-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_4/scaffold_4_19372017-19518140

-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 GlimmerHMM_glimmerT_11258-T1
Valid prediction for snap_scaffold_4-snap.3999-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_11263-T1
Valid prediction for CodingQuarry_transcript_49399-T1
Couldn't classify 63349, 63568
Couldn't classify 65127, 65473
Sorry, prediction pasa_asmbl_42144.p1 fails validation.
(GCG)	 TG	63349-63568	GT	GGG
(GTG)	 AG	65127-65473	TT	GGT
Valid prediction for GlimmerHMM_glimmerT_11245-T1
Couldn't classify 67793, 67830
Couldn't classify 70216, 70601
Sorry, prediction pasa_asmbl_42146.p1 fails validation.
(ATA)	 TG	67793-67830	GT	GGG
(TGA)	 AG	68985-69139	GT	GGG
(AGC)	 AG	69292-69374	GT	AGG
(AAC)	 AG	69591-69684	GT	GGG
(GGC)	 AG	70216-70601	CA	AGC
-recovered pasa_asmbl_42146.p1, internal, 68985, 69139
-recovered pasa_asmbl_42146.p1, internal, 69292, 69374
-recovered pasa_asmbl_42146.p1, internal, 69591, 69684
Couldn't classify 65678, 65830
Couldn't classify 67304, 67574
Sorry, prediction pasa_asmbl_42145.p1 fails validation.
(GCT)	 GA	65678-65830	GT	AGG
(CGT)	 AG	65919-66056	GT	AGG
(GAG)	 AG	66789-67015	GT	AGG
(GTA)	 AG	67304-67574	CT	GTC
-recovered pasa_asmbl_42145.p1, internal, 65919, 66056
-recovered pasa_asmbl_42145.p1, internal, 66789, 67015
Valid prediction for Augustus_model.g7387.t1
Valid prediction for Augustus_model.g7380.t1
Valid prediction for snap_scaffold_4-snap.3990-T1
Valid prediction for GlimmerHMM_glimmerT_11249-T1
Couldn't classify 22487, 22509
Sorry, prediction pasa_asmbl_42140.p2 fails validation.
(ATG)	 CT	20544-20699	GT	AGG
(GGG)	 AG	20938-21107	GT	AGG
(TGG)	 AG	22092-22201	GT	GGG
(CTG)	 AG	22487-22509	CA	CAC
-recovered pasa_asmbl_42140.p2, initial, 20544, 20699
-recovered pasa_asmbl_42140.p2, internal, 20938, 21107
-recovered pasa_asmbl_42140.p2, internal, 22092, 22201
Valid prediction for snap_scaffold_4-snap.3993-T1
Valid prediction for Augustus_model.g7384.t1
Valid prediction for snap_scaffold_4-snap.3997-T1
Valid prediction for GlimmerHMM_glimmerT_11251-T1
Valid prediction for snap_scaffold_4-snap.4014-T1
Valid prediction for snap_scaffold_4-snap.3991-T1
Valid prediction for GlimmerHMM_glimmerT_11261-T1
Valid prediction for Augustus_model.g7382.t1
Valid prediction for snap_scaffold_4-snap.3987-T1
Couldn't classify 56535, 56879
Sorry, prediction pasa_asmbl_42143.p2 fails validation.
(GGT)	 CA	56535-56879	GG	AGG
Valid prediction for Augustus_model.g7386.t1
Valid prediction for Augustus_model.g7388.t1
Couldn't classify 70818, 70976
Couldn't classify 77247, 77335
Sorry, prediction pasa_asmbl_42147.p1 fails validation.
(CAG)	 TG	70818-70976	GT	AGG
(GAG)	 AG	71210-71445	GT	CAG
(GGG)	 AG	71645-71897	GT	AGG
(GAC)	 AG	72602-72819	GT	GGG
(GGC)	 AG	72934-73066	GT	TGG
(GGC)	 AG	73305-73529	GT	CGG
(AAG)	 AG	74026-74180	GT	AGG
(GAC)	 AG	74592-74688	GT	CAG
(GTG)	 AG	75195-75361	GT	AGG
(TGG)	 AG	76170-76540	GT	TGG
(GTA)	 AG	76869-77018	GT	AGG
(GTG)	 AG	77247-77335	GG	GCG
-recovered pasa_asmbl_42147.p1, internal, 71210, 71445
-recovered pasa_asmbl_42147.p1, internal, 71645, 71897
-recovered pasa_asmbl_42147.p1, internal, 72602, 72819
-recovered pasa_asmbl_42147.p1, internal, 72934, 73066
-recovered pasa_asmbl_42147.p1, internal, 73305, 73529
-recovered pasa_asmbl_42147.p1, internal, 74026, 74180
-recovered pasa_asmbl_42147.p1, internal, 74592, 74688
-recovered pasa_asmbl_42147.p1, internal, 75195, 75361
-recovered pasa_asmbl_42147.p1, internal, 76170, 76540
-recovered pasa_asmbl_42147.p1, internal, 76869, 77018
Valid prediction for GlimmerHMM_glimmerT_11257-T1
Valid prediction for GlimmerHMM_glimmerT_11252-T1
Valid prediction for snap_scaffold_4-snap.4013-T1
Valid prediction for GlimmerHMM_glimmerT_11256-T1
Valid prediction for snap_scaffold_4-snap.4011-T1
Valid prediction for GlimmerHMM_glimmerT_11262-T1
Valid prediction for snap_scaffold_4-snap.4005-T1
Valid prediction for snap_scaffold_4-snap.3989-T1
Valid prediction for Augustus_model.g7385.t1
Valid prediction for GlimmerHMM_glimmerT_11247-T1
Couldn't classify 103961, 104162
Couldn't classify 105065, 105193
Sorry, prediction pasa_asmbl_42150.p1 fails validation.
(GGG)	 CT	103961-104162	GT	AGG
(ACA)	 AG	104316-104392	GT	AGG
(GAT)	 AG	105065-105193	CC	GCC
-recovered pasa_asmbl_42150.p1, internal, 104316, 104392
Valid prediction for snap_scaffold_4-snap.4002-T1
Valid prediction for snap_scaffold_4-snap.3985-T1
Valid prediction for GlimmerHMM_glimmerT_11246-T1
Valid prediction for CodingQuarry_transcript_49398-T1
Valid prediction for GlimmerHMM_glimmerT_11253-T1
Valid prediction for GlimmerHMM_glimmerT_11260-T1
Valid prediction for snap_scaffold_4-snap.4001-T1
Valid prediction for snap_scaffold_4-snap.3983-T1
Valid prediction for snap_scaffold_4-snap.4009-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 CodingQuarry_transcript_49401-T1
Valid prediction for Augustus_model.g7383.t1
Couldn't classify 10143, 10202
Sorry, prediction pasa_asmbl_43442.p1 fails validation.
(AAG)	 AC	10143-10202	GT	AGG
(GTG)	 AG	11396-11680	GT	AGG
(GTT)	 AG	11981-12148	GT	AGG
(GCG)	 AG	12267-12478	GT	AGG
(TCC)	 AG	12852-12933	GT	AGG
(GTA)	 AG	13100-13194	GT	CTG
(GTA)	 AG	13379-13547	GT	AGG
(GAT)	 AG	14579-14797	GT	TGG
(GTA)	 AG	14874-15254	AC	GAA
-recovered pasa_asmbl_43442.p1, terminal, 14874, 15254
-recovered pasa_asmbl_43442.p1, internal, 11396, 11680
-recovered pasa_asmbl_43442.p1, internal, 11981, 12148
-recovered pasa_asmbl_43442.p1, internal, 12267, 12478
-recovered pasa_asmbl_43442.p1, internal, 12852, 12933
-recovered pasa_asmbl_43442.p1, internal, 13100, 13194
-recovered pasa_asmbl_43442.p1, internal, 13379, 13547
-recovered pasa_asmbl_43442.p1, internal, 14579, 14797
Valid prediction for snap_scaffold_4-snap.4000-T1
Valid prediction for GlimmerHMM_glimmerT_11255-T1
Valid prediction for pasa_asmbl_43513.p1
Valid prediction for GlimmerHMM_glimmerT_11265-T1
Valid prediction for GlimmerHMM_glimmerT_11264-T1
Valid prediction for Augustus_model.g7381.t1
Valid prediction for snap_scaffold_4-snap.3988-T1
Valid prediction for snap_scaffold_4-snap.4008-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_4-snap.3998-T1
Valid prediction for snap_scaffold_4-snap.4006-T1
Valid prediction for snap_scaffold_4-snap.3992-T1
Valid prediction for snap_scaffold_4-snap.4003-T1
Valid prediction for snap_scaffold_4-snap.4010-T1
Valid prediction for GlimmerHMM_glimmerT_11254-T1
Valid prediction for snap_scaffold_4-snap.3994-T1
Valid prediction for snap_scaffold_4-snap.4004-T1
Valid prediction for snap_scaffold_4-snap.3986-T1
Valid prediction for snap_scaffold_4-snap.3984-T1
Valid prediction for GlimmerHMM_glimmerT_11259-T1
Valid prediction for snap_scaffold_4-snap.3995-T1
Valid prediction for GlimmerHMM_glimmerT_11250-T1
Valid prediction for GlimmerHMM_glimmerT_11248-T1
Valid prediction for snap_scaffold_4-snap.4007-T1
Valid prediction for CodingQuarry_transcript_49402-T1
Valid prediction for snap_scaffold_4-snap.3996-T1
Valid prediction for snap_scaffold_4-snap.3982-T1
Couldn't classify 1822, 1953
Sorry, prediction Augustus_model.g7389.t1 fails validation.
(TGC)	 GC	1822-1953	GT	GGG
(GGA)	 AG	2259-2379	GT	AAG
(CTT)	 AG	2464-2569	GT	CAG
(GTG)	 AG	2643-2699	GT	ATG
(GTG)	 AG	2783-2881	GT	AGG
(ACT)	 AG	3580-3678	GT	AGG
(GCC)	 AG	4958-5044	GT	AGG
(ACT)	 AG	5169-5268	GT	GGG
(GTT)	 AG	5362-5501	GT	AGG
(GTG)	 AG	6383-6523	GT	AGG
(GTG)	 AG	6843-6923	GT	ATG
(GTT)	 AG	7087-7203	GT	CTG
(GAG)	 AG	7789-7905	GT	GGG
(AGG)	 AG	8230-8337	GT	ATG
(GCC)	 AG	8448-8550	GT	CGG
(ATG)	 AG	8965-9107	GT	TGG
(ATC)	 AG	9250-9317	GT	AGG
(ATT)	 AG	9788-9886	GT	ATG
(GTC)	 AG	10115-10202	GT	AGG
(GTG)	 AG	11396-11680	GT	AGG
(GTT)	 AG	11981-12148	GT	AGG
(GCG)	 AG	12267-12478	GT	AGG
(TCC)	 AG	12852-12933	GT	AGG
(GTA)	 AG	13100-13194	GT	CTG
(GTA)	 AG	13379-13547	GT	AGG
(GAT)	 AG	14579-14797	GT	TGG
(GTA)	 AG	14874-15254	AC	GAA
-recovered Augustus_model.g7389.t1, initial, 8965, 9107
-recovered Augustus_model.g7389.t1, terminal, 14874, 15254
-recovered Augustus_model.g7389.t1, internal, 2259, 2379
-recovered Augustus_model.g7389.t1, internal, 2464, 2569
-recovered Augustus_model.g7389.t1, internal, 2643, 2699
-recovered Augustus_model.g7389.t1, internal, 2783, 2881
-recovered Augustus_model.g7389.t1, internal, 3580, 3678
-recovered Augustus_model.g7389.t1, internal, 4958, 5044
-recovered Augustus_model.g7389.t1, internal, 5169, 5268
-recovered Augustus_model.g7389.t1, internal, 5362, 5501
-recovered Augustus_model.g7389.t1, internal, 6383, 6523
-recovered Augustus_model.g7389.t1, internal, 6843, 6923
-recovered Augustus_model.g7389.t1, internal, 7087, 7203
-recovered Augustus_model.g7389.t1, internal, 7789, 7905
-recovered Augustus_model.g7389.t1, internal, 8230, 8337
-recovered Augustus_model.g7389.t1, internal, 8448, 8550
-recovered Augustus_model.g7389.t1, internal, 8965, 9107
-recovered Augustus_model.g7389.t1, internal, 9250, 9317
-recovered Augustus_model.g7389.t1, internal, 9788, 9886
-recovered Augustus_model.g7389.t1, internal, 10115, 10202
-recovered Augustus_model.g7389.t1, internal, 11396, 11680
-recovered Augustus_model.g7389.t1, internal, 11981, 12148
-recovered Augustus_model.g7389.t1, internal, 12267, 12478
-recovered Augustus_model.g7389.t1, internal, 12852, 12933
-recovered Augustus_model.g7389.t1, internal, 13100, 13194
-recovered Augustus_model.g7389.t1, internal, 13379, 13547
-recovered Augustus_model.g7389.t1, internal, 14579, 14797

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 8018, rend_intergenic: 1802  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 9503, rend_intergenic: 8493  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22395, rend_intergenic: 9842  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33538, rend_intergenic: 22597  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37434, rend_intergenic: 33750  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48187, rend_intergenic: 39044  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58185, rend_intergenic: 49760  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79486, rend_intergenic: 58302  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90264, rend_intergenic: 87914  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99264, rend_intergenic: 91683  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102948, rend_intergenic: 100565  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106492, rend_intergenic: 103858  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116318, rend_intergenic: 108354  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119642, rend_intergenic: 116341  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128606, rend_intergenic: 123630  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134684, rend_intergenic: 130510  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 146124
-exon list size: 415


building trellis

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17.3    
17.5    
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18.9    
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19.4    
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20.1    
20.4    
20.6    
20.9    
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21.6    
21.8    
22.1    
22.3    
22.5    
22.8    
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23.3    
23.5    
23.7    
24.0    
24.2    
24.5    
24.7    
24.9    
25.2    
25.4    
25.7    
25.9    
26.1    
26.4    
26.6    
26.9    
27.1    
27.3    
27.6    
27.8    
28.1    
28.3    
28.5    
28.8    
29.0    
29.3    
29.5    
29.7    
30.0    
30.2    
30.5    
30.7    
30.9    
31.2    
31.4    
31.7    
31.9    
32.1    
32.4    
32.6    
32.9    
33.1    
33.3    
33.6    
33.8    
34.1    
34.3    
34.5    
34.8    
35.0    
35.3    
35.5    
35.7    
36.0    
36.2    
36.5    
36.7    
36.9    
37.2    
37.4    
37.6    
37.9    
38.1    
38.4    
38.6    
38.8    
39.1    
39.3    
39.6    
39.8    
40.0    
40.3    
40.5    
40.8    
41.0    
41.2    
41.5    
41.7    
42.0    
42.2    
42.4    
42.7    
42.9    
43.2    
43.4    
43.6    
43.9    
44.1    
44.4    
44.6    
44.8    
45.1    
45.3    
45.6    
45.8    
46.0    
46.3    
46.5    
46.8    
47.0    
47.2    
47.5    
47.7    
48.0    
48.2    
48.4    
48.7    
48.9    
49.2    
49.4    
49.6    
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50.1    
50.4    
50.6    
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51.6    
51.8    
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56.1    
56.4    
56.6    
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57.6    
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77.9    
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78.9    
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79.6    
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82.3    
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86.3    
86.6    
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87.1    
87.3    
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88.0    
88.2    
88.5    
88.7    
89.0    
89.2    
89.4    
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90.2    
90.4    
90.6    
90.9    
91.1    
91.4    
91.6    
91.8    
92.1    
92.3    
92.6    
92.8    
93.0    
93.3    
93.5    
93.8    
94.0    
94.2    
94.5    
94.7    
95.0    
95.2    
95.4    
95.7    
95.9    
96.2    
96.4    
96.6    
96.9    
97.1    
97.4    
97.6    
97.8    
98.1    
98.3    
98.6    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 16 predictions from path traversal
Error with prediction: snap lend_intergenic: 8018, rend_intergenic: 1802  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 9503, rend_intergenic: 8493  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22395, rend_intergenic: 9842  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33538, rend_intergenic: 22597  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37434, rend_intergenic: 33750  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48187, rend_intergenic: 39044  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58185, rend_intergenic: 49760  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79486, rend_intergenic: 58302  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90264, rend_intergenic: 87914  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99264, rend_intergenic: 91683  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102948, rend_intergenic: 100565  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106492, rend_intergenic: 103858  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116318, rend_intergenic: 108354  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119642, rend_intergenic: 116341  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128606, rend_intergenic: 123630  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134684, rend_intergenic: 130510  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 14 predictions persist after filtering for low support