-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_11414462-11606880

-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.2127-T1
Valid prediction for GlimmerHMM_glimmerT_32409-T1
Valid prediction for GlimmerHMM_glimmerT_32416-T1
Valid prediction for Augustus_model.g21636.t1
Valid prediction for HiQ_model.g21650.t1
Valid prediction for snap_scaffold_13-snap.2157-T1
Valid prediction for pasa_asmbl_11276.p1
Valid prediction for pasa_asmbl_11292.p1
Valid prediction for CodingQuarry_transcript_13246-T1
Valid prediction for HiQ_model.g21643.t1
Valid prediction for snap_scaffold_13-snap.2128-T1
Valid prediction for CodingQuarry_transcript_13248-T1
Couldn't classify 185208, 185281
Sorry, prediction CodingQuarry_transcript_13250-T1 fails validation.
(ATG)	 GG	172313-172452	GT	GGG
(ACT)	 AG	174140-174280	GT	AGG
(TCA)	 AG	174546-174729	GT	CGG
(ATG)	 AG	174849-175006	GT	TGG
(GTA)	 AG	175166-175258	GT	AAG
(CTG)	 AG	175387-175475	GT	AAG
(GGT)	 AG	175963-176007	GT	ACG
(ATG)	 AG	176155-176316	GT	TGG
(CTG)	 AG	176494-176655	GT	AGG
(ATG)	 AG	177351-177492	GT	AGG
(GTG)	 AG	177729-177928	GT	AGG
(CTG)	 AG	178129-178185	GT	AGG
(TGG)	 AG	178284-178408	GT	AGG
(TGC)	 AG	178520-178703	GT	AGG
(ACC)	 AG	178797-178971	GT	AGG
(GTT)	 AG	179150-179271	GT	TGG
(CCA)	 AG	180424-180620	GT	AAG
(GCA)	 AG	180995-181121	GT	AGG
(GTG)	 AG	181323-181507	GT	AGG
(GTC)	 AG	181719-181833	GT	GGG
(GCA)	 AG	182028-182184	GT	AAG
(ATC)	 AG	182420-182526	GT	GGG
(GTC)	 AG	182880-182924	GT	CGG
(TCA)	 AG	183203-183339	GT	AGG
(AAA)	 AG	183497-183641	GT	TGG
(AGT)	 AG	183929-183988	GT	AGG
(GAC)	 AG	184223-184290	GT	CGG
(ATA)	 AG	184384-184509	GT	AGG
(TGT)	 AG	185208-185281	AG	AAA
(ATT)	 AG	185549-185582	AA	GAA
-recovered CodingQuarry_transcript_13250-T1, initial, 172313, 172452
-recovered CodingQuarry_transcript_13250-T1, initial, 174849, 175006
add_exon() Sorry, CodingQuarry_transcript_13250-T1 176155-176316-initial-1 is invalid.
-recovered CodingQuarry_transcript_13250-T1, initial, 176155, 176316
add_exon() Sorry, CodingQuarry_transcript_13250-T1 177351-177492-initial-1 is invalid.
-recovered CodingQuarry_transcript_13250-T1, initial, 177351, 177492
add_exon() Sorry, CodingQuarry_transcript_13250-T1 178520-178703-terminal-3 is invalid.
-recovered CodingQuarry_transcript_13250-T1, terminal, 178520, 178703
-recovered CodingQuarry_transcript_13250-T1, terminal, 185549, 185582
-recovered CodingQuarry_transcript_13250-T1, internal, 174140, 174280
-recovered CodingQuarry_transcript_13250-T1, internal, 174546, 174729
-recovered CodingQuarry_transcript_13250-T1, internal, 174849, 175006
-recovered CodingQuarry_transcript_13250-T1, internal, 175166, 175258
-recovered CodingQuarry_transcript_13250-T1, internal, 175387, 175475
-recovered CodingQuarry_transcript_13250-T1, internal, 175963, 176007
-recovered CodingQuarry_transcript_13250-T1, internal, 176155, 176316
-recovered CodingQuarry_transcript_13250-T1, internal, 176494, 176655
-recovered CodingQuarry_transcript_13250-T1, internal, 177351, 177492
-recovered CodingQuarry_transcript_13250-T1, internal, 177729, 177928
-recovered CodingQuarry_transcript_13250-T1, internal, 178129, 178185
-recovered CodingQuarry_transcript_13250-T1, internal, 178284, 178408
-recovered CodingQuarry_transcript_13250-T1, internal, 178520, 178703
-recovered CodingQuarry_transcript_13250-T1, internal, 178797, 178971
-recovered CodingQuarry_transcript_13250-T1, internal, 179150, 179271
-recovered CodingQuarry_transcript_13250-T1, internal, 180424, 180620
-recovered CodingQuarry_transcript_13250-T1, internal, 180995, 181121
-recovered CodingQuarry_transcript_13250-T1, internal, 181323, 181507
-recovered CodingQuarry_transcript_13250-T1, internal, 181719, 181833
-recovered CodingQuarry_transcript_13250-T1, internal, 182028, 182184
-recovered CodingQuarry_transcript_13250-T1, internal, 182420, 182526
-recovered CodingQuarry_transcript_13250-T1, internal, 182880, 182924
-recovered CodingQuarry_transcript_13250-T1, internal, 183203, 183339
-recovered CodingQuarry_transcript_13250-T1, internal, 183497, 183641
-recovered CodingQuarry_transcript_13250-T1, internal, 183929, 183988
-recovered CodingQuarry_transcript_13250-T1, internal, 184223, 184290
-recovered CodingQuarry_transcript_13250-T1, internal, 184384, 184509
Valid prediction for GlimmerHMM_glimmerT_32405-T1
Valid prediction for snap_scaffold_13-snap.2143-T1
Valid prediction for snap_scaffold_13-snap.2159-T1
Valid prediction for snap_scaffold_13-snap.2149-T1
Valid prediction for snap_scaffold_13-snap.2150-T1
Valid prediction for GlimmerHMM_glimmerT_32422-T1
Valid prediction for GlimmerHMM_glimmerT_32421-T1
Couldn't classify 125858, 125914
Couldn't classify 126100, 126254
Sorry, prediction pasa_asmbl_11270.p1 fails validation.
(ATG)	 GA	123973-124047	GT	GGG
(TCT)	 AG	124898-124960	GT	AGG
(TCC)	 AG	125043-125148	GT	GGG
(ATG)	 AG	125292-125394	GT	AGG
(CTC)	 AG	125506-125651	GT	AGG
(ATG)	 AG	125858-125914	AT	ATA
(GCA)	 AC	126100-126254	GT	AGG
(GAA)	 AG	126558-126704	GT	AGG
(GTC)	 AG	126944-127015	GT	AGG
(TTC)	 AG	127145-127153	AG	GAA
-recovered pasa_asmbl_11270.p1, initial, 123973, 124047
-recovered pasa_asmbl_11270.p1, initial, 125292, 125394
-recovered pasa_asmbl_11270.p1, terminal, 127145, 127153
-recovered pasa_asmbl_11270.p1, internal, 124898, 124960
-recovered pasa_asmbl_11270.p1, internal, 125043, 125148
-recovered pasa_asmbl_11270.p1, internal, 125292, 125394
-recovered pasa_asmbl_11270.p1, internal, 125506, 125651
-recovered pasa_asmbl_11270.p1, internal, 126558, 126704
-recovered pasa_asmbl_11270.p1, internal, 126944, 127015
Valid prediction for GlimmerHMM_glimmerT_32406-T1
Valid prediction for GlimmerHMM_glimmerT_32398-T1
Valid prediction for HiQ_model.g21645.t1
Valid prediction for snap_scaffold_13-snap.2153-T1
Valid prediction for snap_scaffold_13-snap.2139-T1
Valid prediction for GlimmerHMM_glimmerT_32399-T1
Valid prediction for HiQ_model.g21647.t1
Valid prediction for GlimmerHMM_glimmerT_32419-T1
Valid prediction for snap_scaffold_13-snap.2141-T1
Valid prediction for snap_scaffold_13-snap.2120-T1
Valid prediction for HiQ_model.g21642.t1
Valid prediction for CodingQuarry_transcript_13251-T1
Valid prediction for Augustus_model.g21633.t1
Valid prediction for pasa_asmbl_11287.p1
Valid prediction for GlimmerHMM_glimmerT_32411-T1
Valid prediction for snap_scaffold_13-snap.2137-T1
Valid prediction for snap_scaffold_13-snap.2161-T1
Valid prediction for snap_scaffold_13-snap.2147-T1
Valid prediction for Augustus_model.g21637.t1
Valid prediction for GlimmerHMM_glimmerT_32417-T1
Valid prediction for snap_scaffold_13-snap.2133-T1
Valid prediction for GlimmerHMM_glimmerT_32394-T1
Valid prediction for Augustus_model.g21648.t1
Valid prediction for snap_scaffold_13-snap.2156-T1
Valid prediction for GlimmerHMM_glimmerT_32395-T1
Valid prediction for snap_scaffold_13-snap.2121-T1
Valid prediction for snap_scaffold_13-snap.2158-T1
Valid prediction for CodingQuarry_transcript_13247-T1
Valid prediction for pasa_asmbl_11280.p2
Valid prediction for snap_scaffold_13-snap.2129-T1
Valid prediction for snap_scaffold_13-snap.2136-T1
Valid prediction for Augustus_model.g21646.t1
Valid prediction for snap_scaffold_13-snap.2131-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 Augustus_model.g21628.t1
Valid prediction for GlimmerHMM_glimmerT_32407-T1
Valid prediction for snap_scaffold_13-snap.2118-T1
Valid prediction for Augustus_model.g21644.t1
Valid prediction for snap_scaffold_13-snap.2132-T1
Valid prediction for snap_scaffold_13-snap.2155-T1
Valid prediction for GlimmerHMM_glimmerT_32402-T1
Valid prediction for Augustus_model.g21641.t1
Valid prediction for snap_scaffold_13-snap.2144-T1
Valid prediction for snap_scaffold_13-snap.2142-T1
Valid prediction for HiQ_model.g21640.t1
Valid prediction for snap_scaffold_13-snap.2134-T1
Valid prediction for GlimmerHMM_glimmerT_32408-T1
Valid prediction for GlimmerHMM_glimmerT_32400-T1
Valid prediction for snap_scaffold_13-snap.2123-T1
Valid prediction for snap_scaffold_13-snap.2135-T1
Valid prediction for GlimmerHMM_glimmerT_32396-T1
Valid prediction for Augustus_model.g21632.t1
Valid prediction for GlimmerHMM_glimmerT_32393-T1
Valid prediction for GlimmerHMM_glimmerT_32415-T1
Valid prediction for snap_scaffold_13-snap.2152-T1
Valid prediction for CodingQuarry_transcript_13245-T1
Valid prediction for Augustus_model.g21635.t1
Valid prediction for Augustus_model.g21639.t1
Valid prediction for snap_scaffold_13-snap.2140-T1
Valid prediction for GlimmerHMM_glimmerT_32420-T1
Valid prediction for snap_scaffold_13-snap.2151-T1
Valid prediction for snap_scaffold_13-snap.2130-T1
Valid prediction for snap_scaffold_13-snap.2146-T1
Valid prediction for pasa_asmbl_10095.p1
Valid prediction for snap_scaffold_13-snap.2125-T1
Valid prediction for GlimmerHMM_glimmerT_32413-T1
Valid prediction for Augustus_model.g21638.t1
Valid prediction for CodingQuarry_transcript_13244-T1
Valid prediction for CodingQuarry_transcript_13249-T1
Valid prediction for snap_scaffold_13-snap.2160-T1
Valid prediction for GlimmerHMM_glimmerT_32401-T1
Valid prediction for snap_scaffold_13-snap.2162-T1
Valid prediction for GlimmerHMM_glimmerT_32403-T1
Valid prediction for HiQ_model.g21630.t1
Valid prediction for snap_scaffold_13-snap.2122-T1
Valid prediction for GlimmerHMM_glimmerT_32397-T1
Valid prediction for snap_scaffold_13-snap.2145-T1
Valid prediction for snap_scaffold_13-snap.2119-T1
Valid prediction for GlimmerHMM_glimmerT_32414-T1
Valid prediction for snap_scaffold_13-snap.2124-T1
Couldn't classify 188313, 188591
Couldn't classify 188737, 188766
Sorry, prediction pasa_asmbl_10403.p1 fails validation.
(CAG)	 AG	188313-188591	GT	AGG
(ATG)	 AG	188737-188766	GA	AGG
-recovered pasa_asmbl_10403.p1, internal, 188313, 188591
Valid prediction for Augustus_model.g21631.t1
Valid prediction for GlimmerHMM_glimmerT_32404-T1
Valid prediction for GlimmerHMM_glimmerT_32418-T1
Valid prediction for snap_scaffold_13-snap.2148-T1
Valid prediction for Augustus_model.g21629.t1
Valid prediction for snap_scaffold_13-snap.2138-T1
Valid prediction for GlimmerHMM_glimmerT_32412-T1
Valid prediction for snap_scaffold_13-snap.2126-T1
Valid prediction for snap_scaffold_13-snap.2154-T1
Valid prediction for Augustus_model.g21634.t1
Valid prediction for HiQ_model.g21649.t1
Couldn't classify 161759, 161783
Sorry, prediction pasa_asmbl_10093.p1 fails validation.
(CTG)	 GG	161759-161783	GT	AAG
(TCC)	 AG	162470-162559	GT	TGG
(ATG)	 AG	162666-162772	GT	AGG
(TTT)	 AG	163004-163129	GT	AGG
(CTT)	 AG	164128-164234	GT	TGG
(TGA)	 AG	164583-164726	GT	AGG
(GAG)	 AG	165122-165212	GT	AGG
(GCT)	 AG	165352-167718	GT	AGG
(GTT)	 AG	167905-167997	GT	AGG
(AGT)	 AG	168191-168309	GT	AGG
(GTG)	 AG	168683-168850	GT	AGG
(GGA)	 AG	169342-169482	GT	AGG
(GTT)	 AG	169576-169781	GT	AGG
(AGC)	 AG	169967-170099	GT	CTG
(GAA)	 AG	170186-170290	GT	ACG
(GCT)	 AG	170740-170950	GT	AGG
(GTC)	 AG	171257-171366	GT	AGG
(GTT)	 AG	171539-171614	CT	AGC
add_exon() Sorry, pasa_asmbl_10093.p1 162666-162772-initial-1 is invalid.
-recovered pasa_asmbl_10093.p1, initial, 162666, 162772
add_exon() Sorry, pasa_asmbl_10093.p1 168191-168309-terminal-2 is invalid.
-recovered pasa_asmbl_10093.p1, terminal, 168191, 168309
-recovered pasa_asmbl_10093.p1, terminal, 171539, 171614
-recovered pasa_asmbl_10093.p1, internal, 162470, 162559
-recovered pasa_asmbl_10093.p1, internal, 162666, 162772
-recovered pasa_asmbl_10093.p1, internal, 163004, 163129
-recovered pasa_asmbl_10093.p1, internal, 164128, 164234
-recovered pasa_asmbl_10093.p1, internal, 164583, 164726
-recovered pasa_asmbl_10093.p1, internal, 165122, 165212
-recovered pasa_asmbl_10093.p1, internal, 165352, 167718
-recovered pasa_asmbl_10093.p1, internal, 167905, 167997
-recovered pasa_asmbl_10093.p1, internal, 168191, 168309
-recovered pasa_asmbl_10093.p1, internal, 168683, 168850
-recovered pasa_asmbl_10093.p1, internal, 169342, 169482
-recovered pasa_asmbl_10093.p1, internal, 169576, 169781
-recovered pasa_asmbl_10093.p1, internal, 169967, 170099
-recovered pasa_asmbl_10093.p1, internal, 170186, 170290
-recovered pasa_asmbl_10093.p1, internal, 170740, 170950
-recovered pasa_asmbl_10093.p1, internal, 171257, 171366
Valid prediction for pasa_asmbl_10409.p2
Valid prediction for GlimmerHMM_glimmerT_32410-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 22479, rend_intergenic: 15760  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58374, rend_intergenic: 55698  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63899, rend_intergenic: 60885  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71564, rend_intergenic: 66216  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88693, rend_intergenic: 86253  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91529, rend_intergenic: 88739  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96299, rend_intergenic: 92734  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102943, rend_intergenic: 101608  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117678, rend_intergenic: 114109  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152587, rend_intergenic: 144169  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187995, rend_intergenic: 178750  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 192419
-exon list size: 386


building trellis

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27.3    
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28.4    
28.6    
28.9    
29.1    
29.4    
29.6    
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30.4    
30.7    
30.9    
31.2    
31.4    
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    
35.1    
35.3    
35.6    
35.8    
36.1    
36.3    
36.6    
36.9    
37.1    
37.4    
37.6    
37.9    
38.1    
38.4    
38.7    
38.9    
39.2    
39.4    
39.7    
39.9    
40.2    
40.5    
40.7    
41.0    
41.2    
41.5    
41.8    
42.0    
42.3    
42.5    
42.8    
43.0    
43.3    
43.6    
43.8    
44.1    
44.3    
44.6    
44.8    
45.1    
45.4    
45.6    
45.9    
46.1    
46.4    
46.6    
46.9    
47.2    
47.4    
47.7    
47.9    
48.2    
48.5    
48.7    
49.0    
49.2    
49.5    
49.7    
50.0    
50.3    
50.5    
50.8    
51.0    
51.3    
51.5    
51.8    
52.1    
52.3    
52.6    
52.8    
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53.4    
53.6    
53.9    
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54.9    
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55.4    
55.7    
55.9    
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82.0    
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83.0    
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84.0    
84.3    
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85.3    
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88.7    
88.9    
89.2    
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89.9    
90.2    
90.5    
90.7    
91.0    
91.2    
91.5    
91.8    
92.0    
92.3    
92.5    
92.8    
93.0    
93.3    
93.6    
93.8    
94.1    
94.3    
94.6    
94.8    
95.1    
95.4    
95.6    
95.9    
96.1    
96.4    
96.6    
96.9    
97.2    
97.4    
97.7    
97.9    
98.2    
98.5    
98.7    
99.0    
99.2    
99.5    
99.7    
-found 32 predictions from path traversal
Error with prediction: snap lend_intergenic: 22479, rend_intergenic: 15760  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58374, rend_intergenic: 55698  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63899, rend_intergenic: 60885  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71564, rend_intergenic: 66216  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88693, rend_intergenic: 86253  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91529, rend_intergenic: 88739  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96299, rend_intergenic: 92734  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102943, rend_intergenic: 101608  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117678, rend_intergenic: 114109  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152587, rend_intergenic: 144169  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187995, rend_intergenic: 178750  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

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