-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_17/scaffold_17_7091227-7339735

-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.71371_t
Valid prediction for GeneMark_model.71333_t
Valid prediction for snap_scaffold_17-snap.1441-T1
Valid prediction for GeneMark_model.71337_t
Valid prediction for GlimmerHMM_glimmerT_41453-T1
Valid prediction for Augustus_model.g27776.t1
Valid prediction for GlimmerHMM_glimmerT_41451-T1
Valid prediction for GeneMark_model.71342_t
Valid prediction for GlimmerHMM_glimmerT_41449-T1
Valid prediction for snap_scaffold_17-snap.1435-T1
Valid prediction for GeneMark_model.71325_t
Valid prediction for GlimmerHMM_glimmerT_41440-T1
Valid prediction for GlimmerHMM_glimmerT_41455-T1
Valid prediction for GlimmerHMM_glimmerT_41462-T1
Valid prediction for Augustus_model.g27768.t1
Valid prediction for snap_scaffold_17-snap.1416-T1
Valid prediction for GeneMark_model.71364_t
Valid prediction for pasa_asmbl_18025.p1
Valid prediction for snap_scaffold_17-snap.1431-T1
Valid prediction for GeneMark_model.71340_t
Valid prediction for snap_scaffold_17-snap.1438-T1
Valid prediction for snap_scaffold_17-snap.1442-T1
Valid prediction for GeneMark_model.71336_t
Valid prediction for GlimmerHMM_glimmerT_41448-T1
Valid prediction for GeneMark_model.71322_t
Couldn't classify 73919, 73970
Sorry, prediction pasa_asmbl_18594.p1 fails validation.
(ATG)	 CC	71948-72038	GT	GGG
(TGA)	 AG	72620-72748	GT	CAG
(AAA)	 AG	72908-72948	GT	AGG
(AAA)	 AG	73091-73166	GT	GTG
(CCT)	 AG	73381-73448	GT	GGG
(GGA)	 AG	73617-73696	GT	AGG
(GTC)	 AG	73919-73970	CT	CTC
-recovered pasa_asmbl_18594.p1, initial, 71948, 72038
-recovered pasa_asmbl_18594.p1, internal, 72620, 72748
-recovered pasa_asmbl_18594.p1, internal, 72908, 72948
-recovered pasa_asmbl_18594.p1, internal, 73091, 73166
-recovered pasa_asmbl_18594.p1, internal, 73381, 73448
-recovered pasa_asmbl_18594.p1, internal, 73617, 73696
Valid prediction for GeneMark_model.71338_t
Valid prediction for CodingQuarry_transcript_21984-T1
Valid prediction for GeneMark_model.71345_t
Valid prediction for GlimmerHMM_glimmerT_41461-T1
Valid prediction for GeneMark_model.71369_t
Valid prediction for snap_scaffold_17-snap.1429-T1
Valid prediction for GeneMark_model.71353_t
Valid prediction for snap_scaffold_17-snap.1423-T1
Valid prediction for GlimmerHMM_glimmerT_41438-T1
Valid prediction for Augustus_model.g27774.t1
Valid prediction for GeneMark_model.71367_t
Valid prediction for GeneMark_model.71310_t
Valid prediction for GeneMark_model.71365_t
Valid prediction for GeneMark_model.71318_t
Valid prediction for snap_scaffold_17-snap.1412-T1
Valid prediction for GeneMark_model.71354_t
Valid prediction for snap_scaffold_17-snap.1421-T1
Valid prediction for pasa_asmbl_18028.p1
Valid prediction for GeneMark_model.71315_t
Valid prediction for Augustus_model.g27763.t1
Valid prediction for snap_scaffold_17-snap.1434-T1
Valid prediction for GlimmerHMM_glimmerT_41439-T1
Valid prediction for snap_scaffold_17-snap.1424-T1
Valid prediction for GeneMark_model.71329_t
Valid prediction for GlimmerHMM_glimmerT_41464-T1
Valid prediction for GeneMark_model.71347_t
Valid prediction for Augustus_model.g27775.t1
Valid prediction for HiQ_model.g27762.t1
Valid prediction for snap_scaffold_17-snap.1405-T1
Valid prediction for GeneMark_model.71308_t
Valid prediction for GlimmerHMM_glimmerT_41446-T1
Valid prediction for Augustus_model.g27772.t1
Valid prediction for GlimmerHMM_glimmerT_41454-T1
Valid prediction for GeneMark_model.71327_t
Valid prediction for GeneMark_model.71323_t
Valid prediction for GeneMark_model.71362_t
Couldn't classify 55501, 55617
Couldn't classify 56785, 56918
Sorry, prediction pasa_asmbl_18027.p1 fails validation.
(GTG)	 AG	55501-55617	GT	GGG
(GTG)	 AG	55860-56041	GT	AGG
(GTA)	 AG	56518-56654	GT	TGG
(TTT)	 AG	56785-56918	GG	GAG
-recovered pasa_asmbl_18027.p1, internal, 55501, 55617
-recovered pasa_asmbl_18027.p1, internal, 55860, 56041
-recovered pasa_asmbl_18027.p1, internal, 56518, 56654
Valid prediction for Augustus_model.g27777.t1
Valid prediction for snap_scaffold_17-snap.1419-T1
Valid prediction for CodingQuarry_transcript_21985-T1
Valid prediction for snap_scaffold_17-snap.1404-T1
Valid prediction for CodingQuarry_transcript_21981-T1
Valid prediction for Augustus_model.g27770.t1
Valid prediction for snap_scaffold_17-snap.1414-T1
Valid prediction for GlimmerHMM_glimmerT_41460-T1
Valid prediction for GlimmerHMM_glimmerT_41457-T1
Valid prediction for GeneMark_model.71375_t
Valid prediction for snap_scaffold_17-snap.1418-T1
Valid prediction for snap_scaffold_17-snap.1407-T1
Valid prediction for GeneMark_model.71373_t
Valid prediction for GeneMark_model.71358_t
Valid prediction for GeneMark_model.71360_t
Valid prediction for GeneMark_model.71368_t
Valid prediction for GlimmerHMM_glimmerT_41459-T1
Valid prediction for GlimmerHMM_glimmerT_41443-T1
Valid prediction for GeneMark_model.71334_t

-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.71341_t
Valid prediction for snap_scaffold_17-snap.1436-T1
Valid prediction for GeneMark_model.71359_t
Valid prediction for snap_scaffold_17-snap.1409-T1
Valid prediction for GeneMark_model.71343_t
Valid prediction for GeneMark_model.71321_t
Valid prediction for GeneMark_model.71350_t
Valid prediction for GeneMark_model.71366_t
Valid prediction for GeneMark_model.71320_t
Valid prediction for Augustus_model.g27766.t1
Valid prediction for GlimmerHMM_glimmerT_41447-T1
Valid prediction for snap_scaffold_17-snap.1420-T1
Valid prediction for GeneMark_model.71370_t
Valid prediction for snap_scaffold_17-snap.1425-T1
Valid prediction for GeneMark_model.71374_t
Valid prediction for GlimmerHMM_glimmerT_41463-T1
Valid prediction for snap_scaffold_17-snap.1443-T1
Valid prediction for GlimmerHMM_glimmerT_41444-T1
Valid prediction for snap_scaffold_17-snap.1444-T1
Valid prediction for GeneMark_model.71357_t
Valid prediction for GeneMark_model.71332_t
Valid prediction for Augustus_model.g27769.t1
Valid prediction for GeneMark_model.71352_t
Valid prediction for GeneMark_model.71363_t
Couldn't classify 222562, 222724
Sorry, prediction pasa_asmbl_19082.p1 fails validation.
(ACC)	 AG	222562-222724	GT	CGG
(AAT)	 AG	222876-222925	GT	AGG
(CTG)	 AG	223152-223253	CC	GAC
-recovered pasa_asmbl_19082.p1, terminal, 223152, 223253
-recovered pasa_asmbl_19082.p1, internal, 222562, 222724
-recovered pasa_asmbl_19082.p1, internal, 222876, 222925
Valid prediction for GeneMark_model.71355_t
Valid prediction for GlimmerHMM_glimmerT_41456-T1
Valid prediction for GlimmerHMM_glimmerT_41458-T1
Valid prediction for snap_scaffold_17-snap.1422-T1
Valid prediction for pasa_asmbl_19090.p1
Valid prediction for GeneMark_model.71326_t
Valid prediction for GeneMark_model.71328_t
Couldn't classify 209999, 210493
Sorry, prediction pasa_asmbl_19091.p1 fails validation.
(ATG)	 GA	209999-210493	GG	GAG
Valid prediction for snap_scaffold_17-snap.1432-T1
Valid prediction for HiQ_model.g27771.t1
Valid prediction for GeneMark_model.71330_t
Valid prediction for snap_scaffold_17-snap.1426-T1
Valid prediction for GlimmerHMM_glimmerT_41442-T1
Valid prediction for snap_scaffold_17-snap.1437-T1
Valid prediction for GeneMark_model.71356_t
Valid prediction for Augustus_model.g27767.t1
Valid prediction for snap_scaffold_17-snap.1408-T1
Valid prediction for GeneMark_model.71319_t
Valid prediction for snap_scaffold_17-snap.1406-T1
Valid prediction for snap_scaffold_17-snap.1410-T1
Valid prediction for CodingQuarry_transcript_21983-T1
Valid prediction for GeneMark_model.71349_t
Valid prediction for GlimmerHMM_glimmerT_41445-T1
Valid prediction for snap_scaffold_17-snap.1417-T1
Valid prediction for Augustus_model.g27764.t1
Valid prediction for GeneMark_model.71344_t
Valid prediction for GeneMark_model.71372_t
Valid prediction for snap_scaffold_17-snap.1446-T1
Valid prediction for Augustus_model.g27773.t1
Valid prediction for snap_scaffold_17-snap.1430-T1
Valid prediction for GeneMark_model.71346_t
Valid prediction for GlimmerHMM_glimmerT_41452-T1
Valid prediction for pasa_asmbl_19093.p1
Valid prediction for snap_scaffold_17-snap.1415-T1
Valid prediction for GlimmerHMM_glimmerT_41450-T1
Valid prediction for GlimmerHMM_glimmerT_41441-T1
Valid prediction for GeneMark_model.71311_t
Valid prediction for GeneMark_model.71309_t
Valid prediction for Augustus_model.g27765.t1
Valid prediction for GeneMark_model.71324_t
Valid prediction for GlimmerHMM_glimmerT_41437-T1
Valid prediction for snap_scaffold_17-snap.1427-T1
Valid prediction for GeneMark_model.71314_t
Valid prediction for snap_scaffold_17-snap.1440-T1
Valid prediction for GeneMark_model.71348_t
Valid prediction for GeneMark_model.71313_t
Valid prediction for GeneMark_model.71339_t
Valid prediction for snap_scaffold_17-snap.1439-T1
Valid prediction for GeneMark_model.71316_t
Valid prediction for GeneMark_model.71361_t
Valid prediction for snap_scaffold_17-snap.1428-T1
Valid prediction for snap_scaffold_17-snap.1433-T1
Valid prediction for snap_scaffold_17-snap.1411-T1
Valid prediction for GeneMark_model.71331_t
Valid prediction for snap_scaffold_17-snap.1413-T1
Valid prediction for GeneMark_model.71335_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 23253, rend_intergenic: 18593  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29094, rend_intergenic: 24420  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49509, rend_intergenic: 42244  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89152, rend_intergenic: 83643  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93469, rend_intergenic: 89359  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113117, rend_intergenic: 93684  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124912, rend_intergenic: 115222  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134994, rend_intergenic: 125158  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138194, rend_intergenic: 135134  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144984, rend_intergenic: 138647  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153804, rend_intergenic: 150320  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184051, rend_intergenic: 171008  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187878, rend_intergenic: 184935  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200805, rend_intergenic: 188126  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 240855, rend_intergenic: 201636  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 248509
-exon list size: 955


building trellis

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64.8    
64.9    
65.0    
65.1    
65.2    
65.3    
65.4    
65.5    
65.6    
65.7    
65.8    
65.9    
66.0    
66.1    
66.2    
66.4    
66.5    
66.6    
66.7    
66.8    
66.9    
67.0    
67.1    
67.2    
67.3    
67.4    
67.5    
67.6    
67.7    
67.8    
67.9    
68.0    
68.1    
68.2    
68.3    
68.4    
68.5    
68.7    
68.8    
68.9    
69.0    
69.1    
69.2    
69.3    
69.4    
69.5    
69.6    
69.7    
69.8    
69.9    
70.0    
70.1    
70.2    
70.3    
70.4    
70.5    
70.6    
70.7    
70.8    
71.0    
71.1    
71.2    
71.3    
71.4    
71.5    
71.6    
71.7    
71.8    
71.9    
72.0    
72.1    
72.2    
72.3    
72.4    
72.5    
72.6    
72.7    
72.8    
72.9    
73.0    
73.1    
73.2    
73.4    
73.5    
73.6    
73.7    
73.8    
73.9    
74.0    
74.1    
74.2    
74.3    
74.4    
74.5    
74.6    
74.7    
74.8    
74.9    
75.0    
75.1    
75.2    
75.3    
75.4    
75.5    
75.7    
75.8    
75.9    
76.0    
76.1    
76.2    
76.3    
76.4    
76.5    
76.6    
76.7    
76.8    
76.9    
77.0    
77.1    
77.2    
77.3    
77.4    
77.5    
77.6    
77.7    
77.8    
78.0    
78.1    
78.2    
78.3    
78.4    
78.5    
78.6    
78.7    
78.8    
78.9    
79.0    
79.1    
79.2    
79.3    
79.4    
79.5    
79.6    
79.7    
79.8    
79.9    
80.0    
80.1    
80.3    
80.4    
80.5    
80.6    
80.7    
80.8    
80.9    
81.0    
81.1    
81.2    
81.3    
81.4    
81.5    
81.6    
81.7    
81.8    
81.9    
82.0    
82.1    
82.2    
82.3    
82.4    
82.5    
82.7    
82.8    
82.9    
83.0    
83.1    
83.2    
83.3    
83.4    
83.5    
83.6    
83.7    
83.8    
83.9    
84.0    
84.1    
84.2    
84.3    
84.4    
84.5    
84.6    
84.7    
84.8    
85.0    
85.1    
85.2    
85.3    
85.4    
85.5    
85.6    
85.7    
85.8    
85.9    
86.0    
86.1    
86.2    
86.3    
86.4    
86.5    
86.6    
86.7    
86.8    
86.9    
87.0    
87.1    
87.3    
87.4    
87.5    
87.6    
87.7    
87.8    
87.9    
88.0    
88.1    
88.2    
88.3    
88.4    
88.5    
88.6    
88.7    
88.8    
88.9    
89.0    
89.1    
89.2    
89.3    
89.4    
89.6    
89.7    
89.8    
89.9    
90.0    
90.1    
90.2    
90.3    
90.4    
90.5    
90.6    
90.7    
90.8    
90.9    
91.0    
91.1    
91.2    
91.3    
91.4    
91.5    
91.6    
91.7    
91.8    
92.0    
92.1    
92.2    
92.3    
92.4    
92.5    
92.6    
92.7    
92.8    
92.9    
93.0    
93.1    
93.2    
93.3    
93.4    
93.5    
93.6    
93.7    
93.8    
93.9    
94.0    
94.1    
94.3    
94.4    
94.5    
94.6    
94.7    
94.8    
94.9    
95.0    
95.1    
95.2    
95.3    
95.4    
95.5    
95.6    
95.7    
95.8    
95.9    
96.0    
96.1    
96.2    
96.3    
96.4    
96.6    
96.7    
96.8    
96.9    
97.0    
97.1    
97.2    
97.3    
97.4    
97.5    
97.6    
97.7    
97.8    
97.9    
98.0    
98.1    
98.2    
98.3    
98.4    
98.5    
98.6    
98.7    
98.9    
99.0    
99.1    
99.2    
99.3    
99.4    
99.5    
99.6    
99.7    
99.8    
99.9    
-found 47 predictions from path traversal
Error with prediction: snap lend_intergenic: 23253, rend_intergenic: 18593  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29094, rend_intergenic: 24420  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49509, rend_intergenic: 42244  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89152, rend_intergenic: 83643  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93469, rend_intergenic: 89359  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113117, rend_intergenic: 93684  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124912, rend_intergenic: 115222  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134994, rend_intergenic: 125158  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138194, rend_intergenic: 135134  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144984, rend_intergenic: 138647  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153804, rend_intergenic: 150320  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184051, rend_intergenic: 171008  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187878, rend_intergenic: 184935  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200805, rend_intergenic: 188126  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 240855, rend_intergenic: 201636  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 10273
-exon list size: 4


building trellis

16.7    
33.3    
50.0    
66.7    
83.3    
-found 1 predictions from path traversal

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