-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_14/scaffold_14_847783-1111154

-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 Augustus_model.g22837.t1
Valid prediction for Augustus_model.g22836.t1
Valid prediction for Augustus_model.g22833.t1
Valid prediction for Augustus_model.g22809.t1
Couldn't classify 67121, 67145
Sorry, prediction pasa_asmbl_11753.p1 fails validation.
(CCA)	 TC	67121-67145	GT	TGG
(GAT)	 AG	67419-67561	GT	TGG
(GAG)	 AG	69677-69820	GT	CGG
(CGG)	 AG	69912-69981	GT	AGG
(GGT)	 AG	70486-70608	GT	TGG
(GTG)	 AG	71559-71677	GT	TTG
(ATT)	 AG	71834-71933	GT	AGG
(ATC)	 AG	72124-72219	GT	CAG
(CAT)	 AG	72326-72407	GT	AGG
(GTG)	 AG	72563-72623	GT	AGG
(GCA)	 AG	72748-72874	GT	AGG
(ATG)	 AG	73468-73503	GT	TGG
(ATT)	 AG	73944-74104	GT	AGG
(CGG)	 AG	74671-74796	GG	AAG
-recovered pasa_asmbl_11753.p1, initial, 73468, 73503
-recovered pasa_asmbl_11753.p1, terminal, 74671, 74796
-recovered pasa_asmbl_11753.p1, internal, 67419, 67561
-recovered pasa_asmbl_11753.p1, internal, 69677, 69820
-recovered pasa_asmbl_11753.p1, internal, 69912, 69981
-recovered pasa_asmbl_11753.p1, internal, 70486, 70608
-recovered pasa_asmbl_11753.p1, internal, 71559, 71677
-recovered pasa_asmbl_11753.p1, internal, 71834, 71933
-recovered pasa_asmbl_11753.p1, internal, 72124, 72219
-recovered pasa_asmbl_11753.p1, internal, 72326, 72407
-recovered pasa_asmbl_11753.p1, internal, 72563, 72623
-recovered pasa_asmbl_11753.p1, internal, 72748, 72874
-recovered pasa_asmbl_11753.p1, internal, 73468, 73503
-recovered pasa_asmbl_11753.p1, internal, 73944, 74104
Valid prediction for HiQ_model.g22806.t1
Valid prediction for CodingQuarry_transcript_15499-T1
Valid prediction for GeneMark_model.58190_t
Valid prediction for CodingQuarry_transcript_15492-T1
Valid prediction for CodingQuarry_transcript_15493-T1
Valid prediction for HiQ_model.g22810.t1
Valid prediction for GlimmerHMM_glimmerT_33963-T1
Valid prediction for CodingQuarry_transcript_15496-T1
Valid prediction for Augustus_model.g22834.t1
Couldn't classify 212985, 213288
Sorry, prediction pasa_asmbl_11760.p1 fails validation.
(ATC)	 GC	212985-213288	GT	AGG
(GAG)	 AG	213788-214014	GT	TGG
(GGG)	 AG	215790-215840	GT	CGG
(AAC)	 AG	215956-216156	GT	AGG
(GTG)	 AG	216357-216728	CC	GAC
-recovered pasa_asmbl_11760.p1, terminal, 216357, 216728
-recovered pasa_asmbl_11760.p1, internal, 213788, 214014
-recovered pasa_asmbl_11760.p1, internal, 215790, 215840
-recovered pasa_asmbl_11760.p1, internal, 215956, 216156
Valid prediction for GlimmerHMM_glimmerT_33945-T1
Valid prediction for Augustus_model.g22830.t1
Valid prediction for HiQ_model.g22835.t1
Valid prediction for GeneMark_model.58179_t
Valid prediction for CodingQuarry_transcript_15491-T1
Valid prediction for pasa_asmbl_11767.p1
Valid prediction for GeneMark_model.58202_t
Valid prediction for GlimmerHMM_glimmerT_33974-T1
Valid prediction for snap_scaffold_14-snap.168-T1
Valid prediction for snap_scaffold_14-snap.179-T1
Valid prediction for snap_scaffold_14-snap.133-T1
Valid prediction for GeneMark_model.58170_t
Valid prediction for GlimmerHMM_glimmerT_33970-T1
Valid prediction for snap_scaffold_14-snap.171-T1
Valid prediction for snap_scaffold_14-snap.160-T1
Valid prediction for snap_scaffold_14-snap.153-T1
Valid prediction for snap_scaffold_14-snap.141-T1
Valid prediction for Augustus_model.g22831.t1
Valid prediction for GeneMark_model.58197_t
Valid prediction for Augustus_model.g22817.t1
Valid prediction for snap_scaffold_14-snap.174-T1
Valid prediction for CodingQuarry_transcript_15495-T1
Valid prediction for snap_scaffold_14-snap.136-T1
Valid prediction for pasa_asmbl_11777.p1
Valid prediction for GlimmerHMM_glimmerT_33973-T1
Valid prediction for snap_scaffold_14-snap.132-T1
Valid prediction for Augustus_model.g22811.t1
Valid prediction for GeneMark_model.58187_t
Valid prediction for GeneMark_model.58199_t
Valid prediction for CodingQuarry_transcript_15490-T1
Valid prediction for snap_scaffold_14-snap.154-T1
Valid prediction for GeneMark_model.58201_t
Valid prediction for GlimmerHMM_glimmerT_33972-T1
Valid prediction for CodingQuarry_transcript_15488-T1
Valid prediction for CodingQuarry_transcript_15494-T1
Valid prediction for Augustus_model.g22822.t1
Valid prediction for GlimmerHMM_glimmerT_33962-T1
Valid prediction for pasa_asmbl_11749.p1
Valid prediction for snap_scaffold_14-snap.180-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_33955-T1
Valid prediction for snap_scaffold_14-snap.170-T1
Valid prediction for GeneMark_model.58174_t
Valid prediction for snap_scaffold_14-snap.176-T1
Valid prediction for GeneMark_model.58195_t
Valid prediction for GlimmerHMM_glimmerT_33946-T1
Valid prediction for GeneMark_model.58173_t
Valid prediction for snap_scaffold_14-snap.151-T1
Valid prediction for GlimmerHMM_glimmerT_33952-T1
Valid prediction for snap_scaffold_14-snap.138-T1
Valid prediction for Augustus_model.g22805.t1
Valid prediction for GlimmerHMM_glimmerT_33951-T1
Valid prediction for HiQ_model.g22829.t1
Valid prediction for GeneMark_model.58185_t
Valid prediction for CodingQuarry_transcript_15497-T1
Valid prediction for GlimmerHMM_glimmerT_33947-T1
Valid prediction for GlimmerHMM_glimmerT_33961-T1
Valid prediction for GlimmerHMM_glimmerT_33958-T1
Valid prediction for GlimmerHMM_glimmerT_33976-T1
Valid prediction for Augustus_model.g22823.t1
Valid prediction for GeneMark_model.58175_t
Valid prediction for snap_scaffold_14-snap.175-T1
Valid prediction for snap_scaffold_14-snap.148-T1
Valid prediction for snap_scaffold_14-snap.139-T1
Valid prediction for GlimmerHMM_glimmerT_33950-T1
Valid prediction for snap_scaffold_14-snap.140-T1
Valid prediction for Augustus_model.g22813.t1
Valid prediction for snap_scaffold_14-snap.172-T1
Valid prediction for CodingQuarry_transcript_15489-T1
Valid prediction for snap_scaffold_14-snap.165-T1
Valid prediction for Augustus_model.g22812.t1
Valid prediction for snap_scaffold_14-snap.156-T1
Valid prediction for snap_scaffold_14-snap.142-T1
Valid prediction for GlimmerHMM_glimmerT_33968-T1
Valid prediction for GlimmerHMM_glimmerT_33975-T1
Valid prediction for snap_scaffold_14-snap.137-T1
Valid prediction for GeneMark_model.58188_t
Valid prediction for GeneMark_model.58203_t
Valid prediction for snap_scaffold_14-snap.177-T1
Valid prediction for GeneMark_model.58186_t

-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_14-snap.159-T1
Valid prediction for snap_scaffold_14-snap.163-T1
Valid prediction for snap_scaffold_14-snap.178-T1
Valid prediction for GlimmerHMM_glimmerT_33965-T1
Valid prediction for GeneMark_model.58191_t
Valid prediction for GlimmerHMM_glimmerT_33969-T1
Valid prediction for Augustus_model.g22824.t1
Valid prediction for Augustus_model.g22819.t1
Valid prediction for Augustus_model.g22808.t1
Valid prediction for snap_scaffold_14-snap.158-T1
Valid prediction for Augustus_model.g22816.t1
Valid prediction for GeneMark_model.58198_t
Valid prediction for snap_scaffold_14-snap.155-T1
Valid prediction for snap_scaffold_14-snap.145-T1
Valid prediction for Augustus_model.g22825.t1
Valid prediction for Augustus_model.g22827.t1
Valid prediction for GeneMark_model.58194_t
Valid prediction for Augustus_model.g22820.t1
Valid prediction for GeneMark_model.58196_t
Valid prediction for Augustus_model.g22804.t1
Valid prediction for snap_scaffold_14-snap.169-T1
Valid prediction for GlimmerHMM_glimmerT_33971-T1
Valid prediction for GeneMark_model.58192_t
Valid prediction for snap_scaffold_14-snap.149-T1
Valid prediction for GlimmerHMM_glimmerT_33956-T1
Valid prediction for snap_scaffold_14-snap.146-T1
Valid prediction for GeneMark_model.58184_t
Valid prediction for snap_scaffold_14-snap.147-T1
Valid prediction for GlimmerHMM_glimmerT_33948-T1
Valid prediction for GlimmerHMM_glimmerT_33949-T1
Valid prediction for Augustus_model.g22814.t1
Valid prediction for snap_scaffold_14-snap.135-T1
Couldn't classify 35878, 36153
Sorry, prediction pasa_asmbl_12838.p1 fails validation.
(CTT)	 AG	35878-36153	GT	AGG
(GAT)	 AG	36333-36396	GT	AGG
(CAA)	 AG	36514-36563	GT	AGG
(GGC)	 AG	36665-36714	GT	ATG
(GAT)	 AG	36882-37024	GT	AGG
(TGG)	 AG	37124-37218	GT	AGG
(CGC)	 AG	37316-37418	GT	AGG
(ATG)	 AG	37515-37975	AC	AGA
add_exon() Sorry, pasa_asmbl_12838.p1 36882-37024-terminal-2 is invalid.
-recovered pasa_asmbl_12838.p1, terminal, 36882, 37024
-recovered pasa_asmbl_12838.p1, terminal, 37515, 37975
-recovered pasa_asmbl_12838.p1, internal, 35878, 36153
-recovered pasa_asmbl_12838.p1, internal, 36333, 36396
-recovered pasa_asmbl_12838.p1, internal, 36514, 36563
-recovered pasa_asmbl_12838.p1, internal, 36665, 36714
-recovered pasa_asmbl_12838.p1, internal, 36882, 37024
-recovered pasa_asmbl_12838.p1, internal, 37124, 37218
-recovered pasa_asmbl_12838.p1, internal, 37316, 37418
Valid prediction for GeneMark_model.58183_t
Valid prediction for GlimmerHMM_glimmerT_33954-T1
Valid prediction for snap_scaffold_14-snap.143-T1
Valid prediction for snap_scaffold_14-snap.167-T1
Valid prediction for snap_scaffold_14-snap.173-T1
Valid prediction for GlimmerHMM_glimmerT_33959-T1
Valid prediction for GlimmerHMM_glimmerT_33966-T1
Valid prediction for snap_scaffold_14-snap.161-T1
Valid prediction for Augustus_model.g22821.t1
Valid prediction for GeneMark_model.58177_t
Valid prediction for GeneMark_model.58176_t
Valid prediction for GlimmerHMM_glimmerT_33964-T1
Valid prediction for GeneMark_model.58181_t
Valid prediction for Augustus_model.g22818.t1
Valid prediction for GlimmerHMM_glimmerT_33953-T1
Valid prediction for snap_scaffold_14-snap.144-T1
Valid prediction for GeneMark_model.58180_t
Valid prediction for snap_scaffold_14-snap.162-T1
Valid prediction for GlimmerHMM_glimmerT_33960-T1
Valid prediction for snap_scaffold_14-snap.134-T1
Couldn't classify 34984, 35439
Sorry, prediction pasa_asmbl_12839.p1 fails validation.
(ATG)	 TC	34361-34401	GT	GGG
(AGA)	 AG	34523-34571	GT	CTG
(ATC)	 AG	34828-34893	GT	CAG
(ACT)	 AG	34984-35439	CT	GCC
-recovered pasa_asmbl_12839.p1, initial, 34361, 34401
-recovered pasa_asmbl_12839.p1, internal, 34523, 34571
-recovered pasa_asmbl_12839.p1, internal, 34828, 34893
Valid prediction for GeneMark_model.58172_t
Valid prediction for GeneMark_model.58189_t
Valid prediction for GeneMark_model.58171_t
Valid prediction for GlimmerHMM_glimmerT_33967-T1
Valid prediction for snap_scaffold_14-snap.166-T1
Valid prediction for HiQ_model.g22832.t1
Valid prediction for GlimmerHMM_glimmerT_33957-T1
Valid prediction for Augustus_model.g22815.t1
Valid prediction for GeneMark_model.58169_t
Valid prediction for GeneMark_model.58200_t
Valid prediction for snap_scaffold_14-snap.131-T1
Valid prediction for GeneMark_model.58182_t
Valid prediction for Augustus_model.g22826.t1
Valid prediction for Augustus_model.g22807.t1
Valid prediction for snap_scaffold_14-snap.150-T1
Valid prediction for snap_scaffold_14-snap.157-T1
Valid prediction for GeneMark_model.58193_t
Valid prediction for snap_scaffold_14-snap.152-T1
Valid prediction for snap_scaffold_14-snap.164-T1
Valid prediction for Augustus_model.g22828.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 16041, rend_intergenic: 13464  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163983, rend_intergenic: 162768  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173178, rend_intergenic: 171341  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177018, rend_intergenic: 173542  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 194570, rend_intergenic: 186729  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 196999, rend_intergenic: 194895  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 208579, rend_intergenic: 205672  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 250091, rend_intergenic: 247101  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 263372
-exon list size: 535


building trellis

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97.6    
97.8    
98.0    
98.1    
98.3    
98.5    
98.7    
98.9    
99.1    
99.3    
99.4    
99.6    
99.8    
-found 41 predictions from path traversal
Error with prediction: snap lend_intergenic: 16041, rend_intergenic: 13464  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163983, rend_intergenic: 162768  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173178, rend_intergenic: 171341  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177018, rend_intergenic: 173542  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 194570, rend_intergenic: 186729  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 196999, rend_intergenic: 194895  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 208579, rend_intergenic: 205672  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 250091, rend_intergenic: 247101  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 36 predictions persist after filtering for low support