-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_23/scaffold_23_8072628-8240067

-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_23-snap.1549-T1
Valid prediction for snap_scaffold_23-snap.1528-T1
Valid prediction for GlimmerHMM_glimmerT_52687-T1
Valid prediction for GeneMark_model.91310_t
Valid prediction for snap_scaffold_23-snap.1556-T1
Valid prediction for GlimmerHMM_glimmerT_52675-T1
Valid prediction for GlimmerHMM_glimmerT_52690-T1
Valid prediction for GlimmerHMM_glimmerT_52676-T1
Valid prediction for GeneMark_model.91315_t
Valid prediction for Augustus_model.g35420.t1
Valid prediction for CodingQuarry_transcript_35692-T1
Valid prediction for GeneMark_model.91334_t
Valid prediction for CodingQuarry_transcript_35693-T1
Valid prediction for GeneMark_model.91309_t
Valid prediction for GeneMark_model.91343_t
Valid prediction for GlimmerHMM_glimmerT_52665-T1
Valid prediction for GlimmerHMM_glimmerT_52666-T1
Valid prediction for GlimmerHMM_glimmerT_52664-T1
Valid prediction for snap_scaffold_23-snap.1559-T1
Valid prediction for snap_scaffold_23-snap.1545-T1
Valid prediction for GlimmerHMM_glimmerT_52674-T1
Valid prediction for snap_scaffold_23-snap.1547-T1
Valid prediction for snap_scaffold_23-snap.1537-T1
Valid prediction for snap_scaffold_23-snap.1539-T1
Valid prediction for GlimmerHMM_glimmerT_52662-T1
Valid prediction for Augustus_model.g35426.t1
Valid prediction for GeneMark_model.91299_t
Valid prediction for CodingQuarry_transcript_35694-T1
Valid prediction for snap_scaffold_23-snap.1534-T1
Valid prediction for GeneMark_model.91347_t
Valid prediction for snap_scaffold_23-snap.1525-T1
Valid prediction for snap_scaffold_23-snap.1562-T1
Valid prediction for snap_scaffold_23-snap.1540-T1
Valid prediction for snap_scaffold_23-snap.1548-T1
Valid prediction for GlimmerHMM_glimmerT_52680-T1
Valid prediction for GeneMark_model.91321_t
Valid prediction for GeneMark_model.91331_t
Valid prediction for snap_scaffold_23-snap.1546-T1
Valid prediction for GeneMark_model.91313_t
Valid prediction for GeneMark_model.91300_t
Valid prediction for GeneMark_model.91344_t
Valid prediction for GeneMark_model.91326_t
Valid prediction for snap_scaffold_23-snap.1554-T1
Valid prediction for GlimmerHMM_glimmerT_52691-T1
Valid prediction for HiQ_model.g35417.t1
Valid prediction for snap_scaffold_23-snap.1560-T1
Valid prediction for GlimmerHMM_glimmerT_52688-T1
Valid prediction for GlimmerHMM_glimmerT_52684-T1
Valid prediction for GlimmerHMM_glimmerT_52685-T1
Valid prediction for GeneMark_model.91336_t
Valid prediction for GlimmerHMM_glimmerT_52673-T1
Valid prediction for snap_scaffold_23-snap.1526-T1
Valid prediction for GlimmerHMM_glimmerT_52681-T1
Valid prediction for GeneMark_model.91327_t
Valid prediction for GlimmerHMM_glimmerT_52682-T1
Valid prediction for GeneMark_model.91319_t
Valid prediction for GlimmerHMM_glimmerT_52679-T1
Valid prediction for CodingQuarry_transcript_35689-T1
Valid prediction for GeneMark_model.91317_t
Valid prediction for GlimmerHMM_glimmerT_52683-T1
Valid prediction for GeneMark_model.91337_t
Valid prediction for GeneMark_model.91324_t
Valid prediction for snap_scaffold_23-snap.1532-T1
Valid prediction for Augustus_model.g35415.t1
Valid prediction for snap_scaffold_23-snap.1550-T1
Valid prediction for Augustus_model.g35429.t1
Valid prediction for GeneMark_model.91304_t
Valid prediction for GeneMark_model.91302_t
Valid prediction for GlimmerHMM_glimmerT_52668-T1
Valid prediction for GlimmerHMM_glimmerT_52671-T1
Valid prediction for CodingQuarry_transcript_35690-T1
Valid prediction for snap_scaffold_23-snap.1557-T1
Valid prediction for GeneMark_model.91345_t
Valid prediction for snap_scaffold_23-snap.1555-T1
Couldn't classify 126345, 126393
Sorry, prediction pasa_asmbl_31063.p1 fails validation.
(ACT)	 CG	126345-126393	GT	CGG
(GTC)	 AG	127355-127475	GT	AAG
(GTA)	 AG	127691-127858	GT	AGG
(TCT)	 AG	128123-128360	GT	GGG
(AAG)	 AG	128705-128838	GT	AAG
(GAC)	 AG	128972-129071	GT	AGG
(GAC)	 AG	130044-130106	GT	AGG
(TTA)	 AG	131264-131328	GT	AGG
(CGG)	 AG	131437-131517	GT	GCG
(GAC)	 AG	131855-131987	GT	AGG
(AAG)	 AG	132356-132455	GT	CGG
(GCC)	 AG	133257-133499	GT	AGG
(CCG)	 AG	135708-135877	GT	TGG
(GTC)	 AG	136254-136425	GT	GGG
(GTT)	 AG	136562-136622	GT	AGG
(GTT)	 AG	137083-137165	GT	AGG
(GCA)	 AG	137402-137700	GA	GAG
-recovered pasa_asmbl_31063.p1, terminal, 127355, 127475
-recovered pasa_asmbl_31063.p1, terminal, 133257, 133499
-recovered pasa_asmbl_31063.p1, terminal, 137402, 137700
-recovered pasa_asmbl_31063.p1, internal, 127355, 127475
-recovered pasa_asmbl_31063.p1, internal, 127691, 127858
-recovered pasa_asmbl_31063.p1, internal, 128123, 128360
-recovered pasa_asmbl_31063.p1, internal, 128705, 128838
-recovered pasa_asmbl_31063.p1, internal, 128972, 129071
-recovered pasa_asmbl_31063.p1, internal, 130044, 130106
-recovered pasa_asmbl_31063.p1, internal, 131264, 131328
-recovered pasa_asmbl_31063.p1, internal, 131437, 131517
-recovered pasa_asmbl_31063.p1, internal, 131855, 131987
-recovered pasa_asmbl_31063.p1, internal, 132356, 132455
-recovered pasa_asmbl_31063.p1, internal, 133257, 133499
-recovered pasa_asmbl_31063.p1, internal, 135708, 135877
-recovered pasa_asmbl_31063.p1, internal, 136254, 136425
-recovered pasa_asmbl_31063.p1, internal, 136562, 136622
-recovered pasa_asmbl_31063.p1, internal, 137083, 137165
Valid prediction for pasa_asmbl_31056.p1
Valid prediction for GeneMark_model.91316_t
Valid prediction for GeneMark_model.91341_t
Valid prediction for GeneMark_model.91339_t
Valid prediction for snap_scaffold_23-snap.1523-T1
Valid prediction for HiQ_model.g35427.t1
Valid prediction for Augustus_model.g35428.t1
Valid prediction for CodingQuarry_transcript_35691-T1
Valid prediction for GeneMark_model.91348_t
Valid prediction for GlimmerHMM_glimmerT_52686-T1
Valid prediction for Augustus_model.g35425.t1
Valid prediction for snap_scaffold_23-snap.1543-T1
Valid prediction for GeneMark_model.91329_t
Valid prediction for pasa_asmbl_31059.p1
Valid prediction for Augustus_model.g35416.t1
Valid prediction for Augustus_model.g35413.t1
Couldn't classify 6711, 6847
Sorry, prediction pasa_asmbl_31200.p1 fails validation.
(GTG)	 CT	6711-6847	GT	AGG
(GCC)	 AG	7150-7320	GT	TGG
(TCA)	 AG	7470-7560	GT	CCG
(GTG)	 AG	7768-8009	GT	AGG
(GTG)	 AG	8297-8449	GT	AGG
(AGT)	 AG	8672-8785	GT	CGG
(AAC)	 AG	9009-9103	GT	AGG
(ACA)	 AG	9306-9379	GT	GGG
(GAC)	 AG	9509-9598	GT	AGG
(ACG)	 AG	9945-10050	GT	CAG
(TTC)	 AG	10132-10235	GT	AAG
(AAG)	 AG	10401-10484	TC	AGT
-recovered pasa_asmbl_31200.p1, terminal, 10401, 10484
-recovered pasa_asmbl_31200.p1, internal, 7150, 7320
-recovered pasa_asmbl_31200.p1, internal, 7470, 7560
-recovered pasa_asmbl_31200.p1, internal, 7768, 8009
-recovered pasa_asmbl_31200.p1, internal, 8297, 8449
-recovered pasa_asmbl_31200.p1, internal, 8672, 8785
-recovered pasa_asmbl_31200.p1, internal, 9009, 9103
-recovered pasa_asmbl_31200.p1, internal, 9306, 9379
-recovered pasa_asmbl_31200.p1, internal, 9509, 9598
-recovered pasa_asmbl_31200.p1, internal, 9945, 10050
-recovered pasa_asmbl_31200.p1, internal, 10132, 10235
Valid prediction for Augustus_model.g35423.t1
Valid prediction for GeneMark_model.91311_t
Valid prediction for GeneMark_model.91308_t
Valid prediction for snap_scaffold_23-snap.1538-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_23-snap.1561-T1
Valid prediction for Augustus_model.g35418.t1
Valid prediction for snap_scaffold_23-snap.1529-T1
Valid prediction for GeneMark_model.91342_t
Valid prediction for GlimmerHMM_glimmerT_52663-T1
Valid prediction for GeneMark_model.91330_t
Valid prediction for Augustus_model.g35414.t1
Valid prediction for GlimmerHMM_glimmerT_52677-T1
Valid prediction for GeneMark_model.91340_t
Valid prediction for GeneMark_model.91332_t
Valid prediction for GeneMark_model.91307_t
Valid prediction for snap_scaffold_23-snap.1524-T1
Valid prediction for Augustus_model.g35422.t1
Valid prediction for snap_scaffold_23-snap.1551-T1
Valid prediction for snap_scaffold_23-snap.1541-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GeneMark_model.91322_t
Valid prediction for snap_scaffold_23-snap.1536-T1
Valid prediction for snap_scaffold_23-snap.1544-T1
Valid prediction for snap_scaffold_23-snap.1552-T1
Valid prediction for snap_scaffold_23-snap.1535-T1
Valid prediction for GeneMark_model.91335_t
Valid prediction for GlimmerHMM_glimmerT_52667-T1
Valid prediction for CodingQuarry_transcript_35688-T1
Couldn't classify 106941, 106957
Couldn't classify 111061, 111126
Sorry, prediction pasa_asmbl_31796.p1 fails validation.
(TGT)	 CG	106941-106957	GT	AAG
(GAT)	 AG	108731-108843	GT	CGG
(CTC)	 AG	109136-109242	GT	GGG
(GTG)	 AG	111061-111126	AA	ACA
-recovered pasa_asmbl_31796.p1, internal, 108731, 108843
-recovered pasa_asmbl_31796.p1, internal, 109136, 109242
Valid prediction for GlimmerHMM_glimmerT_52669-T1
Valid prediction for snap_scaffold_23-snap.1533-T1
Valid prediction for snap_scaffold_23-snap.1527-T1
Valid prediction for GeneMark_model.91346_t
Valid prediction for GeneMark_model.91303_t
Valid prediction for snap_scaffold_23-snap.1530-T1
Valid prediction for Augustus_model.g35419.t1
Valid prediction for GeneMark_model.91314_t
Valid prediction for GeneMark_model.91320_t
Valid prediction for GlimmerHMM_glimmerT_52672-T1
Valid prediction for GeneMark_model.91328_t
Valid prediction for GeneMark_model.91305_t
Valid prediction for GeneMark_model.91323_t
Valid prediction for snap_scaffold_23-snap.1531-T1
Valid prediction for GeneMark_model.91338_t
Valid prediction for GeneMark_model.91301_t
Valid prediction for GlimmerHMM_glimmerT_52678-T1
Valid prediction for GeneMark_model.91306_t
Valid prediction for snap_scaffold_23-snap.1558-T1
Valid prediction for GeneMark_model.91298_t
Valid prediction for GlimmerHMM_glimmerT_52689-T1
Valid prediction for pasa_asmbl_31791.p1
Valid prediction for GlimmerHMM_glimmerT_52670-T1
Valid prediction for GeneMark_model.91318_t
Valid prediction for snap_scaffold_23-snap.1542-T1
Valid prediction for GeneMark_model.91325_t
Valid prediction for GeneMark_model.91333_t
Valid prediction for Augustus_model.g35424.t1
Valid prediction for snap_scaffold_23-snap.1553-T1
Valid prediction for GeneMark_model.91312_t
Valid prediction for Augustus_model.g35421.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 23212, rend_intergenic: 20475  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34568, rend_intergenic: 32360  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58974, rend_intergenic: 57733  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65436, rend_intergenic: 59352  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77232, rend_intergenic: 74061  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94966, rend_intergenic: 86722  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99328, rend_intergenic: 97861  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102528, rend_intergenic: 100620  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132475, rend_intergenic: 120990  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132581, rend_intergenic: 132475  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153064, rend_intergenic: 151185  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161888, rend_intergenic: 159156  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 167440
-exon list size: 735


building trellis

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71.2    
71.4    
71.5    
71.6    
71.8    
71.9    
72.0    
72.2    
72.3    
72.5    
72.6    
72.7    
72.9    
73.0    
73.1    
73.3    
73.4    
73.5    
73.7    
73.8    
73.9    
74.1    
74.2    
74.4    
74.5    
74.6    
74.8    
74.9    
75.0    
75.2    
75.3    
75.4    
75.6    
75.7    
75.8    
76.0    
76.1    
76.3    
76.4    
76.5    
76.7    
76.8    
76.9    
77.1    
77.2    
77.3    
77.5    
77.6    
77.7    
77.9    
78.0    
78.2    
78.3    
78.4    
78.6    
78.7    
78.8    
79.0    
79.1    
79.2    
79.4    
79.5    
79.6    
79.8    
79.9    
80.1    
80.2    
80.3    
80.5    
80.6    
80.7    
80.9    
81.0    
81.1    
81.3    
81.4    
81.5    
81.7    
81.8    
82.0    
82.1    
82.2    
82.4    
82.5    
82.6    
82.8    
82.9    
83.0    
83.2    
83.3    
83.4    
83.6    
83.7    
83.9    
84.0    
84.1    
84.3    
84.4    
84.5    
84.7    
84.8    
84.9    
85.1    
85.2    
85.3    
85.5    
85.6    
85.8    
85.9    
86.0    
86.2    
86.3    
86.4    
86.6    
86.7    
86.8    
87.0    
87.1    
87.2    
87.4    
87.5    
87.7    
87.8    
87.9    
88.1    
88.2    
88.3    
88.5    
88.6    
88.7    
88.9    
89.0    
89.1    
89.3    
89.4    
89.6    
89.7    
89.8    
90.0    
90.1    
90.2    
90.4    
90.5    
90.6    
90.8    
90.9    
91.0    
91.2    
91.3    
91.5    
91.6    
91.7    
91.9    
92.0    
92.1    
92.3    
92.4    
92.5    
92.7    
92.8    
92.9    
93.1    
93.2    
93.4    
93.5    
93.6    
93.8    
93.9    
94.0    
94.2    
94.3    
94.4    
94.6    
94.7    
94.8    
95.0    
95.1    
95.3    
95.4    
95.5    
95.7    
95.8    
95.9    
96.1    
96.2    
96.3    
96.5    
96.6    
96.7    
96.9    
97.0    
97.2    
97.3    
97.4    
97.6    
97.7    
97.8    
98.0    
98.1    
98.2    
98.4    
98.5    
98.6    
98.8    
98.9    
99.1    
99.2    
99.3    
99.5    
99.6    
99.7    
99.9    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 23212, rend_intergenic: 20475  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34568, rend_intergenic: 32360  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58974, rend_intergenic: 57733  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65436, rend_intergenic: 59352  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77232, rend_intergenic: 74061  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94966, rend_intergenic: 86722  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99328, rend_intergenic: 97861  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102528, rend_intergenic: 100620  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132475, rend_intergenic: 120990  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132581, rend_intergenic: 132475  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153064, rend_intergenic: 151185  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161888, rend_intergenic: 159156  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

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