-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_13/scaffold_13_9930674-10162586

-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 Augustus_model.g22123.t1
Valid prediction for CodingQuarry_transcript_13188-T1
Valid prediction for GlimmerHMM_glimmerT_32921-T1
Valid prediction for snap_scaffold_13-snap.1809-T1
Valid prediction for GeneMark_model.56165_t
Valid prediction for GeneMark_model.56148_t
Valid prediction for HiQ_model.g22122.t1
Valid prediction for Augustus_model.g22117.t1
Valid prediction for CodingQuarry_transcript_13189-T1
Valid prediction for snap_scaffold_13-snap.1828-T1
Valid prediction for snap_scaffold_13-snap.1815-T1
Valid prediction for GeneMark_model.56178_t
Valid prediction for GlimmerHMM_glimmerT_32938-T1
Valid prediction for GlimmerHMM_glimmerT_32934-T1
Valid prediction for GeneMark_model.56163_t
Valid prediction for GlimmerHMM_glimmerT_32942-T1
Valid prediction for snap_scaffold_13-snap.1807-T1
Valid prediction for snap_scaffold_13-snap.1838-T1
Valid prediction for snap_scaffold_13-snap.1825-T1
Couldn't classify 23421, 23485
Sorry, prediction pasa_asmbl_11204.p1 fails validation.
(GGG)	 TG	23421-23485	GT	AGG
(AAT)	 AG	23649-23719	GT	TGG
(GCC)	 AG	25516-25812	GT	AGG
(GCA)	 AG	25913-25977	GA	GAG
-recovered pasa_asmbl_11204.p1, terminal, 25913, 25977
-recovered pasa_asmbl_11204.p1, internal, 23649, 23719
-recovered pasa_asmbl_11204.p1, internal, 25516, 25812
Couldn't classify 23260, 23336
Sorry, prediction pasa_asmbl_11201.p1 fails validation.
(ATG)	 TC	21707-21771	GT	GCG
(ATA)	 AG	21887-21996	GT	TGG
(CCA)	 AG	22245-22310	GT	TGG
(GAG)	 AG	22461-22571	GT	CGG
(GCA)	 AG	23001-23144	GT	AGG
(GCT)	 AG	23260-23336	AG	GGA
-recovered pasa_asmbl_11201.p1, initial, 21707, 21771
-recovered pasa_asmbl_11201.p1, internal, 21887, 21996
-recovered pasa_asmbl_11201.p1, internal, 22245, 22310
-recovered pasa_asmbl_11201.p1, internal, 22461, 22571
-recovered pasa_asmbl_11201.p1, internal, 23001, 23144
Valid prediction for HiQ_model.g22109.t1
Valid prediction for snap_scaffold_13-snap.1823-T1
Valid prediction for Augustus_model.g22121.t1
Valid prediction for Augustus_model.g22119.t1
Valid prediction for GlimmerHMM_glimmerT_32941-T1
Valid prediction for Augustus_model.g22112.t1
Valid prediction for GeneMark_model.56160_t
Valid prediction for snap_scaffold_13-snap.1847-T1
Valid prediction for GlimmerHMM_glimmerT_32928-T1
Valid prediction for HiQ_model.g22131.t1
Valid prediction for GeneMark_model.56167_t
Valid prediction for snap_scaffold_13-snap.1836-T1
Valid prediction for GeneMark_model.56150_t
Valid prediction for GlimmerHMM_glimmerT_32919-T1
Valid prediction for GeneMark_model.56152_t
Valid prediction for snap_scaffold_13-snap.1822-T1
Valid prediction for snap_scaffold_13-snap.1848-T1
Valid prediction for GlimmerHMM_glimmerT_32943-T1
Valid prediction for GeneMark_model.56158_t
Valid prediction for GlimmerHMM_glimmerT_32918-T1
Valid prediction for snap_scaffold_13-snap.1845-T1
Valid prediction for pasa_asmbl_11217.p1
Valid prediction for snap_scaffold_13-snap.1830-T1
Couldn't classify 206808, 206857
Sorry, prediction pasa_asmbl_11219.p1 fails validation.
(TCA)	 TC	206808-206857	GT	ATG
(GCC)	 AG	207860-207972	GT	AGG
(AGT)	 AG	208158-208237	GT	AGG
(CCA)	 AG	208339-208401	GT	AGG
(GCT)	 AG	208566-208763	GT	CGG
(TGG)	 AG	209334-209495	GT	AGG
(GCC)	 AG	209647-209781	GT	TGG
(ATT)	 AG	209999-210099	GT	CGG
(GGA)	 AG	210442-210508	GT	AGG
(GAG)	 AG	210650-210814	CT	AAC
-recovered pasa_asmbl_11219.p1, terminal, 210650, 210814
-recovered pasa_asmbl_11219.p1, internal, 207860, 207972
-recovered pasa_asmbl_11219.p1, internal, 208158, 208237
-recovered pasa_asmbl_11219.p1, internal, 208339, 208401
-recovered pasa_asmbl_11219.p1, internal, 208566, 208763
-recovered pasa_asmbl_11219.p1, internal, 209334, 209495
-recovered pasa_asmbl_11219.p1, internal, 209647, 209781
-recovered pasa_asmbl_11219.p1, internal, 209999, 210099
-recovered pasa_asmbl_11219.p1, internal, 210442, 210508
Valid prediction for snap_scaffold_13-snap.1852-T1
Valid prediction for GlimmerHMM_glimmerT_32932-T1
Valid prediction for GeneMark_model.56171_t
Valid prediction for GeneMark_model.56187_t
Valid prediction for snap_scaffold_13-snap.1821-T1
Valid prediction for snap_scaffold_13-snap.1820-T1
Valid prediction for GlimmerHMM_glimmerT_32931-T1
Valid prediction for snap_scaffold_13-snap.1816-T1
Valid prediction for snap_scaffold_13-snap.1814-T1
Valid prediction for snap_scaffold_13-snap.1827-T1
Valid prediction for snap_scaffold_13-snap.1824-T1
Valid prediction for GeneMark_model.56175_t
Valid prediction for HiQ_model.g22114.t1
Valid prediction for snap_scaffold_13-snap.1833-T1
Valid prediction for CodingQuarry_transcript_13190-T1
Valid prediction for snap_scaffold_13-snap.1849-T1
Valid prediction for pasa_asmbl_11213.p1
Valid prediction for Augustus_model.g22116.t1
Valid prediction for GlimmerHMM_glimmerT_32926-T1
Valid prediction for HiQ_model.g22130.t1
Valid prediction for Augustus_model.g22107.t1
Valid prediction for GeneMark_model.56179_t
Valid prediction for CodingQuarry_transcript_13185-T1
Valid prediction for snap_scaffold_13-snap.1839-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_13-snap.1810-T1
Valid prediction for snap_scaffold_13-snap.1842-T1
Valid prediction for GlimmerHMM_glimmerT_32925-T1
Valid prediction for pasa_asmbl_11215.p1
Valid prediction for GlimmerHMM_glimmerT_32924-T1
Valid prediction for GlimmerHMM_glimmerT_32930-T1
Valid prediction for snap_scaffold_13-snap.1851-T1
Valid prediction for GlimmerHMM_glimmerT_32935-T1
Valid prediction for GlimmerHMM_glimmerT_32929-T1
Couldn't classify 58521, 58638
Sorry, prediction pasa_asmbl_11208.p1 fails validation.
(ATG)	 CA	56694-56952	GT	CGG
(CGA)	 AG	57333-57562	GT	GGG
(ACC)	 AG	57655-57753	GT	AGG
(GAC)	 AG	57932-58077	GT	CGG
(GAA)	 AG	58213-58344	GT	ACG
(AAT)	 AG	58521-58638	TA	AGT
-recovered pasa_asmbl_11208.p1, initial, 56694, 56952
-recovered pasa_asmbl_11208.p1, internal, 57333, 57562
-recovered pasa_asmbl_11208.p1, internal, 57655, 57753
-recovered pasa_asmbl_11208.p1, internal, 57932, 58077
-recovered pasa_asmbl_11208.p1, internal, 58213, 58344
Valid prediction for GeneMark_model.56147_t
Valid prediction for snap_scaffold_13-snap.1806-T1
Valid prediction for GeneMark_model.56185_t
Valid prediction for GeneMark_model.56151_t
Valid prediction for HiQ_model.g22120.t1
Valid prediction for Augustus_model.g22126.t1
Valid prediction for snap_scaffold_13-snap.1846-T1
Valid prediction for GeneMark_model.56157_t
Valid prediction for GeneMark_model.56159_t
Valid prediction for GeneMark_model.56161_t
Valid prediction for GeneMark_model.56177_t
Valid prediction for Augustus_model.g22129.t1
Valid prediction for snap_scaffold_13-snap.1829-T1
Valid prediction for snap_scaffold_13-snap.1834-T1
Valid prediction for snap_scaffold_13-snap.1817-T1
Valid prediction for Augustus_model.g22118.t1
Valid prediction for GlimmerHMM_glimmerT_32933-T1
Valid prediction for Augustus_model.g22111.t1
Valid prediction for GeneMark_model.56181_t
Valid prediction for GlimmerHMM_glimmerT_32940-T1
Valid prediction for snap_scaffold_13-snap.1843-T1
Valid prediction for HiQ_model.g22113.t1
Valid prediction for GeneMark_model.56183_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 GlimmerHMM_glimmerT_32922-T1
Valid prediction for GeneMark_model.56168_t
Valid prediction for GeneMark_model.56156_t
Valid prediction for GlimmerHMM_glimmerT_32936-T1
Valid prediction for Augustus_model.g22132.t1
Valid prediction for GeneMark_model.56186_t
Valid prediction for Augustus_model.g22125.t1
Valid prediction for GeneMark_model.56182_t
Valid prediction for Augustus_model.g22110.t1
Valid prediction for GlimmerHMM_glimmerT_32937-T1
Valid prediction for GeneMark_model.56164_t
Valid prediction for snap_scaffold_13-snap.1819-T1
Valid prediction for CodingQuarry_transcript_13187-T1
Valid prediction for GeneMark_model.56176_t
Valid prediction for snap_scaffold_13-snap.1812-T1
Valid prediction for snap_scaffold_13-snap.1831-T1
Valid prediction for GeneMark_model.56172_t
Valid prediction for GeneMark_model.56149_t
Valid prediction for GeneMark_model.56155_t
Valid prediction for GlimmerHMM_glimmerT_32923-T1
Valid prediction for snap_scaffold_13-snap.1826-T1
Valid prediction for GlimmerHMM_glimmerT_32927-T1
Valid prediction for Augustus_model.g22108.t1
Valid prediction for pasa_asmbl_10008.p1
Valid prediction for snap_scaffold_13-snap.1818-T1
Valid prediction for Augustus_model.g22127.t1
Valid prediction for snap_scaffold_13-snap.1837-T1
Valid prediction for GlimmerHMM_glimmerT_32920-T1
Valid prediction for GeneMark_model.56166_t
Valid prediction for CodingQuarry_transcript_13186-T1
Valid prediction for GeneMark_model.56170_t
Valid prediction for Augustus_model.g22115.t1
Valid prediction for snap_scaffold_13-snap.1835-T1
Valid prediction for GeneMark_model.56173_t
Valid prediction for snap_scaffold_13-snap.1813-T1
Valid prediction for GeneMark_model.56188_t
Valid prediction for snap_scaffold_13-snap.1808-T1
Valid prediction for GeneMark_model.56154_t
Valid prediction for GeneMark_model.56174_t
Valid prediction for GeneMark_model.56146_t
Valid prediction for GeneMark_model.56184_t
Valid prediction for GeneMark_model.56169_t
Valid prediction for GeneMark_model.56162_t
Valid prediction for snap_scaffold_13-snap.1840-T1
Couldn't classify 163014, 163127
Sorry, prediction GeneMark_model.56153_t fails validation.
(CCC)	 AG	163014-163127	GT	AGG
(GCA)	 AG	163782-163794	GT	GAG
(AAA)	 AG	163820-163947	GT	AGG
(GCC)	 AG	164285-164990	GT	GAG
(TGA)	 AG	165544-165613	TT	GAT
-recovered GeneMark_model.56153_t, terminal, 165544, 165613
-recovered GeneMark_model.56153_t, internal, 163014, 163127
-recovered GeneMark_model.56153_t, internal, 163782, 163794
-recovered GeneMark_model.56153_t, internal, 163820, 163947
-recovered GeneMark_model.56153_t, internal, 164285, 164990
Valid prediction for GeneMark_model.56180_t
Valid prediction for snap_scaffold_13-snap.1844-T1
Valid prediction for GlimmerHMM_glimmerT_32939-T1
Valid prediction for snap_scaffold_13-snap.1811-T1
Valid prediction for snap_scaffold_13-snap.1832-T1
Valid prediction for snap_scaffold_13-snap.1841-T1
Valid prediction for Augustus_model.g22128.t1
Valid prediction for Augustus_model.g22124.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 112431, rend_intergenic: 108535  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136301, rend_intergenic: 133649  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145397, rend_intergenic: 138154  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146640, rend_intergenic: 145799  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149934, rend_intergenic: 147123  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151203, rend_intergenic: 150907  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166867, rend_intergenic: 151521  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173262, rend_intergenic: 170331  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 231913
-exon list size: 693


building trellis

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83.0    
83.2    
83.3    
83.5    
83.6    
83.7    
83.9    
84.0    
84.2    
84.3    
84.5    
84.6    
84.7    
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    
86.8    
86.9    
87.1    
87.2    
87.3    
87.5    
87.6    
87.8    
87.9    
88.1    
88.2    
88.3    
88.5    
88.6    
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    
91.4    
91.5    
91.7    
91.8    
91.9    
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    
94.0    
94.1    
94.2    
94.4    
94.5    
94.7    
94.8    
95.0    
95.1    
95.3    
95.4    
95.5    
95.7    
95.8    
96.0    
96.1    
96.3    
96.4    
96.5    
96.7    
96.8    
97.0    
97.1    
97.3    
97.4    
97.6    
97.7    
97.8    
98.0    
98.1    
98.3    
98.4    
98.6    
98.7    
98.8    
99.0    
99.1    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 112431, rend_intergenic: 108535  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136301, rend_intergenic: 133649  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145397, rend_intergenic: 138154  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146640, rend_intergenic: 145799  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149934, rend_intergenic: 147123  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151203, rend_intergenic: 150907  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166867, rend_intergenic: 151521  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173262, rend_intergenic: 170331  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.
GOT 5prime partial gene.

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