-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_17/scaffold_17_587706-764331

-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_17-snap.105-T1
Valid prediction for GeneMark_model.69763_t
Couldn't classify 171992, 172645
Sorry, prediction pasa_asmbl_17698.p1 fails validation.
(TCA)	 CC	171992-172645	AC	GGA
Valid prediction for pasa_asmbl_17693.p1
Valid prediction for CodingQuarry_transcript_21785-T1
Valid prediction for Augustus_model.g27145.t1
Valid prediction for Augustus_model.g27148.t1
Valid prediction for GeneMark_model.69773_t
Valid prediction for snap_scaffold_17-snap.112-T1
Valid prediction for GlimmerHMM_glimmerT_40524-T1
Valid prediction for CodingQuarry_transcript_21789-T1
Valid prediction for Augustus_model.g27140.t1
Valid prediction for Augustus_model.g27134.t1
Valid prediction for Augustus_model.g27153.t1
Valid prediction for GlimmerHMM_glimmerT_40531-T1
Valid prediction for snap_scaffold_17-snap.107-T1
Valid prediction for GlimmerHMM_glimmerT_40525-T1
Valid prediction for Augustus_model.g27150.t1
Valid prediction for GlimmerHMM_glimmerT_40526-T1
Valid prediction for GeneMark_model.69772_t
Valid prediction for GlimmerHMM_glimmerT_40532-T1
Valid prediction for GeneMark_model.69748_t
Valid prediction for pasa_asmbl_17682.p1
Valid prediction for HiQ_model.g27143.t1
Valid prediction for GeneMark_model.69759_t
Couldn't classify 164523, 164638
Sorry, prediction pasa_asmbl_17695.p1 fails validation.
(ATG)	 CC	161300-161714	GT	AGG
(GTG)	 AG	163439-164236	GT	CGG
(CTA)	 AG	164523-164638	GT	AGG
-recovered pasa_asmbl_17695.p1, initial, 161300, 161714
-recovered pasa_asmbl_17695.p1, internal, 163439, 164236
-recovered pasa_asmbl_17695.p1, internal, 164523, 164638
Valid prediction for snap_scaffold_17-snap.137-T1
Couldn't classify 87685, 87810
Sorry, prediction pasa_asmbl_17685.p1 fails validation.
(GTG)	 GT	87685-87810	GT	AGG
(GTT)	 AG	88442-88549	GT	TGG
(GAG)	 AG	88706-88771	GT	AGG
(GAG)	 AG	89004-89115	GT	GGG
(CTC)	 AG	89703-89821	GT	AGG
(GGG)	 AG	89988-90134	CC	AGC
-recovered pasa_asmbl_17685.p1, terminal, 89988, 90134
-recovered pasa_asmbl_17685.p1, internal, 88442, 88549
-recovered pasa_asmbl_17685.p1, internal, 88706, 88771
-recovered pasa_asmbl_17685.p1, internal, 89004, 89115
-recovered pasa_asmbl_17685.p1, internal, 89703, 89821
Valid prediction for snap_scaffold_17-snap.118-T1
Couldn't classify 169393, 169528
Sorry, prediction pasa_asmbl_17696.p1 fails validation.
(GTT)	 AG	169393-169528	GT	ACG
(TCA)	 AG	169653-169999	CA	GAC
-recovered pasa_asmbl_17696.p1, terminal, 169653, 169999
-recovered pasa_asmbl_17696.p1, internal, 169393, 169528
Valid prediction for GeneMark_model.69788_t
Valid prediction for snap_scaffold_17-snap.136-T1
Valid prediction for snap_scaffold_17-snap.106-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GeneMark_model.69749_t
Valid prediction for snap_scaffold_17-snap.122-T1
Valid prediction for GeneMark_model.69781_t
Couldn't classify 170819, 171880
Sorry, prediction pasa_asmbl_17697.p1 fails validation.
(ATG)	 CC	170819-171880	CC	CCC
Valid prediction for GeneMark_model.69778_t
Valid prediction for snap_scaffold_17-snap.132-T1
Valid prediction for GeneMark_model.69752_t
Valid prediction for snap_scaffold_17-snap.140-T1
Valid prediction for snap_scaffold_17-snap.135-T1
Valid prediction for snap_scaffold_17-snap.114-T1
Valid prediction for snap_scaffold_17-snap.124-T1
Valid prediction for GeneMark_model.69754_t
Valid prediction for snap_scaffold_17-snap.134-T1
Valid prediction for GeneMark_model.69784_t
Valid prediction for GlimmerHMM_glimmerT_40517-T1
Valid prediction for snap_scaffold_17-snap.120-T1
Valid prediction for GeneMark_model.69779_t
Valid prediction for GeneMark_model.69787_t
Valid prediction for GlimmerHMM_glimmerT_40529-T1
Valid prediction for GlimmerHMM_glimmerT_40519-T1
Couldn't classify 96164, 96257
Sorry, prediction pasa_asmbl_17686.p1 fails validation.
(CTT)	 CT	96164-96257	GT	GTG
(GTG)	 AG	96433-96816	GT	CAG
(CCC)	 AG	97454-97552	GT	AGG
(GTG)	 AG	100532-100584	GT	AGG
(GAA)	 AG	100753-100884	TG	AAT
-recovered pasa_asmbl_17686.p1, terminal, 100753, 100884
-recovered pasa_asmbl_17686.p1, internal, 96433, 96816
-recovered pasa_asmbl_17686.p1, internal, 97454, 97552
-recovered pasa_asmbl_17686.p1, internal, 100532, 100584
Valid prediction for GeneMark_model.69776_t
Valid prediction for GlimmerHMM_glimmerT_40508-T1
Valid prediction for GlimmerHMM_glimmerT_40512-T1
Valid prediction for GlimmerHMM_glimmerT_40534-T1
Valid prediction for GeneMark_model.69768_t
Valid prediction for Augustus_model.g27149.t1
Valid prediction for snap_scaffold_17-snap.139-T1
Valid prediction for GeneMark_model.69765_t
Valid prediction for GeneMark_model.69774_t
Valid prediction for snap_scaffold_17-snap.141-T1
Valid prediction for snap_scaffold_17-snap.121-T1
Valid prediction for GeneMark_model.69767_t
Valid prediction for GeneMark_model.69786_t
Valid prediction for GeneMark_model.69760_t
Valid prediction for snap_scaffold_17-snap.133-T1
Valid prediction for HiQ_model.g27152.t1
Valid prediction for GeneMark_model.69783_t
Valid prediction for snap_scaffold_17-snap.142-T1
Valid prediction for GlimmerHMM_glimmerT_40518-T1
Couldn't classify 127836, 127862
Sorry, prediction pasa_asmbl_17692.p2 fails validation.
(ATG)	 CT	124323-124395	GT	GGG
(ATG)	 AG	125600-125679	GT	CGG
(TTT)	 AG	126264-126345	GT	AGG
(GGG)	 AG	126651-126710	GT	GTG
(TGT)	 AG	126878-126954	GT	AGG
(ATC)	 AG	127836-127862	AC	CCA
-recovered pasa_asmbl_17692.p2, initial, 124323, 124395
add_exon() Sorry, pasa_asmbl_17692.p2 125600-125679-initial-1 is invalid.
-recovered pasa_asmbl_17692.p2, initial, 125600, 125679
-recovered pasa_asmbl_17692.p2, internal, 125600, 125679
-recovered pasa_asmbl_17692.p2, internal, 126264, 126345
-recovered pasa_asmbl_17692.p2, internal, 126651, 126710
-recovered pasa_asmbl_17692.p2, internal, 126878, 126954
Valid prediction for snap_scaffold_17-snap.128-T1
Valid prediction for GlimmerHMM_glimmerT_40533-T1
Valid prediction for GlimmerHMM_glimmerT_40528-T1
Valid prediction for GeneMark_model.69750_t
Valid prediction for GlimmerHMM_glimmerT_40515-T1
Valid prediction for Augustus_model.g27142.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.69758_t
Valid prediction for snap_scaffold_17-snap.123-T1
Valid prediction for snap_scaffold_17-snap.110-T1
Valid prediction for pasa_asmbl_18679.p1
Valid prediction for GeneMark_model.69761_t
Valid prediction for pasa_asmbl_18676.p1
Valid prediction for snap_scaffold_17-snap.126-T1
Valid prediction for GlimmerHMM_glimmerT_40507-T1
Valid prediction for Augustus_model.g27136.t1
Valid prediction for GlimmerHMM_glimmerT_40513-T1
Valid prediction for CodingQuarry_transcript_21784-T1
Valid prediction for GeneMark_model.69782_t
Valid prediction for snap_scaffold_17-snap.125-T1
Valid prediction for snap_scaffold_17-snap.131-T1
Valid prediction for GeneMark_model.69751_t
Valid prediction for Augustus_model.g27146.t1
Valid prediction for snap_scaffold_17-snap.119-T1
Valid prediction for GeneMark_model.69766_t
Valid prediction for HiQ_model.g27137.t1
Valid prediction for GeneMark_model.69764_t
Valid prediction for GeneMark_model.69769_t
Valid prediction for snap_scaffold_17-snap.108-T1
Valid prediction for Augustus_model.g27147.t1
Valid prediction for GeneMark_model.69762_t
Valid prediction for Augustus_model.g27138.t1
Valid prediction for snap_scaffold_17-snap.104-T1
Valid prediction for GlimmerHMM_glimmerT_40511-T1
Valid prediction for pasa_asmbl_18678.p1
Valid prediction for Augustus_model.g27151.t1
Valid prediction for GeneMark_model.69757_t
Valid prediction for GlimmerHMM_glimmerT_40527-T1
Valid prediction for GeneMark_model.69771_t
Valid prediction for CodingQuarry_transcript_21788-T1
Valid prediction for snap_scaffold_17-snap.115-T1
Valid prediction for pasa_asmbl_18685.p1
Valid prediction for HiQ_model.g27135.t1
Valid prediction for GeneMark_model.69775_t
Valid prediction for snap_scaffold_17-snap.129-T1
Valid prediction for GeneMark_model.69756_t
Valid prediction for GlimmerHMM_glimmerT_40522-T1
Valid prediction for snap_scaffold_17-snap.127-T1
Valid prediction for snap_scaffold_17-snap.144-T1
Valid prediction for snap_scaffold_17-snap.130-T1
Valid prediction for GeneMark_model.69753_t
Valid prediction for HiQ_model.g27144.t1
Valid prediction for snap_scaffold_17-snap.116-T1
Valid prediction for GlimmerHMM_glimmerT_40520-T1
Valid prediction for GeneMark_model.69777_t
Valid prediction for GeneMark_model.69755_t
Valid prediction for snap_scaffold_17-snap.138-T1
Couldn't classify 146796, 146849
Couldn't classify 148354, 148383
Sorry, prediction pasa_asmbl_18677.p1 fails validation.
(ATA)	 TG	146796-146849	GT	AGG
(ATC)	 AG	146985-147086	GT	AGG
(AAA)	 AG	147181-147322	GT	AGG
(GCC)	 AG	147517-147717	GT	AGG
(GTG)	 AG	148066-148181	GT	AGG
(CGT)	 AG	148354-148383	AA	CCA
-recovered pasa_asmbl_18677.p1, internal, 146985, 147086
-recovered pasa_asmbl_18677.p1, internal, 147181, 147322
-recovered pasa_asmbl_18677.p1, internal, 147517, 147717
-recovered pasa_asmbl_18677.p1, internal, 148066, 148181
Valid prediction for GlimmerHMM_glimmerT_40521-T1
Valid prediction for HiQ_model.g27141.t1
Valid prediction for snap_scaffold_17-snap.113-T1
Valid prediction for GlimmerHMM_glimmerT_40510-T1
Valid prediction for snap_scaffold_17-snap.111-T1
Valid prediction for GeneMark_model.69785_t
Valid prediction for GlimmerHMM_glimmerT_40516-T1
Couldn't classify 154250, 154357
Sorry, prediction pasa_asmbl_18675.p1 fails validation.
(CCC)	 GT	154250-154357	GT	AGG
(ATC)	 AG	154860-155016	GT	CGG
(GTA)	 AG	155418-155597	GT	AGG
(TGG)	 AG	156385-156408	GT	ATG
(CTG)	 AG	156996-157156	GT	CGG
(CCC)	 AG	157366-157495	GT	AGG
(GCT)	 AG	157617-157749	GT	AGG
(AGT)	 AG	160433-160524	GT	AGG
(ATG)	 AG	160638-160743	GT	AGG
(GTT)	 AG	161426-161573	GG	AGG
add_exon() Sorry, pasa_asmbl_18675.p1 160638-160743-initial-1 is invalid.
-recovered pasa_asmbl_18675.p1, initial, 160638, 160743
-recovered pasa_asmbl_18675.p1, terminal, 161426, 161573
-recovered pasa_asmbl_18675.p1, internal, 154860, 155016
-recovered pasa_asmbl_18675.p1, internal, 155418, 155597
-recovered pasa_asmbl_18675.p1, internal, 156385, 156408
-recovered pasa_asmbl_18675.p1, internal, 156996, 157156
-recovered pasa_asmbl_18675.p1, internal, 157366, 157495
-recovered pasa_asmbl_18675.p1, internal, 157617, 157749
-recovered pasa_asmbl_18675.p1, internal, 160433, 160524
-recovered pasa_asmbl_18675.p1, internal, 160638, 160743
Valid prediction for GlimmerHMM_glimmerT_40514-T1
Valid prediction for GlimmerHMM_glimmerT_40523-T1
Valid prediction for GeneMark_model.69780_t
Valid prediction for snap_scaffold_17-snap.143-T1
Valid prediction for snap_scaffold_17-snap.109-T1
Valid prediction for snap_scaffold_17-snap.117-T1
Valid prediction for GlimmerHMM_glimmerT_40509-T1
Valid prediction for GlimmerHMM_glimmerT_40530-T1
Valid prediction for Augustus_model.g27139.t1
Valid prediction for CodingQuarry_transcript_21787-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 9480, rend_intergenic: 4979  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20412, rend_intergenic: 15054  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48458, rend_intergenic: 47700  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55663, rend_intergenic: 54146  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86247, rend_intergenic: 83445  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90134, rend_intergenic: 86802  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147462, rend_intergenic: 146843  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151546, rend_intergenic: 149016  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166532, rend_intergenic: 163358  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 15057, rend_intergenic: 15054  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 49741, rend_intergenic: 49738  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 176626
-exon list size: 525


building trellis

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92.4    
92.6    
92.8    
93.0    
93.2    
93.4    
93.5    
93.7    
93.9    
94.1    
94.3    
94.5    
94.7    
94.9    
95.1    
95.3    
95.4    
95.6    
95.8    
96.0    
96.2    
96.4    
96.6    
96.8    
97.0    
97.2    
97.3    
97.5    
97.7    
97.9    
98.1    
98.3    
98.5    
98.7    
98.9    
99.1    
99.2    
99.4    
99.6    
99.8    
-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 9480, rend_intergenic: 4979  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20412, rend_intergenic: 15054  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48458, rend_intergenic: 47700  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55663, rend_intergenic: 54146  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86247, rend_intergenic: 83445  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90134, rend_intergenic: 86802  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147462, rend_intergenic: 146843  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151546, rend_intergenic: 149016  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166532, rend_intergenic: 163358  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 15057, rend_intergenic: 15054  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 49741, rend_intergenic: 49738  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 23 predictions persist after filtering for low support