-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_10/scaffold_10_7139532-7519172

-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_10-snap.1489-T1
Valid prediction for snap_scaffold_10-snap.1514-T1
Valid prediction for snap_scaffold_10-snap.1491-T1
Valid prediction for GlimmerHMM_glimmerT_24968-T1
Valid prediction for snap_scaffold_10-snap.1479-T1
Valid prediction for pasa_asmbl_3278.p1
Valid prediction for snap_scaffold_10-snap.1470-T1
Valid prediction for Augustus_model.g16651.t1
Valid prediction for CodingQuarry_transcript_5462-T1
Valid prediction for GlimmerHMM_glimmerT_24979-T1
Couldn't classify 123079, 123330
Couldn't classify 123912, 124010
Sorry, prediction pasa_asmbl_3265.p2 fails validation.
(CAG)	 AC	123079-123330	GT	AGG
(GTG)	 AG	123912-124010	CG	AGC
Valid prediction for GlimmerHMM_glimmerT_24977-T1
Valid prediction for Augustus_model.g16628.t1
Valid prediction for Augustus_model.g16632.t1
Valid prediction for snap_scaffold_10-snap.1487-T1
Valid prediction for Augustus_model.g16636.t1
Valid prediction for GlimmerHMM_glimmerT_24973-T1
Valid prediction for Augustus_model.g16648.t1
Couldn't classify 130528, 130717
Sorry, prediction pasa_asmbl_3269.p1 fails validation.
(AAG)	 CC	130528-130717	GT	AGG
(GGC)	 AG	130946-131107	GT	AGG
(CCT)	 AG	131399-131455	GT	AGG
(ATG)	 AG	131929-132101	GT	AGG
(GAC)	 AG	132274-132405	GT	CGG
(GAG)	 AG	133192-133318	GT	AGG
(GGG)	 AG	133937-134028	GT	AGG
(GAG)	 AG	134154-134288	GT	AGG
(GAC)	 AG	134752-134958	GT	AGG
(GAA)	 AG	135040-135096	GT	AGG
(GAC)	 AG	135374-135509	GT	TAG
(GCT)	 AG	135609-135757	GT	AGG
(ATA)	 AG	135902-135974	GT	TGG
(TGA)	 AG	136122-136327	GT	ATG
(GAG)	 AG	136629-136721	GT	AGG
(GAG)	 AG	136831-136954	GT	AGG
(AAA)	 AG	137309-137334	AA	GAA
add_exon() Sorry, pasa_asmbl_3269.p1 131929-132101-initial-1 is invalid.
-recovered pasa_asmbl_3269.p1, initial, 131929, 132101
add_exon() Sorry, pasa_asmbl_3269.p1 133192-133318-terminal-3 is invalid.
-recovered pasa_asmbl_3269.p1, terminal, 133192, 133318
-recovered pasa_asmbl_3269.p1, terminal, 137309, 137334
-recovered pasa_asmbl_3269.p1, internal, 130946, 131107
-recovered pasa_asmbl_3269.p1, internal, 131399, 131455
-recovered pasa_asmbl_3269.p1, internal, 131929, 132101
-recovered pasa_asmbl_3269.p1, internal, 132274, 132405
-recovered pasa_asmbl_3269.p1, internal, 133192, 133318
-recovered pasa_asmbl_3269.p1, internal, 133937, 134028
-recovered pasa_asmbl_3269.p1, internal, 134154, 134288
-recovered pasa_asmbl_3269.p1, internal, 134752, 134958
-recovered pasa_asmbl_3269.p1, internal, 135040, 135096
-recovered pasa_asmbl_3269.p1, internal, 135374, 135509
-recovered pasa_asmbl_3269.p1, internal, 135609, 135757
-recovered pasa_asmbl_3269.p1, internal, 135902, 135974
-recovered pasa_asmbl_3269.p1, internal, 136122, 136327
-recovered pasa_asmbl_3269.p1, internal, 136629, 136721
-recovered pasa_asmbl_3269.p1, internal, 136831, 136954
Valid prediction for Augustus_model.g16639.t1
Valid prediction for snap_scaffold_10-snap.1513-T1
Valid prediction for snap_scaffold_10-snap.1512-T1
Valid prediction for Augustus_model.g16630.t1
Valid prediction for snap_scaffold_10-snap.1482-T1
Valid prediction for GlimmerHMM_glimmerT_24986-T1
Valid prediction for Augustus_model.g16644.t1
Valid prediction for GlimmerHMM_glimmerT_24969-T1
Valid prediction for snap_scaffold_10-snap.1474-T1
Valid prediction for GlimmerHMM_glimmerT_24967-T1
Valid prediction for GlimmerHMM_glimmerT_24972-T1
Valid prediction for GlimmerHMM_glimmerT_24974-T1
Valid prediction for snap_scaffold_10-snap.1509-T1
Valid prediction for GlimmerHMM_glimmerT_24983-T1
Valid prediction for snap_scaffold_10-snap.1507-T1
Valid prediction for snap_scaffold_10-snap.1502-T1
Couldn't classify 127719, 127838
Couldn't classify 128398, 128608
Sorry, prediction pasa_asmbl_3267.p1 fails validation.
(AAC)	 GG	127719-127838	GT	AGG
(CTG)	 AG	128017-128210	GT	AGG
(AAC)	 AG	128398-128608	AG	GCA
-recovered pasa_asmbl_3267.p1, internal, 128017, 128210
Valid prediction for Augustus_model.g16631.t1
Valid prediction for Augustus_model.g16647.t1
Valid prediction for Augustus_model.g16650.t1
Valid prediction for snap_scaffold_10-snap.1511-T1
Valid prediction for GlimmerHMM_glimmerT_24984-T1
Valid prediction for Augustus_model.g16638.t1
Valid prediction for GlimmerHMM_glimmerT_24970-T1
Valid prediction for snap_scaffold_10-snap.1475-T1
Valid prediction for snap_scaffold_10-snap.1503-T1
Valid prediction for snap_scaffold_10-snap.1480-T1
Valid prediction for snap_scaffold_10-snap.1486-T1
Valid prediction for snap_scaffold_10-snap.1484-T1
Valid prediction for snap_scaffold_10-snap.1510-T1
Couldn't classify 135043, 135096
Sorry, prediction pasa_asmbl_3275.p1 fails validation.
(AAA)	 AA	135043-135096	GT	AGG
(GAC)	 AG	135374-135509	GT	TAG
(GCT)	 AG	135609-135757	GT	AGG
(ATA)	 AG	135902-135974	GT	TGG
(TGA)	 AG	136122-136315	GT	TGG
(GAG)	 AG	136629-136721	GT	AGG
(GAG)	 AG	136831-136954	GT	AGG
(AAA)	 AG	137309-137334	AA	GAA
-recovered pasa_asmbl_3275.p1, terminal, 137309, 137334
-recovered pasa_asmbl_3275.p1, internal, 135374, 135509
-recovered pasa_asmbl_3275.p1, internal, 135609, 135757
-recovered pasa_asmbl_3275.p1, internal, 135902, 135974
-recovered pasa_asmbl_3275.p1, internal, 136122, 136315
-recovered pasa_asmbl_3275.p1, internal, 136629, 136721
-recovered pasa_asmbl_3275.p1, internal, 136831, 136954
Valid prediction for Augustus_model.g16649.t1
Valid prediction for GlimmerHMM_glimmerT_24994-T1
Valid prediction for Augustus_model.g16642.t1
Valid prediction for Augustus_model.g16633.t1
Valid prediction for Augustus_model.g16629.t1
Valid prediction for Augustus_model.g16637.t1
Valid prediction for snap_scaffold_10-snap.1477-T1
Valid prediction for snap_scaffold_10-snap.1490-T1
Valid prediction for Augustus_model.g16635.t1
Valid prediction for snap_scaffold_10-snap.1515-T1
Valid prediction for GlimmerHMM_glimmerT_24993-T1
Couldn't classify 129731, 129830
Couldn't classify 130377, 130467
Sorry, prediction pasa_asmbl_3268.p1 fails validation.
(AGC)	 CC	129731-129830	GT	TGG
(GGT)	 AG	130082-130262	GT	AGG
(ACC)	 AG	130377-130467	AC	ACA
-recovered pasa_asmbl_3268.p1, internal, 130082, 130262
Couldn't classify 346395, 346748
Sorry, prediction pasa_asmbl_3276.p1 fails validation.
(GCC)	 GA	346395-346748	GA	AGG
Valid prediction for snap_scaffold_10-snap.1483-T1
Valid prediction for GlimmerHMM_glimmerT_24980-T1
Couldn't classify 355672, 355779
Couldn't classify 357222, 357533
Sorry, prediction pasa_asmbl_3277.p1 fails validation.
(GTG)	 TG	355672-355779	GT	AGG
(GTA)	 AG	357222-357533	AC	TGA
Valid prediction for snap_scaffold_10-snap.1497-T1
Couldn't classify 127228, 127371
Sorry, prediction pasa_asmbl_3266.p1 fails validation.
(ATG)	 CC	125735-125798	GT	TTG
(GTC)	 AG	125909-126053	GT	AGG
(AAA)	 AG	126275-126651	GT	AGG
(AGT)	 AG	126858-127114	GT	AGG
(AGT)	 AG	127228-127371	TA	GGT
-recovered pasa_asmbl_3266.p1, initial, 125735, 125798
add_exon() Sorry, pasa_asmbl_3266.p1 126275-126651-terminal-2 is invalid.
-recovered pasa_asmbl_3266.p1, terminal, 126275, 126651
-recovered pasa_asmbl_3266.p1, internal, 125909, 126053
-recovered pasa_asmbl_3266.p1, internal, 126275, 126651
-recovered pasa_asmbl_3266.p1, internal, 126858, 127114
Valid prediction for GlimmerHMM_glimmerT_24987-T1
Valid prediction for GlimmerHMM_glimmerT_24975-T1
Couldn't classify 352500, 352808
Sorry, prediction pasa_asmbl_3855.p1 fails validation.
(CTG)	 TC	352500-352808	GA	GGG
Valid prediction for snap_scaffold_10-snap.1494-T1
Valid prediction for snap_scaffold_10-snap.1473-T1
Valid prediction for GlimmerHMM_glimmerT_24966-T1
Valid prediction for GlimmerHMM_glimmerT_24988-T1
Valid prediction for snap_scaffold_10-snap.1508-T1
Valid prediction for GlimmerHMM_glimmerT_24981-T1
Valid prediction for snap_scaffold_10-snap.1485-T1
Valid prediction for snap_scaffold_10-snap.1478-T1
Valid prediction for Augustus_model.g16640.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_24965-T1
Valid prediction for GlimmerHMM_glimmerT_24971-T1
Valid prediction for GlimmerHMM_glimmerT_24985-T1
Valid prediction for HiQ_model.g16645.t1
Valid prediction for pasa_asmbl_4542.p1
Valid prediction for snap_scaffold_10-snap.1493-T1
Valid prediction for CodingQuarry_transcript_5463-T1
Valid prediction for GlimmerHMM_glimmerT_24991-T1
Valid prediction for snap_scaffold_10-snap.1498-T1
Valid prediction for snap_scaffold_10-snap.1499-T1
Valid prediction for GlimmerHMM_glimmerT_24976-T1
Valid prediction for Augustus_model.g16643.t1
Valid prediction for snap_scaffold_10-snap.1488-T1
Valid prediction for snap_scaffold_10-snap.1471-T1
Valid prediction for Augustus_model.g16634.t1
Valid prediction for snap_scaffold_10-snap.1505-T1
Valid prediction for snap_scaffold_10-snap.1506-T1
Valid prediction for snap_scaffold_10-snap.1501-T1
Valid prediction for snap_scaffold_10-snap.1481-T1
Valid prediction for snap_scaffold_10-snap.1496-T1
Valid prediction for GlimmerHMM_glimmerT_24992-T1
Valid prediction for snap_scaffold_10-snap.1472-T1
Valid prediction for snap_scaffold_10-snap.1476-T1
Couldn't classify 262776, 262851
Sorry, prediction pasa_asmbl_4536.p1 fails validation.
(ATG)	 TG	260936-261069	GT	AGG
(AAC)	 AG	262117-262325	GT	TGG
(ATG)	 AG	262444-262606	GT	AGG
(ATC)	 AG	262776-262851	AC	CCA
-recovered pasa_asmbl_4536.p1, initial, 260936, 261069
-recovered pasa_asmbl_4536.p1, initial, 262444, 262606
-recovered pasa_asmbl_4536.p1, internal, 262117, 262325
-recovered pasa_asmbl_4536.p1, internal, 262444, 262606
Valid prediction for pasa_asmbl_4530.p1
Valid prediction for GlimmerHMM_glimmerT_24978-T1
Valid prediction for pasa_asmbl_4540.p1
Valid prediction for GlimmerHMM_glimmerT_24990-T1
Valid prediction for snap_scaffold_10-snap.1492-T1
Valid prediction for snap_scaffold_10-snap.1500-T1
Valid prediction for GlimmerHMM_glimmerT_24989-T1
Valid prediction for HiQ_model.g16646.t1
Valid prediction for CodingQuarry_transcript_5461-T1
Valid prediction for snap_scaffold_10-snap.1517-T1
Valid prediction for CodingQuarry_transcript_5464-T1
Valid prediction for snap_scaffold_10-snap.1516-T1
Valid prediction for pasa_asmbl_4531.p1
Valid prediction for snap_scaffold_10-snap.1504-T1
Valid prediction for snap_scaffold_10-snap.1495-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for Augustus_model.g16627.t1
Valid prediction for GlimmerHMM_glimmerT_24982-T1
Valid prediction for HiQ_model.g16641.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 92747, rend_intergenic: 92744  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22863, rend_intergenic: 20953  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114598, rend_intergenic: 112929  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115712, rend_intergenic: 115103  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137334, rend_intergenic: 127457  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 366236, rend_intergenic: 354063  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 379641
-exon list size: 468


building trellis

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32.6    
32.8    
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33.8    
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41.3    
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83.6    
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84.3    
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84.9    
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86.0    
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86.8    
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87.9    
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90.6    
90.9    
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92.6    
92.8    
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97.9    
98.1    
98.3    
98.5    
98.7    
98.9    
99.1    
99.4    
99.6    
99.8    
-found 45 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 92747, rend_intergenic: 92744  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22863, rend_intergenic: 20953  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114598, rend_intergenic: 112929  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115712, rend_intergenic: 115103  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137334, rend_intergenic: 127457  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 366236, rend_intergenic: 354063  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 39 predictions persist after filtering for low support