-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_19/scaffold_19_12650328-12796329

-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_46185-T1
Valid prediction for snap_scaffold_19-snap.2496-T1
Valid prediction for Augustus_model.g30820.t1
Valid prediction for GlimmerHMM_glimmerT_46191-T1
Valid prediction for CodingQuarry_transcript_25803-T1
Valid prediction for GlimmerHMM_glimmerT_46177-T1
Valid prediction for GeneMark_model.80396_t
Valid prediction for GeneMark_model.80414_t
Valid prediction for GlimmerHMM_glimmerT_46171-T1
Valid prediction for pasa_asmbl_22624.p1
Valid prediction for GeneMark_model.80412_t
Valid prediction for snap_scaffold_19-snap.2492-T1
Valid prediction for GlimmerHMM_glimmerT_46174-T1
Valid prediction for GeneMark_model.80408_t
Valid prediction for GeneMark_model.80409_t
Valid prediction for snap_scaffold_19-snap.2495-T1
Valid prediction for GlimmerHMM_glimmerT_46182-T1
Valid prediction for GeneMark_model.80424_t
Valid prediction for snap_scaffold_19-snap.2503-T1
Valid prediction for snap_scaffold_19-snap.2498-T1
Valid prediction for Augustus_model.g30815.t1
Valid prediction for snap_scaffold_19-snap.2506-T1
Valid prediction for GlimmerHMM_glimmerT_46176-T1
Valid prediction for snap_scaffold_19-snap.2493-T1
Valid prediction for Augustus_model.g30828.t1
Valid prediction for snap_scaffold_19-snap.2486-T1
Valid prediction for GlimmerHMM_glimmerT_46169-T1
Valid prediction for Augustus_model.g30817.t1
Valid prediction for GlimmerHMM_glimmerT_46180-T1
Valid prediction for GeneMark_model.80421_t
Valid prediction for GeneMark_model.80405_t
Valid prediction for pasa_asmbl_22629.p1
Valid prediction for pasa_asmbl_22626.p1
Valid prediction for GeneMark_model.80417_t
Valid prediction for Augustus_model.g30811.t1
Valid prediction for GeneMark_model.80410_t
Valid prediction for GlimmerHMM_glimmerT_46167-T1
Valid prediction for CodingQuarry_transcript_25804-T1
Valid prediction for HiQ_model.g30809.t1
Valid prediction for GeneMark_model.80411_t
Valid prediction for GlimmerHMM_glimmerT_46179-T1
Valid prediction for GeneMark_model.80400_t
Valid prediction for Augustus_model.g30813.t1
Valid prediction for HiQ_model.g30822.t1
Valid prediction for snap_scaffold_19-snap.2501-T1
Valid prediction for GeneMark_model.80413_t
Valid prediction for GlimmerHMM_glimmerT_46184-T1
Valid prediction for CodingQuarry_transcript_25807-T1
Valid prediction for GeneMark_model.80419_t
Valid prediction for GlimmerHMM_glimmerT_46172-T1
Valid prediction for GlimmerHMM_glimmerT_46181-T1
Valid prediction for GeneMark_model.80402_t
Valid prediction for GeneMark_model.80398_t
Valid prediction for GeneMark_model.80403_t
Valid prediction for Augustus_model.g30821.t1
Valid prediction for snap_scaffold_19-snap.2489-T1
Valid prediction for snap_scaffold_19-snap.2482-T1
Valid prediction for snap_scaffold_19-snap.2507-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 GlimmerHMM_glimmerT_46188-T1
Valid prediction for Augustus_model.g30824.t1
Valid prediction for GlimmerHMM_glimmerT_46178-T1
Valid prediction for pasa_asmbl_21745.p1
Valid prediction for snap_scaffold_19-snap.2490-T1
Valid prediction for Augustus_model.g30814.t1
Valid prediction for GlimmerHMM_glimmerT_46168-T1
Valid prediction for snap_scaffold_19-snap.2484-T1
Valid prediction for GeneMark_model.80416_t
Valid prediction for GeneMark_model.80407_t
Couldn't classify 14949, 15257
Sorry, prediction pasa_asmbl_21749.p3 fails validation.
(TAC)	 AC	14949-15257	AC	AGA
Valid prediction for snap_scaffold_19-snap.2487-T1
Valid prediction for CodingQuarry_transcript_25805-T1
Valid prediction for snap_scaffold_19-snap.2494-T1
Valid prediction for GeneMark_model.80423_t
Valid prediction for GlimmerHMM_glimmerT_46190-T1
Valid prediction for GeneMark_model.80404_t
Valid prediction for GeneMark_model.80422_t
Valid prediction for Augustus_model.g30818.t1
Valid prediction for GeneMark_model.80418_t
Valid prediction for Augustus_model.g30810.t1
Valid prediction for snap_scaffold_19-snap.2499-T1
Valid prediction for snap_scaffold_19-snap.2500-T1
Valid prediction for GeneMark_model.80397_t
Valid prediction for GlimmerHMM_glimmerT_46186-T1
Valid prediction for snap_scaffold_19-snap.2488-T1
Valid prediction for Augustus_model.g30819.t1
Valid prediction for GlimmerHMM_glimmerT_46173-T1
Valid prediction for CodingQuarry_transcript_25808-T1
Valid prediction for Augustus_model.g30826.t1
Valid prediction for GlimmerHMM_glimmerT_46189-T1
Valid prediction for snap_scaffold_19-snap.2505-T1
Valid prediction for HiQ_model.g30823.t1
Valid prediction for GlimmerHMM_glimmerT_46175-T1
Valid prediction for Augustus_model.g30825.t1
Valid prediction for CodingQuarry_transcript_25806-T1
Couldn't classify 130511, 130660
Couldn't classify 131593, 131787
Sorry, prediction pasa_asmbl_21737.p1 fails validation.
(CTA)	 CC	130511-130660	GT	AGG
(TTT)	 AG	130854-130979	GT	TGG
(ATA)	 AG	131593-131787	CG	GCC
-recovered pasa_asmbl_21737.p1, internal, 130854, 130979
Valid prediction for snap_scaffold_19-snap.2504-T1
Valid prediction for snap_scaffold_19-snap.2502-T1
Valid prediction for snap_scaffold_19-snap.2483-T1
Valid prediction for GeneMark_model.80415_t
Valid prediction for HiQ_model.g30816.t1
Valid prediction for pasa_asmbl_21738.p1
Valid prediction for GlimmerHMM_glimmerT_46183-T1
Valid prediction for Augustus_model.g30827.t1
Valid prediction for GeneMark_model.80406_t
Valid prediction for GeneMark_model.80420_t
Valid prediction for snap_scaffold_19-snap.2497-T1
Valid prediction for snap_scaffold_19-snap.2491-T1
Valid prediction for Augustus_model.g30812.t1
Valid prediction for GlimmerHMM_glimmerT_46187-T1
Valid prediction for GlimmerHMM_glimmerT_46170-T1
Valid prediction for snap_scaffold_19-snap.2485-T1
Couldn't classify 28212, 28219
Sorry, prediction pasa_asmbl_21747.p1 fails validation.
(CAT)	 AC	28212-28219	GT	AGG
(ATG)	 AG	28296-28965	GT	AGG
(AGC)	 AG	29858-29893	TG	GAT
add_exon() Sorry, pasa_asmbl_21747.p1 28296-28965-initial-1 is invalid.
-recovered pasa_asmbl_21747.p1, initial, 28296, 28965
-recovered pasa_asmbl_21747.p1, terminal, 29858, 29893
-recovered pasa_asmbl_21747.p1, internal, 28296, 28965

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 22030, rend_intergenic: 19065  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54866, rend_intergenic: 50489  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92770, rend_intergenic: 85862  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97061, rend_intergenic: 94236  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121345, rend_intergenic: 113925  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128331, rend_intergenic: 122337  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137964, rend_intergenic: 135277  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 146002
-exon list size: 407


building trellis

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13.9    
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15.9    
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17.1    
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18.6    
18.8    
19.1    
19.3    
19.6    
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20.8    
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23.5    
23.7    
24.0    
24.2    
24.4    
24.7    
24.9    
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25.4    
25.7    
25.9    
26.2    
26.4    
26.7    
26.9    
27.1    
27.4    
27.6    
27.9    
28.1    
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28.6    
28.9    
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29.3    
29.6    
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30.1    
30.3    
30.6    
30.8    
31.1    
31.3    
31.5    
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32.3    
32.5    
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33.3    
33.5    
33.7    
34.0    
34.2    
34.5    
34.7    
35.0    
35.2    
35.5    
35.7    
35.9    
36.2    
36.4    
36.7    
36.9    
37.2    
37.4    
37.7    
37.9    
38.1    
38.4    
38.6    
38.9    
39.1    
39.4    
39.6    
39.9    
40.1    
40.3    
40.6    
40.8    
41.1    
41.3    
41.6    
41.8    
42.1    
42.3    
42.5    
42.8    
43.0    
43.3    
43.5    
43.8    
44.0    
44.3    
44.5    
44.7    
45.0    
45.2    
45.5    
45.7    
46.0    
46.2    
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46.9    
47.2    
47.4    
47.7    
47.9    
48.2    
48.4    
48.7    
48.9    
49.1    
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49.6    
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50.6    
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52.6    
52.8    
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53.3    
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54.3    
54.5    
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55.3    
55.5    
55.7    
56.0    
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56.5    
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57.9    
58.2    
58.4    
58.7    
58.9    
59.2    
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59.9    
60.1    
60.4    
60.6    
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68.9    
69.2    
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79.5    
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80.0    
80.2    
80.4    
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80.9    
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81.9    
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82.6    
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84.1    
84.4    
84.6    
84.8    
85.1    
85.3    
85.6    
85.8    
86.1    
86.3    
86.6    
86.8    
87.0    
87.3    
87.5    
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88.0    
88.3    
88.5    
88.8    
89.0    
89.2    
89.5    
89.7    
90.0    
90.2    
90.5    
90.7    
91.0    
91.2    
91.4    
91.7    
91.9    
92.2    
92.4    
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92.9    
93.2    
93.4    
93.6    
93.9    
94.1    
94.4    
94.6    
94.9    
95.1    
95.4    
95.6    
95.8    
96.1    
96.3    
96.6    
96.8    
97.1    
97.3    
97.6    
97.8    
98.0    
98.3    
98.5    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 23 predictions from path traversal
Error with prediction: snap lend_intergenic: 22030, rend_intergenic: 19065  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54866, rend_intergenic: 50489  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92770, rend_intergenic: 85862  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97061, rend_intergenic: 94236  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121345, rend_intergenic: 113925  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128331, rend_intergenic: 122337  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137964, rend_intergenic: 135277  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support