-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_3/scaffold_3_15607964-15859772

-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_3-snap.3005-T1
Valid prediction for snap_scaffold_3-snap.3017-T1
Valid prediction for snap_scaffold_3-snap.3012-T1
Valid prediction for snap_scaffold_3-snap.3008-T1
Valid prediction for GlimmerHMM_glimmerT_7904-T1
Valid prediction for GlimmerHMM_glimmerT_7925-T1
Valid prediction for GlimmerHMM_glimmerT_7928-T1
Valid prediction for GlimmerHMM_glimmerT_7912-T1
Valid prediction for snap_scaffold_3-snap.3010-T1
Valid prediction for snap_scaffold_3-snap.2993-T1
Valid prediction for Augustus_model.g5230.t1
Valid prediction for snap_scaffold_3-snap.2996-T1
Valid prediction for snap_scaffold_3-snap.2977-T1
Valid prediction for snap_scaffold_3-snap.2992-T1
Valid prediction for Augustus_model.g5218.t1
Valid prediction for snap_scaffold_3-snap.3013-T1
Valid prediction for snap_scaffold_3-snap.3019-T1
Valid prediction for Augustus_model.g5229.t1
Valid prediction for Augustus_model.g5231.t1
Valid prediction for snap_scaffold_3-snap.2988-T1
Valid prediction for snap_scaffold_3-snap.3016-T1
Valid prediction for GlimmerHMM_glimmerT_7911-T1
Valid prediction for snap_scaffold_3-snap.2984-T1
Valid prediction for GlimmerHMM_glimmerT_7923-T1
Valid prediction for snap_scaffold_3-snap.2980-T1
Valid prediction for snap_scaffold_3-snap.2985-T1
Valid prediction for snap_scaffold_3-snap.3022-T1
Valid prediction for GlimmerHMM_glimmerT_7915-T1
Valid prediction for snap_scaffold_3-snap.2997-T1
Valid prediction for GlimmerHMM_glimmerT_7929-T1
Valid prediction for GlimmerHMM_glimmerT_7906-T1
Valid prediction for GlimmerHMM_glimmerT_7917-T1
Valid prediction for GlimmerHMM_glimmerT_7931-T1
Valid prediction for snap_scaffold_3-snap.2990-T1
Couldn't classify 193250, 193561
Sorry, prediction pasa_asmbl_40578.p2 fails validation.
(ATG)	 AG	193250-193561	TA	GGT
Valid prediction for CodingQuarry_transcript_46390-T1
Valid prediction for snap_scaffold_3-snap.2982-T1
Valid prediction for snap_scaffold_3-snap.2991-T1
Valid prediction for snap_scaffold_3-snap.3020-T1
Valid prediction for snap_scaffold_3-snap.2998-T1
Couldn't classify 186114, 186229
Sorry, prediction pasa_asmbl_40884.p1 fails validation.
(ATG)	 AG	185194-185252	GT	TGG
(CAA)	 AG	185356-185470	GT	AGG
(GGT)	 AG	185700-185826	GT	AGG
(GAG)	 AG	186114-186229	AT	CTA
-recovered pasa_asmbl_40884.p1, initial, 185194, 185252
-recovered pasa_asmbl_40884.p1, internal, 185194, 185252
-recovered pasa_asmbl_40884.p1, internal, 185356, 185470
-recovered pasa_asmbl_40884.p1, internal, 185700, 185826
Valid prediction for Augustus_model.g5226.t1
Couldn't classify 215659, 215760
Couldn't classify 222384, 222473
Sorry, prediction pasa_asmbl_40581.p1 fails validation.
(GCG)	 GG	215659-215760	GT	TGG
(AAT)	 AG	216607-216687	GT	AGG
(GTG)	 AG	218303-218397	GT	AGG
(TGG)	 AG	218790-218913	GT	AGG
(GTG)	 AG	219027-219120	GT	ACG
(ACC)	 AG	221486-221601	GT	AGG
(GCC)	 AG	222384-222473	CA	GCC
-recovered pasa_asmbl_40581.p1, internal, 216607, 216687
-recovered pasa_asmbl_40581.p1, internal, 218303, 218397
-recovered pasa_asmbl_40581.p1, internal, 218790, 218913
-recovered pasa_asmbl_40581.p1, internal, 219027, 219120
-recovered pasa_asmbl_40581.p1, internal, 221486, 221601
Valid prediction for Augustus_model.g5228.t1
Valid prediction for GlimmerHMM_glimmerT_7913-T1
Valid prediction for GlimmerHMM_glimmerT_7908-T1
Valid prediction for GlimmerHMM_glimmerT_7927-T1
Valid prediction for GlimmerHMM_glimmerT_7914-T1
Valid prediction for Augustus_model.g5216.t1
Valid prediction for snap_scaffold_3-snap.2981-T1
Valid prediction for snap_scaffold_3-snap.2987-T1
Valid prediction for Augustus_model.g5227.t1
Valid prediction for GlimmerHMM_glimmerT_7907-T1
Valid prediction for snap_scaffold_3-snap.3018-T1
Valid prediction for Augustus_model.g5224.t1
Valid prediction for snap_scaffold_3-snap.2975-T1
Valid prediction for snap_scaffold_3-snap.3014-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 CodingQuarry_transcript_46385-T1
Valid prediction for snap_scaffold_3-snap.3000-T1
Valid prediction for Augustus_model.g5223.t1
Valid prediction for snap_scaffold_3-snap.3004-T1
Valid prediction for snap_scaffold_3-snap.2979-T1
Valid prediction for pasa_asmbl_39446.p1
Valid prediction for GlimmerHMM_glimmerT_7924-T1
Valid prediction for snap_scaffold_3-snap.2986-T1
Valid prediction for pasa_asmbl_39440.p1
Valid prediction for snap_scaffold_3-snap.3021-T1
Valid prediction for CodingQuarry_transcript_46388-T1
Valid prediction for snap_scaffold_3-snap.2989-T1
Valid prediction for GlimmerHMM_glimmerT_7919-T1
Valid prediction for snap_scaffold_3-snap.3015-T1
Valid prediction for CodingQuarry_transcript_46384-T1
Valid prediction for snap_scaffold_3-snap.2976-T1
Valid prediction for Augustus_model.g5221.t1
Valid prediction for GlimmerHMM_glimmerT_7905-T1
Valid prediction for snap_scaffold_3-snap.3009-T1
Valid prediction for Augustus_model.g5232.t1
Couldn't classify 186745, 186877
Couldn't classify 193517, 193540
Sorry, prediction pasa_asmbl_39436.p1 fails validation.
(CTC)	 AG	186745-186877	GT	AGG
(GGA)	 AG	188233-188441	GT	AGG
(GTT)	 AG	190982-191039	GT	AGG
(GTG)	 AG	191329-191417	GT	AGG
(GTA)	 AG	193517-193540	GG	AAG
-recovered pasa_asmbl_39436.p1, internal, 186745, 186877
-recovered pasa_asmbl_39436.p1, internal, 188233, 188441
-recovered pasa_asmbl_39436.p1, internal, 190982, 191039
-recovered pasa_asmbl_39436.p1, internal, 191329, 191417
Valid prediction for pasa_asmbl_39449.p1
Valid prediction for GlimmerHMM_glimmerT_7920-T1
Valid prediction for GlimmerHMM_glimmerT_7909-T1
Valid prediction for CodingQuarry_transcript_46383-T1
Valid prediction for GlimmerHMM_glimmerT_7903-T1
Valid prediction for Augustus_model.g5222.t1
Valid prediction for GlimmerHMM_glimmerT_7926-T1
Valid prediction for GlimmerHMM_glimmerT_7918-T1
Valid prediction for GlimmerHMM_glimmerT_7910-T1
Valid prediction for snap_scaffold_3-snap.3007-T1
Valid prediction for CodingQuarry_transcript_46389-T1
Couldn't classify 1111, 1173
Sorry, prediction pasa_asmbl_39776.p1 fails validation.
(TTT)	 CC	1111-1173	GT	AGG
(CGT)	 AG	1574-1794	GT	TTG
(CAC)	 AG	2735-2874	GT	AGG
(GAT)	 AG	3050-3203	GT	AAG
(AGA)	 AG	4097-4185	GT	CAG
(GAA)	 AG	6666-6742	GT	AGG
(CCC)	 AG	6939-7098	GT	AGG
(ATG)	 AG	7702-7855	GT	AAG
(TTA)	 AG	8296-8372	GT	GGG
(GTG)	 AG	8586-8662	GT	AGG
(GCC)	 AG	8769-8908	GT	AAG
(GTT)	 AG	10633-10687	GT	AGG
(GTG)	 AG	10810-10953	GT	GGG
(ATC)	 AG	12231-12272	CC	AAC
-recovered pasa_asmbl_39776.p1, initial, 7702, 7855
-recovered pasa_asmbl_39776.p1, terminal, 12231, 12272
-recovered pasa_asmbl_39776.p1, internal, 1574, 1794
-recovered pasa_asmbl_39776.p1, internal, 2735, 2874
-recovered pasa_asmbl_39776.p1, internal, 3050, 3203
-recovered pasa_asmbl_39776.p1, internal, 4097, 4185
-recovered pasa_asmbl_39776.p1, internal, 6666, 6742
-recovered pasa_asmbl_39776.p1, internal, 6939, 7098
-recovered pasa_asmbl_39776.p1, internal, 7702, 7855
-recovered pasa_asmbl_39776.p1, internal, 8296, 8372
-recovered pasa_asmbl_39776.p1, internal, 8586, 8662
-recovered pasa_asmbl_39776.p1, internal, 8769, 8908
-recovered pasa_asmbl_39776.p1, internal, 10633, 10687
-recovered pasa_asmbl_39776.p1, internal, 10810, 10953
Valid prediction for GlimmerHMM_glimmerT_7922-T1
Valid prediction for snap_scaffold_3-snap.2995-T1
Valid prediction for snap_scaffold_3-snap.3002-T1
Valid prediction for HiQ_model.g5233.t1
Valid prediction for GlimmerHMM_glimmerT_7930-T1
Valid prediction for snap_scaffold_3-snap.2999-T1
Couldn't classify 96275, 96319
Couldn't classify 97246, 97344
Sorry, prediction pasa_asmbl_39445.p1 fails validation.
(CGC)	 AA	96275-96319	GT	AGG
(GAC)	 AG	96408-96484	GT	AAG
(TGG)	 AG	96600-96687	GT	AGG
(GTG)	 AG	96783-96863	GT	GGG
(GAG)	 AG	97075-97167	GT	AGG
(GCC)	 AG	97246-97344	AA	CCA
-recovered pasa_asmbl_39445.p1, internal, 96408, 96484
-recovered pasa_asmbl_39445.p1, internal, 96600, 96687
-recovered pasa_asmbl_39445.p1, internal, 96783, 96863
-recovered pasa_asmbl_39445.p1, internal, 97075, 97167
Valid prediction for Augustus_model.g5219.t1
Valid prediction for snap_scaffold_3-snap.3003-T1
Couldn't classify 77664, 77716
Couldn't classify 77813, 77813
Sorry, prediction CodingQuarry_transcript_46386-T1 fails validation.
(ATG)	 AG	74573-74729	GT	GGG
(GTG)	 AG	75083-75787	GT	CAG
(GTG)	 AG	76079-76774	GT	CAG
(TGA)	 AG	77096-77179	GT	GAG
(CGT)	 AG	77395-77555	GT	CGG
(ATC)	 AG	77664-77716	TA	TAT
(GGC)	 CA	77813-77813	GC	AGG
-recovered CodingQuarry_transcript_46386-T1, initial, 74573, 74729
-recovered CodingQuarry_transcript_46386-T1, internal, 74573, 74729
-recovered CodingQuarry_transcript_46386-T1, internal, 75083, 75787
-recovered CodingQuarry_transcript_46386-T1, internal, 76079, 76774
-recovered CodingQuarry_transcript_46386-T1, internal, 77096, 77179
-recovered CodingQuarry_transcript_46386-T1, internal, 77395, 77555
Valid prediction for snap_scaffold_3-snap.2983-T1
Valid prediction for CodingQuarry_transcript_46382-T1
Valid prediction for GlimmerHMM_glimmerT_7921-T1
Valid prediction for CodingQuarry_transcript_46387-T1
Valid prediction for snap_scaffold_3-snap.2978-T1
Valid prediction for HiQ_model.g5220.t1
Valid prediction for HiQ_model.g5225.t1
Valid prediction for snap_scaffold_3-snap.3011-T1
Valid prediction for GlimmerHMM_glimmerT_7916-T1
Valid prediction for HiQ_model.g5217.t1
Valid prediction for pasa_asmbl_39444.p1
Valid prediction for snap_scaffold_3-snap.2994-T1
Valid prediction for GlimmerHMM_glimmerT_7932-T1
Valid prediction for snap_scaffold_3-snap.3001-T1
Valid prediction for snap_scaffold_3-snap.3006-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 9121, rend_intergenic: 2877  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34503, rend_intergenic: 30492  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87591, rend_intergenic: 77656  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108336, rend_intergenic: 102256  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114711, rend_intergenic: 109203  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124096, rend_intergenic: 117876  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160295, rend_intergenic: 154486  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177968, rend_intergenic: 172259  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 216334, rend_intergenic: 212633  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 250197, rend_intergenic: 242624  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 251809
-exon list size: 414


building trellis

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-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 9121, rend_intergenic: 2877  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34503, rend_intergenic: 30492  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87591, rend_intergenic: 77656  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108336, rend_intergenic: 102256  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114711, rend_intergenic: 109203  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124096, rend_intergenic: 117876  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160295, rend_intergenic: 154486  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177968, rend_intergenic: 172259  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 216334, rend_intergenic: 212633  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 250197, rend_intergenic: 242624  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

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