-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_7/scaffold_7_7042719-7254564

-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: +)Couldn't classify 186462, 186624
Couldn't classify 189574, 189841
Sorry, prediction pasa_asmbl_50796.p1 fails validation.
(ACC)	 TG	186462-186624	GT	AGG
(GCA)	 AG	186862-187062	GT	CAG
(CCT)	 AG	187575-187854	GT	AGG
(TAT)	 AG	188008-188264	GT	CAG
(ACC)	 AG	188593-188701	GT	AGG
(GAT)	 AG	188835-189071	GT	GAG
(ACT)	 AG	189574-189841	CC	GGC
-recovered pasa_asmbl_50796.p1, terminal, 188835, 189071
-recovered pasa_asmbl_50796.p1, internal, 186862, 187062
-recovered pasa_asmbl_50796.p1, internal, 187575, 187854
-recovered pasa_asmbl_50796.p1, internal, 188008, 188264
-recovered pasa_asmbl_50796.p1, internal, 188593, 188701
-recovered pasa_asmbl_50796.p1, internal, 188835, 189071
Valid prediction for GlimmerHMM_glimmerT_18034-T1
Valid prediction for snap_scaffold_7-snap.1463-T1
Valid prediction for GeneMark_model.30283_t
Valid prediction for GeneMark_model.30277_t
Valid prediction for GlimmerHMM_glimmerT_18055-T1
Valid prediction for GlimmerHMM_glimmerT_18047-T1
Valid prediction for GeneMark_model.30265_t
Valid prediction for GeneMark_model.30254_t
Valid prediction for GlimmerHMM_glimmerT_18048-T1
Valid prediction for snap_scaffold_7-snap.1464-T1
Valid prediction for GlimmerHMM_glimmerT_18051-T1
Couldn't classify 166259, 166490
Couldn't classify 167172, 167278
Sorry, prediction pasa_asmbl_51480.p1 fails validation.
(ACG)	 GG	166259-166490	GT	AGG
(GTG)	 AG	167172-167278	GG	AGG
Couldn't classify 181845, 181886
Couldn't classify 184502, 184536
Sorry, prediction pasa_asmbl_50794.p1 fails validation.
(ATT)	 AT	181845-181886	GT	AGG
(CCT)	 AG	182589-182742	GT	AGG
(CTT)	 AG	182952-183068	GT	AGG
(TTT)	 AG	183152-183306	GT	AGG
(CTG)	 AG	183826-183952	GT	AGG
(CTT)	 AG	184166-184276	GT	TGG
(CCG)	 AG	184502-184536	AC	GCA
-recovered pasa_asmbl_50794.p1, internal, 182589, 182742
-recovered pasa_asmbl_50794.p1, internal, 182952, 183068
-recovered pasa_asmbl_50794.p1, internal, 183152, 183306
-recovered pasa_asmbl_50794.p1, internal, 183826, 183952
-recovered pasa_asmbl_50794.p1, internal, 184166, 184276
Valid prediction for snap_scaffold_7-snap.1467-T1
Couldn't classify 33756, 33898
Sorry, prediction pasa_asmbl_50779.p1 fails validation.
(ATG)	 TT	32032-32320	GT	AGG
(AAA)	 AG	32892-33115	GT	TGG
(GTT)	 AG	33354-33513	GT	TCG
(GGG)	 AG	33756-33898	CT	CCC
-recovered pasa_asmbl_50779.p1, initial, 32032, 32320
-recovered pasa_asmbl_50779.p1, internal, 32892, 33115
-recovered pasa_asmbl_50779.p1, internal, 33354, 33513
Valid prediction for snap_scaffold_7-snap.1455-T1
Valid prediction for snap_scaffold_7-snap.1458-T1
Couldn't classify 174869, 174875
Couldn't classify 177320, 177420
Sorry, prediction pasa_asmbl_50793.p1 fails validation.
(CAC)	 TG	174869-174875	GT	TGG
(CAC)	 AG	175167-175378	GT	AGG
(ATC)	 AG	175633-175841	GT	AGG
(GTA)	 AG	176313-176662	GT	TGG
(GCC)	 AG	177320-177420	CA	TGC
-recovered pasa_asmbl_50793.p1, internal, 175167, 175378
-recovered pasa_asmbl_50793.p1, internal, 175633, 175841
-recovered pasa_asmbl_50793.p1, internal, 176313, 176662
Valid prediction for GeneMark_model.30271_t
Valid prediction for Augustus_model.g12118.t1
Valid prediction for GeneMark_model.30275_t
Valid prediction for GlimmerHMM_glimmerT_18033-T1
Valid prediction for Augustus_model.g12130.t1
Valid prediction for snap_scaffold_7-snap.1450-T1
Valid prediction for GeneMark_model.30258_t
Valid prediction for Augustus_model.g12119.t1
Valid prediction for Augustus_model.g12116.t1
Valid prediction for snap_scaffold_7-snap.1454-T1
Valid prediction for GeneMark_model.30256_t
Valid prediction for GeneMark_model.30263_t
Valid prediction for GeneMark_model.30284_t
Valid prediction for Augustus_model.g12125.t1
Valid prediction for GlimmerHMM_glimmerT_18054-T1
Valid prediction for HiQ_model.g12127.t1
Valid prediction for GeneMark_model.30262_t
Valid prediction for GlimmerHMM_glimmerT_18049-T1
Valid prediction for snap_scaffold_7-snap.1479-T1
Valid prediction for snap_scaffold_7-snap.1462-T1
Couldn't classify 201550, 201750
Couldn't classify 204748, 204965
Sorry, prediction pasa_asmbl_50798.p1 fails validation.
(GTG)	 TA	201550-201750	GT	AGG
(AAA)	 AG	202374-202445	GT	AAG
(GTG)	 AG	203348-203651	GT	AAG
(GTC)	 AG	204748-204965	GT	AGG
-recovered pasa_asmbl_50798.p1, internal, 202374, 202445
-recovered pasa_asmbl_50798.p1, internal, 203348, 203651
-recovered pasa_asmbl_50798.p1, internal, 204748, 204965
Valid prediction for GlimmerHMM_glimmerT_18032-T1
Valid prediction for CodingQuarry_transcript_57391-T1
Valid prediction for GeneMark_model.30279_t
Valid prediction for GeneMark_model.30257_t
Valid prediction for GeneMark_model.30259_t
Valid prediction for GeneMark_model.30289_t
Valid prediction for GlimmerHMM_glimmerT_18044-T1
Valid prediction for GeneMark_model.30281_t
Valid prediction for GeneMark_model.30255_t
Valid prediction for snap_scaffold_7-snap.1472-T1
Valid prediction for GlimmerHMM_glimmerT_18053-T1
Valid prediction for GlimmerHMM_glimmerT_18052-T1
Couldn't classify 190361, 190504
Couldn't classify 196562, 196734
Sorry, prediction pasa_asmbl_50797.p1 fails validation.
(TCG)	 CC	190361-190504	GT	AGG
(GTG)	 AG	190641-190784	GT	CGG
(CTG)	 AG	192619-192748	GT	AGG
(ACA)	 AG	195134-195265	GT	AGG
(GTT)	 AG	195631-195792	GT	AGG
(GTC)	 AG	196562-196734	GG	AAG
-recovered pasa_asmbl_50797.p1, internal, 190641, 190784
-recovered pasa_asmbl_50797.p1, internal, 192619, 192748
-recovered pasa_asmbl_50797.p1, internal, 195134, 195265
-recovered pasa_asmbl_50797.p1, internal, 195631, 195792
Valid prediction for snap_scaffold_7-snap.1460-T1
Valid prediction for Augustus_model.g12129.t1
Valid prediction for GeneMark_model.30276_t
Couldn't classify 208757, 208921
Couldn't classify 209210, 209377
Sorry, prediction pasa_asmbl_50800.p2 fails validation.
(CCC)	 AG	208757-208921	GT	AGG
(GTG)	 AG	209210-209377	GG	CCG
-recovered pasa_asmbl_50800.p2, internal, 208757, 208921
Valid prediction for GeneMark_model.30252_t
Valid prediction for pasa_asmbl_50791.p1
Valid prediction for GlimmerHMM_glimmerT_18035-T1
Valid prediction for pasa_asmbl_50787.p1
Couldn't classify 185190, 185514
Couldn't classify 186200, 186292
Sorry, prediction pasa_asmbl_50795.p1 fails validation.
(GCC)	 AC	185190-185514	GT	AGG
(GCG)	 AG	185603-185778	GT	AGG
(GGC)	 AG	186200-186292	AT	ACA
-recovered pasa_asmbl_50795.p1, internal, 185603, 185778
Valid prediction for snap_scaffold_7-snap.1477-T1
Valid prediction for GlimmerHMM_glimmerT_18042-T1
Valid prediction for snap_scaffold_7-snap.1459-T1
Valid prediction for snap_scaffold_7-snap.1452-T1
Valid prediction for Augustus_model.g12126.t1
Valid prediction for GeneMark_model.30291_t
Valid prediction for HiQ_model.g12128.t1
Valid prediction for snap_scaffold_7-snap.1471-T1
Valid prediction for CodingQuarry_transcript_57390-T1
Valid prediction for snap_scaffold_7-snap.1481-T1
Valid prediction for GlimmerHMM_glimmerT_18031-T1
Valid prediction for Augustus_model.g12120.t1
Valid prediction for HiQ_model.g12117.t1
Valid prediction for snap_scaffold_7-snap.1480-T1
Valid prediction for GeneMark_model.30268_t
Valid prediction for GeneMark_model.30267_t
Valid prediction for GlimmerHMM_glimmerT_18050-T1
Couldn't classify 45592, 45642
Couldn't classify 47163, 47343
Sorry, prediction pasa_asmbl_50780.p1 fails validation.
(TTC)	 GC	45592-45642	GT	CTG
(CTC)	 AG	46352-46452	GT	GGG
(ACT)	 AG	47163-47343	AC	CCA
-recovered pasa_asmbl_50780.p1, internal, 46352, 46452
Valid prediction for Augustus_model.g12123.t1
Couldn't classify 65108, 65146
Sorry, prediction pasa_asmbl_50785.p1 fails validation.
(ACC)	 CC	65108-65146	GT	AGG
(AAC)	 AG	65472-65604	GT	GGG
(GTA)	 AG	65823-65970	GT	TCG
(ATA)	 AG	66067-66157	GT	ATG
(AAC)	 AG	66281-66394	AC	AGA
-recovered pasa_asmbl_50785.p1, terminal, 66281, 66394
-recovered pasa_asmbl_50785.p1, internal, 65472, 65604
-recovered pasa_asmbl_50785.p1, internal, 65823, 65970
-recovered pasa_asmbl_50785.p1, internal, 66067, 66157
Valid prediction for GeneMark_model.30287_t
Valid prediction for snap_scaffold_7-snap.1469-T1
Valid prediction for snap_scaffold_7-snap.1451-T1
Valid prediction for pasa_asmbl_50783.p1
Couldn't classify 168683, 168716
Couldn't classify 170284, 170331
Sorry, prediction pasa_asmbl_51525.p1 fails validation.
(AAG)	 TC	168683-168716	GT	TGG
(AGA)	 AG	168823-168954	GT	AGG
(GGT)	 AG	169229-169360	GT	AGG
(GCA)	 AG	169621-169787	GT	AGG
(GAA)	 AG	170284-170331	CC	AGC
-recovered pasa_asmbl_51525.p1, internal, 168823, 168954
-recovered pasa_asmbl_51525.p1, internal, 169229, 169360
-recovered pasa_asmbl_51525.p1, internal, 169621, 169787
Valid prediction for GeneMark_model.30273_t
Valid prediction for GeneMark_model.30251_t
Valid prediction for Augustus_model.g12115.t1
Couldn't classify 53328, 54161
Sorry, prediction pasa_asmbl_50782.p1 fails validation.
(GCC)	 GC	53328-54161	TA	GAT

-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.30274_t
Valid prediction for snap_scaffold_7-snap.1473-T1
Valid prediction for snap_scaffold_7-snap.1470-T1
Valid prediction for GeneMark_model.30270_t
Valid prediction for GeneMark_model.30261_t
Valid prediction for GlimmerHMM_glimmerT_18045-T1
Valid prediction for snap_scaffold_7-snap.1483-T1
Valid prediction for snap_scaffold_7-snap.1475-T1
Valid prediction for GeneMark_model.30260_t
Valid prediction for Augustus_model.g12122.t1
Valid prediction for GeneMark_model.30253_t
Valid prediction for GeneMark_model.30288_t
Valid prediction for GeneMark_model.30266_t
Valid prediction for Augustus_model.g12124.t1
Valid prediction for snap_scaffold_7-snap.1468-T1
Valid prediction for snap_scaffold_7-snap.1453-T1
Valid prediction for GlimmerHMM_glimmerT_18043-T1
Valid prediction for snap_scaffold_7-snap.1461-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_18041-T1
Valid prediction for GlimmerHMM_glimmerT_18046-T1
Valid prediction for GeneMark_model.30269_t
Valid prediction for snap_scaffold_7-snap.1476-T1
Valid prediction for GlimmerHMM_glimmerT_18030-T1
Valid prediction for snap_scaffold_7-snap.1466-T1
Valid prediction for GeneMark_model.30290_t
Valid prediction for snap_scaffold_7-snap.1486-T1
Valid prediction for GeneMark_model.30278_t
Valid prediction for GlimmerHMM_glimmerT_18036-T1
Valid prediction for GeneMark_model.30286_t
Valid prediction for GlimmerHMM_glimmerT_18038-T1
Valid prediction for GlimmerHMM_glimmerT_18039-T1
Valid prediction for GeneMark_model.30280_t
Valid prediction for GeneMark_model.30285_t
Valid prediction for snap_scaffold_7-snap.1465-T1
Valid prediction for snap_scaffold_7-snap.1478-T1
Valid prediction for snap_scaffold_7-snap.1456-T1
Valid prediction for GeneMark_model.30272_t
Valid prediction for snap_scaffold_7-snap.1474-T1
Valid prediction for snap_scaffold_7-snap.1457-T1
Valid prediction for GlimmerHMM_glimmerT_18037-T1
Valid prediction for Augustus_model.g12121.t1
Valid prediction for GeneMark_model.30264_t
Valid prediction for GeneMark_model.30282_t
Valid prediction for GlimmerHMM_glimmerT_18040-T1
Valid prediction for snap_scaffold_7-snap.1485-T1
Valid prediction for snap_scaffold_7-snap.1484-T1
Sorry, intron length (3) is less than minimum required (10)

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 12800, rend_intergenic: 12320  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18489, rend_intergenic: 13209  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27857, rend_intergenic: 19320  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59088, rend_intergenic: 52323  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76283, rend_intergenic: 73932  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96765, rend_intergenic: 93953  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99968, rend_intergenic: 96904  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105805, rend_intergenic: 101285  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139073, rend_intergenic: 112545  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145624, rend_intergenic: 141926  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 211846
-exon list size: 680


building trellis

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68.5    
68.6    
68.8    
68.9    
69.1    
69.2    
69.4    
69.5    
69.6    
69.8    
69.9    
70.1    
70.2    
70.4    
70.5    
70.7    
70.8    
71.0    
71.1    
71.3    
71.4    
71.6    
71.7    
71.8    
72.0    
72.1    
72.3    
72.4    
72.6    
72.7    
72.9    
73.0    
73.2    
73.3    
73.5    
73.6    
73.8    
73.9    
74.0    
74.2    
74.3    
74.5    
74.6    
74.8    
74.9    
75.1    
75.2    
75.4    
75.5    
75.7    
75.8    
76.0    
76.1    
76.2    
76.4    
76.5    
76.7    
76.8    
77.0    
77.1    
77.3    
77.4    
77.6    
77.7    
77.9    
78.0    
78.2    
78.3    
78.4    
78.6    
78.7    
78.9    
79.0    
79.2    
79.3    
79.5    
79.6    
79.8    
79.9    
80.1    
80.2    
80.4    
80.5    
80.6    
80.8    
80.9    
81.1    
81.2    
81.4    
81.5    
81.7    
81.8    
82.0    
82.1    
82.3    
82.4    
82.6    
82.7    
82.8    
83.0    
83.1    
83.3    
83.4    
83.6    
83.7    
83.9    
84.0    
84.2    
84.3    
84.5    
84.6    
84.8    
84.9    
85.0    
85.2    
85.3    
85.5    
85.6    
85.8    
85.9    
86.1    
86.2    
86.4    
86.5    
86.7    
86.8    
87.0    
87.1    
87.2    
87.4    
87.5    
87.7    
87.8    
88.0    
88.1    
88.3    
88.4    
88.6    
88.7    
88.9    
89.0    
89.1    
89.3    
89.4    
89.6    
89.7    
89.9    
90.0    
90.2    
90.3    
90.5    
90.6    
90.8    
90.9    
91.1    
91.2    
91.3    
91.5    
91.6    
91.8    
91.9    
92.1    
92.2    
92.4    
92.5    
92.7    
92.8    
93.0    
93.1    
93.3    
93.4    
93.5    
93.7    
93.8    
94.0    
94.1    
94.3    
94.4    
94.6    
94.7    
94.9    
95.0    
95.2    
95.3    
95.5    
95.6    
95.7    
95.9    
96.0    
96.2    
96.3    
96.5    
96.6    
96.8    
96.9    
97.1    
97.2    
97.4    
97.5    
97.7    
97.8    
97.9    
98.1    
98.2    
98.4    
98.5    
98.7    
98.8    
99.0    
99.1    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 12800, rend_intergenic: 12320  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18489, rend_intergenic: 13209  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27857, rend_intergenic: 19320  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59088, rend_intergenic: 52323  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76283, rend_intergenic: 73932  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96765, rend_intergenic: 93953  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99968, rend_intergenic: 96904  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105805, rend_intergenic: 101285  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139073, rend_intergenic: 112545  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145624, rend_intergenic: 141926  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 22 predictions persist after filtering for low support