-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_13/scaffold_13_4195825-4471481

-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 CodingQuarry_transcript_13000-T1
Valid prediction for snap_scaffold_13-snap.834-T1
Valid prediction for Augustus_model.g20960.t1
Valid prediction for snap_scaffold_13-snap.842-T1
Valid prediction for CodingQuarry_transcript_12988-T1
Valid prediction for GlimmerHMM_glimmerT_31498-T1
Valid prediction for GlimmerHMM_glimmerT_31518-T1
Valid prediction for snap_scaffold_13-snap.827-T1
Valid prediction for snap_scaffold_13-snap.843-T1
Valid prediction for pasa_asmbl_10788.p1
Valid prediction for CodingQuarry_transcript_12993-T1
Valid prediction for GlimmerHMM_glimmerT_31527-T1
Valid prediction for pasa_asmbl_10777.p1
Valid prediction for snap_scaffold_13-snap.814-T1
Couldn't classify 67443, 67552
Sorry, prediction pasa_asmbl_10771.p1 fails validation.
(ATG)	 TT	66184-66195	GT	AAG
(ATC)	 AG	66327-66512	GT	AGG
(CGC)	 AG	67033-67213	GT	TGG
(AAA)	 AG	67443-67552	GT	AGG
-recovered pasa_asmbl_10771.p1, initial, 66184, 66195
-recovered pasa_asmbl_10771.p1, internal, 66327, 66512
-recovered pasa_asmbl_10771.p1, internal, 67033, 67213
-recovered pasa_asmbl_10771.p1, internal, 67443, 67552
Valid prediction for Augustus_model.g20954.t1
Valid prediction for CodingQuarry_transcript_12982-T1
Valid prediction for snap_scaffold_13-snap.818-T1
Valid prediction for pasa_asmbl_10791.p1
Valid prediction for snap_scaffold_13-snap.813-T1
Valid prediction for pasa_asmbl_10773.p1
Valid prediction for snap_scaffold_13-snap.825-T1
Valid prediction for pasa_asmbl_10769.p1
Valid prediction for CodingQuarry_transcript_12987-T1
Valid prediction for GlimmerHMM_glimmerT_31519-T1
Valid prediction for snap_scaffold_13-snap.826-T1
Valid prediction for snap_scaffold_13-snap.832-T1
Valid prediction for Augustus_model.g20967.t1
Valid prediction for GlimmerHMM_glimmerT_31502-T1
Valid prediction for GlimmerHMM_glimmerT_31513-T1
Valid prediction for GlimmerHMM_glimmerT_31500-T1
Valid prediction for GlimmerHMM_glimmerT_31504-T1
Valid prediction for snap_scaffold_13-snap.828-T1
Valid prediction for pasa_asmbl_10767.p1
Valid prediction for GlimmerHMM_glimmerT_31512-T1
Valid prediction for HiQ_model.g20950.t1
Valid prediction for GlimmerHMM_glimmerT_31520-T1
Valid prediction for Augustus_model.g20976.t1
Valid prediction for GlimmerHMM_glimmerT_31516-T1
Valid prediction for snap_scaffold_13-snap.829-T1
Valid prediction for Augustus_model.g20959.t1
Valid prediction for GlimmerHMM_glimmerT_31511-T1
Valid prediction for pasa_asmbl_10778.p1
Valid prediction for GlimmerHMM_glimmerT_31514-T1
Valid prediction for snap_scaffold_13-snap.798-T1
Valid prediction for Augustus_model.g20963.t1
Valid prediction for HiQ_model.g20977.t1
Valid prediction for pasa_asmbl_10796.p1
Valid prediction for snap_scaffold_13-snap.830-T1
Valid prediction for CodingQuarry_transcript_13001-T1
Valid prediction for snap_scaffold_13-snap.809-T1
Valid prediction for Augustus_model.g20978.t1
Valid prediction for GlimmerHMM_glimmerT_31494-T1
Valid prediction for snap_scaffold_13-snap.812-T1
Valid prediction for CodingQuarry_transcript_12999-T1
Valid prediction for HiQ_model.g20953.t1
Valid prediction for CodingQuarry_transcript_13007-T1
Valid prediction for CodingQuarry_transcript_12996-T1
Valid prediction for snap_scaffold_13-snap.806-T1
Valid prediction for Augustus_model.g20968.t1
Valid prediction for HiQ_model.g20966.t1
Valid prediction for CodingQuarry_transcript_13002-T1
Couldn't classify 95169, 95222
Couldn't classify 97726, 97751
Sorry, prediction pasa_asmbl_10775.p1 fails validation.
(CGC)	 CA	95169-95222	GT	AGG
(TGT)	 AG	95878-95968	GT	CTG
(GTT)	 AG	96284-96349	GT	TGG
(GTA)	 AG	96448-96614	GT	GCG
(GAT)	 AG	96972-97132	GT	AGG
(CTG)	 AG	97323-97393	GT	AGG
(CTC)	 AG	97726-97751	CA	GCC
-recovered pasa_asmbl_10775.p1, internal, 95878, 95968
-recovered pasa_asmbl_10775.p1, internal, 96284, 96349
-recovered pasa_asmbl_10775.p1, internal, 96448, 96614
-recovered pasa_asmbl_10775.p1, internal, 96972, 97132
-recovered pasa_asmbl_10775.p1, internal, 97323, 97393
Valid prediction for GlimmerHMM_glimmerT_31508-T1
Valid prediction for HiQ_model.g20958.t1
Valid prediction for CodingQuarry_transcript_12995-T1
Valid prediction for snap_scaffold_13-snap.824-T1
Valid prediction for GlimmerHMM_glimmerT_31507-T1
Valid prediction for HiQ_model.g20971.t1
Valid prediction for snap_scaffold_13-snap.797-T1
Valid prediction for pasa_asmbl_10774.p1
Valid prediction for GlimmerHMM_glimmerT_31526-T1
Valid prediction for snap_scaffold_13-snap.807-T1
Valid prediction for snap_scaffold_13-snap.841-T1
Valid prediction for snap_scaffold_13-snap.819-T1
Valid prediction for CodingQuarry_transcript_12991-T1
Valid prediction for CodingQuarry_transcript_13005-T1
Valid prediction for GlimmerHMM_glimmerT_31515-T1
Valid prediction for GlimmerHMM_glimmerT_31529-T1
Couldn't classify 146125, 146398
Sorry, prediction pasa_asmbl_10782.p1 fails validation.
(AAT)	 TA	146125-146398	GT	GGG
(CAT)	 AG	146616-146707	GT	AAG
(CTG)	 AG	146821-146931	GT	TGG
(ATG)	 AG	147084-147122	GT	ACG
(GCA)	 AG	147313-147369	GT	AGG
(GAT)	 AG	147499-147560	GT	AAG
(GAA)	 AG	147824-147927	GT	AGG
(AGG)	 AG	148083-148246	GT	AAG
(TCT)	 AG	148436-148598	GT	AGG
(GGC)	 AG	148875-149020	AA	GAA
-recovered pasa_asmbl_10782.p1, initial, 147084, 147122
add_exon() Sorry, pasa_asmbl_10782.p1 147499-147560-terminal-2 is invalid.
-recovered pasa_asmbl_10782.p1, terminal, 147499, 147560
-recovered pasa_asmbl_10782.p1, terminal, 148875, 149020
-recovered pasa_asmbl_10782.p1, internal, 146616, 146707
-recovered pasa_asmbl_10782.p1, internal, 146821, 146931
-recovered pasa_asmbl_10782.p1, internal, 147084, 147122
-recovered pasa_asmbl_10782.p1, internal, 147313, 147369
-recovered pasa_asmbl_10782.p1, internal, 147499, 147560
-recovered pasa_asmbl_10782.p1, internal, 147824, 147927
-recovered pasa_asmbl_10782.p1, internal, 148083, 148246
-recovered pasa_asmbl_10782.p1, internal, 148436, 148598
Valid prediction for GlimmerHMM_glimmerT_31521-T1
Valid prediction for CodingQuarry_transcript_13003-T1
Valid prediction for Augustus_model.g20972.t1
Valid prediction for CodingQuarry_transcript_12992-T1
Valid prediction for HiQ_model.g20969.t1
Valid prediction for HiQ_model.g20962.t1
Valid prediction for GlimmerHMM_glimmerT_31497-T1
Valid prediction for CodingQuarry_transcript_12990-T1
Valid prediction for pasa_asmbl_10779.p1
Valid prediction for GlimmerHMM_glimmerT_31503-T1
Valid prediction for HiQ_model.g20956.t1
Valid prediction for snap_scaffold_13-snap.802-T1
Valid prediction for GlimmerHMM_glimmerT_31528-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_31496-T1
Valid prediction for pasa_asmbl_9618.p1
Valid prediction for GlimmerHMM_glimmerT_31499-T1
Valid prediction for CodingQuarry_transcript_12998-T1
Valid prediction for snap_scaffold_13-snap.839-T1
Valid prediction for pasa_asmbl_9623.p1
Valid prediction for Augustus_model.g20973.t1
Valid prediction for pasa_asmbl_9611.p1
Valid prediction for pasa_asmbl_9624.p1
Valid prediction for snap_scaffold_13-snap.815-T1
Valid prediction for snap_scaffold_13-snap.816-T1
Valid prediction for snap_scaffold_13-snap.831-T1
Valid prediction for HiQ_model.g20955.t1
Valid prediction for snap_scaffold_13-snap.820-T1
Valid prediction for snap_scaffold_13-snap.810-T1
Valid prediction for pasa_asmbl_9627.p1
Valid prediction for CodingQuarry_transcript_13004-T1
Valid prediction for CodingQuarry_transcript_13008-T1
Valid prediction for Augustus_model.g20948.t1
Valid prediction for snap_scaffold_13-snap.836-T1
Valid prediction for snap_scaffold_13-snap.822-T1
Valid prediction for GlimmerHMM_glimmerT_31510-T1
Valid prediction for CodingQuarry_transcript_12985-T1
Valid prediction for GlimmerHMM_glimmerT_31525-T1
Valid prediction for snap_scaffold_13-snap.838-T1
Valid prediction for snap_scaffold_13-snap.800-T1
Valid prediction for snap_scaffold_13-snap.821-T1
Valid prediction for GlimmerHMM_glimmerT_31506-T1
Couldn't classify 264634, 264719
Couldn't classify 269724, 269738
Sorry, prediction pasa_asmbl_9607.p1 fails validation.
(GTG)	 AG	264634-264719	GT	GAG
(TTA)	 AG	267267-267405	GT	AGG
(GTG)	 AG	267745-267892	GT	AGG
(TGG)	 AG	268022-268137	GT	AGG
(ATG)	 AG	268764-268835	GT	AGG
(AAA)	 AG	269057-269158	GT	AGG
(GTT)	 AG	269724-269738	CA	TGC
-recovered pasa_asmbl_9607.p1, initial, 268764, 268835
-recovered pasa_asmbl_9607.p1, internal, 264634, 264719
-recovered pasa_asmbl_9607.p1, internal, 267267, 267405
-recovered pasa_asmbl_9607.p1, internal, 267745, 267892
-recovered pasa_asmbl_9607.p1, internal, 268022, 268137
-recovered pasa_asmbl_9607.p1, internal, 268764, 268835
-recovered pasa_asmbl_9607.p1, internal, 269057, 269158
Valid prediction for pasa_asmbl_9609.p1
Valid prediction for GlimmerHMM_glimmerT_31501-T1
Valid prediction for CodingQuarry_transcript_12984-T1
Couldn't classify 136145, 136178
Sorry, prediction pasa_asmbl_9625.p1 fails validation.
(GGG)	 AA	136145-136178	GT	TGG
(GTA)	 AG	136261-136342	GT	GAG
(ATG)	 AG	136953-137159	GT	AGG
(GAC)	 AG	137288-137421	GT	AGG
(GGG)	 AG	137611-137734	GT	AGG
(CAT)	 AG	137834-138002	AG	GAA
add_exon() Sorry, pasa_asmbl_9625.p1 136953-137159-initial-1 is invalid.
-recovered pasa_asmbl_9625.p1, initial, 136953, 137159
add_exon() Sorry, pasa_asmbl_9625.p1 136261-136342-terminal-3 is invalid.
-recovered pasa_asmbl_9625.p1, terminal, 136261, 136342
add_exon() Sorry, pasa_asmbl_9625.p1 136953-137159-terminal-1 is invalid.
-recovered pasa_asmbl_9625.p1, terminal, 136953, 137159
-recovered pasa_asmbl_9625.p1, terminal, 137834, 138002
-recovered pasa_asmbl_9625.p1, internal, 136261, 136342
-recovered pasa_asmbl_9625.p1, internal, 136953, 137159
-recovered pasa_asmbl_9625.p1, internal, 137288, 137421
-recovered pasa_asmbl_9625.p1, internal, 137611, 137734
Valid prediction for Augustus_model.g20957.t1
Valid prediction for Augustus_model.g20974.t1
Valid prediction for HiQ_model.g20970.t1
Valid prediction for GlimmerHMM_glimmerT_31524-T1
Valid prediction for snap_scaffold_13-snap.803-T1
Valid prediction for snap_scaffold_13-snap.796-T1
Valid prediction for snap_scaffold_13-snap.811-T1
Valid prediction for snap_scaffold_13-snap.840-T1
Valid prediction for CodingQuarry_transcript_12986-T1
Valid prediction for GlimmerHMM_glimmerT_31509-T1
Valid prediction for snap_scaffold_13-snap.835-T1
Valid prediction for GlimmerHMM_glimmerT_31523-T1
Valid prediction for CodingQuarry_transcript_12997-T1
Couldn't classify 167717, 167763
Sorry, prediction pasa_asmbl_9622.p1 fails validation.
(GAG)	 TG	167717-167763	GT	AGG
(CTT)	 AG	168225-168329	GT	GGG
(ATA)	 AG	168423-168468	GT	AGG
(ATG)	 AG	168654-168762	GT	GGG
(AGA)	 AG	168883-168991	GT	GGG
(GAT)	 AG	169541-169692	GT	AGG
(GTG)	 AG	170081-170208	TG	AGT
-recovered pasa_asmbl_9622.p1, initial, 168654, 168762
-recovered pasa_asmbl_9622.p1, terminal, 170081, 170208
-recovered pasa_asmbl_9622.p1, internal, 168225, 168329
-recovered pasa_asmbl_9622.p1, internal, 168423, 168468
-recovered pasa_asmbl_9622.p1, internal, 168654, 168762
-recovered pasa_asmbl_9622.p1, internal, 168883, 168991
-recovered pasa_asmbl_9622.p1, internal, 169541, 169692
Valid prediction for Augustus_model.g20975.t1
Valid prediction for CodingQuarry_transcript_12989-T1
Valid prediction for snap_scaffold_13-snap.833-T1
Valid prediction for GlimmerHMM_glimmerT_31495-T1
Valid prediction for HiQ_model.g20964.t1
Valid prediction for snap_scaffold_13-snap.804-T1
Valid prediction for CodingQuarry_transcript_12983-T1
Valid prediction for HiQ_model.g20951.t1
Couldn't classify 263659, 264162
Sorry, prediction pasa_asmbl_9608.p1 fails validation.
(CCC)	 TG	263659-264162	AC	CCA
Valid prediction for GlimmerHMM_glimmerT_31517-T1
Valid prediction for snap_scaffold_13-snap.837-T1
Valid prediction for Augustus_model.g20952.t1
Valid prediction for snap_scaffold_13-snap.808-T1
Valid prediction for GlimmerHMM_glimmerT_31505-T1
Valid prediction for snap_scaffold_13-snap.799-T1
Valid prediction for GlimmerHMM_glimmerT_31522-T1
Valid prediction for CodingQuarry_transcript_12994-T1
Valid prediction for Augustus_model.g20949.t1
Couldn't classify 194259, 194906
Sorry, prediction pasa_asmbl_9620.p1 fails validation.
(AAG)	 AC	194259-194906	AC	AGA
Valid prediction for snap_scaffold_13-snap.801-T1
Couldn't classify 269948, 270058
Sorry, prediction pasa_asmbl_9606.p1 fails validation.
(TAC)	 TG	269948-270058	GT	CGG
(GAT)	 AG	271107-271241	GT	AGG
(TGT)	 AG	271709-271809	GT	TGG
(CTT)	 AG	272059-272203	CA	GAC
-recovered pasa_asmbl_9606.p1, terminal, 272059, 272203
-recovered pasa_asmbl_9606.p1, internal, 271107, 271241
-recovered pasa_asmbl_9606.p1, internal, 271709, 271809
Valid prediction for snap_scaffold_13-snap.805-T1
Valid prediction for GlimmerHMM_glimmerT_31493-T1
Valid prediction for snap_scaffold_13-snap.817-T1
Valid prediction for Augustus_model.g20965.t1
Valid prediction for Augustus_model.g20961.t1
Valid prediction for snap_scaffold_13-snap.823-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 8487, rend_intergenic: 5726  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41848, rend_intergenic: 34960  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 253684, rend_intergenic: 252468  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 275657
-exon list size: 556


building trellis

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70.6    
70.8    
71.0    
71.1    
71.3    
71.5    
71.7    
71.9    
72.0    
72.2    
72.4    
72.6    
72.8    
72.9    
73.1    
73.3    
73.5    
73.7    
73.8    
74.0    
74.2    
74.4    
74.6    
74.7    
74.9    
75.1    
75.3    
75.4    
75.6    
75.8    
76.0    
76.2    
76.3    
76.5    
76.7    
76.9    
77.1    
77.2    
77.4    
77.6    
77.8    
78.0    
78.1    
78.3    
78.5    
78.7    
78.9    
79.0    
79.2    
79.4    
79.6    
79.7    
79.9    
80.1    
80.3    
80.5    
80.6    
80.8    
81.0    
81.2    
81.4    
81.5    
81.7    
81.9    
82.1    
82.3    
82.4    
82.6    
82.8    
83.0    
83.2    
83.3    
83.5    
83.7    
83.9    
84.1    
84.2    
84.4    
84.6    
84.8    
84.9    
85.1    
85.3    
85.5    
85.7    
85.8    
86.0    
86.2    
86.4    
86.6    
86.7    
86.9    
87.1    
87.3    
87.5    
87.6    
87.8    
88.0    
88.2    
88.4    
88.5    
88.7    
88.9    
89.1    
89.2    
89.4    
89.6    
89.8    
90.0    
90.1    
90.3    
90.5    
90.7    
90.9    
91.0    
91.2    
91.4    
91.6    
91.8    
91.9    
92.1    
92.3    
92.5    
92.7    
92.8    
93.0    
93.2    
93.4    
93.5    
93.7    
93.9    
94.1    
94.3    
94.4    
94.6    
94.8    
95.0    
95.2    
95.3    
95.5    
95.7    
95.9    
96.1    
96.2    
96.4    
96.6    
96.8    
97.0    
97.1    
97.3    
97.5    
97.7    
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 37 predictions from path traversal
Error with prediction: snap lend_intergenic: 8487, rend_intergenic: 5726  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41848, rend_intergenic: 34960  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 253684, rend_intergenic: 252468  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 36 predictions persist after filtering for low support