-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_2/scaffold_2_377806-583461

-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 snap_scaffold_2-snap.85-T1
Valid prediction for GeneMark_model.5052_t
Valid prediction for snap_scaffold_2-snap.114-T1
Valid prediction for GlimmerHMM_glimmerT_3123-T1
Valid prediction for GlimmerHMM_glimmerT_3128-T1
Valid prediction for snap_scaffold_2-snap.100-T1
Valid prediction for Augustus_model.g2107.t1
Valid prediction for GlimmerHMM_glimmerT_3117-T1
Valid prediction for Augustus_model.g2110.t1
Valid prediction for snap_scaffold_2-snap.110-T1
Valid prediction for HiQ_model.g2115.t1
Valid prediction for GeneMark_model.5040_t
Valid prediction for GlimmerHMM_glimmerT_3118-T1
Valid prediction for snap_scaffold_2-snap.118-T1
Valid prediction for snap_scaffold_2-snap.99-T1
Valid prediction for GeneMark_model.5049_t
Valid prediction for snap_scaffold_2-snap.89-T1
Valid prediction for GeneMark_model.5043_t
Valid prediction for GeneMark_model.5055_t
Valid prediction for snap_scaffold_2-snap.108-T1
Valid prediction for GeneMark_model.5070_t
Valid prediction for snap_scaffold_2-snap.130-T1
Valid prediction for GeneMark_model.5034_t
Valid prediction for GeneMark_model.5067_t
Valid prediction for GeneMark_model.5071_t
Valid prediction for snap_scaffold_2-snap.96-T1
Valid prediction for snap_scaffold_2-snap.94-T1
Valid prediction for GlimmerHMM_glimmerT_3110-T1
Valid prediction for snap_scaffold_2-snap.105-T1
Valid prediction for snap_scaffold_2-snap.129-T1
Valid prediction for Augustus_model.g2119.t1
Valid prediction for GeneMark_model.5045_t
Valid prediction for Augustus_model.g2116.t1
Valid prediction for GeneMark_model.5036_t
Valid prediction for snap_scaffold_2-snap.109-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_3116-T1
Valid prediction for snap_scaffold_2-snap.125-T1
Valid prediction for snap_scaffold_2-snap.123-T1
Valid prediction for GlimmerHMM_glimmerT_3107-T1
Valid prediction for Augustus_model.g2118.t1
Valid prediction for snap_scaffold_2-snap.112-T1
Valid prediction for snap_scaffold_2-snap.107-T1
Valid prediction for GlimmerHMM_glimmerT_3126-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GeneMark_model.5059_t
Valid prediction for snap_scaffold_2-snap.84-T1
Valid prediction for snap_scaffold_2-snap.119-T1
Valid prediction for snap_scaffold_2-snap.113-T1
Valid prediction for snap_scaffold_2-snap.102-T1
Valid prediction for GeneMark_model.5037_t
Valid prediction for GlimmerHMM_glimmerT_3114-T1
Valid prediction for GeneMark_model.5057_t
Valid prediction for snap_scaffold_2-snap.88-T1
Valid prediction for GeneMark_model.5062_t
Valid prediction for GeneMark_model.5054_t
Valid prediction for GlimmerHMM_glimmerT_3108-T1
Valid prediction for GlimmerHMM_glimmerT_3127-T1
Valid prediction for GeneMark_model.5038_t
Valid prediction for snap_scaffold_2-snap.106-T1
Valid prediction for GeneMark_model.5051_t
Valid prediction for GeneMark_model.5069_t
Valid prediction for snap_scaffold_2-snap.93-T1
Valid prediction for GeneMark_model.5032_t
Valid prediction for GeneMark_model.5047_t
Valid prediction for snap_scaffold_2-snap.121-T1
Valid prediction for snap_scaffold_2-snap.86-T1
Valid prediction for CodingQuarry_transcript_28368-T1
Valid prediction for GeneMark_model.5065_t
Valid prediction for GlimmerHMM_glimmerT_3120-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.5060_t
Valid prediction for CodingQuarry_transcript_28369-T1
Valid prediction for Augustus_model.g2112.t1
Valid prediction for snap_scaffold_2-snap.120-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_3111-T1
Valid prediction for Augustus_model.g2117.t1
Valid prediction for GeneMark_model.5056_t
Valid prediction for GlimmerHMM_glimmerT_3113-T1
Valid prediction for snap_scaffold_2-snap.126-T1
Valid prediction for Augustus_model.g2114.t1
Valid prediction for snap_scaffold_2-snap.87-T1
Couldn't classify 84587, 84686
Couldn't classify 88665, 88752
Sorry, prediction pasa_asmbl_22836.p1 fails validation.
(CAC)	 CC	84587-84686	GT	GGG
(AGG)	 AG	84893-85059	GT	AGG
(GAG)	 AG	85308-85484	GT	TGG
(GGT)	 AG	86601-86672	GT	TGG
(GTG)	 AG	86888-87015	GT	AGG
(GGT)	 AG	87290-87465	GT	AAG
(CAG)	 AG	87724-87928	GT	AGG
(GAG)	 AG	88191-88394	GT	AGG
(GCT)	 AG	88665-88752	AT	AGA
-recovered pasa_asmbl_22836.p1, internal, 84893, 85059
-recovered pasa_asmbl_22836.p1, internal, 85308, 85484
-recovered pasa_asmbl_22836.p1, internal, 86601, 86672
-recovered pasa_asmbl_22836.p1, internal, 86888, 87015
-recovered pasa_asmbl_22836.p1, internal, 87290, 87465
-recovered pasa_asmbl_22836.p1, internal, 87724, 87928
-recovered pasa_asmbl_22836.p1, internal, 88191, 88394
Valid prediction for GlimmerHMM_glimmerT_3115-T1
Valid prediction for GlimmerHMM_glimmerT_3112-T1
Valid prediction for GeneMark_model.5064_t
Valid prediction for GeneMark_model.5041_t
Valid prediction for GlimmerHMM_glimmerT_3109-T1
Valid prediction for pasa_asmbl_22832.p1
Valid prediction for Augustus_model.g2113.t1
Valid prediction for snap_scaffold_2-snap.90-T1
Valid prediction for CodingQuarry_transcript_28367-T1
Valid prediction for GeneMark_model.5072_t
Valid prediction for GeneMark_model.5073_t
Valid prediction for snap_scaffold_2-snap.92-T1
Valid prediction for GlimmerHMM_glimmerT_3130-T1
Valid prediction for snap_scaffold_2-snap.98-T1
Valid prediction for snap_scaffold_2-snap.117-T1
Valid prediction for GeneMark_model.5068_t
Valid prediction for GlimmerHMM_glimmerT_3124-T1
Valid prediction for GeneMark_model.5061_t
Valid prediction for GeneMark_model.5042_t
Valid prediction for snap_scaffold_2-snap.127-T1
Valid prediction for snap_scaffold_2-snap.104-T1
Valid prediction for snap_scaffold_2-snap.97-T1
Valid prediction for GlimmerHMM_glimmerT_3125-T1
Valid prediction for GeneMark_model.5058_t
Valid prediction for GlimmerHMM_glimmerT_3119-T1
Valid prediction for GeneMark_model.5033_t
Valid prediction for GlimmerHMM_glimmerT_3129-T1
Valid prediction for snap_scaffold_2-snap.83-T1
Valid prediction for snap_scaffold_2-snap.103-T1
Valid prediction for GeneMark_model.5050_t
Valid prediction for snap_scaffold_2-snap.124-T1
Valid prediction for snap_scaffold_2-snap.95-T1
Valid prediction for snap_scaffold_2-snap.111-T1
Couldn't classify 91613, 91728
Sorry, prediction pasa_asmbl_22835.p1 fails validation.
(ATG)	 GC	89154-89222	GT	AGG
(GTA)	 AG	90322-90474	GT	AGG
(TCG)	 AG	91328-91394	GT	TGG
(AAA)	 AG	91613-91728	GG	ACG
-recovered pasa_asmbl_22835.p1, initial, 89154, 89222
-recovered pasa_asmbl_22835.p1, internal, 90322, 90474
-recovered pasa_asmbl_22835.p1, internal, 91328, 91394
Valid prediction for GeneMark_model.5046_t
Valid prediction for snap_scaffold_2-snap.116-T1
Valid prediction for GeneMark_model.5074_t
Valid prediction for Augustus_model.g2120.t1
Valid prediction for CodingQuarry_transcript_28365-T1
Valid prediction for GlimmerHMM_glimmerT_3131-T1
Valid prediction for snap_scaffold_2-snap.101-T1
Valid prediction for GlimmerHMM_glimmerT_3106-T1
Valid prediction for GlimmerHMM_glimmerT_3132-T1
Valid prediction for GeneMark_model.5053_t
Valid prediction for GlimmerHMM_glimmerT_3122-T1
Valid prediction for snap_scaffold_2-snap.122-T1
Valid prediction for Augustus_model.g2108.t1
Valid prediction for GeneMark_model.5066_t
Valid prediction for Augustus_model.g2121.t1
Valid prediction for GeneMark_model.5048_t
Valid prediction for GeneMark_model.5031_t
Valid prediction for snap_scaffold_2-snap.115-T1
Valid prediction for GeneMark_model.5039_t
Valid prediction for Augustus_model.g2109.t1
Valid prediction for snap_scaffold_2-snap.91-T1
Valid prediction for GeneMark_model.5035_t
Valid prediction for GlimmerHMM_glimmerT_3121-T1
Valid prediction for snap_scaffold_2-snap.128-T1
Valid prediction for Augustus_model.g2111.t1
Couldn't classify 93348, 93620
Sorry, prediction pasa_asmbl_22829.p1 fails validation.
(CAG)	 GA	93348-93620	GT	AGG
(GAT)	 AG	94025-94225	GT	GGG
(GAC)	 AG	94583-94690	GT	ATG
(CGG)	 AG	95937-96108	GT	CGG
(GCC)	 AG	97297-97511	GT	AGG
(TTA)	 AG	97811-98555	GT	TGG
(CTT)	 AG	98811-98956	GT	AGG
(GAG)	 AG	99075-99279	GT	AGG
(CAG)	 AG	99588-99725	GT	CAG
(TGG)	 AG	99946-100079	GT	TGG
(GTG)	 AG	100328-100435	GT	CTG
(CAG)	 AG	101517-101700	GT	GGG
(CAG)	 AG	102296-102372	GT	AGG
(GAC)	 AG	102710-102865	GT	AGG
(GGC)	 AG	103132-103283	GT	AAG
(AAT)	 AG	103520-103700	AT	GAA
-recovered pasa_asmbl_22829.p1, terminal, 103520, 103700
-recovered pasa_asmbl_22829.p1, internal, 94025, 94225
-recovered pasa_asmbl_22829.p1, internal, 94583, 94690
-recovered pasa_asmbl_22829.p1, internal, 95937, 96108
-recovered pasa_asmbl_22829.p1, internal, 97297, 97511
-recovered pasa_asmbl_22829.p1, internal, 97811, 98555
-recovered pasa_asmbl_22829.p1, internal, 98811, 98956
-recovered pasa_asmbl_22829.p1, internal, 99075, 99279
-recovered pasa_asmbl_22829.p1, internal, 99588, 99725
-recovered pasa_asmbl_22829.p1, internal, 99946, 100079
-recovered pasa_asmbl_22829.p1, internal, 100328, 100435
-recovered pasa_asmbl_22829.p1, internal, 101517, 101700
-recovered pasa_asmbl_22829.p1, internal, 102296, 102372
-recovered pasa_asmbl_22829.p1, internal, 102710, 102865
-recovered pasa_asmbl_22829.p1, internal, 103132, 103283

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 16639, rend_intergenic: 13136  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41855, rend_intergenic: 26801  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47600, rend_intergenic: 42900  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50520, rend_intergenic: 49948  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57392, rend_intergenic: 50546  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74624, rend_intergenic: 58397  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82518, rend_intergenic: 76351  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85837, rend_intergenic: 84364  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91366, rend_intergenic: 90194  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98753, rend_intergenic: 92810  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125255, rend_intergenic: 104693  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129382, rend_intergenic: 127945  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152598, rend_intergenic: 149420  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162212, rend_intergenic: 159367  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173535, rend_intergenic: 171680  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181635, rend_intergenic: 177670  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187550, rend_intergenic: 182994  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 56157, rend_intergenic: 56154  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 205656
-exon list size: 707


building trellis

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76.9    
77.0    
77.2    
77.3    
77.4    
77.6    
77.7    
77.9    
78.0    
78.1    
78.3    
78.4    
78.6    
78.7    
78.8    
79.0    
79.1    
79.3    
79.4    
79.5    
79.7    
79.8    
80.0    
80.1    
80.3    
80.4    
80.5    
80.7    
80.8    
81.0    
81.1    
81.2    
81.4    
81.5    
81.7    
81.8    
81.9    
82.1    
82.2    
82.4    
82.5    
82.7    
82.8    
82.9    
83.1    
83.2    
83.4    
83.5    
83.6    
83.8    
83.9    
84.1    
84.2    
84.3    
84.5    
84.6    
84.8    
84.9    
85.0    
85.2    
85.3    
85.5    
85.6    
85.8    
85.9    
86.0    
86.2    
86.3    
86.5    
86.6    
86.7    
86.9    
87.0    
87.2    
87.3    
87.4    
87.6    
87.7    
87.9    
88.0    
88.2    
88.3    
88.4    
88.6    
88.7    
88.9    
89.0    
89.1    
89.3    
89.4    
89.6    
89.7    
89.8    
90.0    
90.1    
90.3    
90.4    
90.6    
90.7    
90.8    
91.0    
91.1    
91.3    
91.4    
91.5    
91.7    
91.8    
92.0    
92.1    
92.2    
92.4    
92.5    
92.7    
92.8    
92.9    
93.1    
93.2    
93.4    
93.5    
93.7    
93.8    
93.9    
94.1    
94.2    
94.4    
94.5    
94.6    
94.8    
94.9    
95.1    
95.2    
95.3    
95.5    
95.6    
95.8    
95.9    
96.1    
96.2    
96.3    
96.5    
96.6    
96.8    
96.9    
97.0    
97.2    
97.3    
97.5    
97.6    
97.7    
97.9    
98.0    
98.2    
98.3    
98.4    
98.6    
98.7    
98.9    
99.0    
99.2    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 47 predictions from path traversal
Error with prediction: snap lend_intergenic: 16639, rend_intergenic: 13136  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41855, rend_intergenic: 26801  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47600, rend_intergenic: 42900  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50520, rend_intergenic: 49948  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57392, rend_intergenic: 50546  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74624, rend_intergenic: 58397  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82518, rend_intergenic: 76351  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85837, rend_intergenic: 84364  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91366, rend_intergenic: 90194  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98753, rend_intergenic: 92810  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125255, rend_intergenic: 104693  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129382, rend_intergenic: 127945  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152598, rend_intergenic: 149420  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162212, rend_intergenic: 159367  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173535, rend_intergenic: 171680  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181635, rend_intergenic: 177670  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187550, rend_intergenic: 182994  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 56157, rend_intergenic: 56154  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 25 predictions persist after filtering for low support