-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_24/scaffold_24_6266148-6433115

-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_53941-T1
Couldn't classify 26918, 26934
Couldn't classify 28137, 28190
Sorry, prediction pasa_asmbl_32627.p1 fails validation.
(GAC)	 AT	26918-26934	GT	TGG
(CCA)	 AG	27141-27252	GT	GGG
(CTG)	 AG	27389-27478	GT	AGG
(GCC)	 AG	27573-27759	GT	TGG
(GAG)	 AG	27854-28014	GT	CGG
(CCC)	 AG	28137-28190	GA	ACG
-recovered pasa_asmbl_32627.p1, internal, 27141, 27252
-recovered pasa_asmbl_32627.p1, internal, 27389, 27478
-recovered pasa_asmbl_32627.p1, internal, 27573, 27759
-recovered pasa_asmbl_32627.p1, internal, 27854, 28014
Valid prediction for GeneMark_model.94002_t
Valid prediction for GeneMark_model.93997_t
Valid prediction for Augustus_model.g36100.t1
Valid prediction for GlimmerHMM_glimmerT_53915-T1
Valid prediction for snap_scaffold_24-snap.1242-T1
Valid prediction for GlimmerHMM_glimmerT_53925-T1
Valid prediction for GeneMark_model.94031_t
Valid prediction for snap_scaffold_24-snap.1261-T1
Valid prediction for CodingQuarry_transcript_37256-T1
Valid prediction for snap_scaffold_24-snap.1247-T1
Valid prediction for Augustus_model.g36086.t1
Valid prediction for GeneMark_model.94024_t
Valid prediction for snap_scaffold_24-snap.1240-T1
Valid prediction for GeneMark_model.94009_t
Valid prediction for snap_scaffold_24-snap.1254-T1
Valid prediction for snap_scaffold_24-snap.1246-T1
Valid prediction for snap_scaffold_24-snap.1272-T1
Valid prediction for GeneMark_model.93990_t
Valid prediction for GlimmerHMM_glimmerT_53929-T1
Valid prediction for GlimmerHMM_glimmerT_53923-T1
Valid prediction for GeneMark_model.94005_t
Valid prediction for GeneMark_model.93988_t
Valid prediction for snap_scaffold_24-snap.1256-T1
Valid prediction for GeneMark_model.94000_t
Valid prediction for Augustus_model.g36103.t1
Valid prediction for GeneMark_model.94019_t
Valid prediction for CodingQuarry_transcript_37258-T1
Valid prediction for GeneMark_model.93994_t
Valid prediction for snap_scaffold_24-snap.1239-T1
Valid prediction for GlimmerHMM_glimmerT_53924-T1
Valid prediction for GlimmerHMM_glimmerT_53916-T1
Valid prediction for GeneMark_model.94014_t
Valid prediction for GlimmerHMM_glimmerT_53919-T1
Valid prediction for snap_scaffold_24-snap.1253-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g36110.t1
Valid prediction for Augustus_model.g36099.t1
Valid prediction for snap_scaffold_24-snap.1265-T1
Valid prediction for Augustus_model.g36093.t1
Valid prediction for HiQ_model.g36090.t1
Valid prediction for GlimmerHMM_glimmerT_53918-T1
Valid prediction for Augustus_model.g36092.t1
Valid prediction for snap_scaffold_24-snap.1273-T1
Valid prediction for GlimmerHMM_glimmerT_53936-T1
Valid prediction for GlimmerHMM_glimmerT_53921-T1
Valid prediction for GeneMark_model.94017_t
Valid prediction for snap_scaffold_24-snap.1269-T1
Valid prediction for GeneMark_model.94033_t
Valid prediction for snap_scaffold_24-snap.1248-T1
Valid prediction for GeneMark_model.94013_t
Valid prediction for Augustus_model.g36096.t1
Valid prediction for snap_scaffold_24-snap.1249-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GeneMark_model.94020_t
Couldn't classify 57660, 57765
Couldn't classify 60678, 60715
Sorry, prediction pasa_asmbl_32651.p2 fails validation.
(GAG)	 AG	57660-57765	GT	AGG
(GTG)	 AG	58188-58241	GT	AGG
(ATC)	 AG	59579-59715	GT	AGG
(ACG)	 AG	59857-59917	GT	AGG
(ATC)	 AG	60678-60715	TT	CGT
-recovered pasa_asmbl_32651.p2, internal, 57660, 57765
-recovered pasa_asmbl_32651.p2, internal, 58188, 58241
-recovered pasa_asmbl_32651.p2, internal, 59579, 59715
-recovered pasa_asmbl_32651.p2, internal, 59857, 59917
Valid prediction for GeneMark_model.94012_t
Valid prediction for Augustus_model.g36101.t1
Valid prediction for pasa_asmbl_32313.p1
Valid prediction for Augustus_model.g36109.t1
Valid prediction for GeneMark_model.94035_t
Valid prediction for snap_scaffold_24-snap.1243-T1
Valid prediction for HiQ_model.g36088.t1
Valid prediction for Augustus_model.g36097.t1
Valid prediction for snap_scaffold_24-snap.1263-T1
Valid prediction for GlimmerHMM_glimmerT_53922-T1
Valid prediction for GlimmerHMM_glimmerT_53930-T1
Valid prediction for GeneMark_model.94007_t
Valid prediction for snap_scaffold_24-snap.1276-T1
Valid prediction for snap_scaffold_24-snap.1259-T1
Valid prediction for Augustus_model.g36106.t1
Valid prediction for GeneMark_model.93995_t
Valid prediction for GeneMark_model.94030_t
Couldn't classify 28851, 28997
Sorry, prediction pasa_asmbl_32308.p1 fails validation.
(TTC)	 AC	28851-28997	GT	AGG
(TTA)	 AG	29101-29234	GT	AGG
(CGA)	 AG	30148-30234	GT	AGG
(TGC)	 AG	30354-30479	GT	AGG
(GAG)	 AG	30608-30745	GT	CCG
(CAG)	 AG	30868-30965	GT	GGG
(GTT)	 AG	31192-31395	GT	GAG
(TCA)	 AG	31545-31582	TG	GAT
-recovered pasa_asmbl_32308.p1, terminal, 31545, 31582
-recovered pasa_asmbl_32308.p1, internal, 29101, 29234
-recovered pasa_asmbl_32308.p1, internal, 30148, 30234
-recovered pasa_asmbl_32308.p1, internal, 30354, 30479
-recovered pasa_asmbl_32308.p1, internal, 30608, 30745
-recovered pasa_asmbl_32308.p1, internal, 30868, 30965
-recovered pasa_asmbl_32308.p1, internal, 31192, 31395
Valid prediction for Augustus_model.g36102.t1
Valid prediction for GeneMark_model.94022_t
Valid prediction for GeneMark_model.94003_t
Valid prediction for Augustus_model.g36107.t1
Valid prediction for GeneMark_model.93992_t
Valid prediction for CodingQuarry_transcript_37257-T1
Valid prediction for GlimmerHMM_glimmerT_53933-T1
Valid prediction for GeneMark_model.93987_t
Valid prediction for GlimmerHMM_glimmerT_53934-T1
Couldn't classify 26783, 26911
Sorry, prediction pasa_asmbl_32305.p1 fails validation.
(ATG)	 CG	23610-23634	GT	CGG
(ATC)	 AG	24349-24522	GT	ACG
(ATC)	 AG	25077-25115	GT	AGG
(ATA)	 AG	25918-26084	GT	AGG
(GAG)	 AG	26514-26651	GT	CGG
(GCC)	 AG	26783-26911	AC	TGA
-recovered pasa_asmbl_32305.p1, initial, 23610, 23634
-recovered pasa_asmbl_32305.p1, internal, 24349, 24522
-recovered pasa_asmbl_32305.p1, internal, 25077, 25115
-recovered pasa_asmbl_32305.p1, internal, 25918, 26084
-recovered pasa_asmbl_32305.p1, internal, 26514, 26651
Valid prediction for snap_scaffold_24-snap.1267-T1
Valid prediction for GlimmerHMM_glimmerT_53926-T1
Valid prediction for GeneMark_model.94026_t
Valid prediction for HiQ_model.g36091.t1
Valid prediction for GeneMark_model.94029_t
Valid prediction for GlimmerHMM_glimmerT_53938-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 GeneMark_model.94018_t
Valid prediction for GlimmerHMM_glimmerT_53945-T1
Valid prediction for GeneMark_model.94001_t
Valid prediction for Augustus_model.g36104.t1
Valid prediction for Augustus_model.g36089.t1
Valid prediction for GeneMark_model.93998_t
Valid prediction for Augustus_model.g36112.t1
Valid prediction for HiQ_model.g36095.t1
Valid prediction for CodingQuarry_transcript_37260-T1
Valid prediction for GeneMark_model.94036_t
Valid prediction for GeneMark_model.94010_t
Valid prediction for Augustus_model.g36108.t1
Valid prediction for snap_scaffold_24-snap.1274-T1
Valid prediction for snap_scaffold_24-snap.1266-T1
Valid prediction for snap_scaffold_24-snap.1250-T1
Valid prediction for Augustus_model.g36098.t1
Valid prediction for GeneMark_model.94032_t
Valid prediction for Augustus_model.g36111.t1
Valid prediction for GlimmerHMM_glimmerT_53942-T1
Valid prediction for CodingQuarry_transcript_37261-T1
Valid prediction for snap_scaffold_24-snap.1278-T1
Valid prediction for GeneMark_model.93996_t
Valid prediction for GlimmerHMM_glimmerT_53940-T1
Valid prediction for GlimmerHMM_glimmerT_53931-T1
Valid prediction for pasa_asmbl_32943.p1
Valid prediction for snap_scaffold_24-snap.1275-T1
Valid prediction for GlimmerHMM_glimmerT_53927-T1
Couldn't classify 1924, 1989
Couldn't classify 4608, 4750
Sorry, prediction pasa_asmbl_32946.p1 fails validation.
(TAC)	 CG	1924-1989	GT	AGG
(GTG)	 AG	2582-2738	GT	CCG
(TCG)	 AG	3202-3269	GT	AGG
(GTG)	 AG	3406-3536	GT	GAG
(GTA)	 AG	3704-3851	GT	TGG
(GTC)	 AG	4221-4347	GT	AAG
(GAG)	 AG	4608-4750	GT	ACG
-recovered pasa_asmbl_32946.p1, internal, 2582, 2738
-recovered pasa_asmbl_32946.p1, internal, 3202, 3269
-recovered pasa_asmbl_32946.p1, internal, 3406, 3536
-recovered pasa_asmbl_32946.p1, internal, 3704, 3851
-recovered pasa_asmbl_32946.p1, internal, 4221, 4347
-recovered pasa_asmbl_32946.p1, internal, 4608, 4750
Valid prediction for GlimmerHMM_glimmerT_53932-T1
Valid prediction for snap_scaffold_24-snap.1262-T1
Valid prediction for CodingQuarry_transcript_37259-T1
Valid prediction for GeneMark_model.94027_t
Valid prediction for snap_scaffold_24-snap.1244-T1
Valid prediction for snap_scaffold_24-snap.1271-T1
Valid prediction for pasa_asmbl_32947.p1
Valid prediction for snap_scaffold_24-snap.1277-T1
Valid prediction for GeneMark_model.94021_t
Valid prediction for snap_scaffold_24-snap.1257-T1
Valid prediction for GeneMark_model.94015_t
Valid prediction for GlimmerHMM_glimmerT_53917-T1
Valid prediction for snap_scaffold_24-snap.1270-T1
Valid prediction for GeneMark_model.94034_t
Valid prediction for snap_scaffold_24-snap.1279-T1
Valid prediction for GeneMark_model.93999_t
Valid prediction for snap_scaffold_24-snap.1264-T1
Valid prediction for GeneMark_model.94023_t
Valid prediction for GeneMark_model.93993_t
Valid prediction for GeneMark_model.94016_t
Valid prediction for GeneMark_model.94008_t
Valid prediction for GeneMark_model.94025_t
Valid prediction for snap_scaffold_24-snap.1258-T1
Valid prediction for GlimmerHMM_glimmerT_53939-T1
Valid prediction for GlimmerHMM_glimmerT_53943-T1
Valid prediction for HiQ_model.g36113.t1
Valid prediction for snap_scaffold_24-snap.1241-T1
Valid prediction for snap_scaffold_24-snap.1252-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GeneMark_model.94011_t
Valid prediction for GeneMark_model.94028_t
Valid prediction for GlimmerHMM_glimmerT_53937-T1
Couldn't classify 132847, 132886
Couldn't classify 133362, 133601
Sorry, prediction pasa_asmbl_32942.p1 fails validation.
(TCA)	 AC	132847-132886	GT	TGG
(ACT)	 AG	133163-133242	GT	AGG
(ACA)	 AG	133362-133601	CT	GCC
-recovered pasa_asmbl_32942.p1, internal, 133163, 133242
Valid prediction for Augustus_model.g36094.t1
Valid prediction for Augustus_model.g36087.t1
Valid prediction for GlimmerHMM_glimmerT_53944-T1
Valid prediction for snap_scaffold_24-snap.1268-T1
Valid prediction for Augustus_model.g36105.t1
Valid prediction for snap_scaffold_24-snap.1255-T1
Valid prediction for snap_scaffold_24-snap.1251-T1
Valid prediction for GlimmerHMM_glimmerT_53920-T1
Valid prediction for snap_scaffold_24-snap.1245-T1
Valid prediction for GeneMark_model.93989_t
Couldn't classify 5139, 5207
Couldn't classify 6202, 6303
Sorry, prediction pasa_asmbl_32945.p1 fails validation.
(AGC)	 AA	5139-5207	GT	AGG
(GCC)	 AG	5659-5817	GT	CTG
(GGG)	 AG	6202-6303	TA	CCT
-recovered pasa_asmbl_32945.p1, internal, 5659, 5817
Valid prediction for GlimmerHMM_glimmerT_53928-T1
Valid prediction for GeneMark_model.94004_t
Valid prediction for GlimmerHMM_glimmerT_53914-T1
Valid prediction for GlimmerHMM_glimmerT_53935-T1
Valid prediction for GeneMark_model.94006_t
Valid prediction for snap_scaffold_24-snap.1260-T1
Valid prediction for GeneMark_model.93991_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 21294, rend_intergenic: 19639  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31582, rend_intergenic: 28653  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63876, rend_intergenic: 53025  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64943, rend_intergenic: 64175  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88887, rend_intergenic: 77603  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93611, rend_intergenic: 89658  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112428, rend_intergenic: 103396  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115577, rend_intergenic: 113658  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118584, rend_intergenic: 117329  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128676, rend_intergenic: 119678  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137941, rend_intergenic: 133428  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145560, rend_intergenic: 140126  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149755, rend_intergenic: 148514  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159856, rend_intergenic: 154332  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 166968
-exon list size: 808


building trellis

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56.3    
56.4    
56.5    
56.7    
56.8    
56.9    
57.0    
57.2    
57.3    
57.4    
57.5    
57.7    
57.8    
57.9    
58.0    
58.1    
58.3    
58.4    
58.5    
58.6    
58.8    
58.9    
59.0    
59.1    
59.3    
59.4    
59.5    
59.6    
59.8    
59.9    
60.0    
60.1    
60.2    
60.4    
60.5    
60.6    
60.7    
60.9    
61.0    
61.1    
61.2    
61.4    
61.5    
61.6    
61.7    
61.9    
62.0    
62.1    
62.2    
62.3    
62.5    
62.6    
62.7    
62.8    
63.0    
63.1    
63.2    
63.3    
63.5    
63.6    
63.7    
63.8    
64.0    
64.1    
64.2    
64.3    
64.4    
64.6    
64.7    
64.8    
64.9    
65.1    
65.2    
65.3    
65.4    
65.6    
65.7    
65.8    
65.9    
66.0    
66.2    
66.3    
66.4    
66.5    
66.7    
66.8    
66.9    
67.0    
67.2    
67.3    
67.4    
67.5    
67.7    
67.8    
67.9    
68.0    
68.1    
68.3    
68.4    
68.5    
68.6    
68.8    
68.9    
69.0    
69.1    
69.3    
69.4    
69.5    
69.6    
69.8    
69.9    
70.0    
70.1    
70.2    
70.4    
70.5    
70.6    
70.7    
70.9    
71.0    
71.1    
71.2    
71.4    
71.5    
71.6    
71.7    
71.9    
72.0    
72.1    
72.2    
72.3    
72.5    
72.6    
72.7    
72.8    
73.0    
73.1    
73.2    
73.3    
73.5    
73.6    
73.7    
73.8    
74.0    
74.1    
74.2    
74.3    
74.4    
74.6    
74.7    
74.8    
74.9    
75.1    
75.2    
75.3    
75.4    
75.6    
75.7    
75.8    
75.9    
76.0    
76.2    
76.3    
76.4    
76.5    
76.7    
76.8    
76.9    
77.0    
77.2    
77.3    
77.4    
77.5    
77.7    
77.8    
77.9    
78.0    
78.1    
78.3    
78.4    
78.5    
78.6    
78.8    
78.9    
79.0    
79.1    
79.3    
79.4    
79.5    
79.6    
79.8    
79.9    
80.0    
80.1    
80.2    
80.4    
80.5    
80.6    
80.7    
80.9    
81.0    
81.1    
81.2    
81.4    
81.5    
81.6    
81.7    
81.9    
82.0    
82.1    
82.2    
82.3    
82.5    
82.6    
82.7    
82.8    
83.0    
83.1    
83.2    
83.3    
83.5    
83.6    
83.7    
83.8    
84.0    
84.1    
84.2    
84.3    
84.4    
84.6    
84.7    
84.8    
84.9    
85.1    
85.2    
85.3    
85.4    
85.6    
85.7    
85.8    
85.9    
86.0    
86.2    
86.3    
86.4    
86.5    
86.7    
86.8    
86.9    
87.0    
87.2    
87.3    
87.4    
87.5    
87.7    
87.8    
87.9    
88.0    
88.1    
88.3    
88.4    
88.5    
88.6    
88.8    
88.9    
89.0    
89.1    
89.3    
89.4    
89.5    
89.6    
89.8    
89.9    
90.0    
90.1    
90.2    
90.4    
90.5    
90.6    
90.7    
90.9    
91.0    
91.1    
91.2    
91.4    
91.5    
91.6    
91.7    
91.9    
92.0    
92.1    
92.2    
92.3    
92.5    
92.6    
92.7    
92.8    
93.0    
93.1    
93.2    
93.3    
93.5    
93.6    
93.7    
93.8    
94.0    
94.1    
94.2    
94.3    
94.4    
94.6    
94.7    
94.8    
94.9    
95.1    
95.2    
95.3    
95.4    
95.6    
95.7    
95.8    
95.9    
96.0    
96.2    
96.3    
96.4    
96.5    
96.7    
96.8    
96.9    
97.0    
97.2    
97.3    
97.4    
97.5    
97.7    
97.8    
97.9    
98.0    
98.1    
98.3    
98.4    
98.5    
98.6    
98.8    
98.9    
99.0    
99.1    
99.3    
99.4    
99.5    
99.6    
99.8    
99.9    
-found 36 predictions from path traversal
Error with prediction: snap lend_intergenic: 21294, rend_intergenic: 19639  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31582, rend_intergenic: 28653  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63876, rend_intergenic: 53025  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64943, rend_intergenic: 64175  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88887, rend_intergenic: 77603  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93611, rend_intergenic: 89658  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112428, rend_intergenic: 103396  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115577, rend_intergenic: 113658  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118584, rend_intergenic: 117329  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128676, rend_intergenic: 119678  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137941, rend_intergenic: 133428  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145560, rend_intergenic: 140126  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149755, rend_intergenic: 148514  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159856, rend_intergenic: 154332  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 10075
-exon list size: 6


building trellis

12.5    
25.0    
37.5    
50.0    
62.5    
75.0    
87.5    
-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