-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_16/scaffold_16_8804553-9035864

-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.67773_t
Valid prediction for snap_scaffold_16-snap.1672-T1
Valid prediction for GeneMark_model.67753_t
Valid prediction for GeneMark_model.67776_t
Valid prediction for GlimmerHMM_glimmerT_39595-T1
Valid prediction for GeneMark_model.67789_t
Valid prediction for Augustus_model.g26608.t1
Valid prediction for snap_scaffold_16-snap.1661-T1
Valid prediction for GeneMark_model.67752_t
Couldn't classify 82239, 82331
Sorry, prediction pasa_asmbl_17245.p1 fails validation.
(GGG)	 CA	82239-82331	GT	AGG
(TAT)	 AG	82517-82634	GT	AGG
(AGA)	 AG	82811-82922	GT	CAG
(GTA)	 AG	83495-83621	GG	GAG
-recovered pasa_asmbl_17245.p1, terminal, 83495, 83621
-recovered pasa_asmbl_17245.p1, internal, 82517, 82634
-recovered pasa_asmbl_17245.p1, internal, 82811, 82922
Valid prediction for Augustus_model.g26609.t1
Valid prediction for GeneMark_model.67751_t
Valid prediction for GeneMark_model.67764_t
Valid prediction for GeneMark_model.67780_t
Valid prediction for snap_scaffold_16-snap.1662-T1
Valid prediction for snap_scaffold_16-snap.1654-T1
Valid prediction for GeneMark_model.67727_t
Valid prediction for GlimmerHMM_glimmerT_39597-T1
Valid prediction for GeneMark_model.67747_t
Valid prediction for GeneMark_model.67784_t
Valid prediction for CodingQuarry_transcript_20008-T1
Valid prediction for GeneMark_model.67768_t
Valid prediction for snap_scaffold_16-snap.1669-T1
Valid prediction for GeneMark_model.67758_t
Valid prediction for snap_scaffold_16-snap.1653-T1
Valid prediction for GlimmerHMM_glimmerT_39591-T1
Valid prediction for snap_scaffold_16-snap.1647-T1
Valid prediction for snap_scaffold_16-snap.1640-T1
Valid prediction for snap_scaffold_16-snap.1667-T1
Valid prediction for snap_scaffold_16-snap.1642-T1
Valid prediction for snap_scaffold_16-snap.1638-T1
Valid prediction for snap_scaffold_16-snap.1665-T1
Valid prediction for Augustus_model.g26610.t1
Valid prediction for snap_scaffold_16-snap.1637-T1
Valid prediction for GeneMark_model.67728_t
Valid prediction for snap_scaffold_16-snap.1674-T1
Valid prediction for GeneMark_model.67735_t
Couldn't classify 97398, 97497
Sorry, prediction pasa_asmbl_17249.p1 fails validation.
(GAG)	 CA	97398-97497	GT	CGG
(GCA)	 AG	98099-98156	GT	AGG
(ATT)	 AG	98407-98460	GT	AGG
(GGA)	 AG	100670-100726	GT	GGG
(TGA)	 AG	103582-103711	GT	AGG
(GCC)	 AG	104558-104626	GT	TGG
(TCG)	 AG	105551-105835	AC	AAA
-recovered pasa_asmbl_17249.p1, terminal, 105551, 105835
-recovered pasa_asmbl_17249.p1, internal, 98099, 98156
-recovered pasa_asmbl_17249.p1, internal, 98407, 98460
-recovered pasa_asmbl_17249.p1, internal, 100670, 100726
-recovered pasa_asmbl_17249.p1, internal, 103582, 103711
-recovered pasa_asmbl_17249.p1, internal, 104558, 104626
Valid prediction for GeneMark_model.67761_t
Couldn't classify 86353, 86401
Couldn't classify 92067, 92132
Sorry, prediction pasa_asmbl_17246.p1 fails validation.
(TTT)	 GT	86353-86401	GT	AGG
(TTC)	 AG	86648-86708	GT	ACG
(ATT)	 AG	86915-86954	GT	ATG
(TTC)	 AG	87594-87717	GT	AGG
(GTA)	 AG	88519-88564	GT	CTG
(GCT)	 AG	90118-90198	GT	GGG
(ACC)	 AG	91245-91344	GT	AGG
(GAG)	 AG	91620-91697	GT	AGG
(TCA)	 AG	92067-92132	GG	ATG
-recovered pasa_asmbl_17246.p1, internal, 86648, 86708
-recovered pasa_asmbl_17246.p1, internal, 86915, 86954
-recovered pasa_asmbl_17246.p1, internal, 87594, 87717
-recovered pasa_asmbl_17246.p1, internal, 88519, 88564
-recovered pasa_asmbl_17246.p1, internal, 90118, 90198
-recovered pasa_asmbl_17246.p1, internal, 91245, 91344
-recovered pasa_asmbl_17246.p1, internal, 91620, 91697
Valid prediction for Augustus_model.g26615.t1
Valid prediction for GeneMark_model.67740_t
Valid prediction for CodingQuarry_transcript_20009-T1
Valid prediction for GlimmerHMM_glimmerT_39583-T1
Valid prediction for GeneMark_model.67771_t
Valid prediction for GlimmerHMM_glimmerT_39577-T1
Valid prediction for GlimmerHMM_glimmerT_39587-T1
Valid prediction for HiQ_model.g26620.t1
Valid prediction for GlimmerHMM_glimmerT_39579-T1
Valid prediction for GeneMark_model.67749_t
Valid prediction for snap_scaffold_16-snap.1650-T1
Valid prediction for CodingQuarry_transcript_20007-T1
Valid prediction for Augustus_model.g26617.t1
Valid prediction for GeneMark_model.67770_t
Valid prediction for GlimmerHMM_glimmerT_39592-T1
Valid prediction for GeneMark_model.67733_t
Valid prediction for snap_scaffold_16-snap.1673-T1
Valid prediction for GlimmerHMM_glimmerT_39582-T1
Valid prediction for GeneMark_model.67787_t
Valid prediction for GeneMark_model.67760_t
Valid prediction for GlimmerHMM_glimmerT_39574-T1
Valid prediction for snap_scaffold_16-snap.1658-T1
Valid prediction for GlimmerHMM_glimmerT_39593-T1
Valid prediction for GeneMark_model.67730_t
Valid prediction for snap_scaffold_16-snap.1671-T1
Valid prediction for GlimmerHMM_glimmerT_39588-T1
Valid prediction for snap_scaffold_16-snap.1670-T1
Valid prediction for snap_scaffold_16-snap.1635-T1
Valid prediction for GeneMark_model.67742_t
Valid prediction for GeneMark_model.67775_t
Valid prediction for pasa_asmbl_17253.p1
Valid prediction for Augustus_model.g26605.t1
Valid prediction for Augustus_model.g26614.t1
Valid prediction for snap_scaffold_16-snap.1634-T1
Valid prediction for Augustus_model.g26612.t1
Valid prediction for GeneMark_model.67781_t
Valid prediction for GeneMark_model.67745_t
Valid prediction for Augustus_model.g26606.t1
Valid prediction for GeneMark_model.67731_t
Valid prediction for GeneMark_model.67737_t
Valid prediction for GeneMark_model.67791_t
Valid prediction for GeneMark_model.67755_t
Valid prediction for Augustus_model.g26619.t1
Valid prediction for GeneMark_model.67790_t
Valid prediction for Augustus_model.g26611.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 GeneMark_model.67774_t
Valid prediction for GeneMark_model.67736_t
Valid prediction for GeneMark_model.67729_t
Valid prediction for Augustus_model.g26607.t1
Valid prediction for snap_scaffold_16-snap.1655-T1
Valid prediction for GeneMark_model.67734_t
Valid prediction for GeneMark_model.67785_t
Valid prediction for GeneMark_model.67738_t
Valid prediction for snap_scaffold_16-snap.1664-T1
Valid prediction for snap_scaffold_16-snap.1657-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_39576-T1
Valid prediction for GeneMark_model.67777_t
Valid prediction for GlimmerHMM_glimmerT_39586-T1
Valid prediction for HiQ_model.g26613.t1
Valid prediction for GlimmerHMM_glimmerT_39594-T1
Valid prediction for GlimmerHMM_glimmerT_39584-T1
Valid prediction for snap_scaffold_16-snap.1656-T1
Valid prediction for snap_scaffold_16-snap.1663-T1
Valid prediction for GeneMark_model.67759_t
Valid prediction for snap_scaffold_16-snap.1641-T1
Valid prediction for snap_scaffold_16-snap.1648-T1
Valid prediction for GeneMark_model.67779_t
Valid prediction for GeneMark_model.67788_t
Valid prediction for snap_scaffold_16-snap.1649-T1
Valid prediction for GeneMark_model.67782_t
Valid prediction for GeneMark_model.67762_t
Valid prediction for GeneMark_model.67778_t
Valid prediction for GeneMark_model.67741_t
Valid prediction for snap_scaffold_16-snap.1643-T1
Valid prediction for GeneMark_model.67743_t
Valid prediction for GlimmerHMM_glimmerT_39578-T1
Valid prediction for snap_scaffold_16-snap.1639-T1
Valid prediction for Augustus_model.g26618.t1
Valid prediction for GeneMark_model.67732_t
Valid prediction for GeneMark_model.67757_t
Valid prediction for GlimmerHMM_glimmerT_39580-T1
Valid prediction for GlimmerHMM_glimmerT_39590-T1
Valid prediction for GeneMark_model.67766_t
Valid prediction for snap_scaffold_16-snap.1636-T1
Valid prediction for snap_scaffold_16-snap.1651-T1
Valid prediction for GeneMark_model.67769_t
Valid prediction for GeneMark_model.67783_t
Valid prediction for GlimmerHMM_glimmerT_39575-T1
Valid prediction for GeneMark_model.67763_t
Couldn't classify 158608, 158675
Sorry, prediction pasa_asmbl_16440.p1 fails validation.
(TTG)	 AG	158608-158675	GT	GTG
(AAA)	 AG	159440-160690	GT	AGG
(GAA)	 AG	161049-161225	GT	AGG
(GTC)	 AG	161432-161590	GT	GTG
(GCT)	 AG	161811-161892	GT	AGG
(AAA)	 AG	162044-162245	GT	TGG
(GAG)	 AG	162837-162910	GT	ATG
(AGT)	 AG	163138-163228	GT	CCG
(GGG)	 AG	163365-163512	GT	ATG
(GCA)	 AG	163688-163825	GT	AGG
(TAT)	 AG	164238-164391	GT	TGG
(GTG)	 AG	164469-164583	GT	CAG
(TTA)	 AG	164833-164984	GT	AGG
(ATG)	 AG	165177-165263	GT	GGG
(GAG)	 AG	165465-165668	GG	GAG
-recovered pasa_asmbl_16440.p1, initial, 165177, 165263
-recovered pasa_asmbl_16440.p1, terminal, 165465, 165668
-recovered pasa_asmbl_16440.p1, internal, 158608, 158675
-recovered pasa_asmbl_16440.p1, internal, 159440, 160690
-recovered pasa_asmbl_16440.p1, internal, 161049, 161225
-recovered pasa_asmbl_16440.p1, internal, 161432, 161590
-recovered pasa_asmbl_16440.p1, internal, 161811, 161892
-recovered pasa_asmbl_16440.p1, internal, 162044, 162245
-recovered pasa_asmbl_16440.p1, internal, 162837, 162910
-recovered pasa_asmbl_16440.p1, internal, 163138, 163228
-recovered pasa_asmbl_16440.p1, internal, 163365, 163512
-recovered pasa_asmbl_16440.p1, internal, 163688, 163825
-recovered pasa_asmbl_16440.p1, internal, 164238, 164391
-recovered pasa_asmbl_16440.p1, internal, 164469, 164583
-recovered pasa_asmbl_16440.p1, internal, 164833, 164984
-recovered pasa_asmbl_16440.p1, internal, 165177, 165263
Valid prediction for snap_scaffold_16-snap.1666-T1
Valid prediction for snap_scaffold_16-snap.1652-T1
Valid prediction for GlimmerHMM_glimmerT_39581-T1
Valid prediction for GlimmerHMM_glimmerT_39585-T1
Valid prediction for snap_scaffold_16-snap.1668-T1
Valid prediction for snap_scaffold_16-snap.1659-T1
Valid prediction for GlimmerHMM_glimmerT_39589-T1
Valid prediction for Augustus_model.g26604.t1
Valid prediction for GeneMark_model.67772_t
Valid prediction for GeneMark_model.67750_t
Valid prediction for GeneMark_model.67786_t
Valid prediction for GeneMark_model.67739_t
Valid prediction for GeneMark_model.67746_t
Valid prediction for GeneMark_model.67748_t
Valid prediction for GeneMark_model.67744_t
Valid prediction for Augustus_model.g26616.t1
Valid prediction for GeneMark_model.67754_t
Valid prediction for GlimmerHMM_glimmerT_39596-T1
Valid prediction for snap_scaffold_16-snap.1645-T1
Valid prediction for snap_scaffold_16-snap.1646-T1
Valid prediction for snap_scaffold_16-snap.1644-T1
Valid prediction for snap_scaffold_16-snap.1660-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 6546, rend_intergenic: 4606  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 12084, rend_intergenic: 6560  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14206, rend_intergenic: 13114  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16715, rend_intergenic: 16587  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26683, rend_intergenic: 17473  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40373, rend_intergenic: 28470  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44218, rend_intergenic: 40774  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52968, rend_intergenic: 45595  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105835, rend_intergenic: 88748  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117219, rend_intergenic: 110444  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 231312
-exon list size: 703


building trellis

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76.2    
76.3    
76.5    
76.6    
76.7    
76.9    
77.0    
77.2    
77.3    
77.4    
77.6    
77.7    
77.9    
78.0    
78.2    
78.3    
78.4    
78.6    
78.7    
78.9    
79.0    
79.1    
79.3    
79.4    
79.6    
79.7    
79.9    
80.0    
80.1    
80.3    
80.4    
80.6    
80.7    
80.9    
81.0    
81.1    
81.3    
81.4    
81.6    
81.7    
81.8    
82.0    
82.1    
82.3    
82.4    
82.6    
82.7    
82.8    
83.0    
83.1    
83.3    
83.4    
83.5    
83.7    
83.8    
84.0    
84.1    
84.3    
84.4    
84.5    
84.7    
84.8    
85.0    
85.1    
85.2    
85.4    
85.5    
85.7    
85.8    
86.0    
86.1    
86.2    
86.4    
86.5    
86.7    
86.8    
87.0    
87.1    
87.2    
87.4    
87.5    
87.7    
87.8    
87.9    
88.1    
88.2    
88.4    
88.5    
88.7    
88.8    
88.9    
89.1    
89.2    
89.4    
89.5    
89.6    
89.8    
89.9    
90.1    
90.2    
90.4    
90.5    
90.6    
90.8    
90.9    
91.1    
91.2    
91.3    
91.5    
91.6    
91.8    
91.9    
92.1    
92.2    
92.3    
92.5    
92.6    
92.8    
92.9    
93.0    
93.2    
93.3    
93.5    
93.6    
93.8    
93.9    
94.0    
94.2    
94.3    
94.5    
94.6    
94.8    
94.9    
95.0    
95.2    
95.3    
95.5    
95.6    
95.7    
95.9    
96.0    
96.2    
96.3    
96.5    
96.6    
96.7    
96.9    
97.0    
97.2    
97.3    
97.4    
97.6    
97.7    
97.9    
98.0    
98.2    
98.3    
98.4    
98.6    
98.7    
98.9    
99.0    
99.1    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 39 predictions from path traversal
Error with prediction: snap lend_intergenic: 6546, rend_intergenic: 4606  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 12084, rend_intergenic: 6560  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14206, rend_intergenic: 13114  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16715, rend_intergenic: 16587  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26683, rend_intergenic: 17473  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40373, rend_intergenic: 28470  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44218, rend_intergenic: 40774  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52968, rend_intergenic: 45595  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105835, rend_intergenic: 88748  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117219, rend_intergenic: 110444  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 18 predictions persist after filtering for low support