-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_16/scaffold_16_7634820-7877135

-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 Augustus_model.g26486.t1
Valid prediction for GeneMark_model.67523_t
Valid prediction for Augustus_model.g26487.t1
Valid prediction for snap_scaffold_16-snap.1432-T1
Valid prediction for GlimmerHMM_glimmerT_39420-T1
Valid prediction for snap_scaffold_16-snap.1416-T1
Valid prediction for GlimmerHMM_glimmerT_39446-T1
Valid prediction for snap_scaffold_16-snap.1423-T1
Valid prediction for GeneMark_model.67506_t
Valid prediction for GeneMark_model.67535_t
Valid prediction for GlimmerHMM_glimmerT_39430-T1
Valid prediction for snap_scaffold_16-snap.1429-T1
Valid prediction for Augustus_model.g26491.t1
Valid prediction for snap_scaffold_16-snap.1420-T1
Valid prediction for GlimmerHMM_glimmerT_39422-T1
Valid prediction for GeneMark_model.67502_t
Valid prediction for GeneMark_model.67533_t
Valid prediction for Augustus_model.g26505.t1
Valid prediction for GlimmerHMM_glimmerT_39443-T1
Valid prediction for GeneMark_model.67501_t
Valid prediction for GeneMark_model.67488_t
Valid prediction for Augustus_model.g26500.t1
Valid prediction for Augustus_model.g26488.t1
Valid prediction for snap_scaffold_16-snap.1415-T1
Valid prediction for snap_scaffold_16-snap.1428-T1
Valid prediction for snap_scaffold_16-snap.1410-T1
Valid prediction for GeneMark_model.67526_t
Valid prediction for GlimmerHMM_glimmerT_39437-T1
Valid prediction for snap_scaffold_16-snap.1448-T1
Valid prediction for Augustus_model.g26503.t1
Valid prediction for snap_scaffold_16-snap.1441-T1
Valid prediction for snap_scaffold_16-snap.1436-T1
Valid prediction for Augustus_model.g26485.t1
Valid prediction for GeneMark_model.67518_t
Valid prediction for snap_scaffold_16-snap.1437-T1
Valid prediction for GeneMark_model.67490_t
Valid prediction for GeneMark_model.67515_t
Valid prediction for snap_scaffold_16-snap.1449-T1
Valid prediction for GeneMark_model.67512_t
Valid prediction for GlimmerHMM_glimmerT_39438-T1
Valid prediction for GlimmerHMM_glimmerT_39426-T1
Couldn't classify 72985, 73762
Sorry, prediction pasa_asmbl_17153.p1 fails validation.
(GGA)	 CA	72985-73762	GT	TAG
(ATT)	 AG	74148-74173	CT	GAC
-recovered pasa_asmbl_17153.p1, terminal, 74148, 74173
Valid prediction for GlimmerHMM_glimmerT_39427-T1
Valid prediction for GeneMark_model.67499_t
Valid prediction for GeneMark_model.67510_t
Valid prediction for Augustus_model.g26492.t1
Valid prediction for GeneMark_model.67505_t
Valid prediction for GlimmerHMM_glimmerT_39449-T1
Valid prediction for GeneMark_model.67496_t
Valid prediction for GeneMark_model.67492_t
Valid prediction for snap_scaffold_16-snap.1431-T1
Couldn't classify 192619, 192762
Sorry, prediction pasa_asmbl_17155.p1 fails validation.
(ATG)	 TC	190491-190642	GT	AAG
(GGG)	 AG	190849-190930	GT	AGG
(AAC)	 AG	191025-191144	GT	AGG
(GGA)	 AG	191329-191473	GT	AGG
(GGC)	 AG	191682-191827	GT	CGG
(GCT)	 AG	192417-192542	GT	AGG
(GAG)	 AG	192619-192762	AC	ACA
-recovered pasa_asmbl_17155.p1, initial, 190491, 190642
-recovered pasa_asmbl_17155.p1, internal, 190849, 190930
-recovered pasa_asmbl_17155.p1, internal, 191025, 191144
-recovered pasa_asmbl_17155.p1, internal, 191329, 191473
-recovered pasa_asmbl_17155.p1, internal, 191682, 191827
-recovered pasa_asmbl_17155.p1, internal, 192417, 192542
Valid prediction for snap_scaffold_16-snap.1439-T1
Valid prediction for snap_scaffold_16-snap.1446-T1
Valid prediction for GlimmerHMM_glimmerT_39444-T1
Valid prediction for GeneMark_model.67530_t
Valid prediction for GeneMark_model.67513_t
Valid prediction for snap_scaffold_16-snap.1450-T1
Valid prediction for snap_scaffold_16-snap.1440-T1
Valid prediction for GlimmerHMM_glimmerT_39423-T1
Valid prediction for snap_scaffold_16-snap.1411-T1
Valid prediction for GlimmerHMM_glimmerT_39431-T1
Valid prediction for GeneMark_model.67527_t
Valid prediction for snap_scaffold_16-snap.1442-T1
Valid prediction for snap_scaffold_16-snap.1421-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 43506, 43595
Sorry, prediction pasa_asmbl_16379.p1 fails validation.
(CAG)	 TT	43506-43595	GT	CTG
(GAG)	 AG	44240-44422	GT	AGG
(GGC)	 AG	45667-46383	CA	GAC
-recovered pasa_asmbl_16379.p1, terminal, 45667, 46383
-recovered pasa_asmbl_16379.p1, internal, 44240, 44422
Valid prediction for snap_scaffold_16-snap.1447-T1
Valid prediction for GeneMark_model.67497_t
Valid prediction for GlimmerHMM_glimmerT_39428-T1
Valid prediction for Augustus_model.g26499.t1
Valid prediction for GeneMark_model.67531_t
Valid prediction for snap_scaffold_16-snap.1438-T1
Valid prediction for GeneMark_model.67486_t
Valid prediction for snap_scaffold_16-snap.1444-T1
Valid prediction for GeneMark_model.67520_t
Valid prediction for snap_scaffold_16-snap.1424-T1
Valid prediction for snap_scaffold_16-snap.1433-T1
Valid prediction for Augustus_model.g26494.t1
Valid prediction for GeneMark_model.67514_t
Valid prediction for GeneMark_model.67511_t
Valid prediction for GlimmerHMM_glimmerT_39436-T1
Valid prediction for snap_scaffold_16-snap.1422-T1
Valid prediction for GeneMark_model.67493_t
Valid prediction for GeneMark_model.67491_t
Valid prediction for GlimmerHMM_glimmerT_39425-T1
Valid prediction for GeneMark_model.67498_t
Valid prediction for GeneMark_model.67495_t
Valid prediction for GeneMark_model.67521_t
Valid prediction for snap_scaffold_16-snap.1435-T1
Valid prediction for GlimmerHMM_glimmerT_39421-T1
Valid prediction for snap_scaffold_16-snap.1407-T1
Couldn't classify 37586, 37622
Couldn't classify 42451, 42545
Sorry, prediction pasa_asmbl_16380.p1 fails validation.
(GTT)	 TC	37586-37622	GT	TGG
(CTA)	 AG	38139-38272	GT	AGG
(ACG)	 AG	40524-40604	GT	AGG
(GTG)	 AG	40751-40809	GT	AGG
(GAT)	 AG	41285-41394	GT	AGG
(CTG)	 AG	42451-42545	CT	AGC
add_exon() Sorry, pasa_asmbl_16380.p1 41285-41394-terminal-2 is invalid.
-recovered pasa_asmbl_16380.p1, terminal, 41285, 41394
-recovered pasa_asmbl_16380.p1, internal, 38139, 38272
-recovered pasa_asmbl_16380.p1, internal, 40524, 40604
-recovered pasa_asmbl_16380.p1, internal, 40751, 40809
-recovered pasa_asmbl_16380.p1, internal, 41285, 41394
Valid prediction for GlimmerHMM_glimmerT_39419-T1
Valid prediction for GeneMark_model.67525_t
Valid prediction for GeneMark_model.67519_t
Valid prediction for GlimmerHMM_glimmerT_39435-T1
Valid prediction for GlimmerHMM_glimmerT_39432-T1
Valid prediction for snap_scaffold_16-snap.1414-T1
Valid prediction for GlimmerHMM_glimmerT_39440-T1
Valid prediction for GlimmerHMM_glimmerT_39424-T1
Valid prediction for Augustus_model.g26502.t1
Valid prediction for GeneMark_model.67528_t
Valid prediction for GeneMark_model.67517_t
Valid prediction for GeneMark_model.67532_t
Valid prediction for HiQ_model.g26490.t1
Valid prediction for Augustus_model.g26496.t1
Valid prediction for GlimmerHMM_glimmerT_39445-T1
Valid prediction for Augustus_model.g26484.t1
Valid prediction for GeneMark_model.67524_t
Valid prediction for snap_scaffold_16-snap.1452-T1
Valid prediction for GeneMark_model.67536_t
Valid prediction for GeneMark_model.67509_t
Valid prediction for GlimmerHMM_glimmerT_39439-T1
Valid prediction for GeneMark_model.67507_t
Couldn't classify 172653, 172710
Sorry, prediction pasa_asmbl_16369.p1 fails validation.
(GTA)	 CA	172653-172710	GT	AGG
(ACT)	 AG	173122-173164	GT	TGG
(CGT)	 AG	173265-173304	GT	AGG
(TTG)	 AG	173406-173536	GT	CTG
(CCA)	 AG	173690-173781	GT	TGG
(AGT)	 AG	173966-174087	GT	AAG
(GTA)	 AG	174287-174445	GT	AGG
(AAG)	 AG	174856-175032	CT	GAC
-recovered pasa_asmbl_16369.p1, terminal, 174856, 175032
-recovered pasa_asmbl_16369.p1, internal, 173122, 173164
-recovered pasa_asmbl_16369.p1, internal, 173265, 173304
-recovered pasa_asmbl_16369.p1, internal, 173406, 173536
-recovered pasa_asmbl_16369.p1, internal, 173690, 173781
-recovered pasa_asmbl_16369.p1, internal, 173966, 174087
-recovered pasa_asmbl_16369.p1, internal, 174287, 174445
Valid prediction for Augustus_model.g26495.t1
Valid prediction for snap_scaffold_16-snap.1427-T1
Valid prediction for GeneMark_model.67503_t
Valid prediction for snap_scaffold_16-snap.1412-T1
Valid prediction for GlimmerHMM_glimmerT_39447-T1
Valid prediction for snap_scaffold_16-snap.1419-T1
Valid prediction for snap_scaffold_16-snap.1408-T1
Valid prediction for Augustus_model.g26493.t1
Valid prediction for snap_scaffold_16-snap.1425-T1
Valid prediction for GeneMark_model.67494_t
Valid prediction for GeneMark_model.67529_t
Valid prediction for snap_scaffold_16-snap.1443-T1
Valid prediction for Augustus_model.g26504.t1
Valid prediction for GeneMark_model.67534_t
Valid prediction for GeneMark_model.67537_t
Valid prediction for GeneMark_model.67522_t
Valid prediction for snap_scaffold_16-snap.1426-T1
Valid prediction for snap_scaffold_16-snap.1418-T1
Valid prediction for GeneMark_model.67508_t
Valid prediction for GlimmerHMM_glimmerT_39441-T1
Valid prediction for GeneMark_model.67516_t
Valid prediction for Augustus_model.g26489.t1
Valid prediction for snap_scaffold_16-snap.1451-T1
Valid prediction for GeneMark_model.67500_t
Valid prediction for GlimmerHMM_glimmerT_39450-T1
Valid prediction for snap_scaffold_16-snap.1417-T1
Valid prediction for GlimmerHMM_glimmerT_39448-T1
Valid prediction for GlimmerHMM_glimmerT_39442-T1
Valid prediction for GeneMark_model.67485_t
Valid prediction for GlimmerHMM_glimmerT_39433-T1
Valid prediction for Augustus_model.g26501.t1
Valid prediction for Augustus_model.g26506.t1
Valid prediction for GeneMark_model.67489_t
Valid prediction for snap_scaffold_16-snap.1409-T1
Valid prediction for GlimmerHMM_glimmerT_39434-T1
Valid prediction for GlimmerHMM_glimmerT_39451-T1
Valid prediction for snap_scaffold_16-snap.1413-T1
Valid prediction for GeneMark_model.67487_t
Valid prediction for GeneMark_model.67504_t
Valid prediction for snap_scaffold_16-snap.1430-T1
Valid prediction for GlimmerHMM_glimmerT_39429-T1
Valid prediction for Augustus_model.g26497.t1
Valid prediction for snap_scaffold_16-snap.1434-T1
Valid prediction for snap_scaffold_16-snap.1445-T1
Valid prediction for Augustus_model.g26498.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 12817, rend_intergenic: 12814  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25309, rend_intergenic: 19311  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35292, rend_intergenic: 26110  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48039, rend_intergenic: 44064  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60594, rend_intergenic: 48565  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80541, rend_intergenic: 79891  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90969, rend_intergenic: 82822  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118566, rend_intergenic: 113600  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140486, rend_intergenic: 140405  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169591, rend_intergenic: 162851  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 183362, rend_intergenic: 181366  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 198182, rend_intergenic: 195934  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 215587, rend_intergenic: 211364  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 227841, rend_intergenic: 220718  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 233958, rend_intergenic: 230603  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 242316
-exon list size: 742


building trellis

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72.3    
72.4    
72.6    
72.7    
72.8    
73.0    
73.1    
73.3    
73.4    
73.5    
73.7    
73.8    
73.9    
74.1    
74.2    
74.3    
74.5    
74.6    
74.7    
74.9    
75.0    
75.1    
75.3    
75.4    
75.5    
75.7    
75.8    
75.9    
76.1    
76.2    
76.3    
76.5    
76.6    
76.7    
76.9    
77.0    
77.2    
77.3    
77.4    
77.6    
77.7    
77.8    
78.0    
78.1    
78.2    
78.4    
78.5    
78.6    
78.8    
78.9    
79.0    
79.2    
79.3    
79.4    
79.6    
79.7    
79.8    
80.0    
80.1    
80.2    
80.4    
80.5    
80.6    
80.8    
80.9    
81.0    
81.2    
81.3    
81.5    
81.6    
81.7    
81.9    
82.0    
82.1    
82.3    
82.4    
82.5    
82.7    
82.8    
82.9    
83.1    
83.2    
83.3    
83.5    
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    
87.6    
87.8    
87.9    
88.0    
88.2    
88.3    
88.4    
88.6    
88.7    
88.8    
89.0    
89.1    
89.2    
89.4    
89.5    
89.7    
89.8    
89.9    
90.1    
90.2    
90.3    
90.5    
90.6    
90.7    
90.9    
91.0    
91.1    
91.3    
91.4    
91.5    
91.7    
91.8    
91.9    
92.1    
92.2    
92.3    
92.5    
92.6    
92.7    
92.9    
93.0    
93.1    
93.3    
93.4    
93.5    
93.7    
93.8    
94.0    
94.1    
94.2    
94.4    
94.5    
94.6    
94.8    
94.9    
95.0    
95.2    
95.3    
95.4    
95.6    
95.7    
95.8    
96.0    
96.1    
96.2    
96.4    
96.5    
96.6    
96.8    
96.9    
97.0    
97.2    
97.3    
97.4    
97.6    
97.7    
97.8    
98.0    
98.1    
98.3    
98.4    
98.5    
98.7    
98.8    
98.9    
99.1    
99.2    
99.3    
99.5    
99.6    
99.7    
99.9    
-found 42 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 12817, rend_intergenic: 12814  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25309, rend_intergenic: 19311  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35292, rend_intergenic: 26110  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48039, rend_intergenic: 44064  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60594, rend_intergenic: 48565  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80541, rend_intergenic: 79891  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90969, rend_intergenic: 82822  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118566, rend_intergenic: 113600  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140486, rend_intergenic: 140405  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169591, rend_intergenic: 162851  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 183362, rend_intergenic: 181366  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 198182, rend_intergenic: 195934  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 215587, rend_intergenic: 211364  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 227841, rend_intergenic: 220718  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 233958, rend_intergenic: 230603  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

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