-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_12/scaffold_12_2973894-3150012

-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_29630-T1
Valid prediction for GeneMark_model.51215_t
Valid prediction for GlimmerHMM_glimmerT_29646-T1
Valid prediction for snap_scaffold_12-snap.601-T1
Valid prediction for Augustus_model.g19728.t1
Couldn't classify 125238, 125354
Couldn't classify 129376, 129431
Sorry, prediction pasa_asmbl_8503.p1 fails validation.
(GGG)	 CA	125238-125354	GT	AGG
(ATG)	 AG	125489-125562	GT	TGG
(TCG)	 AG	125934-126012	GT	AGG
(TTG)	 AG	126248-126327	GT	AAG
(AGA)	 AG	126453-126590	GT	AAG
(GTA)	 AG	126847-126932	GT	AGG
(TGA)	 AG	127236-127384	GC	AGG
(GAC)	 AG	127622-127745	GT	TGG
(GAG)	 AG	128153-128250	GT	AGG
(GCG)	 AG	128784-128985	GT	AGG
(ATA)	 AG	129376-129431	GC	ACG
-recovered pasa_asmbl_8503.p1, initial, 125489, 125562
-recovered pasa_asmbl_8503.p1, internal, 125489, 125562
-recovered pasa_asmbl_8503.p1, internal, 125934, 126012
-recovered pasa_asmbl_8503.p1, internal, 126248, 126327
-recovered pasa_asmbl_8503.p1, internal, 126453, 126590
-recovered pasa_asmbl_8503.p1, internal, 126847, 126932
-recovered pasa_asmbl_8503.p1, internal, 127236, 127384
-recovered pasa_asmbl_8503.p1, internal, 127622, 127745
-recovered pasa_asmbl_8503.p1, internal, 128153, 128250
-recovered pasa_asmbl_8503.p1, internal, 128784, 128985
-recovered pasa_asmbl_8503.p1, internal, 129376, 129431
Valid prediction for GeneMark_model.51208_t
Valid prediction for GeneMark_model.51180_t
Valid prediction for GeneMark_model.51186_t
Valid prediction for pasa_asmbl_8496.p2
Valid prediction for CodingQuarry_transcript_10124-T1
Valid prediction for CodingQuarry_transcript_10119-T1
Valid prediction for GeneMark_model.51175_t
Valid prediction for Augustus_model.g19715.t1
Valid prediction for GeneMark_model.51198_t
Valid prediction for GeneMark_model.51177_t
Valid prediction for GlimmerHMM_glimmerT_29637-T1
Valid prediction for GeneMark_model.51211_t
Valid prediction for snap_scaffold_12-snap.622-T1
Valid prediction for GeneMark_model.51188_t
Valid prediction for GeneMark_model.51203_t
Valid prediction for snap_scaffold_12-snap.607-T1
Valid prediction for GeneMark_model.51206_t
Valid prediction for Augustus_model.g19722.t1
Valid prediction for snap_scaffold_12-snap.618-T1
Valid prediction for snap_scaffold_12-snap.631-T1
Valid prediction for snap_scaffold_12-snap.608-T1
Valid prediction for GeneMark_model.51179_t
Valid prediction for snap_scaffold_12-snap.602-T1
Valid prediction for pasa_asmbl_8498.p1
Valid prediction for GlimmerHMM_glimmerT_29636-T1
Valid prediction for GlimmerHMM_glimmerT_29638-T1
Valid prediction for CodingQuarry_transcript_10123-T1
Valid prediction for snap_scaffold_12-snap.624-T1
Valid prediction for GlimmerHMM_glimmerT_29624-T1
Valid prediction for snap_scaffold_12-snap.626-T1
Valid prediction for GlimmerHMM_glimmerT_29639-T1
Valid prediction for Augustus_model.g19719.t1
Valid prediction for GeneMark_model.51182_t
Valid prediction for GeneMark_model.51200_t
Valid prediction for snap_scaffold_12-snap.635-T1
Valid prediction for snap_scaffold_12-snap.621-T1
Valid prediction for GeneMark_model.51196_t
Valid prediction for snap_scaffold_12-snap.598-T1
Valid prediction for GlimmerHMM_glimmerT_29626-T1
Valid prediction for CodingQuarry_transcript_10120-T1
Valid prediction for GeneMark_model.51194_t
Valid prediction for GeneMark_model.51201_t
Valid prediction for snap_scaffold_12-snap.628-T1
Valid prediction for Augustus_model.g19724.t1
Couldn't classify 122305, 122400
Couldn't classify 123453, 123625
Sorry, prediction pasa_asmbl_8502.p2 fails validation.
(CAG)	 CT	122305-122400	GT	AGG
(GTG)	 AG	122688-122781	GT	CAG
(TTC)	 AG	122999-123229	GT	AGG
(ACA)	 AG	123453-123625	GA	GTG
-recovered pasa_asmbl_8502.p2, internal, 122688, 122781
-recovered pasa_asmbl_8502.p2, internal, 122999, 123229
Valid prediction for snap_scaffold_12-snap.614-T1
Valid prediction for snap_scaffold_12-snap.599-T1
Valid prediction for GlimmerHMM_glimmerT_29644-T1
Valid prediction for GeneMark_model.51190_t
Valid prediction for GeneMark_model.51214_t
Valid prediction for GeneMark_model.51184_t
Valid prediction for Augustus_model.g19717.t1
Valid prediction for GlimmerHMM_glimmerT_29642-T1
Valid prediction for GlimmerHMM_glimmerT_29627-T1
Valid prediction for snap_scaffold_12-snap.609-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_29643-T1
Valid prediction for GeneMark_model.51192_t
Valid prediction for snap_scaffold_12-snap.610-T1
Valid prediction for snap_scaffold_12-snap.605-T1
Valid prediction for GeneMark_model.51217_t
Valid prediction for snap_scaffold_12-snap.634-T1
Valid prediction for GeneMark_model.51212_t
Valid prediction for GlimmerHMM_glimmerT_29634-T1
Valid prediction for GlimmerHMM_glimmerT_29647-T1
Valid prediction for CodingQuarry_transcript_10121-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_12-snap.613-T1
Valid prediction for snap_scaffold_12-snap.606-T1
Valid prediction for GeneMark_model.51195_t
Valid prediction for GeneMark_model.51181_t
Valid prediction for snap_scaffold_12-snap.633-T1
Valid prediction for GeneMark_model.51176_t
Valid prediction for GeneMark_model.51193_t
Valid prediction for GeneMark_model.51205_t
Valid prediction for GlimmerHMM_glimmerT_29645-T1
Valid prediction for pasa_asmbl_7480.p1
Valid prediction for Augustus_model.g19721.t1
Valid prediction for GeneMark_model.51189_t
Valid prediction for snap_scaffold_12-snap.617-T1
Valid prediction for GlimmerHMM_glimmerT_29631-T1
Couldn't classify 163876, 164388
Sorry, prediction pasa_asmbl_7476.p1 fails validation.
(CCT)	 CT	163876-164388	TA	AGT
Valid prediction for GlimmerHMM_glimmerT_29648-T1
Valid prediction for GeneMark_model.51202_t
Valid prediction for snap_scaffold_12-snap.604-T1
Valid prediction for GlimmerHMM_glimmerT_29628-T1
Valid prediction for Augustus_model.g19723.t1
Valid prediction for GlimmerHMM_glimmerT_29633-T1
Valid prediction for Augustus_model.g19727.t1
Valid prediction for snap_scaffold_12-snap.625-T1
Valid prediction for GlimmerHMM_glimmerT_29641-T1
Valid prediction for snap_scaffold_12-snap.620-T1
Valid prediction for GlimmerHMM_glimmerT_29632-T1
Valid prediction for snap_scaffold_12-snap.629-T1
Valid prediction for GeneMark_model.51207_t
Couldn't classify 115315, 115536
Couldn't classify 116149, 116232
Sorry, prediction pasa_asmbl_8332.p1 fails validation.
(TTC)	 GG	115315-115536	GT	AGG
(ACG)	 AG	116149-116232	TT	GCT
Valid prediction for GeneMark_model.51199_t
Valid prediction for snap_scaffold_12-snap.623-T1
Valid prediction for snap_scaffold_12-snap.615-T1
Valid prediction for GeneMark_model.51183_t
Valid prediction for GeneMark_model.51210_t
Valid prediction for snap_scaffold_12-snap.630-T1
Valid prediction for snap_scaffold_12-snap.603-T1
Valid prediction for GeneMark_model.51185_t
Valid prediction for GlimmerHMM_glimmerT_29640-T1
Valid prediction for GeneMark_model.51216_t
Valid prediction for GlimmerHMM_glimmerT_29629-T1
Valid prediction for Augustus_model.g19725.t1
Couldn't classify 161290, 161698
Couldn't classify 162446, 162501
Sorry, prediction pasa_asmbl_7477.p1 fails validation.
(TGC)	 AG	161290-161698	GT	AGG
(GTG)	 AG	161852-161935	GT	AGG
(GTG)	 AG	162446-162501	GT	AGG
-recovered pasa_asmbl_7477.p1, internal, 161290, 161698
-recovered pasa_asmbl_7477.p1, internal, 161852, 161935
-recovered pasa_asmbl_7477.p1, internal, 162446, 162501
Couldn't classify 160750, 161169
Sorry, prediction pasa_asmbl_7478.p1 fails validation.
(ATG)	 AC	160750-161169	AA	CCA
Valid prediction for snap_scaffold_12-snap.632-T1
Valid prediction for GeneMark_model.51191_t
Valid prediction for GeneMark_model.51178_t
Couldn't classify 127908, 127970
Sorry, prediction pasa_asmbl_7482.p1 fails validation.
(GTC)	 AG	127908-127970	GT	AGG
(TGC)	 AG	128240-128346	GT	AGG
(TAT)	 AG	128655-128796	GT	AGG
(GTG)	 AG	128987-129121	GT	TGG
(GAC)	 AG	130619-130722	GT	AGG
(CAT)	 AG	130959-131051	GT	AGG
(GTT)	 AG	131355-131598	GT	AGG
(GTG)	 AG	131970-132128	GA	GAG
-recovered pasa_asmbl_7482.p1, terminal, 131970, 132128
-recovered pasa_asmbl_7482.p1, internal, 127908, 127970
-recovered pasa_asmbl_7482.p1, internal, 128240, 128346
-recovered pasa_asmbl_7482.p1, internal, 128655, 128796
-recovered pasa_asmbl_7482.p1, internal, 128987, 129121
-recovered pasa_asmbl_7482.p1, internal, 130619, 130722
-recovered pasa_asmbl_7482.p1, internal, 130959, 131051
-recovered pasa_asmbl_7482.p1, internal, 131355, 131598
Valid prediction for GeneMark_model.51209_t
Valid prediction for GlimmerHMM_glimmerT_29623-T1
Valid prediction for HiQ_model.g19716.t1
Valid prediction for snap_scaffold_12-snap.616-T1
Valid prediction for Augustus_model.g19720.t1
Valid prediction for Augustus_model.g19726.t1
Valid prediction for GlimmerHMM_glimmerT_29635-T1
Valid prediction for snap_scaffold_12-snap.627-T1
Valid prediction for snap_scaffold_12-snap.600-T1
Valid prediction for Augustus_model.g19718.t1
Valid prediction for GeneMark_model.51204_t
Valid prediction for GeneMark_model.51187_t
Valid prediction for snap_scaffold_12-snap.612-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GeneMark_model.51197_t
Valid prediction for snap_scaffold_12-snap.611-T1
Valid prediction for GeneMark_model.51213_t
Valid prediction for GlimmerHMM_glimmerT_29625-T1
Valid prediction for snap_scaffold_12-snap.619-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 66872, rend_intergenic: 44600  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95524, rend_intergenic: 87624  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98867, rend_intergenic: 95652  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129575, rend_intergenic: 121134  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132402, rend_intergenic: 130514  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138772, rend_intergenic: 137706  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141878, rend_intergenic: 141832  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144485, rend_intergenic: 142473  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153490, rend_intergenic: 152365  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 176119
-exon list size: 674


building trellis

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91.9    
92.0    
92.2    
92.3    
92.5    
92.6    
92.8    
92.9    
93.0    
93.2    
93.3    
93.5    
93.6    
93.8    
93.9    
94.1    
94.2    
94.4    
94.5    
94.7    
94.8    
95.0    
95.1    
95.3    
95.4    
95.6    
95.7    
95.9    
96.0    
96.2    
96.3    
96.4    
96.6    
96.7    
96.9    
97.0    
97.2    
97.3    
97.5    
97.6    
97.8    
97.9    
98.1    
98.2    
98.4    
98.5    
98.7    
98.8    
99.0    
99.1    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 23 predictions from path traversal
Error with prediction: snap lend_intergenic: 66872, rend_intergenic: 44600  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95524, rend_intergenic: 87624  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98867, rend_intergenic: 95652  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129575, rend_intergenic: 121134  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132402, rend_intergenic: 130514  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138772, rend_intergenic: 137706  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141878, rend_intergenic: 141832  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144485, rend_intergenic: 142473  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153490, rend_intergenic: 152365  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 18 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 163465 - 176119
-exon list size: 25


building trellis

3.7    
7.4    
11.1    
14.8    
18.5    
22.2    
25.9    
29.6    
33.3    
37.0    
40.7    
44.4    
48.1    
51.9    
55.6    
59.3    
63.0    
66.7    
70.4    
74.1    
77.8    
81.5    
85.2    
88.9    
92.6    
96.3    
-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