-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_10/scaffold_10_10981709-11236356

-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 GeneMark_model.44351_t
Valid prediction for GeneMark_model.44360_t
Valid prediction for snap_scaffold_10-snap.2159-T1
Couldn't classify 123871, 123964
Couldn't classify 130989, 131062
Sorry, prediction pasa_asmbl_4726.p1 fails validation.
(CTT)	 AG	123871-123964	GT	CGG
(ATG)	 AG	124135-124196	GT	TGG
(ATG)	 AG	125750-125821	GT	AGG
(ATG)	 AG	126243-126344	GT	AGG
(GCA)	 AG	127544-127654	GT	CTG
(ATG)	 AG	127866-127970	GT	ATG
(ACG)	 AG	128387-128516	GT	ACG
(GTC)	 AG	128633-128739	GT	TTG
(GGC)	 AG	128845-128939	GT	CGG
(GCC)	 AG	129892-129973	GT	CAG
(ATT)	 AG	130235-130277	GT	AAG
(TCG)	 AG	130502-130570	GT	AGG
(GTA)	 AG	130989-131062	GG	TTG
add_exon() Sorry, pasa_asmbl_4726.p1 124135-124196-initial-1 is invalid.
-recovered pasa_asmbl_4726.p1, initial, 124135, 124196
-recovered pasa_asmbl_4726.p1, initial, 125750, 125821
-recovered pasa_asmbl_4726.p1, initial, 126243, 126344
-recovered pasa_asmbl_4726.p1, initial, 127866, 127970
-recovered pasa_asmbl_4726.p1, internal, 123871, 123964
-recovered pasa_asmbl_4726.p1, internal, 124135, 124196
-recovered pasa_asmbl_4726.p1, internal, 125750, 125821
-recovered pasa_asmbl_4726.p1, internal, 126243, 126344
-recovered pasa_asmbl_4726.p1, internal, 127544, 127654
-recovered pasa_asmbl_4726.p1, internal, 127866, 127970
-recovered pasa_asmbl_4726.p1, internal, 128387, 128516
-recovered pasa_asmbl_4726.p1, internal, 128633, 128739
-recovered pasa_asmbl_4726.p1, internal, 128845, 128939
-recovered pasa_asmbl_4726.p1, internal, 129892, 129973
-recovered pasa_asmbl_4726.p1, internal, 130235, 130277
-recovered pasa_asmbl_4726.p1, internal, 130502, 130570
Valid prediction for snap_scaffold_10-snap.2179-T1
Valid prediction for Augustus_model.g17379.t1
Valid prediction for GlimmerHMM_glimmerT_25893-T1
Valid prediction for GlimmerHMM_glimmerT_25898-T1
Valid prediction for snap_scaffold_10-snap.2153-T1
Valid prediction for GeneMark_model.44378_t
Valid prediction for pasa_asmbl_4721.p1
Valid prediction for GeneMark_model.44367_t
Valid prediction for HiQ_model.g17381.t1
Valid prediction for snap_scaffold_10-snap.2170-T1
Valid prediction for GlimmerHMM_glimmerT_25906-T1
Valid prediction for GlimmerHMM_glimmerT_25912-T1
Valid prediction for GeneMark_model.44347_t
Valid prediction for GeneMark_model.44363_t
Valid prediction for GeneMark_model.44353_t
Valid prediction for snap_scaffold_10-snap.2162-T1
Valid prediction for CodingQuarry_transcript_5556-T1
Valid prediction for snap_scaffold_10-snap.2157-T1
Valid prediction for GlimmerHMM_glimmerT_25913-T1
Couldn't classify 142335, 142496
Sorry, prediction pasa_asmbl_4730.p2 fails validation.
(AGC)	 AC	142335-142496	GT	AGG
(ATC)	 AG	144333-144468	GT	CGG
(TGT)	 AG	146272-146441	GC	GAG
-recovered pasa_asmbl_4730.p2, terminal, 146272, 146441
-recovered pasa_asmbl_4730.p2, internal, 144333, 144468
-recovered pasa_asmbl_4730.p2, internal, 146272, 146441
Valid prediction for snap_scaffold_10-snap.2160-T1
Valid prediction for GeneMark_model.44346_t
Valid prediction for GlimmerHMM_glimmerT_25895-T1
Valid prediction for snap_scaffold_10-snap.2161-T1
Valid prediction for Augustus_model.g17374.t1
Valid prediction for pasa_asmbl_4720.p1
Valid prediction for snap_scaffold_10-snap.2164-T1
Valid prediction for HiQ_model.g17375.t1
Valid prediction for GeneMark_model.44380_t
Valid prediction for GlimmerHMM_glimmerT_25901-T1
Valid prediction for snap_scaffold_10-snap.2156-T1
Valid prediction for snap_scaffold_10-snap.2166-T1
Valid prediction for Augustus_model.g17371.t1
Valid prediction for GlimmerHMM_glimmerT_25892-T1
Valid prediction for HiQ_model.g17376.t1
Valid prediction for Augustus_model.g17378.t1
Valid prediction for GeneMark_model.44365_t
Valid prediction for GlimmerHMM_glimmerT_25902-T1
Valid prediction for GlimmerHMM_glimmerT_25904-T1
Valid prediction for CodingQuarry_transcript_5555-T1
Valid prediction for GlimmerHMM_glimmerT_25896-T1
Valid prediction for Augustus_model.g17373.t1
Valid prediction for Augustus_model.g17385.t1
Valid prediction for CodingQuarry_transcript_5554-T1
Valid prediction for snap_scaffold_10-snap.2165-T1
Valid prediction for snap_scaffold_10-snap.2174-T1
Valid prediction for snap_scaffold_10-snap.2183-T1
Valid prediction for GlimmerHMM_glimmerT_25899-T1
Valid prediction for GeneMark_model.44364_t
Valid prediction for GeneMark_model.44359_t
Valid prediction for GlimmerHMM_glimmerT_25907-T1
Valid prediction for GlimmerHMM_glimmerT_25905-T1
Valid prediction for GeneMark_model.44362_t
Valid prediction for snap_scaffold_10-snap.2167-T1
Valid prediction for GeneMark_model.44357_t
Valid prediction for snap_scaffold_10-snap.2171-T1
Valid prediction for GeneMark_model.44377_t
Valid prediction for snap_scaffold_10-snap.2184-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: -)Couldn't classify 39990, 40697
Sorry, prediction pasa_asmbl_3677.p1 fails validation.
(ATG)	 GC	39990-40697	CA	GCC
Valid prediction for GeneMark_model.44379_t
Valid prediction for Augustus_model.g17380.t1
Couldn't classify 41001, 41825
Sorry, prediction pasa_asmbl_3676.p1 fails validation.
(GGG)	 GG	41001-41825	AG	CAA
Valid prediction for GlimmerHMM_glimmerT_25910-T1
Valid prediction for snap_scaffold_10-snap.2176-T1
Valid prediction for GeneMark_model.44368_t
Valid prediction for snap_scaffold_10-snap.2163-T1
Valid prediction for GlimmerHMM_glimmerT_25911-T1
Valid prediction for snap_scaffold_10-snap.2181-T1
Valid prediction for snap_scaffold_10-snap.2169-T1
Valid prediction for GeneMark_model.44375_t
Valid prediction for GeneMark_model.44349_t
Couldn't classify 88417, 88575
Sorry, prediction pasa_asmbl_3673.p1 fails validation.
(GTT)	 AA	88417-88575	GT	ATG
(CTG)	 AG	89403-89558	CT	GAC
-recovered pasa_asmbl_3673.p1, terminal, 89403, 89558
Valid prediction for GeneMark_model.44374_t
Couldn't classify 149196, 149247
Sorry, prediction pasa_asmbl_3671.p1 fails validation.
(ATG)	 CA	143734-143931	GT	GAG
(GAA)	 AG	144128-144276	GT	AGG
(AAT)	 AG	144525-144761	GT	GGG
(AAT)	 AG	144960-145127	GT	CGG
(GGT)	 AG	145217-145319	GT	AGG
(AGT)	 AG	145822-145931	GT	CGG
(GCT)	 AG	146476-146671	GT	AGG
(GAG)	 AG	147056-147239	GT	CAG
(ATG)	 AG	148389-149079	GT	AGG
(ATG)	 AG	149196-149247	GG	ACG
-recovered pasa_asmbl_3671.p1, initial, 143734, 143931
add_exon() Sorry, pasa_asmbl_3671.p1 148389-149079-initial-1 is invalid.
-recovered pasa_asmbl_3671.p1, initial, 148389, 149079
-recovered pasa_asmbl_3671.p1, internal, 144128, 144276
-recovered pasa_asmbl_3671.p1, internal, 144525, 144761
-recovered pasa_asmbl_3671.p1, internal, 144960, 145127
-recovered pasa_asmbl_3671.p1, internal, 145217, 145319
-recovered pasa_asmbl_3671.p1, internal, 145822, 145931
-recovered pasa_asmbl_3671.p1, internal, 146476, 146671
-recovered pasa_asmbl_3671.p1, internal, 147056, 147239
-recovered pasa_asmbl_3671.p1, internal, 148389, 149079
Valid prediction for Augustus_model.g17372.t1
Valid prediction for GeneMark_model.44355_t
Valid prediction for GlimmerHMM_glimmerT_25908-T1
Valid prediction for GeneMark_model.44376_t
Valid prediction for snap_scaffold_10-snap.2175-T1
Valid prediction for GeneMark_model.44371_t
Valid prediction for GlimmerHMM_glimmerT_25903-T1
Valid prediction for snap_scaffold_10-snap.2155-T1
Valid prediction for GeneMark_model.44352_t
Valid prediction for snap_scaffold_10-snap.2182-T1
Valid prediction for snap_scaffold_10-snap.2178-T1
Valid prediction for HiQ_model.g17377.t1
Valid prediction for Augustus_model.g17382.t1
Valid prediction for GeneMark_model.44356_t
Valid prediction for GeneMark_model.44348_t
Valid prediction for snap_scaffold_10-snap.2173-T1
Valid prediction for snap_scaffold_10-snap.2172-T1
Valid prediction for GeneMark_model.44361_t
Valid prediction for snap_scaffold_10-snap.2158-T1
Valid prediction for GeneMark_model.44366_t
Valid prediction for GeneMark_model.44370_t
Valid prediction for snap_scaffold_10-snap.2180-T1
Valid prediction for GeneMark_model.44354_t
Valid prediction for GeneMark_model.44350_t
Valid prediction for GeneMark_model.44373_t
Valid prediction for GeneMark_model.44369_t
Valid prediction for snap_scaffold_10-snap.2154-T1
Valid prediction for GeneMark_model.44358_t
Valid prediction for Augustus_model.g17383.t1
Valid prediction for GlimmerHMM_glimmerT_25909-T1
Valid prediction for GlimmerHMM_glimmerT_25897-T1
Couldn't classify 77321, 77411
Sorry, prediction pasa_asmbl_3675.p1 fails validation.
(AGG)	 GG	77321-77411	GT	AGG
(CGC)	 AG	78369-78713	GT	AGG
(GAT)	 AG	80608-80752	GT	GAG
(GGA)	 AG	83735-83865	GT	AGG
(GAT)	 AG	83980-84080	TT	AGT
-recovered pasa_asmbl_3675.p1, terminal, 83980, 84080
-recovered pasa_asmbl_3675.p1, internal, 78369, 78713
-recovered pasa_asmbl_3675.p1, internal, 80608, 80752
-recovered pasa_asmbl_3675.p1, internal, 83735, 83865
Valid prediction for GeneMark_model.44372_t
Valid prediction for snap_scaffold_10-snap.2177-T1
Valid prediction for GlimmerHMM_glimmerT_25900-T1
Valid prediction for snap_scaffold_10-snap.2168-T1
Valid prediction for GlimmerHMM_glimmerT_25894-T1
Valid prediction for Augustus_model.g17384.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 22864, rend_intergenic: 19019  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135288, rend_intergenic: 124131  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157111, rend_intergenic: 139584  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 254648
-exon list size: 441


building trellis

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98.2    
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98.9    
99.1    
99.3    
99.5    
99.8    
-found 22 predictions from path traversal
Error with prediction: snap lend_intergenic: 22864, rend_intergenic: 19019  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135288, rend_intergenic: 124131  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157111, rend_intergenic: 139584  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support