-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_19/scaffold_19_196339-451123

-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.77406_t
Valid prediction for GeneMark_model.77439_t
Valid prediction for Augustus_model.g29723.t1
Valid prediction for GeneMark_model.77441_t
Valid prediction for GlimmerHMM_glimmerT_44490-T1
Valid prediction for snap_scaffold_19-snap.56-T1
Valid prediction for GeneMark_model.77392_t
Valid prediction for GeneMark_model.77374_t
Valid prediction for snap_scaffold_19-snap.88-T1
Valid prediction for GeneMark_model.77425_t
Valid prediction for GeneMark_model.77427_t
Valid prediction for snap_scaffold_19-snap.82-T1
Valid prediction for GlimmerHMM_glimmerT_44484-T1
Valid prediction for GeneMark_model.77382_t
Couldn't classify 119830, 119922
Sorry, prediction pasa_asmbl_21987.p1 fails validation.
(ATT)	 GC	119830-119922	GT	TGG
(ACA)	 AG	120220-120315	GT	AGG
(GCA)	 AG	120647-120754	GT	TGG
(GCA)	 AG	120866-121009	GT	AGG
(GAG)	 AG	121309-121482	GT	AGG
(TTT)	 AG	121669-121761	GT	AGG
(AAC)	 AG	121849-121974	GT	AGG
(CCC)	 AG	122676-122759	GT	CAG
(CCT)	 AG	122848-122943	GG	GAG
-recovered pasa_asmbl_21987.p1, terminal, 122848, 122943
-recovered pasa_asmbl_21987.p1, internal, 120220, 120315
-recovered pasa_asmbl_21987.p1, internal, 120647, 120754
-recovered pasa_asmbl_21987.p1, internal, 120866, 121009
-recovered pasa_asmbl_21987.p1, internal, 121309, 121482
-recovered pasa_asmbl_21987.p1, internal, 121669, 121761
-recovered pasa_asmbl_21987.p1, internal, 121849, 121974
-recovered pasa_asmbl_21987.p1, internal, 122676, 122759
Valid prediction for snap_scaffold_19-snap.67-T1
Valid prediction for GlimmerHMM_glimmerT_44491-T1
Valid prediction for GeneMark_model.77429_t
Valid prediction for snap_scaffold_19-snap.95-T1
Valid prediction for HiQ_model.g29724.t1
Valid prediction for GlimmerHMM_glimmerT_44487-T1
Valid prediction for GlimmerHMM_glimmerT_44481-T1
Valid prediction for GlimmerHMM_glimmerT_44483-T1
Valid prediction for GeneMark_model.77431_t
Valid prediction for snap_scaffold_19-snap.48-T1
Valid prediction for GeneMark_model.77448_t
Valid prediction for snap_scaffold_19-snap.65-T1
Valid prediction for GlimmerHMM_glimmerT_44475-T1
Valid prediction for GlimmerHMM_glimmerT_44477-T1
Valid prediction for snap_scaffold_19-snap.72-T1
Valid prediction for GlimmerHMM_glimmerT_44492-T1
Valid prediction for snap_scaffold_19-snap.81-T1
Valid prediction for GeneMark_model.77396_t
Valid prediction for GlimmerHMM_glimmerT_44493-T1
Valid prediction for GeneMark_model.77394_t
Valid prediction for GlimmerHMM_glimmerT_44486-T1
Valid prediction for snap_scaffold_19-snap.85-T1
Valid prediction for snap_scaffold_19-snap.52-T1
Valid prediction for Augustus_model.g29721.t1
Valid prediction for snap_scaffold_19-snap.91-T1
Valid prediction for GeneMark_model.77384_t
Valid prediction for GeneMark_model.77437_t
Valid prediction for snap_scaffold_19-snap.58-T1
Couldn't classify 248128, 248286
Sorry, prediction GeneMark_model.77450_t fails validation.
(ATG)	 GA	247600-247607	GT	GTG
(GGA)	 AG	247694-247720	GT	ACG
(GGG)	 AG	247769-247897	GT	GAG
(ACG)	 AG	247945-248058	GT	CGG
(AAG)	 AG	248128-248286	GT	CAG
-recovered GeneMark_model.77450_t, initial, 247600, 247607
-recovered GeneMark_model.77450_t, internal, 247694, 247720
-recovered GeneMark_model.77450_t, internal, 247769, 247897
-recovered GeneMark_model.77450_t, internal, 247945, 248058
-recovered GeneMark_model.77450_t, internal, 248128, 248286
Valid prediction for GeneMark_model.77434_t
Valid prediction for GeneMark_model.77417_t
Valid prediction for GeneMark_model.77413_t
Valid prediction for GeneMark_model.77400_t
Valid prediction for GeneMark_model.77378_t
Valid prediction for snap_scaffold_19-snap.92-T1
Valid prediction for GeneMark_model.77386_t
Valid prediction for Augustus_model.g29719.t1
Valid prediction for GlimmerHMM_glimmerT_44489-T1
Valid prediction for Augustus_model.g29720.t1
Valid prediction for snap_scaffold_19-snap.74-T1
Valid prediction for snap_scaffold_19-snap.93-T1
Valid prediction for GeneMark_model.77390_t
Valid prediction for snap_scaffold_19-snap.47-T1
Valid prediction for snap_scaffold_19-snap.63-T1
Valid prediction for GlimmerHMM_glimmerT_44470-T1
Valid prediction for GeneMark_model.77407_t
Valid prediction for GeneMark_model.77436_t
Valid prediction for GeneMark_model.77402_t
Valid prediction for GeneMark_model.77414_t
Couldn't classify 92916, 93011
Sorry, prediction pasa_asmbl_22709.p1 fails validation.
(TCG)	 CC	92916-93011	GT	CGG
(GAG)	 AG	93560-93665	GT	AGG
(AGC)	 AG	93758-93891	CA	GAC
-recovered pasa_asmbl_22709.p1, terminal, 93758, 93891
-recovered pasa_asmbl_22709.p1, internal, 93560, 93665
Valid prediction for GeneMark_model.77388_t
Valid prediction for snap_scaffold_19-snap.64-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_19-snap.79-T1
Valid prediction for snap_scaffold_19-snap.61-T1
Valid prediction for CodingQuarry_transcript_25514-T1
Valid prediction for Augustus_model.g29725.t1
Valid prediction for GlimmerHMM_glimmerT_44499-T1
Valid prediction for GeneMark_model.77446_t
Valid prediction for GlimmerHMM_glimmerT_44478-T1
Valid prediction for GeneMark_model.77420_t
Valid prediction for GlimmerHMM_glimmerT_44479-T1
Valid prediction for GeneMark_model.77432_t
Valid prediction for GeneMark_model.77404_t
Valid prediction for snap_scaffold_19-snap.71-T1
Valid prediction for GeneMark_model.77409_t
Valid prediction for GeneMark_model.77422_t
Valid prediction for GeneMark_model.77443_t
Valid prediction for snap_scaffold_19-snap.70-T1
Valid prediction for GeneMark_model.77398_t
Valid prediction for GeneMark_model.77411_t
Valid prediction for snap_scaffold_19-snap.51-T1
Valid prediction for Augustus_model.g29718.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 GlimmerHMM_glimmerT_44480-T1
Valid prediction for GeneMark_model.77449_t
Valid prediction for GeneMark_model.77391_t
Valid prediction for GeneMark_model.77375_t
Valid prediction for GlimmerHMM_glimmerT_44474-T1
Valid prediction for GlimmerHMM_glimmerT_44471-T1
Valid prediction for snap_scaffold_19-snap.57-T1
Valid prediction for snap_scaffold_19-snap.86-T1
Valid prediction for snap_scaffold_19-snap.80-T1
Valid prediction for GeneMark_model.77399_t
Valid prediction for snap_scaffold_19-snap.78-T1
Valid prediction for snap_scaffold_19-snap.53-T1
Valid prediction for GeneMark_model.77401_t
Valid prediction for snap_scaffold_19-snap.76-T1
Valid prediction for snap_scaffold_19-snap.68-T1
Valid prediction for Augustus_model.g29726.t1
Valid prediction for GlimmerHMM_glimmerT_44473-T1
Valid prediction for snap_scaffold_19-snap.87-T1
Valid prediction for GlimmerHMM_glimmerT_44498-T1
Valid prediction for GeneMark_model.77430_t
Valid prediction for snap_scaffold_19-snap.59-T1
Valid prediction for GeneMark_model.77433_t
Valid prediction for GeneMark_model.77387_t
Valid prediction for snap_scaffold_19-snap.73-T1
Valid prediction for GeneMark_model.77405_t
Valid prediction for GeneMark_model.77397_t
Valid prediction for GeneMark_model.77445_t
Valid prediction for GeneMark_model.77423_t
Valid prediction for GeneMark_model.77403_t
Valid prediction for GeneMark_model.77393_t
Valid prediction for GlimmerHMM_glimmerT_44497-T1
Valid prediction for GeneMark_model.77440_t
Valid prediction for GeneMark_model.77395_t
Valid prediction for snap_scaffold_19-snap.62-T1
Valid prediction for snap_scaffold_19-snap.69-T1
Valid prediction for GeneMark_model.77381_t
Valid prediction for snap_scaffold_19-snap.84-T1
Valid prediction for GeneMark_model.77426_t
Valid prediction for GlimmerHMM_glimmerT_44482-T1
Valid prediction for GeneMark_model.77415_t
Valid prediction for snap_scaffold_19-snap.89-T1
Valid prediction for snap_scaffold_19-snap.49-T1
Valid prediction for GlimmerHMM_glimmerT_44501-T1
Valid prediction for GlimmerHMM_glimmerT_44476-T1
Valid prediction for GeneMark_model.77408_t
Valid prediction for GeneMark_model.77416_t
Valid prediction for GeneMark_model.77419_t
Valid prediction for GlimmerHMM_glimmerT_44472-T1
Valid prediction for GeneMark_model.77377_t
Valid prediction for snap_scaffold_19-snap.90-T1
Valid prediction for GeneMark_model.77373_t
Valid prediction for GeneMark_model.77438_t
Valid prediction for snap_scaffold_19-snap.66-T1
Valid prediction for snap_scaffold_19-snap.54-T1
Valid prediction for GlimmerHMM_glimmerT_44496-T1
Valid prediction for GeneMark_model.77379_t
Valid prediction for GlimmerHMM_glimmerT_44500-T1
Valid prediction for GeneMark_model.77435_t
Valid prediction for snap_scaffold_19-snap.94-T1
Valid prediction for snap_scaffold_19-snap.75-T1
Valid prediction for GeneMark_model.77428_t
Valid prediction for GeneMark_model.77421_t
Valid prediction for GeneMark_model.77410_t
Valid prediction for GlimmerHMM_glimmerT_44488-T1
Valid prediction for snap_scaffold_19-snap.60-T1
Valid prediction for GeneMark_model.77389_t
Valid prediction for snap_scaffold_19-snap.83-T1
Valid prediction for GeneMark_model.77418_t
Valid prediction for GeneMark_model.77442_t
Valid prediction for GeneMark_model.77376_t
Valid prediction for GeneMark_model.77383_t
Valid prediction for snap_scaffold_19-snap.50-T1
Valid prediction for GeneMark_model.77447_t
Valid prediction for snap_scaffold_19-snap.77-T1
Valid prediction for GeneMark_model.77424_t
Valid prediction for GlimmerHMM_glimmerT_44485-T1
Valid prediction for GeneMark_model.77380_t
Valid prediction for GlimmerHMM_glimmerT_44494-T1
Valid prediction for GlimmerHMM_glimmerT_44495-T1
Valid prediction for snap_scaffold_19-snap.55-T1
Valid prediction for GeneMark_model.77444_t
Valid prediction for Augustus_model.g29722.t1
Valid prediction for GeneMark_model.77412_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 11889, rend_intergenic: 5354  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14840, rend_intergenic: 13946  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33619, rend_intergenic: 21934  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39530, rend_intergenic: 35578  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47204, rend_intergenic: 43501  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62907, rend_intergenic: 50063  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67428, rend_intergenic: 66921  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74465, rend_intergenic: 68530  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86393, rend_intergenic: 81861  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98612, rend_intergenic: 88147  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123424, rend_intergenic: 118650  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125045, rend_intergenic: 124843  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140957, rend_intergenic: 125845  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180854, rend_intergenic: 164306  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186936, rend_intergenic: 184135  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 194210, rend_intergenic: 189607  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 215923, rend_intergenic: 195323  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 219741, rend_intergenic: 215983  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 254785
-exon list size: 986


building trellis

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56.8    
56.9    
57.0    
57.1    
57.2    
57.3    
57.4    
57.5    
57.6    
57.7    
57.8    
57.9    
58.0    
58.1    
58.2    
58.3    
58.4    
58.5    
58.6    
58.7    
58.8    
58.9    
59.0    
59.1    
59.2    
59.3    
59.4    
59.5    
59.6    
59.7    
59.8    
59.9    
60.0    
60.1    
60.2    
60.3    
60.4    
60.5    
60.6    
60.7    
60.8    
60.9    
61.0    
61.1    
61.2    
61.3    
61.4    
61.5    
61.6    
61.7    
61.8    
61.9    
62.0    
62.1    
62.2    
62.3    
62.4    
62.6    
62.7    
62.8    
62.9    
63.0    
63.1    
63.2    
63.3    
63.4    
63.5    
63.6    
63.7    
63.8    
63.9    
64.0    
64.1    
64.2    
64.3    
64.4    
64.5    
64.6    
64.7    
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    
66.3    
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    
68.6    
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    
70.9    
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    
73.3    
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    
75.6    
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    
77.9    
78.0    
78.1    
78.2    
78.3    
78.4    
78.5    
78.6    
78.7    
78.8    
78.9    
79.0    
79.1    
79.3    
79.4    
79.5    
79.6    
79.7    
79.8    
79.9    
80.0    
80.1    
80.2    
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    
82.6    
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    
84.9    
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    
87.2    
87.3    
87.4    
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    
89.5    
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    
91.9    
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    
94.2    
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    
95.9    
96.0    
96.1    
96.2    
96.3    
96.4    
96.5    
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    
98.8    
98.9    
99.0    
99.1    
99.2    
99.3    
99.4    
99.5    
99.6    
99.7    
99.8    
99.9    
-found 64 predictions from path traversal
Error with prediction: snap lend_intergenic: 11889, rend_intergenic: 5354  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14840, rend_intergenic: 13946  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33619, rend_intergenic: 21934  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39530, rend_intergenic: 35578  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47204, rend_intergenic: 43501  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62907, rend_intergenic: 50063  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67428, rend_intergenic: 66921  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74465, rend_intergenic: 68530  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86393, rend_intergenic: 81861  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98612, rend_intergenic: 88147  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123424, rend_intergenic: 118650  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125045, rend_intergenic: 124843  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140957, rend_intergenic: 125845  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180854, rend_intergenic: 164306  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186936, rend_intergenic: 184135  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 194210, rend_intergenic: 189607  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 215923, rend_intergenic: 195323  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 219741, rend_intergenic: 215983  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 242712 - 254785
-exon list size: 29


building trellis

3.2    
6.5    
9.7    
12.9    
16.1    
19.4    
22.6    
25.8    
29.0    
32.3    
35.5    
38.7    
41.9    
45.2    
48.4    
51.6    
54.8    
58.1    
61.3    
64.5    
67.7    
71.0    
74.2    
77.4    
80.6    
83.9    
87.1    
90.3    
93.5    
96.8    
-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