-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_1/scaffold_1_18023164-18277974

-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_1-snap.3320-T1
Couldn't classify 251884, 252093
Sorry, prediction pasa_asmbl_2545.p1 fails validation.
(GTG)	 TG	251884-252093	GT	GTG
(CTT)	 AG	252189-252300	GT	GGG
(ATC)	 AG	252402-252433	GT	AGG
(GAT)	 AG	252634-252727	GT	GGG
(TTT)	 AG	252828-252877	GT	AGG
(GAT)	 AG	252968-253231	CC	GAC
-recovered pasa_asmbl_2545.p1, terminal, 252968, 253231
-recovered pasa_asmbl_2545.p1, internal, 252189, 252300
-recovered pasa_asmbl_2545.p1, internal, 252402, 252433
-recovered pasa_asmbl_2545.p1, internal, 252634, 252727
-recovered pasa_asmbl_2545.p1, internal, 252828, 252877
Valid prediction for GlimmerHMM_glimmerT_2436-T1
Valid prediction for GlimmerHMM_glimmerT_2427-T1
Couldn't classify 6001, 7440
Sorry, prediction pasa_asmbl_2701.p1 fails validation.
(ACA)	 AG	6001-7440	GG	AGG
Valid prediction for GlimmerHMM_glimmerT_2440-T1
Valid prediction for Augustus_model.g1782.t1
Valid prediction for snap_scaffold_1-snap.3322-T1
Valid prediction for snap_scaffold_1-snap.3314-T1
Valid prediction for GlimmerHMM_glimmerT_2432-T1
Valid prediction for snap_scaffold_1-snap.3287-T1
Valid prediction for snap_scaffold_1-snap.3318-T1
Valid prediction for snap_scaffold_1-snap.3311-T1
Valid prediction for snap_scaffold_1-snap.3325-T1
Valid prediction for CodingQuarry_transcript_2992-T1
Valid prediction for snap_scaffold_1-snap.3317-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g1781.t1
Valid prediction for GlimmerHMM_glimmerT_2438-T1
Valid prediction for Augustus_model.g1777.t1
Valid prediction for CodingQuarry_transcript_2991-T1
Valid prediction for GlimmerHMM_glimmerT_2414-T1
Valid prediction for snap_scaffold_1-snap.3319-T1
Valid prediction for snap_scaffold_1-snap.3289-T1
Valid prediction for snap_scaffold_1-snap.3301-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_1-snap.3295-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_1-snap.3310-T1
Valid prediction for snap_scaffold_1-snap.3279-T1
Valid prediction for snap_scaffold_1-snap.3299-T1
Valid prediction for Augustus_model.g1776.t1
Valid prediction for GlimmerHMM_glimmerT_2437-T1
Valid prediction for GlimmerHMM_glimmerT_2434-T1
Valid prediction for GlimmerHMM_glimmerT_2428-T1
Valid prediction for GlimmerHMM_glimmerT_2424-T1
Valid prediction for snap_scaffold_1-snap.3294-T1
Valid prediction for Augustus_model.g1779.t1
Valid prediction for GlimmerHMM_glimmerT_2420-T1
Valid prediction for snap_scaffold_1-snap.3286-T1
Valid prediction for Augustus_model.g1763.t1
Valid prediction for Augustus_model.g1769.t1
Valid prediction for snap_scaffold_1-snap.3298-T1
Valid prediction for GlimmerHMM_glimmerT_2426-T1
Valid prediction for snap_scaffold_1-snap.3326-T1
Couldn't classify 6110, 6118
Couldn't classify 6845, 7204
Sorry, prediction CodingQuarry_transcript_2983-T1 fails validation.
(ATG)	 AA	6110-6118	CT	ACC
(CTT)	 AC	6845-7204	CC	GAC

-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_2425-T1
Valid prediction for snap_scaffold_1-snap.3285-T1
Valid prediction for snap_scaffold_1-snap.3312-T1
Valid prediction for CodingQuarry_transcript_2989-T1
Valid prediction for CodingQuarry_transcript_2987-T1
Couldn't classify 178045, 178257
Sorry, prediction pasa_asmbl_1094.p1 fails validation.
(ATG)	 AG	174890-175129	GT	AGG
(GCG)	 AG	178045-178257	GT	AGG
-recovered pasa_asmbl_1094.p1, initial, 174890, 175129
-recovered pasa_asmbl_1094.p1, internal, 174890, 175129
-recovered pasa_asmbl_1094.p1, internal, 178045, 178257
Valid prediction for snap_scaffold_1-snap.3305-T1
Valid prediction for Augustus_model.g1778.t1
Valid prediction for snap_scaffold_1-snap.3303-T1
Valid prediction for snap_scaffold_1-snap.3282-T1
Valid prediction for GlimmerHMM_glimmerT_2421-T1
Valid prediction for snap_scaffold_1-snap.3307-T1
Valid prediction for snap_scaffold_1-snap.3321-T1
Valid prediction for Augustus_model.g1773.t1
Valid prediction for snap_scaffold_1-snap.3304-T1
Valid prediction for CodingQuarry_transcript_2986-T1
Valid prediction for Augustus_model.g1767.t1
Valid prediction for Augustus_model.g1765.t1
Valid prediction for snap_scaffold_1-snap.3291-T1
Valid prediction for snap_scaffold_1-snap.3292-T1
Valid prediction for GlimmerHMM_glimmerT_2429-T1
Valid prediction for GlimmerHMM_glimmerT_2430-T1
Valid prediction for snap_scaffold_1-snap.3288-T1
Valid prediction for snap_scaffold_1-snap.3283-T1
Valid prediction for Augustus_model.g1766.t1
Valid prediction for GlimmerHMM_glimmerT_2418-T1
Valid prediction for GlimmerHMM_glimmerT_2417-T1
Valid prediction for CodingQuarry_transcript_2984-T1
Valid prediction for snap_scaffold_1-snap.3324-T1
Valid prediction for GlimmerHMM_glimmerT_2419-T1
Valid prediction for Augustus_model.g1775.t1
Valid prediction for snap_scaffold_1-snap.3290-T1
Valid prediction for snap_scaffold_1-snap.3297-T1
Valid prediction for Augustus_model.g1780.t1
Valid prediction for HiQ_model.g1770.t1
Valid prediction for GlimmerHMM_glimmerT_2422-T1
Valid prediction for GlimmerHMM_glimmerT_2433-T1
Valid prediction for snap_scaffold_1-snap.3300-T1
Valid prediction for snap_scaffold_1-snap.3323-T1
Couldn't classify 232869, 232997
Sorry, prediction pasa_asmbl_1083.p1 fails validation.
(AAA)	 AG	232869-232997	GT	AGG
(GGG)	 AG	233148-233324	GT	CAG
(AAA)	 AG	233469-233590	GT	GAG
(GCT)	 AG	233895-234121	GT	TGG
(GGT)	 AG	234514-234546	GT	GAG
(AAC)	 AG	235047-235211	GT	AGG
(TTC)	 AG	235378-235455	GT	AGG
(TGA)	 AG	235702-235806	GT	CGG
(AGC)	 AG	236192-236369	GT	AGG
(GCT)	 AG	236551-236696	GT	AGG
(CTG)	 AG	236864-236945	GT	AGG
(GTC)	 AG	237062-237173	CT	AAC
-recovered pasa_asmbl_1083.p1, terminal, 234514, 234546
add_exon() Sorry, pasa_asmbl_1083.p1 236551-236696-terminal-2 is invalid.
-recovered pasa_asmbl_1083.p1, terminal, 236551, 236696
-recovered pasa_asmbl_1083.p1, terminal, 237062, 237173
-recovered pasa_asmbl_1083.p1, internal, 232869, 232997
-recovered pasa_asmbl_1083.p1, internal, 233148, 233324
-recovered pasa_asmbl_1083.p1, internal, 233469, 233590
-recovered pasa_asmbl_1083.p1, internal, 233895, 234121
-recovered pasa_asmbl_1083.p1, internal, 234514, 234546
-recovered pasa_asmbl_1083.p1, internal, 235047, 235211
-recovered pasa_asmbl_1083.p1, internal, 235378, 235455
-recovered pasa_asmbl_1083.p1, internal, 235702, 235806
-recovered pasa_asmbl_1083.p1, internal, 236192, 236369
-recovered pasa_asmbl_1083.p1, internal, 236551, 236696
-recovered pasa_asmbl_1083.p1, internal, 236864, 236945
Valid prediction for Augustus_model.g1772.t1
Valid prediction for snap_scaffold_1-snap.3293-T1
Valid prediction for snap_scaffold_1-snap.3284-T1
Valid prediction for GlimmerHMM_glimmerT_2435-T1
Valid prediction for Augustus_model.g1774.t1
Valid prediction for GlimmerHMM_glimmerT_2413-T1
Valid prediction for GlimmerHMM_glimmerT_2439-T1
Valid prediction for GlimmerHMM_glimmerT_2423-T1
Valid prediction for HiQ_model.g1764.t1
Valid prediction for GlimmerHMM_glimmerT_2431-T1
Valid prediction for snap_scaffold_1-snap.3315-T1
Valid prediction for snap_scaffold_1-snap.3309-T1
Valid prediction for Augustus_model.g1768.t1
Couldn't classify 243024, 243566
Sorry, prediction pasa_asmbl_1082.p1 fails validation.
(GTG)	 GG	243024-243566	GA	AGG
Valid prediction for pasa_asmbl_1079.p1
Valid prediction for GlimmerHMM_glimmerT_2415-T1
Valid prediction for snap_scaffold_1-snap.3316-T1
Valid prediction for snap_scaffold_1-snap.3306-T1
Valid prediction for snap_scaffold_1-snap.3308-T1
Valid prediction for snap_scaffold_1-snap.3313-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for snap_scaffold_1-snap.3281-T1
Valid prediction for pasa_asmbl_1087.p1
Valid prediction for snap_scaffold_1-snap.3280-T1
Couldn't classify 181267, 182325
Sorry, prediction pasa_asmbl_1092.p1 fails validation.
(CAG)	 TG	181267-182325	GT	AGG
Valid prediction for snap_scaffold_1-snap.3296-T1
Valid prediction for GlimmerHMM_glimmerT_2416-T1
Valid prediction for Augustus_model.g1771.t1
Valid prediction for snap_scaffold_1-snap.3302-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for CodingQuarry_transcript_2990-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 47531, rend_intergenic: 33621  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91426, rend_intergenic: 85250  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99376, rend_intergenic: 91444  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111658, rend_intergenic: 104843  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121258, rend_intergenic: 115623  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169337, rend_intergenic: 122052  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 183344, rend_intergenic: 173903  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 194766, rend_intergenic: 183813  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 204059, rend_intergenic: 199762  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 225355, rend_intergenic: 221809  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 247070, rend_intergenic: 226328  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 254811
-exon list size: 538


building trellis

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98.1    
98.3    
98.5    
98.7    
98.9    
99.1    
99.3    
99.4    
99.6    
99.8    
-found 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 47531, rend_intergenic: 33621  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91426, rend_intergenic: 85250  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99376, rend_intergenic: 91444  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111658, rend_intergenic: 104843  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121258, rend_intergenic: 115623  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169337, rend_intergenic: 122052  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 183344, rend_intergenic: 173903  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 194766, rend_intergenic: 183813  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 204059, rend_intergenic: 199762  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 225355, rend_intergenic: 221809  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 247070, rend_intergenic: 226328  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 24 predictions persist after filtering for low support