-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_5/scaffold_5_15731330-15911826

-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 snap_scaffold_5-snap.2888-T1
Valid prediction for GlimmerHMM_glimmerT_13280-T1
Valid prediction for GlimmerHMM_glimmerT_13262-T1
Valid prediction for snap_scaffold_5-snap.2922-T1
Valid prediction for GlimmerHMM_glimmerT_13278-T1
Valid prediction for pasa_asmbl_46014.p1
Valid prediction for snap_scaffold_5-snap.2902-T1
Valid prediction for snap_scaffold_5-snap.2894-T1
Valid prediction for snap_scaffold_5-snap.2884-T1
Valid prediction for snap_scaffold_5-snap.2912-T1
Valid prediction for snap_scaffold_5-snap.2908-T1
Valid prediction for GlimmerHMM_glimmerT_13285-T1
Valid prediction for GlimmerHMM_glimmerT_13263-T1
Couldn't classify 162212, 162250
Sorry, prediction pasa_asmbl_46027.p1 fails validation.
(GCT)	 GA	162212-162250	GT	TGG
(TCT)	 AG	162734-162761	GT	TGG
(AGT)	 AG	164766-164909	GT	GGG
(AGA)	 AG	165761-165934	GT	AGG
(GGG)	 AG	166277-166354	GT	AGG
(AAC)	 AG	167729-167757	AG	GAA
add_exon() Sorry, pasa_asmbl_46027.p1 165761-165934-terminal-1 is invalid.
-recovered pasa_asmbl_46027.p1, terminal, 165761, 165934
-recovered pasa_asmbl_46027.p1, terminal, 167729, 167757
-recovered pasa_asmbl_46027.p1, internal, 162734, 162761
-recovered pasa_asmbl_46027.p1, internal, 164766, 164909
-recovered pasa_asmbl_46027.p1, internal, 165761, 165934
-recovered pasa_asmbl_46027.p1, internal, 166277, 166354
Valid prediction for snap_scaffold_5-snap.2905-T1
Valid prediction for snap_scaffold_5-snap.2896-T1
Couldn't classify 144073, 144168
Sorry, prediction pasa_asmbl_46419.p1 fails validation.
(ATG)	 AG	143308-143417	GT	CTG
(GTC)	 AG	143850-143967	GT	TAG
(AGG)	 AG	144073-144168	GG	AGG
-recovered pasa_asmbl_46419.p1, initial, 143308, 143417
-recovered pasa_asmbl_46419.p1, internal, 143308, 143417
-recovered pasa_asmbl_46419.p1, internal, 143850, 143967
Valid prediction for GlimmerHMM_glimmerT_13271-T1
Valid prediction for snap_scaffold_5-snap.2886-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_5-snap.2917-T1
Valid prediction for GlimmerHMM_glimmerT_13270-T1
Valid prediction for Augustus_model.g8820.t1
Valid prediction for GlimmerHMM_glimmerT_13266-T1
Valid prediction for GlimmerHMM_glimmerT_13269-T1
Valid prediction for Augustus_model.g8821.t1
Valid prediction for GlimmerHMM_glimmerT_13281-T1
Valid prediction for GlimmerHMM_glimmerT_13286-T1
Valid prediction for HiQ_model.g8833.t1
Valid prediction for snap_scaffold_5-snap.2893-T1
Valid prediction for GlimmerHMM_glimmerT_13282-T1
Valid prediction for snap_scaffold_5-snap.2915-T1
Valid prediction for snap_scaffold_5-snap.2914-T1
Valid prediction for CodingQuarry_transcript_52401-T1
Valid prediction for GlimmerHMM_glimmerT_13268-T1
Valid prediction for snap_scaffold_5-snap.2906-T1
Valid prediction for Augustus_model.g8816.t1
Valid prediction for GlimmerHMM_glimmerT_13277-T1
Valid prediction for Augustus_model.g8815.t1
Valid prediction for Augustus_model.g8835.t1
Valid prediction for GlimmerHMM_glimmerT_13267-T1
Valid prediction for GlimmerHMM_glimmerT_13284-T1
Valid prediction for snap_scaffold_5-snap.2891-T1
Valid prediction for snap_scaffold_5-snap.2895-T1
Valid prediction for snap_scaffold_5-snap.2907-T1
Valid prediction for Augustus_model.g8831.t1
Valid prediction for Augustus_model.g8819.t1
Valid prediction for snap_scaffold_5-snap.2919-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_5-snap.2910-T1
Valid prediction for snap_scaffold_5-snap.2889-T1
Couldn't classify 120302, 120338
Sorry, prediction pasa_asmbl_44723.p1 fails validation.
(GCC)	 AC	120302-120338	GT	TGG
(GCA)	 AG	120462-120537	GT	GAG
(GAT)	 AG	120673-120739	GT	AGG
(ATT)	 AG	120960-121085	GT	ACG
(GTC)	 AG	121197-121301	AA	GAA
add_exon() Sorry, pasa_asmbl_44723.p1 120462-120537-terminal-3 is invalid.
-recovered pasa_asmbl_44723.p1, terminal, 120462, 120537
-recovered pasa_asmbl_44723.p1, terminal, 121197, 121301
-recovered pasa_asmbl_44723.p1, internal, 120462, 120537
-recovered pasa_asmbl_44723.p1, internal, 120673, 120739
-recovered pasa_asmbl_44723.p1, internal, 120960, 121085
Valid prediction for snap_scaffold_5-snap.2923-T1
Valid prediction for GlimmerHMM_glimmerT_13274-T1
Valid prediction for snap_scaffold_5-snap.2903-T1
Valid prediction for GlimmerHMM_glimmerT_13275-T1
Valid prediction for pasa_asmbl_44730.p1
Valid prediction for Augustus_model.g8817.t1
Valid prediction for GlimmerHMM_glimmerT_13276-T1
Valid prediction for CodingQuarry_transcript_52404-T1
Valid prediction for snap_scaffold_5-snap.2892-T1
Valid prediction for Augustus_model.g8837.t1
Valid prediction for snap_scaffold_5-snap.2885-T1
Valid prediction for snap_scaffold_5-snap.2911-T1
Valid prediction for snap_scaffold_5-snap.2913-T1
Valid prediction for GlimmerHMM_glimmerT_13264-T1
Valid prediction for Augustus_model.g8822.t1
Valid prediction for Augustus_model.g8828.t1
Valid prediction for snap_scaffold_5-snap.2899-T1
Couldn't classify 119300, 119605
Couldn't classify 120215, 120232
Sorry, prediction pasa_asmbl_44724.p1 fails validation.
(ACT)	 GG	119300-119605	GT	AGG
(GTT)	 AG	119706-119750	GT	AGG
(TGG)	 AG	119830-119886	GT	AGG
(ATG)	 AG	119984-120127	GT	AGG
(GTC)	 AG	120215-120232	CC	CAC
-recovered pasa_asmbl_44724.p1, initial, 119984, 120127
-recovered pasa_asmbl_44724.p1, internal, 119706, 119750
-recovered pasa_asmbl_44724.p1, internal, 119830, 119886
-recovered pasa_asmbl_44724.p1, internal, 119984, 120127
Couldn't classify 155954, 156100
Sorry, prediction pasa_asmbl_44722.p1 fails validation.
(GAG)	 AG	155954-156100	GT	GGG
(GAC)	 AG	156186-156238	GT	ACG
(GCT)	 AG	156357-156423	GT	CAG
(GCG)	 AG	156667-156738	TT	GAT
-recovered pasa_asmbl_44722.p1, terminal, 156667, 156738
-recovered pasa_asmbl_44722.p1, internal, 155954, 156100
-recovered pasa_asmbl_44722.p1, internal, 156186, 156238
-recovered pasa_asmbl_44722.p1, internal, 156357, 156423
Valid prediction for Augustus_model.g8834.t1
Valid prediction for Augustus_model.g8824.t1
Valid prediction for CodingQuarry_transcript_52403-T1
Valid prediction for snap_scaffold_5-snap.2898-T1
Valid prediction for Augustus_model.g8830.t1
Valid prediction for Augustus_model.g8832.t1
Valid prediction for snap_scaffold_5-snap.2918-T1
Valid prediction for snap_scaffold_5-snap.2897-T1
Valid prediction for GlimmerHMM_glimmerT_13283-T1
Valid prediction for Augustus_model.g8826.t1
Valid prediction for Augustus_model.g8818.t1
Valid prediction for Augustus_model.g8829.t1
Valid prediction for snap_scaffold_5-snap.2909-T1
Valid prediction for snap_scaffold_5-snap.2921-T1
Valid prediction for HiQ_model.g8825.t1
Valid prediction for snap_scaffold_5-snap.2900-T1
Valid prediction for snap_scaffold_5-snap.2920-T1
Valid prediction for snap_scaffold_5-snap.2916-T1
Valid prediction for Augustus_model.g8823.t1
Valid prediction for Augustus_model.g8836.t1
Valid prediction for GlimmerHMM_glimmerT_13273-T1
Valid prediction for snap_scaffold_5-snap.2887-T1
Valid prediction for GlimmerHMM_glimmerT_13279-T1
Valid prediction for snap_scaffold_5-snap.2901-T1
Valid prediction for Augustus_model.g8827.t1
Valid prediction for GlimmerHMM_glimmerT_13272-T1
Valid prediction for snap_scaffold_5-snap.2890-T1
Valid prediction for GlimmerHMM_glimmerT_13265-T1
Valid prediction for snap_scaffold_5-snap.2904-T1
Valid prediction for CodingQuarry_transcript_52402-T1
Couldn't classify 101047, 101232
Couldn't classify 102232, 102324
Sorry, prediction pasa_asmbl_44733.p1 fails validation.
(GGT)	 CA	101047-101232	GT	AGG
(CAC)	 AG	101523-101615	GT	CGG
(TCC)	 AG	102232-102324	GC	CCG
-recovered pasa_asmbl_44733.p1, internal, 101523, 101615
-recovered pasa_asmbl_44733.p1, internal, 102232, 102324

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 6438, rend_intergenic: 2072  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15470, rend_intergenic: 7220  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16511, rend_intergenic: 15983  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17543, rend_intergenic: 17173  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30564, rend_intergenic: 26682  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83039, rend_intergenic: 78006  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114355, rend_intergenic: 83352  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127661, rend_intergenic: 120598  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130957, rend_intergenic: 130065  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141070, rend_intergenic: 131491  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149560, rend_intergenic: 145628  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167757, rend_intergenic: 164786  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 180497
-exon list size: 436


building trellis

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18.9    
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20.8    
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22.8    
23.1    
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23.5    
23.7    
24.0    
24.2    
24.4    
24.7    
24.9    
25.1    
25.3    
25.6    
25.8    
26.0    
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26.9    
27.2    
27.4    
27.6    
27.9    
28.1    
28.3    
28.5    
28.8    
29.0    
29.2    
29.5    
29.7    
29.9    
30.1    
30.4    
30.6    
30.8    
31.1    
31.3    
31.5    
31.7    
32.0    
32.2    
32.4    
32.6    
32.9    
33.1    
33.3    
33.6    
33.8    
34.0    
34.2    
34.5    
34.7    
34.9    
35.2    
35.4    
35.6    
35.8    
36.1    
36.3    
36.5    
36.8    
37.0    
37.2    
37.4    
37.7    
37.9    
38.1    
38.4    
38.6    
38.8    
39.0    
39.3    
39.5    
39.7    
40.0    
40.2    
40.4    
40.6    
40.9    
41.1    
41.3    
41.6    
41.8    
42.0    
42.2    
42.5    
42.7    
42.9    
43.2    
43.4    
43.6    
43.8    
44.1    
44.3    
44.5    
44.7    
45.0    
45.2    
45.4    
45.7    
45.9    
46.1    
46.3    
46.6    
46.8    
47.0    
47.3    
47.5    
47.7    
47.9    
48.2    
48.4    
48.6    
48.9    
49.1    
49.3    
49.5    
49.8    
50.0    
50.2    
50.5    
50.7    
50.9    
51.1    
51.4    
51.6    
51.8    
52.1    
52.3    
52.5    
52.7    
53.0    
53.2    
53.4    
53.7    
53.9    
54.1    
54.3    
54.6    
54.8    
55.0    
55.3    
55.5    
55.7    
55.9    
56.2    
56.4    
56.6    
56.8    
57.1    
57.3    
57.5    
57.8    
58.0    
58.2    
58.4    
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58.9    
59.1    
59.4    
59.6    
59.8    
60.0    
60.3    
60.5    
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61.0    
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61.4    
61.6    
61.9    
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62.6    
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63.0    
63.2    
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63.7    
63.9    
64.2    
64.4    
64.6    
64.8    
65.1    
65.3    
65.5    
65.8    
66.0    
66.2    
66.4    
66.7    
66.9    
67.1    
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67.6    
67.8    
68.0    
68.3    
68.5    
68.7    
68.9    
69.2    
69.4    
69.6    
69.9    
70.1    
70.3    
70.5    
70.8    
71.0    
71.2    
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71.9    
72.1    
72.4    
72.6    
72.8    
73.1    
73.3    
73.5    
73.7    
74.0    
74.2    
74.4    
74.7    
74.9    
75.1    
75.3    
75.6    
75.8    
76.0    
76.3    
76.5    
76.7    
76.9    
77.2    
77.4    
77.6    
77.9    
78.1    
78.3    
78.5    
78.8    
79.0    
79.2    
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79.7    
79.9    
80.1    
80.4    
80.6    
80.8    
81.1    
81.3    
81.5    
81.7    
82.0    
82.2    
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82.9    
83.1    
83.3    
83.6    
83.8    
84.0    
84.2    
84.5    
84.7    
84.9    
85.2    
85.4    
85.6    
85.8    
86.1    
86.3    
86.5    
86.8    
87.0    
87.2    
87.4    
87.7    
87.9    
88.1    
88.4    
88.6    
88.8    
89.0    
89.3    
89.5    
89.7    
90.0    
90.2    
90.4    
90.6    
90.9    
91.1    
91.3    
91.6    
91.8    
92.0    
92.2    
92.5    
92.7    
92.9    
93.2    
93.4    
93.6    
93.8    
94.1    
94.3    
94.5    
94.7    
95.0    
95.2    
95.4    
95.7    
95.9    
96.1    
96.3    
96.6    
96.8    
97.0    
97.3    
97.5    
97.7    
97.9    
98.2    
98.4    
98.6    
98.9    
99.1    
99.3    
99.5    
99.8    
-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 6438, rend_intergenic: 2072  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15470, rend_intergenic: 7220  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16511, rend_intergenic: 15983  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17543, rend_intergenic: 17173  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30564, rend_intergenic: 26682  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83039, rend_intergenic: 78006  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114355, rend_intergenic: 83352  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127661, rend_intergenic: 120598  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130957, rend_intergenic: 130065  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141070, rend_intergenic: 131491  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149560, rend_intergenic: 145628  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167757, rend_intergenic: 164786  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 23 predictions persist after filtering for low support