-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_13/scaffold_13_1645640-1917055

-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_13-snap.317-T1
Valid prediction for GlimmerHMM_glimmerT_31134-T1
Valid prediction for snap_scaffold_13-snap.305-T1
Valid prediction for snap_scaffold_13-snap.316-T1
Valid prediction for GlimmerHMM_glimmerT_31142-T1
Valid prediction for snap_scaffold_13-snap.323-T1
Valid prediction for snap_scaffold_13-snap.337-T1
Valid prediction for snap_scaffold_13-snap.310-T1
Valid prediction for snap_scaffold_13-snap.336-T1
Valid prediction for snap_scaffold_13-snap.319-T1
Valid prediction for GlimmerHMM_glimmerT_31118-T1
Valid prediction for Augustus_model.g20680.t1
Valid prediction for Augustus_model.g20681.t1
Valid prediction for GlimmerHMM_glimmerT_31126-T1
Valid prediction for GlimmerHMM_glimmerT_31140-T1
Valid prediction for snap_scaffold_13-snap.312-T1
Valid prediction for snap_scaffold_13-snap.313-T1
Valid prediction for snap_scaffold_13-snap.338-T1
Valid prediction for GlimmerHMM_glimmerT_31115-T1
Valid prediction for snap_scaffold_13-snap.330-T1
Valid prediction for GlimmerHMM_glimmerT_31128-T1
Valid prediction for snap_scaffold_13-snap.324-T1
Valid prediction for GlimmerHMM_glimmerT_31136-T1
Valid prediction for snap_scaffold_13-snap.347-T1
Valid prediction for Augustus_model.g20673.t1
Valid prediction for snap_scaffold_13-snap.341-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_13-snap.329-T1
Valid prediction for snap_scaffold_13-snap.303-T1
Valid prediction for snap_scaffold_13-snap.331-T1
Valid prediction for GlimmerHMM_glimmerT_31137-T1
Couldn't classify 189512, 189604
Couldn't classify 190106, 190513
Sorry, prediction pasa_asmbl_10572.p1 fails validation.
(CTG)	 AC	189512-189604	GT	AGG
(GCG)	 AG	189848-189946	GT	AGG
(ATC)	 AG	190106-190513	AA	TGA
-recovered pasa_asmbl_10572.p1, internal, 189848, 189946
Valid prediction for GlimmerHMM_glimmerT_31129-T1
Valid prediction for Augustus_model.g20676.t1
Valid prediction for snap_scaffold_13-snap.344-T1
Valid prediction for snap_scaffold_13-snap.308-T1
Valid prediction for Augustus_model.g20683.t1
Valid prediction for GlimmerHMM_glimmerT_31139-T1
Valid prediction for GlimmerHMM_glimmerT_31123-T1
Couldn't classify 129154, 129216
Couldn't classify 130569, 130592
Sorry, prediction pasa_asmbl_10568.p1 fails validation.
(CCG)	 AC	129154-129216	GT	ATG
(TTA)	 AG	129406-129547	GT	AGG
(GCC)	 AG	129658-129821	GT	AGG
(ACC)	 AG	130052-130186	GT	GAG
(TAC)	 AG	130288-130473	GT	AGG
(GCT)	 AG	130569-130592	GT	AGG
add_exon() Sorry, pasa_asmbl_10568.p1 129406-129547-terminal-3 is invalid.
-recovered pasa_asmbl_10568.p1, terminal, 129406, 129547
-recovered pasa_asmbl_10568.p1, internal, 129406, 129547
-recovered pasa_asmbl_10568.p1, internal, 129658, 129821
-recovered pasa_asmbl_10568.p1, internal, 130052, 130186
-recovered pasa_asmbl_10568.p1, internal, 130288, 130473
-recovered pasa_asmbl_10568.p1, internal, 130569, 130592
Valid prediction for snap_scaffold_13-snap.306-T1
Valid prediction for GlimmerHMM_glimmerT_31116-T1
Valid prediction for GlimmerHMM_glimmerT_31141-T1
Valid prediction for Augustus_model.g20682.t1
Valid prediction for snap_scaffold_13-snap.335-T1
Valid prediction for snap_scaffold_13-snap.333-T1
Valid prediction for snap_scaffold_13-snap.320-T1
Valid prediction for GlimmerHMM_glimmerT_31127-T1
Couldn't classify 192603, 195800
Sorry, prediction pasa_asmbl_10573.p1 fails validation.
(CAA)	 TG	192603-195800	CA	AAC
Valid prediction for snap_scaffold_13-snap.315-T1
Couldn't classify 132266, 132316
Couldn't classify 133161, 133505
Sorry, prediction pasa_asmbl_10569.p1 fails validation.
(ACC)	 AC	132266-132316	GT	AGG
(GAA)	 AG	132437-132754	GT	GTG
(AAA)	 AG	133161-133505	AC	AGA
-recovered pasa_asmbl_10569.p1, internal, 132437, 132754
Valid prediction for snap_scaffold_13-snap.304-T1
Valid prediction for Augustus_model.g20675.t1
Valid prediction for snap_scaffold_13-snap.334-T1
Valid prediction for snap_scaffold_13-snap.309-T1
Valid prediction for GlimmerHMM_glimmerT_31138-T1
Valid prediction for snap_scaffold_13-snap.340-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_13-snap.349-T1
Valid prediction for GlimmerHMM_glimmerT_31135-T1
Valid prediction for snap_scaffold_13-snap.302-T1
Valid prediction for snap_scaffold_13-snap.318-T1
Valid prediction for GlimmerHMM_glimmerT_31121-T1
Valid prediction for pasa_asmbl_9425.p1
Valid prediction for GlimmerHMM_glimmerT_31124-T1
Couldn't classify 155363, 155617
Sorry, prediction pasa_asmbl_9422.p1 fails validation.
(TCC)	 AA	155363-155617	GT	AGG
(AGA)	 AG	156009-156206	AC	GAA
-recovered pasa_asmbl_9422.p1, terminal, 156009, 156206
Valid prediction for Augustus_model.g20668.t1
Valid prediction for snap_scaffold_13-snap.307-T1
Valid prediction for GlimmerHMM_glimmerT_31132-T1
Valid prediction for snap_scaffold_13-snap.348-T1
Valid prediction for Augustus_model.g20672.t1
Valid prediction for CodingQuarry_transcript_12872-T1
Valid prediction for snap_scaffold_13-snap.345-T1
Valid prediction for snap_scaffold_13-snap.301-T1
Valid prediction for GlimmerHMM_glimmerT_31133-T1
Valid prediction for snap_scaffold_13-snap.322-T1
Valid prediction for Augustus_model.g20679.t1
Valid prediction for snap_scaffold_13-snap.314-T1
Valid prediction for Augustus_model.g20685.t1
Valid prediction for Augustus_model.g20674.t1
Valid prediction for GlimmerHMM_glimmerT_31122-T1
Valid prediction for snap_scaffold_13-snap.321-T1
Valid prediction for snap_scaffold_13-snap.342-T1
Valid prediction for Augustus_model.g20669.t1
Valid prediction for GlimmerHMM_glimmerT_31125-T1
Valid prediction for snap_scaffold_13-snap.311-T1
Valid prediction for snap_scaffold_13-snap.325-T1
Valid prediction for snap_scaffold_13-snap.326-T1
Valid prediction for Augustus_model.g20677.t1
Valid prediction for Augustus_model.g20671.t1
Valid prediction for Augustus_model.g20670.t1
Valid prediction for GlimmerHMM_glimmerT_31131-T1
Valid prediction for GlimmerHMM_glimmerT_31117-T1
Valid prediction for snap_scaffold_13-snap.346-T1
Valid prediction for GlimmerHMM_glimmerT_31119-T1
Valid prediction for GlimmerHMM_glimmerT_31130-T1
Valid prediction for GlimmerHMM_glimmerT_31120-T1
Valid prediction for snap_scaffold_13-snap.339-T1
Valid prediction for snap_scaffold_13-snap.343-T1
Valid prediction for GlimmerHMM_glimmerT_31143-T1
Valid prediction for snap_scaffold_13-snap.327-T1
Couldn't classify 152588, 152767
Couldn't classify 155083, 155126
Sorry, prediction pasa_asmbl_9423.p1 fails validation.
(GTG)	 CT	152588-152767	GT	AGG
(CCG)	 AG	152892-153139	GT	AAG
(ATA)	 AG	153331-153473	GT	CAG
(GTG)	 AG	154070-154291	GT	TGG
(ATA)	 AG	154529-154750	GT	CTG
(GTG)	 AG	155083-155126	AT	AGA
-recovered pasa_asmbl_9423.p1, internal, 152892, 153139
-recovered pasa_asmbl_9423.p1, internal, 153331, 153473
-recovered pasa_asmbl_9423.p1, internal, 154070, 154291
-recovered pasa_asmbl_9423.p1, internal, 154529, 154750
Valid prediction for snap_scaffold_13-snap.300-T1
Valid prediction for snap_scaffold_13-snap.332-T1
Valid prediction for Augustus_model.g20678.t1
Valid prediction for snap_scaffold_13-snap.328-T1
Valid prediction for Augustus_model.g20684.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 86539, rend_intergenic: 83116  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165190, rend_intergenic: 158267  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168756, rend_intergenic: 168529  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173085, rend_intergenic: 168977  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 215366, rend_intergenic: 207994  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 257721, rend_intergenic: 252988  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 260595, rend_intergenic: 258827  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 262419, rend_intergenic: 261013  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 271416
-exon list size: 404


building trellis

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3.9    
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23.9    
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25.6    
25.9    
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27.1    
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27.6    
27.8    
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28.6    
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29.6    
29.8    
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30.5    
30.8    
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31.3    
31.5    
31.8    
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32.3    
32.5    
32.8    
33.0    
33.3    
33.5    
33.7    
34.0    
34.2    
34.5    
34.7    
35.0    
35.2    
35.5    
35.7    
36.0    
36.2    
36.5    
36.7    
36.9    
37.2    
37.4    
37.7    
37.9    
38.2    
38.4    
38.7    
38.9    
39.2    
39.4    
39.7    
39.9    
40.1    
40.4    
40.6    
40.9    
41.1    
41.4    
41.6    
41.9    
42.1    
42.4    
42.6    
42.9    
43.1    
43.3    
43.6    
43.8    
44.1    
44.3    
44.6    
44.8    
45.1    
45.3    
45.6    
45.8    
46.1    
46.3    
46.6    
46.8    
47.0    
47.3    
47.5    
47.8    
48.0    
48.3    
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49.0    
49.3    
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53.2    
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53.7    
53.9    
54.2    
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54.9    
55.2    
55.4    
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55.9    
56.2    
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57.6    
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58.1    
58.4    
58.6    
58.9    
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59.4    
59.6    
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60.1    
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60.6    
60.8    
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62.1    
62.3    
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63.1    
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64.0    
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66.3    
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66.7    
67.0    
67.2    
67.5    
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68.0    
68.2    
68.5    
68.7    
69.0    
69.2    
69.5    
69.7    
70.0    
70.2    
70.4    
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70.9    
71.2    
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72.2    
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72.9    
73.2    
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73.6    
73.9    
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74.4    
74.6    
74.9    
75.1    
75.4    
75.6    
75.9    
76.1    
76.4    
76.6    
76.8    
77.1    
77.3    
77.6    
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78.1    
78.3    
78.6    
78.8    
79.1    
79.3    
79.6    
79.8    
80.0    
80.3    
80.5    
80.8    
81.0    
81.3    
81.5    
81.8    
82.0    
82.3    
82.5    
82.8    
83.0    
83.3    
83.5    
83.7    
84.0    
84.2    
84.5    
84.7    
85.0    
85.2    
85.5    
85.7    
86.0    
86.2    
86.5    
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86.9    
87.2    
87.4    
87.7    
87.9    
88.2    
88.4    
88.7    
88.9    
89.2    
89.4    
89.7    
89.9    
90.1    
90.4    
90.6    
90.9    
91.1    
91.4    
91.6    
91.9    
92.1    
92.4    
92.6    
92.9    
93.1    
93.3    
93.6    
93.8    
94.1    
94.3    
94.6    
94.8    
95.1    
95.3    
95.6    
95.8    
96.1    
96.3    
96.6    
96.8    
97.0    
97.3    
97.5    
97.8    
98.0    
98.3    
98.5    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 86539, rend_intergenic: 83116  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165190, rend_intergenic: 158267  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168756, rend_intergenic: 168529  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173085, rend_intergenic: 168977  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 215366, rend_intergenic: 207994  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 257721, rend_intergenic: 252988  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 260595, rend_intergenic: 258827  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 262419, rend_intergenic: 261013  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 26 predictions persist after filtering for low support