-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_13/scaffold_13_14226597-14402773

-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.57402_t
Valid prediction for GeneMark_model.57346_t
Valid prediction for GlimmerHMM_glimmerT_33494-T1
Valid prediction for GeneMark_model.57375_t
Valid prediction for GlimmerHMM_glimmerT_33501-T1
Valid prediction for snap_scaffold_13-snap.2750-T1
Valid prediction for GeneMark_model.57395_t
Valid prediction for GlimmerHMM_glimmerT_33483-T1
Valid prediction for GlimmerHMM_glimmerT_33485-T1
Couldn't classify 19900, 20226
Sorry, prediction pasa_asmbl_11422.p1 fails validation.
(GAG)	 CA	19900-20226	GA	GAG
Valid prediction for GlimmerHMM_glimmerT_33495-T1
Valid prediction for snap_scaffold_13-snap.2746-T1
Valid prediction for snap_scaffold_13-snap.2751-T1
Valid prediction for GeneMark_model.57360_t
Valid prediction for Augustus_model.g22485.t1
Valid prediction for snap_scaffold_13-snap.2755-T1
Valid prediction for GeneMark_model.57400_t
Valid prediction for GeneMark_model.57358_t
Valid prediction for GlimmerHMM_glimmerT_33492-T1
Valid prediction for Augustus_model.g22488.t1
Valid prediction for snap_scaffold_13-snap.2732-T1
Couldn't classify 135222, 135527
Sorry, prediction pasa_asmbl_10153.p1 fails validation.
(ACA)	 TC	135222-135527	GT	GAG
Valid prediction for GlimmerHMM_glimmerT_33496-T1
Valid prediction for GeneMark_model.57403_t
Valid prediction for GeneMark_model.57381_t
Valid prediction for GeneMark_model.57369_t
Valid prediction for GeneMark_model.57377_t
Valid prediction for snap_scaffold_13-snap.2738-T1
Valid prediction for GeneMark_model.57370_t
Valid prediction for GeneMark_model.57383_t
Valid prediction for GlimmerHMM_glimmerT_33486-T1
Valid prediction for GeneMark_model.57356_t
Valid prediction for snap_scaffold_13-snap.2720-T1
Valid prediction for GeneMark_model.57352_t
Valid prediction for snap_scaffold_13-snap.2728-T1
Valid prediction for GeneMark_model.57379_t
Valid prediction for snap_scaffold_13-snap.2743-T1
Valid prediction for GeneMark_model.57389_t
Valid prediction for GeneMark_model.57363_t
Valid prediction for snap_scaffold_13-snap.2740-T1
Valid prediction for snap_scaffold_13-snap.2736-T1
Valid prediction for snap_scaffold_13-snap.2726-T1
Valid prediction for snap_scaffold_13-snap.2753-T1
Valid prediction for Augustus_model.g22491.t1
Valid prediction for Augustus_model.g22492.t1
Valid prediction for snap_scaffold_13-snap.2737-T1
Valid prediction for GlimmerHMM_glimmerT_33504-T1
Valid prediction for snap_scaffold_13-snap.2752-T1
Valid prediction for GeneMark_model.57350_t
Couldn't classify 4593, 4724
Sorry, prediction pasa_asmbl_11635.p1 fails validation.
(ATG)	 TC	2346-2466	GT	AGG
(GTG)	 AG	2627-2709	GT	AGG
(GCC)	 AG	2948-3524	GT	AGG
(CCC)	 AG	3917-4062	GT	AGG
(GAC)	 AG	4593-4724	GT	AGG
-recovered pasa_asmbl_11635.p1, initial, 2346, 2466
-recovered pasa_asmbl_11635.p1, internal, 2627, 2709
-recovered pasa_asmbl_11635.p1, internal, 2948, 3524
-recovered pasa_asmbl_11635.p1, internal, 3917, 4062
-recovered pasa_asmbl_11635.p1, internal, 4593, 4724
Valid prediction for GeneMark_model.57397_t
Valid prediction for GeneMark_model.57372_t
Valid prediction for Augustus_model.g22493.t1
Valid prediction for GeneMark_model.57347_t
Valid prediction for Augustus_model.g22484.t1
Valid prediction for GeneMark_model.57385_t
Valid prediction for GeneMark_model.57392_t
Valid prediction for GeneMark_model.57365_t
Valid prediction for snap_scaffold_13-snap.2748-T1
Valid prediction for Augustus_model.g22489.t1
Valid prediction for GeneMark_model.57367_t
Valid prediction for GeneMark_model.57390_t
Valid prediction for Augustus_model.g22486.t1
Valid prediction for GlimmerHMM_glimmerT_33489-T1
Valid prediction for snap_scaffold_13-snap.2723-T1
Valid prediction for GeneMark_model.57387_t
Valid prediction for GlimmerHMM_glimmerT_33481-T1
Valid prediction for GeneMark_model.57354_t
Valid prediction for GlimmerHMM_glimmerT_33487-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 GeneMark_model.57357_t
Valid prediction for GeneMark_model.57399_t
Valid prediction for snap_scaffold_13-snap.2733-T1
Valid prediction for GeneMark_model.57366_t
Valid prediction for snap_scaffold_13-snap.2739-T1
Valid prediction for GlimmerHMM_glimmerT_33482-T1
Valid prediction for snap_scaffold_13-snap.2725-T1
Valid prediction for snap_scaffold_13-snap.2741-T1
Valid prediction for snap_scaffold_13-snap.2722-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_33500-T1
Valid prediction for GeneMark_model.57378_t
Valid prediction for GeneMark_model.57373_t
Couldn't classify 91279, 91371
Couldn't classify 92467, 92625
Sorry, prediction pasa_asmbl_10294.p1 fails validation.
(TCC)	 AG	91279-91371	GT	AGG
(TCC)	 AG	91989-92219	GT	AGG
(GAG)	 AG	92467-92625	GT	AGG
-recovered pasa_asmbl_10294.p1, internal, 91279, 91371
-recovered pasa_asmbl_10294.p1, internal, 91989, 92219
-recovered pasa_asmbl_10294.p1, internal, 92467, 92625
Valid prediction for snap_scaffold_13-snap.2731-T1
Valid prediction for GeneMark_model.57364_t
Valid prediction for GeneMark_model.57386_t
Valid prediction for GlimmerHMM_glimmerT_33490-T1
Valid prediction for GeneMark_model.57359_t
Valid prediction for GeneMark_model.57382_t
Valid prediction for snap_scaffold_13-snap.2745-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for GeneMark_model.57384_t
Valid prediction for GlimmerHMM_glimmerT_33503-T1
Valid prediction for GlimmerHMM_glimmerT_33484-T1
Couldn't classify 36445, 36521
Couldn't classify 37931, 38017
Sorry, prediction pasa_asmbl_10354.p1 fails validation.
(GCC)	 AT	36445-36521	GT	GGG
(GAA)	 AG	36639-36721	GT	TGG
(GAA)	 AG	37266-37390	GT	AGG
(GTG)	 AG	37931-38017	GT	GCG
-recovered pasa_asmbl_10354.p1, internal, 36639, 36721
-recovered pasa_asmbl_10354.p1, internal, 37266, 37390
-recovered pasa_asmbl_10354.p1, internal, 37931, 38017
Valid prediction for snap_scaffold_13-snap.2724-T1
Valid prediction for snap_scaffold_13-snap.2744-T1
Valid prediction for snap_scaffold_13-snap.2747-T1
Valid prediction for GeneMark_model.57368_t
Valid prediction for snap_scaffold_13-snap.2742-T1
Valid prediction for GeneMark_model.57371_t
Valid prediction for GeneMark_model.57349_t
Valid prediction for GeneMark_model.57362_t
Valid prediction for GlimmerHMM_glimmerT_33502-T1
Valid prediction for GeneMark_model.57398_t
Valid prediction for snap_scaffold_13-snap.2729-T1
Valid prediction for GeneMark_model.57401_t
Valid prediction for Augustus_model.g22487.t1
Valid prediction for snap_scaffold_13-snap.2734-T1
Valid prediction for GlimmerHMM_glimmerT_33493-T1
Valid prediction for snap_scaffold_13-snap.2730-T1
Valid prediction for GeneMark_model.57353_t
Valid prediction for snap_scaffold_13-snap.2735-T1
Valid prediction for GeneMark_model.57394_t
Valid prediction for snap_scaffold_13-snap.2749-T1
Valid prediction for GlimmerHMM_glimmerT_33497-T1
Valid prediction for GeneMark_model.57348_t
Valid prediction for GeneMark_model.57396_t
Valid prediction for GlimmerHMM_glimmerT_33498-T1
Valid prediction for GeneMark_model.57388_t
Valid prediction for snap_scaffold_13-snap.2754-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GeneMark_model.57355_t
Valid prediction for GeneMark_model.57351_t
Valid prediction for GlimmerHMM_glimmerT_33488-T1
Valid prediction for GeneMark_model.57376_t
Valid prediction for GeneMark_model.57380_t
Valid prediction for snap_scaffold_13-snap.2721-T1
Valid prediction for GlimmerHMM_glimmerT_33491-T1
Valid prediction for GeneMark_model.57393_t
Valid prediction for GeneMark_model.57374_t
Valid prediction for GeneMark_model.57361_t
Valid prediction for Augustus_model.g22490.t1
Valid prediction for GlimmerHMM_glimmerT_33499-T1
Couldn't classify 96037, 96156
Couldn't classify 96704, 96851
Sorry, prediction pasa_asmbl_10148.p1 fails validation.
(AGG)	 AG	96037-96156	GT	AGG
(AGT)	 AG	96323-96429	GT	AGG
(CCA)	 AG	96704-96851	TG	AGT
-recovered pasa_asmbl_10148.p1, internal, 96037, 96156
-recovered pasa_asmbl_10148.p1, internal, 96323, 96429
Valid prediction for snap_scaffold_13-snap.2727-T1
Valid prediction for GeneMark_model.57391_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 6589, rend_intergenic: 3082  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 11346, rend_intergenic: 9070  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20226, rend_intergenic: 11577  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21981, rend_intergenic: 20247  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36891, rend_intergenic: 28026  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42100, rend_intergenic: 37983  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51070, rend_intergenic: 44867  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78060, rend_intergenic: 68090  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89395, rend_intergenic: 79324  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95788, rend_intergenic: 93303  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103776, rend_intergenic: 96005  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103829, rend_intergenic: 103800  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128648, rend_intergenic: 103889  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130390, rend_intergenic: 128701  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137637, rend_intergenic: 132805  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144341, rend_intergenic: 144103  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147353, rend_intergenic: 144342  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171231, rend_intergenic: 167141  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 176177
-exon list size: 730


building trellis

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89.1    
89.2    
89.3    
89.5    
89.6    
89.8    
89.9    
90.0    
90.2    
90.3    
90.4    
90.6    
90.7    
90.8    
91.0    
91.1    
91.3    
91.4    
91.5    
91.7    
91.8    
91.9    
92.1    
92.2    
92.3    
92.5    
92.6    
92.8    
92.9    
93.0    
93.2    
93.3    
93.4    
93.6    
93.7    
93.9    
94.0    
94.1    
94.3    
94.4    
94.5    
94.7    
94.8    
94.9    
95.1    
95.2    
95.4    
95.5    
95.6    
95.8    
95.9    
96.0    
96.2    
96.3    
96.4    
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 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 6589, rend_intergenic: 3082  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 11346, rend_intergenic: 9070  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20226, rend_intergenic: 11577  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21981, rend_intergenic: 20247  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36891, rend_intergenic: 28026  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42100, rend_intergenic: 37983  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51070, rend_intergenic: 44867  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78060, rend_intergenic: 68090  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89395, rend_intergenic: 79324  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95788, rend_intergenic: 93303  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103776, rend_intergenic: 96005  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103829, rend_intergenic: 103800  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128648, rend_intergenic: 103889  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130390, rend_intergenic: 128701  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137637, rend_intergenic: 132805  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144341, rend_intergenic: 144103  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147353, rend_intergenic: 144342  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171231, rend_intergenic: 167141  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support