-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_4/scaffold_4_11225628-11391934

-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_10220-T1
Valid prediction for Augustus_model.g6656.t1
Valid prediction for snap_scaffold_4-snap.2427-T1
Valid prediction for snap_scaffold_4-snap.2425-T1
Valid prediction for Augustus_model.g6668.t1
Valid prediction for Augustus_model.g6659.t1
Valid prediction for Augustus_model.g6652.t1
Valid prediction for GlimmerHMM_glimmerT_10244-T1
Valid prediction for snap_scaffold_4-snap.2432-T1
Valid prediction for Augustus_model.g6660.t1
Valid prediction for snap_scaffold_4-snap.2435-T1
Valid prediction for GlimmerHMM_glimmerT_10234-T1
Couldn't classify 73813, 73820
Sorry, prediction pasa_asmbl_41702.p1 fails validation.
(CAC)	 AA	73813-73820	GT	AGG
(GAC)	 AG	73920-74154	GT	AGG
(GTG)	 AG	74296-74490	GT	AGG
(GTG)	 AG	74659-75046	GT	TGG
(GCT)	 AG	75919-76095	GT	AGG
(GTA)	 AG	76279-76449	GT	GGG
(GGG)	 AG	76563-76739	GT	CGG
(GTA)	 AG	78477-78579	GT	TGG
(GAA)	 AG	79283-79556	GT	AGG
(GGG)	 AG	79816-80064	CA	GAC
-recovered pasa_asmbl_41702.p1, terminal, 79816, 80064
-recovered pasa_asmbl_41702.p1, internal, 73920, 74154
-recovered pasa_asmbl_41702.p1, internal, 74296, 74490
-recovered pasa_asmbl_41702.p1, internal, 74659, 75046
-recovered pasa_asmbl_41702.p1, internal, 75919, 76095
-recovered pasa_asmbl_41702.p1, internal, 76279, 76449
-recovered pasa_asmbl_41702.p1, internal, 76563, 76739
-recovered pasa_asmbl_41702.p1, internal, 78477, 78579
-recovered pasa_asmbl_41702.p1, internal, 79283, 79556
Valid prediction for snap_scaffold_4-snap.2428-T1
Valid prediction for pasa_asmbl_41704.p1
Valid prediction for Augustus_model.g6664.t1
Valid prediction for snap_scaffold_4-snap.2444-T1
Valid prediction for GlimmerHMM_glimmerT_10224-T1
Valid prediction for GlimmerHMM_glimmerT_10236-T1
Valid prediction for GlimmerHMM_glimmerT_10223-T1
Valid prediction for snap_scaffold_4-snap.2463-T1
Valid prediction for GlimmerHMM_glimmerT_10225-T1
Valid prediction for snap_scaffold_4-snap.2449-T1
Valid prediction for snap_scaffold_4-snap.2451-T1
Valid prediction for Augustus_model.g6669.t1
Valid prediction for Augustus_model.g6650.t1
Valid prediction for snap_scaffold_4-snap.2466-T1
Valid prediction for Augustus_model.g6654.t1
Valid prediction for snap_scaffold_4-snap.2464-T1
Couldn't classify 71724, 71881
Couldn't classify 72646, 72686
Sorry, prediction pasa_asmbl_42242.p1 fails validation.
(CTA)	 AG	71724-71881	GT	AGG
(GGC)	 AG	72392-72519	GT	AGG
(AGC)	 AG	72646-72686	AA	CCA
-recovered pasa_asmbl_42242.p1, internal, 71724, 71881
-recovered pasa_asmbl_42242.p1, internal, 72392, 72519
Valid prediction for snap_scaffold_4-snap.2433-T1
Valid prediction for snap_scaffold_4-snap.2459-T1
Valid prediction for GlimmerHMM_glimmerT_10229-T1
Valid prediction for Augustus_model.g6661.t1
Valid prediction for Augustus_model.g6663.t1
Valid prediction for snap_scaffold_4-snap.2455-T1
Valid prediction for Augustus_model.g6658.t1
Valid prediction for snap_scaffold_4-snap.2467-T1
Valid prediction for GlimmerHMM_glimmerT_10227-T1
Valid prediction for snap_scaffold_4-snap.2440-T1
Valid prediction for snap_scaffold_4-snap.2436-T1
Valid prediction for Augustus_model.g6653.t1
Valid prediction for GlimmerHMM_glimmerT_10231-T1
Valid prediction for snap_scaffold_4-snap.2457-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_4-snap.2439-T1
Valid prediction for GlimmerHMM_glimmerT_10222-T1
Valid prediction for GlimmerHMM_glimmerT_10243-T1
Valid prediction for GlimmerHMM_glimmerT_10233-T1
Valid prediction for snap_scaffold_4-snap.2453-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_10242-T1
Valid prediction for snap_scaffold_4-snap.2461-T1
Valid prediction for snap_scaffold_4-snap.2448-T1
Valid prediction for Augustus_model.g6651.t1
Valid prediction for GlimmerHMM_glimmerT_10228-T1
Valid prediction for snap_scaffold_4-snap.2441-T1
Valid prediction for pasa_asmbl_42880.p1
Valid prediction for HiQ_model.g6667.t1
Valid prediction for snap_scaffold_4-snap.2450-T1
Valid prediction for snap_scaffold_4-snap.2446-T1
Valid prediction for snap_scaffold_4-snap.2443-T1
Valid prediction for snap_scaffold_4-snap.2430-T1
Valid prediction for GlimmerHMM_glimmerT_10239-T1
Valid prediction for snap_scaffold_4-snap.2456-T1
Valid prediction for GlimmerHMM_glimmerT_10241-T1
Valid prediction for snap_scaffold_4-snap.2454-T1
Valid prediction for CodingQuarry_transcript_49137-T1
Valid prediction for snap_scaffold_4-snap.2442-T1
Valid prediction for Augustus_model.g6655.t1
Valid prediction for snap_scaffold_4-snap.2452-T1
Valid prediction for GlimmerHMM_glimmerT_10235-T1
Couldn't classify 56526, 56560
Couldn't classify 56941, 57226
Sorry, prediction pasa_asmbl_43534.p1 fails validation.
(CTG)	 GC	56526-56560	GT	AGG
(GCT)	 AG	56695-56835	GT	AGG
(GGA)	 AG	56941-57226	GG	GAG
-recovered pasa_asmbl_43534.p1, internal, 56695, 56835
Valid prediction for snap_scaffold_4-snap.2437-T1
Valid prediction for snap_scaffold_4-snap.2434-T1
Valid prediction for Augustus_model.g6657.t1
Valid prediction for Augustus_model.g6662.t1
Valid prediction for GlimmerHMM_glimmerT_10221-T1
Valid prediction for CodingQuarry_transcript_49138-T1
Valid prediction for GlimmerHMM_glimmerT_10232-T1
Valid prediction for snap_scaffold_4-snap.2429-T1
Valid prediction for snap_scaffold_4-snap.2438-T1
Valid prediction for snap_scaffold_4-snap.2465-T1
Valid prediction for snap_scaffold_4-snap.2458-T1
Valid prediction for snap_scaffold_4-snap.2462-T1
Valid prediction for pasa_asmbl_43659.p1
Valid prediction for GlimmerHMM_glimmerT_10226-T1
Valid prediction for Augustus_model.g6649.t1
Valid prediction for GlimmerHMM_glimmerT_10238-T1
Valid prediction for snap_scaffold_4-snap.2426-T1
Valid prediction for GlimmerHMM_glimmerT_10237-T1
Valid prediction for CodingQuarry_transcript_49136-T1
Valid prediction for snap_scaffold_4-snap.2447-T1
Valid prediction for Augustus_model.g6665.t1
Valid prediction for GlimmerHMM_glimmerT_10240-T1
Valid prediction for GlimmerHMM_glimmerT_10230-T1
Valid prediction for snap_scaffold_4-snap.2460-T1
Valid prediction for snap_scaffold_4-snap.2445-T1
Valid prediction for snap_scaffold_4-snap.2431-T1
Valid prediction for HiQ_model.g6666.t1
Couldn't classify 53834, 53910
Couldn't classify 56050, 56195
Sorry, prediction pasa_asmbl_42879.p1 fails validation.
(CAC)	 AT	53834-53910	GT	AGG
(TCC)	 AG	54198-54360	GT	AGG
(ATC)	 AG	55365-55479	GT	GGG
(GCG)	 AG	56050-56195	GG	GTG
-recovered pasa_asmbl_42879.p1, internal, 54198, 54360
-recovered pasa_asmbl_42879.p1, internal, 55365, 55479

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 7608, rend_intergenic: 4888  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17698, rend_intergenic: 7899  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21046, rend_intergenic: 17717  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31080, rend_intergenic: 23689  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31443, rend_intergenic: 31246  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37002, rend_intergenic: 31595  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40749, rend_intergenic: 37174  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45201, rend_intergenic: 41072  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58304, rend_intergenic: 49089  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63794, rend_intergenic: 60860  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75279, rend_intergenic: 64361  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79961, rend_intergenic: 75815  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90161, rend_intergenic: 84102  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105162, rend_intergenic: 100044  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113532, rend_intergenic: 110681  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116594, rend_intergenic: 113792  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136509, rend_intergenic: 134291  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 166307
-exon list size: 457


building trellis

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27.9    
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28.8    
29.0    
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29.6    
29.8    
30.1    
30.3    
30.5    
30.7    
30.9    
31.2    
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31.6    
31.8    
32.0    
32.2    
32.5    
32.7    
32.9    
33.1    
33.3    
33.6    
33.8    
34.0    
34.2    
34.4    
34.6    
34.9    
35.1    
35.3    
35.5    
35.7    
35.9    
36.2    
36.4    
36.6    
36.8    
37.0    
37.3    
37.5    
37.7    
37.9    
38.1    
38.3    
38.6    
38.8    
39.0    
39.2    
39.4    
39.7    
39.9    
40.1    
40.3    
40.5    
40.7    
41.0    
41.2    
41.4    
41.6    
41.8    
42.0    
42.3    
42.5    
42.7    
42.9    
43.1    
43.4    
43.6    
43.8    
44.0    
44.2    
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44.9    
45.1    
45.3    
45.5    
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46.0    
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46.6    
46.8    
47.1    
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47.9    
48.1    
48.4    
48.6    
48.8    
49.0    
49.2    
49.5    
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51.0    
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60.1    
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62.1    
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64.3    
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66.4    
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80.0    
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80.4    
80.6    
80.8    
81.0    
81.3    
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81.7    
81.9    
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82.4    
82.6    
82.8    
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83.2    
83.4    
83.7    
83.9    
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84.5    
84.7    
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85.4    
85.6    
85.8    
86.1    
86.3    
86.5    
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86.9    
87.1    
87.4    
87.6    
87.8    
88.0    
88.2    
88.5    
88.7    
88.9    
89.1    
89.3    
89.5    
89.8    
90.0    
90.2    
90.4    
90.6    
90.8    
91.1    
91.3    
91.5    
91.7    
91.9    
92.2    
92.4    
92.6    
92.8    
93.0    
93.2    
93.5    
93.7    
93.9    
94.1    
94.3    
94.6    
94.8    
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95.2    
95.4    
95.6    
95.9    
96.1    
96.3    
96.5    
96.7    
96.9    
97.2    
97.4    
97.6    
97.8    
98.0    
98.3    
98.5    
98.7    
98.9    
99.1    
99.3    
99.6    
99.8    
-found 25 predictions from path traversal
Error with prediction: snap lend_intergenic: 7608, rend_intergenic: 4888  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17698, rend_intergenic: 7899  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21046, rend_intergenic: 17717  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31080, rend_intergenic: 23689  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31443, rend_intergenic: 31246  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37002, rend_intergenic: 31595  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40749, rend_intergenic: 37174  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45201, rend_intergenic: 41072  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58304, rend_intergenic: 49089  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63794, rend_intergenic: 60860  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75279, rend_intergenic: 64361  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79961, rend_intergenic: 75815  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90161, rend_intergenic: 84102  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105162, rend_intergenic: 100044  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113532, rend_intergenic: 110681  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116594, rend_intergenic: 113792  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136509, rend_intergenic: 134291  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support