-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_15/scaffold_15_2457670-2636394

-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_35738-T1
Valid prediction for pasa_asmbl_15067.p2
Valid prediction for snap_scaffold_15-snap.532-T1
Valid prediction for GlimmerHMM_glimmerT_35756-T1
Valid prediction for snap_scaffold_15-snap.507-T1
Valid prediction for GlimmerHMM_glimmerT_35754-T1
Valid prediction for CodingQuarry_transcript_17932-T1
Valid prediction for GlimmerHMM_glimmerT_35761-T1
Valid prediction for GlimmerHMM_glimmerT_35749-T1
Couldn't classify 95179, 95256
Couldn't classify 95319, 95435
Sorry, prediction CodingQuarry_transcript_17934-T1 fails validation.
(ATG)	 GG	95179-95256	CT	ACC
(CTG)	 AC	95319-95435	GC	AGG
Valid prediction for HiQ_model.g23849.t1
Valid prediction for snap_scaffold_15-snap.519-T1
Valid prediction for GlimmerHMM_glimmerT_35760-T1
Valid prediction for snap_scaffold_15-snap.514-T1
Valid prediction for GlimmerHMM_glimmerT_35742-T1
Valid prediction for GlimmerHMM_glimmerT_35751-T1
Valid prediction for GlimmerHMM_glimmerT_35763-T1
Valid prediction for Augustus_model.g23854.t1
Valid prediction for snap_scaffold_15-snap.537-T1
Valid prediction for Augustus_model.g23852.t1
Valid prediction for GlimmerHMM_glimmerT_35750-T1
Valid prediction for snap_scaffold_15-snap.504-T1
Valid prediction for Augustus_model.g23853.t1
Valid prediction for Augustus_model.g23841.t1
Couldn't classify 86539, 86638
Couldn't classify 87730, 87854
Sorry, prediction pasa_asmbl_15955.p1 fails validation.
(ATT)	 AG	86539-86638	GT	AGG
(GGC)	 AG	86781-86885	GT	AGG
(TGC)	 AG	87730-87854	GT	CAG
-recovered pasa_asmbl_15955.p1, internal, 86539, 86638
-recovered pasa_asmbl_15955.p1, internal, 86781, 86885
-recovered pasa_asmbl_15955.p1, internal, 87730, 87854
Valid prediction for GlimmerHMM_glimmerT_35766-T1
Valid prediction for snap_scaffold_15-snap.529-T1
Valid prediction for snap_scaffold_15-snap.526-T1
Valid prediction for snap_scaffold_15-snap.517-T1
Valid prediction for GlimmerHMM_glimmerT_35757-T1
Valid prediction for snap_scaffold_15-snap.535-T1
Valid prediction for Augustus_model.g23845.t1
Valid prediction for snap_scaffold_15-snap.505-T1
Valid prediction for snap_scaffold_15-snap.506-T1
Valid prediction for Augustus_model.g23846.t1
Valid prediction for snap_scaffold_15-snap.540-T1
Couldn't classify 156401, 156709
Sorry, prediction pasa_asmbl_14918.p3 fails validation.
(TCT)	 TC	156401-156709	CT	CCC
Valid prediction for GlimmerHMM_glimmerT_35741-T1
Couldn't classify 81445, 81505
Couldn't classify 82176, 82240
Sorry, prediction pasa_asmbl_15060.p1 fails validation.
(AGC)	 AC	81445-81505	GT	GGG
(TGA)	 AG	81913-82086	GT	CGG
(ATC)	 AG	82176-82240	AC	GCA
-recovered pasa_asmbl_15060.p1, internal, 81913, 82086
Valid prediction for snap_scaffold_15-snap.510-T1
Valid prediction for GlimmerHMM_glimmerT_35752-T1
Valid prediction for Augustus_model.g23851.t1
Valid prediction for GlimmerHMM_glimmerT_35744-T1
Valid prediction for pasa_asmbl_15057.p1
Valid prediction for HiQ_model.g23839.t1
Valid prediction for CodingQuarry_transcript_17933-T1
Valid prediction for CodingQuarry_transcript_17936-T1
Valid prediction for snap_scaffold_15-snap.521-T1
Valid prediction for snap_scaffold_15-snap.503-T1
Valid prediction for snap_scaffold_15-snap.501-T1
Valid prediction for snap_scaffold_15-snap.511-T1
Couldn't classify 172720, 173046
Sorry, prediction pasa_asmbl_14029.p1 fails validation.
(CTA)	 GA	172720-173046	CC	AAC
Valid prediction for GlimmerHMM_glimmerT_35759-T1
Valid prediction for snap_scaffold_15-snap.528-T1
Valid prediction for GlimmerHMM_glimmerT_35743-T1
Valid prediction for snap_scaffold_15-snap.525-T1
Valid prediction for HiQ_model.g23840.t1
Valid prediction for snap_scaffold_15-snap.515-T1
Valid prediction for snap_scaffold_15-snap.509-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 GlimmerHMM_glimmerT_35740-T1
Valid prediction for snap_scaffold_15-snap.518-T1
Valid prediction for Augustus_model.g23855.t1
Valid prediction for snap_scaffold_15-snap.531-T1
Valid prediction for snap_scaffold_15-snap.516-T1
Valid prediction for HiQ_model.g23848.t1
Valid prediction for CodingQuarry_transcript_17939-T1
Valid prediction for snap_scaffold_15-snap.523-T1
Valid prediction for GlimmerHMM_glimmerT_35747-T1
Valid prediction for Augustus_model.g23842.t1
Valid prediction for GlimmerHMM_glimmerT_35758-T1
Valid prediction for HiQ_model.g23850.t1
Valid prediction for snap_scaffold_15-snap.530-T1
Valid prediction for CodingQuarry_transcript_17935-T1
Valid prediction for HiQ_model.g23844.t1
Valid prediction for pasa_asmbl_14021.p1
Valid prediction for GlimmerHMM_glimmerT_35753-T1
Valid prediction for GlimmerHMM_glimmerT_35762-T1
Valid prediction for snap_scaffold_15-snap.522-T1
Valid prediction for GlimmerHMM_glimmerT_35764-T1
Valid prediction for snap_scaffold_15-snap.500-T1
Valid prediction for snap_scaffold_15-snap.539-T1
Valid prediction for GlimmerHMM_glimmerT_35746-T1
Valid prediction for snap_scaffold_15-snap.520-T1
Valid prediction for snap_scaffold_15-snap.533-T1
Valid prediction for GlimmerHMM_glimmerT_35739-T1
Valid prediction for CodingQuarry_transcript_17937-T1
Valid prediction for snap_scaffold_15-snap.513-T1
Valid prediction for snap_scaffold_15-snap.508-T1
Valid prediction for GlimmerHMM_glimmerT_35745-T1
Couldn't classify 112514, 112678
Sorry, prediction pasa_asmbl_14843.p1 fails validation.
(ATG)	 TG	111579-111592	GT	GAG
(AGA)	 AG	112158-112266	GT	AGG
(GTA)	 AG	112514-112678	TG	AGT
-recovered pasa_asmbl_14843.p1, initial, 111579, 111592
-recovered pasa_asmbl_14843.p1, internal, 112158, 112266
Valid prediction for GlimmerHMM_glimmerT_35755-T1
Valid prediction for GlimmerHMM_glimmerT_35748-T1
Couldn't classify 168481, 168596
Couldn't classify 168723, 168855
Sorry, prediction CodingQuarry_transcript_17931-T1 fails validation.
(ATG)	 TT	168481-168596	AG	AAA
(GGA)	 GG	168723-168855	AT	AGA
Valid prediction for snap_scaffold_15-snap.524-T1
Valid prediction for snap_scaffold_15-snap.512-T1
Valid prediction for snap_scaffold_15-snap.538-T1
Valid prediction for snap_scaffold_15-snap.536-T1
Valid prediction for snap_scaffold_15-snap.534-T1
Couldn't classify 24100, 24205
Sorry, prediction pasa_asmbl_14027.p2 fails validation.
(GGC)	 CA	24100-24205	GT	GGG
(GGA)	 AG	24421-24527	GT	AGG
(CCT)	 AG	26123-26275	GT	GAG
-recovered pasa_asmbl_14027.p2, terminal, 26123, 26275
-recovered pasa_asmbl_14027.p2, internal, 24421, 24527
-recovered pasa_asmbl_14027.p2, internal, 26123, 26275
Valid prediction for HiQ_model.g23843.t1
Valid prediction for snap_scaffold_15-snap.502-T1
Couldn't classify 113278, 113321
Sorry, prediction pasa_asmbl_14017.p1 fails validation.
(AGC)	 CA	113278-113321	GT	GGG
(ATT)	 AG	113830-113945	GT	GGG
(GCC)	 AG	114288-114496	GA	GAG
-recovered pasa_asmbl_14017.p1, terminal, 114288, 114496
-recovered pasa_asmbl_14017.p1, internal, 113830, 113945
Valid prediction for snap_scaffold_15-snap.527-T1
Couldn't classify 75971, 76195
Sorry, prediction pasa_asmbl_14020.p1 fails validation.
(ATA)	 GA	75971-76195	GT	AGG
(GCA)	 AG	76608-76778	CG	GAC
-recovered pasa_asmbl_14020.p1, terminal, 76608, 76778
Valid prediction for CodingQuarry_transcript_17938-T1
Valid prediction for Augustus_model.g23847.t1
Valid prediction for GlimmerHMM_glimmerT_35765-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 27376, rend_intergenic: 1753  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36555, rend_intergenic: 34569  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52105, rend_intergenic: 47132  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62848, rend_intergenic: 52352  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66055, rend_intergenic: 64230  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80855, rend_intergenic: 69333  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81801, rend_intergenic: 81008  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85238, rend_intergenic: 83548  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88829, rend_intergenic: 85928  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91744, rend_intergenic: 89177  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92541, rend_intergenic: 92151  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94864, rend_intergenic: 92809  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107199, rend_intergenic: 105497  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110778, rend_intergenic: 107565  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124213, rend_intergenic: 114967  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145681, rend_intergenic: 127199  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152985, rend_intergenic: 149001  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165763, rend_intergenic: 153275  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173165, rend_intergenic: 166268  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 124213, rend_intergenic: 124210  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 178725
-exon list size: 362


building trellis

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26.6    
26.9    
27.2    
27.5    
27.7    
28.0    
28.3    
28.6    
28.8    
29.1    
29.4    
29.7    
29.9    
30.2    
30.5    
30.8    
31.0    
31.3    
31.6    
31.9    
32.1    
32.4    
32.7    
33.0    
33.2    
33.5    
33.8    
34.1    
34.3    
34.6    
34.9    
35.2    
35.4    
35.7    
36.0    
36.3    
36.5    
36.8    
37.1    
37.4    
37.6    
37.9    
38.2    
38.5    
38.7    
39.0    
39.3    
39.6    
39.8    
40.1    
40.4    
40.7    
40.9    
41.2    
41.5    
41.8    
42.0    
42.3    
42.6    
42.9    
43.1    
43.4    
43.7    
44.0    
44.2    
44.5    
44.8    
45.1    
45.3    
45.6    
45.9    
46.2    
46.4    
46.7    
47.0    
47.3    
47.5    
47.8    
48.1    
48.4    
48.6    
48.9    
49.2    
49.5    
49.7    
50.0    
50.3    
50.5    
50.8    
51.1    
51.4    
51.6    
51.9    
52.2    
52.5    
52.7    
53.0    
53.3    
53.6    
53.8    
54.1    
54.4    
54.7    
54.9    
55.2    
55.5    
55.8    
56.0    
56.3    
56.6    
56.9    
57.1    
57.4    
57.7    
58.0    
58.2    
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58.8    
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60.2    
60.4    
60.7    
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61.3    
61.5    
61.8    
62.1    
62.4    
62.6    
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64.0    
64.3    
64.6    
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65.1    
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89.3    
89.6    
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90.4    
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92.6    
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97.3    
97.5    
97.8    
98.1    
98.4    
98.6    
98.9    
99.2    
99.5    
99.7    
-found 32 predictions from path traversal
Error with prediction: snap lend_intergenic: 27376, rend_intergenic: 1753  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36555, rend_intergenic: 34569  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52105, rend_intergenic: 47132  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62848, rend_intergenic: 52352  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66055, rend_intergenic: 64230  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80855, rend_intergenic: 69333  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81801, rend_intergenic: 81008  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85238, rend_intergenic: 83548  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88829, rend_intergenic: 85928  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91744, rend_intergenic: 89177  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92541, rend_intergenic: 92151  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94864, rend_intergenic: 92809  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107199, rend_intergenic: 105497  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110778, rend_intergenic: 107565  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124213, rend_intergenic: 114967  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145681, rend_intergenic: 127199  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152985, rend_intergenic: 149001  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165763, rend_intergenic: 153275  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173165, rend_intergenic: 166268  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 124213, rend_intergenic: 124210  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 24 predictions persist after filtering for low support