-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_2/scaffold_2_10158837-10353981

-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.2049-T1
Valid prediction for GeneMark_model.7200_t
Valid prediction for GlimmerHMM_glimmerT_4496-T1
Valid prediction for GeneMark_model.7197_t
Valid prediction for GlimmerHMM_glimmerT_4511-T1
Valid prediction for GlimmerHMM_glimmerT_4512-T1
Valid prediction for GeneMark_model.7221_t
Valid prediction for GlimmerHMM_glimmerT_4507-T1
Valid prediction for GeneMark_model.7217_t
Valid prediction for GeneMark_model.7215_t
Valid prediction for snap_scaffold_2-snap.2043-T1
Valid prediction for snap_scaffold_2-snap.2035-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GeneMark_model.7219_t
Valid prediction for snap_scaffold_2-snap.2047-T1
Valid prediction for snap_scaffold_2-snap.2033-T1
Valid prediction for snap_scaffold_2-snap.2052-T1
Valid prediction for snap_scaffold_2-snap.2041-T1
Valid prediction for GeneMark_model.7213_t
Valid prediction for GlimmerHMM_glimmerT_4499-T1
Valid prediction for snap_scaffold_2-snap.2039-T1
Valid prediction for GeneMark_model.7225_t
Valid prediction for snap_scaffold_2-snap.2026-T1
Valid prediction for snap_scaffold_2-snap.2027-T1
Valid prediction for GeneMark_model.7223_t
Valid prediction for snap_scaffold_2-snap.2060-T1
Valid prediction for GeneMark_model.7233_t
Valid prediction for GlimmerHMM_glimmerT_4497-T1
Valid prediction for snap_scaffold_2-snap.2032-T1
Valid prediction for snap_scaffold_2-snap.2030-T1
Valid prediction for snap_scaffold_2-snap.2028-T1
Valid prediction for GeneMark_model.7232_t
Valid prediction for GeneMark_model.7240_t
Valid prediction for GeneMark_model.7230_t
Valid prediction for GeneMark_model.7204_t
Valid prediction for snap_scaffold_2-snap.2037-T1
Valid prediction for GeneMark_model.7242_t
Valid prediction for GeneMark_model.7228_t
Valid prediction for Augustus_model.g3016.t1
Valid prediction for snap_scaffold_2-snap.2057-T1
Valid prediction for GeneMark_model.7198_t
Valid prediction for GeneMark_model.7206_t
Valid prediction for GeneMark_model.7216_t
Valid prediction for GeneMark_model.7195_t
Valid prediction for snap_scaffold_2-snap.2029-T1
Valid prediction for Augustus_model.g3023.t1
Valid prediction for GeneMark_model.7192_t
Valid prediction for snap_scaffold_2-snap.2054-T1
Valid prediction for snap_scaffold_2-snap.2050-T1
Valid prediction for GlimmerHMM_glimmerT_4505-T1
Valid prediction for GeneMark_model.7190_t
Valid prediction for GeneMark_model.7210_t
Valid prediction for GeneMark_model.7238_t
Valid prediction for snap_scaffold_2-snap.2058-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.7193_t
Valid prediction for GeneMark_model.7227_t
Valid prediction for GeneMark_model.7218_t
Valid prediction for Augustus_model.g3021.t1
Valid prediction for Augustus_model.g3017.t1
Valid prediction for GlimmerHMM_glimmerT_4509-T1
Valid prediction for GeneMark_model.7214_t
Valid prediction for Augustus_model.g3020.t1
Valid prediction for GeneMark_model.7220_t
Valid prediction for snap_scaffold_2-snap.2023-T1
Valid prediction for GlimmerHMM_glimmerT_4502-T1
Valid prediction for GlimmerHMM_glimmerT_4508-T1
Valid prediction for snap_scaffold_2-snap.2040-T1
Valid prediction for GeneMark_model.7212_t
Valid prediction for snap_scaffold_2-snap.2059-T1
Valid prediction for GeneMark_model.7226_t
Valid prediction for Augustus_model.g3027.t1
Valid prediction for snap_scaffold_2-snap.2051-T1
Valid prediction for GlimmerHMM_glimmerT_4514-T1
Valid prediction for GeneMark_model.7191_t
Valid prediction for GlimmerHMM_glimmerT_4513-T1
Valid prediction for GeneMark_model.7237_t
Valid prediction for Augustus_model.g3015.t1
Valid prediction for GeneMark_model.7207_t
Valid prediction for GeneMark_model.7203_t
Valid prediction for GeneMark_model.7208_t
Valid prediction for GeneMark_model.7231_t
Valid prediction for GeneMark_model.7234_t
Valid prediction for GeneMark_model.7209_t
Valid prediction for Augustus_model.g3022.t1
Valid prediction for snap_scaffold_2-snap.2053-T1
Valid prediction for Augustus_model.g3019.t1
Valid prediction for GeneMark_model.7196_t
Valid prediction for snap_scaffold_2-snap.2038-T1
Valid prediction for snap_scaffold_2-snap.2056-T1
Valid prediction for snap_scaffold_2-snap.2045-T1
Valid prediction for snap_scaffold_2-snap.2044-T1
Valid prediction for snap_scaffold_2-snap.2046-T1
Valid prediction for snap_scaffold_2-snap.2055-T1
Valid prediction for snap_scaffold_2-snap.2062-T1
Valid prediction for snap_scaffold_2-snap.2042-T1
Valid prediction for snap_scaffold_2-snap.2034-T1
Valid prediction for GlimmerHMM_glimmerT_4501-T1
Valid prediction for GlimmerHMM_glimmerT_4495-T1
Valid prediction for snap_scaffold_2-snap.2024-T1
Valid prediction for Augustus_model.g3024.t1
Valid prediction for Augustus_model.g3026.t1
Valid prediction for GlimmerHMM_glimmerT_4516-T1
Valid prediction for GlimmerHMM_glimmerT_4506-T1
Valid prediction for GlimmerHMM_glimmerT_4494-T1
Valid prediction for snap_scaffold_2-snap.2025-T1
Valid prediction for GlimmerHMM_glimmerT_4504-T1
Valid prediction for GeneMark_model.7236_t
Valid prediction for GlimmerHMM_glimmerT_4500-T1
Valid prediction for GlimmerHMM_glimmerT_4498-T1
Valid prediction for GeneMark_model.7224_t
Valid prediction for GlimmerHMM_glimmerT_4503-T1
Couldn't classify 175113, 175331
Sorry, prediction pasa_asmbl_23420.p1 fails validation.
(TGC)	 AG	175113-175331	GT	ATG
(GGC)	 AG	176481-176573	GT	AGG
(GCA)	 AG	178966-179077	GT	AGG
(ACC)	 AG	180002-180063	GT	AGG
(GAC)	 AG	180251-180580	GT	AGG
(ATG)	 AG	181411-181478	GT	AGG
(CTG)	 AG	181775-181849	GT	TGG
(GTC)	 AG	182755-182815	GT	AGG
(AAT)	 AG	183571-183706	GT	GAG
(GGA)	 AG	185307-185442	GT	AAG
(GAT)	 AG	185593-185721	GT	AGG
(AGA)	 AG	185897-186047	GT	AGG
(GAG)	 AG	186980-187091	GT	ACG
(GCT)	 AG	187259-187347	GT	TGG
(AAT)	 AG	187620-187742	GT	AGG
(AAC)	 AG	187905-188030	GT	TCG
(ATC)	 AG	188383-188571	GT	AGG
(CCT)	 AG	189225-189413	AC	GAA
-recovered pasa_asmbl_23420.p1, initial, 181411, 181478
add_exon() Sorry, pasa_asmbl_23420.p1 183571-183706-terminal-3 is invalid.
-recovered pasa_asmbl_23420.p1, terminal, 183571, 183706
-recovered pasa_asmbl_23420.p1, terminal, 189225, 189413
-recovered pasa_asmbl_23420.p1, internal, 175113, 175331
-recovered pasa_asmbl_23420.p1, internal, 176481, 176573
-recovered pasa_asmbl_23420.p1, internal, 178966, 179077
-recovered pasa_asmbl_23420.p1, internal, 180002, 180063
-recovered pasa_asmbl_23420.p1, internal, 180251, 180580
-recovered pasa_asmbl_23420.p1, internal, 181411, 181478
-recovered pasa_asmbl_23420.p1, internal, 181775, 181849
-recovered pasa_asmbl_23420.p1, internal, 182755, 182815
-recovered pasa_asmbl_23420.p1, internal, 183571, 183706
-recovered pasa_asmbl_23420.p1, internal, 185307, 185442
-recovered pasa_asmbl_23420.p1, internal, 185593, 185721
-recovered pasa_asmbl_23420.p1, internal, 185897, 186047
-recovered pasa_asmbl_23420.p1, internal, 186980, 187091
-recovered pasa_asmbl_23420.p1, internal, 187259, 187347
-recovered pasa_asmbl_23420.p1, internal, 187620, 187742
-recovered pasa_asmbl_23420.p1, internal, 187905, 188030
-recovered pasa_asmbl_23420.p1, internal, 188383, 188571
Valid prediction for Augustus_model.g3014.t1
Valid prediction for GlimmerHMM_glimmerT_4510-T1
Valid prediction for GeneMark_model.7241_t
Valid prediction for snap_scaffold_2-snap.2036-T1
Valid prediction for snap_scaffold_2-snap.2031-T1
Valid prediction for Augustus_model.g3018.t1
Valid prediction for GeneMark_model.7202_t
Valid prediction for GeneMark_model.7189_t
Valid prediction for GeneMark_model.7222_t
Valid prediction for GeneMark_model.7239_t
Valid prediction for GeneMark_model.7229_t
Couldn't classify 137558, 137606
Couldn't classify 138565, 138951
Sorry, prediction pasa_asmbl_23423.p1 fails validation.
(GCT)	 AC	137558-137606	GT	GGG
(ATT)	 AG	137934-138229	GT	AGG
(GTG)	 AG	138565-138951	CA	GTC
-recovered pasa_asmbl_23423.p1, internal, 137934, 138229
Valid prediction for snap_scaffold_2-snap.2048-T1
Valid prediction for GeneMark_model.7235_t
Valid prediction for GeneMark_model.7194_t
Valid prediction for GeneMark_model.7211_t
Couldn't classify 99254, 99407
Couldn't classify 99633, 99832
Sorry, prediction pasa_asmbl_23979.p2 fails validation.
(ATC)	 CC	99254-99407	GT	TCG
(CCA)	 AG	99633-99832	GA	AGG
Valid prediction for GeneMark_model.7199_t
Valid prediction for GeneMark_model.7205_t
Valid prediction for GeneMark_model.7201_t
Valid prediction for GlimmerHMM_glimmerT_4515-T1
Valid prediction for snap_scaffold_2-snap.2061-T1
Valid prediction for Augustus_model.g3025.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 36533, rend_intergenic: 6794  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40052, rend_intergenic: 37050  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46720, rend_intergenic: 41837  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59041, rend_intergenic: 56087  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63810, rend_intergenic: 63260  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67951, rend_intergenic: 64423  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80367, rend_intergenic: 79156  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95575, rend_intergenic: 89363  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102764, rend_intergenic: 100978  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121015, rend_intergenic: 103625  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153050, rend_intergenic: 150552  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154231, rend_intergenic: 153272  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167360, rend_intergenic: 162030  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168631, rend_intergenic: 167434  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 195145
-exon list size: 684


building trellis

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92.1    
92.3    
92.4    
92.6    
92.7    
92.9    
93.0    
93.1    
93.3    
93.4    
93.6    
93.7    
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    
95.8    
95.9    
96.1    
96.2    
96.4    
96.5    
96.6    
96.8    
96.9    
97.1    
97.2    
97.4    
97.5    
97.7    
97.8    
98.0    
98.1    
98.3    
98.4    
98.5    
98.7    
98.8    
99.0    
99.1    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 23 predictions from path traversal
Error with prediction: snap lend_intergenic: 36533, rend_intergenic: 6794  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40052, rend_intergenic: 37050  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46720, rend_intergenic: 41837  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59041, rend_intergenic: 56087  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63810, rend_intergenic: 63260  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67951, rend_intergenic: 64423  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80367, rend_intergenic: 79156  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95575, rend_intergenic: 89363  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102764, rend_intergenic: 100978  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121015, rend_intergenic: 103625  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153050, rend_intergenic: 150552  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154231, rend_intergenic: 153272  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167360, rend_intergenic: 162030  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168631, rend_intergenic: 167434  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 15 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 181878 - 195145
-exon list size: 10


building trellis

8.3    
16.7    
25.0    
33.3    
41.7    
50.0    
58.3    
66.7    
75.0    
83.3    
91.7    
-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

-building DP trellis

-building trellis in range 184616 - 195145
-exon list size: 7


building trellis

11.1    
22.2    
33.3    
44.4    
55.6    
66.7    
77.8    
88.9    
-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