-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_9/scaffold_9_15036522-15223470

-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 GeneMark_model.41080_t
Valid prediction for GlimmerHMM_glimmerT_23936-T1
Valid prediction for CodingQuarry_transcript_62248-T1
Valid prediction for Augustus_model.g16031.t1
Valid prediction for snap_scaffold_9-snap.3107-T1
Valid prediction for GeneMark_model.41084_t
Valid prediction for GeneMark_model.41063_t
Valid prediction for CodingQuarry_transcript_62247-T1
Valid prediction for GeneMark_model.41079_t
Valid prediction for snap_scaffold_9-snap.3083-T1
Valid prediction for pasa_asmbl_54524.p1
Valid prediction for snap_scaffold_9-snap.3099-T1
Valid prediction for pasa_asmbl_54525.p1
Valid prediction for GeneMark_model.41064_t
Valid prediction for snap_scaffold_9-snap.3101-T1
Valid prediction for snap_scaffold_9-snap.3082-T1
Valid prediction for snap_scaffold_9-snap.3105-T1
Valid prediction for snap_scaffold_9-snap.3079-T1
Valid prediction for GlimmerHMM_glimmerT_23930-T1
Valid prediction for GlimmerHMM_glimmerT_23928-T1
Valid prediction for snap_scaffold_9-snap.3091-T1
Valid prediction for snap_scaffold_9-snap.3094-T1
Valid prediction for snap_scaffold_9-snap.3108-T1
Valid prediction for GlimmerHMM_glimmerT_23940-T1
Valid prediction for snap_scaffold_9-snap.3076-T1
Valid prediction for GlimmerHMM_glimmerT_23924-T1
Valid prediction for snap_scaffold_9-snap.3111-T1
Valid prediction for GeneMark_model.41086_t
Valid prediction for snap_scaffold_9-snap.3092-T1
Valid prediction for GeneMark_model.41088_t
Valid prediction for GeneMark_model.41095_t
Valid prediction for GeneMark_model.41076_t
Valid prediction for HiQ_model.g16029.t1
Valid prediction for snap_scaffold_9-snap.3096-T1
Valid prediction for GeneMark_model.41066_t
Valid prediction for snap_scaffold_9-snap.3089-T1
Valid prediction for GeneMark_model.41068_t
Valid prediction for GlimmerHMM_glimmerT_23935-T1
Valid prediction for Augustus_model.g16028.t1
Valid prediction for GeneMark_model.41092_t
Valid prediction for snap_scaffold_9-snap.3072-T1
Valid prediction for GlimmerHMM_glimmerT_23925-T1
Valid prediction for Augustus_model.g16037.t1
Valid prediction for snap_scaffold_9-snap.3073-T1
Valid prediction for Augustus_model.g16034.t1
Valid prediction for snap_scaffold_9-snap.3077-T1
Valid prediction for GeneMark_model.41072_t
Valid prediction for GeneMark_model.41090_t
Valid prediction for GlimmerHMM_glimmerT_23932-T1
Valid prediction for snap_scaffold_9-snap.3112-T1
Valid prediction for GlimmerHMM_glimmerT_23939-T1
Valid prediction for GeneMark_model.41070_t
Valid prediction for snap_scaffold_9-snap.3098-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.41065_t
Valid prediction for Augustus_model.g16044.t1
Valid prediction for GlimmerHMM_glimmerT_23934-T1
Valid prediction for GlimmerHMM_glimmerT_23921-T1
Valid prediction for snap_scaffold_9-snap.3075-T1
Valid prediction for GeneMark_model.41083_t
Valid prediction for GlimmerHMM_glimmerT_23922-T1
Valid prediction for snap_scaffold_9-snap.3097-T1
Valid prediction for Augustus_model.g16043.t1
Valid prediction for GeneMark_model.41091_t
Valid prediction for Augustus_model.g16041.t1
Valid prediction for snap_scaffold_9-snap.3081-T1
Valid prediction for Augustus_model.g16030.t1
Valid prediction for snap_scaffold_9-snap.3087-T1
Valid prediction for GlimmerHMM_glimmerT_23945-T1
Valid prediction for GlimmerHMM_glimmerT_23931-T1
Valid prediction for GlimmerHMM_glimmerT_23926-T1
Valid prediction for GeneMark_model.41094_t
Valid prediction for snap_scaffold_9-snap.3074-T1
Valid prediction for snap_scaffold_9-snap.3071-T1
Valid prediction for GeneMark_model.41071_t
Valid prediction for GlimmerHMM_glimmerT_23929-T1
Couldn't classify 60574, 61110
Sorry, prediction pasa_asmbl_55473.p1 fails validation.
(GTA)	 CT	60574-61110	GC	GAG
Couldn't classify 15989, 16153
Sorry, prediction pasa_asmbl_55475.p1 fails validation.
(ATG)	 CA	87-184	GT	AGG
(AAG)	 AG	1703-2484	GT	AAG
(GTT)	 AG	4478-4583	GT	AGG
(TCG)	 AG	5789-5925	GT	AGG
(CCT)	 AG	6027-6110	GT	AGG
(CTC)	 AG	6235-6330	GT	AAG
(GCT)	 AG	6467-6618	GT	TGG
(ATC)	 AG	7081-7116	GT	TTG
(ATG)	 AG	7214-7309	GT	AGG
(CTT)	 AG	7403-7495	GT	CTG
(GGC)	 AG	7701-7862	GT	AGG
(GAT)	 AG	7967-8035	GT	AGG
(AAC)	 AG	8145-8310	GT	GAG
(ACA)	 AG	8432-8549	GT	TGG
(TGA)	 AG	8708-8864	GT	AGG
(ACA)	 AG	9922-10075	GT	TGG
(GCG)	 AG	10190-10418	GT	AGG
(CCA)	 AG	10591-10709	GT	AGG
(GTG)	 AG	10800-11004	GT	GGG
(GAG)	 AG	11169-11269	GT	GGG
(CCA)	 AG	11362-11536	GT	AGG
(GGA)	 AG	11651-11792	GT	AGG
(GTG)	 AG	12155-12346	GT	CGG
(GTT)	 AG	12500-12651	GT	AGG
(AGG)	 AG	13027-13184	GT	AGG
(GCT)	 AG	13275-13348	GT	TGG
(GCC)	 AG	13446-13645	GT	TGG
(GTA)	 AG	13774-13901	GT	CGG
(ATG)	 AG	13999-14150	GT	AAG
(AAC)	 AG	14267-14409	GT	TGG
(CCC)	 AG	14496-14652	GT	AGG
(CGA)	 AG	15180-15278	GT	AGG
(GTG)	 AG	15396-15510	GT	AGG
(GAA)	 AG	15708-15862	GT	TGG
(CTG)	 AG	15989-16153	GT	AGG
-recovered pasa_asmbl_55475.p1, initial, 87, 184
-recovered pasa_asmbl_55475.p1, initial, 7214, 7309
add_exon() Sorry, pasa_asmbl_55475.p1 13999-14150-initial-1 is invalid.
-recovered pasa_asmbl_55475.p1, initial, 13999, 14150
-recovered pasa_asmbl_55475.p1, internal, 1703, 2484
-recovered pasa_asmbl_55475.p1, internal, 4478, 4583
-recovered pasa_asmbl_55475.p1, internal, 5789, 5925
-recovered pasa_asmbl_55475.p1, internal, 6027, 6110
-recovered pasa_asmbl_55475.p1, internal, 6235, 6330
-recovered pasa_asmbl_55475.p1, internal, 6467, 6618
-recovered pasa_asmbl_55475.p1, internal, 7081, 7116
-recovered pasa_asmbl_55475.p1, internal, 7214, 7309
-recovered pasa_asmbl_55475.p1, internal, 7403, 7495
-recovered pasa_asmbl_55475.p1, internal, 7701, 7862
-recovered pasa_asmbl_55475.p1, internal, 7967, 8035
-recovered pasa_asmbl_55475.p1, internal, 8145, 8310
-recovered pasa_asmbl_55475.p1, internal, 8432, 8549
-recovered pasa_asmbl_55475.p1, internal, 8708, 8864
-recovered pasa_asmbl_55475.p1, internal, 9922, 10075
-recovered pasa_asmbl_55475.p1, internal, 10190, 10418
-recovered pasa_asmbl_55475.p1, internal, 10591, 10709
-recovered pasa_asmbl_55475.p1, internal, 10800, 11004
-recovered pasa_asmbl_55475.p1, internal, 11169, 11269
-recovered pasa_asmbl_55475.p1, internal, 11362, 11536
-recovered pasa_asmbl_55475.p1, internal, 11651, 11792
-recovered pasa_asmbl_55475.p1, internal, 12155, 12346
-recovered pasa_asmbl_55475.p1, internal, 12500, 12651
-recovered pasa_asmbl_55475.p1, internal, 13027, 13184
-recovered pasa_asmbl_55475.p1, internal, 13275, 13348
-recovered pasa_asmbl_55475.p1, internal, 13446, 13645
-recovered pasa_asmbl_55475.p1, internal, 13774, 13901
-recovered pasa_asmbl_55475.p1, internal, 13999, 14150
-recovered pasa_asmbl_55475.p1, internal, 14267, 14409
-recovered pasa_asmbl_55475.p1, internal, 14496, 14652
-recovered pasa_asmbl_55475.p1, internal, 15180, 15278
-recovered pasa_asmbl_55475.p1, internal, 15396, 15510
-recovered pasa_asmbl_55475.p1, internal, 15708, 15862
-recovered pasa_asmbl_55475.p1, internal, 15989, 16153
Valid prediction for Augustus_model.g16035.t1
Valid prediction for GlimmerHMM_glimmerT_23949-T1
Valid prediction for snap_scaffold_9-snap.3085-T1
Valid prediction for GeneMark_model.41089_t
Valid prediction for Augustus_model.g16047.t1
Valid prediction for snap_scaffold_9-snap.3100-T1
Valid prediction for Augustus_model.g16036.t1
Valid prediction for Augustus_model.g16048.t1
Valid prediction for snap_scaffold_9-snap.3110-T1
Valid prediction for Augustus_model.g16033.t1
Valid prediction for GlimmerHMM_glimmerT_23950-T1
Valid prediction for GeneMark_model.41087_t
Valid prediction for GlimmerHMM_glimmerT_23946-T1
Valid prediction for GlimmerHMM_glimmerT_23947-T1
Valid prediction for snap_scaffold_9-snap.3070-T1
Valid prediction for GlimmerHMM_glimmerT_23937-T1
Valid prediction for snap_scaffold_9-snap.3106-T1
Valid prediction for GeneMark_model.41067_t
Valid prediction for GlimmerHMM_glimmerT_23938-T1
Valid prediction for GeneMark_model.41074_t
Valid prediction for snap_scaffold_9-snap.3095-T1
Valid prediction for snap_scaffold_9-snap.3109-T1
Valid prediction for GeneMark_model.41077_t
Valid prediction for Augustus_model.g16032.t1
Valid prediction for GeneMark_model.41062_t
Valid prediction for Augustus_model.g16027.t1
Valid prediction for GeneMark_model.41075_t
Valid prediction for GlimmerHMM_glimmerT_23941-T1
Valid prediction for Augustus_model.g16039.t1
Valid prediction for GlimmerHMM_glimmerT_23942-T1
Valid prediction for Augustus_model.g16045.t1
Valid prediction for snap_scaffold_9-snap.3090-T1
Couldn't classify 16350, 16499
Sorry, prediction pasa_asmbl_55474.p1 fails validation.
(AGC)	 TC	16350-16499	GT	GGG
(CTG)	 AG	16668-16781	GT	AGG
(TTG)	 AG	16865-16959	GT	AGG
(CCG)	 AG	17162-17265	GT	AGG
(GAT)	 AG	17467-17663	TC	GAT
-recovered pasa_asmbl_55474.p1, terminal, 17467, 17663
-recovered pasa_asmbl_55474.p1, internal, 16668, 16781
-recovered pasa_asmbl_55474.p1, internal, 16865, 16959
-recovered pasa_asmbl_55474.p1, internal, 17162, 17265
Valid prediction for snap_scaffold_9-snap.3088-T1
Valid prediction for GlimmerHMM_glimmerT_23943-T1
Valid prediction for snap_scaffold_9-snap.3084-T1
Valid prediction for snap_scaffold_9-snap.3078-T1
Valid prediction for GeneMark_model.41078_t
Valid prediction for GeneMark_model.41082_t
Valid prediction for snap_scaffold_9-snap.3093-T1
Valid prediction for CodingQuarry_transcript_62250-T1
Valid prediction for Augustus_model.g16046.t1
Valid prediction for snap_scaffold_9-snap.3102-T1
Valid prediction for snap_scaffold_9-snap.3103-T1
Valid prediction for Augustus_model.g16038.t1
Valid prediction for GeneMark_model.41069_t
Valid prediction for Augustus_model.g16042.t1
Valid prediction for GlimmerHMM_glimmerT_23923-T1
Valid prediction for snap_scaffold_9-snap.3080-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GeneMark_model.41093_t
Valid prediction for snap_scaffold_9-snap.3104-T1
Valid prediction for GeneMark_model.41096_t
Valid prediction for GlimmerHMM_glimmerT_23944-T1
Valid prediction for Augustus_model.g16040.t1
Valid prediction for GlimmerHMM_glimmerT_23933-T1
Valid prediction for GlimmerHMM_glimmerT_23927-T1
Valid prediction for GeneMark_model.41073_t
Valid prediction for snap_scaffold_9-snap.3086-T1
Valid prediction for GeneMark_model.41085_t
Valid prediction for HiQ_model.g16049.t1
Valid prediction for GeneMark_model.41061_t
Valid prediction for GeneMark_model.41081_t
Valid prediction for Augustus_model.g16026.t1
Valid prediction for GlimmerHMM_glimmerT_23948-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 29706, rend_intergenic: 25694  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31117, rend_intergenic: 29714  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51028, rend_intergenic: 50965  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100860, rend_intergenic: 92696  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105355, rend_intergenic: 103253  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118409, rend_intergenic: 115516  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124754, rend_intergenic: 118638  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126747, rend_intergenic: 125840  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130858, rend_intergenic: 130818  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147978, rend_intergenic: 145290  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158997, rend_intergenic: 153727  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166206, rend_intergenic: 162870  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186863, rend_intergenic: 181479  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 186949
-exon list size: 673


building trellis

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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    
74.1    
74.2    
74.4    
74.5    
74.7    
74.8    
75.0    
75.1    
75.3    
75.4    
75.6    
75.7    
75.9    
76.0    
76.1    
76.3    
76.4    
76.6    
76.7    
76.9    
77.0    
77.2    
77.3    
77.5    
77.6    
77.8    
77.9    
78.1    
78.2    
78.4    
78.5    
78.7    
78.8    
79.0    
79.1    
79.3    
79.4    
79.6    
79.7    
79.9    
80.0    
80.1    
80.3    
80.4    
80.6    
80.7    
80.9    
81.0    
81.2    
81.3    
81.5    
81.6    
81.8    
81.9    
82.1    
82.2    
82.4    
82.5    
82.7    
82.8    
83.0    
83.1    
83.3    
83.4    
83.6    
83.7    
83.9    
84.0    
84.1    
84.3    
84.4    
84.6    
84.7    
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    
87.3    
87.4    
87.6    
87.7    
87.9    
88.0    
88.1    
88.3    
88.4    
88.6    
88.7    
88.9    
89.0    
89.2    
89.3    
89.5    
89.6    
89.8    
89.9    
90.1    
90.2    
90.4    
90.5    
90.7    
90.8    
91.0    
91.1    
91.3    
91.4    
91.6    
91.7    
91.9    
92.0    
92.1    
92.3    
92.4    
92.6    
92.7    
92.9    
93.0    
93.2    
93.3    
93.5    
93.6    
93.8    
93.9    
94.1    
94.2    
94.4    
94.5    
94.7    
94.8    
95.0    
95.1    
95.3    
95.4    
95.6    
95.7    
95.9    
96.0    
96.1    
96.3    
96.4    
96.6    
96.7    
96.9    
97.0    
97.2    
97.3    
97.5    
97.6    
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 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 29706, rend_intergenic: 25694  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31117, rend_intergenic: 29714  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51028, rend_intergenic: 50965  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100860, rend_intergenic: 92696  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105355, rend_intergenic: 103253  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118409, rend_intergenic: 115516  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124754, rend_intergenic: 118638  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126747, rend_intergenic: 125840  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130858, rend_intergenic: 130818  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147978, rend_intergenic: 145290  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158997, rend_intergenic: 153727  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166206, rend_intergenic: 162870  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186863, rend_intergenic: 181479  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 24 predictions persist after filtering for low support