-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_25/scaffold_25_4600710-4805618

-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_25-snap.950-T1
Valid prediction for GlimmerHMM_glimmerT_54051-T1
Valid prediction for snap_scaffold_25-snap.968-T1
Valid prediction for Augustus_model.g35876.t1
Valid prediction for GlimmerHMM_glimmerT_54057-T1
Valid prediction for GlimmerHMM_glimmerT_54040-T1
Valid prediction for Augustus_model.g35878.t1
Valid prediction for GlimmerHMM_glimmerT_54061-T1
Valid prediction for GlimmerHMM_glimmerT_54063-T1
Valid prediction for snap_scaffold_25-snap.981-T1
Valid prediction for snap_scaffold_25-snap.976-T1
Valid prediction for GlimmerHMM_glimmerT_54035-T1
Valid prediction for GlimmerHMM_glimmerT_54047-T1
Valid prediction for Augustus_model.g35875.t1
Valid prediction for snap_scaffold_25-snap.957-T1
Valid prediction for snap_scaffold_25-snap.963-T1
Valid prediction for snap_scaffold_25-snap.959-T1
Valid prediction for GlimmerHMM_glimmerT_54053-T1
Valid prediction for snap_scaffold_25-snap.965-T1
Valid prediction for snap_scaffold_25-snap.973-T1
Valid prediction for HiQ_model.g35881.t1
Valid prediction for snap_scaffold_25-snap.970-T1
Valid prediction for snap_scaffold_25-snap.978-T1
Valid prediction for GlimmerHMM_glimmerT_54054-T1
Couldn't classify 167630, 167700
Couldn't classify 168550, 168576
Sorry, prediction pasa_asmbl_33527.p1 fails validation.
(ACA)	 TG	167630-167700	GT	AAG
(GAT)	 AG	168104-168323	GT	AGG
(AAC)	 AG	168550-168576	AA	GTA
-recovered pasa_asmbl_33527.p1, internal, 168104, 168323
Valid prediction for snap_scaffold_25-snap.954-T1
Valid prediction for snap_scaffold_25-snap.964-T1
Valid prediction for GlimmerHMM_glimmerT_54039-T1
Valid prediction for Augustus_model.g35880.t1
Valid prediction for snap_scaffold_25-snap.971-T1
Valid prediction for GlimmerHMM_glimmerT_54056-T1
Valid prediction for snap_scaffold_25-snap.961-T1
Valid prediction for snap_scaffold_25-snap.956-T1
Valid prediction for Augustus_model.g35879.t1
Valid prediction for GlimmerHMM_glimmerT_54046-T1
Valid prediction for GlimmerHMM_glimmerT_54034-T1
Valid prediction for snap_scaffold_25-snap.988-T1
Valid prediction for snap_scaffold_25-snap.979-T1
Valid prediction for snap_scaffold_25-snap.952-T1
Valid prediction for snap_scaffold_25-snap.989-T1
Valid prediction for Augustus_model.g35869.t1
Valid prediction for Augustus_model.g35866.t1
Valid prediction for snap_scaffold_25-snap.984-T1
Valid prediction for GlimmerHMM_glimmerT_54058-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_54032-T1
Couldn't classify 25487, 25690
Couldn't classify 26476, 26512
Sorry, prediction pasa_asmbl_34222.p2 fails validation.
(GTT)	 CA	25487-25690	GT	AGG
(GTG)	 AG	25923-26047	GT	CGG
(CCA)	 AG	26476-26512	CC	CCC
-recovered pasa_asmbl_34222.p2, internal, 25923, 26047
Valid prediction for GlimmerHMM_glimmerT_54052-T1
Valid prediction for snap_scaffold_25-snap.969-T1
Valid prediction for snap_scaffold_25-snap.960-T1
Valid prediction for HiQ_model.g35882.t1
Valid prediction for GlimmerHMM_glimmerT_54050-T1
Valid prediction for GlimmerHMM_glimmerT_54045-T1
Valid prediction for GlimmerHMM_glimmerT_54042-T1
Valid prediction for GlimmerHMM_glimmerT_54036-T1
Valid prediction for Augustus_model.g35868.t1
Valid prediction for Augustus_model.g35877.t1
Valid prediction for snap_scaffold_25-snap.980-T1
Valid prediction for snap_scaffold_25-snap.982-T1
Valid prediction for snap_scaffold_25-snap.955-T1
Valid prediction for GlimmerHMM_glimmerT_54062-T1
Valid prediction for Augustus_model.g35884.t1
Valid prediction for snap_scaffold_25-snap.986-T1
Valid prediction for snap_scaffold_25-snap.967-T1
Couldn't classify 26597, 27073
Sorry, prediction pasa_asmbl_34221.p1 fails validation.
(TCC)	 CC	26597-27073	CC	AGC
Valid prediction for GlimmerHMM_glimmerT_54044-T1
Valid prediction for GlimmerHMM_glimmerT_54055-T1
Valid prediction for Augustus_model.g35874.t1
Valid prediction for Augustus_model.g35872.t1
Valid prediction for snap_scaffold_25-snap.966-T1
Valid prediction for GlimmerHMM_glimmerT_54049-T1
Valid prediction for snap_scaffold_25-snap.974-T1
Valid prediction for snap_scaffold_25-snap.985-T1
Valid prediction for snap_scaffold_25-snap.983-T1
Valid prediction for GlimmerHMM_glimmerT_54064-T1
Valid prediction for GlimmerHMM_glimmerT_54043-T1
Valid prediction for snap_scaffold_25-snap.977-T1
Valid prediction for Augustus_model.g35873.t1
Valid prediction for Augustus_model.g35883.t1
Valid prediction for GlimmerHMM_glimmerT_54059-T1
Valid prediction for GlimmerHMM_glimmerT_54048-T1
Valid prediction for snap_scaffold_25-snap.949-T1
Valid prediction for GlimmerHMM_glimmerT_54060-T1
Valid prediction for snap_scaffold_25-snap.991-T1
Valid prediction for Augustus_model.g35867.t1
Valid prediction for GlimmerHMM_glimmerT_54038-T1
Valid prediction for snap_scaffold_25-snap.987-T1
Couldn't classify 162679, 162789
Couldn't classify 165708, 165814
Sorry, prediction pasa_asmbl_34596.p2 fails validation.
(CAA)	 AG	162679-162789	GT	AGG
(CAC)	 AG	165033-165141	GT	AGG
(ATA)	 AG	165708-165814	GG	TAG
-recovered pasa_asmbl_34596.p2, internal, 162679, 162789
-recovered pasa_asmbl_34596.p2, internal, 165033, 165141
Valid prediction for HiQ_model.g35871.t1
Valid prediction for snap_scaffold_25-snap.962-T1
Valid prediction for snap_scaffold_25-snap.975-T1
Valid prediction for snap_scaffold_25-snap.951-T1
Valid prediction for snap_scaffold_25-snap.990-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for HiQ_model.g35870.t1
Valid prediction for snap_scaffold_25-snap.953-T1
Valid prediction for CodingQuarry_transcript_38712-T1
Valid prediction for GlimmerHMM_glimmerT_54041-T1
Valid prediction for GlimmerHMM_glimmerT_54065-T1
Valid prediction for snap_scaffold_25-snap.958-T1
Couldn't classify 14733, 14825
Couldn't classify 21851, 21996
Sorry, prediction pasa_asmbl_34224.p1 fails validation.
(TAC)	 AG	14733-14825	GT	AAG
(AAG)	 AG	15997-16055	GT	AGG
(AAT)	 AG	17468-17576	GT	AGG
(AGC)	 AG	17882-18014	GT	GGG
(CCC)	 AG	18603-18784	GT	AGG
(GTT)	 AG	20354-20515	GT	AGG
(GTG)	 AG	21612-21774	GT	CCG
(TGG)	 AG	21851-21996	GG	TAG
-recovered pasa_asmbl_34224.p1, internal, 14733, 14825
-recovered pasa_asmbl_34224.p1, internal, 15997, 16055
-recovered pasa_asmbl_34224.p1, internal, 17468, 17576
-recovered pasa_asmbl_34224.p1, internal, 17882, 18014
-recovered pasa_asmbl_34224.p1, internal, 18603, 18784
-recovered pasa_asmbl_34224.p1, internal, 20354, 20515
-recovered pasa_asmbl_34224.p1, internal, 21612, 21774
Valid prediction for GlimmerHMM_glimmerT_54037-T1
Valid prediction for CodingQuarry_transcript_38711-T1
Couldn't classify 201161, 201194
Couldn't classify 204768, 204857
Sorry, prediction pasa_asmbl_34217.p1 fails validation.
(AGT)	 AC	201161-201194	GT	CTG
(ACA)	 AG	201350-201458	GT	GAG
(CAA)	 AG	201633-201667	GT	AAG
(GCA)	 AG	201917-202026	GT	AGG
(AGC)	 AG	202473-202563	GT	TTG
(ACG)	 AG	202680-202756	GT	ACG
(GGT)	 AG	202912-202948	GT	GGG
(GTC)	 AG	203114-203211	GT	GGG
(AGT)	 AG	203489-203614	GT	ACG
(AGG)	 AG	203732-203889	GT	AGG
(TGC)	 AG	204191-204326	GT	AGG
(GCC)	 AG	204481-204630	GT	AGG
(AGA)	 AG	204768-204857	TG	CAT
add_exon() Sorry, pasa_asmbl_34217.p1 201350-201458-terminal-3 is invalid.
-recovered pasa_asmbl_34217.p1, terminal, 201350, 201458
-recovered pasa_asmbl_34217.p1, internal, 201350, 201458
-recovered pasa_asmbl_34217.p1, internal, 201633, 201667
-recovered pasa_asmbl_34217.p1, internal, 201917, 202026
-recovered pasa_asmbl_34217.p1, internal, 202473, 202563
-recovered pasa_asmbl_34217.p1, internal, 202680, 202756
-recovered pasa_asmbl_34217.p1, internal, 202912, 202948
-recovered pasa_asmbl_34217.p1, internal, 203114, 203211
-recovered pasa_asmbl_34217.p1, internal, 203489, 203614
-recovered pasa_asmbl_34217.p1, internal, 203732, 203889
-recovered pasa_asmbl_34217.p1, internal, 204191, 204326
-recovered pasa_asmbl_34217.p1, internal, 204481, 204630
Valid prediction for snap_scaffold_25-snap.972-T1
Valid prediction for GlimmerHMM_glimmerT_54033-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 17938, rend_intergenic: 15523  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22899, rend_intergenic: 19660  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26026, rend_intergenic: 23461  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37782, rend_intergenic: 26755  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42079, rend_intergenic: 38149  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46583, rend_intergenic: 42619  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49106, rend_intergenic: 48123  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51058, rend_intergenic: 50022  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61381, rend_intergenic: 51748  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103405, rend_intergenic: 102064  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106575, rend_intergenic: 104319  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112195, rend_intergenic: 106640  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115488, rend_intergenic: 112494  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121448, rend_intergenic: 116555  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144562, rend_intergenic: 131415  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163391, rend_intergenic: 150250  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169299, rend_intergenic: 168161  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186474, rend_intergenic: 179703  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195416, rend_intergenic: 186557  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 204909
-exon list size: 400


building trellis

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18.7    
18.9    
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19.4    
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19.9    
20.1    
20.4    
20.6    
20.9    
21.1    
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21.6    
21.9    
22.1    
22.4    
22.6    
22.9    
23.1    
23.4    
23.6    
23.9    
24.1    
24.4    
24.6    
24.9    
25.1    
25.4    
25.6    
25.9    
26.1    
26.4    
26.6    
26.9    
27.1    
27.4    
27.6    
27.9    
28.1    
28.4    
28.6    
28.9    
29.1    
29.4    
29.6    
29.9    
30.1    
30.3    
30.6    
30.8    
31.1    
31.3    
31.6    
31.8    
32.1    
32.3    
32.6    
32.8    
33.1    
33.3    
33.6    
33.8    
34.1    
34.3    
34.6    
34.8    
35.1    
35.3    
35.6    
35.8    
36.1    
36.3    
36.6    
36.8    
37.1    
37.3    
37.6    
37.8    
38.1    
38.3    
38.6    
38.8    
39.1    
39.3    
39.6    
39.8    
40.0    
40.3    
40.5    
40.8    
41.0    
41.3    
41.5    
41.8    
42.0    
42.3    
42.5    
42.8    
43.0    
43.3    
43.5    
43.8    
44.0    
44.3    
44.5    
44.8    
45.0    
45.3    
45.5    
45.8    
46.0    
46.3    
46.5    
46.8    
47.0    
47.3    
47.5    
47.8    
48.0    
48.3    
48.5    
48.8    
49.0    
49.3    
49.5    
49.8    
50.0    
50.2    
50.5    
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51.0    
51.2    
51.5    
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52.0    
52.2    
52.5    
52.7    
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53.2    
53.5    
53.7    
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54.2    
54.5    
54.7    
55.0    
55.2    
55.5    
55.7    
56.0    
56.2    
56.5    
56.7    
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60.4    
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60.9    
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63.9    
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66.2    
66.4    
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68.9    
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97.5    
97.8    
98.0    
98.3    
98.5    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 17938, rend_intergenic: 15523  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22899, rend_intergenic: 19660  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26026, rend_intergenic: 23461  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37782, rend_intergenic: 26755  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42079, rend_intergenic: 38149  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46583, rend_intergenic: 42619  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49106, rend_intergenic: 48123  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51058, rend_intergenic: 50022  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61381, rend_intergenic: 51748  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103405, rend_intergenic: 102064  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106575, rend_intergenic: 104319  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112195, rend_intergenic: 106640  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115488, rend_intergenic: 112494  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121448, rend_intergenic: 116555  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144562, rend_intergenic: 131415  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163391, rend_intergenic: 150250  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169299, rend_intergenic: 168161  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186474, rend_intergenic: 179703  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195416, rend_intergenic: 186557  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support