-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_6/scaffold_6_2890240-3084624

-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_14238-T1
Valid prediction for snap_scaffold_6-snap.710-T1
Sorry, intron length (3) is less than minimum required (10)
Sorry, intron length (9) is less than minimum required (10)
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for CodingQuarry_transcript_54968-T1
Valid prediction for pasa_asmbl_46807.p1
Valid prediction for GlimmerHMM_glimmerT_14262-T1
Valid prediction for snap_scaffold_6-snap.691-T1
Valid prediction for pasa_asmbl_46793.p1
Valid prediction for snap_scaffold_6-snap.694-T1
Valid prediction for CodingQuarry_transcript_54966-T1
Valid prediction for CodingQuarry_transcript_54960-T1
Valid prediction for GlimmerHMM_glimmerT_14263-T1
Valid prediction for snap_scaffold_6-snap.715-T1
Valid prediction for CodingQuarry_transcript_54958-T1
Valid prediction for GlimmerHMM_glimmerT_14242-T1
Valid prediction for pasa_asmbl_46792.p1
Valid prediction for Augustus_model.g9457.t1
Valid prediction for GlimmerHMM_glimmerT_14246-T1
Valid prediction for HiQ_model.g9440.t1
Valid prediction for snap_scaffold_6-snap.712-T1
Valid prediction for snap_scaffold_6-snap.707-T1
Valid prediction for snap_scaffold_6-snap.720-T1
Valid prediction for snap_scaffold_6-snap.700-T1
Valid prediction for HiQ_model.g9459.t1
Valid prediction for snap_scaffold_6-snap.693-T1
Valid prediction for pasa_asmbl_46801.p1
Valid prediction for GlimmerHMM_glimmerT_14250-T1
Valid prediction for snap_scaffold_6-snap.703-T1
Valid prediction for HiQ_model.g9453.t1
Valid prediction for HiQ_model.g9460.t1
Valid prediction for snap_scaffold_6-snap.685-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for HiQ_model.g9458.t1
Valid prediction for snap_scaffold_6-snap.705-T1
Valid prediction for GlimmerHMM_glimmerT_14239-T1
Valid prediction for GlimmerHMM_glimmerT_14257-T1
Valid prediction for GlimmerHMM_glimmerT_14259-T1
Valid prediction for Augustus_model.g9439.t1
Valid prediction for HiQ_model.g9445.t1
Valid prediction for GlimmerHMM_glimmerT_14253-T1
Valid prediction for CodingQuarry_transcript_54965-T1
Valid prediction for snap_scaffold_6-snap.699-T1
Valid prediction for snap_scaffold_6-snap.697-T1
Valid prediction for CodingQuarry_transcript_54962-T1
Valid prediction for snap_scaffold_6-snap.682-T1
Couldn't classify 12720, 13156
Sorry, prediction pasa_asmbl_46783.p1 fails validation.
(ATG)	 AA	11950-12030	GT	AGG
(GAG)	 AG	12369-12606	GT	AGG
(AGG)	 AG	12720-13156	TG	GAT
-recovered pasa_asmbl_46783.p1, initial, 11950, 12030
-recovered pasa_asmbl_46783.p1, internal, 12369, 12606
Valid prediction for snap_scaffold_6-snap.709-T1
Valid prediction for snap_scaffold_6-snap.695-T1
Valid prediction for snap_scaffold_6-snap.719-T1
Valid prediction for snap_scaffold_6-snap.716-T1
Valid prediction for snap_scaffold_6-snap.718-T1
Valid prediction for CodingQuarry_transcript_54967-T1
Valid prediction for Augustus_model.g9456.t1
Valid prediction for snap_scaffold_6-snap.683-T1
Valid prediction for snap_scaffold_6-snap.717-T1
Valid prediction for pasa_asmbl_46785.p1

-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 Augustus_model.g9451.t1
Valid prediction for Augustus_model.g9461.t1
Valid prediction for GlimmerHMM_glimmerT_14240-T1
Valid prediction for snap_scaffold_6-snap.704-T1
Valid prediction for GlimmerHMM_glimmerT_14252-T1
Valid prediction for HiQ_model.g9444.t1
Valid prediction for snap_scaffold_6-snap.701-T1
Valid prediction for GlimmerHMM_glimmerT_14260-T1
Valid prediction for snap_scaffold_6-snap.711-T1
Valid prediction for snap_scaffold_6-snap.702-T1
Valid prediction for snap_scaffold_6-snap.687-T1
Valid prediction for Augustus_model.g9437.t1
Couldn't classify 98814, 99265
Sorry, prediction pasa_asmbl_48208.p1 fails validation.
(GGT)	 AG	98814-99265	GT	AGG
(GCT)	 AG	100224-100284	GT	AGG
(GAT)	 AG	100377-100472	GT	AGG
(GAG)	 AG	100589-100750	GT	AGG
(TTT)	 AG	101342-101467	GT	CAG
(AAC)	 AG	101618-101838	GT	AGG
(GAT)	 AG	101982-102025	GT	AGG
(AGA)	 AG	102161-102243	GT	AGG
(ATC)	 AG	102465-102506	TC	GAT
-recovered pasa_asmbl_48208.p1, terminal, 102465, 102506
-recovered pasa_asmbl_48208.p1, internal, 98814, 99265
-recovered pasa_asmbl_48208.p1, internal, 100224, 100284
-recovered pasa_asmbl_48208.p1, internal, 100377, 100472
-recovered pasa_asmbl_48208.p1, internal, 100589, 100750
-recovered pasa_asmbl_48208.p1, internal, 101342, 101467
-recovered pasa_asmbl_48208.p1, internal, 101618, 101838
-recovered pasa_asmbl_48208.p1, internal, 101982, 102025
-recovered pasa_asmbl_48208.p1, internal, 102161, 102243
Valid prediction for GlimmerHMM_glimmerT_14264-T1
Valid prediction for Augustus_model.g9448.t1
Valid prediction for GlimmerHMM_glimmerT_14248-T1
Valid prediction for HiQ_model.g9438.t1
Couldn't classify 149023, 149371
Couldn't classify 149769, 149953
Sorry, prediction pasa_asmbl_48201.p2 fails validation.
(ATG)	 AG	148342-148803	GT	AGG
(GAG)	 AG	149023-149371	AT	TGA
(TTA)	 AC	149769-149953	GT	CTG
(GGC)	 AG	150963-151073	GT	AGG
(TTC)	 AG	151282-151401	GT	AGG
(ATG)	 AG	151532-151669	GT	CTG
(CCA)	 AG	151863-152036	AA	AAA
-recovered pasa_asmbl_48201.p2, initial, 148342, 148803
-recovered pasa_asmbl_48201.p2, initial, 151532, 151669
-recovered pasa_asmbl_48201.p2, terminal, 151863, 152036
-recovered pasa_asmbl_48201.p2, internal, 148342, 148803
-recovered pasa_asmbl_48201.p2, internal, 150963, 151073
-recovered pasa_asmbl_48201.p2, internal, 151282, 151401
-recovered pasa_asmbl_48201.p2, internal, 151532, 151669
Valid prediction for Augustus_model.g9447.t1
Valid prediction for snap_scaffold_6-snap.696-T1
Couldn't classify 170632, 171030
Sorry, prediction pasa_asmbl_48188.p2 fails validation.
(GAG)	 CT	170632-171030	TT	AGT
Valid prediction for snap_scaffold_6-snap.706-T1
Couldn't classify 168669, 168721
Couldn't classify 169778, 169923
Sorry, prediction pasa_asmbl_48190.p1 fails validation.
(CTC)	 AC	168669-168721	GT	GGG
(ACA)	 AG	168864-168978	GT	AGG
(CAA)	 AG	169190-169255	GT	TGG
(GAA)	 AG	169490-169679	GT	AGG
(GTG)	 AG	169778-169923	GT	TGG
-recovered pasa_asmbl_48190.p1, internal, 168864, 168978
-recovered pasa_asmbl_48190.p1, internal, 169190, 169255
-recovered pasa_asmbl_48190.p1, internal, 169490, 169679
-recovered pasa_asmbl_48190.p1, internal, 169778, 169923
Couldn't classify 165374, 165904
Sorry, prediction pasa_asmbl_48191.p1 fails validation.
(GCC)	 CT	165374-165904	CC	CCC
Valid prediction for CodingQuarry_transcript_54957-T1
Valid prediction for snap_scaffold_6-snap.688-T1
Valid prediction for pasa_asmbl_48215.p1
Valid prediction for Augustus_model.g9450.t1
Valid prediction for snap_scaffold_6-snap.684-T1
Valid prediction for snap_scaffold_6-snap.689-T1
Valid prediction for GlimmerHMM_glimmerT_14255-T1
Valid prediction for GlimmerHMM_glimmerT_14245-T1
Couldn't classify 147491, 147612
Sorry, prediction pasa_asmbl_48203.p1 fails validation.
(ATG)	 AG	145348-145413	GT	AGG
(CCC)	 AG	145553-145726	GT	AGG
(GTG)	 AG	145839-145926	GT	AGG
(GCG)	 AG	146045-146187	GT	AGG
(GAC)	 AG	146870-146897	GT	AGG
(ATG)	 AG	147023-147236	GT	AGG
(GGA)	 AG	147322-147395	GT	AGG
(GAG)	 AG	147491-147612	CC	CAC
-recovered pasa_asmbl_48203.p1, initial, 145348, 145413
-recovered pasa_asmbl_48203.p1, initial, 147023, 147236
-recovered pasa_asmbl_48203.p1, internal, 145348, 145413
-recovered pasa_asmbl_48203.p1, internal, 145553, 145726
-recovered pasa_asmbl_48203.p1, internal, 145839, 145926
-recovered pasa_asmbl_48203.p1, internal, 146045, 146187
-recovered pasa_asmbl_48203.p1, internal, 146870, 146897
-recovered pasa_asmbl_48203.p1, internal, 147023, 147236
-recovered pasa_asmbl_48203.p1, internal, 147322, 147395
Valid prediction for Augustus_model.g9455.t1
Couldn't classify 189815, 190225
Sorry, prediction pasa_asmbl_48185.p1 fails validation.
(CTG)	 AG	189815-190225	GA	CAG
Valid prediction for HiQ_model.g9454.t1
Valid prediction for GlimmerHMM_glimmerT_14247-T1
Valid prediction for snap_scaffold_6-snap.681-T1
Valid prediction for snap_scaffold_6-snap.686-T1
Valid prediction for snap_scaffold_6-snap.692-T1
Valid prediction for Augustus_model.g9441.t1
Valid prediction for HiQ_model.g9452.t1
Couldn't classify 134482, 134599
Sorry, prediction pasa_asmbl_48206.p1 fails validation.
(TTT)	 TA	134482-134599	GT	AGG
(CCA)	 AG	135439-135728	GT	AGG
(GAC)	 AG	135888-135989	GT	CGG
(GTT)	 AG	136176-136350	GT	GGG
(GTG)	 AG	136466-136587	GT	AGG
(TTC)	 AG	136671-136736	GT	TGG
(CAA)	 AG	136837-136938	GT	TGG
(AGT)	 AG	137048-137158	GT	AGG
(ATG)	 AG	137371-137456	GT	GAG
(GGA)	 AG	137578-137636	GT	TGG
(TGC)	 AG	137751-137860	GT	AGG
(GGC)	 AG	137943-138110	GT	AGG
(GAA)	 AG	138254-138334	AG	GAA
-recovered pasa_asmbl_48206.p1, initial, 137371, 137456
-recovered pasa_asmbl_48206.p1, terminal, 138254, 138334
-recovered pasa_asmbl_48206.p1, internal, 135439, 135728
-recovered pasa_asmbl_48206.p1, internal, 135888, 135989
-recovered pasa_asmbl_48206.p1, internal, 136176, 136350
-recovered pasa_asmbl_48206.p1, internal, 136466, 136587
-recovered pasa_asmbl_48206.p1, internal, 136671, 136736
-recovered pasa_asmbl_48206.p1, internal, 136837, 136938
-recovered pasa_asmbl_48206.p1, internal, 137048, 137158
-recovered pasa_asmbl_48206.p1, internal, 137371, 137456
-recovered pasa_asmbl_48206.p1, internal, 137578, 137636
-recovered pasa_asmbl_48206.p1, internal, 137751, 137860
-recovered pasa_asmbl_48206.p1, internal, 137943, 138110
Valid prediction for snap_scaffold_6-snap.713-T1
Valid prediction for pasa_asmbl_48213.p1
Valid prediction for snap_scaffold_6-snap.690-T1
Valid prediction for GlimmerHMM_glimmerT_14268-T1
Valid prediction for Augustus_model.g9446.t1
Couldn't classify 85059, 85064
Sorry, prediction pasa_asmbl_48210.p1 fails validation.
(GCT)	 AC	85059-85064	GT	ATG
(GTA)	 AG	85464-85584	GT	CAG
(GTT)	 AG	86540-86673	GT	GTG
(GTT)	 AG	87113-87186	GT	AGG
(CCC)	 AG	87310-87377	GT	AGG
(ACC)	 AG	87627-87722	GT	AGG
(GCC)	 AG	88431-88592	GT	GTG
(CCC)	 AG	88696-88844	GT	AGG
(GAG)	 AG	90781-90912	GT	GGG
(GGC)	 AG	91066-91195	GT	AGG
(GTG)	 AG	91380-91557	GT	TGG
(GAG)	 AG	92501-92729	GG	GAG
-recovered pasa_asmbl_48210.p1, terminal, 92501, 92729
-recovered pasa_asmbl_48210.p1, internal, 85464, 85584
-recovered pasa_asmbl_48210.p1, internal, 86540, 86673
-recovered pasa_asmbl_48210.p1, internal, 87113, 87186
-recovered pasa_asmbl_48210.p1, internal, 87310, 87377
-recovered pasa_asmbl_48210.p1, internal, 87627, 87722
-recovered pasa_asmbl_48210.p1, internal, 88431, 88592
-recovered pasa_asmbl_48210.p1, internal, 88696, 88844
-recovered pasa_asmbl_48210.p1, internal, 90781, 90912
-recovered pasa_asmbl_48210.p1, internal, 91066, 91195
-recovered pasa_asmbl_48210.p1, internal, 91380, 91557
Valid prediction for pasa_asmbl_48194.p1
Valid prediction for snap_scaffold_6-snap.721-T1
Valid prediction for GlimmerHMM_glimmerT_14249-T1
Valid prediction for snap_scaffold_6-snap.722-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for Augustus_model.g9449.t1
Valid prediction for GlimmerHMM_glimmerT_14267-T1
Couldn't classify 143533, 144183
Couldn't classify 144433, 144549
Sorry, prediction pasa_asmbl_48205.p1 fails validation.
(ACC)	 CA	143533-144183	GT	AGG
(ACG)	 AG	144433-144549	TC	CGT
Valid prediction for GlimmerHMM_glimmerT_14244-T1
Valid prediction for Augustus_model.g9443.t1
Valid prediction for Augustus_model.g9442.t1
Valid prediction for GlimmerHMM_glimmerT_14237-T1
Valid prediction for GlimmerHMM_glimmerT_14265-T1
Valid prediction for snap_scaffold_6-snap.680-T1
Valid prediction for GlimmerHMM_glimmerT_14261-T1
Valid prediction for GlimmerHMM_glimmerT_14256-T1
Valid prediction for snap_scaffold_6-snap.708-T1
Valid prediction for snap_scaffold_6-snap.714-T1
Valid prediction for CodingQuarry_transcript_54963-T1
Valid prediction for snap_scaffold_6-snap.698-T1
Valid prediction for GlimmerHMM_glimmerT_14254-T1
Valid prediction for GlimmerHMM_glimmerT_14251-T1
Valid prediction for GlimmerHMM_glimmerT_14258-T1
Valid prediction for GlimmerHMM_glimmerT_14243-T1
Valid prediction for CodingQuarry_transcript_54961-T1
Valid prediction for CodingQuarry_transcript_54959-T1
Valid prediction for pasa_asmbl_48186.p1
Valid prediction for GlimmerHMM_glimmerT_14266-T1
Valid prediction for GlimmerHMM_glimmerT_14241-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 29099, rend_intergenic: 23799  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73629, rend_intergenic: 68021  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77524, rend_intergenic: 74079  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80825, rend_intergenic: 78152  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81587, rend_intergenic: 81113  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83747, rend_intergenic: 81994  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89322, rend_intergenic: 88067  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99868, rend_intergenic: 92036  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114128, rend_intergenic: 104690  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123621, rend_intergenic: 121620  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126167, rend_intergenic: 125065  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135368, rend_intergenic: 131013  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 194385
-exon list size: 486


building trellis

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69.9    
70.1    
70.3    
70.5    
70.7    
70.9    
71.1    
71.3    
71.5    
71.7    
71.9    
72.1    
72.3    
72.5    
72.7    
73.0    
73.2    
73.4    
73.6    
73.8    
74.0    
74.2    
74.4    
74.6    
74.8    
75.0    
75.2    
75.4    
75.6    
75.8    
76.0    
76.2    
76.4    
76.6    
76.8    
77.0    
77.3    
77.5    
77.7    
77.9    
78.1    
78.3    
78.5    
78.7    
78.9    
79.1    
79.3    
79.5    
79.7    
79.9    
80.1    
80.3    
80.5    
80.7    
80.9    
81.1    
81.4    
81.6    
81.8    
82.0    
82.2    
82.4    
82.6    
82.8    
83.0    
83.2    
83.4    
83.6    
83.8    
84.0    
84.2    
84.4    
84.6    
84.8    
85.0    
85.2    
85.5    
85.7    
85.9    
86.1    
86.3    
86.5    
86.7    
86.9    
87.1    
87.3    
87.5    
87.7    
87.9    
88.1    
88.3    
88.5    
88.7    
88.9    
89.1    
89.3    
89.5    
89.8    
90.0    
90.2    
90.4    
90.6    
90.8    
91.0    
91.2    
91.4    
91.6    
91.8    
92.0    
92.2    
92.4    
92.6    
92.8    
93.0    
93.2    
93.4    
93.6    
93.9    
94.1    
94.3    
94.5    
94.7    
94.9    
95.1    
95.3    
95.5    
95.7    
95.9    
96.1    
96.3    
96.5    
96.7    
96.9    
97.1    
97.3    
97.5    
97.7    
98.0    
98.2    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 35 predictions from path traversal
Error with prediction: snap lend_intergenic: 29099, rend_intergenic: 23799  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73629, rend_intergenic: 68021  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77524, rend_intergenic: 74079  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80825, rend_intergenic: 78152  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81587, rend_intergenic: 81113  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83747, rend_intergenic: 81994  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89322, rend_intergenic: 88067  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99868, rend_intergenic: 92036  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114128, rend_intergenic: 104690  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123621, rend_intergenic: 121620  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126167, rend_intergenic: 125065  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135368, rend_intergenic: 131013  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 34 predictions persist after filtering for low support