-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_27/scaffold_27_520696-749237

-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_56564-T1
Valid prediction for GlimmerHMM_glimmerT_56576-T1
Valid prediction for GlimmerHMM_glimmerT_56577-T1
Valid prediction for snap_scaffold_27-snap.157-T1
Valid prediction for snap_scaffold_27-snap.153-T1
Valid prediction for GlimmerHMM_glimmerT_56560-T1
Valid prediction for snap_scaffold_27-snap.134-T1
Couldn't classify 133969, 134008
Sorry, prediction pasa_asmbl_35965.p1 fails validation.
(GAT)	 TG	133969-134008	GT	AGG
(GCT)	 AG	134320-134420	GT	AGG
(ATG)	 AG	134553-134723	GT	ACG
(GTG)	 AG	134887-135066	GA	GAG
-recovered pasa_asmbl_35965.p1, initial, 134553, 134723
-recovered pasa_asmbl_35965.p1, terminal, 134887, 135066
-recovered pasa_asmbl_35965.p1, internal, 134320, 134420
-recovered pasa_asmbl_35965.p1, internal, 134553, 134723
Valid prediction for GlimmerHMM_glimmerT_56562-T1
Valid prediction for snap_scaffold_27-snap.162-T1
Valid prediction for snap_scaffold_27-snap.143-T1
Valid prediction for snap_scaffold_27-snap.124-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for Augustus_model.g37481.t1
Valid prediction for GlimmerHMM_glimmerT_56558-T1
Valid prediction for GlimmerHMM_glimmerT_56572-T1
Valid prediction for GlimmerHMM_glimmerT_56565-T1
Valid prediction for Augustus_model.g37479.t1
Valid prediction for snap_scaffold_27-snap.158-T1
Valid prediction for GlimmerHMM_glimmerT_56569-T1
Valid prediction for snap_scaffold_27-snap.165-T1
Valid prediction for pasa_asmbl_35961.p1
Valid prediction for snap_scaffold_27-snap.154-T1
Valid prediction for Augustus_model.g37487.t1
Valid prediction for snap_scaffold_27-snap.161-T1
Couldn't classify 52833, 52907
Sorry, prediction pasa_asmbl_35951.p1 fails validation.
(ATG)	 TC	50964-51410	GT	AGG
(GCG)	 AG	52305-52667	GT	AGG
(GTG)	 AG	52833-52907	AC	GCA
-recovered pasa_asmbl_35951.p1, initial, 50964, 51410
-recovered pasa_asmbl_35951.p1, internal, 52305, 52667
Valid prediction for Augustus_model.g37478.t1
Valid prediction for Augustus_model.g37471.t1
Valid prediction for snap_scaffold_27-snap.128-T1
Valid prediction for GlimmerHMM_glimmerT_56568-T1
Valid prediction for snap_scaffold_27-snap.151-T1
Valid prediction for GlimmerHMM_glimmerT_56574-T1
Valid prediction for HiQ_model.g37482.t1
Couldn't classify 4454, 4547
Sorry, prediction pasa_asmbl_35948.p1 fails validation.
(AAA)	 AC	4454-4547	GT	GTG
(CTG)	 AG	4839-4876	GT	AGG
(GAG)	 AG	5077-5175	GT	AGG
(GTG)	 AG	5416-5532	GT	AGG
(ATC)	 AG	5743-5870	GT	AGG
(GTA)	 AG	5990-6017	GA	GAG
-recovered pasa_asmbl_35948.p1, terminal, 5990, 6017
-recovered pasa_asmbl_35948.p1, internal, 4839, 4876
-recovered pasa_asmbl_35948.p1, internal, 5077, 5175
-recovered pasa_asmbl_35948.p1, internal, 5416, 5532
-recovered pasa_asmbl_35948.p1, internal, 5743, 5870
Valid prediction for snap_scaffold_27-snap.148-T1
Valid prediction for snap_scaffold_27-snap.169-T1
Valid prediction for snap_scaffold_27-snap.163-T1
Valid prediction for Augustus_model.g37480.t1
Valid prediction for snap_scaffold_27-snap.167-T1
Valid prediction for GlimmerHMM_glimmerT_56575-T1
Valid prediction for CodingQuarry_transcript_41748-T1
Valid prediction for CodingQuarry_transcript_41745-T1
Valid prediction for GlimmerHMM_glimmerT_56544-T1
Couldn't classify 131026, 131107
Couldn't classify 132959, 132967
Sorry, prediction pasa_asmbl_35964.p1 fails validation.
(GGG)	 GA	131026-131107	GT	AGG
(TCT)	 AG	131494-131575	GT	GGG
(GTG)	 AG	131760-131849	GT	AGG
(TCC)	 AG	132141-132256	GT	AAG
(AGT)	 AG	132384-132556	GT	AGG
(AAA)	 AG	132664-132807	GT	AGG
(CTT)	 AG	132959-132967	CA	AGC
-recovered pasa_asmbl_35964.p1, internal, 131494, 131575
-recovered pasa_asmbl_35964.p1, internal, 131760, 131849
-recovered pasa_asmbl_35964.p1, internal, 132141, 132256
-recovered pasa_asmbl_35964.p1, internal, 132384, 132556
-recovered pasa_asmbl_35964.p1, internal, 132664, 132807
Valid prediction for snap_scaffold_27-snap.127-T1
Valid prediction for Augustus_model.g37486.t1
Valid prediction for HiQ_model.g37484.t1
Valid prediction for pasa_asmbl_35958.p1
Valid prediction for Augustus_model.g37491.t1
Valid prediction for snap_scaffold_27-snap.126-T1
Valid prediction for snap_scaffold_27-snap.140-T1
Valid prediction for GlimmerHMM_glimmerT_56547-T1
Valid prediction for Augustus_model.g37494.t1
Couldn't classify 124918, 125298
Sorry, prediction pasa_asmbl_35963.p1 fails validation.
(CCC)	 AG	124918-125298	TG	GGT
Valid prediction for Augustus_model.g37475.t1
Valid prediction for GlimmerHMM_glimmerT_56563-T1
Valid prediction for CodingQuarry_transcript_41753-T1
Valid prediction for snap_scaffold_27-snap.137-T1
Valid prediction for pasa_asmbl_35959.p1
Valid prediction for snap_scaffold_27-snap.168-T1
Valid prediction for snap_scaffold_27-snap.146-T1
Valid prediction for snap_scaffold_27-snap.142-T1
Valid prediction for Augustus_model.g37492.t1
Valid prediction for HiQ_model.g37469.t1
Valid prediction for CodingQuarry_transcript_41751-T1
Valid prediction for GlimmerHMM_glimmerT_56556-T1
Valid prediction for Augustus_model.g37493.t1
Valid prediction for snap_scaffold_27-snap.129-T1
Valid prediction for pasa_asmbl_35947.p2
Valid prediction for GlimmerHMM_glimmerT_56555-T1
Valid prediction for GlimmerHMM_glimmerT_56551-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_56561-T1
Valid prediction for CodingQuarry_transcript_41750-T1
Valid prediction for GlimmerHMM_glimmerT_56571-T1
Valid prediction for snap_scaffold_27-snap.141-T1
Valid prediction for GlimmerHMM_glimmerT_56553-T1
Valid prediction for snap_scaffold_27-snap.173-T1
Valid prediction for GlimmerHMM_glimmerT_56567-T1
Valid prediction for snap_scaffold_27-snap.160-T1
Valid prediction for Augustus_model.g37488.t1
Valid prediction for snap_scaffold_27-snap.170-T1
Valid prediction for snap_scaffold_27-snap.155-T1
Valid prediction for CodingQuarry_transcript_41746-T1
Valid prediction for snap_scaffold_27-snap.174-T1
Valid prediction for GlimmerHMM_glimmerT_56573-T1
Valid prediction for snap_scaffold_27-snap.125-T1
Valid prediction for snap_scaffold_27-snap.152-T1
Valid prediction for snap_scaffold_27-snap.135-T1
Valid prediction for pasa_asmbl_36699.p1
Valid prediction for GlimmerHMM_glimmerT_56557-T1
Valid prediction for snap_scaffold_27-snap.149-T1
Valid prediction for GlimmerHMM_glimmerT_56552-T1
Valid prediction for snap_scaffold_27-snap.136-T1
Valid prediction for HiQ_model.g37483.t1
Valid prediction for GlimmerHMM_glimmerT_56570-T1
Valid prediction for snap_scaffold_27-snap.133-T1
Valid prediction for Augustus_model.g37490.t1
Valid prediction for pasa_asmbl_36702.p1
Valid prediction for GlimmerHMM_glimmerT_56549-T1
Valid prediction for snap_scaffold_27-snap.130-T1
Valid prediction for snap_scaffold_27-snap.138-T1
Valid prediction for Augustus_model.g37476.t1
Valid prediction for snap_scaffold_27-snap.175-T1
Valid prediction for GlimmerHMM_glimmerT_56566-T1
Valid prediction for snap_scaffold_27-snap.164-T1
Valid prediction for GlimmerHMM_glimmerT_56546-T1
Valid prediction for GlimmerHMM_glimmerT_56554-T1
Valid prediction for snap_scaffold_27-snap.156-T1
Valid prediction for CodingQuarry_transcript_41752-T1
Valid prediction for Augustus_model.g37470.t1
Valid prediction for snap_scaffold_27-snap.172-T1
Valid prediction for snap_scaffold_27-snap.159-T1
Valid prediction for Augustus_model.g37489.t1
Valid prediction for CodingQuarry_transcript_41749-T1
Valid prediction for snap_scaffold_27-snap.131-T1
Valid prediction for snap_scaffold_27-snap.144-T1
Valid prediction for GlimmerHMM_glimmerT_56545-T1
Valid prediction for Augustus_model.g37472.t1
Valid prediction for HiQ_model.g37477.t1
Valid prediction for HiQ_model.g37485.t1
Valid prediction for snap_scaffold_27-snap.150-T1
Valid prediction for snap_scaffold_27-snap.147-T1
Valid prediction for GlimmerHMM_glimmerT_56548-T1
Valid prediction for Augustus_model.g37474.t1
Valid prediction for snap_scaffold_27-snap.139-T1
Valid prediction for snap_scaffold_27-snap.145-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_27-snap.132-T1
Valid prediction for GlimmerHMM_glimmerT_56559-T1
Valid prediction for pasa_asmbl_36711.p1
Valid prediction for snap_scaffold_27-snap.166-T1
Valid prediction for Augustus_model.g37473.t1
Valid prediction for snap_scaffold_27-snap.171-T1
Valid prediction for GlimmerHMM_glimmerT_56550-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 8640, rend_intergenic: 3109  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25915, rend_intergenic: 21383  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31858, rend_intergenic: 26430  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35975, rend_intergenic: 33096  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43017, rend_intergenic: 42389  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48609, rend_intergenic: 44171  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84338, rend_intergenic: 63501  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93748, rend_intergenic: 89203  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99647, rend_intergenic: 96899  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103912, rend_intergenic: 100737  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144605, rend_intergenic: 140804  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168755, rend_intergenic: 165632  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180644, rend_intergenic: 170489  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182032, rend_intergenic: 181884  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 221588, rend_intergenic: 194849  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 228542
-exon list size: 471


building trellis

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23.9    
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27.9    
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28.8    
29.0    
29.2    
29.4    
29.6    
29.8    
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30.4    
30.7    
30.9    
31.1    
31.3    
31.5    
31.7    
31.9    
32.1    
32.3    
32.6    
32.8    
33.0    
33.2    
33.4    
33.6    
33.8    
34.0    
34.2    
34.5    
34.7    
34.9    
35.1    
35.3    
35.5    
35.7    
35.9    
36.2    
36.4    
36.6    
36.8    
37.0    
37.2    
37.4    
37.6    
37.8    
38.1    
38.3    
38.5    
38.7    
38.9    
39.1    
39.3    
39.5    
39.7    
40.0    
40.2    
40.4    
40.6    
40.8    
41.0    
41.2    
41.4    
41.6    
41.9    
42.1    
42.3    
42.5    
42.7    
42.9    
43.1    
43.3    
43.6    
43.8    
44.0    
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44.6    
44.8    
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45.2    
45.5    
45.7    
45.9    
46.1    
46.3    
46.5    
46.7    
46.9    
47.1    
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47.6    
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48.0    
48.2    
48.4    
48.6    
48.8    
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49.3    
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49.9    
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50.3    
50.5    
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59.6    
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78.9    
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80.3    
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82.9    
83.1    
83.3    
83.5    
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83.9    
84.1    
84.4    
84.6    
84.8    
85.0    
85.2    
85.4    
85.6    
85.8    
86.0    
86.3    
86.5    
86.7    
86.9    
87.1    
87.3    
87.5    
87.7    
87.9    
88.2    
88.4    
88.6    
88.8    
89.0    
89.2    
89.4    
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89.9    
90.1    
90.3    
90.5    
90.7    
90.9    
91.1    
91.3    
91.5    
91.8    
92.0    
92.2    
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92.6    
92.8    
93.0    
93.2    
93.4    
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93.9    
94.1    
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94.9    
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95.3    
95.6    
95.8    
96.0    
96.2    
96.4    
96.6    
96.8    
97.0    
97.3    
97.5    
97.7    
97.9    
98.1    
98.3    
98.5    
98.7    
98.9    
99.2    
99.4    
99.6    
99.8    
-found 35 predictions from path traversal
Error with prediction: snap lend_intergenic: 8640, rend_intergenic: 3109  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25915, rend_intergenic: 21383  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31858, rend_intergenic: 26430  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35975, rend_intergenic: 33096  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43017, rend_intergenic: 42389  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48609, rend_intergenic: 44171  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84338, rend_intergenic: 63501  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93748, rend_intergenic: 89203  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99647, rend_intergenic: 96899  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103912, rend_intergenic: 100737  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144605, rend_intergenic: 140804  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168755, rend_intergenic: 165632  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180644, rend_intergenic: 170489  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182032, rend_intergenic: 181884  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 221588, rend_intergenic: 194849  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 30 predictions persist after filtering for low support