-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_17/scaffold_17_5185983-5395175

-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_40288-T1
Valid prediction for Augustus_model.g26844.t1
Valid prediction for Augustus_model.g26839.t1
Valid prediction for pasa_asmbl_18819.p1
Valid prediction for GlimmerHMM_glimmerT_40295-T1
Valid prediction for snap_scaffold_17-snap.1073-T1
Valid prediction for snap_scaffold_17-snap.1089-T1
Valid prediction for GlimmerHMM_glimmerT_40291-T1
Valid prediction for GlimmerHMM_glimmerT_40274-T1
Valid prediction for Augustus_model.g26826.t1
Valid prediction for snap_scaffold_17-snap.1105-T1
Valid prediction for GlimmerHMM_glimmerT_40292-T1
Valid prediction for snap_scaffold_17-snap.1107-T1
Valid prediction for Augustus_model.g26827.t1
Valid prediction for snap_scaffold_17-snap.1097-T1
Valid prediction for snap_scaffold_17-snap.1093-T1
Valid prediction for snap_scaffold_17-snap.1076-T1
Valid prediction for Augustus_model.g26843.t1
Valid prediction for Augustus_model.g26835.t1
Valid prediction for snap_scaffold_17-snap.1088-T1
Valid prediction for CodingQuarry_transcript_21983-T1
Valid prediction for snap_scaffold_17-snap.1090-T1
Valid prediction for GlimmerHMM_glimmerT_40296-T1
Valid prediction for Augustus_model.g26837.t1
Valid prediction for Augustus_model.g26845.t1
Valid prediction for Augustus_model.g26834.t1
Valid prediction for snap_scaffold_17-snap.1072-T1
Valid prediction for snap_scaffold_17-snap.1106-T1
Valid prediction for snap_scaffold_17-snap.1096-T1
Couldn't classify 130423, 130526
Sorry, prediction pasa_asmbl_18816.p1 fails validation.
(CAG)	 CC	130423-130526	GT	TGG
(CTG)	 AG	130640-130774	GT	GGG
(ATT)	 AG	132465-132582	GT	AGG
(ATT)	 AG	133141-133233	GT	AGG
(GAT)	 AG	133683-133779	GT	AGG
(TGG)	 AG	136536-136587	GT	AGG
(AAC)	 AG	137062-137190	GT	AAG
(GAG)	 AG	138260-138395	GT	AGG
(CTG)	 AG	138805-138950	GT	AGG
(AAC)	 AG	139204-139240	AA	AAA
-recovered pasa_asmbl_18816.p1, terminal, 139204, 139240
-recovered pasa_asmbl_18816.p1, internal, 130640, 130774
-recovered pasa_asmbl_18816.p1, internal, 132465, 132582
-recovered pasa_asmbl_18816.p1, internal, 133141, 133233
-recovered pasa_asmbl_18816.p1, internal, 133683, 133779
-recovered pasa_asmbl_18816.p1, internal, 136536, 136587
-recovered pasa_asmbl_18816.p1, internal, 137062, 137190
-recovered pasa_asmbl_18816.p1, internal, 138260, 138395
-recovered pasa_asmbl_18816.p1, internal, 138805, 138950
Valid prediction for GlimmerHMM_glimmerT_40279-T1
Valid prediction for GlimmerHMM_glimmerT_40293-T1
Couldn't classify 177228, 177260
Couldn't classify 177935, 177953
Sorry, prediction pasa_asmbl_19501.p1 fails validation.
(GTG)	 AG	177228-177260	GT	TGG
(ACA)	 AG	177417-177524	GT	AGG
(CGC)	 AG	177635-177807	GT	ACG
(AAA)	 AG	177935-177953	AC	ACA
-recovered pasa_asmbl_19501.p1, internal, 177228, 177260
-recovered pasa_asmbl_19501.p1, internal, 177417, 177524
-recovered pasa_asmbl_19501.p1, internal, 177635, 177807
Valid prediction for snap_scaffold_17-snap.1108-T1
Valid prediction for GlimmerHMM_glimmerT_40281-T1
Valid prediction for Augustus_model.g26831.t1
Valid prediction for GlimmerHMM_glimmerT_40284-T1
Valid prediction for snap_scaffold_17-snap.1067-T1
Valid prediction for Augustus_model.g26836.t1
Valid prediction for GlimmerHMM_glimmerT_40289-T1
Valid prediction for HiQ_model.g26841.t1
Valid prediction for GlimmerHMM_glimmerT_40286-T1
Valid prediction for snap_scaffold_17-snap.1102-T1
Valid prediction for snap_scaffold_17-snap.1066-T1
Valid prediction for snap_scaffold_17-snap.1099-T1
Valid prediction for Augustus_model.g26830.t1
Valid prediction for Augustus_model.g26829.t1
Valid prediction for GlimmerHMM_glimmerT_40287-T1
Valid prediction for GlimmerHMM_glimmerT_40276-T1
Valid prediction for snap_scaffold_17-snap.1077-T1
Valid prediction for HiQ_model.g26838.t1
Couldn't classify 144281, 145126
Sorry, prediction pasa_asmbl_18818.p1 fails validation.
(ATG)	 CG	144281-145126	GA	ATG
Valid prediction for GlimmerHMM_glimmerT_40278-T1
Valid prediction for snap_scaffold_17-snap.1104-T1
Valid prediction for GlimmerHMM_glimmerT_40294-T1
Valid prediction for snap_scaffold_17-snap.1081-T1
Valid prediction for GlimmerHMM_glimmerT_40277-T1
Valid prediction for Augustus_model.g26846.t1
Valid prediction for snap_scaffold_17-snap.1083-T1
Valid prediction for snap_scaffold_17-snap.1095-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 snap_scaffold_17-snap.1078-T1
Valid prediction for Augustus_model.g26842.t1
Valid prediction for snap_scaffold_17-snap.1079-T1
Valid prediction for snap_scaffold_17-snap.1071-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_17-snap.1101-T1
Valid prediction for snap_scaffold_17-snap.1068-T1
Valid prediction for snap_scaffold_17-snap.1103-T1
Valid prediction for GlimmerHMM_glimmerT_40280-T1
Valid prediction for GlimmerHMM_glimmerT_40290-T1
Valid prediction for Augustus_model.g26825.t1
Valid prediction for GlimmerHMM_glimmerT_40275-T1
Valid prediction for GlimmerHMM_glimmerT_40282-T1
Valid prediction for snap_scaffold_17-snap.1087-T1
Valid prediction for snap_scaffold_17-snap.1086-T1
Valid prediction for GlimmerHMM_glimmerT_40283-T1
Valid prediction for Augustus_model.g26828.t1
Valid prediction for Augustus_model.g26840.t1
Valid prediction for pasa_asmbl_17929.p1
Couldn't classify 127583, 127647
Sorry, prediction pasa_asmbl_17928.p2 fails validation.
(ATG)	 CG	125333-125374	GT	TGG
(AAC)	 AG	126494-126673	GT	AGG
(CAA)	 AG	126796-126886	GT	GGG
(TAA)	 AG	127583-127647	TA	CGT
-recovered pasa_asmbl_17928.p2, initial, 125333, 125374
-recovered pasa_asmbl_17928.p2, internal, 126494, 126673
-recovered pasa_asmbl_17928.p2, internal, 126796, 126886
Valid prediction for snap_scaffold_17-snap.1100-T1
Couldn't classify 134282, 134347
Sorry, prediction pasa_asmbl_17926.p1 fails validation.
(CAG)	 CC	134282-134347	GC	TGG
(GTG)	 AG	134721-134916	GT	TGG
(AGA)	 AG	135024-135115	GT	AGG
(GCG)	 AG	135334-135489	GT	AGG
(AAA)	 AG	135674-135757	GT	ATG
(CGA)	 AG	135883-136083	GT	AGG
(GGT)	 AG	136351-136501	GT	AGG
(GTG)	 AG	136845-137009	GT	AGG
(CCG)	 AG	137384-137585	GT	ACG
(GTC)	 AG	139015-139094	GT	TGG
(ACG)	 AG	139290-139388	GT	AGG
(CCA)	 AG	140067-140198	GT	AGG
(GAA)	 AG	140290-140387	GT	GCG
(AAG)	 AG	140489-140656	AC	AGA
-recovered pasa_asmbl_17926.p1, terminal, 140489, 140656
-recovered pasa_asmbl_17926.p1, internal, 134721, 134916
-recovered pasa_asmbl_17926.p1, internal, 135024, 135115
-recovered pasa_asmbl_17926.p1, internal, 135334, 135489
-recovered pasa_asmbl_17926.p1, internal, 135674, 135757
-recovered pasa_asmbl_17926.p1, internal, 135883, 136083
-recovered pasa_asmbl_17926.p1, internal, 136351, 136501
-recovered pasa_asmbl_17926.p1, internal, 136845, 137009
-recovered pasa_asmbl_17926.p1, internal, 137384, 137585
-recovered pasa_asmbl_17926.p1, internal, 139015, 139094
-recovered pasa_asmbl_17926.p1, internal, 139290, 139388
-recovered pasa_asmbl_17926.p1, internal, 140067, 140198
-recovered pasa_asmbl_17926.p1, internal, 140290, 140387
Valid prediction for HiQ_model.g26833.t1
Valid prediction for GlimmerHMM_glimmerT_40285-T1
Valid prediction for snap_scaffold_17-snap.1098-T1
Valid prediction for snap_scaffold_17-snap.1084-T1
Valid prediction for snap_scaffold_17-snap.1082-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for snap_scaffold_17-snap.1075-T1
Couldn't classify 131364, 131433
Couldn't classify 133286, 133351
Sorry, prediction pasa_asmbl_17927.p1 fails validation.
(ATT)	 GT	131364-131433	GT	AGG
(GTT)	 AG	131561-131670	GT	TGG
(GCC)	 AG	131794-131886	GT	AGG
(CAA)	 AG	132673-132787	GT	CGG
(GGC)	 AG	133048-133169	GT	AGG
(CAA)	 AG	133286-133351	CT	TCC
-recovered pasa_asmbl_17927.p1, internal, 131561, 131670
-recovered pasa_asmbl_17927.p1, internal, 131794, 131886
-recovered pasa_asmbl_17927.p1, internal, 132673, 132787
-recovered pasa_asmbl_17927.p1, internal, 133048, 133169
Valid prediction for snap_scaffold_17-snap.1085-T1
Valid prediction for snap_scaffold_17-snap.1069-T1
Valid prediction for CodingQuarry_transcript_21982-T1
Valid prediction for snap_scaffold_17-snap.1092-T1
Valid prediction for Augustus_model.g26832.t1
Valid prediction for snap_scaffold_17-snap.1091-T1
Valid prediction for snap_scaffold_17-snap.1080-T1
Valid prediction for snap_scaffold_17-snap.1094-T1
Valid prediction for snap_scaffold_17-snap.1074-T1
Valid prediction for snap_scaffold_17-snap.1070-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 19426, rend_intergenic: 13536  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27500, rend_intergenic: 23265  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45060, rend_intergenic: 40354  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47424, rend_intergenic: 45363  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51486, rend_intergenic: 49460  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59313, rend_intergenic: 56250  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64805, rend_intergenic: 59577  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128920, rend_intergenic: 117598  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136663, rend_intergenic: 130617  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139930, rend_intergenic: 137069  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149236, rend_intergenic: 144893  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158520, rend_intergenic: 151756  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165024, rend_intergenic: 160188  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 209193
-exon list size: 401


building trellis

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25.6    
25.8    
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26.6    
26.8    
27.0    
27.3    
27.5    
27.8    
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30.5    
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31.3    
31.5    
31.8    
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32.3    
32.5    
32.8    
33.0    
33.3    
33.5    
33.7    
34.0    
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35.2    
35.5    
35.7    
36.0    
36.2    
36.5    
36.7    
37.0    
37.2    
37.5    
37.7    
38.0    
38.2    
38.5    
38.7    
39.0    
39.2    
39.5    
39.7    
40.0    
40.2    
40.4    
40.7    
40.9    
41.2    
41.4    
41.7    
41.9    
42.2    
42.4    
42.7    
42.9    
43.2    
43.4    
43.7    
43.9    
44.2    
44.4    
44.7    
44.9    
45.2    
45.4    
45.7    
45.9    
46.2    
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46.9    
47.1    
47.4    
47.6    
47.9    
48.1    
48.4    
48.6    
48.9    
49.1    
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96.5    
96.8    
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97.3    
97.5    
97.8    
98.0    
98.3    
98.5    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 19426, rend_intergenic: 13536  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27500, rend_intergenic: 23265  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45060, rend_intergenic: 40354  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47424, rend_intergenic: 45363  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51486, rend_intergenic: 49460  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59313, rend_intergenic: 56250  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64805, rend_intergenic: 59577  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128920, rend_intergenic: 117598  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136663, rend_intergenic: 130617  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139930, rend_intergenic: 137069  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149236, rend_intergenic: 144893  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158520, rend_intergenic: 151756  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165024, rend_intergenic: 160188  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 25 predictions persist after filtering for low support