-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_28/scaffold_28_2244575-2462081

-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 pasa_asmbl_37818.p1
Valid prediction for snap_scaffold_28-snap.582-T1
Valid prediction for Augustus_model.g38615.t1
Couldn't classify 186885, 187442
Sorry, prediction pasa_asmbl_37368.p1 fails validation.
(CCC)	 GG	186885-187442	TA	AAT
Valid prediction for GlimmerHMM_glimmerT_58336-T1
Valid prediction for GlimmerHMM_glimmerT_58311-T1
Valid prediction for snap_scaffold_28-snap.592-T1
Valid prediction for GlimmerHMM_glimmerT_58333-T1
Valid prediction for GlimmerHMM_glimmerT_58346-T1
Valid prediction for snap_scaffold_28-snap.557-T1
Valid prediction for CodingQuarry_transcript_43561-T1
Valid prediction for Augustus_model.g38619.t1
Valid prediction for GlimmerHMM_glimmerT_58341-T1
Valid prediction for snap_scaffold_28-snap.605-T1
Valid prediction for snap_scaffold_28-snap.600-T1
Valid prediction for CodingQuarry_transcript_43559-T1
Valid prediction for snap_scaffold_28-snap.584-T1
Valid prediction for snap_scaffold_28-snap.594-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for pasa_asmbl_37364.p1
Valid prediction for snap_scaffold_28-snap.571-T1
Valid prediction for CodingQuarry_transcript_43554-T1
Valid prediction for HiQ_model.g38602.t1
Valid prediction for GlimmerHMM_glimmerT_58307-T1
Valid prediction for snap_scaffold_28-snap.597-T1
Valid prediction for GlimmerHMM_glimmerT_58334-T1
Couldn't classify 208162, 208205
Couldn't classify 214089, 214232
Sorry, prediction pasa_asmbl_37369.p1 fails validation.
(CGC)	 AC	208162-208205	GT	ACG
(TTC)	 AG	210987-211089	GT	TGG
(AAG)	 AG	212856-213100	GT	AAG
(TGG)	 AG	213189-213345	GT	AGG
(GCG)	 AG	214089-214232	GG	AAG
-recovered pasa_asmbl_37369.p1, internal, 210987, 211089
-recovered pasa_asmbl_37369.p1, internal, 212856, 213100
-recovered pasa_asmbl_37369.p1, internal, 213189, 213345
Valid prediction for GlimmerHMM_glimmerT_58326-T1
Valid prediction for Augustus_model.g38635.t1
Valid prediction for GlimmerHMM_glimmerT_58321-T1
Valid prediction for HiQ_model.g38605.t1
Valid prediction for Augustus_model.g38608.t1
Valid prediction for GlimmerHMM_glimmerT_58335-T1
Valid prediction for snap_scaffold_28-snap.554-T1
Valid prediction for GlimmerHMM_glimmerT_58309-T1
Valid prediction for snap_scaffold_28-snap.564-T1
Valid prediction for GlimmerHMM_glimmerT_58319-T1
Valid prediction for GlimmerHMM_glimmerT_58345-T1
Valid prediction for CodingQuarry_transcript_43563-T1
Valid prediction for snap_scaffold_28-snap.590-T1
Valid prediction for snap_scaffold_28-snap.574-T1
Valid prediction for pasa_asmbl_37360.p1
Valid prediction for GlimmerHMM_glimmerT_58331-T1
Valid prediction for Augustus_model.g38625.t1
Valid prediction for Augustus_model.g38632.t1
Valid prediction for snap_scaffold_28-snap.595-T1
Valid prediction for Augustus_model.g38624.t1
Valid prediction for snap_scaffold_28-snap.580-T1
Valid prediction for Augustus_model.g38610.t1
Valid prediction for GlimmerHMM_glimmerT_58315-T1
Valid prediction for GlimmerHMM_glimmerT_58343-T1
Valid prediction for HiQ_model.g38627.t1
Valid prediction for Augustus_model.g38622.t1
Valid prediction for GlimmerHMM_glimmerT_58344-T1
Valid prediction for snap_scaffold_28-snap.588-T1
Valid prediction for GlimmerHMM_glimmerT_58338-T1
Valid prediction for Augustus_model.g38630.t1
Valid prediction for Augustus_model.g38626.t1
Valid prediction for CodingQuarry_transcript_43562-T1
Couldn't classify 185130, 185167
Couldn't classify 185843, 186608
Sorry, prediction pasa_asmbl_37367.p1 fails validation.
(CAA)	 GG	185130-185167	GT	AGG
(GCC)	 AG	185843-186608	GA	AGG
Valid prediction for snap_scaffold_28-snap.573-T1
Valid prediction for snap_scaffold_28-snap.585-T1
Valid prediction for Augustus_model.g38607.t1
Valid prediction for snap_scaffold_28-snap.591-T1
Sorry, intron length (4) is less than minimum required (10)
Couldn't classify 29023, 29656
Sorry, prediction pasa_asmbl_37358.p1 fails validation.
(TCA)	 TC	29023-29656	GT	AGG
(ACC)	 AG	29778-29923	GT	AGG
(TTC)	 AG	30072-30177	GT	AGG
(GTG)	 AG	30285-30461	GT	AGG
(GTT)	 AG	30681-30940	AA	GAA
-recovered pasa_asmbl_37358.p1, terminal, 30681, 30940
-recovered pasa_asmbl_37358.p1, internal, 29778, 29923
-recovered pasa_asmbl_37358.p1, internal, 30072, 30177
-recovered pasa_asmbl_37358.p1, internal, 30285, 30461
Valid prediction for HiQ_model.g38613.t1
Valid prediction for GlimmerHMM_glimmerT_58312-T1
Valid prediction for snap_scaffold_28-snap.602-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 pasa_asmbl_38032.p1
Valid prediction for snap_scaffold_28-snap.586-T1
Valid prediction for GlimmerHMM_glimmerT_58322-T1
Valid prediction for snap_scaffold_28-snap.562-T1
Valid prediction for snap_scaffold_28-snap.555-T1
Valid prediction for snap_scaffold_28-snap.565-T1
Valid prediction for snap_scaffold_28-snap.560-T1
Valid prediction for snap_scaffold_28-snap.558-T1
Valid prediction for snap_scaffold_28-snap.551-T1
Valid prediction for GlimmerHMM_glimmerT_58317-T1
Valid prediction for GlimmerHMM_glimmerT_58325-T1
Valid prediction for snap_scaffold_28-snap.566-T1
Valid prediction for GlimmerHMM_glimmerT_58320-T1
Valid prediction for snap_scaffold_28-snap.581-T1
Couldn't classify 162272, 162281
Sorry, prediction pasa_asmbl_38035.p1 fails validation.
(ATC)	 TC	162272-162281	GT	AGG
(TGG)	 AG	162398-162564	GT	AAG
(ATT)	 AG	162659-162809	GT	AGG
(ATG)	 AG	162905-163091	GT	GAG
(TTA)	 AG	163207-163427	GT	AGG
(GTG)	 AG	163999-164153	GT	AGG
(GAC)	 AG	164394-164556	GT	CAG
(TAA)	 AG	164725-164852	CA	GAC
add_exon() Sorry, pasa_asmbl_38035.p1 162905-163091-initial-1 is invalid.
-recovered pasa_asmbl_38035.p1, initial, 162905, 163091
-recovered pasa_asmbl_38035.p1, terminal, 164725, 164852
-recovered pasa_asmbl_38035.p1, internal, 162398, 162564
-recovered pasa_asmbl_38035.p1, internal, 162659, 162809
-recovered pasa_asmbl_38035.p1, internal, 162905, 163091
-recovered pasa_asmbl_38035.p1, internal, 163207, 163427
-recovered pasa_asmbl_38035.p1, internal, 163999, 164153
-recovered pasa_asmbl_38035.p1, internal, 164394, 164556
Valid prediction for GlimmerHMM_glimmerT_58305-T1
Valid prediction for GlimmerHMM_glimmerT_58340-T1
Valid prediction for snap_scaffold_28-snap.593-T1
Valid prediction for Augustus_model.g38612.t1
Valid prediction for CodingQuarry_transcript_43557-T1
Valid prediction for snap_scaffold_28-snap.601-T1
Valid prediction for Augustus_model.g38634.t1
Valid prediction for GlimmerHMM_glimmerT_58310-T1
Valid prediction for snap_scaffold_28-snap.563-T1
Valid prediction for Augustus_model.g38628.t1
Couldn't classify 94496, 94627
Couldn't classify 95300, 95406
Sorry, prediction pasa_asmbl_38052.p1 fails validation.
(GGC)	 TG	94496-94627	GT	CGG
(ATA)	 AG	94907-95021	GT	CGG
(CTT)	 AG	95300-95406	GG	CTG
-recovered pasa_asmbl_38052.p1, internal, 94907, 95021
Valid prediction for HiQ_model.g38603.t1
Valid prediction for CodingQuarry_transcript_43555-T1
Valid prediction for GlimmerHMM_glimmerT_58316-T1
Valid prediction for HiQ_model.g38618.t1
Valid prediction for snap_scaffold_28-snap.569-T1
Valid prediction for Augustus_model.g38616.t1
Valid prediction for snap_scaffold_28-snap.599-T1
Valid prediction for snap_scaffold_28-snap.552-T1
Valid prediction for Augustus_model.g38623.t1
Couldn't classify 24196, 24281
Couldn't classify 29572, 29686
Sorry, prediction pasa_asmbl_38059.p1 fails validation.
(CTC)	 GT	24196-24281	GT	TGG
(CCC)	 AG	26690-26726	GT	AGG
(TTC)	 AG	28578-28706	GT	AGG
(GTT)	 AG	29028-29446	GT	AGG
(CCC)	 AG	29572-29686	AG	CCA
-recovered pasa_asmbl_38059.p1, internal, 26690, 26726
-recovered pasa_asmbl_38059.p1, internal, 28578, 28706
-recovered pasa_asmbl_38059.p1, internal, 29028, 29446
Valid prediction for pasa_asmbl_38050.p1
Valid prediction for Augustus_model.g38609.t1
Valid prediction for snap_scaffold_28-snap.576-T1
Valid prediction for GlimmerHMM_glimmerT_58330-T1
Valid prediction for pasa_asmbl_38024.p1
Valid prediction for snap_scaffold_28-snap.561-T1
Valid prediction for snap_scaffold_28-snap.596-T1
Valid prediction for snap_scaffold_28-snap.607-T1
Valid prediction for HiQ_model.g38604.t1
Couldn't classify 125248, 125386
Sorry, prediction pasa_asmbl_38043.p2 fails validation.
(GGC)	 AC	125248-125386	GT	AGG
(GTT)	 AG	125551-125759	CC	GAC
-recovered pasa_asmbl_38043.p2, terminal, 125551, 125759
Valid prediction for snap_scaffold_28-snap.572-T1
Valid prediction for GlimmerHMM_glimmerT_58308-T1
Valid prediction for snap_scaffold_28-snap.603-T1
Valid prediction for GlimmerHMM_glimmerT_58306-T1
Valid prediction for GlimmerHMM_glimmerT_58342-T1
Valid prediction for HiQ_model.g38617.t1
Valid prediction for Augustus_model.g38620.t1
Valid prediction for snap_scaffold_28-snap.589-T1
Couldn't classify 152966, 153449
Sorry, prediction pasa_asmbl_38041.p1 fails validation.
(CTT)	 AG	152966-153449	GT	AGG
(ATT)	 AG	153534-153661	CG	AAC
add_exon() Sorry, pasa_asmbl_38041.p1 152966-153449-terminal-3 is invalid.
-recovered pasa_asmbl_38041.p1, terminal, 152966, 153449
-recovered pasa_asmbl_38041.p1, terminal, 153534, 153661
-recovered pasa_asmbl_38041.p1, internal, 152966, 153449
Valid prediction for snap_scaffold_28-snap.567-T1
Valid prediction for HiQ_model.g38611.t1
Valid prediction for CodingQuarry_transcript_43556-T1
Valid prediction for Augustus_model.g38614.t1
Valid prediction for GlimmerHMM_glimmerT_58337-T1
Valid prediction for Augustus_model.g38629.t1
Valid prediction for GlimmerHMM_glimmerT_58324-T1
Valid prediction for snap_scaffold_28-snap.578-T1
Valid prediction for snap_scaffold_28-snap.606-T1
Valid prediction for GlimmerHMM_glimmerT_58323-T1
Valid prediction for Augustus_model.g38633.t1
Valid prediction for snap_scaffold_28-snap.579-T1
Valid prediction for GlimmerHMM_glimmerT_58327-T1
Valid prediction for snap_scaffold_28-snap.583-T1
Valid prediction for pasa_asmbl_38023.p1
Valid prediction for GlimmerHMM_glimmerT_58328-T1
Valid prediction for snap_scaffold_28-snap.568-T1
Valid prediction for GlimmerHMM_glimmerT_58318-T1
Valid prediction for GlimmerHMM_glimmerT_58314-T1
Valid prediction for Augustus_model.g38631.t1
Valid prediction for GlimmerHMM_glimmerT_58339-T1
Valid prediction for Augustus_model.g38621.t1
Valid prediction for CodingQuarry_transcript_43560-T1
Valid prediction for snap_scaffold_28-snap.575-T1
Valid prediction for snap_scaffold_28-snap.553-T1
Valid prediction for pasa_asmbl_38033.p1
Couldn't classify 35169, 35273
Sorry, prediction pasa_asmbl_38056.p1 fails validation.
(ATG)	 GA	33503-33925	GT	CGG
(GTC)	 AG	34066-34181	GT	AGG
(GTT)	 AG	34779-34950	GT	AGG
(ATT)	 AG	35169-35273	GG	ATG
-recovered pasa_asmbl_38056.p1, initial, 33503, 33925
-recovered pasa_asmbl_38056.p1, internal, 34066, 34181
-recovered pasa_asmbl_38056.p1, internal, 34779, 34950
Valid prediction for Augustus_model.g38606.t1
Valid prediction for snap_scaffold_28-snap.604-T1
Valid prediction for snap_scaffold_28-snap.587-T1
Valid prediction for GlimmerHMM_glimmerT_58313-T1
Valid prediction for GlimmerHMM_glimmerT_58329-T1
Valid prediction for snap_scaffold_28-snap.570-T1
Couldn't classify 162161, 162265
Sorry, prediction pasa_asmbl_38036.p1 fails validation.
(ATG)	 GG	158830-158838	GT	AGG
(GAA)	 AG	159368-159501	GT	AGG
(AAA)	 AG	159656-159815	GT	AGG
(GAC)	 AG	159958-160000	GT	AGG
(GTT)	 AG	160413-160630	GT	AGG
(ACG)	 AG	160727-160933	GT	AGG
(AGG)	 AG	161133-161279	GT	AGG
(GAT)	 AG	161487-161576	GT	AGG
(GAA)	 AG	161746-161844	GT	AGG
(ATA)	 AG	162161-162265	CC	AGC
-recovered pasa_asmbl_38036.p1, initial, 158830, 158838
-recovered pasa_asmbl_38036.p1, internal, 159368, 159501
-recovered pasa_asmbl_38036.p1, internal, 159656, 159815
-recovered pasa_asmbl_38036.p1, internal, 159958, 160000
-recovered pasa_asmbl_38036.p1, internal, 160413, 160630
-recovered pasa_asmbl_38036.p1, internal, 160727, 160933
-recovered pasa_asmbl_38036.p1, internal, 161133, 161279
-recovered pasa_asmbl_38036.p1, internal, 161487, 161576
-recovered pasa_asmbl_38036.p1, internal, 161746, 161844
Valid prediction for snap_scaffold_28-snap.577-T1
Valid prediction for snap_scaffold_28-snap.556-T1
Valid prediction for GlimmerHMM_glimmerT_58332-T1
Valid prediction for Augustus_model.g38601.t1
Valid prediction for CodingQuarry_transcript_43558-T1
Valid prediction for snap_scaffold_28-snap.559-T1
Valid prediction for snap_scaffold_28-snap.598-T1
Valid prediction for pasa_asmbl_38047.p1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 126545, rend_intergenic: 124060  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132322, rend_intergenic: 127761  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140128, rend_intergenic: 135242  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174341, rend_intergenic: 172942  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192782, rend_intergenic: 187773  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 214530, rend_intergenic: 210957  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 217507
-exon list size: 590


building trellis

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70.1    
70.3    
70.4    
70.6    
70.8    
70.9    
71.1    
71.3    
71.5    
71.6    
71.8    
72.0    
72.1    
72.3    
72.5    
72.6    
72.8    
73.0    
73.1    
73.3    
73.5    
73.6    
73.8    
74.0    
74.2    
74.3    
74.5    
74.7    
74.8    
75.0    
75.2    
75.3    
75.5    
75.7    
75.8    
76.0    
76.2    
76.4    
76.5    
76.7    
76.9    
77.0    
77.2    
77.4    
77.5    
77.7    
77.9    
78.0    
78.2    
78.4    
78.5    
78.7    
78.9    
79.1    
79.2    
79.4    
79.6    
79.7    
79.9    
80.1    
80.2    
80.4    
80.6    
80.7    
80.9    
81.1    
81.2    
81.4    
81.6    
81.8    
81.9    
82.1    
82.3    
82.4    
82.6    
82.8    
82.9    
83.1    
83.3    
83.4    
83.6    
83.8    
84.0    
84.1    
84.3    
84.5    
84.6    
84.8    
85.0    
85.1    
85.3    
85.5    
85.6    
85.8    
86.0    
86.1    
86.3    
86.5    
86.7    
86.8    
87.0    
87.2    
87.3    
87.5    
87.7    
87.8    
88.0    
88.2    
88.3    
88.5    
88.7    
88.9    
89.0    
89.2    
89.4    
89.5    
89.7    
89.9    
90.0    
90.2    
90.4    
90.5    
90.7    
90.9    
91.0    
91.2    
91.4    
91.6    
91.7    
91.9    
92.1    
92.2    
92.4    
92.6    
92.7    
92.9    
93.1    
93.2    
93.4    
93.6    
93.8    
93.9    
94.1    
94.3    
94.4    
94.6    
94.8    
94.9    
95.1    
95.3    
95.4    
95.6    
95.8    
95.9    
96.1    
96.3    
96.5    
96.6    
96.8    
97.0    
97.1    
97.3    
97.5    
97.6    
97.8    
98.0    
98.1    
98.3    
98.5    
98.6    
98.8    
99.0    
99.2    
99.3    
99.5    
99.7    
99.8    
-found 46 predictions from path traversal
Error with prediction: snap lend_intergenic: 126545, rend_intergenic: 124060  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132322, rend_intergenic: 127761  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140128, rend_intergenic: 135242  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174341, rend_intergenic: 172942  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192782, rend_intergenic: 187773  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 214530, rend_intergenic: 210957  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 41 predictions persist after filtering for low support