-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_27/scaffold_27_6324326-6540191

-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 GlimmerHMM_glimmerT_58836-T1
Valid prediction for CodingQuarry_transcript_41829-T1
Valid prediction for Augustus_model.g39197.t1
Valid prediction for snap_scaffold_27-snap.1529-T1
Valid prediction for Augustus_model.g39191.t1
Valid prediction for GeneMark_model.102553_t
Valid prediction for GeneMark_model.102536_t
Valid prediction for GeneMark_model.102540_t
Valid prediction for snap_scaffold_27-snap.1525-T1
Valid prediction for GeneMark_model.102495_t
Valid prediction for GeneMark_model.102489_t
Valid prediction for Augustus_model.g39189.t1
Valid prediction for Augustus_model.g39198.t1
Valid prediction for GeneMark_model.102519_t
Valid prediction for GeneMark_model.102488_t
Valid prediction for GlimmerHMM_glimmerT_58832-T1
Valid prediction for snap_scaffold_27-snap.1551-T1
Valid prediction for GeneMark_model.102492_t
Valid prediction for Augustus_model.g39190.t1
Valid prediction for snap_scaffold_27-snap.1523-T1
Valid prediction for GeneMark_model.102510_t
Valid prediction for GlimmerHMM_glimmerT_58851-T1
Valid prediction for snap_scaffold_27-snap.1562-T1
Valid prediction for HiQ_model.g39208.t1
Valid prediction for GeneMark_model.102483_t
Valid prediction for snap_scaffold_27-snap.1555-T1
Valid prediction for GlimmerHMM_glimmerT_58846-T1
Valid prediction for GeneMark_model.102547_t
Valid prediction for snap_scaffold_27-snap.1553-T1
Valid prediction for snap_scaffold_27-snap.1532-T1
Valid prediction for GeneMark_model.102526_t
Valid prediction for GeneMark_model.102544_t
Valid prediction for snap_scaffold_27-snap.1564-T1
Valid prediction for GeneMark_model.102508_t
Valid prediction for GeneMark_model.102501_t
Valid prediction for GlimmerHMM_glimmerT_58829-T1
Valid prediction for snap_scaffold_27-snap.1542-T1
Valid prediction for snap_scaffold_27-snap.1535-T1
Valid prediction for GlimmerHMM_glimmerT_58844-T1
Valid prediction for GeneMark_model.102493_t
Valid prediction for GeneMark_model.102542_t
Valid prediction for snap_scaffold_27-snap.1539-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_58834-T1
Valid prediction for GlimmerHMM_glimmerT_58833-T1
Valid prediction for snap_scaffold_27-snap.1522-T1
Valid prediction for GeneMark_model.102482_t
Valid prediction for GeneMark_model.102499_t
Valid prediction for GlimmerHMM_glimmerT_58828-T1
Valid prediction for GeneMark_model.102505_t
Valid prediction for snap_scaffold_27-snap.1526-T1
Valid prediction for snap_scaffold_27-snap.1557-T1
Valid prediction for snap_scaffold_27-snap.1540-T1
Valid prediction for GlimmerHMM_glimmerT_58826-T1
Valid prediction for GlimmerHMM_glimmerT_58831-T1
Valid prediction for snap_scaffold_27-snap.1524-T1
Valid prediction for Augustus_model.g39188.t1
Valid prediction for GlimmerHMM_glimmerT_58847-T1
Valid prediction for GeneMark_model.102486_t
Valid prediction for GeneMark_model.102521_t
Valid prediction for GeneMark_model.102517_t
Valid prediction for snap_scaffold_27-snap.1534-T1
Valid prediction for GlimmerHMM_glimmerT_58854-T1
Valid prediction for GlimmerHMM_glimmerT_58843-T1
Valid prediction for pasa_asmbl_36354.p1
Valid prediction for snap_scaffold_27-snap.1546-T1
Valid prediction for GeneMark_model.102514_t
Valid prediction for GeneMark_model.102543_t
Valid prediction for snap_scaffold_27-snap.1548-T1
Valid prediction for Augustus_model.g39199.t1
Valid prediction for snap_scaffold_27-snap.1569-T1
Valid prediction for GeneMark_model.102551_t
Valid prediction for snap_scaffold_27-snap.1560-T1
Valid prediction for snap_scaffold_27-snap.1536-T1
Valid prediction for GeneMark_model.102507_t
Valid prediction for snap_scaffold_27-snap.1570-T1
Valid prediction for GeneMark_model.102524_t
Valid prediction for GlimmerHMM_glimmerT_58850-T1
Valid prediction for GeneMark_model.102485_t
Valid prediction for snap_scaffold_27-snap.1566-T1
Valid prediction for GlimmerHMM_glimmerT_58838-T1
Valid prediction for GeneMark_model.102512_t
Valid prediction for GeneMark_model.102532_t
Valid prediction for GeneMark_model.102538_t
Valid prediction for GeneMark_model.102504_t
Valid prediction for GeneMark_model.102484_t
Valid prediction for snap_scaffold_27-snap.1550-T1
Valid prediction for snap_scaffold_27-snap.1544-T1
Valid prediction for GlimmerHMM_glimmerT_58827-T1
Valid prediction for GeneMark_model.102534_t
Valid prediction for GeneMark_model.102549_t
Valid prediction for GlimmerHMM_glimmerT_58830-T1
Valid prediction for GeneMark_model.102528_t
Valid prediction for snap_scaffold_27-snap.1538-T1
Valid prediction for GlimmerHMM_glimmerT_58845-T1
Valid prediction for GeneMark_model.102516_t
Valid prediction for snap_scaffold_27-snap.1528-T1
Valid prediction for GeneMark_model.102497_t
Valid prediction for GeneMark_model.102523_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 Augustus_model.g39187.t1
Valid prediction for GeneMark_model.102527_t
Valid prediction for Augustus_model.g39204.t1
Valid prediction for GlimmerHMM_glimmerT_58825-T1
Valid prediction for snap_scaffold_27-snap.1558-T1
Valid prediction for snap_scaffold_27-snap.1556-T1
Valid prediction for snap_scaffold_27-snap.1527-T1
Valid prediction for snap_scaffold_27-snap.1543-T1
Valid prediction for GeneMark_model.102533_t
Valid prediction for GeneMark_model.102496_t
Valid prediction for snap_scaffold_27-snap.1520-T1
Valid prediction for GeneMark_model.102545_t
Valid prediction for GlimmerHMM_glimmerT_58840-T1
Valid prediction for CodingQuarry_transcript_41828-T1
Valid prediction for snap_scaffold_27-snap.1554-T1
Couldn't classify 171623, 171661
Sorry, prediction GeneMark_model.102487_t fails validation.
(GCA)	 AG	171623-171661	GC	GGG
(GGG)	 AG	171697-171711	GT	GAG
(AGG)	 AG	171773-171787	GT	GAG
(TGA)	 AG	171811-171831	GT	TTG
(AGG)	 AG	171873-171953	GC	AGG
(ACA)	 AG	172907-173153	CG	AAC
-recovered GeneMark_model.102487_t, terminal, 172907, 173153
-recovered GeneMark_model.102487_t, internal, 171623, 171661
-recovered GeneMark_model.102487_t, internal, 171697, 171711
-recovered GeneMark_model.102487_t, internal, 171773, 171787
-recovered GeneMark_model.102487_t, internal, 171811, 171831
-recovered GeneMark_model.102487_t, internal, 171873, 171953
Valid prediction for snap_scaffold_27-snap.1547-T1
Valid prediction for GeneMark_model.102498_t
Valid prediction for GeneMark_model.102502_t
Valid prediction for Augustus_model.g39195.t1
Valid prediction for GeneMark_model.102520_t
Valid prediction for GeneMark_model.102509_t
Valid prediction for Augustus_model.g39196.t1
Valid prediction for GlimmerHMM_glimmerT_58839-T1
Valid prediction for GeneMark_model.102525_t
Valid prediction for pasa_asmbl_37012.p1
Valid prediction for snap_scaffold_27-snap.1568-T1
Valid prediction for snap_scaffold_27-snap.1521-T1
Valid prediction for Augustus_model.g39203.t1
Valid prediction for GlimmerHMM_glimmerT_58837-T1
Valid prediction for snap_scaffold_27-snap.1549-T1
Valid prediction for snap_scaffold_27-snap.1533-T1
Valid prediction for Augustus_model.g39194.t1
Valid prediction for GlimmerHMM_glimmerT_58835-T1
Valid prediction for Augustus_model.g39207.t1
Valid prediction for snap_scaffold_27-snap.1519-T1
Valid prediction for GeneMark_model.102548_t
Valid prediction for GeneMark_model.102515_t
Valid prediction for GeneMark_model.102513_t
Valid prediction for snap_scaffold_27-snap.1567-T1
Valid prediction for snap_scaffold_27-snap.1552-T1
Valid prediction for GlimmerHMM_glimmerT_58853-T1
Valid prediction for Augustus_model.g39206.t1
Valid prediction for GeneMark_model.102550_t
Valid prediction for GeneMark_model.102531_t
Valid prediction for snap_scaffold_27-snap.1559-T1
Valid prediction for snap_scaffold_27-snap.1565-T1
Valid prediction for HiQ_model.g39201.t1
Valid prediction for GlimmerHMM_glimmerT_58824-T1
Valid prediction for GeneMark_model.102522_t
Valid prediction for snap_scaffold_27-snap.1537-T1
Valid prediction for snap_scaffold_27-snap.1545-T1
Valid prediction for GeneMark_model.102539_t
Valid prediction for GeneMark_model.102552_t
Valid prediction for GlimmerHMM_glimmerT_58841-T1
Valid prediction for GeneMark_model.102518_t
Valid prediction for Augustus_model.g39186.t1
Valid prediction for GeneMark_model.102506_t
Valid prediction for snap_scaffold_27-snap.1541-T1
Valid prediction for GeneMark_model.102530_t
Valid prediction for snap_scaffold_27-snap.1563-T1
Valid prediction for GlimmerHMM_glimmerT_58849-T1
Valid prediction for GeneMark_model.102535_t
Valid prediction for GeneMark_model.102541_t
Valid prediction for Augustus_model.g39200.t1
Valid prediction for GeneMark_model.102490_t
Valid prediction for GlimmerHMM_glimmerT_58842-T1
Valid prediction for GeneMark_model.102500_t
Valid prediction for snap_scaffold_27-snap.1530-T1
Valid prediction for Augustus_model.g39192.t1
Valid prediction for GeneMark_model.102511_t
Valid prediction for GeneMark_model.102529_t
Valid prediction for snap_scaffold_27-snap.1531-T1
Valid prediction for GeneMark_model.102491_t
Valid prediction for GlimmerHMM_glimmerT_58852-T1
Valid prediction for Augustus_model.g39193.t1
Valid prediction for GeneMark_model.102537_t
Valid prediction for snap_scaffold_27-snap.1561-T1
Valid prediction for GeneMark_model.102503_t
Valid prediction for Augustus_model.g39202.t1
Valid prediction for GlimmerHMM_glimmerT_58848-T1
Valid prediction for Augustus_model.g39205.t1
Valid prediction for GeneMark_model.102546_t
Valid prediction for GeneMark_model.102481_t
Valid prediction for GeneMark_model.102494_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 64668, rend_intergenic: 55586  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68259, rend_intergenic: 67097  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80888, rend_intergenic: 72021  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86686, rend_intergenic: 83162  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101966, rend_intergenic: 87853  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107399, rend_intergenic: 102476  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111679, rend_intergenic: 108788  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115827, rend_intergenic: 112165  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118927, rend_intergenic: 118772  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121172, rend_intergenic: 119295  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129269, rend_intergenic: 121444  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137550, rend_intergenic: 133261  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140699, rend_intergenic: 137957  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146296, rend_intergenic: 141636  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150127, rend_intergenic: 146432  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161867, rend_intergenic: 158971  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170921, rend_intergenic: 164239  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175419, rend_intergenic: 171536  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176788, rend_intergenic: 176035  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180281, rend_intergenic: 177018  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186380, rend_intergenic: 181370  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189729, rend_intergenic: 187260  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200107, rend_intergenic: 190242  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 201583, rend_intergenic: 200410  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 215866
-exon list size: 876


building trellis

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60.9    
61.0    
61.2    
61.3    
61.4    
61.5    
61.6    
61.7    
61.8    
62.0    
62.1    
62.2    
62.3    
62.4    
62.5    
62.6    
62.8    
62.9    
63.0    
63.1    
63.2    
63.3    
63.4    
63.6    
63.7    
63.8    
63.9    
64.0    
64.1    
64.2    
64.4    
64.5    
64.6    
64.7    
64.8    
64.9    
65.0    
65.1    
65.3    
65.4    
65.5    
65.6    
65.7    
65.8    
65.9    
66.1    
66.2    
66.3    
66.4    
66.5    
66.6    
66.7    
66.9    
67.0    
67.1    
67.2    
67.3    
67.4    
67.5    
67.7    
67.8    
67.9    
68.0    
68.1    
68.2    
68.3    
68.5    
68.6    
68.7    
68.8    
68.9    
69.0    
69.1    
69.2    
69.4    
69.5    
69.6    
69.7    
69.8    
69.9    
70.0    
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    
71.8    
71.9    
72.0    
72.1    
72.2    
72.3    
72.4    
72.6    
72.7    
72.8    
72.9    
73.0    
73.1    
73.2    
73.3    
73.5    
73.6    
73.7    
73.8    
73.9    
74.0    
74.1    
74.3    
74.4    
74.5    
74.6    
74.7    
74.8    
74.9    
75.1    
75.2    
75.3    
75.4    
75.5    
75.6    
75.7    
75.9    
76.0    
76.1    
76.2    
76.3    
76.4    
76.5    
76.7    
76.8    
76.9    
77.0    
77.1    
77.2    
77.3    
77.4    
77.6    
77.7    
77.8    
77.9    
78.0    
78.1    
78.2    
78.4    
78.5    
78.6    
78.7    
78.8    
78.9    
79.0    
79.2    
79.3    
79.4    
79.5    
79.6    
79.7    
79.8    
80.0    
80.1    
80.2    
80.3    
80.4    
80.5    
80.6    
80.8    
80.9    
81.0    
81.1    
81.2    
81.3    
81.4    
81.5    
81.7    
81.8    
81.9    
82.0    
82.1    
82.2    
82.3    
82.5    
82.6    
82.7    
82.8    
82.9    
83.0    
83.1    
83.3    
83.4    
83.5    
83.6    
83.7    
83.8    
83.9    
84.1    
84.2    
84.3    
84.4    
84.5    
84.6    
84.7    
84.9    
85.0    
85.1    
85.2    
85.3    
85.4    
85.5    
85.6    
85.8    
85.9    
86.0    
86.1    
86.2    
86.3    
86.4    
86.6    
86.7    
86.8    
86.9    
87.0    
87.1    
87.2    
87.4    
87.5    
87.6    
87.7    
87.8    
87.9    
88.0    
88.2    
88.3    
88.4    
88.5    
88.6    
88.7    
88.8    
89.0    
89.1    
89.2    
89.3    
89.4    
89.5    
89.6    
89.7    
89.9    
90.0    
90.1    
90.2    
90.3    
90.4    
90.5    
90.7    
90.8    
90.9    
91.0    
91.1    
91.2    
91.3    
91.5    
91.6    
91.7    
91.8    
91.9    
92.0    
92.1    
92.3    
92.4    
92.5    
92.6    
92.7    
92.8    
92.9    
93.1    
93.2    
93.3    
93.4    
93.5    
93.6    
93.7    
93.8    
94.0    
94.1    
94.2    
94.3    
94.4    
94.5    
94.6    
94.8    
94.9    
95.0    
95.1    
95.2    
95.3    
95.4    
95.6    
95.7    
95.8    
95.9    
96.0    
96.1    
96.2    
96.4    
96.5    
96.6    
96.7    
96.8    
96.9    
97.0    
97.2    
97.3    
97.4    
97.5    
97.6    
97.7    
97.8    
97.9    
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    
99.7    
99.8    
99.9    
-found 42 predictions from path traversal
Error with prediction: snap lend_intergenic: 64668, rend_intergenic: 55586  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68259, rend_intergenic: 67097  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80888, rend_intergenic: 72021  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86686, rend_intergenic: 83162  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101966, rend_intergenic: 87853  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107399, rend_intergenic: 102476  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111679, rend_intergenic: 108788  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115827, rend_intergenic: 112165  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118927, rend_intergenic: 118772  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121172, rend_intergenic: 119295  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129269, rend_intergenic: 121444  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137550, rend_intergenic: 133261  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140699, rend_intergenic: 137957  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146296, rend_intergenic: 141636  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150127, rend_intergenic: 146432  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161867, rend_intergenic: 158971  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170921, rend_intergenic: 164239  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175419, rend_intergenic: 171536  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176788, rend_intergenic: 176035  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180281, rend_intergenic: 177018  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186380, rend_intergenic: 181370  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189729, rend_intergenic: 187260  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200107, rend_intergenic: 190242  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 201583, rend_intergenic: 200410  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 26 predictions persist after filtering for low support