-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_2/scaffold_2_507380-651794

-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: +)Couldn't classify 76089, 76330
Couldn't classify 76465, 77041
Sorry, prediction pasa_asmbl_24088.p2 fails validation.
(TCG)	 AG	76089-76330	GT	GGG
(GTA)	 AG	76465-77041	CT	ACC
-recovered pasa_asmbl_24088.p2, internal, 76089, 76330
Valid prediction for GlimmerHMM_glimmerT_3077-T1
Valid prediction for snap_scaffold_2-snap.119-T1
Valid prediction for snap_scaffold_2-snap.118-T1
Valid prediction for Augustus_model.g2085.t1
Valid prediction for snap_scaffold_2-snap.146-T1
Valid prediction for Augustus_model.g2086.t1
Valid prediction for snap_scaffold_2-snap.142-T1
Valid prediction for GlimmerHMM_glimmerT_3067-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_2-snap.150-T1
Valid prediction for snap_scaffold_2-snap.120-T1
Couldn't classify 77705, 78100
Sorry, prediction pasa_asmbl_24089.p1 fails validation.
(CCC)	 CG	77705-78100	CG	GAC
Valid prediction for snap_scaffold_2-snap.137-T1
Valid prediction for snap_scaffold_2-snap.124-T1
Valid prediction for snap_scaffold_2-snap.125-T1
Valid prediction for GlimmerHMM_glimmerT_3063-T1
Valid prediction for snap_scaffold_2-snap.126-T1
Sorry, intron length (9) is less than minimum required (10)
Couldn't classify 135624, 135821
Sorry, prediction pasa_asmbl_24090.p1 fails validation.
(TCA)	 TG	135624-135821	GT	AGG
(GCG)	 AG	136915-137031	GT	CTG
(GTG)	 AG	137628-137777	GT	AGG
(ATC)	 AG	138180-138344	GT	AGG
(GAA)	 AG	138515-138631	GT	AGG
(GAC)	 AG	139462-139566	GT	AGG
(GGA)	 AG	139789-139885	GT	GGG
(GTG)	 AG	140302-140414	GT	GAG
(TCG)	 AG	141030-141120	GT	AGG
(AGC)	 AG	141306-141445	GT	AGG
(CTT)	 AG	141554-141679	CC	GAC
-recovered pasa_asmbl_24090.p1, terminal, 141554, 141679
-recovered pasa_asmbl_24090.p1, internal, 136915, 137031
-recovered pasa_asmbl_24090.p1, internal, 137628, 137777
-recovered pasa_asmbl_24090.p1, internal, 138180, 138344
-recovered pasa_asmbl_24090.p1, internal, 138515, 138631
-recovered pasa_asmbl_24090.p1, internal, 139462, 139566
-recovered pasa_asmbl_24090.p1, internal, 139789, 139885
-recovered pasa_asmbl_24090.p1, internal, 140302, 140414
-recovered pasa_asmbl_24090.p1, internal, 141030, 141120
-recovered pasa_asmbl_24090.p1, internal, 141306, 141445
Valid prediction for snap_scaffold_2-snap.144-T1
Valid prediction for snap_scaffold_2-snap.136-T1
Valid prediction for GlimmerHMM_glimmerT_3082-T1
Valid prediction for Augustus_model.g2083.t1
Valid prediction for snap_scaffold_2-snap.131-T1
Valid prediction for GlimmerHMM_glimmerT_3068-T1
Valid prediction for Augustus_model.g2092.t1
Valid prediction for snap_scaffold_2-snap.138-T1
Valid prediction for GlimmerHMM_glimmerT_3075-T1
Valid prediction for GlimmerHMM_glimmerT_3081-T1
Valid prediction for snap_scaffold_2-snap.148-T1
Valid prediction for snap_scaffold_2-snap.129-T1
Valid prediction for GlimmerHMM_glimmerT_3080-T1
Valid prediction for GlimmerHMM_glimmerT_3074-T1
Valid prediction for GlimmerHMM_glimmerT_3065-T1
Valid prediction for snap_scaffold_2-snap.151-T1
Valid prediction for HiQ_model.g2093.t1
Valid prediction for snap_scaffold_2-snap.127-T1
Valid prediction for HiQ_model.g2089.t1
Valid prediction for GlimmerHMM_glimmerT_3083-T1
Valid prediction for snap_scaffold_2-snap.140-T1
Valid prediction for GlimmerHMM_glimmerT_3085-T1
Valid prediction for snap_scaffold_2-snap.147-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_3084-T1
Valid prediction for CodingQuarry_transcript_28426-T1
Valid prediction for Augustus_model.g2091.t1
Valid prediction for snap_scaffold_2-snap.139-T1
Valid prediction for GlimmerHMM_glimmerT_3078-T1
Valid prediction for GlimmerHMM_glimmerT_3076-T1
Valid prediction for GlimmerHMM_glimmerT_3073-T1
Valid prediction for CodingQuarry_transcript_28428-T1
Valid prediction for GlimmerHMM_glimmerT_3072-T1
Valid prediction for GlimmerHMM_glimmerT_3071-T1
Valid prediction for Augustus_model.g2084.t1
Valid prediction for snap_scaffold_2-snap.145-T1
Valid prediction for GlimmerHMM_glimmerT_3064-T1
Valid prediction for snap_scaffold_2-snap.135-T1
Valid prediction for GlimmerHMM_glimmerT_3069-T1
Valid prediction for snap_scaffold_2-snap.152-T1
Valid prediction for snap_scaffold_2-snap.128-T1
Valid prediction for snap_scaffold_2-snap.122-T1
Valid prediction for snap_scaffold_2-snap.132-T1
Couldn't classify 58683, 58798
Sorry, prediction pasa_asmbl_22811.p1 fails validation.
(GTG)	 GT	58683-58798	GT	AGG
(CGA)	 AG	58908-58991	GT	AGG
(AGA)	 AG	59144-59234	GT	ATG
(ATC)	 AG	59330-59443	GT	AGG
(GTG)	 AG	59718-59801	GT	TGG
(AAC)	 AG	60435-60545	GT	CCG
(GTG)	 AG	61820-61915	GT	AGG
(ATA)	 AG	62128-62241	GT	AGG
(CTT)	 AG	62904-63014	CC	AAC
-recovered pasa_asmbl_22811.p1, terminal, 62904, 63014
-recovered pasa_asmbl_22811.p1, internal, 58908, 58991
-recovered pasa_asmbl_22811.p1, internal, 59144, 59234
-recovered pasa_asmbl_22811.p1, internal, 59330, 59443
-recovered pasa_asmbl_22811.p1, internal, 59718, 59801
-recovered pasa_asmbl_22811.p1, internal, 60435, 60545
-recovered pasa_asmbl_22811.p1, internal, 61820, 61915
-recovered pasa_asmbl_22811.p1, internal, 62128, 62241
Valid prediction for snap_scaffold_2-snap.123-T1
Valid prediction for Augustus_model.g2087.t1
Valid prediction for snap_scaffold_2-snap.134-T1
Valid prediction for GlimmerHMM_glimmerT_3079-T1
Valid prediction for snap_scaffold_2-snap.143-T1
Valid prediction for snap_scaffold_2-snap.133-T1
Valid prediction for Augustus_model.g2088.t1
Valid prediction for snap_scaffold_2-snap.141-T1
Valid prediction for Augustus_model.g2090.t1
Valid prediction for snap_scaffold_2-snap.130-T1
Valid prediction for GlimmerHMM_glimmerT_3066-T1
Valid prediction for snap_scaffold_2-snap.149-T1
Valid prediction for snap_scaffold_2-snap.121-T1
Valid prediction for GlimmerHMM_glimmerT_3070-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 23024, rend_intergenic: 19941  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32638, rend_intergenic: 29793  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46984, rend_intergenic: 43448  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52061, rend_intergenic: 48096  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57976, rend_intergenic: 53420  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73491, rend_intergenic: 71617  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83228, rend_intergenic: 80543  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91998, rend_intergenic: 83859  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92789, rend_intergenic: 91999  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108689, rend_intergenic: 92820  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120048, rend_intergenic: 118488  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121447, rend_intergenic: 120066  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127015, rend_intergenic: 125192  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133377, rend_intergenic: 132065  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141679, rend_intergenic: 136802  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 144415
-exon list size: 275


building trellis

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25.6    
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32.5    
32.9    
33.2    
33.6    
33.9    
34.3    
34.7    
35.0    
35.4    
35.7    
36.1    
36.5    
36.8    
37.2    
37.5    
37.9    
38.3    
38.6    
39.0    
39.4    
39.7    
40.1    
40.4    
40.8    
41.2    
41.5    
41.9    
42.2    
42.6    
43.0    
43.3    
43.7    
44.0    
44.4    
44.8    
45.1    
45.5    
45.8    
46.2    
46.6    
46.9    
47.3    
47.7    
48.0    
48.4    
48.7    
49.1    
49.5    
49.8    
50.2    
50.5    
50.9    
51.3    
51.6    
52.0    
52.3    
52.7    
53.1    
53.4    
53.8    
54.2    
54.5    
54.9    
55.2    
55.6    
56.0    
56.3    
56.7    
57.0    
57.4    
57.8    
58.1    
58.5    
58.8    
59.2    
59.6    
59.9    
60.3    
60.6    
61.0    
61.4    
61.7    
62.1    
62.5    
62.8    
63.2    
63.5    
63.9    
64.3    
64.6    
65.0    
65.3    
65.7    
66.1    
66.4    
66.8    
67.1    
67.5    
67.9    
68.2    
68.6    
69.0    
69.3    
69.7    
70.0    
70.4    
70.8    
71.1    
71.5    
71.8    
72.2    
72.6    
72.9    
73.3    
73.6    
74.0    
74.4    
74.7    
75.1    
75.5    
75.8    
76.2    
76.5    
76.9    
77.3    
77.6    
78.0    
78.3    
78.7    
79.1    
79.4    
79.8    
80.1    
80.5    
80.9    
81.2    
81.6    
81.9    
82.3    
82.7    
83.0    
83.4    
83.8    
84.1    
84.5    
84.8    
85.2    
85.6    
85.9    
86.3    
86.6    
87.0    
87.4    
87.7    
88.1    
88.4    
88.8    
89.2    
89.5    
89.9    
90.3    
90.6    
91.0    
91.3    
91.7    
92.1    
92.4    
92.8    
93.1    
93.5    
93.9    
94.2    
94.6    
94.9    
95.3    
95.7    
96.0    
96.4    
96.8    
97.1    
97.5    
97.8    
98.2    
98.6    
98.9    
99.3    
99.6    
-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 23024, rend_intergenic: 19941  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32638, rend_intergenic: 29793  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46984, rend_intergenic: 43448  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52061, rend_intergenic: 48096  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57976, rend_intergenic: 53420  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73491, rend_intergenic: 71617  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83228, rend_intergenic: 80543  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91998, rend_intergenic: 83859  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92789, rend_intergenic: 91999  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108689, rend_intergenic: 92820  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120048, rend_intergenic: 118488  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121447, rend_intergenic: 120066  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127015, rend_intergenic: 125192  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133377, rend_intergenic: 132065  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141679, rend_intergenic: 136802  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

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

-building DP trellis

-building trellis in range 1 - 19810
-exon list size: 8


building trellis

10.0    
20.0    
30.0    
40.0    
50.0    
60.0    
70.0    
80.0    
90.0    
-found 3 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support