-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_23/scaffold_23_4449725-4915542

-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_50945-T1
Valid prediction for CodingQuarry_transcript_35640-T1
Valid prediction for GlimmerHMM_glimmerT_50937-T1
Valid prediction for GlimmerHMM_glimmerT_50942-T1
Couldn't classify 127802, 127942
Couldn't classify 129786, 129829
Sorry, prediction pasa_asmbl_31977.p1 fails validation.
(GGA)	 CT	127802-127942	GT	AGG
(GTC)	 AG	128101-128208	GT	AGG
(GCT)	 AG	128383-128506	GT	CGG
(CTC)	 AG	129786-129829	GC	TGG
-recovered pasa_asmbl_31977.p1, internal, 128101, 128208
-recovered pasa_asmbl_31977.p1, internal, 128383, 128506
-recovered pasa_asmbl_31977.p1, internal, 129786, 129829
Valid prediction for snap_scaffold_23-snap.861-T1
Valid prediction for snap_scaffold_23-snap.856-T1
Valid prediction for snap_scaffold_23-snap.896-T1
Valid prediction for GlimmerHMM_glimmerT_50959-T1
Couldn't classify 132003, 132027
Sorry, prediction pasa_asmbl_31519.p1 fails validation.
(ATC)	 AC	132003-132027	GT	AGG
(ATG)	 AG	133111-133210	GT	AGG
(ACC)	 AG	134435-134546	GT	CGG
(GGT)	 AG	136053-136193	GT	AGG
(GCA)	 AG	136642-136748	GT	CAG
(TGA)	 AG	137462-137541	GT	AGG
(ACG)	 AG	138183-138326	GT	AGG
(ATG)	 AG	140143-140190	GC	AGG
(ACA)	 AG	141127-141249	GT	TGG
(GCC)	 AG	141556-141667	GT	TCG
(AAT)	 AG	142775-142861	GT	AAG
(TGT)	 AG	143372-143507	GT	AGG
(AGT)	 AG	143877-143944	GT	ATG
(GAG)	 AG	145329-145464	AC	AAA
add_exon() Sorry, pasa_asmbl_31519.p1 133111-133210-initial-1 is invalid.
-recovered pasa_asmbl_31519.p1, initial, 133111, 133210
add_exon() Sorry, pasa_asmbl_31519.p1 140143-140190-initial-1 is invalid.
-recovered pasa_asmbl_31519.p1, initial, 140143, 140190
-recovered pasa_asmbl_31519.p1, terminal, 145329, 145464
-recovered pasa_asmbl_31519.p1, internal, 133111, 133210
-recovered pasa_asmbl_31519.p1, internal, 134435, 134546
-recovered pasa_asmbl_31519.p1, internal, 136053, 136193
-recovered pasa_asmbl_31519.p1, internal, 136642, 136748
-recovered pasa_asmbl_31519.p1, internal, 137462, 137541
-recovered pasa_asmbl_31519.p1, internal, 138183, 138326
-recovered pasa_asmbl_31519.p1, internal, 140143, 140190
-recovered pasa_asmbl_31519.p1, internal, 141127, 141249
-recovered pasa_asmbl_31519.p1, internal, 141556, 141667
-recovered pasa_asmbl_31519.p1, internal, 142775, 142861
-recovered pasa_asmbl_31519.p1, internal, 143372, 143507
-recovered pasa_asmbl_31519.p1, internal, 143877, 143944
Valid prediction for Augustus_model.g34069.t1
Valid prediction for snap_scaffold_23-snap.897-T1
Valid prediction for CodingQuarry_transcript_35645-T1
Valid prediction for snap_scaffold_23-snap.857-T1
Valid prediction for Augustus_model.g34068.t1
Valid prediction for CodingQuarry_transcript_35641-T1
Valid prediction for snap_scaffold_23-snap.892-T1
Valid prediction for Augustus_model.g34070.t1
Valid prediction for snap_scaffold_23-snap.899-T1
Valid prediction for Augustus_model.g34071.t1
Valid prediction for HiQ_model.g34047.t1
Couldn't classify 236063, 236096
Couldn't classify 239693, 239887
Sorry, prediction pasa_asmbl_31525.p1 fails validation.
(TTT)	 AG	236063-236096	GT	AGG
(GTC)	 AG	236737-236895	GT	AGG
(GTG)	 AG	237952-238076	GT	AGG
(GTT)	 AG	239693-239887	GT	AAG
add_exon() Sorry, pasa_asmbl_31525.p1 236737-236895-terminal-1 is invalid.
-recovered pasa_asmbl_31525.p1, terminal, 236737, 236895
-recovered pasa_asmbl_31525.p1, internal, 236063, 236096
-recovered pasa_asmbl_31525.p1, internal, 236737, 236895
-recovered pasa_asmbl_31525.p1, internal, 237952, 238076
-recovered pasa_asmbl_31525.p1, internal, 239693, 239887
Valid prediction for GlimmerHMM_glimmerT_50954-T1
Valid prediction for GlimmerHMM_glimmerT_50936-T1
Valid prediction for snap_scaffold_23-snap.858-T1
Valid prediction for snap_scaffold_23-snap.846-T1
Valid prediction for snap_scaffold_23-snap.879-T1
Valid prediction for Augustus_model.g34077.t1
Valid prediction for CodingQuarry_transcript_35643-T1
Valid prediction for GlimmerHMM_glimmerT_50949-T1
Valid prediction for Augustus_model.g34063.t1
Valid prediction for snap_scaffold_23-snap.900-T1
Valid prediction for snap_scaffold_23-snap.860-T1
Valid prediction for CodingQuarry_transcript_35642-T1
Valid prediction for Augustus_model.g34055.t1
Valid prediction for GlimmerHMM_glimmerT_50968-T1
Valid prediction for Augustus_model.g34053.t1
Valid prediction for snap_scaffold_23-snap.887-T1
Valid prediction for snap_scaffold_23-snap.890-T1
Valid prediction for snap_scaffold_23-snap.849-T1
Valid prediction for snap_scaffold_23-snap.895-T1
Valid prediction for snap_scaffold_23-snap.848-T1
Valid prediction for snap_scaffold_23-snap.850-T1
Valid prediction for snap_scaffold_23-snap.889-T1
Couldn't classify 339404, 339908
Couldn't classify 341282, 341415
Sorry, prediction pasa_asmbl_31939.p1 fails validation.
(AGT)	 TC	339404-339908	GT	AGG
(GTG)	 AG	341282-341415	CC	GAC
Valid prediction for snap_scaffold_23-snap.854-T1
Valid prediction for Augustus_model.g34074.t1
Valid prediction for pasa_asmbl_31516.p1
Valid prediction for Augustus_model.g34082.t1
Valid prediction for snap_scaffold_23-snap.874-T1
Valid prediction for snap_scaffold_23-snap.884-T1
Valid prediction for Augustus_model.g34067.t1
Valid prediction for Augustus_model.g34078.t1
Valid prediction for pasa_asmbl_31528.p1
Valid prediction for CodingQuarry_transcript_35646-T1
Valid prediction for HiQ_model.g34051.t1
Valid prediction for Augustus_model.g34066.t1
Valid prediction for snap_scaffold_23-snap.876-T1
Valid prediction for Augustus_model.g34054.t1
Valid prediction for snap_scaffold_23-snap.859-T1
Valid prediction for snap_scaffold_23-snap.847-T1
Valid prediction for snap_scaffold_23-snap.898-T1
Valid prediction for snap_scaffold_23-snap.869-T1
Couldn't classify 126812, 126883
Couldn't classify 127579, 127629
Sorry, prediction pasa_asmbl_31962.p1 fails validation.
(CGA)	 TC	126812-126883	GT	AGG
(GCT)	 AG	127054-127162	GT	TGG
(CCT)	 AG	127374-127498	GT	CAG
(GAT)	 AG	127579-127629	GG	CAG
-recovered pasa_asmbl_31962.p1, internal, 127054, 127162
-recovered pasa_asmbl_31962.p1, internal, 127374, 127498
Valid prediction for GlimmerHMM_glimmerT_50960-T1
Valid prediction for snap_scaffold_23-snap.891-T1
Valid prediction for snap_scaffold_23-snap.877-T1
Valid prediction for snap_scaffold_23-snap.903-T1
Valid prediction for GlimmerHMM_glimmerT_50967-T1
Valid prediction for snap_scaffold_23-snap.886-T1
Valid prediction for GlimmerHMM_glimmerT_50956-T1
Valid prediction for pasa_asmbl_31526.p1
Valid prediction for Augustus_model.g34049.t1
Valid prediction for Augustus_model.g34062.t1
Valid prediction for snap_scaffold_23-snap.872-T1
Valid prediction for GlimmerHMM_glimmerT_50948-T1
Valid prediction for GlimmerHMM_glimmerT_50963-T1
Valid prediction for GlimmerHMM_glimmerT_50962-T1
Valid prediction for GlimmerHMM_glimmerT_50951-T1
Valid prediction for HiQ_model.g34081.t1
Valid prediction for GlimmerHMM_glimmerT_50940-T1
Valid prediction for GlimmerHMM_glimmerT_50941-T1
Valid prediction for snap_scaffold_23-snap.888-T1
Valid prediction for GlimmerHMM_glimmerT_50964-T1
Valid prediction for Augustus_model.g34056.t1
Couldn't classify 19611, 19636
Sorry, prediction pasa_asmbl_31511.p1 fails validation.
(CCC)	 AC	19611-19636	GT	AGG
(CTA)	 AG	21032-21133	GT	AGG
(GGT)	 AG	21295-21395	GT	TCG
(CCC)	 AG	23250-23342	GT	TGG
(CAT)	 AG	23803-23876	GT	GAG
-recovered pasa_asmbl_31511.p1, terminal, 23803, 23876
-recovered pasa_asmbl_31511.p1, internal, 21032, 21133
-recovered pasa_asmbl_31511.p1, internal, 21295, 21395
-recovered pasa_asmbl_31511.p1, internal, 23250, 23342
-recovered pasa_asmbl_31511.p1, internal, 23803, 23876
Valid prediction for Augustus_model.g34060.t1
Valid prediction for snap_scaffold_23-snap.885-T1
Valid prediction for snap_scaffold_23-snap.893-T1
Couldn't classify 58031, 58134
Couldn't classify 59265, 59275
Sorry, prediction CodingQuarry_transcript_35644-T1 fails validation.
(ATG)	 GG	53701-53797	GT	TGG
(GTC)	 AG	54709-55128	GT	AGG
(GGG)	 AG	55376-55521	GT	AGG
(GGT)	 AG	56153-56255	GT	CAG
(AGT)	 AG	56694-56857	GT	AGG
(GGA)	 AG	57394-57497	GT	AAG
(GTG)	 AG	58031-58134	TA	GGT
(CCA)	 GC	59265-59275	CA	AAC
-recovered CodingQuarry_transcript_35644-T1, initial, 53701, 53797
-recovered CodingQuarry_transcript_35644-T1, internal, 54709, 55128
-recovered CodingQuarry_transcript_35644-T1, internal, 55376, 55521
-recovered CodingQuarry_transcript_35644-T1, internal, 56153, 56255
-recovered CodingQuarry_transcript_35644-T1, internal, 56694, 56857
-recovered CodingQuarry_transcript_35644-T1, internal, 57394, 57497
Valid prediction for snap_scaffold_23-snap.855-T1
Valid prediction for snap_scaffold_23-snap.865-T1
Valid prediction for GlimmerHMM_glimmerT_50958-T1
Couldn't classify 42886, 43090
Sorry, prediction pasa_asmbl_31513.p1 fails validation.
(CCC)	 AC	42886-43090	GT	AGG
(AAG)	 AG	43312-43427	GT	AAG
(GCT)	 AG	43652-43775	GT	AGG
(GAG)	 AG	44071-44115	GC	AGG
(ACC)	 AG	44218-44424	GT	TGG
(AGC)	 AG	44600-44766	GC	GAG
add_exon() Sorry, pasa_asmbl_31513.p1 43652-43775-terminal-3 is invalid.
-recovered pasa_asmbl_31513.p1, terminal, 43652, 43775
-recovered pasa_asmbl_31513.p1, terminal, 44600, 44766
-recovered pasa_asmbl_31513.p1, internal, 43312, 43427
-recovered pasa_asmbl_31513.p1, internal, 43652, 43775
-recovered pasa_asmbl_31513.p1, internal, 44071, 44115
-recovered pasa_asmbl_31513.p1, internal, 44218, 44424
-recovered pasa_asmbl_31513.p1, internal, 44600, 44766
Valid prediction for GlimmerHMM_glimmerT_50943-T1
Valid prediction for GlimmerHMM_glimmerT_50955-T1
Valid prediction for Augustus_model.g34046.t1
Valid prediction for snap_scaffold_23-snap.853-T1
Valid prediction for snap_scaffold_23-snap.875-T1
Valid prediction for Augustus_model.g34076.t1
Valid prediction for GlimmerHMM_glimmerT_50965-T1
Valid prediction for HiQ_model.g34061.t1
Valid prediction for snap_scaffold_23-snap.873-T1
Valid prediction for Augustus_model.g34052.t1
Valid prediction for snap_scaffold_23-snap.878-T1
Valid prediction for GlimmerHMM_glimmerT_50944-T1
Valid prediction for Augustus_model.g34048.t1
Valid prediction for Augustus_model.g34073.t1
Valid prediction for GlimmerHMM_glimmerT_50957-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 snap_scaffold_23-snap.902-T1
Valid prediction for snap_scaffold_23-snap.866-T1
Valid prediction for Augustus_model.g34083.t1
Valid prediction for GlimmerHMM_glimmerT_50939-T1
Valid prediction for Augustus_model.g34057.t1
Valid prediction for snap_scaffold_23-snap.863-T1
Valid prediction for snap_scaffold_23-snap.852-T1
Couldn't classify 201227, 201940
Sorry, prediction pasa_asmbl_30873.p1 fails validation.
(GTG)	 GT	201227-201940	AC	GGA
Valid prediction for snap_scaffold_23-snap.880-T1
Valid prediction for Augustus_model.g34058.t1
Valid prediction for snap_scaffold_23-snap.862-T1
Valid prediction for GlimmerHMM_glimmerT_50961-T1
Valid prediction for pasa_asmbl_30875.p1
Valid prediction for HiQ_model.g34059.t1
Valid prediction for snap_scaffold_23-snap.851-T1
Valid prediction for Augustus_model.g34079.t1
Valid prediction for GlimmerHMM_glimmerT_50946-T1
Valid prediction for snap_scaffold_23-snap.883-T1
Valid prediction for GlimmerHMM_glimmerT_50953-T1
Valid prediction for Augustus_model.g34064.t1
Valid prediction for Augustus_model.g34072.t1
Valid prediction for snap_scaffold_23-snap.864-T1
Valid prediction for pasa_asmbl_30872.p1
Valid prediction for snap_scaffold_23-snap.894-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g34075.t1
Valid prediction for Augustus_model.g34065.t1
Valid prediction for snap_scaffold_23-snap.882-T1
Valid prediction for snap_scaffold_23-snap.881-T1
Valid prediction for GlimmerHMM_glimmerT_50938-T1
Valid prediction for GlimmerHMM_glimmerT_50950-T1
Valid prediction for Augustus_model.g34050.t1
Valid prediction for snap_scaffold_23-snap.901-T1
Valid prediction for snap_scaffold_23-snap.871-T1
Valid prediction for snap_scaffold_23-snap.904-T1
Valid prediction for GlimmerHMM_glimmerT_50947-T1
Valid prediction for GlimmerHMM_glimmerT_50966-T1
Valid prediction for HiQ_model.g34080.t1
Valid prediction for snap_scaffold_23-snap.870-T1
Valid prediction for GlimmerHMM_glimmerT_50952-T1
Valid prediction for snap_scaffold_23-snap.867-T1
Valid prediction for snap_scaffold_23-snap.868-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 178116, rend_intergenic: 169235  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 202615, rend_intergenic: 200904  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 465818
-exon list size: 493


building trellis

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92.1    
92.3    
92.5    
92.7    
92.9    
93.1    
93.3    
93.5    
93.7    
93.9    
94.1    
94.3    
94.5    
94.7    
94.9    
95.2    
95.4    
95.6    
95.8    
96.0    
96.2    
96.4    
96.6    
96.8    
97.0    
97.2    
97.4    
97.6    
97.8    
98.0    
98.2    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 50 predictions from path traversal
Error with prediction: snap lend_intergenic: 178116, rend_intergenic: 169235  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 202615, rend_intergenic: 200904  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 47 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 455665 - 465818
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-found 1 predictions from path traversal
GOT 5prime partial gene.

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

-building DP trellis

-building trellis in range 455665 - 465721
-exon list size: 1


building trellis

33.3    
66.7    
-found 1 predictions from path traversal
GOT 5prime partial gene.

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