_asmbl_37194.p1 fails validation.
(GAT)	 AG	202099-202122	GT	AGG
(AGG)	 AG	202308-202418	GT	AGG
(GCC)	 AG	202534-202677	GT	CGG
(ATG)	 AG	202878-202988	GT	AGG
(GTG)	 AG	203310-203330	AG	CCA
-recovered pasa_asmbl_37194.p1, initial, 202878, 202988
-recovered pasa_asmbl_37194.p1, internal, 202099, 202122
-recovered pasa_asmbl_37194.p1, internal, 202308, 202418
-recovered pasa_asmbl_37194.p1, internal, 202534, 202677
-recovered pasa_asmbl_37194.p1, internal, 202878, 202988
Valid prediction for snap_scaffold_27-snap.994-T1
Valid prediction for Augustus_model.g37893.t1
Valid prediction for pasa_asmbl_36945.p1
Valid prediction for CodingQuarry_transcript_41869-T1
Valid prediction for snap_scaffold_27-snap.965-T1
Valid prediction for snap_scaffold_27-snap.976-T1
Valid prediction for Augustus_model.g37880.t1
Valid prediction for GlimmerHMM_glimmerT_57165-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 14347, rend_intergenic: 7417  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73870, rend_intergenic: 70162  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134624, rend_intergenic: 128858  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138700, rend_intergenic: 137816  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142366, rend_intergenic: 142269  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144932, rend_intergenic: 142538  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181847, rend_intergenic: 180394  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187969, rend_intergenic: 186802  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 191676, rend_intergenic: 188338  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195450, rend_intergenic: 192697  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 202577, rend_intergenic: 195766  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 214537
-exon list size: 595


building trellis

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57.3    
57.5    
57.6    
57.8    
58.0    
58.1    
58.3    
58.5    
58.6    
58.8    
59.0    
59.1    
59.3    
59.5    
59.6    
59.8    
60.0    
60.1    
60.3    
60.5    
60.6    
60.8    
61.0    
61.1    
61.3    
61.5    
61.6    
61.8    
62.0    
62.1    
62.3    
62.5    
62.6    
62.8    
63.0    
63.1    
63.3    
63.5    
63.7    
63.8    
64.0    
64.2    
64.3    
64.5    
64.7    
64.8    
65.0    
65.2    
65.3    
65.5    
65.7    
65.8    
66.0    
66.2    
66.3    
66.5    
66.7    
66.8    
67.0    
67.2    
67.3    
67.5    
67.7    
67.8    
68.0    
68.2    
68.3    
68.5    
68.7    
68.8    
69.0    
69.2    
69.3    
69.5    
69.7    
69.8    
70.0    
70.2    
70.4    
70.5    
70.7    
70.9    
71.0    
71.2    
71.4    
71.5    
71.7    
71.9    
72.0    
72.2    
72.4    
72.5    
72.7    
72.9    
73.0    
73.2    
73.4    
73.5    
73.7    
73.9    
74.0    
74.2    
74.4    
74.5    
74.7    
74.9    
75.0    
75.2    
75.4    
75.5    
75.7    
75.9    
76.0    
76.2    
76.4    
76.5    
76.7    
76.9    
77.1    
77.2    
77.4    
77.6    
77.7    
77.9    
78.1    
78.2    
78.4    
78.6    
78.7    
78.9    
79.1    
79.2    
79.4    
79.6    
79.7    
79.9    
80.1    
80.2    
80.4    
80.6    
80.7    
80.9    
81.1    
81.2    
81.4    
81.6    
81.7    
81.9    
82.1    
82.2    
82.4    
82.6    
82.7    
82.9    
83.1    
83.2    
83.4    
83.6    
83.8    
83.9    
84.1    
84.3    
84.4    
84.6    
84.8    
84.9    
85.1    
85.3    
85.4    
85.6    
85.8    
85.9    
86.1    
86.3    
86.4    
86.6    
86.8    
86.9    
87.1    
87.3    
87.4    
87.6    
87.8    
87.9    
88.1    
88.3    
88.4    
88.6    
88.8    
88.9    
89.1    
89.3    
89.4    
89.6    
89.8    
89.9    
90.1    
90.3    
90.5    
90.6    
90.8    
91.0    
91.1    
91.3    
91.5    
91.6    
91.8    
92.0    
92.1    
92.3    
92.5    
92.6    
92.8    
93.0    
93.1    
93.3    
93.5    
93.6    
93.8    
94.0    
94.1    
94.3    
94.5    
94.6    
94.8    
95.0    
95.1    
95.3    
95.5    
95.6    
95.8    
96.0    
96.1    
96.3    
96.5    
96.6    
96.8    
97.0    
97.2    
97.3    
97.5    
97.7    
97.8    
98.0    
98.2    
98.3    
98.5    
98.7    
98.8    
99.0    
99.2    
99.3    
99.5    
99.7    
99.8    
-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 14347, rend_intergenic: 7417  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73870, rend_intergenic: 70162  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134624, rend_intergenic: 128858  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138700, rend_intergenic: 137816  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142366, rend_intergenic: 142269  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144932, rend_intergenic: 142538  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181847, rend_intergenic: 180394  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187969, rend_intergenic: 186802  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 191676, rend_intergenic: 188338  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195450, rend_intergenic: 192697  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 202577, rend_intergenic: 195766  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

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