-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_2/scaffold_2_2386324-2594493

-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 Augustus_model.g2265.t1
Valid prediction for GlimmerHMM_glimmerT_3368-T1
Valid prediction for snap_scaffold_2-snap.559-T1
Valid prediction for Augustus_model.g2250.t1
add_exon() Sorry, Augustus_model.g2250.t1 54923-55283-initial-1 is invalid.
add_exon() Sorry, Augustus_model.g2250.t1 55611-55777-internal-2 is invalid.
add_exon() Sorry, Augustus_model.g2250.t1 56110-56296-internal-1 is invalid.
add_exon() Sorry, Augustus_model.g2250.t1 56418-56615-internal-2 is invalid.
add_exon() Sorry, Augustus_model.g2250.t1 56956-57034-internal-2 is invalid.
add_exon() Sorry, Augustus_model.g2250.t1 57344-57529-internal-3 is invalid.
add_exon() Sorry, Augustus_model.g2250.t1 58155-58292-internal-3 is invalid.
add_exon() Sorry, Augustus_model.g2250.t1 60630-60941-internal-1 is invalid.
add_exon() Sorry, Augustus_model.g2250.t1 61525-61643-internal-1 is invalid.
add_exon() Sorry, Augustus_model.g2250.t1 62195-62422-internal-3 is invalid.
add_exon() Sorry, Augustus_model.g2250.t1 63254-63332-terminal-2 is invalid.
Valid prediction for pasa_asmbl_24242.p1
Valid prediction for GlimmerHMM_glimmerT_3392-T1
Valid prediction for Augustus_model.g2262.t1
Valid prediction for GlimmerHMM_glimmerT_3371-T1
Valid prediction for GlimmerHMM_glimmerT_3367-T1
Couldn't classify 39880, 39932
Couldn't classify 40919, 41105
Sorry, prediction pasa_asmbl_24241.p1 fails validation.
(GGA)	 GA	39880-39932	GT	AGG
(GTC)	 AG	40504-40620	GT	ATG
(CTT)	 AG	40919-41105	GG	AGG
-recovered pasa_asmbl_24241.p1, internal, 40504, 40620
Valid prediction for snap_scaffold_2-snap.588-T1
Valid prediction for snap_scaffold_2-snap.565-T1
Valid prediction for snap_scaffold_2-snap.578-T1
Valid prediction for GlimmerHMM_glimmerT_3387-T1
Couldn't classify 186866, 186891
Couldn't classify 189004, 189120
Sorry, prediction pasa_asmbl_24250.p1 fails validation.
(GCC)	 AG	186866-186891	GT	AGG
(GTA)	 AG	187316-187436	GT	AGG
(GCG)	 AG	187758-187839	GT	CGG
(ACT)	 AG	188155-188319	GT	TGG
(GAG)	 AG	188497-188621	GT	AGG
(GTG)	 AG	189004-189120	AG	GTA
-recovered pasa_asmbl_24250.p1, internal, 186866, 186891
-recovered pasa_asmbl_24250.p1, internal, 187316, 187436
-recovered pasa_asmbl_24250.p1, internal, 187758, 187839
-recovered pasa_asmbl_24250.p1, internal, 188155, 188319
-recovered pasa_asmbl_24250.p1, internal, 188497, 188621
Couldn't classify 193690, 193759
Couldn't classify 196504, 196694
Sorry, prediction pasa_asmbl_25418.p1 fails validation.
(CTG)	 AC	193690-193759	GT	AGG
(CAG)	 AG	194019-194167	GT	GGG
(ATG)	 AG	194512-194703	GT	TGG
(GCC)	 AG	195095-195216	GT	AGG
(GAT)	 AG	195489-195627	GT	AGG
(GTG)	 AG	195861-195981	GT	TGG
(GGG)	 AG	196504-196694	GC	TTG
-recovered pasa_asmbl_25418.p1, initial, 194512, 194703
-recovered pasa_asmbl_25418.p1, internal, 194019, 194167
-recovered pasa_asmbl_25418.p1, internal, 194512, 194703
-recovered pasa_asmbl_25418.p1, internal, 195095, 195216
-recovered pasa_asmbl_25418.p1, internal, 195489, 195627
-recovered pasa_asmbl_25418.p1, internal, 195861, 195981
-recovered pasa_asmbl_25418.p1, internal, 196504, 196694
Valid prediction for GlimmerHMM_glimmerT_3377-T1
Valid prediction for Augustus_model.g2267.t1
Valid prediction for Augustus_model.g2249.t1
Valid prediction for snap_scaffold_2-snap.584-T1
Valid prediction for snap_scaffold_2-snap.563-T1
Valid prediction for snap_scaffold_2-snap.570-T1
Valid prediction for snap_scaffold_2-snap.569-T1
Valid prediction for GlimmerHMM_glimmerT_3360-T1
Valid prediction for GlimmerHMM_glimmerT_3389-T1
Valid prediction for snap_scaffold_2-snap.595-T1
Valid prediction for GlimmerHMM_glimmerT_3382-T1
Valid prediction for snap_scaffold_2-snap.576-T1
Couldn't classify 138966, 138993
Couldn't classify 140719, 140841
Sorry, prediction pasa_asmbl_24243.p1 fails validation.
(GAA)	 CG	138966-138993	GT	AGG
(ATG)	 AG	139076-139180	GT	CTG
(CCT)	 AG	139420-139576	GT	CGG
(CCC)	 AG	140127-140199	GT	AGG
(GTG)	 AG	140719-140841	GG	GGG
add_exon() Sorry, pasa_asmbl_24243.p1 139076-139180-initial-1 is invalid.
-recovered pasa_asmbl_24243.p1, initial, 139076, 139180
-recovered pasa_asmbl_24243.p1, internal, 139076, 139180
-recovered pasa_asmbl_24243.p1, internal, 139420, 139576
-recovered pasa_asmbl_24243.p1, internal, 140127, 140199
Valid prediction for Augustus_model.g2261.t1
Valid prediction for snap_scaffold_2-snap.567-T1
Valid prediction for snap_scaffold_2-snap.600-T1
Valid prediction for GlimmerHMM_glimmerT_3376-T1
Couldn't classify 196899, 197028
Sorry, prediction pasa_asmbl_25347.p1 fails validation.
(CAG)	 AG	196899-197028	GT	AGG
(ACC)	 AG	197110-197273	GT	AGG
(CTG)	 AG	197728-197857	GT	CTG
(ACG)	 AG	198262-198390	GT	TGG
(ACT)	 AG	198550-198626	GT	AGG
(CTG)	 AG	199026-199178	GA	GAG
-recovered pasa_asmbl_25347.p1, terminal, 199026, 199178
-recovered pasa_asmbl_25347.p1, internal, 196899, 197028
-recovered pasa_asmbl_25347.p1, internal, 197110, 197273
-recovered pasa_asmbl_25347.p1, internal, 197728, 197857
-recovered pasa_asmbl_25347.p1, internal, 198262, 198390
-recovered pasa_asmbl_25347.p1, internal, 198550, 198626
Valid prediction for snap_scaffold_2-snap.580-T1
Valid prediction for Augustus_model.g2248.t1
Valid prediction for snap_scaffold_2-snap.604-T1
Valid prediction for Augustus_model.g2258.t1
Valid prediction for GlimmerHMM_glimmerT_3366-T1
Valid prediction for snap_scaffold_2-snap.579-T1
Valid prediction for GlimmerHMM_glimmerT_3361-T1
Valid prediction for snap_scaffold_2-snap.583-T1
Valid prediction for snap_scaffold_2-snap.573-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g2256.t1
Valid prediction for GlimmerHMM_glimmerT_3388-T1
Valid prediction for GlimmerHMM_glimmerT_3379-T1
Valid prediction for snap_scaffold_2-snap.586-T1
Valid prediction for Augustus_model.g2259.t1
Valid prediction for GlimmerHMM_glimmerT_3384-T1
Couldn't classify 192371, 192559
Couldn't classify 192967, 193092
Sorry, prediction pasa_asmbl_25444.p2 fails validation.
(GTG)	 AA	192371-192559	GT	AGG
(GTC)	 AG	192967-193092	TC	GGT
Valid prediction for GlimmerHMM_glimmerT_3364-T1
Couldn't classify 182014, 182032
Couldn't classify 183073, 183099
Sorry, prediction pasa_asmbl_24248.p1 fails validation.
(GGG)	 CA	182014-182032	GT	TGG
(ACC)	 AG	182205-182369	GT	AGG
(CCC)	 AG	182716-182891	GT	AGG
(GTG)	 AG	183073-183099	GA	ACG
-recovered pasa_asmbl_24248.p1, internal, 182205, 182369
-recovered pasa_asmbl_24248.p1, internal, 182716, 182891
Valid prediction for snap_scaffold_2-snap.568-T1
Valid prediction for snap_scaffold_2-snap.594-T1
Valid prediction for GlimmerHMM_glimmerT_3378-T1
Valid prediction for GlimmerHMM_glimmerT_3373-T1
Valid prediction for snap_scaffold_2-snap.597-T1
Valid prediction for GlimmerHMM_glimmerT_3393-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 GlimmerHMM_glimmerT_3375-T1
Valid prediction for snap_scaffold_2-snap.592-T1
Valid prediction for HiQ_model.g2263.t1
Valid prediction for CodingQuarry_transcript_28475-T1
Valid prediction for snap_scaffold_2-snap.591-T1
Valid prediction for HiQ_model.g2251.t1
Valid prediction for snap_scaffold_2-snap.560-T1
Valid prediction for snap_scaffold_2-snap.603-T1
Valid prediction for GlimmerHMM_glimmerT_3370-T1
Valid prediction for snap_scaffold_2-snap.587-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for CodingQuarry_transcript_28474-T1
Valid prediction for Augustus_model.g2253.t1
Valid prediction for snap_scaffold_2-snap.599-T1
Valid prediction for snap_scaffold_2-snap.566-T1
Valid prediction for GlimmerHMM_glimmerT_3391-T1
Valid prediction for snap_scaffold_2-snap.581-T1
Valid prediction for HiQ_model.g2266.t1
Valid prediction for GlimmerHMM_glimmerT_3390-T1
Valid prediction for snap_scaffold_2-snap.602-T1
Valid prediction for GlimmerHMM_glimmerT_3374-T1
Valid prediction for CodingQuarry_transcript_28476-T1
Valid prediction for snap_scaffold_2-snap.574-T1
Valid prediction for snap_scaffold_2-snap.598-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_3365-T1
Valid prediction for snap_scaffold_2-snap.589-T1
Valid prediction for snap_scaffold_2-snap.572-T1
Valid prediction for snap_scaffold_2-snap.593-T1
Valid prediction for snap_scaffold_2-snap.585-T1
Valid prediction for snap_scaffold_2-snap.590-T1
Valid prediction for snap_scaffold_2-snap.596-T1
Valid prediction for Augustus_model.g2255.t1
Valid prediction for snap_scaffold_2-snap.562-T1
Valid prediction for GlimmerHMM_glimmerT_3380-T1
Valid prediction for pasa_asmbl_22907.p1
Valid prediction for snap_scaffold_2-snap.601-T1
Valid prediction for GlimmerHMM_glimmerT_3362-T1
Valid prediction for pasa_asmbl_22897.p1
Valid prediction for GlimmerHMM_glimmerT_3369-T1
Valid prediction for GlimmerHMM_glimmerT_3381-T1
Valid prediction for GlimmerHMM_glimmerT_3359-T1
Valid prediction for GlimmerHMM_glimmerT_3372-T1
Valid prediction for GlimmerHMM_glimmerT_3383-T1
Valid prediction for snap_scaffold_2-snap.577-T1
Valid prediction for Augustus_model.g2264.t1
Valid prediction for snap_scaffold_2-snap.571-T1
Valid prediction for CodingQuarry_transcript_28479-T1
Valid prediction for GlimmerHMM_glimmerT_3386-T1
Valid prediction for Augustus_model.g2257.t1
Valid prediction for pasa_asmbl_22895.p1
Valid prediction for Augustus_model.g2254.t1
Valid prediction for snap_scaffold_2-snap.582-T1
Valid prediction for snap_scaffold_2-snap.561-T1
Valid prediction for CodingQuarry_transcript_28480-T1
Valid prediction for CodingQuarry_transcript_28473-T1
Valid prediction for snap_scaffold_2-snap.575-T1
Valid prediction for pasa_asmbl_22900.p1
Valid prediction for snap_scaffold_2-snap.564-T1
Valid prediction for GlimmerHMM_glimmerT_3385-T1
Valid prediction for Augustus_model.g2252.t1
Valid prediction for CodingQuarry_transcript_28478-T1
Valid prediction for GlimmerHMM_glimmerT_3363-T1
Valid prediction for HiQ_model.g2260.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 17561, rend_intergenic: 5460  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34716, rend_intergenic: 17994  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37471, rend_intergenic: 35981  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50763, rend_intergenic: 45811  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77733, rend_intergenic: 73693  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80559, rend_intergenic: 78767  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98954, rend_intergenic: 80789  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103599, rend_intergenic: 98964  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108305, rend_intergenic: 103608  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111684, rend_intergenic: 108797  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126529, rend_intergenic: 121500  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153006, rend_intergenic: 135237  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171760, rend_intergenic: 167280  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175220, rend_intergenic: 172966  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182115, rend_intergenic: 179814  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199178, rend_intergenic: 182249  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 208170
-exon list size: 551


building trellis

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90.8    
91.0    
91.1    
91.3    
91.5    
91.7    
91.9    
92.0    
92.2    
92.4    
92.6    
92.8    
92.9    
93.1    
93.3    
93.5    
93.7    
93.9    
94.0    
94.2    
94.4    
94.6    
94.8    
94.9    
95.1    
95.3    
95.5    
95.7    
95.8    
96.0    
96.2    
96.4    
96.6    
96.7    
96.9    
97.1    
97.3    
97.5    
97.6    
97.8    
98.0    
98.2    
98.4    
98.6    
98.7    
98.9    
99.1    
99.3    
99.5    
99.6    
99.8    
-found 36 predictions from path traversal
Error with prediction: snap lend_intergenic: 17561, rend_intergenic: 5460  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34716, rend_intergenic: 17994  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37471, rend_intergenic: 35981  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50763, rend_intergenic: 45811  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77733, rend_intergenic: 73693  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80559, rend_intergenic: 78767  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98954, rend_intergenic: 80789  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103599, rend_intergenic: 98964  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108305, rend_intergenic: 103608  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111684, rend_intergenic: 108797  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126529, rend_intergenic: 121500  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153006, rend_intergenic: 135237  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171760, rend_intergenic: 167280  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175220, rend_intergenic: 172966  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182115, rend_intergenic: 179814  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199178, rend_intergenic: 182249  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 26 predictions persist after filtering for low support