-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_4/scaffold_4_17538657-17761372

-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 snap_scaffold_4-snap.3598-T1
Valid prediction for pasa_asmbl_42065.p1
Valid prediction for snap_scaffold_4-snap.3614-T1
Valid prediction for HiQ_model.g7225.t1
Valid prediction for GlimmerHMM_glimmerT_11019-T1
Valid prediction for GlimmerHMM_glimmerT_11035-T1
Valid prediction for snap_scaffold_4-snap.3629-T1
Valid prediction for snap_scaffold_4-snap.3613-T1
Valid prediction for CodingQuarry_transcript_49339-T1
Valid prediction for snap_scaffold_4-snap.3602-T1
Valid prediction for snap_scaffold_4-snap.3600-T1
Valid prediction for snap_scaffold_4-snap.3611-T1
Valid prediction for GlimmerHMM_glimmerT_11025-T1
Valid prediction for CodingQuarry_transcript_49340-T1
Valid prediction for snap_scaffold_4-snap.3640-T1
Valid prediction for CodingQuarry_transcript_49342-T1
Valid prediction for Augustus_model.g7245.t1
Valid prediction for snap_scaffold_4-snap.3633-T1
Valid prediction for GlimmerHMM_glimmerT_11038-T1
Valid prediction for Augustus_model.g7240.t1
Valid prediction for GlimmerHMM_glimmerT_11021-T1
Valid prediction for snap_scaffold_4-snap.3619-T1
Valid prediction for CodingQuarry_transcript_49338-T1
Valid prediction for Augustus_model.g7231.t1
Valid prediction for snap_scaffold_4-snap.3638-T1
Valid prediction for pasa_asmbl_42221.p1
Valid prediction for snap_scaffold_4-snap.3606-T1
Couldn't classify 16279, 16341
Sorry, prediction pasa_asmbl_42167.p1 fails validation.
(ATG)	 AA	14718-14764	GT	TGG
(GTC)	 AG	15212-15344	GT	AGG
(GCT)	 AG	15600-15743	GT	CTG
(TAT)	 AG	16014-16091	GT	AGG
(CCT)	 AG	16279-16341	CC	CCC
-recovered pasa_asmbl_42167.p1, initial, 14718, 14764
-recovered pasa_asmbl_42167.p1, internal, 15212, 15344
-recovered pasa_asmbl_42167.p1, internal, 15600, 15743
-recovered pasa_asmbl_42167.p1, internal, 16014, 16091
Valid prediction for HiQ_model.g7226.t1
Valid prediction for snap_scaffold_4-snap.3624-T1
Valid prediction for snap_scaffold_4-snap.3632-T1
Valid prediction for CodingQuarry_transcript_49346-T1
Valid prediction for GlimmerHMM_glimmerT_11028-T1
Valid prediction for snap_scaffold_4-snap.3618-T1
Valid prediction for CodingQuarry_transcript_49343-T1
Valid prediction for pasa_asmbl_42058.p1
Valid prediction for snap_scaffold_4-snap.3608-T1
Valid prediction for pasa_asmbl_42068.p1
Valid prediction for HiQ_model.g7228.t1
Valid prediction for GlimmerHMM_glimmerT_11022-T1
Valid prediction for pasa_asmbl_42064.p1
Valid prediction for CodingQuarry_transcript_49336-T1
Valid prediction for snap_scaffold_4-snap.3626-T1
Valid prediction for snap_scaffold_4-snap.3620-T1
Valid prediction for snap_scaffold_4-snap.3604-T1
Valid prediction for snap_scaffold_4-snap.3596-T1
Valid prediction for HiQ_model.g7238.t1
Valid prediction for snap_scaffold_4-snap.3595-T1
Valid prediction for GlimmerHMM_glimmerT_11016-T1
Valid prediction for snap_scaffold_4-snap.3607-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_4-snap.3627-T1
Valid prediction for Augustus_model.g7235.t1
Valid prediction for snap_scaffold_4-snap.3636-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_11029-T1
Valid prediction for HiQ_model.g7232.t1
Valid prediction for CodingQuarry_transcript_49341-T1
Valid prediction for CodingQuarry_transcript_49334-T1
Valid prediction for GlimmerHMM_glimmerT_11023-T1
Valid prediction for HiQ_model.g7234.t1
Valid prediction for pasa_asmbl_42066.p1
Valid prediction for GlimmerHMM_glimmerT_11017-T1
Valid prediction for snap_scaffold_4-snap.3609-T1
Valid prediction for GlimmerHMM_glimmerT_11024-T1
Valid prediction for snap_scaffold_4-snap.3605-T1
Valid prediction for Augustus_model.g7233.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 HiQ_model.g7243.t1
Valid prediction for snap_scaffold_4-snap.3639-T1
Valid prediction for CodingQuarry_transcript_49345-T1
Valid prediction for GlimmerHMM_glimmerT_11039-T1
Valid prediction for pasa_asmbl_43288.p1
Valid prediction for snap_scaffold_4-snap.3625-T1
Couldn't classify 40974, 41048
Couldn't classify 44368, 44553
Sorry, prediction pasa_asmbl_43313.p1 fails validation.
(GAA)	 AT	40974-41048	GT	AGG
(GAG)	 AG	43663-43751	GT	AAG
(GAC)	 AG	43953-44076	GT	AGG
(GTG)	 AG	44368-44553	GA	AGG
-recovered pasa_asmbl_43313.p1, internal, 43663, 43751
-recovered pasa_asmbl_43313.p1, internal, 43953, 44076
Couldn't classify 209857, 210001
Sorry, prediction pasa_asmbl_43283.p1 fails validation.
(GAA)	 AA	209857-210001	GT	AAG
(ACG)	 AG	211259-212214	GG	AGG
-recovered pasa_asmbl_43283.p1, terminal, 211259, 212214
Valid prediction for CodingQuarry_transcript_49344-T1
Valid prediction for GlimmerHMM_glimmerT_11032-T1
Valid prediction for snap_scaffold_4-snap.3628-T1
Valid prediction for snap_scaffold_4-snap.3622-T1
Valid prediction for Augustus_model.g7229.t1
Couldn't classify 73125, 73490
Sorry, prediction pasa_asmbl_43303.p1 fails validation.
(CCC)	 AC	73125-73490	GT	AGG
(GTC)	 AG	74034-74096	GC	GAG
-recovered pasa_asmbl_43303.p1, terminal, 74034, 74096
-recovered pasa_asmbl_43303.p1, internal, 74034, 74096
Valid prediction for HiQ_model.g7241.t1
Valid prediction for GlimmerHMM_glimmerT_11040-T1
Valid prediction for snap_scaffold_4-snap.3601-T1
Valid prediction for GlimmerHMM_glimmerT_11033-T1
Valid prediction for Augustus_model.g7244.t1
Valid prediction for Augustus_model.g7246.t1
Valid prediction for pasa_asmbl_43308.p1
Couldn't classify 133377, 133439
Sorry, prediction pasa_asmbl_43556.p1 fails validation.
(GGG)	 CA	133377-133439	GT	AGG
(GCT)	 AG	134759-134870	GT	AGG
(ACA)	 AG	135023-135221	GT	AGG
(ACA)	 AG	135347-135479	GT	AGG
(GGC)	 AG	135743-135868	GT	AGG
(GGC)	 AG	136211-136309	AG	GAA
-recovered pasa_asmbl_43556.p1, terminal, 136211, 136309
-recovered pasa_asmbl_43556.p1, internal, 134759, 134870
-recovered pasa_asmbl_43556.p1, internal, 135023, 135221
-recovered pasa_asmbl_43556.p1, internal, 135347, 135479
-recovered pasa_asmbl_43556.p1, internal, 135743, 135868
Valid prediction for snap_scaffold_4-snap.3615-T1
Couldn't classify 131550, 131691
Sorry, prediction pasa_asmbl_43291.p1 fails validation.
(ATG)	 CC	128287-128311	GT	AGG
(GTG)	 AG	128524-128591	GT	AGG
(CTT)	 AG	128672-128746	GT	AAG
(CGA)	 AG	128836-128925	GT	CGG
(CAA)	 AG	129083-129211	GT	CGG
(AAC)	 AG	129302-129397	GT	AGG
(GAT)	 AG	129560-129773	GT	ACG
(CTC)	 AG	129902-130029	GT	CAG
(GAG)	 AG	130127-130183	GT	AGG
(TCA)	 AG	130312-131233	GT	GAG
(GTT)	 AG	131324-131429	GT	CCG
(GAT)	 AG	131550-131691	GT	AGG
-recovered pasa_asmbl_43291.p1, initial, 128287, 128311
-recovered pasa_asmbl_43291.p1, internal, 128524, 128591
-recovered pasa_asmbl_43291.p1, internal, 128672, 128746
-recovered pasa_asmbl_43291.p1, internal, 128836, 128925
-recovered pasa_asmbl_43291.p1, internal, 129083, 129211
-recovered pasa_asmbl_43291.p1, internal, 129302, 129397
-recovered pasa_asmbl_43291.p1, internal, 129560, 129773
-recovered pasa_asmbl_43291.p1, internal, 129902, 130029
-recovered pasa_asmbl_43291.p1, internal, 130127, 130183
-recovered pasa_asmbl_43291.p1, internal, 130312, 131233
-recovered pasa_asmbl_43291.p1, internal, 131324, 131429
-recovered pasa_asmbl_43291.p1, internal, 131550, 131691
Valid prediction for GlimmerHMM_glimmerT_11036-T1
Valid prediction for GlimmerHMM_glimmerT_11020-T1
Valid prediction for snap_scaffold_4-snap.3603-T1
Valid prediction for snap_scaffold_4-snap.3621-T1
Valid prediction for GlimmerHMM_glimmerT_11031-T1
Valid prediction for CodingQuarry_transcript_49347-T1
Couldn't classify 117714, 117784
Sorry, prediction pasa_asmbl_43298.p1 fails validation.
(GAT)	 GC	117714-117784	GT	CGG
(AAA)	 AG	118150-118215	GT	AGG
(CTC)	 AG	119004-119250	GT	AGG
(CTC)	 AG	119340-119380	GT	AGG
(GAC)	 AG	119906-119978	GA	AGG
-recovered pasa_asmbl_43298.p1, terminal, 119906, 119978
-recovered pasa_asmbl_43298.p1, internal, 118150, 118215
-recovered pasa_asmbl_43298.p1, internal, 119004, 119250
-recovered pasa_asmbl_43298.p1, internal, 119340, 119380
Valid prediction for snap_scaffold_4-snap.3610-T1
Valid prediction for snap_scaffold_4-snap.3630-T1
Couldn't classify 71889, 72485
Sorry, prediction pasa_asmbl_43305.p1 fails validation.
(CGA)	 AT	71889-72485	GT	TGG
Valid prediction for snap_scaffold_4-snap.3634-T1
Valid prediction for GlimmerHMM_glimmerT_11041-T1
Valid prediction for GlimmerHMM_glimmerT_11034-T1
Couldn't classify 80674, 80775
Sorry, prediction pasa_asmbl_43301.p1 fails validation.
(ATG)	 GA	77281-77347	GT	CAG
(TCC)	 AG	79811-79961	GT	AGG
(TAA)	 AG	80431-80497	GT	AGG
(GGC)	 AG	80674-80775	GA	GAG
-recovered pasa_asmbl_43301.p1, initial, 77281, 77347
-recovered pasa_asmbl_43301.p1, internal, 79811, 79961
-recovered pasa_asmbl_43301.p1, internal, 80431, 80497
Valid prediction for CodingQuarry_transcript_49348-T1
Valid prediction for Augustus_model.g7239.t1
Valid prediction for snap_scaffold_4-snap.3623-T1
Sorry, intron length (6) is less than minimum required (10)
Couldn't classify 39255, 39314
Couldn't classify 40083, 40295
Sorry, prediction pasa_asmbl_43314.p1 fails validation.
(GCC)	 GA	39255-39314	GT	AGG
(GAG)	 AG	39554-39652	GT	ACG
(GTG)	 AG	40083-40295	GT	AGG
-recovered pasa_asmbl_43314.p1, internal, 39554, 39652
-recovered pasa_asmbl_43314.p1, internal, 40083, 40295
Valid prediction for Augustus_model.g7247.t1
Valid prediction for snap_scaffold_4-snap.3637-T1
Couldn't classify 32240, 32400
Couldn't classify 34450, 34572
Sorry, prediction pasa_asmbl_43315.p1 fails validation.
(ATC)	 AG	32240-32400	GT	AGG
(GGC)	 AG	32821-32929	GT	AGG
(GTG)	 AG	33176-33307	GT	AGG
(CTG)	 AG	33663-33869	GT	AGG
(GAC)	 AG	34012-34149	GT	AGG
(GAG)	 AG	34450-34572	GG	AAG
-recovered pasa_asmbl_43315.p1, internal, 32240, 32400
-recovered pasa_asmbl_43315.p1, internal, 32821, 32929
-recovered pasa_asmbl_43315.p1, internal, 33176, 33307
-recovered pasa_asmbl_43315.p1, internal, 33663, 33869
-recovered pasa_asmbl_43315.p1, internal, 34012, 34149
Valid prediction for snap_scaffold_4-snap.3635-T1
Valid prediction for GlimmerHMM_glimmerT_11037-T1
Valid prediction for snap_scaffold_4-snap.3631-T1
Valid prediction for GlimmerHMM_glimmerT_11030-T1
Valid prediction for Augustus_model.g7242.t1
Valid prediction for Augustus_model.g7236.t1
Valid prediction for snap_scaffold_4-snap.3599-T1
Valid prediction for GlimmerHMM_glimmerT_11026-T1
Valid prediction for Augustus_model.g7227.t1
Valid prediction for snap_scaffold_4-snap.3617-T1
Valid prediction for snap_scaffold_4-snap.3612-T1
Valid prediction for GlimmerHMM_glimmerT_11018-T1
Valid prediction for GlimmerHMM_glimmerT_11027-T1
Valid prediction for CodingQuarry_transcript_49337-T1
Valid prediction for snap_scaffold_4-snap.3616-T1
Valid prediction for pasa_asmbl_43295.p1
Valid prediction for HiQ_model.g7237.t1
Couldn't classify 72483, 72953
Sorry, prediction pasa_asmbl_43304.p1 fails validation.
(GTG)	 GG	72483-72953	CC	CCC
Valid prediction for Augustus_model.g7230.t1
Valid prediction for snap_scaffold_4-snap.3597-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 23020, rend_intergenic: 19046  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36557, rend_intergenic: 32646  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65018, rend_intergenic: 64569  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69106, rend_intergenic: 66230  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77436, rend_intergenic: 72410  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89669, rend_intergenic: 86408  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113840, rend_intergenic: 105077  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125747, rend_intergenic: 118714  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138110, rend_intergenic: 136630  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143685, rend_intergenic: 138898  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155892, rend_intergenic: 151199  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189216, rend_intergenic: 173964  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192220, rend_intergenic: 189414  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 204290, rend_intergenic: 195071  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 213575, rend_intergenic: 204462  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 216755, rend_intergenic: 213613  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 222716
-exon list size: 531


building trellis

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76.9    
77.1    
77.3    
77.5    
77.7    
77.9    
78.0    
78.2    
78.4    
78.6    
78.8    
79.0    
79.2    
79.4    
79.5    
79.7    
79.9    
80.1    
80.3    
80.5    
80.7    
80.9    
81.1    
81.2    
81.4    
81.6    
81.8    
82.0    
82.2    
82.4    
82.6    
82.7    
82.9    
83.1    
83.3    
83.5    
83.7    
83.9    
84.1    
84.2    
84.4    
84.6    
84.8    
85.0    
85.2    
85.4    
85.6    
85.7    
85.9    
86.1    
86.3    
86.5    
86.7    
86.9    
87.1    
87.2    
87.4    
87.6    
87.8    
88.0    
88.2    
88.4    
88.6    
88.7    
88.9    
89.1    
89.3    
89.5    
89.7    
89.9    
90.1    
90.2    
90.4    
90.6    
90.8    
91.0    
91.2    
91.4    
91.6    
91.7    
91.9    
92.1    
92.3    
92.5    
92.7    
92.9    
93.1    
93.2    
93.4    
93.6    
93.8    
94.0    
94.2    
94.4    
94.6    
94.7    
94.9    
95.1    
95.3    
95.5    
95.7    
95.9    
96.1    
96.2    
96.4    
96.6    
96.8    
97.0    
97.2    
97.4    
97.6    
97.7    
97.9    
98.1    
98.3    
98.5    
98.7    
98.9    
99.1    
99.2    
99.4    
99.6    
99.8    
-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 23020, rend_intergenic: 19046  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36557, rend_intergenic: 32646  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65018, rend_intergenic: 64569  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69106, rend_intergenic: 66230  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77436, rend_intergenic: 72410  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89669, rend_intergenic: 86408  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113840, rend_intergenic: 105077  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125747, rend_intergenic: 118714  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138110, rend_intergenic: 136630  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143685, rend_intergenic: 138898  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155892, rend_intergenic: 151199  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189216, rend_intergenic: 173964  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192220, rend_intergenic: 189414  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 204290, rend_intergenic: 195071  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 213575, rend_intergenic: 204462  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 216755, rend_intergenic: 213613  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 27 predictions persist after filtering for low support