-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_12/scaffold_12_9151662-9354694

-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_12-snap.1759-T1
Valid prediction for GeneMark_model.52567_t
Valid prediction for Augustus_model.g20264.t1
Valid prediction for snap_scaffold_12-snap.1744-T1
Valid prediction for snap_scaffold_12-snap.1776-T1
Valid prediction for snap_scaffold_12-snap.1750-T1
Valid prediction for GeneMark_model.52585_t
Valid prediction for GeneMark_model.52565_t
Valid prediction for snap_scaffold_12-snap.1755-T1
Valid prediction for snap_scaffold_12-snap.1749-T1
Valid prediction for GlimmerHMM_glimmerT_30428-T1
Valid prediction for GlimmerHMM_glimmerT_30419-T1
Valid prediction for GlimmerHMM_glimmerT_30421-T1
Valid prediction for GlimmerHMM_glimmerT_30426-T1
Valid prediction for snap_scaffold_12-snap.1769-T1
Valid prediction for snap_scaffold_12-snap.1752-T1
Valid prediction for GeneMark_model.52580_t
Valid prediction for GeneMark_model.52573_t
Valid prediction for GeneMark_model.52571_t
Valid prediction for GeneMark_model.52576_t
Valid prediction for GeneMark_model.52591_t
Valid prediction for Augustus_model.g20263.t1
Valid prediction for GeneMark_model.52562_t
Valid prediction for snap_scaffold_12-snap.1778-T1
Valid prediction for GlimmerHMM_glimmerT_30416-T1
Valid prediction for GlimmerHMM_glimmerT_30430-T1
Valid prediction for GeneMark_model.52587_t
Valid prediction for GeneMark_model.52589_t
Valid prediction for Augustus_model.g20266.t1
Valid prediction for Augustus_model.g20276.t1
Valid prediction for snap_scaffold_12-snap.1770-T1
Valid prediction for snap_scaffold_12-snap.1753-T1
Valid prediction for GlimmerHMM_glimmerT_30417-T1
Valid prediction for GlimmerHMM_glimmerT_30425-T1
Valid prediction for snap_scaffold_12-snap.1742-T1
Valid prediction for snap_scaffold_12-snap.1748-T1
Valid prediction for snap_scaffold_12-snap.1745-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_12-snap.1747-T1
Valid prediction for GlimmerHMM_glimmerT_30411-T1
Valid prediction for CodingQuarry_transcript_10307-T1
Valid prediction for snap_scaffold_12-snap.1760-T1
Valid prediction for snap_scaffold_12-snap.1763-T1
Valid prediction for GlimmerHMM_glimmerT_30410-T1
Valid prediction for Augustus_model.g20265.t1
Valid prediction for snap_scaffold_12-snap.1751-T1
Valid prediction for GeneMark_model.52572_t
Valid prediction for GeneMark_model.52574_t
Valid prediction for GlimmerHMM_glimmerT_30423-T1
Valid prediction for snap_scaffold_12-snap.1777-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_30409-T1
Valid prediction for snap_scaffold_12-snap.1775-T1
Valid prediction for GeneMark_model.52570_t
Valid prediction for snap_scaffold_12-snap.1766-T1
Valid prediction for Augustus_model.g20280.t1
Valid prediction for GlimmerHMM_glimmerT_30412-T1
Valid prediction for GeneMark_model.52592_t
Valid prediction for GeneMark_model.52582_t
Valid prediction for Augustus_model.g20281.t1
Valid prediction for snap_scaffold_12-snap.1767-T1
Valid prediction for snap_scaffold_12-snap.1765-T1
Valid prediction for snap_scaffold_12-snap.1772-T1
Couldn't classify 84162, 84198
Sorry, prediction pasa_asmbl_8826.p1 fails validation.
(AAC)	 CT	84162-84198	GT	CAG
(CCC)	 AG	85378-85421	GT	AGG
(ACT)	 AG	86046-86113	GT	GTG
(CTT)	 AG	86211-86304	GT	AGG
(TTC)	 AG	86506-86633	GT	TGG
(GAT)	 AG	86799-86928	GT	ATG
(TCC)	 AG	87112-87239	GT	AGG
(TAT)	 AG	87703-87814	GT	AGG
(CAA)	 AG	87941-88020	GT	AGG
(CAT)	 AG	88119-88224	GT	AGG
(GAG)	 AG	89005-89137	GT	CTG
(TCC)	 AG	89245-89364	GT	GAG
(CGT)	 AG	89533-89590	GT	GGG
(GAT)	 AG	89744-89903	GT	CCG
(GCG)	 AG	90076-90227	GT	TGG
(GTC)	 AG	90337-90448	GT	AGG
(GAC)	 AG	90653-90824	GT	AGG
(GTA)	 AG	92983-93050	TG	AGT
-recovered pasa_asmbl_8826.p1, terminal, 92983, 93050
-recovered pasa_asmbl_8826.p1, internal, 85378, 85421
-recovered pasa_asmbl_8826.p1, internal, 86046, 86113
-recovered pasa_asmbl_8826.p1, internal, 86211, 86304
-recovered pasa_asmbl_8826.p1, internal, 86506, 86633
-recovered pasa_asmbl_8826.p1, internal, 86799, 86928
-recovered pasa_asmbl_8826.p1, internal, 87112, 87239
-recovered pasa_asmbl_8826.p1, internal, 87703, 87814
-recovered pasa_asmbl_8826.p1, internal, 87941, 88020
-recovered pasa_asmbl_8826.p1, internal, 88119, 88224
-recovered pasa_asmbl_8826.p1, internal, 89005, 89137
-recovered pasa_asmbl_8826.p1, internal, 89245, 89364
-recovered pasa_asmbl_8826.p1, internal, 89533, 89590
-recovered pasa_asmbl_8826.p1, internal, 89744, 89903
-recovered pasa_asmbl_8826.p1, internal, 90076, 90227
-recovered pasa_asmbl_8826.p1, internal, 90337, 90448
-recovered pasa_asmbl_8826.p1, internal, 90653, 90824
Valid prediction for HiQ_model.g20270.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_12-snap.1764-T1
Valid prediction for CodingQuarry_transcript_10304-T1
Valid prediction for snap_scaffold_12-snap.1761-T1
Couldn't classify 194592, 194634
Sorry, prediction pasa_asmbl_7781.p1 fails validation.
(TCT)	 CT	194592-194634	GT	GGG
(ACT)	 AG	195472-195601	GT	AGG
(GCT)	 AG	195820-196000	GT	AGG
(CGT)	 AG	196088-196192	GT	AGG
(AGA)	 AG	196309-196362	GT	AGG
(AGA)	 AG	196481-196688	GT	GGG
(AGA)	 AG	196796-196982	GT	AGG
(CCC)	 AG	197219-197505	GT	AGG
(AGA)	 AG	197710-197717	CC	GAC
-recovered pasa_asmbl_7781.p1, terminal, 196796, 196982
-recovered pasa_asmbl_7781.p1, terminal, 197710, 197717
-recovered pasa_asmbl_7781.p1, internal, 195472, 195601
-recovered pasa_asmbl_7781.p1, internal, 195820, 196000
-recovered pasa_asmbl_7781.p1, internal, 196088, 196192
-recovered pasa_asmbl_7781.p1, internal, 196309, 196362
-recovered pasa_asmbl_7781.p1, internal, 196481, 196688
-recovered pasa_asmbl_7781.p1, internal, 196796, 196982
-recovered pasa_asmbl_7781.p1, internal, 197219, 197505
Valid prediction for GeneMark_model.52563_t
Valid prediction for GlimmerHMM_glimmerT_30414-T1
Valid prediction for GeneMark_model.52593_t
Valid prediction for Augustus_model.g20273.t1
Valid prediction for GlimmerHMM_glimmerT_30406-T1
Valid prediction for snap_scaffold_12-snap.1743-T1
Valid prediction for GlimmerHMM_glimmerT_30420-T1
Valid prediction for CodingQuarry_transcript_10303-T1
Valid prediction for snap_scaffold_12-snap.1758-T1
Valid prediction for snap_scaffold_12-snap.1756-T1
Valid prediction for GeneMark_model.52597_t
Valid prediction for Augustus_model.g20271.t1
Valid prediction for Augustus_model.g20262.t1
Valid prediction for GlimmerHMM_glimmerT_30407-T1
Valid prediction for CodingQuarry_transcript_10302-T1
Valid prediction for GlimmerHMM_glimmerT_30427-T1
Valid prediction for GeneMark_model.52583_t
Valid prediction for Augustus_model.g20277.t1
Valid prediction for Augustus_model.g20278.t1
Valid prediction for GeneMark_model.52584_t
Valid prediction for GeneMark_model.52568_t
Valid prediction for Augustus_model.g20267.t1
Valid prediction for GeneMark_model.52590_t
Valid prediction for snap_scaffold_12-snap.1773-T1
Valid prediction for Augustus_model.g20261.t1
Valid prediction for GeneMark_model.52594_t
Valid prediction for Augustus_model.g20272.t1
Valid prediction for GeneMark_model.52564_t
Valid prediction for GlimmerHMM_glimmerT_30422-T1
Valid prediction for pasa_asmbl_7787.p1
Valid prediction for GeneMark_model.52569_t
Valid prediction for CodingQuarry_transcript_10305-T1
Valid prediction for Augustus_model.g20268.t1
Valid prediction for snap_scaffold_12-snap.1768-T1
Valid prediction for GlimmerHMM_glimmerT_30408-T1
Valid prediction for GeneMark_model.52579_t
Couldn't classify 132509, 132637
Sorry, prediction pasa_asmbl_7782.p1 fails validation.
(GAC)	 TG	132509-132637	GT	AGG
(GGG)	 AG	132759-132818	GT	TGG
(ACC)	 AG	133992-134138	GT	AGG
(GAA)	 AG	134998-135084	GT	AAG
(GGG)	 AG	135247-135328	GT	AGG
(GGA)	 AG	135789-135904	GT	AGG
(ACT)	 AG	136184-136360	GT	AGG
(AGG)	 AG	137419-137439	GT	AGG
(GAT)	 AG	138795-138891	GT	TTG
(GCA)	 AG	139199-139285	GT	AGG
(CTG)	 AG	139524-139623	GT	AAG
(GAG)	 AG	139781-139835	GT	AGG
(GAG)	 AG	140042-140164	AC	GAA
-recovered pasa_asmbl_7782.p1, terminal, 140042, 140164
-recovered pasa_asmbl_7782.p1, internal, 132759, 132818
-recovered pasa_asmbl_7782.p1, internal, 133992, 134138
-recovered pasa_asmbl_7782.p1, internal, 134998, 135084
-recovered pasa_asmbl_7782.p1, internal, 135247, 135328
-recovered pasa_asmbl_7782.p1, internal, 135789, 135904
-recovered pasa_asmbl_7782.p1, internal, 136184, 136360
-recovered pasa_asmbl_7782.p1, internal, 137419, 137439
-recovered pasa_asmbl_7782.p1, internal, 138795, 138891
-recovered pasa_asmbl_7782.p1, internal, 139199, 139285
-recovered pasa_asmbl_7782.p1, internal, 139524, 139623
-recovered pasa_asmbl_7782.p1, internal, 139781, 139835
Valid prediction for GlimmerHMM_glimmerT_30424-T1
Valid prediction for GeneMark_model.52588_t
Valid prediction for Augustus_model.g20283.t1
Valid prediction for GlimmerHMM_glimmerT_30429-T1
Valid prediction for CodingQuarry_transcript_10306-T1
Valid prediction for GeneMark_model.52595_t
Valid prediction for Augustus_model.g20275.t1
Valid prediction for GeneMark_model.52566_t
Valid prediction for GlimmerHMM_glimmerT_30418-T1
Valid prediction for GlimmerHMM_glimmerT_30415-T1
Valid prediction for GeneMark_model.52561_t
Valid prediction for Augustus_model.g20274.t1
Valid prediction for snap_scaffold_12-snap.1762-T1
Valid prediction for HiQ_model.g20269.t1
Valid prediction for snap_scaffold_12-snap.1754-T1
Valid prediction for pasa_asmbl_7783.p1
Valid prediction for GeneMark_model.52586_t
Valid prediction for snap_scaffold_12-snap.1757-T1
Valid prediction for GeneMark_model.52596_t
Valid prediction for GeneMark_model.52578_t
Valid prediction for snap_scaffold_12-snap.1771-T1
Valid prediction for GlimmerHMM_glimmerT_30413-T1
Valid prediction for GeneMark_model.52575_t
Valid prediction for Augustus_model.g20279.t1
Valid prediction for GeneMark_model.52577_t
Valid prediction for Augustus_model.g20282.t1
Valid prediction for GlimmerHMM_glimmerT_30405-T1
Valid prediction for snap_scaffold_12-snap.1774-T1
Valid prediction for snap_scaffold_12-snap.1746-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 24289, rend_intergenic: 5434  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66911, rend_intergenic: 62870  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71517, rend_intergenic: 67137  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108563, rend_intergenic: 106059  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109629, rend_intergenic: 109432  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123446, rend_intergenic: 117845  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129227, rend_intergenic: 124160  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140860, rend_intergenic: 138073  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 203033
-exon list size: 546


building trellis

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99.1    
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99.8    
-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 24289, rend_intergenic: 5434  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66911, rend_intergenic: 62870  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71517, rend_intergenic: 67137  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108563, rend_intergenic: 106059  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109629, rend_intergenic: 109432  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123446, rend_intergenic: 117845  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129227, rend_intergenic: 124160  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140860, rend_intergenic: 138073  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 23 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 191372 - 203033
-exon list size: 11


building trellis

7.7    
15.4    
23.1    
30.8    
38.5    
46.2    
53.8    
61.5    
69.2    
76.9    
84.6    
92.3    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 1 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 191372 - 202399
-exon list size: 9


building trellis

9.1    
18.2    
27.3    
36.4    
45.5    
54.5    
63.6    
72.7    
81.8    
90.9    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 191754 - 202399
-exon list size: 8


building trellis

10.0    
20.0    
30.0    
40.0    
50.0    
60.0    
70.0    
80.0    
90.0    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support