-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_11/scaffold_11_2958445-3116840

-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.47151_t
Valid prediction for GeneMark_model.47154_t
Valid prediction for snap_scaffold_11-snap.761-T1
Valid prediction for Augustus_model.g18215.t1
Valid prediction for Augustus_model.g18225.t1
Couldn't classify 153656, 153874
Couldn't classify 156335, 156466
Sorry, prediction pasa_asmbl_5364.p1 fails validation.
(ACT)	 AC	153656-153874	GT	AGG
(TTG)	 AG	154096-154191	GT	AGG
(ACA)	 AG	154388-154552	GT	AGG
(GCC)	 AG	155031-155125	GT	GGG
(TGC)	 AG	155781-155847	GT	AGG
(AGC)	 AG	155983-156020	GT	AGG
(ATT)	 AG	156112-156244	GT	AGG
(GAA)	 AG	156335-156466	GT	AGG
-recovered pasa_asmbl_5364.p1, internal, 154096, 154191
-recovered pasa_asmbl_5364.p1, internal, 154388, 154552
-recovered pasa_asmbl_5364.p1, internal, 155031, 155125
-recovered pasa_asmbl_5364.p1, internal, 155781, 155847
-recovered pasa_asmbl_5364.p1, internal, 155983, 156020
-recovered pasa_asmbl_5364.p1, internal, 156112, 156244
-recovered pasa_asmbl_5364.p1, internal, 156335, 156466
Valid prediction for GeneMark_model.47150_t
Valid prediction for HiQ_model.g18219.t1
Valid prediction for GeneMark_model.47167_t
Valid prediction for GeneMark_model.47169_t
Valid prediction for GeneMark_model.47171_t
Valid prediction for GeneMark_model.47181_t
Valid prediction for GlimmerHMM_glimmerT_27309-T1
Valid prediction for Augustus_model.g18214.t1
Valid prediction for GeneMark_model.47163_t
Valid prediction for GeneMark_model.47165_t
Couldn't classify 63116, 63180
Sorry, prediction pasa_asmbl_5357.p1 fails validation.
(CCA)	 CC	63116-63180	GT	GTG
(GCT)	 AG	64547-64619	GT	ATG
(GTG)	 AG	64757-64833	GT	TGG
(GAT)	 AG	64926-65046	GT	AGG
(GAC)	 AG	65466-65579	GT	AGG
(AGT)	 AG	65848-66016	GT	GGG
(CCT)	 AG	68002-68012	AA	AGA
-recovered pasa_asmbl_5357.p1, terminal, 68002, 68012
-recovered pasa_asmbl_5357.p1, internal, 64547, 64619
-recovered pasa_asmbl_5357.p1, internal, 64757, 64833
-recovered pasa_asmbl_5357.p1, internal, 64926, 65046
-recovered pasa_asmbl_5357.p1, internal, 65466, 65579
-recovered pasa_asmbl_5357.p1, internal, 65848, 66016
Valid prediction for GlimmerHMM_glimmerT_27299-T1
Valid prediction for GlimmerHMM_glimmerT_27319-T1
Valid prediction for Augustus_model.g18227.t1
Valid prediction for GlimmerHMM_glimmerT_27298-T1
Valid prediction for GeneMark_model.47193_t
Valid prediction for GeneMark_model.47186_t
Valid prediction for snap_scaffold_11-snap.759-T1
Valid prediction for GeneMark_model.47146_t
Valid prediction for GlimmerHMM_glimmerT_27304-T1
Valid prediction for GlimmerHMM_glimmerT_27314-T1
Valid prediction for GlimmerHMM_glimmerT_27307-T1
Valid prediction for GlimmerHMM_glimmerT_27292-T1
Valid prediction for GeneMark_model.47153_t
Valid prediction for CodingQuarry_transcript_7976-T1
Valid prediction for GlimmerHMM_glimmerT_27311-T1
Valid prediction for Augustus_model.g18220.t1
Valid prediction for GeneMark_model.47190_t
Valid prediction for GlimmerHMM_glimmerT_27316-T1
Valid prediction for GeneMark_model.47160_t
Valid prediction for snap_scaffold_11-snap.782-T1
Valid prediction for GeneMark_model.47183_t
Valid prediction for GeneMark_model.47179_t
Valid prediction for Augustus_model.g18230.t1
Valid prediction for snap_scaffold_11-snap.780-T1
Valid prediction for snap_scaffold_11-snap.786-T1
Valid prediction for snap_scaffold_11-snap.762-T1
Couldn't classify 33626, 33674
Couldn't classify 39372, 39481
Sorry, prediction pasa_asmbl_5351.p1 fails validation.
(CCA)	 GT	33626-33674	GT	CAG
(TTT)	 AG	34051-34091	GT	AGG
(ATG)	 AG	34608-34773	GT	AGG
(ACA)	 AG	36956-37023	GT	CTG
(AGA)	 AG	37240-37402	GT	AGG
(GTT)	 AG	39372-39481	GC	CAG
-recovered pasa_asmbl_5351.p1, initial, 34608, 34773
-recovered pasa_asmbl_5351.p1, internal, 34051, 34091
-recovered pasa_asmbl_5351.p1, internal, 34608, 34773
-recovered pasa_asmbl_5351.p1, internal, 36956, 37023
-recovered pasa_asmbl_5351.p1, internal, 37240, 37402
-recovered pasa_asmbl_5351.p1, internal, 39372, 39481
Valid prediction for GeneMark_model.47176_t
Valid prediction for snap_scaffold_11-snap.765-T1
Valid prediction for snap_scaffold_11-snap.776-T1
Valid prediction for GlimmerHMM_glimmerT_27295-T1
Valid prediction for GeneMark_model.47188_t
Valid prediction for GlimmerHMM_glimmerT_27313-T1
Valid prediction for GlimmerHMM_glimmerT_27317-T1
Valid prediction for snap_scaffold_11-snap.781-T1
Valid prediction for Augustus_model.g18228.t1
Valid prediction for snap_scaffold_11-snap.775-T1
Valid prediction for snap_scaffold_11-snap.783-T1
Valid prediction for GeneMark_model.47156_t
Valid prediction for GeneMark_model.47178_t
Valid prediction for snap_scaffold_11-snap.757-T1
Valid prediction for CodingQuarry_transcript_7977-T1
Valid prediction for Augustus_model.g18216.t1
Valid prediction for snap_scaffold_11-snap.770-T1
Valid prediction for GlimmerHMM_glimmerT_27305-T1
Valid prediction for Augustus_model.g18223.t1
Valid prediction for GeneMark_model.47192_t
Valid prediction for GlimmerHMM_glimmerT_27315-T1
Valid prediction for pasa_asmbl_5353.p1
Valid prediction for snap_scaffold_11-snap.769-T1
Valid prediction for Augustus_model.g18226.t1
Valid prediction for snap_scaffold_11-snap.760-T1
Valid prediction for GlimmerHMM_glimmerT_27312-T1
Couldn't classify 133245, 133326
Couldn't classify 135531, 135595
Sorry, prediction pasa_asmbl_5360.p1 fails validation.
(GAC)	 CA	133245-133326	GT	AGG
(TCC)	 AG	134259-134543	GT	ACG
(AGC)	 AG	135531-135595	GG	GCG
-recovered pasa_asmbl_5360.p1, internal, 134259, 134543
Valid prediction for GeneMark_model.47173_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.47149_t
Couldn't classify 13669, 13797
Couldn't classify 14317, 14435
Sorry, prediction pasa_asmbl_7259.p1 fails validation.
(CGG)	 AA	13669-13797	GT	AGG
(GTT)	 AG	13912-14042	GT	CAG
(GAC)	 AG	14157-14197	GT	AGG
(ATG)	 AG	14317-14435	CC	CCC
-recovered pasa_asmbl_7259.p1, internal, 13912, 14042
-recovered pasa_asmbl_7259.p1, internal, 14157, 14197
Valid prediction for GeneMark_model.47175_t
Valid prediction for GlimmerHMM_glimmerT_27301-T1
Valid prediction for GeneMark_model.47152_t
Valid prediction for GlimmerHMM_glimmerT_27302-T1
Valid prediction for Augustus_model.g18229.t1
Valid prediction for GeneMark_model.47164_t
Valid prediction for GeneMark_model.47189_t
Valid prediction for snap_scaffold_11-snap.764-T1
Valid prediction for GeneMark_model.47174_t
Valid prediction for Augustus_model.g18222.t1
Valid prediction for GlimmerHMM_glimmerT_27297-T1
Valid prediction for snap_scaffold_11-snap.767-T1
Valid prediction for GeneMark_model.47184_t
Valid prediction for GeneMark_model.47148_t
Valid prediction for GlimmerHMM_glimmerT_27294-T1
Valid prediction for GeneMark_model.47177_t
Valid prediction for snap_scaffold_11-snap.778-T1
Valid prediction for GeneMark_model.47158_t
Valid prediction for snap_scaffold_11-snap.766-T1
Valid prediction for GeneMark_model.47147_t
Valid prediction for GeneMark_model.47172_t
Valid prediction for GeneMark_model.47191_t
Valid prediction for GeneMark_model.47161_t
Valid prediction for snap_scaffold_11-snap.773-T1
Valid prediction for GeneMark_model.47145_t
Valid prediction for GeneMark_model.47185_t
Valid prediction for GlimmerHMM_glimmerT_27293-T1
Valid prediction for snap_scaffold_11-snap.763-T1
Valid prediction for snap_scaffold_11-snap.784-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GeneMark_model.47166_t
Valid prediction for Augustus_model.g18217.t1
Couldn't classify 114604, 114654
Sorry, prediction pasa_asmbl_6497.p1 fails validation.
(GGG)	 CG	114604-114654	GT	AGG
(CTG)	 AG	114796-114902	GT	AGG
(GTA)	 AG	115084-115258	CA	AAC
-recovered pasa_asmbl_6497.p1, terminal, 115084, 115258
-recovered pasa_asmbl_6497.p1, internal, 114796, 114902
Valid prediction for GeneMark_model.47155_t
Valid prediction for Augustus_model.g18218.t1
Valid prediction for GlimmerHMM_glimmerT_27296-T1
Valid prediction for GlimmerHMM_glimmerT_27303-T1
Valid prediction for GlimmerHMM_glimmerT_27300-T1
Valid prediction for GeneMark_model.47159_t
Valid prediction for snap_scaffold_11-snap.785-T1
Valid prediction for GeneMark_model.47187_t
Valid prediction for GlimmerHMM_glimmerT_27308-T1
Couldn't classify 112892, 112945
Couldn't classify 113781, 114010
Sorry, prediction pasa_asmbl_6498.p1 fails validation.
(GGC)	 AC	112892-112945	GT	CGG
(GTG)	 AG	113056-113158	GT	TGG
(AGA)	 AG	113423-113572	GT	TGG
(GAG)	 AG	113781-114010	TG	GGT
-recovered pasa_asmbl_6498.p1, internal, 113056, 113158
-recovered pasa_asmbl_6498.p1, internal, 113423, 113572
Valid prediction for CodingQuarry_transcript_7978-T1
Valid prediction for HiQ_model.g18221.t1
Valid prediction for GeneMark_model.47157_t
Valid prediction for GeneMark_model.47170_t
Valid prediction for snap_scaffold_11-snap.774-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_11-snap.768-T1
Valid prediction for Augustus_model.g18224.t1
Valid prediction for GlimmerHMM_glimmerT_27306-T1
Couldn't classify 14745, 15053
Sorry, prediction pasa_asmbl_6503.p1 fails validation.
(TGC)	 CC	14745-15053	CC	CCC
Valid prediction for GeneMark_model.47182_t
Valid prediction for GeneMark_model.47168_t
Valid prediction for snap_scaffold_11-snap.787-T1
Valid prediction for snap_scaffold_11-snap.779-T1
Valid prediction for snap_scaffold_11-snap.772-T1
Valid prediction for snap_scaffold_11-snap.777-T1
Couldn't classify 84684, 84822
Sorry, prediction pasa_asmbl_6501.p1 fails validation.
(ATC)	 AG	84684-84822	GT	AGG
(GCA)	 AG	85017-85129	GT	CTG
(AGT)	 AG	85350-85506	GT	AGG
(TGG)	 AG	85989-86146	AC	GAA
-recovered pasa_asmbl_6501.p1, terminal, 85989, 86146
-recovered pasa_asmbl_6501.p1, internal, 84684, 84822
-recovered pasa_asmbl_6501.p1, internal, 85017, 85129
-recovered pasa_asmbl_6501.p1, internal, 85350, 85506
Valid prediction for snap_scaffold_11-snap.756-T1
Valid prediction for GeneMark_model.47180_t
Valid prediction for GlimmerHMM_glimmerT_27310-T1
Valid prediction for snap_scaffold_11-snap.758-T1
Valid prediction for snap_scaffold_11-snap.771-T1
Valid prediction for GeneMark_model.47162_t
Valid prediction for GlimmerHMM_glimmerT_27318-T1
Valid prediction for pasa_asmbl_6502.p1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 16490, rend_intergenic: 15161  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28545, rend_intergenic: 16492  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34310, rend_intergenic: 31254  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36968, rend_intergenic: 34608  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103305, rend_intergenic: 90825  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111566, rend_intergenic: 106524  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137080, rend_intergenic: 133242  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156877, rend_intergenic: 149320  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 158396
-exon list size: 717


building trellis

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78.9    
79.0    
79.1    
79.3    
79.4    
79.6    
79.7    
79.8    
80.0    
80.1    
80.3    
80.4    
80.5    
80.7    
80.8    
80.9    
81.1    
81.2    
81.4    
81.5    
81.6    
81.8    
81.9    
82.1    
82.2    
82.3    
82.5    
82.6    
82.8    
82.9    
83.0    
83.2    
83.3    
83.4    
83.6    
83.7    
83.9    
84.0    
84.1    
84.3    
84.4    
84.6    
84.7    
84.8    
85.0    
85.1    
85.3    
85.4    
85.5    
85.7    
85.8    
86.0    
86.1    
86.2    
86.4    
86.5    
86.6    
86.8    
86.9    
87.1    
87.2    
87.3    
87.5    
87.6    
87.8    
87.9    
88.0    
88.2    
88.3    
88.5    
88.6    
88.7    
88.9    
89.0    
89.2    
89.3    
89.4    
89.6    
89.7    
89.8    
90.0    
90.1    
90.3    
90.4    
90.5    
90.7    
90.8    
91.0    
91.1    
91.2    
91.4    
91.5    
91.7    
91.8    
91.9    
92.1    
92.2    
92.4    
92.5    
92.6    
92.8    
92.9    
93.0    
93.2    
93.3    
93.5    
93.6    
93.7    
93.9    
94.0    
94.2    
94.3    
94.4    
94.6    
94.7    
94.9    
95.0    
95.1    
95.3    
95.4    
95.5    
95.7    
95.8    
96.0    
96.1    
96.2    
96.4    
96.5    
96.7    
96.8    
96.9    
97.1    
97.2    
97.4    
97.5    
97.6    
97.8    
97.9    
98.1    
98.2    
98.3    
98.5    
98.6    
98.7    
98.9    
99.0    
99.2    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 16490, rend_intergenic: 15161  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28545, rend_intergenic: 16492  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34310, rend_intergenic: 31254  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36968, rend_intergenic: 34608  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103305, rend_intergenic: 90825  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111566, rend_intergenic: 106524  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137080, rend_intergenic: 133242  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156877, rend_intergenic: 149320  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