-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_5/scaffold_5_12620179-12893747

-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 Augustus_model.g8507.t1
Couldn't classify 197196, 197999
Sorry, prediction pasa_asmbl_45822.p1 fails validation.
(ATG)	 TT	195278-195304	GT	AGG
(AGA)	 AG	195886-195907	GT	AGG
(TGC)	 AG	196719-196798	GT	AGG
(AAC)	 AG	197196-197999	CC	CCC
-recovered pasa_asmbl_45822.p1, initial, 195278, 195304
-recovered pasa_asmbl_45822.p1, internal, 195886, 195907
-recovered pasa_asmbl_45822.p1, internal, 196719, 196798
Valid prediction for HiQ_model.g8499.t1
Valid prediction for GlimmerHMM_glimmerT_12850-T1
Valid prediction for CodingQuarry_transcript_52291-T1
Valid prediction for Augustus_model.g8515.t1
Couldn't classify 72504, 72641
Sorry, prediction pasa_asmbl_46368.p1 fails validation.
(ATG)	 AG	72070-72255	GT	AGG
(GTG)	 AG	72504-72641	AT	TGA
-recovered pasa_asmbl_46368.p1, initial, 72070, 72255
-recovered pasa_asmbl_46368.p1, internal, 72070, 72255
Valid prediction for snap_scaffold_5-snap.2378-T1
Valid prediction for GlimmerHMM_glimmerT_12857-T1
Valid prediction for snap_scaffold_5-snap.2374-T1
Valid prediction for GlimmerHMM_glimmerT_12831-T1
Valid prediction for snap_scaffold_5-snap.2371-T1
Valid prediction for snap_scaffold_5-snap.2369-T1
Valid prediction for Augustus_model.g8498.t1
Valid prediction for GlimmerHMM_glimmerT_12833-T1
Valid prediction for snap_scaffold_5-snap.2386-T1
Valid prediction for GlimmerHMM_glimmerT_12848-T1
Valid prediction for snap_scaffold_5-snap.2362-T1
Valid prediction for GlimmerHMM_glimmerT_12827-T1
Valid prediction for pasa_asmbl_45831.p1
Valid prediction for GlimmerHMM_glimmerT_12839-T1
Valid prediction for GlimmerHMM_glimmerT_12852-T1
Valid prediction for GlimmerHMM_glimmerT_12825-T1
Valid prediction for CodingQuarry_transcript_52292-T1
Valid prediction for GlimmerHMM_glimmerT_12846-T1
Valid prediction for snap_scaffold_5-snap.2345-T1
Valid prediction for HiQ_model.g8516.t1
Couldn't classify 15582, 15695
Sorry, prediction pasa_asmbl_45804.p1 fails validation.
(CAG)	 TT	15582-15695	GT	GGG
(GCC)	 AG	15844-16016	GT	AGG
(GCC)	 AG	16115-16509	GT	CAG
(GAC)	 AG	16710-16781	GT	AGG
(GTA)	 AG	17386-17517	GT	TGG
(GTC)	 AG	17811-17938	GT	AGG
(CTC)	 AG	19702-19794	GT	AGG
(CCC)	 AG	21809-21907	GT	AGG
(GGT)	 AG	22558-22815	GT	GGG
(GTC)	 AG	22904-23209	GT	GGG
(CTG)	 AG	23592-23693	GT	GAG
(AGC)	 AG	23854-23916	GT	AGG
(GGA)	 AG	24230-24328	GT	AGG
(AAC)	 AG	24519-24857	CT	AGC
-recovered pasa_asmbl_45804.p1, terminal, 24519, 24857
-recovered pasa_asmbl_45804.p1, internal, 15844, 16016
-recovered pasa_asmbl_45804.p1, internal, 16115, 16509
-recovered pasa_asmbl_45804.p1, internal, 16710, 16781
-recovered pasa_asmbl_45804.p1, internal, 17386, 17517
-recovered pasa_asmbl_45804.p1, internal, 17811, 17938
-recovered pasa_asmbl_45804.p1, internal, 19702, 19794
-recovered pasa_asmbl_45804.p1, internal, 21809, 21907
-recovered pasa_asmbl_45804.p1, internal, 22558, 22815
-recovered pasa_asmbl_45804.p1, internal, 22904, 23209
-recovered pasa_asmbl_45804.p1, internal, 23592, 23693
-recovered pasa_asmbl_45804.p1, internal, 23854, 23916
-recovered pasa_asmbl_45804.p1, internal, 24230, 24328
Valid prediction for snap_scaffold_5-snap.2354-T1
Valid prediction for GlimmerHMM_glimmerT_12844-T1
Valid prediction for snap_scaffold_5-snap.2387-T1
Valid prediction for pasa_asmbl_45815.p1
Valid prediction for GlimmerHMM_glimmerT_12851-T1
Valid prediction for GlimmerHMM_glimmerT_12830-T1
Valid prediction for snap_scaffold_5-snap.2360-T1
Valid prediction for snap_scaffold_5-snap.2365-T1
Valid prediction for snap_scaffold_5-snap.2348-T1
Valid prediction for Augustus_model.g8502.t1
Valid prediction for pasa_asmbl_45823.p1
Valid prediction for Augustus_model.g8511.t1
Valid prediction for snap_scaffold_5-snap.2364-T1
Valid prediction for HiQ_model.g8509.t1
Valid prediction for GlimmerHMM_glimmerT_12837-T1
Valid prediction for GlimmerHMM_glimmerT_12855-T1
Valid prediction for snap_scaffold_5-snap.2355-T1
Valid prediction for snap_scaffold_5-snap.2382-T1
Valid prediction for snap_scaffold_5-snap.2376-T1
Valid prediction for pasa_asmbl_45807.p1
Valid prediction for Augustus_model.g8497.t1
Valid prediction for CodingQuarry_transcript_52293-T1
Valid prediction for snap_scaffold_5-snap.2385-T1
Valid prediction for Augustus_model.g8512.t1
Valid prediction for snap_scaffold_5-snap.2349-T1
Valid prediction for GlimmerHMM_glimmerT_12824-T1
Valid prediction for CodingQuarry_transcript_52286-T1
Valid prediction for GlimmerHMM_glimmerT_12823-T1
Valid prediction for GlimmerHMM_glimmerT_12856-T1
Valid prediction for snap_scaffold_5-snap.2357-T1
Valid prediction for Augustus_model.g8503.t1
Valid prediction for HiQ_model.g8513.t1
Valid prediction for GlimmerHMM_glimmerT_12829-T1
Valid prediction for snap_scaffold_5-snap.2380-T1
Valid prediction for pasa_asmbl_45825.p1
Valid prediction for Augustus_model.g8501.t1
Valid prediction for CodingQuarry_transcript_52287-T1
Valid prediction for snap_scaffold_5-snap.2379-T1
Valid prediction for snap_scaffold_5-snap.2368-T1
Valid prediction for snap_scaffold_5-snap.2352-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_12840-T1
Valid prediction for snap_scaffold_5-snap.2356-T1
Valid prediction for GlimmerHMM_glimmerT_12845-T1
Valid prediction for GlimmerHMM_glimmerT_12847-T1
Valid prediction for GlimmerHMM_glimmerT_12834-T1
Valid prediction for GlimmerHMM_glimmerT_12841-T1
Valid prediction for GlimmerHMM_glimmerT_12849-T1
Valid prediction for GlimmerHMM_glimmerT_12854-T1
Couldn't classify 137044, 137103
Sorry, prediction pasa_asmbl_44483.p1 fails validation.
(GCC)	 AT	137044-137103	GT	TTG
(GTG)	 AG	137862-138410	CC	AGC
-recovered pasa_asmbl_44483.p1, terminal, 137862, 138410
Valid prediction for snap_scaffold_5-snap.2353-T1
Valid prediction for GlimmerHMM_glimmerT_12826-T1
Valid prediction for GlimmerHMM_glimmerT_12835-T1
Valid prediction for GlimmerHMM_glimmerT_12828-T1
Valid prediction for GlimmerHMM_glimmerT_12832-T1
Valid prediction for snap_scaffold_5-snap.2370-T1
Valid prediction for HiQ_model.g8505.t1
Valid prediction for GlimmerHMM_glimmerT_12853-T1
Valid prediction for pasa_asmbl_44478.p1
Valid prediction for pasa_asmbl_44490.p1
Valid prediction for snap_scaffold_5-snap.2381-T1
Valid prediction for snap_scaffold_5-snap.2377-T1
Couldn't classify 143169, 143414
Sorry, prediction pasa_asmbl_44480.p1 fails validation.
(ATG)	 CA	142124-142405	GT	AAG
(ACC)	 AG	143169-143414	TA	GGT
-recovered pasa_asmbl_44480.p1, initial, 142124, 142405
Valid prediction for snap_scaffold_5-snap.2347-T1
Valid prediction for snap_scaffold_5-snap.2366-T1
Valid prediction for CodingQuarry_transcript_52290-T1
Valid prediction for CodingQuarry_transcript_52289-T1
Valid prediction for GlimmerHMM_glimmerT_12836-T1
Valid prediction for Augustus_model.g8506.t1
Valid prediction for GlimmerHMM_glimmerT_12838-T1
Valid prediction for GlimmerHMM_glimmerT_12842-T1
Valid prediction for CodingQuarry_transcript_52288-T1
Valid prediction for snap_scaffold_5-snap.2383-T1
Valid prediction for snap_scaffold_5-snap.2367-T1
Valid prediction for HiQ_model.g8504.t1
Valid prediction for snap_scaffold_5-snap.2373-T1
Valid prediction for Augustus_model.g8514.t1
Valid prediction for snap_scaffold_5-snap.2350-T1
Valid prediction for snap_scaffold_5-snap.2358-T1
Valid prediction for snap_scaffold_5-snap.2363-T1
Valid prediction for snap_scaffold_5-snap.2361-T1
Valid prediction for snap_scaffold_5-snap.2346-T1
Valid prediction for Augustus_model.g8508.t1
Valid prediction for HiQ_model.g8510.t1
Valid prediction for pasa_asmbl_44489.p1
Valid prediction for Augustus_model.g8500.t1
Valid prediction for snap_scaffold_5-snap.2351-T1
Valid prediction for snap_scaffold_5-snap.2359-T1
Valid prediction for snap_scaffold_5-snap.2384-T1
Valid prediction for snap_scaffold_5-snap.2372-T1
Valid prediction for GlimmerHMM_glimmerT_12843-T1
Valid prediction for snap_scaffold_5-snap.2375-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 24857, rend_intergenic: 6920  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56489, rend_intergenic: 52503  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63174, rend_intergenic: 59813  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67599, rend_intergenic: 63389  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72465, rend_intergenic: 67737  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74914, rend_intergenic: 72689  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75325, rend_intergenic: 75208  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94957, rend_intergenic: 77730  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118871, rend_intergenic: 113177  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130290, rend_intergenic: 127225  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137837, rend_intergenic: 132517  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157760, rend_intergenic: 146165  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173261, rend_intergenic: 170374  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176329, rend_intergenic: 173800  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185973, rend_intergenic: 177705  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 238296, rend_intergenic: 238261  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 243290, rend_intergenic: 240120  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 273569
-exon list size: 424


building trellis

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25.6    
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30.5    
30.8    
31.0    
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31.9    
32.2    
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32.9    
33.1    
33.3    
33.6    
33.8    
34.0    
34.3    
34.5    
34.7    
35.0    
35.2    
35.4    
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35.9    
36.2    
36.4    
36.6    
36.9    
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37.3    
37.6    
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38.0    
38.3    
38.5    
38.7    
39.0    
39.2    
39.4    
39.7    
39.9    
40.1    
40.4    
40.6    
40.8    
41.1    
41.3    
41.5    
41.8    
42.0    
42.3    
42.5    
42.7    
43.0    
43.2    
43.4    
43.7    
43.9    
44.1    
44.4    
44.6    
44.8    
45.1    
45.3    
45.5    
45.8    
46.0    
46.2    
46.5    
46.7    
46.9    
47.2    
47.4    
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48.4    
48.6    
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96.9    
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97.4    
97.7    
97.9    
98.1    
98.4    
98.6    
98.8    
99.1    
99.3    
99.5    
99.8    
-found 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 24857, rend_intergenic: 6920  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56489, rend_intergenic: 52503  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63174, rend_intergenic: 59813  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67599, rend_intergenic: 63389  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72465, rend_intergenic: 67737  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74914, rend_intergenic: 72689  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75325, rend_intergenic: 75208  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94957, rend_intergenic: 77730  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118871, rend_intergenic: 113177  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130290, rend_intergenic: 127225  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137837, rend_intergenic: 132517  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157760, rend_intergenic: 146165  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173261, rend_intergenic: 170374  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176329, rend_intergenic: 173800  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185973, rend_intergenic: 177705  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 238296, rend_intergenic: 238261  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 243290, rend_intergenic: 240120  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support