-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_6/scaffold_6_5253545-5429823

-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 Augustus_model.g9979.t1
Valid prediction for HiQ_model.g9975.t1
Valid prediction for GlimmerHMM_glimmerT_14992-T1
Valid prediction for GeneMark_model.25394_t
Valid prediction for snap_scaffold_6-snap.1255-T1
Valid prediction for GeneMark_model.25371_t
Valid prediction for snap_scaffold_6-snap.1257-T1
Valid prediction for GlimmerHMM_glimmerT_14984-T1
Valid prediction for GeneMark_model.25404_t
Valid prediction for CodingQuarry_transcript_54904-T1
Valid prediction for GeneMark_model.25385_t
Valid prediction for GlimmerHMM_glimmerT_15007-T1
Valid prediction for GeneMark_model.25412_t
Valid prediction for pasa_asmbl_46876.p1
Valid prediction for snap_scaffold_6-snap.1275-T1
Valid prediction for GeneMark_model.25396_t
Valid prediction for GeneMark_model.25406_t
Valid prediction for GeneMark_model.25367_t
Valid prediction for GlimmerHMM_glimmerT_15000-T1
Valid prediction for Augustus_model.g9982.t1
Valid prediction for snap_scaffold_6-snap.1236-T1
Valid prediction for GeneMark_model.25378_t
Valid prediction for snap_scaffold_6-snap.1272-T1
Valid prediction for GeneMark_model.25392_t
Valid prediction for Augustus_model.g9978.t1
Valid prediction for GeneMark_model.25400_t
Valid prediction for snap_scaffold_6-snap.1261-T1
Valid prediction for pasa_asmbl_46885.p1
Valid prediction for GeneMark_model.25369_t
Valid prediction for GeneMark_model.25373_t
Valid prediction for snap_scaffold_6-snap.1251-T1
Valid prediction for GlimmerHMM_glimmerT_14996-T1
Valid prediction for GeneMark_model.25381_t
Valid prediction for Augustus_model.g9976.t1
Valid prediction for GlimmerHMM_glimmerT_14988-T1
Valid prediction for snap_scaffold_6-snap.1258-T1
Valid prediction for GeneMark_model.25365_t
Valid prediction for snap_scaffold_6-snap.1244-T1
Couldn't classify 28426, 28437
Couldn't classify 30082, 30085
Sorry, prediction pasa_asmbl_46883.p1 fails validation.
(GTT)	 GT	28426-28437	GT	GGG
(TAC)	 AG	28589-28662	GT	GGG
(GTG)	 AG	28822-28905	GT	CCG
(GCT)	 AG	28999-29142	GT	AGG
(GCT)	 AG	29483-29594	GT	AGG
(TCC)	 AG	29907-29983	GT	AGG
(GAC)	 AG	30082-30085	AG	CCA
-recovered pasa_asmbl_46883.p1, internal, 28589, 28662
-recovered pasa_asmbl_46883.p1, internal, 28822, 28905
-recovered pasa_asmbl_46883.p1, internal, 28999, 29142
-recovered pasa_asmbl_46883.p1, internal, 29483, 29594
-recovered pasa_asmbl_46883.p1, internal, 29907, 29983
Valid prediction for Augustus_model.g9992.t1
Valid prediction for GlimmerHMM_glimmerT_14999-T1
Valid prediction for Augustus_model.g9994.t1
Valid prediction for snap_scaffold_6-snap.1253-T1
Valid prediction for GeneMark_model.25374_t
Valid prediction for GeneMark_model.25376_t
Valid prediction for Augustus_model.g9989.t1
Valid prediction for GlimmerHMM_glimmerT_14980-T1
Valid prediction for GlimmerHMM_glimmerT_14998-T1
Valid prediction for GlimmerHMM_glimmerT_14983-T1
Valid prediction for GlimmerHMM_glimmerT_14985-T1
Valid prediction for GlimmerHMM_glimmerT_14987-T1
Valid prediction for snap_scaffold_6-snap.1273-T1
Valid prediction for Augustus_model.g9983.t1
Valid prediction for GeneMark_model.25389_t
Valid prediction for snap_scaffold_6-snap.1270-T1
Valid prediction for GeneMark_model.25383_t
Valid prediction for snap_scaffold_6-snap.1238-T1
Valid prediction for snap_scaffold_6-snap.1249-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_6-snap.1263-T1
Valid prediction for GeneMark_model.25386_t
Valid prediction for snap_scaffold_6-snap.1247-T1
Valid prediction for snap_scaffold_6-snap.1266-T1
Valid prediction for GeneMark_model.25370_t
Valid prediction for Augustus_model.g9990.t1
Valid prediction for GlimmerHMM_glimmerT_15003-T1
Valid prediction for snap_scaffold_6-snap.1240-T1
Valid prediction for GlimmerHMM_glimmerT_15002-T1
Valid prediction for GlimmerHMM_glimmerT_14977-T1
Valid prediction for snap_scaffold_6-snap.1252-T1
Valid prediction for snap_scaffold_6-snap.1250-T1
Valid prediction for GeneMark_model.25398_t
Valid prediction for snap_scaffold_6-snap.1256-T1
Valid prediction for snap_scaffold_6-snap.1269-T1
Valid prediction for GeneMark_model.25410_t
Valid prediction for GlimmerHMM_glimmerT_14991-T1
Valid prediction for GeneMark_model.25402_t
Valid prediction for snap_scaffold_6-snap.1246-T1
Valid prediction for GlimmerHMM_glimmerT_14979-T1
Valid prediction for GeneMark_model.25415_t
Couldn't classify 32149, 32172
Sorry, prediction pasa_asmbl_46884.p1 fails validation.
(CTG)	 AG	32149-32172	GT	GGG
(GAG)	 AG	32351-32553	GT	ACG
(GTA)	 AG	32846-33080	GT	CGG
(CAA)	 AG	33214-33282	GT	AGG
(ATC)	 AG	33377-33457	GT	TTG
(CTG)	 AG	33603-33732	GT	AGG
(TGT)	 AG	33867-34030	GT	AGG
(GAG)	 AG	34185-34286	GT	AGG
(CAA)	 AG	34440-34538	GT	AGG
(CAG)	 AG	34635-34743	GT	AGG
(ACC)	 AG	34935-34999	GG	GAG
add_exon() Sorry, pasa_asmbl_46884.p1 33603-33732-terminal-3 is invalid.
-recovered pasa_asmbl_46884.p1, terminal, 33603, 33732
-recovered pasa_asmbl_46884.p1, terminal, 34935, 34999
-recovered pasa_asmbl_46884.p1, internal, 32149, 32172
-recovered pasa_asmbl_46884.p1, internal, 32351, 32553
-recovered pasa_asmbl_46884.p1, internal, 32846, 33080
-recovered pasa_asmbl_46884.p1, internal, 33214, 33282
-recovered pasa_asmbl_46884.p1, internal, 33377, 33457
-recovered pasa_asmbl_46884.p1, internal, 33603, 33732
-recovered pasa_asmbl_46884.p1, internal, 33867, 34030
-recovered pasa_asmbl_46884.p1, internal, 34185, 34286
-recovered pasa_asmbl_46884.p1, internal, 34440, 34538
-recovered pasa_asmbl_46884.p1, internal, 34635, 34743
Valid prediction for CodingQuarry_transcript_54902-T1
Couldn't classify 18190, 18255
Couldn't classify 18887, 18988
Sorry, prediction pasa_asmbl_47900.p1 fails validation.
(TTG)	 AG	18190-18255	GT	AAG
(GCC)	 AG	18410-18521	GT	AGG
(AAC)	 AG	18632-18777	GT	AGG
(GTT)	 AG	18887-18988	GG	CTG
-recovered pasa_asmbl_47900.p1, internal, 18190, 18255
-recovered pasa_asmbl_47900.p1, internal, 18410, 18521
-recovered pasa_asmbl_47900.p1, internal, 18632, 18777
Valid prediction for GlimmerHMM_glimmerT_15005-T1
Valid prediction for GeneMark_model.25407_t
Valid prediction for snap_scaffold_6-snap.1239-T1
Valid prediction for Augustus_model.g9986.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: -)Couldn't classify 25771, 26226
Sorry, prediction pasa_asmbl_48356.p1 fails validation.
(CGC)	 CC	25771-26226	GA	GGG
Valid prediction for GeneMark_model.25397_t
Valid prediction for GeneMark_model.25387_t
Valid prediction for GeneMark_model.25364_t
Valid prediction for GeneMark_model.25382_t
Valid prediction for GlimmerHMM_glimmerT_14993-T1
Valid prediction for GlimmerHMM_glimmerT_14982-T1
Valid prediction for HiQ_model.g9974.t1
Valid prediction for GlimmerHMM_glimmerT_14989-T1
Valid prediction for HiQ_model.g9977.t1
Valid prediction for GeneMark_model.25414_t
Valid prediction for pasa_asmbl_48353.p1
Valid prediction for GeneMark_model.25413_t
Valid prediction for pasa_asmbl_48349.p1
Valid prediction for snap_scaffold_6-snap.1268-T1
Valid prediction for Augustus_model.g9993.t1
Couldn't classify 151745, 151789
Sorry, prediction pasa_asmbl_48352.p1 fails validation.
(TCC)	 TT	151745-151789	GT	AAG
(ACG)	 AG	152358-152394	GT	CAG
(ATT)	 AG	152581-152667	GT	AGG
(ACG)	 AG	152896-153005	GT	AGG
(AAA)	 AG	153090-153186	GT	AAG
(CGA)	 AG	153482-153581	GT	ACG
(GAA)	 AG	153735-153936	GT	AGG
(ATT)	 AG	154133-154189	AG	GAA
-recovered pasa_asmbl_48352.p1, terminal, 154133, 154189
-recovered pasa_asmbl_48352.p1, internal, 152358, 152394
-recovered pasa_asmbl_48352.p1, internal, 152581, 152667
-recovered pasa_asmbl_48352.p1, internal, 152896, 153005
-recovered pasa_asmbl_48352.p1, internal, 153090, 153186
-recovered pasa_asmbl_48352.p1, internal, 153482, 153581
-recovered pasa_asmbl_48352.p1, internal, 153735, 153936
Valid prediction for GlimmerHMM_glimmerT_14978-T1
Valid prediction for GlimmerHMM_glimmerT_14997-T1
Valid prediction for GeneMark_model.25384_t
Valid prediction for GeneMark_model.25395_t
Valid prediction for snap_scaffold_6-snap.1267-T1
Valid prediction for GeneMark_model.25408_t
Valid prediction for GlimmerHMM_glimmerT_15004-T1
Valid prediction for snap_scaffold_6-snap.1265-T1
Valid prediction for HiQ_model.g9988.t1
Valid prediction for GlimmerHMM_glimmerT_14981-T1
Valid prediction for GeneMark_model.25403_t
Valid prediction for GeneMark_model.25379_t
Couldn't classify 23328, 23652
Sorry, prediction pasa_asmbl_48358.p1 fails validation.
(ATG)	 TC	21300-21326	GT	AGG
(CTG)	 AG	21473-21559	GT	AAG
(GAC)	 AG	22472-22615	GT	AGG
(AGG)	 AG	22792-22922	GT	CGG
(AAC)	 AG	23328-23652	GA	GGG
-recovered pasa_asmbl_48358.p1, initial, 21300, 21326
-recovered pasa_asmbl_48358.p1, internal, 21473, 21559
-recovered pasa_asmbl_48358.p1, internal, 22472, 22615
-recovered pasa_asmbl_48358.p1, internal, 22792, 22922
Valid prediction for Augustus_model.g9985.t1
Valid prediction for Augustus_model.g9987.t1
Valid prediction for snap_scaffold_6-snap.1264-T1
Valid prediction for Augustus_model.g9991.t1
Valid prediction for snap_scaffold_6-snap.1241-T1
Valid prediction for GeneMark_model.25405_t
Valid prediction for Augustus_model.g9984.t1
Valid prediction for Augustus_model.g9980.t1
Valid prediction for snap_scaffold_6-snap.1237-T1
Valid prediction for GeneMark_model.25391_t
Valid prediction for GeneMark_model.25390_t
Valid prediction for snap_scaffold_6-snap.1260-T1
Valid prediction for GeneMark_model.25372_t
Valid prediction for snap_scaffold_6-snap.1254-T1
Valid prediction for snap_scaffold_6-snap.1271-T1
Valid prediction for snap_scaffold_6-snap.1243-T1
Valid prediction for CodingQuarry_transcript_54903-T1
Valid prediction for GeneMark_model.25409_t
Valid prediction for GeneMark_model.25399_t
Valid prediction for GeneMark_model.25393_t
Valid prediction for GeneMark_model.25366_t
Valid prediction for GlimmerHMM_glimmerT_14995-T1
Valid prediction for snap_scaffold_6-snap.1242-T1
Couldn't classify 26248, 27258
Sorry, prediction pasa_asmbl_48355.p1 fails validation.
(CCA)	 CC	26248-27258	GG	GAG
Valid prediction for GeneMark_model.25401_t
Valid prediction for snap_scaffold_6-snap.1245-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_6-snap.1248-T1
Valid prediction for GlimmerHMM_glimmerT_15001-T1
Couldn't classify 23722, 25500
Sorry, prediction pasa_asmbl_48357.p1 fails validation.
(TCC)	 GC	23722-25500	TC	ACT
Valid prediction for GeneMark_model.25377_t
Valid prediction for Augustus_model.g9981.t1
Valid prediction for snap_scaffold_6-snap.1262-T1
Valid prediction for CodingQuarry_transcript_54901-T1
Valid prediction for GlimmerHMM_glimmerT_14994-T1
Valid prediction for GeneMark_model.25411_t
Valid prediction for snap_scaffold_6-snap.1259-T1
Valid prediction for GeneMark_model.25375_t
Valid prediction for snap_scaffold_6-snap.1274-T1
Valid prediction for GlimmerHMM_glimmerT_15008-T1
Valid prediction for GeneMark_model.25368_t
Valid prediction for GlimmerHMM_glimmerT_15006-T1
Valid prediction for snap_scaffold_6-snap.1276-T1
Valid prediction for GeneMark_model.25388_t
Valid prediction for GlimmerHMM_glimmerT_14986-T1
Valid prediction for GlimmerHMM_glimmerT_14990-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 3885, rend_intergenic: 3746  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 10182, rend_intergenic: 4126  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34999, rend_intergenic: 28291  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41918, rend_intergenic: 40049  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65909, rend_intergenic: 42795  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71075, rend_intergenic: 66897  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80855, rend_intergenic: 75953  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91578, rend_intergenic: 89022  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100546, rend_intergenic: 92246  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115513, rend_intergenic: 112576  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141957, rend_intergenic: 139990  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164917, rend_intergenic: 152102  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 176279
-exon list size: 708


building trellis

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66.6    
66.8    
66.9    
67.0    
67.2    
67.3    
67.5    
67.6    
67.7    
67.9    
68.0    
68.2    
68.3    
68.5    
68.6    
68.7    
68.9    
69.0    
69.2    
69.3    
69.4    
69.6    
69.7    
69.9    
70.0    
70.1    
70.3    
70.4    
70.6    
70.7    
70.8    
71.0    
71.1    
71.3    
71.4    
71.5    
71.7    
71.8    
72.0    
72.1    
72.3    
72.4    
72.5    
72.7    
72.8    
73.0    
73.1    
73.2    
73.4    
73.5    
73.7    
73.8    
73.9    
74.1    
74.2    
74.4    
74.5    
74.6    
74.8    
74.9    
75.1    
75.2    
75.4    
75.5    
75.6    
75.8    
75.9    
76.1    
76.2    
76.3    
76.5    
76.6    
76.8    
76.9    
77.0    
77.2    
77.3    
77.5    
77.6    
77.7    
77.9    
78.0    
78.2    
78.3    
78.5    
78.6    
78.7    
78.9    
79.0    
79.2    
79.3    
79.4    
79.6    
79.7    
79.9    
80.0    
80.1    
80.3    
80.4    
80.6    
80.7    
80.8    
81.0    
81.1    
81.3    
81.4    
81.5    
81.7    
81.8    
82.0    
82.1    
82.3    
82.4    
82.5    
82.7    
82.8    
83.0    
83.1    
83.2    
83.4    
83.5    
83.7    
83.8    
83.9    
84.1    
84.2    
84.4    
84.5    
84.6    
84.8    
84.9    
85.1    
85.2    
85.4    
85.5    
85.6    
85.8    
85.9    
86.1    
86.2    
86.3    
86.5    
86.6    
86.8    
86.9    
87.0    
87.2    
87.3    
87.5    
87.6    
87.7    
87.9    
88.0    
88.2    
88.3    
88.5    
88.6    
88.7    
88.9    
89.0    
89.2    
89.3    
89.4    
89.6    
89.7    
89.9    
90.0    
90.1    
90.3    
90.4    
90.6    
90.7    
90.8    
91.0    
91.1    
91.3    
91.4    
91.5    
91.7    
91.8    
92.0    
92.1    
92.3    
92.4    
92.5    
92.7    
92.8    
93.0    
93.1    
93.2    
93.4    
93.5    
93.7    
93.8    
93.9    
94.1    
94.2    
94.4    
94.5    
94.6    
94.8    
94.9    
95.1    
95.2    
95.4    
95.5    
95.6    
95.8    
95.9    
96.1    
96.2    
96.3    
96.5    
96.6    
96.8    
96.9    
97.0    
97.2    
97.3    
97.5    
97.6    
97.7    
97.9    
98.0    
98.2    
98.3    
98.5    
98.6    
98.7    
98.9    
99.0    
99.2    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 45 predictions from path traversal
Error with prediction: snap lend_intergenic: 3885, rend_intergenic: 3746  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 10182, rend_intergenic: 4126  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34999, rend_intergenic: 28291  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41918, rend_intergenic: 40049  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65909, rend_intergenic: 42795  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71075, rend_intergenic: 66897  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80855, rend_intergenic: 75953  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91578, rend_intergenic: 89022  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100546, rend_intergenic: 92246  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115513, rend_intergenic: 112576  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141957, rend_intergenic: 139990  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164917, rend_intergenic: 152102  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support