-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_10/scaffold_10_1738580-1944013

-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.42192_t
Valid prediction for GlimmerHMM_glimmerT_24697-T1
Valid prediction for GeneMark_model.42194_t
Valid prediction for snap_scaffold_10-snap.404-T1
Valid prediction for GlimmerHMM_glimmerT_24700-T1
Valid prediction for GeneMark_model.42159_t
Valid prediction for snap_scaffold_10-snap.402-T1
Valid prediction for GlimmerHMM_glimmerT_24710-T1
Valid prediction for Augustus_model.g16566.t1
Valid prediction for GeneMark_model.42168_t
Valid prediction for HiQ_model.g16567.t1
Valid prediction for Augustus_model.g16569.t1
Valid prediction for GeneMark_model.42179_t
Valid prediction for GeneMark_model.42154_t
Valid prediction for GeneMark_model.42180_t
Valid prediction for snap_scaffold_10-snap.387-T1
Valid prediction for GlimmerHMM_glimmerT_24701-T1
Valid prediction for snap_scaffold_10-snap.389-T1
Valid prediction for Augustus_model.g16560.t1
Valid prediction for GeneMark_model.42187_t
Valid prediction for Augustus_model.g16565.t1
Valid prediction for Augustus_model.g16561.t1
Valid prediction for GeneMark_model.42156_t
Valid prediction for GlimmerHMM_glimmerT_24715-T1
Couldn't classify 122856, 123062
Couldn't classify 123186, 123326
Sorry, prediction pasa_asmbl_5132.p1 fails validation.
(AGG)	 GC	122856-123062	GT	AGG
(GCA)	 AG	123186-123326	AA	CCA
Valid prediction for GlimmerHMM_glimmerT_24699-T1
Valid prediction for snap_scaffold_10-snap.396-T1
Valid prediction for snap_scaffold_10-snap.400-T1
Valid prediction for Augustus_model.g16556.t1
Valid prediction for snap_scaffold_10-snap.377-T1
Valid prediction for GlimmerHMM_glimmerT_24705-T1
Valid prediction for snap_scaffold_10-snap.392-T1
Valid prediction for snap_scaffold_10-snap.393-T1
Couldn't classify 32663, 32767
Sorry, prediction pasa_asmbl_4237.p1 fails validation.
(ATG)	 CC	30042-30159	GT	CGG
(AAT)	 AG	30527-30544	GT	AGG
(GTA)	 AG	30657-30739	GT	TTG
(GTG)	 AG	32663-32767	GT	AGG
-recovered pasa_asmbl_4237.p1, initial, 30042, 30159
-recovered pasa_asmbl_4237.p1, internal, 30527, 30544
-recovered pasa_asmbl_4237.p1, internal, 30657, 30739
-recovered pasa_asmbl_4237.p1, internal, 32663, 32767
Couldn't classify 52607, 52724
Sorry, prediction pasa_asmbl_5102.p1 fails validation.
(ATG)	 AG	48860-48948	GT	GTG
(GTC)	 AG	49292-49394	GT	AGG
(ACC)	 AG	49518-49649	GT	CTG
(ATG)	 AG	49980-50099	GT	AGG
(GGA)	 AG	50321-50539	GT	AGG
(AGG)	 AG	50716-51051	GT	TGG
(ACC)	 AG	51274-51494	GT	TGG
(CAT)	 AG	51580-51782	GT	ATG
(GTT)	 AG	51977-52062	GT	TGG
(AGT)	 AG	52156-52289	GT	AGG
(TGT)	 AG	52607-52724	GT	CGG
-recovered pasa_asmbl_5102.p1, initial, 48860, 48948
-recovered pasa_asmbl_5102.p1, initial, 49980, 50099
-recovered pasa_asmbl_5102.p1, internal, 48860, 48948
-recovered pasa_asmbl_5102.p1, internal, 49292, 49394
-recovered pasa_asmbl_5102.p1, internal, 49518, 49649
-recovered pasa_asmbl_5102.p1, internal, 49980, 50099
-recovered pasa_asmbl_5102.p1, internal, 50321, 50539
-recovered pasa_asmbl_5102.p1, internal, 50716, 51051
-recovered pasa_asmbl_5102.p1, internal, 51274, 51494
-recovered pasa_asmbl_5102.p1, internal, 51580, 51782
-recovered pasa_asmbl_5102.p1, internal, 51977, 52062
-recovered pasa_asmbl_5102.p1, internal, 52156, 52289
-recovered pasa_asmbl_5102.p1, internal, 52607, 52724
Valid prediction for GeneMark_model.42176_t
Valid prediction for GeneMark_model.42153_t
Valid prediction for GeneMark_model.42177_t
Valid prediction for GeneMark_model.42189_t
Couldn't classify 43663, 43743
Couldn't classify 44387, 44553
Sorry, prediction pasa_asmbl_4239.p1 fails validation.
(TCA)	 AG	43663-43743	GT	CTG
(GGT)	 AG	43902-44199	GT	GGG
(GCC)	 AG	44387-44553	GT	GGG
-recovered pasa_asmbl_4239.p1, internal, 43663, 43743
-recovered pasa_asmbl_4239.p1, internal, 43902, 44199
-recovered pasa_asmbl_4239.p1, internal, 44387, 44553
Valid prediction for GeneMark_model.42161_t
Valid prediction for Augustus_model.g16570.t1
Valid prediction for GlimmerHMM_glimmerT_24709-T1
Valid prediction for snap_scaffold_10-snap.398-T1
Valid prediction for GlimmerHMM_glimmerT_24706-T1
Valid prediction for GlimmerHMM_glimmerT_24711-T1
Valid prediction for Augustus_model.g16558.t1
Valid prediction for Augustus_model.g16562.t1
Valid prediction for GlimmerHMM_glimmerT_24698-T1
Valid prediction for Augustus_model.g16559.t1
Valid prediction for GeneMark_model.42195_t
Valid prediction for snap_scaffold_10-snap.373-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for snap_scaffold_10-snap.382-T1
Valid prediction for GlimmerHMM_glimmerT_24712-T1
Valid prediction for Augustus_model.g16568.t1
Valid prediction for GlimmerHMM_glimmerT_24703-T1
Valid prediction for GeneMark_model.42196_t
Valid prediction for snap_scaffold_10-snap.378-T1
Valid prediction for GeneMark_model.42184_t
Valid prediction for GlimmerHMM_glimmerT_24704-T1
Valid prediction for GlimmerHMM_glimmerT_24707-T1
Valid prediction for GlimmerHMM_glimmerT_24708-T1
Valid prediction for Augustus_model.g16564.t1
Valid prediction for GeneMark_model.42174_t
Valid prediction for snap_scaffold_10-snap.397-T1
Valid prediction for GeneMark_model.42164_t
Valid prediction for GeneMark_model.42183_t
Valid prediction for snap_scaffold_10-snap.385-T1
Couldn't classify 190345, 190430
Couldn't classify 195442, 195531
Sorry, prediction pasa_asmbl_4248.p1 fails validation.
(AAA)	 TG	190345-190430	GT	AGG
(GTA)	 AG	190533-190581	GT	AGG
(TAT)	 AG	190735-190884	GT	AGG
(AAC)	 AG	193852-194028	GT	AGG
(GTG)	 AG	194354-194437	GT	AGG
(GAC)	 AG	195098-195184	GT	TGG
(ATG)	 AG	195442-195531	AC	TGA
-recovered pasa_asmbl_4248.p1, internal, 190533, 190581
-recovered pasa_asmbl_4248.p1, internal, 190735, 190884
-recovered pasa_asmbl_4248.p1, internal, 193852, 194028
-recovered pasa_asmbl_4248.p1, internal, 194354, 194437
-recovered pasa_asmbl_4248.p1, internal, 195098, 195184
Valid prediction for GeneMark_model.42149_t
Valid prediction for GlimmerHMM_glimmerT_24696-T1
Valid prediction for GeneMark_model.42186_t
Valid prediction for GeneMark_model.42172_t
Valid prediction for Augustus_model.g16557.t1
Couldn't classify 111671, 111710
Couldn't classify 113104, 113218
Sorry, prediction pasa_asmbl_4242.p1 fails validation.
(GCC)	 TG	111671-111710	GT	CAG
(ATA)	 AG	112538-112672	GT	AGG
(CCC)	 AG	112767-112872	GT	AGG
(GAT)	 AG	113104-113218	CA	CGC
add_exon() Sorry, pasa_asmbl_4242.p1 112538-112672-terminal-1 is invalid.
-recovered pasa_asmbl_4242.p1, terminal, 112538, 112672
-recovered pasa_asmbl_4242.p1, internal, 112538, 112672
-recovered pasa_asmbl_4242.p1, internal, 112767, 112872
Valid prediction for GeneMark_model.42166_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 Augustus_model.g16563.t1
Valid prediction for GlimmerHMM_glimmerT_24714-T1
Valid prediction for snap_scaffold_10-snap.375-T1
Valid prediction for GeneMark_model.42165_t
Valid prediction for GeneMark_model.42150_t
Valid prediction for snap_scaffold_10-snap.381-T1
Valid prediction for snap_scaffold_10-snap.406-T1
Valid prediction for GeneMark_model.42157_t
Valid prediction for CodingQuarry_transcript_5283-T1
Valid prediction for GlimmerHMM_glimmerT_24702-T1
Valid prediction for GeneMark_model.42160_t
Valid prediction for GeneMark_model.42147_t
Valid prediction for GeneMark_model.42158_t
Valid prediction for GeneMark_model.42178_t
Valid prediction for snap_scaffold_10-snap.388-T1
Valid prediction for snap_scaffold_10-snap.390-T1
Valid prediction for snap_scaffold_10-snap.384-T1
Valid prediction for GeneMark_model.42169_t
Valid prediction for GeneMark_model.42167_t
Valid prediction for snap_scaffold_10-snap.376-T1
Valid prediction for snap_scaffold_10-snap.374-T1
Valid prediction for GeneMark_model.42175_t
Valid prediction for GeneMark_model.42182_t
Valid prediction for GlimmerHMM_glimmerT_24692-T1
Valid prediction for Augustus_model.g16555.t1
Valid prediction for snap_scaffold_10-snap.386-T1
Valid prediction for snap_scaffold_10-snap.405-T1
Valid prediction for snap_scaffold_10-snap.379-T1
Valid prediction for snap_scaffold_10-snap.391-T1
Valid prediction for snap_scaffold_10-snap.372-T1
Couldn't classify 191554, 191643
Couldn't classify 193286, 193300
Sorry, prediction pasa_asmbl_4066.p1 fails validation.
(TTC)	 CC	191554-191643	GT	CGG
(GAG)	 AG	192112-192198	GT	AGG
(TGT)	 AG	192538-192645	GT	TGG
(CTC)	 AG	193286-193300	CC	AGC
-recovered pasa_asmbl_4066.p1, internal, 192112, 192198
-recovered pasa_asmbl_4066.p1, internal, 192538, 192645
Valid prediction for GeneMark_model.42152_t
Valid prediction for GlimmerHMM_glimmerT_24695-T1
Valid prediction for snap_scaffold_10-snap.401-T1
Valid prediction for GeneMark_model.42148_t
Valid prediction for GlimmerHMM_glimmerT_24693-T1
Valid prediction for snap_scaffold_10-snap.394-T1
Valid prediction for GlimmerHMM_glimmerT_24694-T1
Valid prediction for GlimmerHMM_glimmerT_24713-T1
Valid prediction for GeneMark_model.42191_t
Valid prediction for snap_scaffold_10-snap.383-T1
Valid prediction for snap_scaffold_10-snap.399-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GeneMark_model.42173_t
Valid prediction for GeneMark_model.42193_t
Valid prediction for GeneMark_model.42197_t
Valid prediction for snap_scaffold_10-snap.403-T1
Valid prediction for Augustus_model.g16554.t1
Valid prediction for GeneMark_model.42155_t
Valid prediction for GeneMark_model.42181_t
Valid prediction for GeneMark_model.42151_t
Valid prediction for GeneMark_model.42185_t
Valid prediction for GeneMark_model.42163_t
Valid prediction for GeneMark_model.42162_t
Valid prediction for Augustus_model.g16553.t1
Valid prediction for snap_scaffold_10-snap.380-T1
Valid prediction for GeneMark_model.42170_t
Valid prediction for GeneMark_model.42171_t
Valid prediction for snap_scaffold_10-snap.371-T1
Valid prediction for snap_scaffold_10-snap.395-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 17696, rend_intergenic: 13034  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20678, rend_intergenic: 17763  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53102, rend_intergenic: 36383  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70067, rend_intergenic: 62875  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85040, rend_intergenic: 72720  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88458, rend_intergenic: 86452  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89436, rend_intergenic: 88811  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109705, rend_intergenic: 90002  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111770, rend_intergenic: 109813  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134847, rend_intergenic: 123151  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174374, rend_intergenic: 168811  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 191814, rend_intergenic: 189433  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 198575, rend_intergenic: 195100  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 205434
-exon list size: 732


building trellis

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76.4    
76.6    
76.7    
76.8    
77.0    
77.1    
77.2    
77.4    
77.5    
77.7    
77.8    
77.9    
78.1    
78.2    
78.3    
78.5    
78.6    
78.7    
78.9    
79.0    
79.2    
79.3    
79.4    
79.6    
79.7    
79.8    
80.0    
80.1    
80.2    
80.4    
80.5    
80.7    
80.8    
80.9    
81.1    
81.2    
81.3    
81.5    
81.6    
81.7    
81.9    
82.0    
82.2    
82.3    
82.4    
82.6    
82.7    
82.8    
83.0    
83.1    
83.2    
83.4    
83.5    
83.7    
83.8    
83.9    
84.1    
84.2    
84.3    
84.5    
84.6    
84.7    
84.9    
85.0    
85.1    
85.3    
85.4    
85.6    
85.7    
85.8    
86.0    
86.1    
86.2    
86.4    
86.5    
86.6    
86.8    
86.9    
87.1    
87.2    
87.3    
87.5    
87.6    
87.7    
87.9    
88.0    
88.1    
88.3    
88.4    
88.6    
88.7    
88.8    
89.0    
89.1    
89.2    
89.4    
89.5    
89.6    
89.8    
89.9    
90.1    
90.2    
90.3    
90.5    
90.6    
90.7    
90.9    
91.0    
91.1    
91.3    
91.4    
91.6    
91.7    
91.8    
92.0    
92.1    
92.2    
92.4    
92.5    
92.6    
92.8    
92.9    
93.1    
93.2    
93.3    
93.5    
93.6    
93.7    
93.9    
94.0    
94.1    
94.3    
94.4    
94.6    
94.7    
94.8    
95.0    
95.1    
95.2    
95.4    
95.5    
95.6    
95.8    
95.9    
96.0    
96.2    
96.3    
96.5    
96.6    
96.7    
96.9    
97.0    
97.1    
97.3    
97.4    
97.5    
97.7    
97.8    
98.0    
98.1    
98.2    
98.4    
98.5    
98.6    
98.8    
98.9    
99.0    
99.2    
99.3    
99.5    
99.6    
99.7    
99.9    
-found 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 17696, rend_intergenic: 13034  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20678, rend_intergenic: 17763  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53102, rend_intergenic: 36383  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70067, rend_intergenic: 62875  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85040, rend_intergenic: 72720  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88458, rend_intergenic: 86452  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89436, rend_intergenic: 88811  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109705, rend_intergenic: 90002  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111770, rend_intergenic: 109813  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134847, rend_intergenic: 123151  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174374, rend_intergenic: 168811  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 191814, rend_intergenic: 189433  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 198575, rend_intergenic: 195100  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

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