-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_6/scaffold_6_15732396-15885943

-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_6-snap.3321-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_6-snap.3325-T1
Valid prediction for snap_scaffold_6-snap.3317-T1
Couldn't classify 132703, 132756
Sorry, prediction pasa_asmbl_47674.p1 fails validation.
(ATG)	 AC	127092-127173	GT	TCG
(GCG)	 AG	128499-128690	GT	TGG
(GGT)	 AG	129299-129324	GT	AGG
(GGA)	 AG	129530-129565	GT	GAG
(GGT)	 AG	130478-130570	GT	GAG
(AAC)	 AG	131509-131577	GT	TGG
(GGT)	 AG	131957-132001	GT	GCG
(GGC)	 AG	132703-132756	GT	CTG
-recovered pasa_asmbl_47674.p1, initial, 127092, 127173
-recovered pasa_asmbl_47674.p1, internal, 128499, 128690
-recovered pasa_asmbl_47674.p1, internal, 129299, 129324
-recovered pasa_asmbl_47674.p1, internal, 129530, 129565
-recovered pasa_asmbl_47674.p1, internal, 130478, 130570
-recovered pasa_asmbl_47674.p1, internal, 131509, 131577
-recovered pasa_asmbl_47674.p1, internal, 131957, 132001
-recovered pasa_asmbl_47674.p1, internal, 132703, 132756
Valid prediction for snap_scaffold_6-snap.3337-T1
Valid prediction for HiQ_model.g10853.t1
Valid prediction for Augustus_model.g10862.t1
Valid prediction for snap_scaffold_6-snap.3340-T1
Valid prediction for GlimmerHMM_glimmerT_16149-T1
Valid prediction for GlimmerHMM_glimmerT_16163-T1
Valid prediction for GlimmerHMM_glimmerT_16156-T1
Valid prediction for GlimmerHMM_glimmerT_16168-T1
Valid prediction for GlimmerHMM_glimmerT_16160-T1
Valid prediction for snap_scaffold_6-snap.3341-T1
Valid prediction for Augustus_model.g10855.t1
Valid prediction for GlimmerHMM_glimmerT_16158-T1
Valid prediction for snap_scaffold_6-snap.3332-T1
Valid prediction for snap_scaffold_6-snap.3320-T1
Valid prediction for GlimmerHMM_glimmerT_16157-T1
Valid prediction for pasa_asmbl_47672.p1
Valid prediction for Augustus_model.g10854.t1
Valid prediction for GlimmerHMM_glimmerT_16171-T1
Valid prediction for Augustus_model.g10856.t1
Valid prediction for snap_scaffold_6-snap.3311-T1
Valid prediction for snap_scaffold_6-snap.3331-T1
Valid prediction for Augustus_model.g10851.t1
Valid prediction for HiQ_model.g10863.t1
Valid prediction for GlimmerHMM_glimmerT_16153-T1
Valid prediction for GlimmerHMM_glimmerT_16152-T1
Valid prediction for snap_scaffold_6-snap.3323-T1
Valid prediction for GlimmerHMM_glimmerT_16166-T1
Valid prediction for HiQ_model.g10861.t1
Valid prediction for snap_scaffold_6-snap.3330-T1
Valid prediction for snap_scaffold_6-snap.3327-T1
Valid prediction for GlimmerHMM_glimmerT_16172-T1
Valid prediction for snap_scaffold_6-snap.3313-T1
Valid prediction for Augustus_model.g10857.t1
Valid prediction for Augustus_model.g10848.t1
Valid prediction for GlimmerHMM_glimmerT_16154-T1
Valid prediction for GlimmerHMM_glimmerT_16159-T1
Valid prediction for snap_scaffold_6-snap.3339-T1
Couldn't classify 141230, 141392
Couldn't classify 141857, 141909
Sorry, prediction CodingQuarry_transcript_55370-T1 fails validation.
(ATG)	 TC	139473-139502	GT	CTG
(GGT)	 AG	139613-139666	GT	TCG
(GGC)	 AG	139795-139848	GT	CTG
(GGA)	 AG	140164-140217	GT	AGG
(GGA)	 AG	140325-140378	GT	AGG
(GGC)	 AG	140574-140618	GT	GAG
(GGT)	 AG	140793-140891	GT	AGG
(GGT)	 AG	141001-141108	GT	GAG
(GGA)	 AG	141230-141392	TG	TGT
(GTG)	 TA	141857-141909	GT	CCG
(GGC)	 AG	142139-142246	GT	AGG
(GGA)	 AG	142402-142455	GT	CTG
(GGT)	 AG	142750-142803	GT	CTG
(GGC)	 AG	142972-143133	GT	CTG
(GGT)	 AG	143671-143778	GT	CTG
(GGA)	 AG	143913-144020	GT	AGG
(GGA)	 AG	144134-144187	GT	AGG
(GGA)	 AG	144344-144451	GT	CTG
(GGT)	 AG	144646-144699	GT	CTG
(GGA)	 AG	144925-145032	GT	CCG
(GGA)	 AG	145204-145257	GT	GAG
(GGA)	 AG	145403-145510	GT	CTG
(GGA)	 AG	145678-145960	GT	CGG
(GCG)	 AG	146115-146305	GT	AGG
(TTC)	 AG	146781-147023	GT	CGG
(TCG)	 AG	147245-147391	AA	AAA
-recovered CodingQuarry_transcript_55370-T1, initial, 139473, 139502
-recovered CodingQuarry_transcript_55370-T1, terminal, 147245, 147391
-recovered CodingQuarry_transcript_55370-T1, internal, 139613, 139666
-recovered CodingQuarry_transcript_55370-T1, internal, 139795, 139848
-recovered CodingQuarry_transcript_55370-T1, internal, 140164, 140217
-recovered CodingQuarry_transcript_55370-T1, internal, 140325, 140378
-recovered CodingQuarry_transcript_55370-T1, internal, 140574, 140618
-recovered CodingQuarry_transcript_55370-T1, internal, 140793, 140891
-recovered CodingQuarry_transcript_55370-T1, internal, 141001, 141108
-recovered CodingQuarry_transcript_55370-T1, internal, 142139, 142246
-recovered CodingQuarry_transcript_55370-T1, internal, 142402, 142455
-recovered CodingQuarry_transcript_55370-T1, internal, 142750, 142803
-recovered CodingQuarry_transcript_55370-T1, internal, 142972, 143133
-recovered CodingQuarry_transcript_55370-T1, internal, 143671, 143778
-recovered CodingQuarry_transcript_55370-T1, internal, 143913, 144020
-recovered CodingQuarry_transcript_55370-T1, internal, 144134, 144187
-recovered CodingQuarry_transcript_55370-T1, internal, 144344, 144451
-recovered CodingQuarry_transcript_55370-T1, internal, 144646, 144699
-recovered CodingQuarry_transcript_55370-T1, internal, 144925, 145032
-recovered CodingQuarry_transcript_55370-T1, internal, 145204, 145257
-recovered CodingQuarry_transcript_55370-T1, internal, 145403, 145510
-recovered CodingQuarry_transcript_55370-T1, internal, 145678, 145960
-recovered CodingQuarry_transcript_55370-T1, internal, 146115, 146305
-recovered CodingQuarry_transcript_55370-T1, internal, 146781, 147023

-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_16155-T1
Valid prediction for GlimmerHMM_glimmerT_16167-T1
Valid prediction for snap_scaffold_6-snap.3335-T1
Couldn't classify 126329, 126385
Sorry, prediction pasa_asmbl_49082.p1 fails validation.
(ATG)	 AG	120835-120952	GT	CGG
(GTT)	 AG	121611-121752	GT	TGG
(GTA)	 AG	123424-123495	GT	ACG
(GTT)	 AG	123579-123763	GT	CAG
(CGC)	 AG	124649-124738	GT	AGG
(ACG)	 AG	124936-125013	GT	CGG
(CCA)	 AG	125264-125340	GT	AGG
(AAC)	 AG	125458-125556	GT	AGG
(ATG)	 AG	126329-126385	AT	ACA
-recovered pasa_asmbl_49082.p1, initial, 120835, 120952
-recovered pasa_asmbl_49082.p1, internal, 120835, 120952
-recovered pasa_asmbl_49082.p1, internal, 121611, 121752
-recovered pasa_asmbl_49082.p1, internal, 123424, 123495
-recovered pasa_asmbl_49082.p1, internal, 123579, 123763
-recovered pasa_asmbl_49082.p1, internal, 124649, 124738
-recovered pasa_asmbl_49082.p1, internal, 124936, 125013
-recovered pasa_asmbl_49082.p1, internal, 125264, 125340
-recovered pasa_asmbl_49082.p1, internal, 125458, 125556
Valid prediction for GlimmerHMM_glimmerT_16148-T1
Valid prediction for snap_scaffold_6-snap.3328-T1
Valid prediction for GlimmerHMM_glimmerT_16151-T1
Valid prediction for snap_scaffold_6-snap.3316-T1
Valid prediction for Augustus_model.g10850.t1
Valid prediction for GlimmerHMM_glimmerT_16150-T1
Valid prediction for Augustus_model.g10858.t1
Valid prediction for GlimmerHMM_glimmerT_16169-T1
Valid prediction for snap_scaffold_6-snap.3315-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_16170-T1
Valid prediction for snap_scaffold_6-snap.3310-T1
Valid prediction for snap_scaffold_6-snap.3333-T1
Valid prediction for Augustus_model.g10860.t1
Valid prediction for snap_scaffold_6-snap.3318-T1
Valid prediction for GlimmerHMM_glimmerT_16165-T1
Valid prediction for snap_scaffold_6-snap.3338-T1
Valid prediction for Augustus_model.g10852.t1
Valid prediction for Augustus_model.g10849.t1
Valid prediction for snap_scaffold_6-snap.3322-T1
Valid prediction for GlimmerHMM_glimmerT_16164-T1
Valid prediction for snap_scaffold_6-snap.3312-T1
Valid prediction for CodingQuarry_transcript_55367-T1
Valid prediction for snap_scaffold_6-snap.3324-T1
Valid prediction for snap_scaffold_6-snap.3326-T1
Valid prediction for GlimmerHMM_glimmerT_16161-T1
Valid prediction for Augustus_model.g10859.t1
Valid prediction for snap_scaffold_6-snap.3314-T1
Valid prediction for snap_scaffold_6-snap.3342-T1
Valid prediction for CodingQuarry_transcript_55369-T1
Valid prediction for snap_scaffold_6-snap.3334-T1
Valid prediction for snap_scaffold_6-snap.3309-T1
Valid prediction for GlimmerHMM_glimmerT_16162-T1
Valid prediction for snap_scaffold_6-snap.3329-T1
Valid prediction for snap_scaffold_6-snap.3319-T1
Valid prediction for snap_scaffold_6-snap.3336-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 18050, rend_intergenic: 15962  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29993, rend_intergenic: 26105  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43249, rend_intergenic: 40429  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46156, rend_intergenic: 43793  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57008, rend_intergenic: 50465  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68180, rend_intergenic: 64607  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73822, rend_intergenic: 72809  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76749, rend_intergenic: 74605  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79969, rend_intergenic: 77013  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82462, rend_intergenic: 79971  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97579, rend_intergenic: 82835  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106117, rend_intergenic: 98076  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120776, rend_intergenic: 114400  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147391, rend_intergenic: 138700  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 153548
-exon list size: 462


building trellis

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19.6    
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21.1    
21.3    
21.6    
21.8    
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22.2    
22.4    
22.6    
22.8    
23.1    
23.3    
23.5    
23.7    
23.9    
24.1    
24.4    
24.6    
24.8    
25.0    
25.2    
25.4    
25.6    
25.9    
26.1    
26.3    
26.5    
26.7    
26.9    
27.2    
27.4    
27.6    
27.8    
28.0    
28.2    
28.4    
28.7    
28.9    
29.1    
29.3    
29.5    
29.7    
30.0    
30.2    
30.4    
30.6    
30.8    
31.0    
31.2    
31.5    
31.7    
31.9    
32.1    
32.3    
32.5    
32.8    
33.0    
33.2    
33.4    
33.6    
33.8    
34.1    
34.3    
34.5    
34.7    
34.9    
35.1    
35.3    
35.6    
35.8    
36.0    
36.2    
36.4    
36.6    
36.9    
37.1    
37.3    
37.5    
37.7    
37.9    
38.1    
38.4    
38.6    
38.8    
39.0    
39.2    
39.4    
39.7    
39.9    
40.1    
40.3    
40.5    
40.7    
40.9    
41.2    
41.4    
41.6    
41.8    
42.0    
42.2    
42.5    
42.7    
42.9    
43.1    
43.3    
43.5    
43.8    
44.0    
44.2    
44.4    
44.6    
44.8    
45.0    
45.3    
45.5    
45.7    
45.9    
46.1    
46.3    
46.6    
46.8    
47.0    
47.2    
47.4    
47.6    
47.8    
48.1    
48.3    
48.5    
48.7    
48.9    
49.1    
49.4    
49.6    
49.8    
50.0    
50.2    
50.4    
50.6    
50.9    
51.1    
51.3    
51.5    
51.7    
51.9    
52.2    
52.4    
52.6    
52.8    
53.0    
53.2    
53.4    
53.7    
53.9    
54.1    
54.3    
54.5    
54.7    
55.0    
55.2    
55.4    
55.6    
55.8    
56.0    
56.2    
56.5    
56.7    
56.9    
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57.8    
58.0    
58.2    
58.4    
58.6    
58.8    
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59.3    
59.5    
59.7    
59.9    
60.1    
60.3    
60.6    
60.8    
61.0    
61.2    
61.4    
61.6    
61.9    
62.1    
62.3    
62.5    
62.7    
62.9    
63.1    
63.4    
63.6    
63.8    
64.0    
64.2    
64.4    
64.7    
64.9    
65.1    
65.3    
65.5    
65.7    
65.9    
66.2    
66.4    
66.6    
66.8    
67.0    
67.2    
67.5    
67.7    
67.9    
68.1    
68.3    
68.5    
68.8    
69.0    
69.2    
69.4    
69.6    
69.8    
70.0    
70.3    
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70.7    
70.9    
71.1    
71.3    
71.6    
71.8    
72.0    
72.2    
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72.6    
72.8    
73.1    
73.3    
73.5    
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73.9    
74.1    
74.4    
74.6    
74.8    
75.0    
75.2    
75.4    
75.6    
75.9    
76.1    
76.3    
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76.9    
77.2    
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77.6    
77.8    
78.0    
78.2    
78.4    
78.7    
78.9    
79.1    
79.3    
79.5    
79.7    
80.0    
80.2    
80.4    
80.6    
80.8    
81.0    
81.2    
81.5    
81.7    
81.9    
82.1    
82.3    
82.5    
82.8    
83.0    
83.2    
83.4    
83.6    
83.8    
84.1    
84.3    
84.5    
84.7    
84.9    
85.1    
85.3    
85.6    
85.8    
86.0    
86.2    
86.4    
86.6    
86.9    
87.1    
87.3    
87.5    
87.7    
87.9    
88.1    
88.4    
88.6    
88.8    
89.0    
89.2    
89.4    
89.7    
89.9    
90.1    
90.3    
90.5    
90.7    
90.9    
91.2    
91.4    
91.6    
91.8    
92.0    
92.2    
92.5    
92.7    
92.9    
93.1    
93.3    
93.5    
93.8    
94.0    
94.2    
94.4    
94.6    
94.8    
95.0    
95.3    
95.5    
95.7    
95.9    
96.1    
96.3    
96.6    
96.8    
97.0    
97.2    
97.4    
97.6    
97.8    
98.1    
98.3    
98.5    
98.7    
98.9    
99.1    
99.4    
99.6    
99.8    
-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 18050, rend_intergenic: 15962  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29993, rend_intergenic: 26105  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43249, rend_intergenic: 40429  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46156, rend_intergenic: 43793  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57008, rend_intergenic: 50465  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68180, rend_intergenic: 64607  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73822, rend_intergenic: 72809  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76749, rend_intergenic: 74605  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79969, rend_intergenic: 77013  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82462, rend_intergenic: 79971  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97579, rend_intergenic: 82835  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106117, rend_intergenic: 98076  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120776, rend_intergenic: 114400  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147391, rend_intergenic: 138700  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 18 predictions persist after filtering for low support