-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_737010-887066

-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.189-T1
Valid prediction for snap_scaffold_6-snap.202-T1
Valid prediction for Augustus_model.g9282.t1
Valid prediction for GlimmerHMM_glimmerT_13962-T1
Valid prediction for snap_scaffold_6-snap.183-T1
Valid prediction for snap_scaffold_6-snap.208-T1
Valid prediction for Augustus_model.g9281.t1
Valid prediction for snap_scaffold_6-snap.168-T1
Valid prediction for Augustus_model.g9290.t1
Valid prediction for GlimmerHMM_glimmerT_13956-T1
Valid prediction for GlimmerHMM_glimmerT_13953-T1
Valid prediction for snap_scaffold_6-snap.191-T1
Valid prediction for GlimmerHMM_glimmerT_13955-T1
Valid prediction for GlimmerHMM_glimmerT_13948-T1
Valid prediction for snap_scaffold_6-snap.182-T1
Valid prediction for GlimmerHMM_glimmerT_13960-T1
Valid prediction for snap_scaffold_6-snap.184-T1
Valid prediction for snap_scaffold_6-snap.193-T1
Valid prediction for snap_scaffold_6-snap.173-T1
Valid prediction for snap_scaffold_6-snap.197-T1
Valid prediction for snap_scaffold_6-snap.165-T1
Valid prediction for GlimmerHMM_glimmerT_13958-T1
Valid prediction for GlimmerHMM_glimmerT_13970-T1
Valid prediction for snap_scaffold_6-snap.174-T1
Valid prediction for snap_scaffold_6-snap.175-T1
Valid prediction for Augustus_model.g9285.t1
Valid prediction for snap_scaffold_6-snap.176-T1
Couldn't classify 104208, 104476
Couldn't classify 106816, 106930
Sorry, prediction pasa_asmbl_46679.p1 fails validation.
(ACT)	 TG	104208-104476	GT	CGG
(ACT)	 AG	106816-106930	AA	GGA
Valid prediction for GlimmerHMM_glimmerT_13952-T1
Couldn't classify 125918, 126000
Couldn't classify 132405, 132448
Sorry, prediction pasa_asmbl_47931.p1 fails validation.
(AGA)	 AC	125918-126000	GT	GGG
(CCC)	 AG	126324-126399	GT	TGG
(GTG)	 AG	127331-127429	GT	AGG
(TAC)	 AG	128557-128680	GT	AGG
(GCA)	 AG	129720-129820	GT	AGG
(ATG)	 AG	130206-130286	GT	AAG
(GAC)	 AG	130637-130765	GT	AGG
(GAT)	 AG	131196-131277	GT	AGG
(CTG)	 AG	131613-131723	GT	AGG
(GAA)	 AG	131968-132123	GT	AGG
(GGT)	 AG	132405-132448	GA	ACG
-recovered pasa_asmbl_47931.p1, initial, 130206, 130286
add_exon() Sorry, pasa_asmbl_47931.p1 131196-131277-terminal-3 is invalid.
-recovered pasa_asmbl_47931.p1, terminal, 131196, 131277
add_exon() Sorry, pasa_asmbl_47931.p1 131968-132123-terminal-1 is invalid.
-recovered pasa_asmbl_47931.p1, terminal, 131968, 132123
-recovered pasa_asmbl_47931.p1, internal, 126324, 126399
-recovered pasa_asmbl_47931.p1, internal, 127331, 127429
-recovered pasa_asmbl_47931.p1, internal, 128557, 128680
-recovered pasa_asmbl_47931.p1, internal, 129720, 129820
-recovered pasa_asmbl_47931.p1, internal, 130206, 130286
-recovered pasa_asmbl_47931.p1, internal, 130637, 130765
-recovered pasa_asmbl_47931.p1, internal, 131196, 131277
-recovered pasa_asmbl_47931.p1, internal, 131613, 131723
-recovered pasa_asmbl_47931.p1, internal, 131968, 132123
Valid prediction for snap_scaffold_6-snap.171-T1
Valid prediction for snap_scaffold_6-snap.206-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_6-snap.188-T1
Valid prediction for GlimmerHMM_glimmerT_13968-T1
Valid prediction for GlimmerHMM_glimmerT_13961-T1
Valid prediction for GlimmerHMM_glimmerT_13957-T1
Valid prediction for Augustus_model.g9286.t1
Valid prediction for snap_scaffold_6-snap.179-T1
Couldn't classify 61508, 61547
Couldn't classify 61940, 62868
Sorry, prediction pasa_asmbl_46675.p1 fails validation.
(GGG)	 CG	61508-61547	GT	GGG
(GTG)	 AG	61940-62868	AC	TGA
Valid prediction for GlimmerHMM_glimmerT_13959-T1
Couldn't classify 107536, 108216
Sorry, prediction pasa_asmbl_46680.p1 fails validation.
(GGG)	 GA	107536-108216	CC	GAC

-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_6-snap.198-T1
Valid prediction for Augustus_model.g9284.t1
Valid prediction for snap_scaffold_6-snap.199-T1
Valid prediction for GlimmerHMM_glimmerT_13965-T1
Valid prediction for HiQ_model.g9292.t1
Valid prediction for snap_scaffold_6-snap.190-T1
Valid prediction for Augustus_model.g9278.t1
Valid prediction for snap_scaffold_6-snap.203-T1
Valid prediction for Augustus_model.g9291.t1
Valid prediction for GlimmerHMM_glimmerT_13966-T1
Couldn't classify 27500, 27594
Sorry, prediction pasa_asmbl_48081.p1 fails validation.
(ATG)	 TC	25696-25838	GT	ATG
(AGA)	 AG	26673-26721	GT	TGG
(GCG)	 AG	27005-27146	GT	GGG
(CTG)	 AG	27500-27594	AC	CCA
-recovered pasa_asmbl_48081.p1, initial, 25696, 25838
-recovered pasa_asmbl_48081.p1, internal, 26673, 26721
-recovered pasa_asmbl_48081.p1, internal, 27005, 27146
Valid prediction for snap_scaffold_6-snap.180-T1
Valid prediction for pasa_asmbl_48074.p2
Valid prediction for GlimmerHMM_glimmerT_13951-T1
Valid prediction for Augustus_model.g9280.t1
Couldn't classify 28308, 28435
Couldn't classify 29231, 29342
Sorry, prediction pasa_asmbl_48080.p1 fails validation.
(CAG)	 TC	28308-28435	GT	AGG
(GTG)	 AG	28584-28978	GT	GGG
(AAA)	 AG	29088-29115	GT	AGG
(TCC)	 AG	29231-29342	CC	CCC
-recovered pasa_asmbl_48080.p1, internal, 28584, 28978
-recovered pasa_asmbl_48080.p1, internal, 29088, 29115
Valid prediction for snap_scaffold_6-snap.178-T1
Couldn't classify 132909, 133029
Couldn't classify 135197, 135351
Sorry, prediction pasa_asmbl_48064.p1 fails validation.
(TGC)	 CG	132909-133029	GT	CTG
(ACA)	 AG	134008-134129	GT	AGG
(GTG)	 AG	134421-134505	GT	AGG
(CTT)	 AG	135197-135351	GG	GGG
-recovered pasa_asmbl_48064.p1, internal, 134008, 134129
-recovered pasa_asmbl_48064.p1, internal, 134421, 134505
Valid prediction for Augustus_model.g9279.t1
Valid prediction for snap_scaffold_6-snap.205-T1
Valid prediction for snap_scaffold_6-snap.207-T1
Valid prediction for GlimmerHMM_glimmerT_13964-T1
Valid prediction for GlimmerHMM_glimmerT_13950-T1
Valid prediction for snap_scaffold_6-snap.169-T1
Valid prediction for snap_scaffold_6-snap.185-T1
Valid prediction for snap_scaffold_6-snap.170-T1
Valid prediction for snap_scaffold_6-snap.201-T1
Couldn't classify 29769, 30068
Couldn't classify 30475, 30606
Sorry, prediction pasa_asmbl_48079.p1 fails validation.
(CCA)	 CG	29769-30068	GT	AGG
(GCC)	 AG	30475-30606	GT	AGG
-recovered pasa_asmbl_48079.p1, internal, 30475, 30606
Valid prediction for HiQ_model.g9287.t1
Valid prediction for GlimmerHMM_glimmerT_13963-T1
Valid prediction for pasa_asmbl_48084.p1
Valid prediction for GlimmerHMM_glimmerT_13967-T1
Valid prediction for snap_scaffold_6-snap.186-T1
Valid prediction for snap_scaffold_6-snap.172-T1
Valid prediction for snap_scaffold_6-snap.192-T1
Valid prediction for GlimmerHMM_glimmerT_13969-T1
Valid prediction for snap_scaffold_6-snap.187-T1
Valid prediction for snap_scaffold_6-snap.166-T1
Valid prediction for snap_scaffold_6-snap.195-T1
Valid prediction for snap_scaffold_6-snap.181-T1
Valid prediction for GlimmerHMM_glimmerT_13949-T1
Valid prediction for CodingQuarry_transcript_54910-T1
Valid prediction for CodingQuarry_transcript_54909-T1
Valid prediction for Augustus_model.g9288.t1
Valid prediction for snap_scaffold_6-snap.167-T1
Valid prediction for snap_scaffold_6-snap.194-T1
Valid prediction for GlimmerHMM_glimmerT_13954-T1
Valid prediction for Augustus_model.g9289.t1
Valid prediction for snap_scaffold_6-snap.177-T1
Couldn't classify 138925, 140214
Sorry, prediction pasa_asmbl_48061.p1 fails validation.
(GGA)	 GA	138925-140214	GC	AGG
Couldn't classify 9784, 10137
Sorry, prediction pasa_asmbl_48083.p1 fails validation.
(CTC)	 AA	9784-10137	CC	AAC
Valid prediction for snap_scaffold_6-snap.200-T1
Valid prediction for CodingQuarry_transcript_54907-T1
Valid prediction for HiQ_model.g9283.t1
Valid prediction for CodingQuarry_transcript_54911-T1
Valid prediction for snap_scaffold_6-snap.204-T1
Couldn't classify 4826, 4947
Sorry, prediction pasa_asmbl_48088.p1 fails validation.
(ATG)	 AA	1395-1450	GT	GGG
(AAG)	 AG	1553-1697	GT	AGG
(TAT)	 AG	2273-2369	GT	ACG
(AGT)	 AG	3177-3310	GT	CGG
(TAT)	 AG	3761-3826	GT	TAG
(TGC)	 AG	4573-4714	GT	AGG
(GTG)	 AG	4826-4947	TT	GCT
-recovered pasa_asmbl_48088.p1, initial, 1395, 1450
-recovered pasa_asmbl_48088.p1, internal, 1553, 1697
-recovered pasa_asmbl_48088.p1, internal, 2273, 2369
-recovered pasa_asmbl_48088.p1, internal, 3177, 3310
-recovered pasa_asmbl_48088.p1, internal, 3761, 3826
-recovered pasa_asmbl_48088.p1, internal, 4573, 4714
Valid prediction for snap_scaffold_6-snap.196-T1
Couldn't classify 11598, 11733
Couldn't classify 11758, 12073
Sorry, prediction CodingQuarry_transcript_54912-T1 fails validation.
(ATG)	 AA	11009-11405	GT	AGG
(GCA)	 AG	11598-11733	TA	GGT
(CAG)	 AA	11758-12073	AC	AGA
-recovered CodingQuarry_transcript_54912-T1, initial, 11009, 11405

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 7022, rend_intergenic: 5302  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17601, rend_intergenic: 13700  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24672, rend_intergenic: 21530  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41209, rend_intergenic: 24905  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46481, rend_intergenic: 44966  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58528, rend_intergenic: 49337  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66910, rend_intergenic: 61918  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79304, rend_intergenic: 70526  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82265, rend_intergenic: 80663  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96379, rend_intergenic: 92844  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108216, rend_intergenic: 104921  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119840, rend_intergenic: 118161  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134426, rend_intergenic: 126908  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145892, rend_intergenic: 138110  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149456, rend_intergenic: 146830  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 150057
-exon list size: 359


building trellis

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11.1    
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11.9    
12.2    
12.5    
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14.4    
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17.5    
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18.0    
18.3    
18.6    
18.8    
19.1    
19.4    
19.7    
19.9    
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20.8    
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21.9    
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22.4    
22.7    
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23.5    
23.8    
24.1    
24.4    
24.7    
24.9    
25.2    
25.5    
25.8    
26.0    
26.3    
26.6    
26.9    
27.1    
27.4    
27.7    
28.0    
28.3    
28.5    
28.8    
29.1    
29.4    
29.6    
29.9    
30.2    
30.5    
30.7    
31.0    
31.3    
31.6    
31.9    
32.1    
32.4    
32.7    
33.0    
33.2    
33.5    
33.8    
34.1    
34.3    
34.6    
34.9    
35.2    
35.5    
35.7    
36.0    
36.3    
36.6    
36.8    
37.1    
37.4    
37.7    
38.0    
38.2    
38.5    
38.8    
39.1    
39.3    
39.6    
39.9    
40.2    
40.4    
40.7    
41.0    
41.3    
41.6    
41.8    
42.1    
42.4    
42.7    
42.9    
43.2    
43.5    
43.8    
44.0    
44.3    
44.6    
44.9    
45.2    
45.4    
45.7    
46.0    
46.3    
46.5    
46.8    
47.1    
47.4    
47.6    
47.9    
48.2    
48.5    
48.8    
49.0    
49.3    
49.6    
49.9    
50.1    
50.4    
50.7    
51.0    
51.2    
51.5    
51.8    
52.1    
52.4    
52.6    
52.9    
53.2    
53.5    
53.7    
54.0    
54.3    
54.6    
54.8    
55.1    
55.4    
55.7    
56.0    
56.2    
56.5    
56.8    
57.1    
57.3    
57.6    
57.9    
58.2    
58.4    
58.7    
59.0    
59.3    
59.6    
59.8    
60.1    
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60.9    
61.2    
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65.1    
65.4    
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67.6    
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85.6    
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86.1    
86.4    
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87.0    
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88.1    
88.4    
88.6    
88.9    
89.2    
89.5    
89.8    
90.0    
90.3    
90.6    
90.9    
91.1    
91.4    
91.7    
92.0    
92.2    
92.5    
92.8    
93.1    
93.4    
93.6    
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96.1    
96.4    
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97.0    
97.2    
97.5    
97.8    
98.1    
98.3    
98.6    
98.9    
99.2    
99.4    
99.7    
-found 23 predictions from path traversal
Error with prediction: snap lend_intergenic: 7022, rend_intergenic: 5302  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17601, rend_intergenic: 13700  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24672, rend_intergenic: 21530  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41209, rend_intergenic: 24905  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46481, rend_intergenic: 44966  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58528, rend_intergenic: 49337  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66910, rend_intergenic: 61918  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79304, rend_intergenic: 70526  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82265, rend_intergenic: 80663  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96379, rend_intergenic: 92844  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108216, rend_intergenic: 104921  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119840, rend_intergenic: 118161  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134426, rend_intergenic: 126908  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145892, rend_intergenic: 138110  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149456, rend_intergenic: 146830  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support