-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_14/scaffold_14_13377952-13580046

-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.61308_t
Valid prediction for GeneMark_model.61312_t
Valid prediction for GeneMark_model.61310_t
Valid prediction for GlimmerHMM_glimmerT_35774-T1
Valid prediction for HiQ_model.g24077.t1
Valid prediction for snap_scaffold_14-snap.2809-T1
Valid prediction for GeneMark_model.61322_t
Valid prediction for GeneMark_model.61299_t
Valid prediction for GeneMark_model.61328_t
Valid prediction for snap_scaffold_14-snap.2786-T1
Valid prediction for GeneMark_model.61287_t
Valid prediction for GlimmerHMM_glimmerT_35761-T1
Valid prediction for Augustus_model.g24079.t1
Valid prediction for GlimmerHMM_glimmerT_35756-T1
Valid prediction for GlimmerHMM_glimmerT_35768-T1
Valid prediction for snap_scaffold_14-snap.2804-T1
Valid prediction for GlimmerHMM_glimmerT_35770-T1
Couldn't classify 118656, 118806
Couldn't classify 119721, 119826
Sorry, prediction pasa_asmbl_12694.p1 fails validation.
(CCT)	 TC	118656-118806	GT	AGG
(GAG)	 AG	119000-119123	GT	CGG
(AGG)	 AG	119721-119826	AC	GAA
-recovered pasa_asmbl_12694.p1, internal, 119000, 119123
Valid prediction for GeneMark_model.61286_t
Valid prediction for snap_scaffold_14-snap.2801-T1
Valid prediction for GlimmerHMM_glimmerT_35757-T1
Valid prediction for Augustus_model.g24076.t1
Valid prediction for Augustus_model.g24072.t1
Valid prediction for snap_scaffold_14-snap.2810-T1
Valid prediction for GlimmerHMM_glimmerT_35753-T1
Valid prediction for snap_scaffold_14-snap.2790-T1
Valid prediction for GeneMark_model.61314_t
Valid prediction for pasa_asmbl_12464.p1
Valid prediction for snap_scaffold_14-snap.2787-T1
Valid prediction for GeneMark_model.61281_t
Valid prediction for GeneMark_model.61279_t
Valid prediction for snap_scaffold_14-snap.2797-T1
Valid prediction for GeneMark_model.61280_t
Valid prediction for GeneMark_model.61316_t
Valid prediction for GlimmerHMM_glimmerT_35755-T1
Valid prediction for GeneMark_model.61317_t
Valid prediction for CodingQuarry_transcript_15857-T1
Valid prediction for Augustus_model.g24073.t1
Valid prediction for GlimmerHMM_glimmerT_35758-T1
Valid prediction for snap_scaffold_14-snap.2789-T1
Valid prediction for GeneMark_model.61324_t
Valid prediction for snap_scaffold_14-snap.2777-T1
Valid prediction for Augustus_model.g24084.t1
Valid prediction for GeneMark_model.61293_t
Valid prediction for GeneMark_model.61289_t
Valid prediction for GlimmerHMM_glimmerT_35766-T1
Valid prediction for snap_scaffold_14-snap.2816-T1
Valid prediction for GlimmerHMM_glimmerT_35763-T1
Valid prediction for CodingQuarry_transcript_15859-T1
Valid prediction for snap_scaffold_14-snap.2813-T1
Valid prediction for GeneMark_model.61296_t
Valid prediction for snap_scaffold_14-snap.2795-T1
Valid prediction for GeneMark_model.61320_t
Valid prediction for GlimmerHMM_glimmerT_35762-T1
Valid prediction for Augustus_model.g24080.t1
Valid prediction for snap_scaffold_14-snap.2779-T1
Valid prediction for GeneMark_model.61327_t
Valid prediction for GeneMark_model.61305_t
Valid prediction for GeneMark_model.61325_t
Valid prediction for GlimmerHMM_glimmerT_35764-T1
Valid prediction for GeneMark_model.61303_t
Valid prediction for snap_scaffold_14-snap.2807-T1
Couldn't classify 61938, 62014
Sorry, prediction pasa_asmbl_12461.p1 fails validation.
(CTG)	 TG	61938-62014	GT	AGG
(GTC)	 AG	62581-62765	GT	AAG
(ACT)	 AG	63069-63164	GT	GGG
(GGG)	 AG	63359-63517	GT	AGG
(AGT)	 AG	64328-64421	GT	AGG
(GCG)	 AG	64569-64632	CC	AAC
-recovered pasa_asmbl_12461.p1, terminal, 64569, 64632
-recovered pasa_asmbl_12461.p1, internal, 62581, 62765
-recovered pasa_asmbl_12461.p1, internal, 63069, 63164
-recovered pasa_asmbl_12461.p1, internal, 63359, 63517
-recovered pasa_asmbl_12461.p1, internal, 64328, 64421
Valid prediction for snap_scaffold_14-snap.2794-T1
Valid prediction for GeneMark_model.61295_t
Valid prediction for GeneMark_model.61301_t
Valid prediction for GlimmerHMM_glimmerT_35771-T1
Valid prediction for snap_scaffold_14-snap.2800-T1
Valid prediction for GlimmerHMM_glimmerT_35767-T1
Valid prediction for Augustus_model.g24075.t1
Valid prediction for snap_scaffold_14-snap.2793-T1
Valid prediction for snap_scaffold_14-snap.2815-T1
Valid prediction for Augustus_model.g24070.t1
Valid prediction for GeneMark_model.61292_t
Valid prediction for GeneMark_model.61285_t
Valid prediction for Augustus_model.g24081.t1
Valid prediction for GeneMark_model.61284_t
Couldn't classify 60122, 60604
Couldn't classify 61819, 61856
Sorry, prediction pasa_asmbl_12460.p1 fails validation.
(AGT)	 AC	60122-60604	GT	CGG
(TTG)	 AG	60795-61068	GT	AGG
(ACC)	 AG	61819-61856	GG	GGG
-recovered pasa_asmbl_12460.p1, internal, 60795, 61068

-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_35773-T1
Valid prediction for GeneMark_model.61291_t
Valid prediction for snap_scaffold_14-snap.2798-T1
Valid prediction for GeneMark_model.61321_t
Couldn't classify 192759, 192834
Sorry, prediction pasa_asmbl_13795.p1 fails validation.
(CAC)	 TG	192759-192834	GT	GAG
(GTC)	 AG	193277-193629	CT	AAC
-recovered pasa_asmbl_13795.p1, terminal, 193277, 193629
Valid prediction for Augustus_model.g24082.t1
Valid prediction for GeneMark_model.61306_t
Valid prediction for GeneMark_model.61277_t
Valid prediction for GeneMark_model.61319_t
Valid prediction for GeneMark_model.61315_t
Valid prediction for GeneMark_model.61309_t
Valid prediction for snap_scaffold_14-snap.2806-T1
Valid prediction for snap_scaffold_14-snap.2783-T1
Valid prediction for GlimmerHMM_glimmerT_35752-T1
Valid prediction for GeneMark_model.61326_t
Valid prediction for snap_scaffold_14-snap.2785-T1
Valid prediction for CodingQuarry_transcript_15856-T1
Valid prediction for snap_scaffold_14-snap.2802-T1
Valid prediction for pasa_asmbl_13621.p1
Valid prediction for GeneMark_model.61283_t
Valid prediction for GeneMark_model.61300_t
Valid prediction for GlimmerHMM_glimmerT_35772-T1
Valid prediction for snap_scaffold_14-snap.2773-T1
Valid prediction for snap_scaffold_14-snap.2788-T1
Valid prediction for GlimmerHMM_glimmerT_35754-T1
Valid prediction for GeneMark_model.61278_t
Valid prediction for snap_scaffold_14-snap.2814-T1
Valid prediction for Augustus_model.g24071.t1
Valid prediction for snap_scaffold_14-snap.2811-T1
Valid prediction for snap_scaffold_14-snap.2803-T1
Valid prediction for GlimmerHMM_glimmerT_35765-T1
Valid prediction for GeneMark_model.61311_t
Valid prediction for GeneMark_model.61294_t
Valid prediction for Augustus_model.g24083.t1
Valid prediction for CodingQuarry_transcript_15854-T1
Valid prediction for snap_scaffold_14-snap.2792-T1
Valid prediction for snap_scaffold_14-snap.2776-T1
Valid prediction for snap_scaffold_14-snap.2774-T1
Valid prediction for CodingQuarry_transcript_15855-T1
Valid prediction for GeneMark_model.61323_t
Valid prediction for GlimmerHMM_glimmerT_35769-T1
Valid prediction for CodingQuarry_transcript_15858-T1
Valid prediction for HiQ_model.g24068.t1
Valid prediction for snap_scaffold_14-snap.2791-T1
Valid prediction for snap_scaffold_14-snap.2778-T1
Valid prediction for snap_scaffold_14-snap.2799-T1
Valid prediction for snap_scaffold_14-snap.2812-T1
Valid prediction for snap_scaffold_14-snap.2781-T1
Valid prediction for GlimmerHMM_glimmerT_35759-T1
Valid prediction for GeneMark_model.61313_t
Valid prediction for GeneMark_model.61318_t
Valid prediction for snap_scaffold_14-snap.2780-T1
Valid prediction for GeneMark_model.61307_t
Valid prediction for GeneMark_model.61298_t
Valid prediction for snap_scaffold_14-snap.2782-T1
Valid prediction for snap_scaffold_14-snap.2796-T1
Valid prediction for snap_scaffold_14-snap.2808-T1
Valid prediction for snap_scaffold_14-snap.2805-T1
Valid prediction for HiQ_model.g24074.t1
Valid prediction for snap_scaffold_14-snap.2775-T1
Couldn't classify 192733, 192758
Sorry, prediction pasa_asmbl_13845.p1 fails validation.
(ATG)	 CA	191276-191340	GT	AAG
(GAA)	 AG	191631-191749	GT	AGG
(GGG)	 AG	191914-192069	GT	AGG
(AGG)	 AG	192172-192276	GT	AGG
(GTC)	 AG	192381-192593	GC	AGG
(GAA)	 AG	192733-192758	CA	TGC
-recovered pasa_asmbl_13845.p1, initial, 191276, 191340
add_exon() Sorry, pasa_asmbl_13845.p1 192172-192276-terminal-1 is invalid.
-recovered pasa_asmbl_13845.p1, terminal, 192172, 192276
-recovered pasa_asmbl_13845.p1, internal, 191631, 191749
-recovered pasa_asmbl_13845.p1, internal, 191914, 192069
-recovered pasa_asmbl_13845.p1, internal, 192172, 192276
-recovered pasa_asmbl_13845.p1, internal, 192381, 192593
Valid prediction for GeneMark_model.61297_t
Valid prediction for GeneMark_model.61282_t
Valid prediction for GlimmerHMM_glimmerT_35760-T1
Valid prediction for HiQ_model.g24069.t1
Valid prediction for Augustus_model.g24078.t1
Valid prediction for snap_scaffold_14-snap.2784-T1
Valid prediction for GeneMark_model.61288_t
Valid prediction for GeneMark_model.61302_t
Valid prediction for pasa_asmbl_13624.p1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 16065, rend_intergenic: 15377  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18121, rend_intergenic: 16477  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25064, rend_intergenic: 20995  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64860, rend_intergenic: 61446  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105317, rend_intergenic: 102307  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122772, rend_intergenic: 108655  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137286, rend_intergenic: 131386  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155518, rend_intergenic: 147621  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169886, rend_intergenic: 164085  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173896, rend_intergenic: 170681  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181825, rend_intergenic: 175532  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186567, rend_intergenic: 182486  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 202095
-exon list size: 691


building trellis

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93.4    
93.5    
93.7    
93.8    
93.9    
94.1    
94.2    
94.4    
94.5    
94.7    
94.8    
94.9    
95.1    
95.2    
95.4    
95.5    
95.7    
95.8    
96.0    
96.1    
96.2    
96.4    
96.5    
96.7    
96.8    
97.0    
97.1    
97.3    
97.4    
97.5    
97.7    
97.8    
98.0    
98.1    
98.3    
98.4    
98.6    
98.7    
98.8    
99.0    
99.1    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 32 predictions from path traversal
Error with prediction: snap lend_intergenic: 16065, rend_intergenic: 15377  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18121, rend_intergenic: 16477  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25064, rend_intergenic: 20995  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64860, rend_intergenic: 61446  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105317, rend_intergenic: 102307  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122772, rend_intergenic: 108655  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137286, rend_intergenic: 131386  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155518, rend_intergenic: 147621  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169886, rend_intergenic: 164085  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173896, rend_intergenic: 170681  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181825, rend_intergenic: 175532  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186567, rend_intergenic: 182486  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support