-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_21/scaffold_21_6337448-6502719

-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.85046_t
Valid prediction for pasa_asmbl_28670.p1
Valid prediction for GlimmerHMM_glimmerT_49059-T1
Valid prediction for snap_scaffold_21-snap.1309-T1
Valid prediction for GlimmerHMM_glimmerT_49048-T1
Valid prediction for GlimmerHMM_glimmerT_49050-T1
Valid prediction for GeneMark_model.85039_t
Valid prediction for HiQ_model.g32878.t1
Valid prediction for snap_scaffold_21-snap.1299-T1
Valid prediction for GeneMark_model.85064_t
Valid prediction for Augustus_model.g32865.t1
Valid prediction for Augustus_model.g32872.t1
Valid prediction for Augustus_model.g32882.t1
Valid prediction for snap_scaffold_21-snap.1307-T1
Valid prediction for snap_scaffold_21-snap.1313-T1
Valid prediction for Augustus_model.g32887.t1
Valid prediction for snap_scaffold_21-snap.1325-T1
Valid prediction for snap_scaffold_21-snap.1326-T1
Valid prediction for CodingQuarry_transcript_32521-T1
Valid prediction for GeneMark_model.85031_t
Valid prediction for GlimmerHMM_glimmerT_49054-T1
Couldn't classify 53510, 53629
Couldn't classify 63596, 64004
Sorry, prediction pasa_asmbl_28655.p1 fails validation.
(CAG)	 TC	53510-53629	GT	ATG
(ACC)	 AG	54766-54795	GT	CTG
(GTC)	 AG	55961-56043	GT	AGG
(ATG)	 AG	57038-57204	GT	AGG
(GTG)	 AG	57603-57699	GT	AAG
(GTT)	 AG	59190-59303	GT	AGG
(GCA)	 AG	59397-59596	GT	CGG
(ACT)	 AG	61153-61281	GT	GGG
(AGT)	 AG	61497-61608	GT	AAG
(CTG)	 AG	62128-62323	GT	AGG
(GGT)	 AG	62432-62617	GT	TGG
(GTC)	 AG	62825-62995	GT	TGG
(GTG)	 AG	63127-63281	GT	AGG
(GCT)	 AG	63596-64004	CC	TCC
add_exon() Sorry, pasa_asmbl_28655.p1 57038-57204-initial-1 is invalid.
-recovered pasa_asmbl_28655.p1, initial, 57038, 57204
-recovered pasa_asmbl_28655.p1, internal, 54766, 54795
-recovered pasa_asmbl_28655.p1, internal, 55961, 56043
-recovered pasa_asmbl_28655.p1, internal, 57038, 57204
-recovered pasa_asmbl_28655.p1, internal, 57603, 57699
-recovered pasa_asmbl_28655.p1, internal, 59190, 59303
-recovered pasa_asmbl_28655.p1, internal, 59397, 59596
-recovered pasa_asmbl_28655.p1, internal, 61153, 61281
-recovered pasa_asmbl_28655.p1, internal, 61497, 61608
-recovered pasa_asmbl_28655.p1, internal, 62128, 62323
-recovered pasa_asmbl_28655.p1, internal, 62432, 62617
-recovered pasa_asmbl_28655.p1, internal, 62825, 62995
-recovered pasa_asmbl_28655.p1, internal, 63127, 63281
Valid prediction for GeneMark_model.85054_t
Valid prediction for Augustus_model.g32867.t1
Couldn't classify 64116, 65258
Sorry, prediction pasa_asmbl_28658.p1 fails validation.
(AGC)	 GC	64116-65258	GT	TCG
(ACG)	 AG	65511-65621	GT	AGG
(GTC)	 AG	65793-65881	GT	AGG
(GAA)	 AG	66114-66291	GA	GAG
-recovered pasa_asmbl_28658.p1, terminal, 66114, 66291
-recovered pasa_asmbl_28658.p1, internal, 65511, 65621
-recovered pasa_asmbl_28658.p1, internal, 65793, 65881
Valid prediction for GlimmerHMM_glimmerT_49044-T1
Valid prediction for Augustus_model.g32884.t1
Valid prediction for snap_scaffold_21-snap.1312-T1
Valid prediction for snap_scaffold_21-snap.1327-T1
Valid prediction for GeneMark_model.85033_t
Valid prediction for HiQ_model.g32886.t1
Valid prediction for GlimmerHMM_glimmerT_49052-T1
Valid prediction for snap_scaffold_21-snap.1314-T1
Valid prediction for HiQ_model.g32888.t1
Valid prediction for GlimmerHMM_glimmerT_49047-T1
Valid prediction for snap_scaffold_21-snap.1315-T1
Couldn't classify 73280, 73325
Sorry, prediction pasa_asmbl_28659.p1 fails validation.
(GAT)	 CA	73280-73325	GT	TGG
(CAC)	 AG	73491-73655	GT	TGG
(TTC)	 AG	73740-73885	GT	AGG
(CTG)	 AG	73992-74084	GT	AGG
(GAA)	 AG	74202-74268	GT	AAG
(ATG)	 AG	74340-74503	GT	AGG
(CTG)	 AG	74685-74864	AG	AGA
add_exon() Sorry, pasa_asmbl_28659.p1 74340-74503-initial-1 is invalid.
-recovered pasa_asmbl_28659.p1, initial, 74340, 74503
-recovered pasa_asmbl_28659.p1, terminal, 74685, 74864
-recovered pasa_asmbl_28659.p1, internal, 73491, 73655
-recovered pasa_asmbl_28659.p1, internal, 73740, 73885
-recovered pasa_asmbl_28659.p1, internal, 73992, 74084
-recovered pasa_asmbl_28659.p1, internal, 74202, 74268
-recovered pasa_asmbl_28659.p1, internal, 74340, 74503
Valid prediction for GeneMark_model.85063_t
Valid prediction for pasa_asmbl_28661.p1
Valid prediction for snap_scaffold_21-snap.1329-T1
Valid prediction for snap_scaffold_21-snap.1302-T1
Valid prediction for snap_scaffold_21-snap.1321-T1
Valid prediction for GlimmerHMM_glimmerT_49045-T1
Valid prediction for snap_scaffold_21-snap.1324-T1
Valid prediction for GeneMark_model.85042_t
Valid prediction for snap_scaffold_21-snap.1318-T1
Valid prediction for Augustus_model.g32869.t1
Valid prediction for GlimmerHMM_glimmerT_49064-T1
Valid prediction for GeneMark_model.85060_t
Valid prediction for GlimmerHMM_glimmerT_49065-T1
Valid prediction for snap_scaffold_21-snap.1296-T1
Valid prediction for Augustus_model.g32875.t1
Valid prediction for GeneMark_model.85058_t
Valid prediction for CodingQuarry_transcript_32522-T1
Valid prediction for GeneMark_model.85038_t
Valid prediction for snap_scaffold_21-snap.1322-T1
Valid prediction for GeneMark_model.85029_t
Valid prediction for GeneMark_model.85066_t
Valid prediction for GeneMark_model.85048_t
Valid prediction for snap_scaffold_21-snap.1294-T1
Valid prediction for GeneMark_model.85035_t
Valid prediction for GeneMark_model.85062_t
Valid prediction for GeneMark_model.85052_t
Couldn't classify 111325, 111589
Sorry, prediction pasa_asmbl_28666.p1 fails validation.
(GAA)	 AA	111325-111589	GT	AGG
(CCT)	 AG	111791-111860	GT	GGG
(AAT)	 AG	112021-112126	GT	TGG
(GAC)	 AG	112314-112439	AC	GAA
-recovered pasa_asmbl_28666.p1, terminal, 112314, 112439
-recovered pasa_asmbl_28666.p1, internal, 111791, 111860
-recovered pasa_asmbl_28666.p1, internal, 112021, 112126
Valid prediction for CodingQuarry_transcript_32519-T1
Valid prediction for GlimmerHMM_glimmerT_49062-T1
Valid prediction for CodingQuarry_transcript_32518-T1
Valid prediction for GlimmerHMM_glimmerT_49063-T1
Valid prediction for GlimmerHMM_glimmerT_49040-T1
Valid prediction for HiQ_model.g32873.t1
Valid prediction for HiQ_model.g32876.t1
Valid prediction for Augustus_model.g32870.t1
Valid prediction for GeneMark_model.85023_t
Valid prediction for Augustus_model.g32885.t1
Valid prediction for GeneMark_model.85045_t
Valid prediction for GeneMark_model.85036_t
Valid prediction for GeneMark_model.85026_t
Valid prediction for GeneMark_model.85043_t
Valid prediction for snap_scaffold_21-snap.1306-T1
Valid prediction for snap_scaffold_21-snap.1317-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_21-snap.1304-T1
Couldn't classify 138527, 138598
Sorry, prediction pasa_asmbl_27747.p1 fails validation.
(GAA)	 TT	138527-138598	GT	AGG
(ATA)	 AG	138781-138823	GT	AGG
(AAA)	 AG	138929-139011	GT	AGG
(AAA)	 AG	139163-139252	GT	CGG
(TAC)	 AG	139348-139454	GT	CTG
(ACC)	 AG	139650-139727	GT	TGG
(GTA)	 AG	139941-140103	GT	AGG
(GAA)	 AG	140240-140311	GT	CTG
(ATA)	 AG	140503-140625	GT	AGG
(GAA)	 AG	140738-140854	GT	TTG
(GGA)	 AG	141586-141699	CC	AAC
-recovered pasa_asmbl_27747.p1, terminal, 141586, 141699
-recovered pasa_asmbl_27747.p1, internal, 138781, 138823
-recovered pasa_asmbl_27747.p1, internal, 138929, 139011
-recovered pasa_asmbl_27747.p1, internal, 139163, 139252
-recovered pasa_asmbl_27747.p1, internal, 139348, 139454
-recovered pasa_asmbl_27747.p1, internal, 139650, 139727
-recovered pasa_asmbl_27747.p1, internal, 139941, 140103
-recovered pasa_asmbl_27747.p1, internal, 140240, 140311
-recovered pasa_asmbl_27747.p1, internal, 140503, 140625
-recovered pasa_asmbl_27747.p1, internal, 140738, 140854
Valid prediction for GlimmerHMM_glimmerT_49061-T1
Valid prediction for GeneMark_model.85047_t
Valid prediction for snap_scaffold_21-snap.1316-T1
Valid prediction for GeneMark_model.85059_t
Valid prediction for GeneMark_model.85027_t
Valid prediction for GeneMark_model.85049_t
Valid prediction for Augustus_model.g32866.t1
Valid prediction for snap_scaffold_21-snap.1295-T1
Valid prediction for GeneMark_model.85040_t
Valid prediction for snap_scaffold_21-snap.1320-T1
Valid prediction for GeneMark_model.85025_t
Valid prediction for HiQ_model.g32877.t1
Valid prediction for GeneMark_model.85044_t
Valid prediction for GlimmerHMM_glimmerT_49038-T1
Valid prediction for snap_scaffold_21-snap.1328-T1
Valid prediction for GeneMark_model.85053_t
Valid prediction for GlimmerHMM_glimmerT_49041-T1
Valid prediction for GeneMark_model.85028_t
Valid prediction for GeneMark_model.85050_t
Valid prediction for GlimmerHMM_glimmerT_49039-T1
Valid prediction for snap_scaffold_21-snap.1301-T1
Valid prediction for snap_scaffold_21-snap.1300-T1
Valid prediction for snap_scaffold_21-snap.1297-T1
Valid prediction for Augustus_model.g32874.t1
Valid prediction for snap_scaffold_21-snap.1298-T1
Valid prediction for HiQ_model.g32883.t1
Valid prediction for GeneMark_model.85057_t
Valid prediction for GlimmerHMM_glimmerT_49058-T1
Valid prediction for GeneMark_model.85024_t
Valid prediction for GlimmerHMM_glimmerT_49057-T1
Valid prediction for GlimmerHMM_glimmerT_49042-T1
Valid prediction for GeneMark_model.85032_t
Valid prediction for Augustus_model.g32871.t1
Valid prediction for CodingQuarry_transcript_32520-T1
Valid prediction for GeneMark_model.85061_t
Valid prediction for Augustus_model.g32868.t1
Valid prediction for GlimmerHMM_glimmerT_49055-T1
Valid prediction for snap_scaffold_21-snap.1305-T1
Valid prediction for snap_scaffold_21-snap.1310-T1
Sorry, intron length (3) is less than minimum required (10)
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for Augustus_model.g32879.t1
Valid prediction for snap_scaffold_21-snap.1323-T1
Valid prediction for snap_scaffold_21-snap.1303-T1
Valid prediction for GlimmerHMM_glimmerT_49053-T1
Valid prediction for snap_scaffold_21-snap.1308-T1
Valid prediction for GeneMark_model.85037_t
Valid prediction for GeneMark_model.85051_t
Valid prediction for GeneMark_model.85056_t
Valid prediction for GlimmerHMM_glimmerT_49056-T1
Valid prediction for GeneMark_model.85034_t
Valid prediction for GeneMark_model.85041_t
Valid prediction for GlimmerHMM_glimmerT_49060-T1
Valid prediction for GeneMark_model.85030_t
Valid prediction for GlimmerHMM_glimmerT_49051-T1
Valid prediction for Augustus_model.g32880.t1
Couldn't classify 37994, 38024
Sorry, prediction pasa_asmbl_27750.p1 fails validation.
(TCA)	 TC	37994-38024	GT	AGG
(CCA)	 AG	38250-38362	GT	AGG
(GAC)	 AG	38691-38765	GT	AGG
(GAT)	 AG	38891-39040	GT	AGG
(ACC)	 AG	39285-39410	CC	AAC
-recovered pasa_asmbl_27750.p1, terminal, 39285, 39410
-recovered pasa_asmbl_27750.p1, internal, 38250, 38362
-recovered pasa_asmbl_27750.p1, internal, 38691, 38765
-recovered pasa_asmbl_27750.p1, internal, 38891, 39040
Valid prediction for GlimmerHMM_glimmerT_49046-T1
Valid prediction for GlimmerHMM_glimmerT_49043-T1
Valid prediction for snap_scaffold_21-snap.1319-T1
Valid prediction for GeneMark_model.85065_t
Valid prediction for snap_scaffold_21-snap.1293-T1
Valid prediction for GlimmerHMM_glimmerT_49049-T1
Valid prediction for Augustus_model.g32881.t1
Couldn't classify 26177, 26218
Sorry, prediction pasa_asmbl_27751.p1 fails validation.
(CGT)	 GC	26177-26218	GT	GGG
(TCC)	 AG	26576-26672	GT	TGG
(GCA)	 AG	26930-27053	GT	GGG
(GTA)	 AG	27233-27306	GT	ACG
(ACC)	 AG	27407-27552	GT	AGG
(GAG)	 AG	27773-27916	GG	GAG
-recovered pasa_asmbl_27751.p1, terminal, 27773, 27916
-recovered pasa_asmbl_27751.p1, internal, 26576, 26672
-recovered pasa_asmbl_27751.p1, internal, 26930, 27053
-recovered pasa_asmbl_27751.p1, internal, 27233, 27306
-recovered pasa_asmbl_27751.p1, internal, 27407, 27552
Valid prediction for snap_scaffold_21-snap.1311-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 5389, rend_intergenic: 3709  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 6987, rend_intergenic: 6479  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 9981, rend_intergenic: 7483  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 11801, rend_intergenic: 10137  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14767, rend_intergenic: 11817  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20595, rend_intergenic: 15066  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47556, rend_intergenic: 34608  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58800, rend_intergenic: 55696  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62242, rend_intergenic: 59139  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66291, rend_intergenic: 64287  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123433, rend_intergenic: 117241  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132214, rend_intergenic: 129729  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 165272
-exon list size: 619


building trellis

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67.0    
67.1    
67.3    
67.5    
67.6    
67.8    
68.0    
68.1    
68.3    
68.4    
68.6    
68.8    
68.9    
69.1    
69.2    
69.4    
69.6    
69.7    
69.9    
70.0    
70.2    
70.4    
70.5    
70.7    
70.9    
71.0    
71.2    
71.3    
71.5    
71.7    
71.8    
72.0    
72.1    
72.3    
72.5    
72.6    
72.8    
72.9    
73.1    
73.3    
73.4    
73.6    
73.8    
73.9    
74.1    
74.2    
74.4    
74.6    
74.7    
74.9    
75.0    
75.2    
75.4    
75.5    
75.7    
75.8    
76.0    
76.2    
76.3    
76.5    
76.7    
76.8    
77.0    
77.1    
77.3    
77.5    
77.6    
77.8    
77.9    
78.1    
78.3    
78.4    
78.6    
78.7    
78.9    
79.1    
79.2    
79.4    
79.5    
79.7    
79.9    
80.0    
80.2    
80.4    
80.5    
80.7    
80.8    
81.0    
81.2    
81.3    
81.5    
81.6    
81.8    
82.0    
82.1    
82.3    
82.4    
82.6    
82.8    
82.9    
83.1    
83.3    
83.4    
83.6    
83.7    
83.9    
84.1    
84.2    
84.4    
84.5    
84.7    
84.9    
85.0    
85.2    
85.3    
85.5    
85.7    
85.8    
86.0    
86.2    
86.3    
86.5    
86.6    
86.8    
87.0    
87.1    
87.3    
87.4    
87.6    
87.8    
87.9    
88.1    
88.2    
88.4    
88.6    
88.7    
88.9    
89.0    
89.2    
89.4    
89.5    
89.7    
89.9    
90.0    
90.2    
90.3    
90.5    
90.7    
90.8    
91.0    
91.1    
91.3    
91.5    
91.6    
91.8    
91.9    
92.1    
92.3    
92.4    
92.6    
92.8    
92.9    
93.1    
93.2    
93.4    
93.6    
93.7    
93.9    
94.0    
94.2    
94.4    
94.5    
94.7    
94.8    
95.0    
95.2    
95.3    
95.5    
95.7    
95.8    
96.0    
96.1    
96.3    
96.5    
96.6    
96.8    
96.9    
97.1    
97.3    
97.4    
97.6    
97.7    
97.9    
98.1    
98.2    
98.4    
98.6    
98.7    
98.9    
99.0    
99.2    
99.4    
99.5    
99.7    
99.8    
-found 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 5389, rend_intergenic: 3709  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 6987, rend_intergenic: 6479  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 9981, rend_intergenic: 7483  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 11801, rend_intergenic: 10137  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14767, rend_intergenic: 11817  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20595, rend_intergenic: 15066  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47556, rend_intergenic: 34608  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58800, rend_intergenic: 55696  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62242, rend_intergenic: 59139  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66291, rend_intergenic: 64287  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123433, rend_intergenic: 117241  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132214, rend_intergenic: 129729  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