-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_21/scaffold_21_11866942-12046431

-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_48702-T1
Valid prediction for GlimmerHMM_glimmerT_48700-T1
Valid prediction for Augustus_model.g32526.t1
Valid prediction for snap_scaffold_21-snap.2580-T1
Valid prediction for snap_scaffold_21-snap.2574-T1
Valid prediction for snap_scaffold_21-snap.2572-T1
Valid prediction for snap_scaffold_21-snap.2559-T1
Couldn't classify 89395, 89460
Sorry, prediction pasa_asmbl_28946.p1 fails validation.
(ATG)	 CA	81832-81916	GT	GGG
(AGA)	 AG	82720-82890	GT	TGG
(GAG)	 AG	83544-84005	GT	TGG
(CTC)	 AG	84113-84250	GT	CAG
(GTC)	 AG	85510-85624	GT	AGG
(TGA)	 AG	85754-85970	GT	AGG
(GGT)	 AG	86451-86609	GT	AGG
(GAG)	 AG	88227-88310	GT	AGG
(CTG)	 AG	89395-89460	AG	GCA
-recovered pasa_asmbl_28946.p1, initial, 81832, 81916
-recovered pasa_asmbl_28946.p1, internal, 82720, 82890
-recovered pasa_asmbl_28946.p1, internal, 83544, 84005
-recovered pasa_asmbl_28946.p1, internal, 84113, 84250
-recovered pasa_asmbl_28946.p1, internal, 85510, 85624
-recovered pasa_asmbl_28946.p1, internal, 85754, 85970
-recovered pasa_asmbl_28946.p1, internal, 86451, 86609
-recovered pasa_asmbl_28946.p1, internal, 88227, 88310
Valid prediction for snap_scaffold_21-snap.2602-T1
Valid prediction for snap_scaffold_21-snap.2566-T1
Valid prediction for GlimmerHMM_glimmerT_48715-T1
Valid prediction for snap_scaffold_21-snap.2589-T1
Couldn't classify 35253, 35609
Sorry, prediction pasa_asmbl_28943.p1 fails validation.
(GTT)	 GT	35253-35609	GC	AGG
Valid prediction for Augustus_model.g32530.t1
Valid prediction for snap_scaffold_21-snap.2568-T1
Valid prediction for GlimmerHMM_glimmerT_48701-T1
Valid prediction for snap_scaffold_21-snap.2557-T1
Valid prediction for GlimmerHMM_glimmerT_48722-T1
Valid prediction for snap_scaffold_21-snap.2582-T1
Valid prediction for snap_scaffold_21-snap.2577-T1
Valid prediction for Augustus_model.g32527.t1
Valid prediction for Augustus_model.g32533.t1
Valid prediction for snap_scaffold_21-snap.2578-T1
Valid prediction for GlimmerHMM_glimmerT_48710-T1
Valid prediction for snap_scaffold_21-snap.2586-T1
Valid prediction for GlimmerHMM_glimmerT_48724-T1
Valid prediction for snap_scaffold_21-snap.2585-T1
Valid prediction for GlimmerHMM_glimmerT_48726-T1
Valid prediction for GlimmerHMM_glimmerT_48708-T1
Valid prediction for snap_scaffold_21-snap.2594-T1
Valid prediction for GlimmerHMM_glimmerT_48716-T1
Valid prediction for snap_scaffold_21-snap.2588-T1
Valid prediction for GlimmerHMM_glimmerT_48703-T1
Valid prediction for GlimmerHMM_glimmerT_48704-T1
Valid prediction for snap_scaffold_21-snap.2592-T1
Couldn't classify 25497, 25547
Couldn't classify 26133, 26401
Sorry, prediction pasa_asmbl_28939.p1 fails validation.
(GGC)	 AT	25497-25547	GT	AGG
(AAC)	 AG	25914-26052	GT	CAG
(AGC)	 AG	26133-26401	GC	CAG
-recovered pasa_asmbl_28939.p1, internal, 25914, 26052
-recovered pasa_asmbl_28939.p1, internal, 26133, 26401
Valid prediction for GlimmerHMM_glimmerT_48712-T1
Valid prediction for GlimmerHMM_glimmerT_48711-T1
Valid prediction for GlimmerHMM_glimmerT_48709-T1
Valid prediction for snap_scaffold_21-snap.2562-T1
Valid prediction for snap_scaffold_21-snap.2595-T1
Valid prediction for snap_scaffold_21-snap.2570-T1
Valid prediction for snap_scaffold_21-snap.2564-T1
Valid prediction for snap_scaffold_21-snap.2587-T1
Valid prediction for Augustus_model.g32529.t1
Valid prediction for Augustus_model.g32524.t1
Valid prediction for GlimmerHMM_glimmerT_48706-T1
Valid prediction for Augustus_model.g32532.t1
Couldn't classify 35712, 35878
Sorry, prediction pasa_asmbl_28944.p1 fails validation.
(CTG)	 CT	35712-35878	GT	AGG
(CTG)	 AG	36112-36205	GT	AGG
(GTG)	 AG	36514-36634	GT	GGG
(GTG)	 AG	36777-36896	GT	AGG
(GCA)	 AG	37251-37303	AC	GAA
-recovered pasa_asmbl_28944.p1, terminal, 37251, 37303
-recovered pasa_asmbl_28944.p1, internal, 36112, 36205
-recovered pasa_asmbl_28944.p1, internal, 36514, 36634
-recovered pasa_asmbl_28944.p1, internal, 36777, 36896
Valid prediction for Augustus_model.g32528.t1
Valid prediction for snap_scaffold_21-snap.2590-T1
Valid prediction for snap_scaffold_21-snap.2561-T1
Valid prediction for snap_scaffold_21-snap.2579-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 CodingQuarry_transcript_32758-T1
Valid prediction for snap_scaffold_21-snap.2584-T1
Valid prediction for snap_scaffold_21-snap.2596-T1
Valid prediction for snap_scaffold_21-snap.2591-T1
Valid prediction for snap_scaffold_21-snap.2575-T1
Valid prediction for CodingQuarry_transcript_32756-T1
Valid prediction for snap_scaffold_21-snap.2573-T1
Valid prediction for snap_scaffold_21-snap.2560-T1
Valid prediction for snap_scaffold_21-snap.2571-T1
Valid prediction for snap_scaffold_21-snap.2565-T1
Valid prediction for pasa_asmbl_28142.p3
Valid prediction for GlimmerHMM_glimmerT_48699-T1
Valid prediction for snap_scaffold_21-snap.2567-T1
Couldn't classify 17628, 17729
Sorry, prediction pasa_asmbl_28148.p1 fails validation.
(CTG)	 AT	17628-17729	GT	AGG
(GGA)	 AG	17872-18294	CA	AAC
-recovered pasa_asmbl_28148.p1, terminal, 17872, 18294
Couldn't classify 55116, 55161
Sorry, prediction pasa_asmbl_28146.p1 fails validation.
(ATG)	 AG	52811-52816	GT	AGG
(GCT)	 AG	52952-53055	GT	AGG
(GGG)	 AG	54340-54567	GT	AGG
(GTA)	 AG	55116-55161	AA	AGA
-recovered pasa_asmbl_28146.p1, initial, 52811, 52816
-recovered pasa_asmbl_28146.p1, internal, 52811, 52816
-recovered pasa_asmbl_28146.p1, internal, 52952, 53055
-recovered pasa_asmbl_28146.p1, internal, 54340, 54567
Couldn't classify 16382, 16502
Couldn't classify 17173, 17480
Sorry, prediction pasa_asmbl_28149.p1 fails validation.
(CAG)	 AC	16382-16502	GT	AGG
(ATG)	 AG	17173-17480	CC	GCC
Valid prediction for GlimmerHMM_glimmerT_48707-T1
Couldn't classify 71194, 71295
Couldn't classify 72125, 72172
Sorry, prediction pasa_asmbl_28170.p1 fails validation.
(AAC)	 TC	71194-71295	GT	AGG
(GCT)	 AG	71559-71705	GT	AGG
(ATC)	 AG	72125-72172	TC	CGT
-recovered pasa_asmbl_28170.p1, internal, 71559, 71705
Valid prediction for GlimmerHMM_glimmerT_48723-T1
Valid prediction for Augustus_model.g32531.t1
Valid prediction for GlimmerHMM_glimmerT_48718-T1
Valid prediction for GlimmerHMM_glimmerT_48713-T1
Valid prediction for GlimmerHMM_glimmerT_48721-T1
Couldn't classify 67334, 67339
Couldn't classify 70782, 70823
Sorry, prediction pasa_asmbl_28145.p1 fails validation.
(CAG)	 CA	67334-67339	GT	AGG
(GAT)	 AG	67814-67858	GT	ATG
(AGA)	 AG	69381-69422	GT	AGG
(TTT)	 AG	70167-70382	GT	AGG
(GAA)	 AG	70485-70640	GT	AGG
(ATC)	 AG	70782-70823	CG	GCC
-recovered pasa_asmbl_28145.p1, internal, 67814, 67858
-recovered pasa_asmbl_28145.p1, internal, 69381, 69422
-recovered pasa_asmbl_28145.p1, internal, 70167, 70382
-recovered pasa_asmbl_28145.p1, internal, 70485, 70640
Valid prediction for snap_scaffold_21-snap.2563-T1
Valid prediction for GlimmerHMM_glimmerT_48725-T1
Valid prediction for snap_scaffold_21-snap.2598-T1
Valid prediction for Augustus_model.g32525.t1
Valid prediction for snap_scaffold_21-snap.2597-T1
Valid prediction for GlimmerHMM_glimmerT_48719-T1
Valid prediction for snap_scaffold_21-snap.2593-T1
Valid prediction for snap_scaffold_21-snap.2581-T1
Couldn't classify 60426, 60452
Couldn't classify 62163, 62243
Sorry, prediction pasa_asmbl_28175.p2 fails validation.
(AAA)	 AG	60426-60452	GT	TCG
(GAC)	 AG	61091-61204	GT	AGG
(GTG)	 AG	61973-62086	GT	AGG
(AAA)	 AG	62163-62243	GC	CCG
-recovered pasa_asmbl_28175.p2, internal, 60426, 60452
-recovered pasa_asmbl_28175.p2, internal, 61091, 61204
-recovered pasa_asmbl_28175.p2, internal, 61973, 62086
-recovered pasa_asmbl_28175.p2, internal, 62163, 62243
Valid prediction for Augustus_model.g32534.t1
Valid prediction for snap_scaffold_21-snap.2601-T1
Valid prediction for GlimmerHMM_glimmerT_48705-T1
Valid prediction for snap_scaffold_21-snap.2583-T1
Valid prediction for GlimmerHMM_glimmerT_48714-T1
Valid prediction for snap_scaffold_21-snap.2599-T1
Valid prediction for snap_scaffold_21-snap.2569-T1
Valid prediction for snap_scaffold_21-snap.2576-T1
Valid prediction for GlimmerHMM_glimmerT_48717-T1
Valid prediction for snap_scaffold_21-snap.2558-T1
Valid prediction for GlimmerHMM_glimmerT_48720-T1
Valid prediction for snap_scaffold_21-snap.2600-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 13234, rend_intergenic: 6144  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19272, rend_intergenic: 18306  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21163, rend_intergenic: 19664  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26737, rend_intergenic: 24949  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42298, rend_intergenic: 38952  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45725, rend_intergenic: 45342  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50422, rend_intergenic: 47443  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60932, rend_intergenic: 53872  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63446, rend_intergenic: 61637  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70327, rend_intergenic: 65263  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90612, rend_intergenic: 85408  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91232, rend_intergenic: 90801  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129614, rend_intergenic: 98409  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140670, rend_intergenic: 136969  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155306, rend_intergenic: 146549  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176193, rend_intergenic: 175023  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 98378, rend_intergenic: 98375  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 179490
-exon list size: 427


building trellis

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25.6    
25.9    
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26.6    
26.8    
27.0    
27.3    
27.5    
27.7    
28.0    
28.2    
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28.9    
29.1    
29.4    
29.6    
29.8    
30.1    
30.3    
30.5    
30.8    
31.0    
31.2    
31.5    
31.7    
31.9    
32.2    
32.4    
32.6    
32.9    
33.1    
33.3    
33.6    
33.8    
34.0    
34.3    
34.5    
34.7    
35.0    
35.2    
35.4    
35.7    
35.9    
36.1    
36.4    
36.6    
36.8    
37.1    
37.3    
37.5    
37.8    
38.0    
38.2    
38.5    
38.7    
38.9    
39.2    
39.4    
39.6    
39.9    
40.1    
40.3    
40.6    
40.8    
41.0    
41.3    
41.5    
41.7    
42.0    
42.2    
42.4    
42.7    
42.9    
43.1    
43.4    
43.6    
43.8    
44.1    
44.3    
44.5    
44.8    
45.0    
45.2    
45.5    
45.7    
45.9    
46.2    
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46.6    
46.9    
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47.8    
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48.7    
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89.3    
89.5    
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96.7    
97.0    
97.2    
97.4    
97.7    
97.9    
98.1    
98.4    
98.6    
98.8    
99.1    
99.3    
99.5    
99.8    
-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 13234, rend_intergenic: 6144  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19272, rend_intergenic: 18306  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21163, rend_intergenic: 19664  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26737, rend_intergenic: 24949  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42298, rend_intergenic: 38952  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45725, rend_intergenic: 45342  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50422, rend_intergenic: 47443  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60932, rend_intergenic: 53872  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63446, rend_intergenic: 61637  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70327, rend_intergenic: 65263  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90612, rend_intergenic: 85408  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91232, rend_intergenic: 90801  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129614, rend_intergenic: 98409  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140670, rend_intergenic: 136969  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155306, rend_intergenic: 146549  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176193, rend_intergenic: 175023  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 98378, rend_intergenic: 98375  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 22 predictions persist after filtering for low support