-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_9/scaffold_9_5125201-5295739

-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_9-snap.1091-T1
Valid prediction for GlimmerHMM_glimmerT_22130-T1
Valid prediction for HiQ_model.g14706.t1
Valid prediction for GlimmerHMM_glimmerT_22118-T1
Valid prediction for GlimmerHMM_glimmerT_22108-T1
Valid prediction for snap_scaffold_9-snap.1079-T1
Valid prediction for GlimmerHMM_glimmerT_22135-T1
Valid prediction for snap_scaffold_9-snap.1086-T1
Valid prediction for Augustus_model.g14707.t1
Valid prediction for snap_scaffold_9-snap.1094-T1
Valid prediction for snap_scaffold_9-snap.1084-T1
Valid prediction for GlimmerHMM_glimmerT_22137-T1
Valid prediction for CodingQuarry_transcript_62173-T1
Valid prediction for GlimmerHMM_glimmerT_22115-T1
Valid prediction for snap_scaffold_9-snap.1093-T1
Valid prediction for GlimmerHMM_glimmerT_22125-T1
Valid prediction for HiQ_model.g14708.t1
Valid prediction for GlimmerHMM_glimmerT_22139-T1
Valid prediction for snap_scaffold_9-snap.1090-T1
Valid prediction for snap_scaffold_9-snap.1097-T1
Valid prediction for Augustus_model.g14700.t1
Valid prediction for pasa_asmbl_54011.p1
Valid prediction for snap_scaffold_9-snap.1083-T1
Valid prediction for pasa_asmbl_54001.p1
Couldn't classify 91156, 91292
Sorry, prediction pasa_asmbl_54002.p1 fails validation.
(ATG)	 CC	89866-90085	GT	AGG
(ACG)	 AG	90221-90463	GT	AGG
(AAA)	 AG	90582-90828	GT	AGG
(ATC)	 AG	90949-91022	GT	TTG
(ACA)	 AG	91156-91292	AA	TGA
-recovered pasa_asmbl_54002.p1, initial, 89866, 90085
-recovered pasa_asmbl_54002.p1, internal, 90221, 90463
-recovered pasa_asmbl_54002.p1, internal, 90582, 90828
-recovered pasa_asmbl_54002.p1, internal, 90949, 91022
Valid prediction for snap_scaffold_9-snap.1095-T1
Valid prediction for snap_scaffold_9-snap.1077-T1
Valid prediction for snap_scaffold_9-snap.1074-T1
Valid prediction for snap_scaffold_9-snap.1098-T1
Valid prediction for GlimmerHMM_glimmerT_22132-T1
Valid prediction for snap_scaffold_9-snap.1082-T1
Valid prediction for snap_scaffold_9-snap.1068-T1
Valid prediction for snap_scaffold_9-snap.1107-T1
Valid prediction for pasa_asmbl_53997.p1
Valid prediction for CodingQuarry_transcript_62172-T1
Valid prediction for GlimmerHMM_glimmerT_22124-T1
Couldn't classify 47416, 47527
Sorry, prediction pasa_asmbl_54000.p1 fails validation.
(GAC)	 GC	47416-47527	GT	AGG
(GCG)	 AG	47724-47837	GT	AAG
(GTG)	 AG	48147-48268	GT	CCG
(CTG)	 AG	48560-48700	GT	AGG
(GAA)	 AG	48844-48933	GT	AGG
(TTT)	 AG	49170-49265	CA	AGC
-recovered pasa_asmbl_54000.p1, terminal, 49170, 49265
-recovered pasa_asmbl_54000.p1, internal, 47724, 47837
-recovered pasa_asmbl_54000.p1, internal, 48147, 48268
-recovered pasa_asmbl_54000.p1, internal, 48560, 48700
-recovered pasa_asmbl_54000.p1, internal, 48844, 48933
Valid prediction for snap_scaffold_9-snap.1078-T1
Valid prediction for GlimmerHMM_glimmerT_22127-T1
Valid prediction for GlimmerHMM_glimmerT_22128-T1
Valid prediction for Augustus_model.g14710.t1
Valid prediction for pasa_asmbl_54004.p2
Valid prediction for snap_scaffold_9-snap.1071-T1
Valid prediction for snap_scaffold_9-snap.1099-T1
Valid prediction for CodingQuarry_transcript_62174-T1
Valid prediction for GlimmerHMM_glimmerT_22111-T1
Valid prediction for snap_scaffold_9-snap.1102-T1
Valid prediction for GlimmerHMM_glimmerT_22133-T1
Valid prediction for HiQ_model.g14712.t1
Valid prediction for GlimmerHMM_glimmerT_22123-T1
Valid prediction for snap_scaffold_9-snap.1081-T1
Valid prediction for snap_scaffold_9-snap.1104-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_9-snap.1105-T1
Valid prediction for GlimmerHMM_glimmerT_22114-T1
Couldn't classify 91433, 91532
Sorry, prediction pasa_asmbl_54006.p1 fails validation.
(GTG)	 AG	91433-91532	GT	GGG
(GGG)	 AG	91645-91757	GT	TCG
(GAT)	 AG	91891-92157	GT	AGG
(ATC)	 AG	92399-92521	GT	AGG
(GTG)	 AG	92607-92735	GT	AGG
(ACA)	 AG	93995-94163	GT	AGG
(CCA)	 AG	95054-95326	GT	AGG
(TCT)	 AG	95435-95580	GT	AGG
(AGC)	 AG	95690-95857	GT	AGG
(TAT)	 AG	96000-96116	CT	AAC
-recovered pasa_asmbl_54006.p1, terminal, 96000, 96116
-recovered pasa_asmbl_54006.p1, internal, 91433, 91532
-recovered pasa_asmbl_54006.p1, internal, 91645, 91757
-recovered pasa_asmbl_54006.p1, internal, 91891, 92157
-recovered pasa_asmbl_54006.p1, internal, 92399, 92521
-recovered pasa_asmbl_54006.p1, internal, 92607, 92735
-recovered pasa_asmbl_54006.p1, internal, 93995, 94163
-recovered pasa_asmbl_54006.p1, internal, 95054, 95326
-recovered pasa_asmbl_54006.p1, internal, 95435, 95580
-recovered pasa_asmbl_54006.p1, internal, 95690, 95857
Valid prediction for HiQ_model.g14699.t1
Valid prediction for Augustus_model.g14695.t1
Valid prediction for HiQ_model.g14702.t1
Valid prediction for HiQ_model.g14714.t1
Couldn't classify 155239, 155299
Sorry, prediction pasa_asmbl_54020.p1 fails validation.
(ATG)	 AC	154066-154122	GT	TGG
(AAA)	 AG	154303-154362	GT	AGG
(GTG)	 AG	154489-154623	GT	TGG
(ACG)	 AG	154758-154870	GT	AGG
(GCA)	 AG	155239-155299	TA	GCT
-recovered pasa_asmbl_54020.p1, initial, 154066, 154122
-recovered pasa_asmbl_54020.p1, internal, 154303, 154362
-recovered pasa_asmbl_54020.p1, internal, 154489, 154623
-recovered pasa_asmbl_54020.p1, internal, 154758, 154870
Valid prediction for snap_scaffold_9-snap.1106-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 Augustus_model.g14709.t1
Valid prediction for GlimmerHMM_glimmerT_22119-T1
Valid prediction for snap_scaffold_9-snap.1101-T1
Valid prediction for snap_scaffold_9-snap.1073-T1
Valid prediction for Augustus_model.g14704.t1
Couldn't classify 149325, 150155
Sorry, prediction pasa_asmbl_54992.p1 fails validation.
(GTG)	 GC	149325-150155	CA	AAC
Valid prediction for snap_scaffold_9-snap.1103-T1
Valid prediction for GlimmerHMM_glimmerT_22112-T1
Valid prediction for GlimmerHMM_glimmerT_22113-T1
Valid prediction for GlimmerHMM_glimmerT_22129-T1
Valid prediction for snap_scaffold_9-snap.1088-T1
Valid prediction for GlimmerHMM_glimmerT_22131-T1
Valid prediction for snap_scaffold_9-snap.1089-T1
Valid prediction for GlimmerHMM_glimmerT_22126-T1
Valid prediction for Augustus_model.g14697.t1
Couldn't classify 162485, 162634
Sorry, prediction pasa_asmbl_55722.p1 fails validation.
(ATT)	 GT	162485-162634	GT	AGG
(ATC)	 AG	163099-163171	GT	TCG
(GTG)	 AG	163399-163501	GT	AAG
(AGA)	 AG	163651-163816	GT	AGG
(TAC)	 AG	163989-164089	GT	CGG
(CGA)	 AG	164243-164354	GT	AGG
(AGG)	 AG	164460-164597	TT	AGT
-recovered pasa_asmbl_55722.p1, terminal, 164460, 164597
-recovered pasa_asmbl_55722.p1, internal, 163099, 163171
-recovered pasa_asmbl_55722.p1, internal, 163399, 163501
-recovered pasa_asmbl_55722.p1, internal, 163651, 163816
-recovered pasa_asmbl_55722.p1, internal, 163989, 164089
-recovered pasa_asmbl_55722.p1, internal, 164243, 164354
Valid prediction for HiQ_model.g14696.t1
Valid prediction for snap_scaffold_9-snap.1076-T1
Valid prediction for GlimmerHMM_glimmerT_22120-T1
Valid prediction for snap_scaffold_9-snap.1070-T1
Valid prediction for Augustus_model.g14698.t1
Couldn't classify 69781, 69852
Sorry, prediction pasa_asmbl_54997.p1 fails validation.
(GGA)	 CC	69781-69852	GT	AGG
(GCT)	 AG	70107-70379	GT	CGG
(CTA)	 AG	70515-70595	GT	AGG
(CCT)	 AG	70980-71084	GT	ATG
(TCC)	 AG	71217-71323	GT	AGG
(GGA)	 AG	71451-71601	GT	TCG
(TTG)	 AG	71711-71744	GT	AGG
(ACT)	 AG	71875-72006	GT	GAG
(GCT)	 AG	72148-72344	GT	GGG
(GCC)	 AG	72458-72547	GC	GAG
-recovered pasa_asmbl_54997.p1, terminal, 72458, 72547
-recovered pasa_asmbl_54997.p1, internal, 70107, 70379
-recovered pasa_asmbl_54997.p1, internal, 70515, 70595
-recovered pasa_asmbl_54997.p1, internal, 70980, 71084
-recovered pasa_asmbl_54997.p1, internal, 71217, 71323
-recovered pasa_asmbl_54997.p1, internal, 71451, 71601
-recovered pasa_asmbl_54997.p1, internal, 71711, 71744
-recovered pasa_asmbl_54997.p1, internal, 71875, 72006
-recovered pasa_asmbl_54997.p1, internal, 72148, 72344
-recovered pasa_asmbl_54997.p1, internal, 72458, 72547
Valid prediction for pasa_asmbl_54993.p1
Valid prediction for snap_scaffold_9-snap.1072-T1
Valid prediction for GlimmerHMM_glimmerT_22138-T1
Valid prediction for Augustus_model.g14715.t1
Valid prediction for CodingQuarry_transcript_62170-T1
Valid prediction for GlimmerHMM_glimmerT_22116-T1
Valid prediction for snap_scaffold_9-snap.1085-T1
Valid prediction for CodingQuarry_transcript_62169-T1
Valid prediction for snap_scaffold_9-snap.1100-T1
Valid prediction for Augustus_model.g14711.t1
Valid prediction for GlimmerHMM_glimmerT_22136-T1
Valid prediction for GlimmerHMM_glimmerT_22122-T1
Valid prediction for CodingQuarry_transcript_62171-T1
Couldn't classify 59727, 60038
Sorry, prediction pasa_asmbl_54009.p2 fails validation.
(CGT)	 AC	59727-60038	GA	GAG
Valid prediction for snap_scaffold_9-snap.1087-T1
Valid prediction for snap_scaffold_9-snap.1108-T1
Valid prediction for snap_scaffold_9-snap.1075-T1
Valid prediction for snap_scaffold_9-snap.1110-T1
Valid prediction for Augustus_model.g14713.t1
Valid prediction for snap_scaffold_9-snap.1109-T1
Couldn't classify 93270, 93448
Sorry, prediction pasa_asmbl_54996.p1 fails validation.
(ATG)	 TC	92835-92925	GT	GGG
(GTG)	 AG	93270-93448	AA	CCA
-recovered pasa_asmbl_54996.p1, initial, 92835, 92925
Valid prediction for snap_scaffold_9-snap.1069-T1
Valid prediction for GlimmerHMM_glimmerT_22110-T1
Valid prediction for Augustus_model.g14705.t1
Valid prediction for GlimmerHMM_glimmerT_22121-T1
Valid prediction for pasa_asmbl_54991.p1
Couldn't classify 67132, 67180
Couldn't classify 68238, 68343
Couldn't classify 68632, 68691
Couldn't classify 69175, 69289
Sorry, prediction pasa_asmbl_54998.p1 fails validation.
(CGA)	 CG	67132-67180	GT	TGG
(ACT)	 AG	68238-68343	AT	CTA
(CTA)	 AC	68632-68691	GT	AGG
(GCA)	 AG	68934-69065	GT	TTG
(AAA)	 AG	69175-69289	GA	TGG
-recovered pasa_asmbl_54998.p1, internal, 68934, 69065
Valid prediction for GlimmerHMM_glimmerT_22117-T1
Valid prediction for snap_scaffold_9-snap.1092-T1
Valid prediction for GlimmerHMM_glimmerT_22109-T1
Valid prediction for snap_scaffold_9-snap.1096-T1
Valid prediction for GlimmerHMM_glimmerT_22134-T1
Valid prediction for Augustus_model.g14703.t1
Valid prediction for HiQ_model.g14701.t1
Valid prediction for snap_scaffold_9-snap.1080-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 12398, rend_intergenic: 11897  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13863, rend_intergenic: 12648  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18527, rend_intergenic: 17699  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31888, rend_intergenic: 21352  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62182, rend_intergenic: 58092  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67186, rend_intergenic: 65015  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75348, rend_intergenic: 68091  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83216, rend_intergenic: 76471  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86387, rend_intergenic: 84031  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104533, rend_intergenic: 97707  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114469, rend_intergenic: 109457  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123660, rend_intergenic: 119855  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128435, rend_intergenic: 124380  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165246, rend_intergenic: 151639  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 170539
-exon list size: 532


building trellis

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85.8    
86.0    
86.1    
86.3    
86.5    
86.7    
86.9    
87.1    
87.3    
87.5    
87.6    
87.8    
88.0    
88.2    
88.4    
88.6    
88.8    
89.0    
89.1    
89.3    
89.5    
89.7    
89.9    
90.1    
90.3    
90.4    
90.6    
90.8    
91.0    
91.2    
91.4    
91.6    
91.8    
91.9    
92.1    
92.3    
92.5    
92.7    
92.9    
93.1    
93.3    
93.4    
93.6    
93.8    
94.0    
94.2    
94.4    
94.6    
94.8    
94.9    
95.1    
95.3    
95.5    
95.7    
95.9    
96.1    
96.3    
96.4    
96.6    
96.8    
97.0    
97.2    
97.4    
97.6    
97.8    
97.9    
98.1    
98.3    
98.5    
98.7    
98.9    
99.1    
99.3    
99.4    
99.6    
99.8    
-found 24 predictions from path traversal
Error with prediction: snap lend_intergenic: 12398, rend_intergenic: 11897  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13863, rend_intergenic: 12648  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18527, rend_intergenic: 17699  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31888, rend_intergenic: 21352  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62182, rend_intergenic: 58092  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67186, rend_intergenic: 65015  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75348, rend_intergenic: 68091  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83216, rend_intergenic: 76471  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86387, rend_intergenic: 84031  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104533, rend_intergenic: 97707  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114469, rend_intergenic: 109457  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123660, rend_intergenic: 119855  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128435, rend_intergenic: 124380  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165246, rend_intergenic: 151639  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 156331 - 170539
-exon list size: 20


building trellis

4.5    
9.1    
13.6    
18.2    
22.7    
27.3    
31.8    
36.4    
40.9    
45.5    
50.0    
54.5    
59.1    
63.6    
68.2    
72.7    
77.3    
81.8    
86.4    
90.9    
95.5    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support