-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_11/scaffold_11_3782510-3936095

-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 CodingQuarry_transcript_8001-T1
Valid prediction for GeneMark_model.47403_t
Valid prediction for Augustus_model.g18310.t1
Valid prediction for GeneMark_model.47382_t
Valid prediction for snap_scaffold_11-snap.954-T1
Valid prediction for Augustus_model.g18323.t1
Valid prediction for GeneMark_model.47411_t
Valid prediction for CodingQuarry_transcript_7999-T1
Valid prediction for CodingQuarry_transcript_8000-T1
Valid prediction for GeneMark_model.47384_t
Valid prediction for snap_scaffold_11-snap.970-T1
Valid prediction for GeneMark_model.47379_t
Valid prediction for HiQ_model.g18317.t1
Valid prediction for GlimmerHMM_glimmerT_27449-T1
Valid prediction for Augustus_model.g18321.t1
Couldn't classify 116739, 116769
Sorry, prediction pasa_asmbl_5430.p1 fails validation.
(TTA)	 GC	116739-116769	GT	GGG
(CGG)	 AG	117118-117269	GT	AGG
(TAC)	 AG	117398-117464	GT	AGG
(ACA)	 AG	117587-117679	GT	AAG
(GAG)	 AG	118031-118143	TG	AAT
-recovered pasa_asmbl_5430.p1, terminal, 118031, 118143
-recovered pasa_asmbl_5430.p1, internal, 117118, 117269
-recovered pasa_asmbl_5430.p1, internal, 117398, 117464
-recovered pasa_asmbl_5430.p1, internal, 117587, 117679
Valid prediction for snap_scaffold_11-snap.957-T1
Valid prediction for pasa_asmbl_5423.p1
Valid prediction for GeneMark_model.47401_t
Valid prediction for GeneMark_model.47413_t
Valid prediction for snap_scaffold_11-snap.972-T1
Valid prediction for snap_scaffold_11-snap.945-T1
Valid prediction for Augustus_model.g18318.t1
Valid prediction for GlimmerHMM_glimmerT_27462-T1
Valid prediction for GeneMark_model.47387_t
Valid prediction for GlimmerHMM_glimmerT_27452-T1
Valid prediction for snap_scaffold_11-snap.966-T1
Valid prediction for Augustus_model.g18314.t1
Valid prediction for snap_scaffold_11-snap.969-T1
Valid prediction for GlimmerHMM_glimmerT_27454-T1
Valid prediction for Augustus_model.g18307.t1
Valid prediction for GeneMark_model.47397_t
Valid prediction for snap_scaffold_11-snap.943-T1
Valid prediction for GlimmerHMM_glimmerT_27453-T1
Valid prediction for HiQ_model.g18313.t1
Valid prediction for snap_scaffold_11-snap.964-T1
Valid prediction for GlimmerHMM_glimmerT_27446-T1
Valid prediction for GeneMark_model.47391_t
Valid prediction for snap_scaffold_11-snap.938-T1
Valid prediction for GlimmerHMM_glimmerT_27458-T1
Valid prediction for GeneMark_model.47395_t
Valid prediction for snap_scaffold_11-snap.950-T1
Valid prediction for snap_scaffold_11-snap.951-T1
Valid prediction for GeneMark_model.47393_t
Valid prediction for Augustus_model.g18315.t1
Valid prediction for GeneMark_model.47399_t
Couldn't classify 95444, 95620
Sorry, prediction pasa_asmbl_5427.p1 fails validation.
(CAG)	 TG	95444-95620	GT	AGG
(GTC)	 AG	96814-96985	GT	AGG
(GTG)	 AG	98490-98644	AG	AGA
-recovered pasa_asmbl_5427.p1, terminal, 98490, 98644
-recovered pasa_asmbl_5427.p1, internal, 96814, 96985
Valid prediction for GlimmerHMM_glimmerT_27451-T1
Valid prediction for Augustus_model.g18316.t1
Valid prediction for snap_scaffold_11-snap.963-T1
Valid prediction for snap_scaffold_11-snap.953-T1
Valid prediction for GlimmerHMM_glimmerT_27460-T1
Valid prediction for GlimmerHMM_glimmerT_27465-T1
Valid prediction for GeneMark_model.47380_t
Valid prediction for GeneMark_model.47392_t
Valid prediction for GeneMark_model.47417_t
Valid prediction for GlimmerHMM_glimmerT_27461-T1
Valid prediction for snap_scaffold_11-snap.947-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GeneMark_model.47405_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.47390_t
Couldn't classify 15384, 15479
Sorry, prediction pasa_asmbl_7339.p1 fails validation.
(GAC)	 CA	15384-15479	GT	AGG
(TGC)	 AG	16154-16295	GT	TGG
(GTA)	 AG	16586-16769	GT	AGG
(AGA)	 AG	16897-17068	GC	GAG
-recovered pasa_asmbl_7339.p1, terminal, 16897, 17068
-recovered pasa_asmbl_7339.p1, internal, 16154, 16295
-recovered pasa_asmbl_7339.p1, internal, 16586, 16769
-recovered pasa_asmbl_7339.p1, internal, 16897, 17068
Valid prediction for GlimmerHMM_glimmerT_27467-T1
Valid prediction for snap_scaffold_11-snap.968-T1
Couldn't classify 136650, 137104
Sorry, prediction pasa_asmbl_6562.p1 fails validation.
(ATG)	 CC	136371-136503	GT	GGG
(AGG)	 AG	136650-137104	GA	TGG
-recovered pasa_asmbl_6562.p1, initial, 136371, 136503
Valid prediction for snap_scaffold_11-snap.962-T1
Valid prediction for snap_scaffold_11-snap.961-T1
Valid prediction for GeneMark_model.47398_t
Valid prediction for Augustus_model.g18309.t1
Valid prediction for Augustus_model.g18319.t1
Valid prediction for snap_scaffold_11-snap.942-T1
Valid prediction for GlimmerHMM_glimmerT_27447-T1
Valid prediction for HiQ_model.g18308.t1
Valid prediction for GeneMark_model.47412_t
Valid prediction for GeneMark_model.47414_t
Valid prediction for snap_scaffold_11-snap.952-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GeneMark_model.47396_t
Valid prediction for snap_scaffold_11-snap.948-T1
Valid prediction for GeneMark_model.47388_t
Valid prediction for snap_scaffold_11-snap.937-T1
Valid prediction for GlimmerHMM_glimmerT_27455-T1
Valid prediction for GlimmerHMM_glimmerT_27463-T1
Valid prediction for snap_scaffold_11-snap.941-T1
Valid prediction for snap_scaffold_11-snap.971-T1
Valid prediction for snap_scaffold_11-snap.965-T1
Valid prediction for CodingQuarry_transcript_7998-T1
Couldn't classify 22801, 22845
Sorry, prediction pasa_asmbl_6564.p1 fails validation.
(GCA)	 TA	22801-22845	GT	AGG
(GCA)	 AG	23038-23181	GT	CGG
(GAC)	 AG	23314-23623	GT	AAG
(GTT)	 AG	23967-24088	GT	AGG
(TAC)	 AG	24294-24329	AA	AAA
-recovered pasa_asmbl_6564.p1, terminal, 24294, 24329
-recovered pasa_asmbl_6564.p1, internal, 23038, 23181
-recovered pasa_asmbl_6564.p1, internal, 23314, 23623
-recovered pasa_asmbl_6564.p1, internal, 23967, 24088
Valid prediction for GlimmerHMM_glimmerT_27448-T1
Valid prediction for snap_scaffold_11-snap.960-T1
Valid prediction for pasa_asmbl_6559.p1
Valid prediction for GlimmerHMM_glimmerT_27459-T1
Valid prediction for GeneMark_model.47383_t
Valid prediction for GeneMark_model.47378_t
Valid prediction for snap_scaffold_11-snap.955-T1
Valid prediction for GeneMark_model.47394_t
Valid prediction for GlimmerHMM_glimmerT_27464-T1
Valid prediction for snap_scaffold_11-snap.940-T1
Valid prediction for GeneMark_model.47404_t
Valid prediction for snap_scaffold_11-snap.967-T1
Valid prediction for snap_scaffold_11-snap.944-T1
Valid prediction for GeneMark_model.47406_t
Valid prediction for snap_scaffold_11-snap.959-T1
Valid prediction for HiQ_model.g18320.t1
Valid prediction for snap_scaffold_11-snap.974-T1
Couldn't classify 137261, 137286
Sorry, prediction pasa_asmbl_6561.p1 fails validation.
(ACA)	 TC	137261-137286	GT	CAG
(AAT)	 AG	137505-137616	GT	AGG
(GAG)	 AG	138180-138302	GT	CGG
(TGC)	 AG	138398-138492	GT	AGG
(CTT)	 AG	138619-138726	GT	AGG
(GGT)	 AG	138936-139062	GT	AGG
(CCA)	 AG	139189-139311	GT	AGG
(GAG)	 AG	139392-139547	GT	AGG
(GGC)	 AG	139790-139911	GT	AGG
(TGA)	 AG	140086-140233	GA	GAG
-recovered pasa_asmbl_6561.p1, terminal, 140086, 140233
-recovered pasa_asmbl_6561.p1, internal, 137505, 137616
-recovered pasa_asmbl_6561.p1, internal, 138180, 138302
-recovered pasa_asmbl_6561.p1, internal, 138398, 138492
-recovered pasa_asmbl_6561.p1, internal, 138619, 138726
-recovered pasa_asmbl_6561.p1, internal, 138936, 139062
-recovered pasa_asmbl_6561.p1, internal, 139189, 139311
-recovered pasa_asmbl_6561.p1, internal, 139392, 139547
-recovered pasa_asmbl_6561.p1, internal, 139790, 139911
Valid prediction for Augustus_model.g18312.t1
Valid prediction for snap_scaffold_11-snap.973-T1
Valid prediction for GlimmerHMM_glimmerT_27445-T1
Valid prediction for GeneMark_model.47386_t
Valid prediction for CodingQuarry_transcript_7997-T1
Valid prediction for GlimmerHMM_glimmerT_27456-T1
Valid prediction for GeneMark_model.47416_t
Valid prediction for Augustus_model.g18311.t1
Valid prediction for snap_scaffold_11-snap.946-T1
Valid prediction for GeneMark_model.47400_t
Valid prediction for snap_scaffold_11-snap.949-T1
Valid prediction for GlimmerHMM_glimmerT_27457-T1
Valid prediction for CodingQuarry_transcript_7996-T1
Valid prediction for snap_scaffold_11-snap.958-T1
Valid prediction for GlimmerHMM_glimmerT_27468-T1
Valid prediction for snap_scaffold_11-snap.956-T1
Valid prediction for snap_scaffold_11-snap.939-T1
Valid prediction for GlimmerHMM_glimmerT_27450-T1
Valid prediction for HiQ_model.g18306.t1
Valid prediction for GeneMark_model.47409_t
Valid prediction for GeneMark_model.47415_t
Valid prediction for GlimmerHMM_glimmerT_27466-T1
Valid prediction for GeneMark_model.47407_t
Valid prediction for GeneMark_model.47402_t
Valid prediction for GeneMark_model.47385_t
Valid prediction for Augustus_model.g18322.t1
Valid prediction for GeneMark_model.47410_t
Valid prediction for GeneMark_model.47389_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 35884, rend_intergenic: 34540  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40093, rend_intergenic: 37570  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52713, rend_intergenic: 46801  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58909, rend_intergenic: 52807  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79577, rend_intergenic: 75039  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94687, rend_intergenic: 84224  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105810, rend_intergenic: 95473  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108954, rend_intergenic: 106937  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119255, rend_intergenic: 117126  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123385, rend_intergenic: 119844  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128828, rend_intergenic: 127582  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140958, rend_intergenic: 136589  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 132980, rend_intergenic: 132977  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 153586
-exon list size: 674


building trellis

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91.0    
91.1    
91.3    
91.4    
91.6    
91.7    
91.9    
92.0    
92.2    
92.3    
92.5    
92.6    
92.8    
92.9    
93.0    
93.2    
93.3    
93.5    
93.6    
93.8    
93.9    
94.1    
94.2    
94.4    
94.5    
94.7    
94.8    
95.0    
95.1    
95.3    
95.4    
95.6    
95.7    
95.9    
96.0    
96.2    
96.3    
96.4    
96.6    
96.7    
96.9    
97.0    
97.2    
97.3    
97.5    
97.6    
97.8    
97.9    
98.1    
98.2    
98.4    
98.5    
98.7    
98.8    
99.0    
99.1    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 39 predictions from path traversal
Error with prediction: snap lend_intergenic: 35884, rend_intergenic: 34540  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40093, rend_intergenic: 37570  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52713, rend_intergenic: 46801  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58909, rend_intergenic: 52807  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79577, rend_intergenic: 75039  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94687, rend_intergenic: 84224  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105810, rend_intergenic: 95473  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108954, rend_intergenic: 106937  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119255, rend_intergenic: 117126  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123385, rend_intergenic: 119844  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128828, rend_intergenic: 127582  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140958, rend_intergenic: 136589  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 132980, rend_intergenic: 132977  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