-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_17/scaffold_17_6714475-6877475

-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 snap_scaffold_17-snap.1337-T1
Couldn't classify 80774, 80807
Couldn't classify 82816, 82884
Sorry, prediction pasa_asmbl_18000.p1 fails validation.
(TCT)	 AA	80774-80807	GT	TGG
(ACT)	 AG	80904-81173	GT	CGG
(GAG)	 AG	81295-81348	GT	TGG
(GAG)	 AG	81565-81860	GT	AGG
(CCC)	 AG	82159-82231	GT	AGG
(GTG)	 AG	82366-82700	GT	AGG
(GCT)	 AG	82816-82884	CC	CTC
-recovered pasa_asmbl_18000.p1, internal, 80904, 81173
-recovered pasa_asmbl_18000.p1, internal, 81295, 81348
-recovered pasa_asmbl_18000.p1, internal, 81565, 81860
-recovered pasa_asmbl_18000.p1, internal, 82159, 82231
-recovered pasa_asmbl_18000.p1, internal, 82366, 82700
Valid prediction for GlimmerHMM_glimmerT_41389-T1
Valid prediction for GeneMark_model.71232_t
Valid prediction for snap_scaffold_17-snap.1354-T1
Valid prediction for snap_scaffold_17-snap.1344-T1
Valid prediction for snap_scaffold_17-snap.1338-T1
Valid prediction for GeneMark_model.71226_t
Valid prediction for HiQ_model.g27733.t1
Valid prediction for GeneMark_model.71237_t
Valid prediction for GlimmerHMM_glimmerT_41382-T1
Valid prediction for Augustus_model.g27731.t1
Valid prediction for snap_scaffold_17-snap.1351-T1
Valid prediction for GeneMark_model.71255_t
Valid prediction for GlimmerHMM_glimmerT_41393-T1
Valid prediction for GeneMark_model.71228_t
Valid prediction for GeneMark_model.71239_t
Valid prediction for GeneMark_model.71251_t
Valid prediction for GeneMark_model.71230_t
Valid prediction for snap_scaffold_17-snap.1357-T1
Valid prediction for snap_scaffold_17-snap.1342-T1
Valid prediction for snap_scaffold_17-snap.1349-T1
Valid prediction for CodingQuarry_transcript_21962-T1
Valid prediction for GlimmerHMM_glimmerT_41391-T1
Valid prediction for Augustus_model.g27724.t1
Valid prediction for GeneMark_model.71241_t
Valid prediction for GeneMark_model.71245_t
Valid prediction for GeneMark_model.71235_t
Valid prediction for GlimmerHMM_glimmerT_41385-T1
Valid prediction for Augustus_model.g27722.t1
Valid prediction for GeneMark_model.71229_t
Valid prediction for snap_scaffold_17-snap.1347-T1
Valid prediction for snap_scaffold_17-snap.1359-T1
Valid prediction for Augustus_model.g27725.t1
Valid prediction for GlimmerHMM_glimmerT_41383-T1
Valid prediction for GlimmerHMM_glimmerT_41388-T1
Couldn't classify 85709, 85819
Sorry, prediction pasa_asmbl_18003.p1 fails validation.
(CCC)	 AC	85709-85819	GT	AGG
(AGT)	 AG	85935-86003	GT	AGG
(ATG)	 AG	86607-86825	GT	CTG
(GAG)	 AG	86943-87050	GT	AGG
(ACA)	 AG	87296-87442	GT	AGG
(GTG)	 AG	87552-87650	TT	AGT
-recovered pasa_asmbl_18003.p1, initial, 86607, 86825
-recovered pasa_asmbl_18003.p1, terminal, 87552, 87650
-recovered pasa_asmbl_18003.p1, internal, 85935, 86003
-recovered pasa_asmbl_18003.p1, internal, 86607, 86825
-recovered pasa_asmbl_18003.p1, internal, 86943, 87050
-recovered pasa_asmbl_18003.p1, internal, 87296, 87442
Valid prediction for CodingQuarry_transcript_21960-T1
Valid prediction for GeneMark_model.71247_t
Valid prediction for Augustus_model.g27729.t1
Valid prediction for snap_scaffold_17-snap.1358-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_17-snap.1341-T1
Valid prediction for GeneMark_model.71253_t
Valid prediction for Augustus_model.g27726.t1
Valid prediction for snap_scaffold_17-snap.1336-T1
Valid prediction for snap_scaffold_17-snap.1355-T1
Valid prediction for GlimmerHMM_glimmerT_41397-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 46169, 46318
Couldn't classify 46443, 46646
Sorry, prediction CodingQuarry_transcript_21964-T1 fails validation.
(ATG)	 AG	40949-41116	GT	AGG
(GAG)	 AG	41233-41439	GT	AGG
(TAT)	 AG	41650-41877	GT	AGG
(GTG)	 AG	42064-42282	GT	GGG
(CTC)	 AG	42542-42745	GT	AGG
(TTC)	 AG	44017-44242	GT	GGG
(CTG)	 AG	44651-44877	GT	AGG
(GCG)	 AG	45075-45197	GT	AGG
(ATG)	 AG	45335-45436	GT	AGG
(GGT)	 AG	45639-45740	GT	AGG
(CAC)	 AG	45830-46003	GT	AGG
(CAC)	 AG	46169-46318	AC	AAA
(CCC)	 CT	46443-46646	GT	AGG
(GCG)	 AG	46811-46939	GT	TAG
(GAG)	 AG	47047-47229	GT	GGG
(GCT)	 AG	47381-47536	GT	AGG
(GTG)	 AG	47730-47936	GT	AGG
(TTC)	 AG	48123-48242	GT	AGG
(GAG)	 AG	48429-48598	GT	AGG
(ACA)	 AG	48776-48935	GT	AGG
(GCG)	 AG	49034-49228	GT	AGG
(GCA)	 AG	49353-49625	GT	AGG
(GTG)	 AG	49744-49932	GT	AGG
(GTG)	 AG	50041-50152	GT	ACG
(GTA)	 AG	50348-50511	GT	AGG
(CTG)	 AG	50636-50798	GT	TAG
(AGT)	 AG	51058-51212	GT	AGG
(GTG)	 AG	51581-51655	GT	GGG
(TTC)	 AG	52496-52513	GT	AGG
(TTC)	 AG	53230-53347	GT	AGG
(TGC)	 AG	53926-53991	GT	AGG
(CTC)	 AG	56207-56424	GT	GGG
(TCC)	 AG	57092-57208	GT	AGG
(GGG)	 AG	57652-57763	GT	CGG
(ACC)	 AG	57990-58234	AG	AGA
-recovered CodingQuarry_transcript_21964-T1, initial, 40949, 41116
-recovered CodingQuarry_transcript_21964-T1, initial, 45335, 45436
-recovered CodingQuarry_transcript_21964-T1, terminal, 53926, 53991
-recovered CodingQuarry_transcript_21964-T1, terminal, 57990, 58234
-recovered CodingQuarry_transcript_21964-T1, internal, 40949, 41116
-recovered CodingQuarry_transcript_21964-T1, internal, 41233, 41439
-recovered CodingQuarry_transcript_21964-T1, internal, 41650, 41877
-recovered CodingQuarry_transcript_21964-T1, internal, 42064, 42282
-recovered CodingQuarry_transcript_21964-T1, internal, 42542, 42745
-recovered CodingQuarry_transcript_21964-T1, internal, 44017, 44242
-recovered CodingQuarry_transcript_21964-T1, internal, 44651, 44877
-recovered CodingQuarry_transcript_21964-T1, internal, 45075, 45197
-recovered CodingQuarry_transcript_21964-T1, internal, 45335, 45436
-recovered CodingQuarry_transcript_21964-T1, internal, 45639, 45740
-recovered CodingQuarry_transcript_21964-T1, internal, 45830, 46003
-recovered CodingQuarry_transcript_21964-T1, internal, 46811, 46939
-recovered CodingQuarry_transcript_21964-T1, internal, 47047, 47229
-recovered CodingQuarry_transcript_21964-T1, internal, 47381, 47536
-recovered CodingQuarry_transcript_21964-T1, internal, 47730, 47936
-recovered CodingQuarry_transcript_21964-T1, internal, 48123, 48242
-recovered CodingQuarry_transcript_21964-T1, internal, 48429, 48598
-recovered CodingQuarry_transcript_21964-T1, internal, 48776, 48935
-recovered CodingQuarry_transcript_21964-T1, internal, 49034, 49228
-recovered CodingQuarry_transcript_21964-T1, internal, 49353, 49625
-recovered CodingQuarry_transcript_21964-T1, internal, 49744, 49932
-recovered CodingQuarry_transcript_21964-T1, internal, 50041, 50152
-recovered CodingQuarry_transcript_21964-T1, internal, 50348, 50511
-recovered CodingQuarry_transcript_21964-T1, internal, 50636, 50798
-recovered CodingQuarry_transcript_21964-T1, internal, 51058, 51212
-recovered CodingQuarry_transcript_21964-T1, internal, 51581, 51655
-recovered CodingQuarry_transcript_21964-T1, internal, 52496, 52513
-recovered CodingQuarry_transcript_21964-T1, internal, 53230, 53347
-recovered CodingQuarry_transcript_21964-T1, internal, 53926, 53991
-recovered CodingQuarry_transcript_21964-T1, internal, 56207, 56424
-recovered CodingQuarry_transcript_21964-T1, internal, 57092, 57208
-recovered CodingQuarry_transcript_21964-T1, internal, 57652, 57763
Couldn't classify 89712, 89772
Sorry, prediction pasa_asmbl_19028.p1 fails validation.
(TTC)	 GG	89712-89772	GT	AGG
(CGG)	 AG	91083-91249	GT	AGG
(GTG)	 AG	91506-91685	GC	AGG
-recovered pasa_asmbl_19028.p1, terminal, 91506, 91685
-recovered pasa_asmbl_19028.p1, internal, 91083, 91249
-recovered pasa_asmbl_19028.p1, internal, 91506, 91685
Valid prediction for GeneMark_model.71227_t
Valid prediction for GlimmerHMM_glimmerT_41396-T1
Valid prediction for GeneMark_model.71249_t
Valid prediction for GeneMark_model.71233_t
Valid prediction for GeneMark_model.71236_t
Valid prediction for GlimmerHMM_glimmerT_41387-T1
Valid prediction for GeneMark_model.71250_t
Valid prediction for GeneMark_model.71246_t
Valid prediction for GeneMark_model.71256_t
Couldn't classify 18259, 18990
Couldn't classify 19600, 20103
Sorry, prediction pasa_asmbl_19036.p1 fails validation.
(GAG)	 GT	18259-18990	GT	AGG
(ATC)	 AG	19600-20103	GG	TAG
Valid prediction for GeneMark_model.71244_t
Valid prediction for HiQ_model.g27732.t1
Valid prediction for snap_scaffold_17-snap.1352-T1
Valid prediction for snap_scaffold_17-snap.1340-T1
Couldn't classify 2570, 4036
Sorry, prediction pasa_asmbl_19041.p1 fails validation.
(AAC)	 TG	2570-4036	GT	GGG
Valid prediction for GlimmerHMM_glimmerT_41386-T1
Valid prediction for GeneMark_model.71240_t
Couldn't classify 32421, 32906
Sorry, prediction pasa_asmbl_19538.p2 fails validation.
(CTG)	 AC	32421-32906	CC	CTC
Valid prediction for GeneMark_model.71234_t
Valid prediction for Augustus_model.g27723.t1
Valid prediction for CodingQuarry_transcript_21965-T1
Valid prediction for GlimmerHMM_glimmerT_41384-T1
Valid prediction for snap_scaffold_17-snap.1350-T1
Valid prediction for Augustus_model.g27728.t1
Valid prediction for snap_scaffold_17-snap.1353-T1
Valid prediction for GlimmerHMM_glimmerT_41392-T1
Valid prediction for Augustus_model.g27727.t1
Valid prediction for GeneMark_model.71242_t
Valid prediction for GeneMark_model.71254_t
Valid prediction for Augustus_model.g27734.t1
Valid prediction for CodingQuarry_transcript_21961-T1
Valid prediction for pasa_asmbl_19030.p1
Couldn't classify 31548, 32099
Sorry, prediction pasa_asmbl_19034.p1 fails validation.
(GTG)	 TG	31548-32099	GG	GTG
Valid prediction for snap_scaffold_17-snap.1343-T1
Valid prediction for CodingQuarry_transcript_21963-T1
Valid prediction for snap_scaffold_17-snap.1339-T1
Valid prediction for GeneMark_model.71231_t
Couldn't classify 7659, 7766
Couldn't classify 10150, 10182
Sorry, prediction pasa_asmbl_19039.p1 fails validation.
(ACA)	 TT	7659-7766	GT	AAG
(GAG)	 AG	7875-8027	GT	AGG
(GAG)	 AG	8239-8535	GT	AGG
(GTG)	 AG	9399-9548	GT	AGG
(GAA)	 AG	9730-9963	GT	GGG
(GCC)	 AG	10150-10182	GG	AGG
-recovered pasa_asmbl_19039.p1, internal, 7875, 8027
-recovered pasa_asmbl_19039.p1, internal, 8239, 8535
-recovered pasa_asmbl_19039.p1, internal, 9399, 9548
-recovered pasa_asmbl_19039.p1, internal, 9730, 9963
Valid prediction for snap_scaffold_17-snap.1345-T1
Valid prediction for HiQ_model.g27735.t1
Couldn't classify 10629, 10874
Couldn't classify 11018, 11179
Sorry, prediction pasa_asmbl_19038.p1 fails validation.
(CCA)	 CC	10629-10874	GT	AGG
(CTG)	 AG	11018-11179	AA	CCA
Valid prediction for snap_scaffold_17-snap.1346-T1
Valid prediction for Augustus_model.g27736.t1
Valid prediction for GlimmerHMM_glimmerT_41395-T1
Couldn't classify 4496, 7156
Sorry, prediction pasa_asmbl_19040.p1 fails validation.
(ATG)	 GA	4496-7156	TT	GCT
Valid prediction for GlimmerHMM_glimmerT_41390-T1
Valid prediction for GeneMark_model.71252_t
Valid prediction for CodingQuarry_transcript_21966-T1
Valid prediction for GeneMark_model.71238_t
Valid prediction for pasa_asmbl_19031.p1
Valid prediction for snap_scaffold_17-snap.1348-T1
Valid prediction for GeneMark_model.71248_t
Valid prediction for GlimmerHMM_glimmerT_41394-T1
Valid prediction for snap_scaffold_17-snap.1356-T1
Valid prediction for GeneMark_model.71243_t
Couldn't classify 11976, 12170
Couldn't classify 16697, 16896
Sorry, prediction pasa_asmbl_19521.p1 fails validation.
(CTA)	 GC	11976-12170	GT	AGG
(AAA)	 AG	12341-12658	GT	AGG
(GAA)	 AG	12809-12975	GT	AGG
(GTT)	 AG	14077-14233	GT	AGG
(GAC)	 AG	14461-14572	GT	AGG
(GTG)	 AG	14778-14846	GT	AGG
(ACA)	 AG	15474-15712	GT	AGG
(GTG)	 AG	15867-15996	GT	AGG
(ACG)	 AG	16697-16896	GT	AGG
add_exon() Sorry, pasa_asmbl_19521.p1 15867-15996-terminal-3 is invalid.
-recovered pasa_asmbl_19521.p1, terminal, 15867, 15996
-recovered pasa_asmbl_19521.p1, internal, 12341, 12658
-recovered pasa_asmbl_19521.p1, internal, 12809, 12975
-recovered pasa_asmbl_19521.p1, internal, 14077, 14233
-recovered pasa_asmbl_19521.p1, internal, 14461, 14572
-recovered pasa_asmbl_19521.p1, internal, 14778, 14846
-recovered pasa_asmbl_19521.p1, internal, 15474, 15712
-recovered pasa_asmbl_19521.p1, internal, 15867, 15996
-recovered pasa_asmbl_19521.p1, internal, 16697, 16896
Valid prediction for Augustus_model.g27730.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 87650, rend_intergenic: 82442  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100394, rend_intergenic: 99820  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107793, rend_intergenic: 105130  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108868, rend_intergenic: 108277  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134268, rend_intergenic: 121926  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140691, rend_intergenic: 134397  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155655, rend_intergenic: 141488  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 163001
-exon list size: 525


building trellis

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78.0    
78.2    
78.4    
78.6    
78.7    
78.9    
79.1    
79.3    
79.5    
79.7    
79.9    
80.1    
80.3    
80.5    
80.6    
80.8    
81.0    
81.2    
81.4    
81.6    
81.8    
82.0    
82.2    
82.4    
82.5    
82.7    
82.9    
83.1    
83.3    
83.5    
83.7    
83.9    
84.1    
84.3    
84.4    
84.6    
84.8    
85.0    
85.2    
85.4    
85.6    
85.8    
86.0    
86.1    
86.3    
86.5    
86.7    
86.9    
87.1    
87.3    
87.5    
87.7    
87.9    
88.0    
88.2    
88.4    
88.6    
88.8    
89.0    
89.2    
89.4    
89.6    
89.8    
89.9    
90.1    
90.3    
90.5    
90.7    
90.9    
91.1    
91.3    
91.5    
91.7    
91.8    
92.0    
92.2    
92.4    
92.6    
92.8    
93.0    
93.2    
93.4    
93.5    
93.7    
93.9    
94.1    
94.3    
94.5    
94.7    
94.9    
95.1    
95.3    
95.4    
95.6    
95.8    
96.0    
96.2    
96.4    
96.6    
96.8    
97.0    
97.2    
97.3    
97.5    
97.7    
97.9    
98.1    
98.3    
98.5    
98.7    
98.9    
99.1    
99.2    
99.4    
99.6    
99.8    
-found 19 predictions from path traversal
Error with prediction: snap lend_intergenic: 87650, rend_intergenic: 82442  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100394, rend_intergenic: 99820  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107793, rend_intergenic: 105130  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108868, rend_intergenic: 108277  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134268, rend_intergenic: 121926  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140691, rend_intergenic: 134397  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155655, rend_intergenic: 141488  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 14 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 10882
-exon list size: 8


building trellis

10.0    
20.0    
30.0    
40.0    
50.0    
60.0    
70.0    
80.0    
90.0    
-found 1 predictions from path traversal
GOT 5prime partial gene.

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