-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_3842755-4019005

-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.710-T1
Valid prediction for GlimmerHMM_glimmerT_31463-T1
Valid prediction for pasa_asmbl_10753.p1
Valid prediction for snap_scaffold_13-snap.733-T1
Valid prediction for snap_scaffold_13-snap.721-T1
Valid prediction for Augustus_model.g20925.t1
Valid prediction for snap_scaffold_13-snap.718-T1
Valid prediction for snap_scaffold_13-snap.711-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_13-snap.716-T1
Valid prediction for GlimmerHMM_glimmerT_31440-T1
Valid prediction for snap_scaffold_13-snap.706-T1
Valid prediction for snap_scaffold_13-snap.727-T1
Valid prediction for Augustus_model.g20903.t1
Valid prediction for GlimmerHMM_glimmerT_31444-T1
Valid prediction for snap_scaffold_13-snap.748-T1
Valid prediction for snap_scaffold_13-snap.747-T1
Valid prediction for Augustus_model.g20916.t1
Valid prediction for Augustus_model.g20905.t1
Valid prediction for CodingQuarry_transcript_12977-T1
Valid prediction for snap_scaffold_13-snap.717-T1
Valid prediction for snap_scaffold_13-snap.713-T1
Valid prediction for Augustus_model.g20907.t1
Valid prediction for snap_scaffold_13-snap.735-T1
Valid prediction for snap_scaffold_13-snap.746-T1
Couldn't classify 61064, 61191
Sorry, prediction pasa_asmbl_10748.p1 fails validation.
(GTT)	 AG	61064-61191	GT	AGG
(GAA)	 AG	61422-61652	GT	AGG
(CTA)	 AG	61907-62141	GT	TGG
(GGT)	 AG	62334-62483	GT	AGG
(GTG)	 AG	63054-63188	CT	AGC
-recovered pasa_asmbl_10748.p1, terminal, 63054, 63188
-recovered pasa_asmbl_10748.p1, internal, 61064, 61191
-recovered pasa_asmbl_10748.p1, internal, 61422, 61652
-recovered pasa_asmbl_10748.p1, internal, 61907, 62141
-recovered pasa_asmbl_10748.p1, internal, 62334, 62483
Couldn't classify 76076, 76177
Sorry, prediction pasa_asmbl_11673.p1 fails validation.
(TCT)	 GC	76076-76177	GT	AGG
(GAG)	 AG	76621-76713	GT	TGG
(GCC)	 AG	76807-76874	GT	GGG
(GTT)	 AG	76959-77037	GT	AAG
(AAT)	 AG	77125-77207	GT	AGG
(CAT)	 AG	77296-77348	GT	CAG
(AAA)	 AG	77461-77471	TT	GAT
-recovered pasa_asmbl_11673.p1, terminal, 77461, 77471
-recovered pasa_asmbl_11673.p1, internal, 76621, 76713
-recovered pasa_asmbl_11673.p1, internal, 76807, 76874
-recovered pasa_asmbl_11673.p1, internal, 76959, 77037
-recovered pasa_asmbl_11673.p1, internal, 77125, 77207
-recovered pasa_asmbl_11673.p1, internal, 77296, 77348
Valid prediction for Augustus_model.g20906.t1
Valid prediction for GlimmerHMM_glimmerT_31442-T1
Couldn't classify 35278, 35429
Sorry, prediction pasa_asmbl_10746.p1 fails validation.
(GCA)	 GA	35278-35429	GT	AGG
(GGC)	 AG	35557-35646	GT	AGG
(GTT)	 AG	35790-35851	GT	ATG
(ACG)	 AG	35948-36111	GT	AGG
(GTA)	 AG	36242-36418	AG	AAA
-recovered pasa_asmbl_10746.p1, terminal, 36242, 36418
-recovered pasa_asmbl_10746.p1, internal, 35557, 35646
-recovered pasa_asmbl_10746.p1, internal, 35790, 35851
-recovered pasa_asmbl_10746.p1, internal, 35948, 36111
Couldn't classify 170688, 170969
Sorry, prediction pasa_asmbl_10751.p1 fails validation.
(ATG)	 AA	170688-170969	GA	GCG
Valid prediction for GlimmerHMM_glimmerT_31438-T1
Valid prediction for GlimmerHMM_glimmerT_31446-T1
Valid prediction for HiQ_model.g20904.t1
Valid prediction for CodingQuarry_transcript_12978-T1
Valid prediction for CodingQuarry_transcript_12979-T1
Valid prediction for GlimmerHMM_glimmerT_31456-T1
Valid prediction for Augustus_model.g20926.t1
Valid prediction for snap_scaffold_13-snap.715-T1
Valid prediction for GlimmerHMM_glimmerT_31449-T1
Valid prediction for pasa_asmbl_10749.p1
Valid prediction for snap_scaffold_13-snap.707-T1
Valid prediction for Augustus_model.g20909.t1
Valid prediction for snap_scaffold_13-snap.709-T1
Valid prediction for GlimmerHMM_glimmerT_31445-T1
Valid prediction for GlimmerHMM_glimmerT_31447-T1
Valid prediction for GlimmerHMM_glimmerT_31441-T1
Valid prediction for snap_scaffold_13-snap.726-T1
Valid prediction for Augustus_model.g20911.t1
Valid prediction for snap_scaffold_13-snap.738-T1
Valid prediction for CodingQuarry_transcript_12976-T1
Couldn't classify 58865, 58939
Couldn't classify 59637, 59686
Sorry, prediction pasa_asmbl_11586.p1 fails validation.
(AAT)	 CC	58865-58939	GT	AGG
(GTG)	 AG	59151-59391	GT	TGG
(GCA)	 AG	59637-59686	AC	CCA
-recovered pasa_asmbl_11586.p1, internal, 59151, 59391
Valid prediction for GlimmerHMM_glimmerT_31464-T1
Couldn't classify 57932, 57943
Sorry, prediction pasa_asmbl_10747.p1 fails validation.
(ATG)	 AG	55774-55858	GT	AGG
(GAG)	 AG	56931-57033	GT	AGG
(GCT)	 AG	57329-57566	GT	AGG
(GTG)	 AG	57932-57943	AA	GGA
-recovered pasa_asmbl_10747.p1, initial, 55774, 55858
-recovered pasa_asmbl_10747.p1, internal, 55774, 55858
-recovered pasa_asmbl_10747.p1, internal, 56931, 57033
-recovered pasa_asmbl_10747.p1, internal, 57329, 57566
Valid prediction for HiQ_model.g20908.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.744-T1
Couldn't classify 65530, 65700
Sorry, prediction pasa_asmbl_9595.p1 fails validation.
(ATG)	 TG	63163-63264	GT	AGG
(GAC)	 AG	63386-63484	GT	AGG
(GAG)	 AG	63908-64072	GT	ATG
(GCC)	 AG	64333-64432	GT	AAG
(ACT)	 AG	64580-64734	GT	TGG
(GTT)	 AG	64932-65054	GT	AGG
(GTT)	 AG	65221-65403	GT	AGG
(GTG)	 AG	65530-65700	GG	ACG
-recovered pasa_asmbl_9595.p1, initial, 63163, 63264
-recovered pasa_asmbl_9595.p1, internal, 63386, 63484
-recovered pasa_asmbl_9595.p1, internal, 63908, 64072
-recovered pasa_asmbl_9595.p1, internal, 64333, 64432
-recovered pasa_asmbl_9595.p1, internal, 64580, 64734
-recovered pasa_asmbl_9595.p1, internal, 64932, 65054
-recovered pasa_asmbl_9595.p1, internal, 65221, 65403
Valid prediction for snap_scaffold_13-snap.728-T1
Valid prediction for GlimmerHMM_glimmerT_31455-T1
Valid prediction for GlimmerHMM_glimmerT_31451-T1
Valid prediction for GlimmerHMM_glimmerT_31450-T1
Valid prediction for Augustus_model.g20924.t1
Valid prediction for GlimmerHMM_glimmerT_31454-T1
Valid prediction for snap_scaffold_13-snap.725-T1
Valid prediction for snap_scaffold_13-snap.734-T1
Valid prediction for Augustus_model.g20922.t1
Valid prediction for snap_scaffold_13-snap.722-T1
Valid prediction for Augustus_model.g20914.t1
Valid prediction for snap_scaffold_13-snap.712-T1
Valid prediction for GlimmerHMM_glimmerT_31453-T1
Valid prediction for snap_scaffold_13-snap.742-T1
Valid prediction for snap_scaffold_13-snap.719-T1
Couldn't classify 55084, 55461
Sorry, prediction pasa_asmbl_9597.p1 fails validation.
(CCA)	 AG	55084-55461	GT	AGG
-recovered pasa_asmbl_9597.p1, internal, 55084, 55461
Valid prediction for GlimmerHMM_glimmerT_31452-T1
Valid prediction for GlimmerHMM_glimmerT_31457-T1
Valid prediction for GlimmerHMM_glimmerT_31461-T1
Valid prediction for Augustus_model.g20912.t1
Valid prediction for pasa_asmbl_9600.p1
Valid prediction for snap_scaffold_13-snap.732-T1
Valid prediction for Augustus_model.g20915.t1
Valid prediction for snap_scaffold_13-snap.708-T1
Valid prediction for GlimmerHMM_glimmerT_31462-T1
Valid prediction for Augustus_model.g20918.t1
Valid prediction for CodingQuarry_transcript_12980-T1
Valid prediction for GlimmerHMM_glimmerT_31460-T1
Valid prediction for snap_scaffold_13-snap.736-T1
Valid prediction for snap_scaffold_13-snap.714-T1
Valid prediction for snap_scaffold_13-snap.729-T1
Valid prediction for GlimmerHMM_glimmerT_31439-T1
Valid prediction for HiQ_model.g20910.t1
Valid prediction for GlimmerHMM_glimmerT_31448-T1
Valid prediction for snap_scaffold_13-snap.724-T1
Valid prediction for Augustus_model.g20917.t1
Valid prediction for snap_scaffold_13-snap.739-T1
Valid prediction for snap_scaffold_13-snap.730-T1
Valid prediction for snap_scaffold_13-snap.740-T1
Valid prediction for snap_scaffold_13-snap.731-T1
Valid prediction for snap_scaffold_13-snap.723-T1
Valid prediction for snap_scaffold_13-snap.737-T1
Valid prediction for pasa_asmbl_9598.p1
Couldn't classify 92774, 92798
Sorry, prediction pasa_asmbl_9591.p1 fails validation.
(CCC)	 AG	92774-92798	GT	AGG
(GAG)	 AG	92901-93049	GT	GGG
(GAA)	 AG	93530-93736	GT	AGG
(ACA)	 AG	93851-93980	GT	AAG
(ATG)	 AG	94096-94157	GT	AGG
(GAG)	 AG	94249-94321	GT	AGG
(TGT)	 AG	94519-94670	GT	AGG
(GCG)	 AG	95512-95593	GT	AGG
(AAG)	 AG	95720-95814	GT	AGG
(CAA)	 AG	96297-96343	GT	ACG
(GGA)	 AG	96548-96675	GT	CGG
(GTT)	 AG	96780-97075	CC	GAC
-recovered pasa_asmbl_9591.p1, initial, 94096, 94157
-recovered pasa_asmbl_9591.p1, terminal, 96780, 97075
-recovered pasa_asmbl_9591.p1, internal, 92774, 92798
-recovered pasa_asmbl_9591.p1, internal, 92901, 93049
-recovered pasa_asmbl_9591.p1, internal, 93530, 93736
-recovered pasa_asmbl_9591.p1, internal, 93851, 93980
-recovered pasa_asmbl_9591.p1, internal, 94096, 94157
-recovered pasa_asmbl_9591.p1, internal, 94249, 94321
-recovered pasa_asmbl_9591.p1, internal, 94519, 94670
-recovered pasa_asmbl_9591.p1, internal, 95512, 95593
-recovered pasa_asmbl_9591.p1, internal, 95720, 95814
-recovered pasa_asmbl_9591.p1, internal, 96297, 96343
-recovered pasa_asmbl_9591.p1, internal, 96548, 96675
Valid prediction for GlimmerHMM_glimmerT_31443-T1
Valid prediction for GlimmerHMM_glimmerT_31458-T1
Valid prediction for Augustus_model.g20913.t1
Valid prediction for snap_scaffold_13-snap.741-T1
Valid prediction for snap_scaffold_13-snap.743-T1
Valid prediction for HiQ_model.g20923.t1
Valid prediction for HiQ_model.g20921.t1
Valid prediction for Augustus_model.g20919.t1
Valid prediction for snap_scaffold_13-snap.720-T1
Valid prediction for snap_scaffold_13-snap.745-T1
Valid prediction for Augustus_model.g20920.t1
Couldn't classify 16477, 16726
Sorry, prediction pasa_asmbl_9603.p1 fails validation.
(AAG)	 GG	16477-16726	GT	AGG
(GAG)	 AG	16855-17057	AA	GAA
-recovered pasa_asmbl_9603.p1, terminal, 16855, 17057
Valid prediction for GlimmerHMM_glimmerT_31459-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 16437, rend_intergenic: 15268  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20659, rend_intergenic: 16762  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56422, rend_intergenic: 52737  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107706, rend_intergenic: 104391  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116694, rend_intergenic: 110357  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128150, rend_intergenic: 123487  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135251, rend_intergenic: 132551  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139172, rend_intergenic: 137917  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 176251
-exon list size: 395


building trellis

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13.9    
14.1    
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14.9    
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15.4    
15.6    
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16.6    
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17.1    
17.4    
17.6    
17.9    
18.1    
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18.6    
18.9    
19.1    
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20.7    
20.9    
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22.7    
22.9    
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23.4    
23.7    
23.9    
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24.4    
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24.9    
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25.4    
25.7    
25.9    
26.2    
26.4    
26.7    
27.0    
27.2    
27.5    
27.7    
28.0    
28.2    
28.5    
28.7    
29.0    
29.2    
29.5    
29.7    
30.0    
30.2    
30.5    
30.7    
31.0    
31.2    
31.5    
31.7    
32.0    
32.2    
32.5    
32.7    
33.0    
33.2    
33.5    
33.8    
34.0    
34.3    
34.5    
34.8    
35.0    
35.3    
35.5    
35.8    
36.0    
36.3    
36.5    
36.8    
37.0    
37.3    
37.5    
37.8    
38.0    
38.3    
38.5    
38.8    
39.0    
39.3    
39.5    
39.8    
40.1    
40.3    
40.6    
40.8    
41.1    
41.3    
41.6    
41.8    
42.1    
42.3    
42.6    
42.8    
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    
46.9    
47.1    
47.4    
47.6    
47.9    
48.1    
48.4    
48.6    
48.9    
49.1    
49.4    
49.6    
49.9    
50.1    
50.4    
50.6    
50.9    
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51.4    
51.6    
51.9    
52.1    
52.4    
52.6    
52.9    
53.1    
53.4    
53.7    
53.9    
54.2    
54.4    
54.7    
54.9    
55.2    
55.4    
55.7    
55.9    
56.2    
56.4    
56.7    
56.9    
57.2    
57.4    
57.7    
57.9    
58.2    
58.4    
58.7    
58.9    
59.2    
59.4    
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59.9    
60.2    
60.5    
60.7    
61.0    
61.2    
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67.0    
67.3    
67.5    
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68.0    
68.3    
68.5    
68.8    
69.0    
69.3    
69.5    
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70.0    
70.3    
70.5    
70.8    
71.0    
71.3    
71.5    
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72.0    
72.3    
72.5    
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73.0    
73.3    
73.6    
73.8    
74.1    
74.3    
74.6    
74.8    
75.1    
75.3    
75.6    
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76.1    
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76.6    
76.8    
77.1    
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77.6    
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78.3    
78.6    
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81.6    
81.9    
82.1    
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82.9    
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83.4    
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84.4    
84.6    
84.9    
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87.4    
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87.9    
88.2    
88.4    
88.7    
88.9    
89.2    
89.4    
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89.9    
90.2    
90.4    
90.7    
90.9    
91.2    
91.4    
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91.9    
92.2    
92.4    
92.7    
92.9    
93.2    
93.5    
93.7    
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94.2    
94.5    
94.7    
95.0    
95.2    
95.5    
95.7    
96.0    
96.2    
96.5    
96.7    
97.0    
97.2    
97.5    
97.7    
98.0    
98.2    
98.5    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 16437, rend_intergenic: 15268  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20659, rend_intergenic: 16762  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56422, rend_intergenic: 52737  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107706, rend_intergenic: 104391  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116694, rend_intergenic: 110357  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128150, rend_intergenic: 123487  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135251, rend_intergenic: 132551  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139172, rend_intergenic: 137917  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 28 predictions persist after filtering for low support