-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_17/scaffold_17_6637328-6885327

-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 pasa_asmbl_18868.p1
Valid prediction for snap_scaffold_17-snap.1350-T1
Valid prediction for CodingQuarry_transcript_22008-T1
Valid prediction for Augustus_model.g26965.t1
Valid prediction for snap_scaffold_17-snap.1352-T1
Valid prediction for snap_scaffold_17-snap.1341-T1
Valid prediction for snap_scaffold_17-snap.1335-T1
Valid prediction for HiQ_model.g26960.t1
Valid prediction for Augustus_model.g26953.t1
Valid prediction for snap_scaffold_17-snap.1331-T1
Couldn't classify 157921, 157954
Couldn't classify 159963, 160031
Sorry, prediction pasa_asmbl_18871.p1 fails validation.
(TCT)	 AA	157921-157954	GT	TGG
(ACT)	 AG	158051-158320	GT	CGG
(GAG)	 AG	158442-158495	GT	TGG
(GAG)	 AG	158712-159007	GT	AGG
(CCC)	 AG	159306-159378	GT	AGG
(GTG)	 AG	159513-159847	GT	AGG
(GCT)	 AG	159963-160031	CC	CTC
-recovered pasa_asmbl_18871.p1, internal, 158051, 158320
-recovered pasa_asmbl_18871.p1, internal, 158442, 158495
-recovered pasa_asmbl_18871.p1, internal, 158712, 159007
-recovered pasa_asmbl_18871.p1, internal, 159306, 159378
-recovered pasa_asmbl_18871.p1, internal, 159513, 159847
Valid prediction for HiQ_model.g26959.t1
Valid prediction for GlimmerHMM_glimmerT_40455-T1
Valid prediction for snap_scaffold_17-snap.1338-T1
Valid prediction for snap_scaffold_17-snap.1347-T1
Valid prediction for CodingQuarry_transcript_22003-T1
Valid prediction for snap_scaffold_17-snap.1329-T1
Valid prediction for Augustus_model.g26967.t1
Valid prediction for snap_scaffold_17-snap.1322-T1
Valid prediction for pasa_asmbl_18867.p1
Valid prediction for snap_scaffold_17-snap.1332-T1
Valid prediction for Augustus_model.g26966.t1
Valid prediction for snap_scaffold_17-snap.1320-T1
Valid prediction for GlimmerHMM_glimmerT_40469-T1
Valid prediction for snap_scaffold_17-snap.1336-T1
Valid prediction for snap_scaffold_17-snap.1328-T1
Valid prediction for GlimmerHMM_glimmerT_40467-T1
Valid prediction for GlimmerHMM_glimmerT_40465-T1
Valid prediction for Augustus_model.g26954.t1
Valid prediction for Augustus_model.g26970.t1
Valid prediction for snap_scaffold_17-snap.1354-T1
Valid prediction for snap_scaffold_17-snap.1321-T1
Valid prediction for GlimmerHMM_glimmerT_40452-T1
Valid prediction for snap_scaffold_17-snap.1319-T1
Valid prediction for snap_scaffold_17-snap.1345-T1
Valid prediction for snap_scaffold_17-snap.1326-T1
Valid prediction for GlimmerHMM_glimmerT_40464-T1
Valid prediction for GlimmerHMM_glimmerT_40453-T1
Valid prediction for HiQ_model.g26974.t1
Valid prediction for Augustus_model.g26972.t1
Valid prediction for CodingQuarry_transcript_22005-T1
Valid prediction for GlimmerHMM_glimmerT_40457-T1
Valid prediction for snap_scaffold_17-snap.1330-T1
Valid prediction for snap_scaffold_17-snap.1351-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_17-snap.1343-T1
Valid prediction for Augustus_model.g26952.t1
Couldn't classify 162856, 162966
Sorry, prediction pasa_asmbl_18874.p1 fails validation.
(CCC)	 AC	162856-162966	GT	AGG
(AGT)	 AG	163082-163150	GT	AGG
(ATG)	 AG	163754-163972	GT	CTG
(GAG)	 AG	164090-164197	GT	AGG
(ACA)	 AG	164443-164589	GT	AGG
(GTG)	 AG	164699-164797	TT	AGT
-recovered pasa_asmbl_18874.p1, initial, 163754, 163972
-recovered pasa_asmbl_18874.p1, terminal, 164699, 164797
-recovered pasa_asmbl_18874.p1, internal, 163082, 163150
-recovered pasa_asmbl_18874.p1, internal, 163754, 163972
-recovered pasa_asmbl_18874.p1, internal, 164090, 164197
-recovered pasa_asmbl_18874.p1, internal, 164443, 164589
Valid prediction for snap_scaffold_17-snap.1348-T1
Valid prediction for snap_scaffold_17-snap.1325-T1
Valid prediction for GlimmerHMM_glimmerT_40460-T1
Valid prediction for Augustus_model.g26963.t1
Valid prediction for snap_scaffold_17-snap.1318-T1
Valid prediction for GlimmerHMM_glimmerT_40459-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 HiQ_model.g26973.t1
Valid prediction for pasa_asmbl_17987.p1
Valid prediction for GlimmerHMM_glimmerT_40450-T1
Couldn't classify 196856, 197035
Sorry, prediction pasa_asmbl_17981.p1 fails validation.
(ATG)	 AC	195210-195220	GT	AGG
(GGT)	 AG	195771-195891	GT	AGG
(GAA)	 AG	196007-196129	GT	TGG
(ACA)	 AG	196452-196601	GT	AGG
(GGA)	 AG	196856-197035	AA	GCA
-recovered pasa_asmbl_17981.p1, initial, 195210, 195220
-recovered pasa_asmbl_17981.p1, internal, 195771, 195891
-recovered pasa_asmbl_17981.p1, internal, 196007, 196129
-recovered pasa_asmbl_17981.p1, internal, 196452, 196601
Couldn't classify 97564, 97624
Sorry, prediction pasa_asmbl_17985.p1 fails validation.
(TTC)	 GG	97564-97624	GT	AGG
(CGG)	 AG	98935-99101	GT	AGG
(GTG)	 AG	99358-99537	GC	AGG
-recovered pasa_asmbl_17985.p1, terminal, 99358, 99537
-recovered pasa_asmbl_17985.p1, internal, 98935, 99101
-recovered pasa_asmbl_17985.p1, internal, 99358, 99537
Valid prediction for snap_scaffold_17-snap.1337-T1
Valid prediction for CodingQuarry_transcript_22012-T1
Valid prediction for Augustus_model.g26961.t1
Valid prediction for GlimmerHMM_glimmerT_40451-T1
Valid prediction for CodingQuarry_transcript_22009-T1
Couldn't classify 15511, 15618
Couldn't classify 18002, 18034
Sorry, prediction pasa_asmbl_18000.p1 fails validation.
(ACA)	 TT	15511-15618	GT	AAG
(GAG)	 AG	15727-15879	GT	AGG
(GAG)	 AG	16091-16387	GT	AGG
(GTG)	 AG	17251-17400	GT	AGG
(GAA)	 AG	17582-17815	GT	GGG
(GCC)	 AG	18002-18034	GG	AGG
-recovered pasa_asmbl_18000.p1, internal, 15727, 15879
-recovered pasa_asmbl_18000.p1, internal, 16091, 16387
-recovered pasa_asmbl_18000.p1, internal, 17251, 17400
-recovered pasa_asmbl_18000.p1, internal, 17582, 17815
Valid prediction for snap_scaffold_17-snap.1339-T1
Valid prediction for Augustus_model.g26969.t1
Couldn't classify 26111, 26842
Couldn't classify 27452, 27955
Sorry, prediction pasa_asmbl_17997.p1 fails validation.
(GAG)	 GT	26111-26842	GT	AGG
(ATC)	 AG	27452-27955	GG	TAG
Valid prediction for CodingQuarry_transcript_22011-T1
Valid prediction for HiQ_model.g26957.t1
Valid prediction for snap_scaffold_17-snap.1346-T1
Couldn't classify 10422, 11888
Sorry, prediction pasa_asmbl_18002.p1 fails validation.
(AAC)	 TG	10422-11888	GT	GGG
Valid prediction for Augustus_model.g26977.t1
Valid prediction for GlimmerHMM_glimmerT_40454-T1
Valid prediction for HiQ_model.g26976.t1
Valid prediction for GlimmerHMM_glimmerT_40471-T1
Valid prediction for Augustus_model.g26955.t1
Couldn't classify 18481, 18726
Couldn't classify 18870, 19031
Sorry, prediction pasa_asmbl_17999.p1 fails validation.
(CCA)	 CC	18481-18726	GT	AGG
(CTG)	 AG	18870-19031	AA	CCA
Valid prediction for CodingQuarry_transcript_22007-T1
Valid prediction for snap_scaffold_17-snap.1349-T1
Valid prediction for GlimmerHMM_glimmerT_40468-T1
Valid prediction for GlimmerHMM_glimmerT_40466-T1
Valid prediction for Augustus_model.g26956.t1
Couldn't classify 54021, 54170
Couldn't classify 54295, 54498
Sorry, prediction CodingQuarry_transcript_22010-T1 fails validation.
(ATG)	 AG	48801-48968	GT	AGG
(GAG)	 AG	49085-49291	GT	AGG
(TAT)	 AG	49502-49729	GT	AGG
(GTG)	 AG	49916-50134	GT	GGG
(CTC)	 AG	50394-50597	GT	AGG
(TTC)	 AG	51869-52094	GT	GGG
(CTG)	 AG	52503-52729	GT	AGG
(GCG)	 AG	52927-53049	GT	AGG
(ATG)	 AG	53187-53288	GT	AGG
(GGT)	 AG	53491-53592	GT	AGG
(CAC)	 AG	53682-53855	GT	AGG
(CAC)	 AG	54021-54170	AC	AAA
(CCC)	 CT	54295-54498	GT	AGG
(GCG)	 AG	54663-54791	GT	TAG
(GAG)	 AG	54899-55081	GT	GGG
(GCT)	 AG	55233-55388	GT	AGG
(GTG)	 AG	55582-55788	GT	AGG
(TTC)	 AG	55975-56094	GT	AGG
(GAG)	 AG	56281-56450	GT	AGG
(ACA)	 AG	56628-56787	GT	AGG
(GCG)	 AG	56886-57080	GT	AGG
(GCA)	 AG	57205-57477	GT	AGG
(GTG)	 AG	57596-57784	GT	AGG
(GTG)	 AG	57893-58004	GT	ACG
(GTA)	 AG	58200-58363	GT	AGG
(CTG)	 AG	58488-58650	GT	TAG
(AGT)	 AG	58910-59064	GT	AGG
(GTG)	 AG	59433-59507	GT	GGG
(TTC)	 AG	60348-60365	GT	AGG
(TTC)	 AG	61082-61199	GT	AGG
(TGA)	 AG	62312-62344	GT	AGG
(CTC)	 AG	64059-64276	GT	GGG
(TCC)	 AG	64944-65060	GT	AGG
(GGG)	 AG	65504-65615	GT	CGG
(ACC)	 AG	65842-66086	AG	AGA
-recovered CodingQuarry_transcript_22010-T1, initial, 48801, 48968
-recovered CodingQuarry_transcript_22010-T1, initial, 53187, 53288
-recovered CodingQuarry_transcript_22010-T1, terminal, 65842, 66086
-recovered CodingQuarry_transcript_22010-T1, internal, 48801, 48968
-recovered CodingQuarry_transcript_22010-T1, internal, 49085, 49291
-recovered CodingQuarry_transcript_22010-T1, internal, 49502, 49729
-recovered CodingQuarry_transcript_22010-T1, internal, 49916, 50134
-recovered CodingQuarry_transcript_22010-T1, internal, 50394, 50597
-recovered CodingQuarry_transcript_22010-T1, internal, 51869, 52094
-recovered CodingQuarry_transcript_22010-T1, internal, 52503, 52729
-recovered CodingQuarry_transcript_22010-T1, internal, 52927, 53049
-recovered CodingQuarry_transcript_22010-T1, internal, 53187, 53288
-recovered CodingQuarry_transcript_22010-T1, internal, 53491, 53592
-recovered CodingQuarry_transcript_22010-T1, internal, 53682, 53855
-recovered CodingQuarry_transcript_22010-T1, internal, 54663, 54791
-recovered CodingQuarry_transcript_22010-T1, internal, 54899, 55081
-recovered CodingQuarry_transcript_22010-T1, internal, 55233, 55388
-recovered CodingQuarry_transcript_22010-T1, internal, 55582, 55788
-recovered CodingQuarry_transcript_22010-T1, internal, 55975, 56094
-recovered CodingQuarry_transcript_22010-T1, internal, 56281, 56450
-recovered CodingQuarry_transcript_22010-T1, internal, 56628, 56787
-recovered CodingQuarry_transcript_22010-T1, internal, 56886, 57080
-recovered CodingQuarry_transcript_22010-T1, internal, 57205, 57477
-recovered CodingQuarry_transcript_22010-T1, internal, 57596, 57784
-recovered CodingQuarry_transcript_22010-T1, internal, 57893, 58004
-recovered CodingQuarry_transcript_22010-T1, internal, 58200, 58363
-recovered CodingQuarry_transcript_22010-T1, internal, 58488, 58650
-recovered CodingQuarry_transcript_22010-T1, internal, 58910, 59064
-recovered CodingQuarry_transcript_22010-T1, internal, 59433, 59507
-recovered CodingQuarry_transcript_22010-T1, internal, 60348, 60365
-recovered CodingQuarry_transcript_22010-T1, internal, 61082, 61199
-recovered CodingQuarry_transcript_22010-T1, internal, 62312, 62344
-recovered CodingQuarry_transcript_22010-T1, internal, 64059, 64276
-recovered CodingQuarry_transcript_22010-T1, internal, 64944, 65060
-recovered CodingQuarry_transcript_22010-T1, internal, 65504, 65615
Valid prediction for Augustus_model.g26968.t1
Valid prediction for Augustus_model.g26962.t1
Valid prediction for CodingQuarry_transcript_22006-T1
Valid prediction for GlimmerHMM_glimmerT_40461-T1
Valid prediction for Augustus_model.g26971.t1
Valid prediction for Augustus_model.g26964.t1
Valid prediction for snap_scaffold_17-snap.1324-T1
Valid prediction for snap_scaffold_17-snap.1317-T1
Valid prediction for pasa_asmbl_17993.p1
Valid prediction for CodingQuarry_transcript_22002-T1
Valid prediction for snap_scaffold_17-snap.1340-T1
Valid prediction for snap_scaffold_17-snap.1323-T1
Valid prediction for GlimmerHMM_glimmerT_40472-T1
Valid prediction for Augustus_model.g26958.t1
Valid prediction for GlimmerHMM_glimmerT_40463-T1
Valid prediction for GlimmerHMM_glimmerT_40470-T1
Valid prediction for Augustus_model.g26951.t1
Valid prediction for snap_scaffold_17-snap.1327-T1
Couldn't classify 12567, 15008
Sorry, prediction pasa_asmbl_18001.p1 fails validation.
(ATG)	 AG	12567-15008	TT	GCT
Valid prediction for GlimmerHMM_glimmerT_40456-T1
Valid prediction for snap_scaffold_17-snap.1344-T1
Couldn't classify 40273, 40758
Sorry, prediction pasa_asmbl_18469.p2 fails validation.
(CTG)	 AC	40273-40758	CC	CTC
Valid prediction for snap_scaffold_17-snap.1342-T1
Valid prediction for snap_scaffold_17-snap.1333-T1
Valid prediction for GlimmerHMM_glimmerT_40458-T1
Valid prediction for snap_scaffold_17-snap.1334-T1
Couldn't classify 39460, 39951
Sorry, prediction pasa_asmbl_17995.p1 fails validation.
(ATG)	 TA	39460-39951	GG	GTG
Valid prediction for GlimmerHMM_glimmerT_40462-T1
Couldn't classify 19828, 20022
Couldn't classify 24549, 24748
Sorry, prediction pasa_asmbl_18463.p1 fails validation.
(CTA)	 GC	19828-20022	GT	AGG
(AAA)	 AG	20193-20510	GT	AGG
(GAA)	 AG	20661-20827	GT	AGG
(GTT)	 AG	21929-22085	GT	AGG
(GAC)	 AG	22313-22424	GT	AGG
(GTG)	 AG	22630-22698	GT	AGG
(ACA)	 AG	23326-23564	GT	AGG
(GTG)	 AG	23719-23848	GT	AGG
(ACG)	 AG	24549-24748	GT	AGG
add_exon() Sorry, pasa_asmbl_18463.p1 23719-23848-terminal-3 is invalid.
-recovered pasa_asmbl_18463.p1, terminal, 23719, 23848
-recovered pasa_asmbl_18463.p1, internal, 20193, 20510
-recovered pasa_asmbl_18463.p1, internal, 20661, 20827
-recovered pasa_asmbl_18463.p1, internal, 21929, 22085
-recovered pasa_asmbl_18463.p1, internal, 22313, 22424
-recovered pasa_asmbl_18463.p1, internal, 22630, 22698
-recovered pasa_asmbl_18463.p1, internal, 23326, 23564
-recovered pasa_asmbl_18463.p1, internal, 23719, 23848
-recovered pasa_asmbl_18463.p1, internal, 24549, 24748
Valid prediction for Augustus_model.g26975.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 37153, rend_intergenic: 34080  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75293, rend_intergenic: 71083  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164797, rend_intergenic: 159589  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177541, rend_intergenic: 176967  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 193805, rend_intergenic: 182277  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 210227, rend_intergenic: 199073  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 217838, rend_intergenic: 211544  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 232802, rend_intergenic: 218653  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 248000
-exon list size: 491


building trellis

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66.3    
66.5    
66.7    
66.9    
67.1    
67.3    
67.5    
67.7    
68.0    
68.2    
68.4    
68.6    
68.8    
69.0    
69.2    
69.4    
69.6    
69.8    
70.0    
70.2    
70.4    
70.6    
70.8    
71.0    
71.2    
71.4    
71.6    
71.8    
72.0    
72.2    
72.4    
72.6    
72.8    
73.0    
73.2    
73.4    
73.6    
73.8    
74.0    
74.2    
74.4    
74.6    
74.8    
75.1    
75.3    
75.5    
75.7    
75.9    
76.1    
76.3    
76.5    
76.7    
76.9    
77.1    
77.3    
77.5    
77.7    
77.9    
78.1    
78.3    
78.5    
78.7    
78.9    
79.1    
79.3    
79.5    
79.7    
79.9    
80.1    
80.3    
80.5    
80.7    
80.9    
81.1    
81.3    
81.5    
81.7    
81.9    
82.2    
82.4    
82.6    
82.8    
83.0    
83.2    
83.4    
83.6    
83.8    
84.0    
84.2    
84.4    
84.6    
84.8    
85.0    
85.2    
85.4    
85.6    
85.8    
86.0    
86.2    
86.4    
86.6    
86.8    
87.0    
87.2    
87.4    
87.6    
87.8    
88.0    
88.2    
88.4    
88.6    
88.8    
89.0    
89.2    
89.5    
89.7    
89.9    
90.1    
90.3    
90.5    
90.7    
90.9    
91.1    
91.3    
91.5    
91.7    
91.9    
92.1    
92.3    
92.5    
92.7    
92.9    
93.1    
93.3    
93.5    
93.7    
93.9    
94.1    
94.3    
94.5    
94.7    
94.9    
95.1    
95.3    
95.5    
95.7    
95.9    
96.1    
96.3    
96.6    
96.8    
97.0    
97.2    
97.4    
97.6    
97.8    
98.0    
98.2    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 37153, rend_intergenic: 34080  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75293, rend_intergenic: 71083  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164797, rend_intergenic: 159589  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177541, rend_intergenic: 176967  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 193805, rend_intergenic: 182277  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 210227, rend_intergenic: 199073  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 217838, rend_intergenic: 211544  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 232802, rend_intergenic: 218653  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 27 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 232599 - 248000
-exon list size: 11


building trellis

7.7    
15.4    
23.1    
30.8    
38.5    
46.2    
53.8    
61.5    
69.2    
76.9    
84.6    
92.3    
-found 2 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support