-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_9/scaffold_9_7549269-7820008

-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_22501-T1
Valid prediction for snap_scaffold_9-snap.1619-T1
Valid prediction for snap_scaffold_9-snap.1632-T1
Valid prediction for snap_scaffold_9-snap.1598-T1
Valid prediction for Augustus_model.g14956.t1
Valid prediction for snap_scaffold_9-snap.1625-T1
Valid prediction for GlimmerHMM_glimmerT_22497-T1
Valid prediction for GlimmerHMM_glimmerT_22514-T1
Valid prediction for snap_scaffold_9-snap.1609-T1
Valid prediction for snap_scaffold_9-snap.1631-T1
Valid prediction for Augustus_model.g14961.t1
Valid prediction for GlimmerHMM_glimmerT_22507-T1
Valid prediction for snap_scaffold_9-snap.1602-T1
Valid prediction for snap_scaffold_9-snap.1605-T1
Valid prediction for snap_scaffold_9-snap.1588-T1
Valid prediction for Augustus_model.g14966.t1
Valid prediction for GlimmerHMM_glimmerT_22517-T1
Valid prediction for GlimmerHMM_glimmerT_22519-T1
Valid prediction for Augustus_model.g14955.t1
Valid prediction for snap_scaffold_9-snap.1612-T1
Valid prediction for GlimmerHMM_glimmerT_22520-T1
Valid prediction for snap_scaffold_9-snap.1620-T1
Valid prediction for GlimmerHMM_glimmerT_22512-T1
Valid prediction for HiQ_model.g14965.t1
Valid prediction for snap_scaffold_9-snap.1597-T1
Valid prediction for snap_scaffold_9-snap.1634-T1
Valid prediction for Augustus_model.g14963.t1
Valid prediction for Augustus_model.g14962.t1
Valid prediction for Augustus_model.g14967.t1
Valid prediction for snap_scaffold_9-snap.1618-T1
Couldn't classify 246072, 246281
Sorry, prediction CodingQuarry_transcript_62229-T1 fails validation.
(ATG)	 GG	233031-233130	GT	AGG
(TGC)	 AG	233258-233418	GT	AGG
(GCT)	 AG	234197-234307	GT	GGG
(GTG)	 AG	234883-235037	GT	AGG
(AAA)	 AG	235437-235536	GT	AGG
(ATC)	 AG	235629-235800	GT	AGG
(AGG)	 AG	236124-236377	GT	AGG
(TAT)	 AG	236463-236606	GT	ACG
(ATT)	 AG	236705-236873	GT	AGG
(GCA)	 AG	236966-237056	GT	AGG
(ACG)	 AG	237150-237232	GT	GAG
(GTG)	 AG	237518-237668	GT	AGG
(GTG)	 AG	238122-238225	GT	GGG
(GTA)	 AG	238316-238501	GT	AGG
(GAG)	 AG	239237-239438	GT	AGG
(GGG)	 AG	239739-239860	GT	AGG
(ACT)	 AG	239946-240133	GT	AGG
(GGT)	 AG	240230-240324	GT	AGG
(GGC)	 AG	240434-241026	GT	AGG
(GGT)	 AG	241235-241332	GT	AGG
(GTT)	 AG	241458-241628	GT	AGG
(CTG)	 AG	241765-241905	GT	AGG
(ACG)	 AG	242664-242843	GT	AGG
(ACC)	 AG	243777-243941	GT	AGG
(AAG)	 AG	244271-244345	GT	CGG
(GTG)	 AG	244448-244618	GT	AGG
(GTG)	 CT	246072-246281	GT	TTG
(ATT)	 AG	247250-247387	GT	GGG
(CTG)	 AG	248177-248337	GT	AGG
(TCT)	 AG	248550-248757	GT	AGG
(AAT)	 AG	249084-249233	GT	CAG
(ATC)	 AG	249324-249422	GT	CTG
(TGG)	 AG	249505-249588	GT	AGG
(CAA)	 AG	250729-250839	GT	AGG
(CTA)	 AG	251034-251320	GT	AGG
(GAG)	 AG	251427-251688	CA	GAC
-recovered CodingQuarry_transcript_62229-T1, initial, 233031, 233130
add_exon() Sorry, CodingQuarry_transcript_62229-T1 237518-237668-terminal-3 is invalid.
-recovered CodingQuarry_transcript_62229-T1, terminal, 237518, 237668
add_exon() Sorry, CodingQuarry_transcript_62229-T1 240434-241026-terminal-2 is invalid.
-recovered CodingQuarry_transcript_62229-T1, terminal, 240434, 241026
-recovered CodingQuarry_transcript_62229-T1, terminal, 251427, 251688
-recovered CodingQuarry_transcript_62229-T1, internal, 233258, 233418
-recovered CodingQuarry_transcript_62229-T1, internal, 234197, 234307
-recovered CodingQuarry_transcript_62229-T1, internal, 234883, 235037
-recovered CodingQuarry_transcript_62229-T1, internal, 235437, 235536
-recovered CodingQuarry_transcript_62229-T1, internal, 235629, 235800
-recovered CodingQuarry_transcript_62229-T1, internal, 236124, 236377
-recovered CodingQuarry_transcript_62229-T1, internal, 236463, 236606
-recovered CodingQuarry_transcript_62229-T1, internal, 236705, 236873
-recovered CodingQuarry_transcript_62229-T1, internal, 236966, 237056
-recovered CodingQuarry_transcript_62229-T1, internal, 237150, 237232
-recovered CodingQuarry_transcript_62229-T1, internal, 237518, 237668
-recovered CodingQuarry_transcript_62229-T1, internal, 238122, 238225
-recovered CodingQuarry_transcript_62229-T1, internal, 238316, 238501
-recovered CodingQuarry_transcript_62229-T1, internal, 239237, 239438
-recovered CodingQuarry_transcript_62229-T1, internal, 239739, 239860
-recovered CodingQuarry_transcript_62229-T1, internal, 239946, 240133
-recovered CodingQuarry_transcript_62229-T1, internal, 240230, 240324
-recovered CodingQuarry_transcript_62229-T1, internal, 240434, 241026
-recovered CodingQuarry_transcript_62229-T1, internal, 241235, 241332
-recovered CodingQuarry_transcript_62229-T1, internal, 241458, 241628
-recovered CodingQuarry_transcript_62229-T1, internal, 241765, 241905
-recovered CodingQuarry_transcript_62229-T1, internal, 242664, 242843
-recovered CodingQuarry_transcript_62229-T1, internal, 243777, 243941
-recovered CodingQuarry_transcript_62229-T1, internal, 244271, 244345
-recovered CodingQuarry_transcript_62229-T1, internal, 244448, 244618
-recovered CodingQuarry_transcript_62229-T1, internal, 247250, 247387
-recovered CodingQuarry_transcript_62229-T1, internal, 248177, 248337
-recovered CodingQuarry_transcript_62229-T1, internal, 248550, 248757
-recovered CodingQuarry_transcript_62229-T1, internal, 249084, 249233
-recovered CodingQuarry_transcript_62229-T1, internal, 249324, 249422
-recovered CodingQuarry_transcript_62229-T1, internal, 249505, 249588
-recovered CodingQuarry_transcript_62229-T1, internal, 250729, 250839
-recovered CodingQuarry_transcript_62229-T1, internal, 251034, 251320
Valid prediction for GlimmerHMM_glimmerT_22492-T1
Valid prediction for GlimmerHMM_glimmerT_22516-T1
Valid prediction for snap_scaffold_9-snap.1592-T1
Valid prediction for Augustus_model.g14951.t1
Valid prediction for snap_scaffold_9-snap.1589-T1
Valid prediction for GlimmerHMM_glimmerT_22498-T1
Valid prediction for snap_scaffold_9-snap.1623-T1
Valid prediction for GlimmerHMM_glimmerT_22499-T1
Valid prediction for GlimmerHMM_glimmerT_22522-T1
Valid prediction for snap_scaffold_9-snap.1604-T1
Valid prediction for Augustus_model.g14953.t1
Valid prediction for snap_scaffold_9-snap.1611-T1
Valid prediction for pasa_asmbl_54142.p1
Valid prediction for snap_scaffold_9-snap.1586-T1
Valid prediction for GlimmerHMM_glimmerT_22505-T1
Valid prediction for CodingQuarry_transcript_62231-T1
Valid prediction for snap_scaffold_9-snap.1607-T1
Valid prediction for snap_scaffold_9-snap.1593-T1
Valid prediction for snap_scaffold_9-snap.1635-T1
Valid prediction for GlimmerHMM_glimmerT_22513-T1
Valid prediction for GlimmerHMM_glimmerT_22511-T1
Valid prediction for GlimmerHMM_glimmerT_22518-T1
Valid prediction for snap_scaffold_9-snap.1614-T1
Couldn't classify 196190, 196231
Sorry, prediction pasa_asmbl_54131.p1 fails validation.
(CGG)	 GA	196190-196231	GT	TGG
(GGT)	 AG	198438-198514	GT	CAG
(CTT)	 AG	199093-199204	GT	AGG
(GAG)	 AG	200789-200925	GT	AGG
(ACT)	 AG	201014-201077	GT	AGG
(ATT)	 AG	201670-201798	GT	GTG
(GGT)	 AG	202497-202566	GT	ACG
(TCC)	 AG	203473-203586	GT	AGG
(GAC)	 AG	204675-204774	GT	AGG
(TCT)	 AG	205033-205152	GT	GGG
(CAT)	 AG	205258-205402	GT	AGG
(GCA)	 AG	205602-205766	AG	AAA
-recovered pasa_asmbl_54131.p1, terminal, 205602, 205766
-recovered pasa_asmbl_54131.p1, internal, 198438, 198514
-recovered pasa_asmbl_54131.p1, internal, 199093, 199204
-recovered pasa_asmbl_54131.p1, internal, 200789, 200925
-recovered pasa_asmbl_54131.p1, internal, 201014, 201077
-recovered pasa_asmbl_54131.p1, internal, 201670, 201798
-recovered pasa_asmbl_54131.p1, internal, 202497, 202566
-recovered pasa_asmbl_54131.p1, internal, 203473, 203586
-recovered pasa_asmbl_54131.p1, internal, 204675, 204774
-recovered pasa_asmbl_54131.p1, internal, 205033, 205152
-recovered pasa_asmbl_54131.p1, internal, 205258, 205402
Valid prediction for snap_scaffold_9-snap.1626-T1
Valid prediction for snap_scaffold_9-snap.1595-T1
Valid prediction for snap_scaffold_9-snap.1610-T1
Valid prediction for pasa_asmbl_54140.p1
Valid prediction for snap_scaffold_9-snap.1636-T1
Valid prediction for snap_scaffold_9-snap.1624-T1
Valid prediction for Augustus_model.g14960.t1
Valid prediction for CodingQuarry_transcript_62230-T1
Valid prediction for Augustus_model.g14954.t1
Valid prediction for GlimmerHMM_glimmerT_22495-T1
Valid prediction for GlimmerHMM_glimmerT_22506-T1
Valid prediction for snap_scaffold_9-snap.1628-T1
Valid prediction for GlimmerHMM_glimmerT_22521-T1
Valid prediction for snap_scaffold_9-snap.1633-T1
Couldn't classify 245991, 246281
Sorry, prediction pasa_asmbl_54141.p1 fails validation.
(GTC)	 CT	245991-246281	GT	TTG
(ATT)	 AG	247250-247387	GT	GGG
(CTG)	 AG	248177-248337	GT	AGG
(TCT)	 AG	248550-248757	GT	AGG
(AAT)	 AG	249084-249233	GT	CAG
(ATC)	 AG	249324-249422	GT	CTG
(TGG)	 AG	249505-249588	GT	AGG
(CAA)	 AG	250729-250839	GT	AGG
(CTA)	 AG	251034-251320	GT	AGG
(GAG)	 AG	251427-251688	CA	GAC
-recovered pasa_asmbl_54141.p1, terminal, 251427, 251688
-recovered pasa_asmbl_54141.p1, internal, 247250, 247387
-recovered pasa_asmbl_54141.p1, internal, 248177, 248337
-recovered pasa_asmbl_54141.p1, internal, 248550, 248757
-recovered pasa_asmbl_54141.p1, internal, 249084, 249233
-recovered pasa_asmbl_54141.p1, internal, 249324, 249422
-recovered pasa_asmbl_54141.p1, internal, 249505, 249588
-recovered pasa_asmbl_54141.p1, internal, 250729, 250839
-recovered pasa_asmbl_54141.p1, internal, 251034, 251320
Valid prediction for snap_scaffold_9-snap.1630-T1
Valid prediction for GlimmerHMM_glimmerT_22493-T1
Valid prediction for snap_scaffold_9-snap.1622-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_9-snap.1594-T1
Valid prediction for snap_scaffold_9-snap.1601-T1
Valid prediction for GlimmerHMM_glimmerT_22508-T1
Valid prediction for HiQ_model.g14959.t1
Valid prediction for Augustus_model.g14958.t1
Valid prediction for snap_scaffold_9-snap.1590-T1
Valid prediction for snap_scaffold_9-snap.1617-T1
Valid prediction for Augustus_model.g14948.t1
Valid prediction for snap_scaffold_9-snap.1616-T1
Valid prediction for snap_scaffold_9-snap.1629-T1
Valid prediction for snap_scaffold_9-snap.1585-T1
Valid prediction for snap_scaffold_9-snap.1591-T1
Valid prediction for snap_scaffold_9-snap.1608-T1
Valid prediction for GlimmerHMM_glimmerT_22494-T1
Valid prediction for snap_scaffold_9-snap.1606-T1
Valid prediction for GlimmerHMM_glimmerT_22509-T1
Valid prediction for snap_scaffold_9-snap.1615-T1
Valid prediction for snap_scaffold_9-snap.1613-T1
Valid prediction for CodingQuarry_transcript_62228-T1
Valid prediction for Augustus_model.g14964.t1
Valid prediction for Augustus_model.g14949.t1
Valid prediction for snap_scaffold_9-snap.1603-T1
Couldn't classify 208723, 208899
Sorry, prediction pasa_asmbl_55107.p1 fails validation.
(TTG)	 GG	208723-208899	GT	AGG
(GTG)	 AG	209940-210107	GT	GGG
(GCC)	 AG	210198-210298	GT	AAG
(ACA)	 AG	210414-210759	GC	AGG
-recovered pasa_asmbl_55107.p1, terminal, 210414, 210759
-recovered pasa_asmbl_55107.p1, internal, 209940, 210107
-recovered pasa_asmbl_55107.p1, internal, 210198, 210298
-recovered pasa_asmbl_55107.p1, internal, 210414, 210759
Valid prediction for Augustus_model.g14952.t1
Valid prediction for GlimmerHMM_glimmerT_22510-T1
Valid prediction for snap_scaffold_9-snap.1621-T1
Valid prediction for GlimmerHMM_glimmerT_22515-T1
Valid prediction for snap_scaffold_9-snap.1627-T1
Valid prediction for GlimmerHMM_glimmerT_22500-T1
Valid prediction for GlimmerHMM_glimmerT_22504-T1
Valid prediction for Augustus_model.g14946.t1
Valid prediction for snap_scaffold_9-snap.1587-T1
Valid prediction for snap_scaffold_9-snap.1600-T1
Valid prediction for snap_scaffold_9-snap.1599-T1
Valid prediction for snap_scaffold_9-snap.1596-T1
Valid prediction for GlimmerHMM_glimmerT_22503-T1
Valid prediction for Augustus_model.g14957.t1
Couldn't classify 203727, 203905
Sorry, prediction pasa_asmbl_55108.p1 fails validation.
(ATG)	 TT	194276-194396	GT	AGG
(AAC)	 AG	197005-197135	GT	TGG
(TTC)	 AG	199174-199288	GT	AGG
(TGT)	 AG	200575-200686	GT	CGG
(GCT)	 AG	200775-200890	GT	GAG
(TGA)	 AG	203727-203905	TG	AGT
-recovered pasa_asmbl_55108.p1, initial, 194276, 194396
add_exon() Sorry, pasa_asmbl_55108.p1 200775-200890-terminal-2 is invalid.
-recovered pasa_asmbl_55108.p1, terminal, 200775, 200890
-recovered pasa_asmbl_55108.p1, internal, 197005, 197135
-recovered pasa_asmbl_55108.p1, internal, 199174, 199288
-recovered pasa_asmbl_55108.p1, internal, 200575, 200686
-recovered pasa_asmbl_55108.p1, internal, 200775, 200890
Valid prediction for GlimmerHMM_glimmerT_22496-T1
Couldn't classify 208723, 208899
Couldn't classify 212263, 212591
Sorry, prediction pasa_asmbl_55106.p1 fails validation.
(TTG)	 GG	208723-208899	GT	AGG
(GTG)	 AG	209940-210107	GT	GGG
(GCC)	 AG	210198-210298	GT	AAG
(ACA)	 AG	210414-210646	GT	ATG
(CTC)	 AG	212263-212591	TT	ACT
-recovered pasa_asmbl_55106.p1, internal, 209940, 210107
-recovered pasa_asmbl_55106.p1, internal, 210198, 210298
-recovered pasa_asmbl_55106.p1, internal, 210414, 210646
Valid prediction for GlimmerHMM_glimmerT_22502-T1
Valid prediction for pasa_asmbl_55110.p1
Valid prediction for Augustus_model.g14950.t1
Valid prediction for Augustus_model.g14947.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 35228, rend_intergenic: 30751  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40236, rend_intergenic: 36022  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49840, rend_intergenic: 46587  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66997, rend_intergenic: 64648  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69518, rend_intergenic: 68475  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73827, rend_intergenic: 69523  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 226666, rend_intergenic: 223054  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 270740
-exon list size: 480


building trellis

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64.7    
64.9    
65.1    
65.4    
65.6    
65.8    
66.0    
66.2    
66.4    
66.6    
66.8    
67.0    
67.2    
67.4    
67.6    
67.8    
68.0    
68.3    
68.5    
68.7    
68.9    
69.1    
69.3    
69.5    
69.7    
69.9    
70.1    
70.3    
70.5    
70.7    
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    
73.7    
73.9    
74.1    
74.3    
74.5    
74.7    
74.9    
75.1    
75.3    
75.5    
75.7    
75.9    
76.1    
76.3    
76.6    
76.8    
77.0    
77.2    
77.4    
77.6    
77.8    
78.0    
78.2    
78.4    
78.6    
78.8    
79.0    
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    
82.0    
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    
84.9    
85.1    
85.3    
85.5    
85.7    
85.9    
86.1    
86.3    
86.5    
86.7    
86.9    
87.1    
87.3    
87.6    
87.8    
88.0    
88.2    
88.4    
88.6    
88.8    
89.0    
89.2    
89.4    
89.6    
89.8    
90.0    
90.2    
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    
93.2    
93.4    
93.6    
93.8    
94.0    
94.2    
94.4    
94.6    
94.8    
95.0    
95.2    
95.4    
95.6    
95.9    
96.1    
96.3    
96.5    
96.7    
96.9    
97.1    
97.3    
97.5    
97.7    
97.9    
98.1    
98.3    
98.5    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 39 predictions from path traversal
Error with prediction: snap lend_intergenic: 35228, rend_intergenic: 30751  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40236, rend_intergenic: 36022  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49840, rend_intergenic: 46587  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66997, rend_intergenic: 64648  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69518, rend_intergenic: 68475  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73827, rend_intergenic: 69523  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 226666, rend_intergenic: 223054  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 33 predictions persist after filtering for low support