-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_3/scaffold_3_3189754-3441523

-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 GeneMark_model.10482_t
Valid prediction for CodingQuarry_transcript_45992-T1
Valid prediction for Augustus_model.g4183.t1
Valid prediction for snap_scaffold_3-snap.730-T1
Valid prediction for snap_scaffold_3-snap.742-T1
Valid prediction for snap_scaffold_3-snap.719-T1
Valid prediction for CodingQuarry_transcript_45994-T1
Valid prediction for snap_scaffold_3-snap.697-T1
Valid prediction for CodingQuarry_transcript_45995-T1
Valid prediction for GlimmerHMM_glimmerT_6392-T1
Valid prediction for snap_scaffold_3-snap.706-T1
Valid prediction for snap_scaffold_3-snap.722-T1
Valid prediction for snap_scaffold_3-snap.707-T1
Valid prediction for snap_scaffold_3-snap.725-T1
Valid prediction for GlimmerHMM_glimmerT_6411-T1
Valid prediction for GlimmerHMM_glimmerT_6413-T1
Valid prediction for GeneMark_model.10501_t
Valid prediction for GeneMark_model.10506_t
Valid prediction for pasa_asmbl_39899.p2
Valid prediction for snap_scaffold_3-snap.703-T1
Valid prediction for snap_scaffold_3-snap.702-T1
Valid prediction for Augustus_model.g4181.t1
Valid prediction for GeneMark_model.10498_t
Valid prediction for HiQ_model.g4184.t1
Valid prediction for GlimmerHMM_glimmerT_6390-T1
Valid prediction for GeneMark_model.10473_t
Valid prediction for GeneMark_model.10514_t
Valid prediction for GeneMark_model.10503_t
Valid prediction for snap_scaffold_3-snap.734-T1
Valid prediction for GeneMark_model.10509_t
Valid prediction for snap_scaffold_3-snap.705-T1
Valid prediction for GeneMark_model.10476_t
Valid prediction for snap_scaffold_3-snap.731-T1
Valid prediction for snap_scaffold_3-snap.708-T1
Valid prediction for snap_scaffold_3-snap.728-T1
Valid prediction for GlimmerHMM_glimmerT_6387-T1
Valid prediction for GlimmerHMM_glimmerT_6403-T1
Valid prediction for GlimmerHMM_glimmerT_6385-T1
Valid prediction for GeneMark_model.10518_t
Valid prediction for GeneMark_model.10495_t
Valid prediction for GlimmerHMM_glimmerT_6404-T1
Valid prediction for snap_scaffold_3-snap.739-T1
Valid prediction for GeneMark_model.10512_t
Valid prediction for GeneMark_model.10481_t
Valid prediction for snap_scaffold_3-snap.699-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GeneMark_model.10491_t
Valid prediction for snap_scaffold_3-snap.738-T1
Valid prediction for Augustus_model.g4196.t1
Valid prediction for GeneMark_model.10488_t
Valid prediction for snap_scaffold_3-snap.744-T1
Valid prediction for GeneMark_model.10505_t
Valid prediction for GeneMark_model.10484_t
Valid prediction for GeneMark_model.10478_t
Valid prediction for GlimmerHMM_glimmerT_6402-T1
Valid prediction for CodingQuarry_transcript_45993-T1
Valid prediction for GeneMark_model.10474_t
Valid prediction for GeneMark_model.10507_t
Valid prediction for GeneMark_model.10479_t
Valid prediction for GlimmerHMM_glimmerT_6412-T1
Valid prediction for snap_scaffold_3-snap.711-T1
Valid prediction for GeneMark_model.10516_t

-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_6393-T1
Valid prediction for snap_scaffold_3-snap.696-T1
Valid prediction for Augustus_model.g4182.t1
Valid prediction for GlimmerHMM_glimmerT_6400-T1
Valid prediction for GeneMark_model.10519_t
Valid prediction for snap_scaffold_3-snap.712-T1
Valid prediction for GeneMark_model.10499_t
Valid prediction for GeneMark_model.10508_t
Valid prediction for Augustus_model.g4192.t1
Valid prediction for pasa_asmbl_38726.p2
Valid prediction for snap_scaffold_3-snap.715-T1
Valid prediction for GeneMark_model.10483_t
Valid prediction for GlimmerHMM_glimmerT_6388-T1
Valid prediction for GlimmerHMM_glimmerT_6398-T1
Valid prediction for GeneMark_model.10485_t
Valid prediction for snap_scaffold_3-snap.740-T1
Couldn't classify 159169, 159182
Couldn't classify 159784, 159914
Sorry, prediction pasa_asmbl_38723.p1 fails validation.
(TAT)	 CA	159169-159182	GT	AGG
(GTC)	 AG	159349-159656	GT	GGG
(TTC)	 AG	159784-159914	GA	AGG
-recovered pasa_asmbl_38723.p1, internal, 159349, 159656
Valid prediction for GeneMark_model.10490_t
Valid prediction for snap_scaffold_3-snap.745-T1
Valid prediction for GeneMark_model.10515_t
Valid prediction for Augustus_model.g4189.t1
Valid prediction for GeneMark_model.10486_t
Valid prediction for GeneMark_model.10502_t
Valid prediction for CodingQuarry_transcript_45997-T1
Valid prediction for snap_scaffold_3-snap.701-T1
Valid prediction for GeneMark_model.10475_t
Valid prediction for Augustus_model.g4193.t1
Valid prediction for GlimmerHMM_glimmerT_6396-T1
Valid prediction for GlimmerHMM_glimmerT_6408-T1
Valid prediction for HiQ_model.g4187.t1
Couldn't classify 238186, 238515
Sorry, prediction pasa_asmbl_38715.p1 fails validation.
(CTG)	 TG	238186-238515	GG	CTG
Valid prediction for snap_scaffold_3-snap.710-T1
Valid prediction for Augustus_model.g4197.t1
Valid prediction for snap_scaffold_3-snap.723-T1
Valid prediction for GeneMark_model.10496_t
Valid prediction for CodingQuarry_transcript_45998-T1
Valid prediction for snap_scaffold_3-snap.721-T1
Valid prediction for snap_scaffold_3-snap.714-T1
Valid prediction for GeneMark_model.10492_t
Valid prediction for snap_scaffold_3-snap.709-T1
Valid prediction for Augustus_model.g4180.t1
Valid prediction for HiQ_model.g4190.t1
Valid prediction for GlimmerHMM_glimmerT_6410-T1
Valid prediction for snap_scaffold_3-snap.735-T1
Valid prediction for GlimmerHMM_glimmerT_6391-T1
Valid prediction for Augustus_model.g4188.t1
Valid prediction for snap_scaffold_3-snap.716-T1
Valid prediction for GlimmerHMM_glimmerT_6409-T1
Valid prediction for snap_scaffold_3-snap.718-T1
Valid prediction for snap_scaffold_3-snap.732-T1
Valid prediction for pasa_asmbl_38727.p1
Couldn't classify 122566, 123631
Couldn't classify 123704, 123719
Sorry, prediction CodingQuarry_transcript_46001-T1 fails validation.
(ATG)	 AT	121984-121990	GT	AGG
(ATC)	 AG	122566-123631	CT	ACC
(CTC)	 AC	123704-123719	TC	AAT
-recovered CodingQuarry_transcript_46001-T1, initial, 121984, 121990
Valid prediction for GeneMark_model.10517_t
Valid prediction for snap_scaffold_3-snap.726-T1
Valid prediction for GlimmerHMM_glimmerT_6407-T1
Valid prediction for snap_scaffold_3-snap.720-T1
Valid prediction for snap_scaffold_3-snap.733-T1
Valid prediction for GeneMark_model.10477_t
Valid prediction for GlimmerHMM_glimmerT_6389-T1
Valid prediction for HiQ_model.g4191.t1
Valid prediction for Augustus_model.g4185.t1
Valid prediction for GeneMark_model.10487_t
Valid prediction for GeneMark_model.10513_t
Valid prediction for GlimmerHMM_glimmerT_6386-T1
Valid prediction for snap_scaffold_3-snap.736-T1
Valid prediction for CodingQuarry_transcript_46002-T1
Valid prediction for snap_scaffold_3-snap.698-T1
Valid prediction for snap_scaffold_3-snap.724-T1
Valid prediction for snap_scaffold_3-snap.737-T1
Couldn't classify 249360, 249668
Sorry, prediction pasa_asmbl_38714.p1 fails validation.
(GAC)	 CA	249360-249668	GA	CCG
Valid prediction for GlimmerHMM_glimmerT_6397-T1
Valid prediction for CodingQuarry_transcript_45996-T1
Valid prediction for GlimmerHMM_glimmerT_6399-T1
Valid prediction for Augustus_model.g4186.t1
Valid prediction for snap_scaffold_3-snap.717-T1
Valid prediction for GeneMark_model.10504_t
Valid prediction for GeneMark_model.10493_t
Valid prediction for GlimmerHMM_glimmerT_6405-T1
Valid prediction for Augustus_model.g4195.t1
Valid prediction for pasa_asmbl_38724.p1
Valid prediction for snap_scaffold_3-snap.704-T1
Valid prediction for snap_scaffold_3-snap.700-T1
Valid prediction for snap_scaffold_3-snap.743-T1
Valid prediction for GeneMark_model.10489_t
Valid prediction for GlimmerHMM_glimmerT_6395-T1
Valid prediction for GeneMark_model.10480_t
Valid prediction for GlimmerHMM_glimmerT_6406-T1
Valid prediction for Augustus_model.g4194.t1
Valid prediction for GeneMark_model.10494_t
Valid prediction for GeneMark_model.10497_t
Valid prediction for GeneMark_model.10510_t
Valid prediction for GlimmerHMM_glimmerT_6401-T1
Valid prediction for snap_scaffold_3-snap.729-T1
Valid prediction for pasa_asmbl_38717.p1
Valid prediction for GeneMark_model.10511_t
Valid prediction for snap_scaffold_3-snap.741-T1
Valid prediction for GlimmerHMM_glimmerT_6394-T1
Valid prediction for GeneMark_model.10500_t
Valid prediction for snap_scaffold_3-snap.713-T1
Valid prediction for snap_scaffold_3-snap.727-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 13561, rend_intergenic: 9018  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31307, rend_intergenic: 19380  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144970, rend_intergenic: 139412  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151183, rend_intergenic: 148529  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157406, rend_intergenic: 153590  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163805, rend_intergenic: 159598  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167320, rend_intergenic: 163855  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177586, rend_intergenic: 171368  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181720, rend_intergenic: 178950  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187101, rend_intergenic: 183559  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 201298, rend_intergenic: 195880  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 203557, rend_intergenic: 202143  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 237390, rend_intergenic: 230849  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 240108, rend_intergenic: 239419  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 243590, rend_intergenic: 241253  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 247200, rend_intergenic: 246003  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 251770
-exon list size: 681


building trellis

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97.1    
97.2    
97.4    
97.5    
97.7    
97.8    
98.0    
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 39 predictions from path traversal
Error with prediction: snap lend_intergenic: 13561, rend_intergenic: 9018  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31307, rend_intergenic: 19380  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144970, rend_intergenic: 139412  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151183, rend_intergenic: 148529  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157406, rend_intergenic: 153590  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163805, rend_intergenic: 159598  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167320, rend_intergenic: 163855  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177586, rend_intergenic: 171368  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181720, rend_intergenic: 178950  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187101, rend_intergenic: 183559  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 201298, rend_intergenic: 195880  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 203557, rend_intergenic: 202143  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 237390, rend_intergenic: 230849  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 240108, rend_intergenic: 239419  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 243590, rend_intergenic: 241253  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 247200, rend_intergenic: 246003  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

-building DP trellis

-building trellis in range 236268 - 251770
-exon list size: 62


building trellis

1.6    
3.1    
4.7    
6.2    
7.8    
9.4    
10.9    
12.5    
14.1    
15.6    
17.2    
18.8    
20.3    
21.9    
23.4    
25.0    
26.6    
28.1    
29.7    
31.2    
32.8    
34.4    
35.9    
37.5    
39.1    
40.6    
42.2    
43.8    
45.3    
46.9    
48.4    
50.0    
51.6    
53.1    
54.7    
56.2    
57.8    
59.4    
60.9    
62.5    
64.1    
65.6    
67.2    
68.8    
70.3    
71.9    
73.4    
75.0    
76.6    
78.1    
79.7    
81.2    
82.8    
84.4    
85.9    
87.5    
89.1    
90.6    
92.2    
93.8    
95.3    
96.9    
98.4    
-found 2 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 1 predictions persist after filtering for low support