-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_11/scaffold_11_12128879-12329216

-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_11-snap.2628-T1
Valid prediction for GeneMark_model.49376_t
Valid prediction for snap_scaffold_11-snap.2620-T1
Valid prediction for snap_scaffold_11-snap.2605-T1
Valid prediction for GlimmerHMM_glimmerT_28598-T1
Valid prediction for GlimmerHMM_glimmerT_28581-T1
Valid prediction for GeneMark_model.49355_t
Valid prediction for GlimmerHMM_glimmerT_28604-T1
Valid prediction for GeneMark_model.49334_t
Valid prediction for snap_scaffold_11-snap.2598-T1
Valid prediction for snap_scaffold_11-snap.2636-T1
Valid prediction for Augustus_model.g19099.t1
Valid prediction for GlimmerHMM_glimmerT_28595-T1
Valid prediction for GlimmerHMM_glimmerT_28596-T1
Valid prediction for GeneMark_model.49349_t
Valid prediction for GeneMark_model.49379_t
Couldn't classify 93606, 93744
Couldn't classify 98689, 98763
Sorry, prediction pasa_asmbl_5980.p1 fails validation.
(GAC)	 TA	93606-93744	GT	AGG
(CCT)	 AG	95742-95774	GT	AGG
(GGA)	 AG	97377-97602	GT	GGG
(GTG)	 AG	98225-98327	GT	AGG
(TAC)	 AG	98689-98763	GA	ACG
-recovered pasa_asmbl_5980.p1, internal, 95742, 95774
-recovered pasa_asmbl_5980.p1, internal, 97377, 97602
-recovered pasa_asmbl_5980.p1, internal, 98225, 98327
Couldn't classify 154098, 154229
Couldn't classify 154410, 154580
Sorry, prediction pasa_asmbl_6259.p1 fails validation.
(GTA)	 CA	154098-154229	GT	AAG
(GAC)	 AG	154410-154580	CA	AGC
Valid prediction for GlimmerHMM_glimmerT_28587-T1
Valid prediction for Augustus_model.g19094.t1
Valid prediction for snap_scaffold_11-snap.2630-T1
Valid prediction for GeneMark_model.49337_t
Valid prediction for GlimmerHMM_glimmerT_28609-T1
Valid prediction for GeneMark_model.49364_t
Couldn't classify 64049, 64098
Sorry, prediction pasa_asmbl_5976.p1 fails validation.
(AGC)	 TC	64049-64098	GT	AGG
(GCT)	 AG	64350-64425	GT	AGG
(GTG)	 AG	64620-64769	GT	TGG
(GCC)	 AG	64906-65143	GT	GGG
(GTG)	 AG	65938-66138	GT	ACG
(TGG)	 AG	66542-66726	AC	AAA
-recovered pasa_asmbl_5976.p1, terminal, 66542, 66726
-recovered pasa_asmbl_5976.p1, internal, 64350, 64425
-recovered pasa_asmbl_5976.p1, internal, 64620, 64769
-recovered pasa_asmbl_5976.p1, internal, 64906, 65143
-recovered pasa_asmbl_5976.p1, internal, 65938, 66138
Valid prediction for GeneMark_model.49375_t
Valid prediction for GlimmerHMM_glimmerT_28608-T1
Valid prediction for GlimmerHMM_glimmerT_28610-T1
Valid prediction for GeneMark_model.49340_t
Valid prediction for snap_scaffold_11-snap.2625-T1
Valid prediction for GeneMark_model.49351_t
Valid prediction for GlimmerHMM_glimmerT_28584-T1
Valid prediction for Augustus_model.g19087.t1
Valid prediction for GeneMark_model.49363_t
Valid prediction for snap_scaffold_11-snap.2615-T1
Valid prediction for GeneMark_model.49392_t
Valid prediction for GlimmerHMM_glimmerT_28605-T1
Valid prediction for GeneMark_model.49381_t
Valid prediction for GeneMark_model.49390_t
Valid prediction for GlimmerHMM_glimmerT_28599-T1
Valid prediction for snap_scaffold_11-snap.2626-T1
Valid prediction for snap_scaffold_11-snap.2609-T1
Valid prediction for snap_scaffold_11-snap.2613-T1
Valid prediction for GeneMark_model.49370_t
Valid prediction for snap_scaffold_11-snap.2627-T1
Valid prediction for GeneMark_model.49373_t
Valid prediction for GeneMark_model.49366_t
Valid prediction for GeneMark_model.49348_t
Valid prediction for GlimmerHMM_glimmerT_28600-T1
Valid prediction for snap_scaffold_11-snap.2602-T1
Valid prediction for Augustus_model.g19086.t1
Couldn't classify 48959, 49354
Sorry, prediction pasa_asmbl_5975.p1 fails validation.
(GAG)	 AT	48959-49354	GA	TGG
Valid prediction for GeneMark_model.49357_t
Valid prediction for GlimmerHMM_glimmerT_28606-T1
Valid prediction for Augustus_model.g19093.t1
Valid prediction for GlimmerHMM_glimmerT_28585-T1
Valid prediction for Augustus_model.g19095.t1
Valid prediction for Augustus_model.g19101.t1
Valid prediction for Augustus_model.g19100.t1
Valid prediction for snap_scaffold_11-snap.2600-T1
Valid prediction for snap_scaffold_11-snap.2606-T1
Valid prediction for snap_scaffold_11-snap.2621-T1
Valid prediction for snap_scaffold_11-snap.2632-T1
Valid prediction for Augustus_model.g19097.t1
Valid prediction for GeneMark_model.49380_t
Valid prediction for GeneMark_model.49342_t
Valid prediction for GeneMark_model.49345_t
Valid prediction for GeneMark_model.49386_t
Valid prediction for GeneMark_model.49372_t
Valid prediction for Augustus_model.g19091.t1
Valid prediction for snap_scaffold_11-snap.2603-T1
Valid prediction for GeneMark_model.49338_t
Valid prediction for GeneMark_model.49368_t
Valid prediction for snap_scaffold_11-snap.2612-T1
Valid prediction for Augustus_model.g19090.t1
Valid prediction for GlimmerHMM_glimmerT_28593-T1
Valid prediction for snap_scaffold_11-snap.2624-T1
Valid prediction for GlimmerHMM_glimmerT_28611-T1
Valid prediction for GeneMark_model.49388_t
Valid prediction for GeneMark_model.49361_t
Valid prediction for GeneMark_model.49353_t
Valid prediction for GlimmerHMM_glimmerT_28590-T1
Valid prediction for GlimmerHMM_glimmerT_28601-T1
Valid prediction for snap_scaffold_11-snap.2618-T1
Valid prediction for Augustus_model.g19096.t1
Valid prediction for Augustus_model.g19085.t1
Valid prediction for GlimmerHMM_glimmerT_28588-T1
Valid prediction for GlimmerHMM_glimmerT_28591-T1
Valid prediction for GlimmerHMM_glimmerT_28582-T1
Valid prediction for GeneMark_model.49384_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 GeneMark_model.49343_t
Valid prediction for GeneMark_model.49362_t
Valid prediction for GeneMark_model.49356_t
Valid prediction for snap_scaffold_11-snap.2601-T1
Valid prediction for snap_scaffold_11-snap.2604-T1
Valid prediction for GeneMark_model.49358_t
Valid prediction for snap_scaffold_11-snap.2611-T1
Valid prediction for snap_scaffold_11-snap.2608-T1
Valid prediction for Augustus_model.g19088.t1
Valid prediction for GeneMark_model.49360_t
Valid prediction for GeneMark_model.49387_t
Valid prediction for GeneMark_model.49354_t
Valid prediction for Augustus_model.g19098.t1
Valid prediction for GeneMark_model.49367_t
Valid prediction for snap_scaffold_11-snap.2635-T1
Valid prediction for GlimmerHMM_glimmerT_28613-T1
Valid prediction for GeneMark_model.49383_t
Valid prediction for GeneMark_model.49377_t
Valid prediction for Augustus_model.g19089.t1
Valid prediction for snap_scaffold_11-snap.2633-T1
Valid prediction for GeneMark_model.49335_t
Valid prediction for snap_scaffold_11-snap.2599-T1
Valid prediction for GlimmerHMM_glimmerT_28589-T1
Valid prediction for snap_scaffold_11-snap.2614-T1
Valid prediction for GlimmerHMM_glimmerT_28592-T1
Valid prediction for GlimmerHMM_glimmerT_28586-T1
Valid prediction for snap_scaffold_11-snap.2623-T1
Valid prediction for GeneMark_model.49389_t
Valid prediction for snap_scaffold_11-snap.2619-T1
Valid prediction for GeneMark_model.49344_t
Valid prediction for GeneMark_model.49346_t
Valid prediction for snap_scaffold_11-snap.2634-T1
Valid prediction for GlimmerHMM_glimmerT_28597-T1
Valid prediction for snap_scaffold_11-snap.2629-T1
Valid prediction for snap_scaffold_11-snap.2637-T1
Valid prediction for GeneMark_model.49365_t
Valid prediction for GeneMark_model.49339_t
Valid prediction for Augustus_model.g19102.t1
Valid prediction for GeneMark_model.49350_t
Valid prediction for GeneMark_model.49347_t
Valid prediction for GeneMark_model.49391_t
Valid prediction for GlimmerHMM_glimmerT_28607-T1
Valid prediction for snap_scaffold_11-snap.2617-T1
Valid prediction for GeneMark_model.49352_t
Valid prediction for GlimmerHMM_glimmerT_28612-T1
Valid prediction for snap_scaffold_11-snap.2607-T1
Valid prediction for GlimmerHMM_glimmerT_28602-T1
Valid prediction for snap_scaffold_11-snap.2610-T1
Valid prediction for GeneMark_model.49359_t
Valid prediction for GeneMark_model.49378_t
Valid prediction for GlimmerHMM_glimmerT_28583-T1
Valid prediction for GeneMark_model.49382_t
Valid prediction for GeneMark_model.49371_t
Valid prediction for snap_scaffold_11-snap.2622-T1
Valid prediction for snap_scaffold_11-snap.2616-T1
Valid prediction for GeneMark_model.49385_t
Valid prediction for GeneMark_model.49336_t
Valid prediction for GlimmerHMM_glimmerT_28594-T1
Valid prediction for Augustus_model.g19092.t1
Valid prediction for GeneMark_model.49341_t
Valid prediction for GeneMark_model.49369_t
Valid prediction for GeneMark_model.49374_t
Valid prediction for GlimmerHMM_glimmerT_28603-T1
Valid prediction for snap_scaffold_11-snap.2631-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 8076, rend_intergenic: 5587  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17670, rend_intergenic: 11929  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29757, rend_intergenic: 18300  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30506, rend_intergenic: 29831  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34704, rend_intergenic: 30992  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47433, rend_intergenic: 37804  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66726, rend_intergenic: 54679  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80717, rend_intergenic: 76547  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87559, rend_intergenic: 81313  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96751, rend_intergenic: 88471  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102504, rend_intergenic: 97033  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105386, rend_intergenic: 102675  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134845, rend_intergenic: 125475  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172519, rend_intergenic: 167685  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182057, rend_intergenic: 174878  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185777, rend_intergenic: 182277  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189885, rend_intergenic: 187033  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 200338
-exon list size: 732


building trellis

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87.2    
87.3    
87.5    
87.6    
87.7    
87.9    
88.0    
88.1    
88.3    
88.4    
88.6    
88.7    
88.8    
89.0    
89.1    
89.2    
89.4    
89.5    
89.6    
89.8    
89.9    
90.1    
90.2    
90.3    
90.5    
90.6    
90.7    
90.9    
91.0    
91.1    
91.3    
91.4    
91.6    
91.7    
91.8    
92.0    
92.1    
92.2    
92.4    
92.5    
92.6    
92.8    
92.9    
93.1    
93.2    
93.3    
93.5    
93.6    
93.7    
93.9    
94.0    
94.1    
94.3    
94.4    
94.6    
94.7    
94.8    
95.0    
95.1    
95.2    
95.4    
95.5    
95.6    
95.8    
95.9    
96.0    
96.2    
96.3    
96.5    
96.6    
96.7    
96.9    
97.0    
97.1    
97.3    
97.4    
97.5    
97.7    
97.8    
98.0    
98.1    
98.2    
98.4    
98.5    
98.6    
98.8    
98.9    
99.0    
99.2    
99.3    
99.5    
99.6    
99.7    
99.9    
-found 40 predictions from path traversal
Error with prediction: snap lend_intergenic: 8076, rend_intergenic: 5587  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17670, rend_intergenic: 11929  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29757, rend_intergenic: 18300  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30506, rend_intergenic: 29831  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34704, rend_intergenic: 30992  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47433, rend_intergenic: 37804  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66726, rend_intergenic: 54679  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80717, rend_intergenic: 76547  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87559, rend_intergenic: 81313  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96751, rend_intergenic: 88471  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102504, rend_intergenic: 97033  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105386, rend_intergenic: 102675  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134845, rend_intergenic: 125475  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172519, rend_intergenic: 167685  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182057, rend_intergenic: 174878  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185777, rend_intergenic: 182277  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189885, rend_intergenic: 187033  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 14 predictions persist after filtering for low support