-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_10/scaffold_10_961835-1151748

-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 GlimmerHMM_glimmerT_24609-T1
Valid prediction for GlimmerHMM_glimmerT_24597-T1
Valid prediction for GeneMark_model.41980_t
Valid prediction for snap_scaffold_10-snap.223-T1
Valid prediction for Augustus_model.g16504.t1
Valid prediction for snap_scaffold_10-snap.225-T1
Valid prediction for GlimmerHMM_glimmerT_24600-T1
Valid prediction for GeneMark_model.41957_t
Valid prediction for GeneMark_model.41976_t
Valid prediction for HiQ_model.g16506.t1
Valid prediction for GlimmerHMM_glimmerT_24612-T1
Valid prediction for snap_scaffold_10-snap.247-T1
Valid prediction for snap_scaffold_10-snap.234-T1
Valid prediction for snap_scaffold_10-snap.246-T1
Valid prediction for GeneMark_model.41960_t
Valid prediction for snap_scaffold_10-snap.231-T1
Valid prediction for GeneMark_model.41955_t
Valid prediction for GlimmerHMM_glimmerT_24605-T1
Valid prediction for GlimmerHMM_glimmerT_24589-T1
Couldn't classify 155105, 155213
Sorry, prediction pasa_asmbl_4186.p1 fails validation.
(ATG)	 CA	152804-152918	GT	ATG
(CCT)	 AG	154412-154484	GT	GTG
(GTT)	 AG	154661-154786	GT	GGG
(AAT)	 AG	155105-155213	TA	AGT
-recovered pasa_asmbl_4186.p1, initial, 152804, 152918
-recovered pasa_asmbl_4186.p1, internal, 154412, 154484
-recovered pasa_asmbl_4186.p1, internal, 154661, 154786
Couldn't classify 4472, 4486
Couldn't classify 7850, 7981
Sorry, prediction pasa_asmbl_4177.p1 fails validation.
(AGC)	 AC	4472-4486	GT	CGG
(CTG)	 AG	4664-4749	GT	AGG
(TCT)	 AG	5437-5582	GT	TGG
(GTG)	 AG	5670-5848	GT	GGG
(GTG)	 AG	6192-6392	GT	AGG
(GGC)	 AG	6611-6703	GT	AGG
(GCG)	 AG	6792-6944	GT	AGG
(TGT)	 AG	7075-7212	GT	AGG
(GTA)	 AG	7299-7373	GT	AGG
(GCA)	 AG	7530-7763	GT	AGG
(TGT)	 AG	7850-7981	GT	AGG
-recovered pasa_asmbl_4177.p1, internal, 4664, 4749
-recovered pasa_asmbl_4177.p1, internal, 5437, 5582
-recovered pasa_asmbl_4177.p1, internal, 5670, 5848
-recovered pasa_asmbl_4177.p1, internal, 6192, 6392
-recovered pasa_asmbl_4177.p1, internal, 6611, 6703
-recovered pasa_asmbl_4177.p1, internal, 6792, 6944
-recovered pasa_asmbl_4177.p1, internal, 7075, 7212
-recovered pasa_asmbl_4177.p1, internal, 7299, 7373
-recovered pasa_asmbl_4177.p1, internal, 7530, 7763
-recovered pasa_asmbl_4177.p1, internal, 7850, 7981
Valid prediction for GlimmerHMM_glimmerT_24602-T1
Valid prediction for Augustus_model.g16503.t1
Valid prediction for GeneMark_model.41979_t
Valid prediction for GeneMark_model.41982_t
Valid prediction for GlimmerHMM_glimmerT_24606-T1
Valid prediction for snap_scaffold_10-snap.240-T1
Valid prediction for GeneMark_model.41978_t
Valid prediction for GlimmerHMM_glimmerT_24585-T1
Valid prediction for Augustus_model.g16510.t1
Valid prediction for Augustus_model.g16497.t1
Valid prediction for Augustus_model.g16498.t1
Valid prediction for GeneMark_model.41974_t
Valid prediction for GeneMark_model.41952_t
Valid prediction for pasa_asmbl_4185.p1
Valid prediction for GlimmerHMM_glimmerT_24601-T1
Valid prediction for snap_scaffold_10-snap.228-T1
Valid prediction for GlimmerHMM_glimmerT_24611-T1
Valid prediction for snap_scaffold_10-snap.244-T1
Valid prediction for GlimmerHMM_glimmerT_24590-T1
Valid prediction for Augustus_model.g16499.t1
Valid prediction for snap_scaffold_10-snap.250-T1
Valid prediction for GeneMark_model.41969_t
Valid prediction for GeneMark_model.41954_t
Valid prediction for HiQ_model.g16505.t1
Valid prediction for snap_scaffold_10-snap.248-T1
Valid prediction for snap_scaffold_10-snap.237-T1
Valid prediction for GlimmerHMM_glimmerT_24607-T1
Valid prediction for GeneMark_model.41962_t
Valid prediction for GlimmerHMM_glimmerT_24608-T1
Valid prediction for GeneMark_model.41964_t
Valid prediction for GeneMark_model.41967_t
Valid prediction for Augustus_model.g16492.t1
Valid prediction for snap_scaffold_10-snap.226-T1
Valid prediction for Augustus_model.g16508.t1
Valid prediction for snap_scaffold_10-snap.236-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 snap_scaffold_10-snap.224-T1
Valid prediction for snap_scaffold_10-snap.233-T1
Valid prediction for CodingQuarry_transcript_5263-T1
Valid prediction for GeneMark_model.41965_t
Valid prediction for GeneMark_model.41972_t
Valid prediction for snap_scaffold_10-snap.232-T1
Couldn't classify 148160, 148322
Sorry, prediction pasa_asmbl_2948.p1 fails validation.
(ATG)	 GG	141275-141345	GT	AGG
(CTG)	 AG	144259-144311	GT	AGG
(CCC)	 AG	145333-145394	GT	ACG
(CAA)	 AG	146393-146503	GT	CGG
(AAC)	 AG	147306-147382	GT	TCG
(GAA)	 AG	147472-147595	GT	AGG
(GAT)	 AG	147859-148064	GT	GGG
(GGT)	 AG	148160-148322	GT	AGG
-recovered pasa_asmbl_2948.p1, initial, 141275, 141345
-recovered pasa_asmbl_2948.p1, internal, 144259, 144311
-recovered pasa_asmbl_2948.p1, internal, 145333, 145394
-recovered pasa_asmbl_2948.p1, internal, 146393, 146503
-recovered pasa_asmbl_2948.p1, internal, 147306, 147382
-recovered pasa_asmbl_2948.p1, internal, 147472, 147595
-recovered pasa_asmbl_2948.p1, internal, 147859, 148064
-recovered pasa_asmbl_2948.p1, internal, 148160, 148322
Valid prediction for GeneMark_model.41956_t
Valid prediction for snap_scaffold_10-snap.227-T1
Valid prediction for GlimmerHMM_glimmerT_24599-T1
Valid prediction for Augustus_model.g16501.t1
Valid prediction for CodingQuarry_transcript_5266-T1
Valid prediction for Augustus_model.g16491.t1
Valid prediction for CodingQuarry_transcript_5267-T1
Valid prediction for GlimmerHMM_glimmerT_24586-T1
Valid prediction for pasa_asmbl_2953.p1
Valid prediction for Augustus_model.g16500.t1
Valid prediction for snap_scaffold_10-snap.230-T1
Valid prediction for snap_scaffold_10-snap.243-T1
Valid prediction for GeneMark_model.41971_t
Valid prediction for GeneMark_model.41953_t
Valid prediction for GeneMark_model.41973_t
Valid prediction for GlimmerHMM_glimmerT_24603-T1
Valid prediction for GlimmerHMM_glimmerT_24592-T1
Valid prediction for GeneMark_model.41958_t
Valid prediction for snap_scaffold_10-snap.241-T1
Valid prediction for pasa_asmbl_2937.p1
Valid prediction for CodingQuarry_transcript_5271-T1
Valid prediction for HiQ_model.g16495.t1
Valid prediction for GlimmerHMM_glimmerT_24610-T1
Valid prediction for GeneMark_model.41977_t
Couldn't classify 172926, 173113
Sorry, prediction pasa_asmbl_2940.p1 fails validation.
(ATG)	 AC	155301-155408	GT	AGG
(ATC)	 AG	155605-155721	GT	ACG
(GAG)	 AG	155820-155966	GT	AGG
(GCC)	 AG	156125-156246	GT	AGG
(CGC)	 AG	156414-156553	GT	AGG
(GTG)	 AG	159254-159394	GT	AGG
(CCG)	 AG	159651-159766	GT	AGG
(CTC)	 AG	160410-160571	GT	AGG
(CTC)	 AG	161063-161164	GT	AGG
(GCT)	 AG	161359-161474	GT	AGG
(GGA)	 AG	161613-162057	GT	CGG
(ACG)	 AG	162150-163773	GT	AGG
(CAC)	 AG	164373-164486	GT	AGG
(ACG)	 AG	164979-165127	GT	AGG
(AAC)	 AG	165359-165720	GT	AGG
(GAT)	 AG	165939-166171	GT	AGG
(GAG)	 AG	166531-166582	GT	AGG
(ACT)	 AG	168940-169130	GT	CGG
(GGG)	 AG	171732-172082	GT	AGG
(ACC)	 AG	172281-172406	GT	AGG
(CAG)	 AG	172681-172797	GT	AGG
(ACA)	 AG	172926-173113	AG	ACA
-recovered pasa_asmbl_2940.p1, initial, 155301, 155408
-recovered pasa_asmbl_2940.p1, internal, 155605, 155721
-recovered pasa_asmbl_2940.p1, internal, 155820, 155966
-recovered pasa_asmbl_2940.p1, internal, 156125, 156246
-recovered pasa_asmbl_2940.p1, internal, 156414, 156553
-recovered pasa_asmbl_2940.p1, internal, 159254, 159394
-recovered pasa_asmbl_2940.p1, internal, 159651, 159766
-recovered pasa_asmbl_2940.p1, internal, 160410, 160571
-recovered pasa_asmbl_2940.p1, internal, 161063, 161164
-recovered pasa_asmbl_2940.p1, internal, 161359, 161474
-recovered pasa_asmbl_2940.p1, internal, 161613, 162057
-recovered pasa_asmbl_2940.p1, internal, 162150, 163773
-recovered pasa_asmbl_2940.p1, internal, 164373, 164486
-recovered pasa_asmbl_2940.p1, internal, 164979, 165127
-recovered pasa_asmbl_2940.p1, internal, 165359, 165720
-recovered pasa_asmbl_2940.p1, internal, 165939, 166171
-recovered pasa_asmbl_2940.p1, internal, 166531, 166582
-recovered pasa_asmbl_2940.p1, internal, 168940, 169130
-recovered pasa_asmbl_2940.p1, internal, 171732, 172082
-recovered pasa_asmbl_2940.p1, internal, 172281, 172406
-recovered pasa_asmbl_2940.p1, internal, 172681, 172797
Valid prediction for snap_scaffold_10-snap.242-T1
Valid prediction for GlimmerHMM_glimmerT_24588-T1
Couldn't classify 151499, 151636
Couldn't classify 152753, 152872
Sorry, prediction pasa_asmbl_2947.p1 fails validation.
(CAG)	 TC	151499-151636	GT	AGG
(GCT)	 AG	151853-151972	GT	AGG
(ATT)	 AG	152260-152352	GC	AGG
(GGG)	 AG	152575-152652	GT	AGG
(GTT)	 AG	152753-152872	AA	AGA
-recovered pasa_asmbl_2947.p1, internal, 151853, 151972
-recovered pasa_asmbl_2947.p1, internal, 152260, 152352
-recovered pasa_asmbl_2947.p1, internal, 152575, 152652
Valid prediction for CodingQuarry_transcript_5270-T1
Valid prediction for Augustus_model.g16494.t1
Valid prediction for GeneMark_model.41963_t
Valid prediction for Augustus_model.g16509.t1
Valid prediction for snap_scaffold_10-snap.221-T1
Valid prediction for Augustus_model.g16502.t1
Valid prediction for GeneMark_model.41970_t
Couldn't classify 153037, 153153
Couldn't classify 154183, 154263
Sorry, prediction pasa_asmbl_2946.p1 fails validation.
(GCA)	 CG	153037-153153	GT	AGG
(GAG)	 AG	153307-153417	GT	AGG
(CAA)	 AG	153585-153722	GT	CCG
(AAC)	 AG	153918-154097	GT	AGG
(GAC)	 AG	154183-154263	AA	TGA
-recovered pasa_asmbl_2946.p1, internal, 153307, 153417
-recovered pasa_asmbl_2946.p1, internal, 153585, 153722
-recovered pasa_asmbl_2946.p1, internal, 153918, 154097
Valid prediction for GeneMark_model.41951_t
Valid prediction for GlimmerHMM_glimmerT_24594-T1
Valid prediction for GeneMark_model.41959_t
Valid prediction for CodingQuarry_transcript_5268-T1
Valid prediction for Augustus_model.g16507.t1
Valid prediction for GeneMark_model.41961_t
Couldn't classify 89196, 89579
Sorry, prediction pasa_asmbl_2955.p1 fails validation.
(CCT)	 AC	89196-89579	GC	GAG
Valid prediction for GlimmerHMM_glimmerT_24593-T1
Valid prediction for GeneMark_model.41966_t
Valid prediction for GeneMark_model.41975_t
Valid prediction for CodingQuarry_transcript_5265-T1
Valid prediction for snap_scaffold_10-snap.249-T1
Valid prediction for snap_scaffold_10-snap.238-T1
Valid prediction for snap_scaffold_10-snap.245-T1
Valid prediction for GeneMark_model.41981_t
Valid prediction for GlimmerHMM_glimmerT_24587-T1
Valid prediction for HiQ_model.g16496.t1
Valid prediction for snap_scaffold_10-snap.229-T1
Valid prediction for GlimmerHMM_glimmerT_24598-T1
Valid prediction for snap_scaffold_10-snap.222-T1
Couldn't classify 70266, 70387
Sorry, prediction pasa_asmbl_2959.p1 fails validation.
(TTA)	 CC	70266-70387	GT	ATG
(TTA)	 AG	70786-70879	GT	AGG
(CTG)	 AG	71022-71166	GT	CGG
(GGC)	 AG	71623-71710	GT	AGG
(GCT)	 AG	72002-72226	GT	CGG
(GGA)	 AG	72403-72922	GT	AGG
(GTC)	 AG	74114-74240	GT	CGG
(ATG)	 AG	74478-74782	CT	AGC
-recovered pasa_asmbl_2959.p1, terminal, 74478, 74782
-recovered pasa_asmbl_2959.p1, internal, 70786, 70879
-recovered pasa_asmbl_2959.p1, internal, 71022, 71166
-recovered pasa_asmbl_2959.p1, internal, 71623, 71710
-recovered pasa_asmbl_2959.p1, internal, 72002, 72226
-recovered pasa_asmbl_2959.p1, internal, 72403, 72922
-recovered pasa_asmbl_2959.p1, internal, 74114, 74240
Valid prediction for snap_scaffold_10-snap.239-T1
Valid prediction for GlimmerHMM_glimmerT_24604-T1
Valid prediction for GlimmerHMM_glimmerT_24591-T1
Valid prediction for pasa_asmbl_2962.p1
Valid prediction for Augustus_model.g16493.t1
Valid prediction for snap_scaffold_10-snap.235-T1
Valid prediction for GlimmerHMM_glimmerT_24595-T1
Valid prediction for GlimmerHMM_glimmerT_24596-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 18350, rend_intergenic: 14026  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19690, rend_intergenic: 19409  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39828, rend_intergenic: 26377  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41581, rend_intergenic: 40061  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46365, rend_intergenic: 43087  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74151, rend_intergenic: 68751  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91060, rend_intergenic: 87101  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141814, rend_intergenic: 129726  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 189914
-exon list size: 564


building trellis

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74.0    
74.2    
74.4    
74.6    
74.7    
74.9    
75.1    
75.3    
75.4    
75.6    
75.8    
76.0    
76.1    
76.3    
76.5    
76.7    
76.9    
77.0    
77.2    
77.4    
77.6    
77.7    
77.9    
78.1    
78.3    
78.4    
78.6    
78.8    
79.0    
79.2    
79.3    
79.5    
79.7    
79.9    
80.0    
80.2    
80.4    
80.6    
80.7    
80.9    
81.1    
81.3    
81.4    
81.6    
81.8    
82.0    
82.2    
82.3    
82.5    
82.7    
82.9    
83.0    
83.2    
83.4    
83.6    
83.7    
83.9    
84.1    
84.3    
84.5    
84.6    
84.8    
85.0    
85.2    
85.3    
85.5    
85.7    
85.9    
86.0    
86.2    
86.4    
86.6    
86.7    
86.9    
87.1    
87.3    
87.5    
87.6    
87.8    
88.0    
88.2    
88.3    
88.5    
88.7    
88.9    
89.0    
89.2    
89.4    
89.6    
89.8    
89.9    
90.1    
90.3    
90.5    
90.6    
90.8    
91.0    
91.2    
91.3    
91.5    
91.7    
91.9    
92.0    
92.2    
92.4    
92.6    
92.8    
92.9    
93.1    
93.3    
93.5    
93.6    
93.8    
94.0    
94.2    
94.3    
94.5    
94.7    
94.9    
95.1    
95.2    
95.4    
95.6    
95.8    
95.9    
96.1    
96.3    
96.5    
96.6    
96.8    
97.0    
97.2    
97.3    
97.5    
97.7    
97.9    
98.1    
98.2    
98.4    
98.6    
98.8    
98.9    
99.1    
99.3    
99.5    
99.6    
99.8    
-found 20 predictions from path traversal
Error with prediction: snap lend_intergenic: 18350, rend_intergenic: 14026  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19690, rend_intergenic: 19409  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39828, rend_intergenic: 26377  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41581, rend_intergenic: 40061  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46365, rend_intergenic: 43087  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74151, rend_intergenic: 68751  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91060, rend_intergenic: 87101  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141814, rend_intergenic: 129726  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support