-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_16/scaffold_16_6987297-7199664

-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: +)Couldn't classify 70219, 70259
Couldn't classify 70774, 70919
Sorry, prediction pasa_asmbl_17115.p3 fails validation.
(AAC)	 TC	70219-70259	GT	AGG
(AGC)	 AG	70379-70527	GT	CGG
(GCG)	 AG	70774-70919	AA	AGA
-recovered pasa_asmbl_17115.p3, internal, 70379, 70527
Valid prediction for GeneMark_model.67354_t
Valid prediction for snap_scaffold_16-snap.1322-T1
Valid prediction for Augustus_model.g26434.t1
Valid prediction for Augustus_model.g26444.t1
Valid prediction for GeneMark_model.67346_t
Valid prediction for GeneMark_model.67345_t
Valid prediction for GeneMark_model.67347_t
Valid prediction for snap_scaffold_16-snap.1308-T1
Valid prediction for snap_scaffold_16-snap.1319-T1
Valid prediction for snap_scaffold_16-snap.1301-T1
Valid prediction for GeneMark_model.67353_t
Valid prediction for GeneMark_model.67362_t
Valid prediction for Augustus_model.g26446.t1
Valid prediction for snap_scaffold_16-snap.1325-T1
Valid prediction for snap_scaffold_16-snap.1296-T1
Valid prediction for GlimmerHMM_glimmerT_39368-T1
Valid prediction for Augustus_model.g26441.t1
Valid prediction for Augustus_model.g26438.t1
Valid prediction for GlimmerHMM_glimmerT_39357-T1
Valid prediction for GlimmerHMM_glimmerT_39361-T1
Valid prediction for GeneMark_model.67382_t
Valid prediction for GeneMark_model.67389_t
Valid prediction for snap_scaffold_16-snap.1316-T1
Valid prediction for pasa_asmbl_17122.p1
Valid prediction for GeneMark_model.67350_t
Valid prediction for pasa_asmbl_17113.p1
Valid prediction for snap_scaffold_16-snap.1303-T1
Valid prediction for GlimmerHMM_glimmerT_39348-T1
Valid prediction for GeneMark_model.67364_t
Valid prediction for GeneMark_model.67366_t
Valid prediction for Augustus_model.g26440.t1
Valid prediction for GlimmerHMM_glimmerT_39345-T1
Valid prediction for GlimmerHMM_glimmerT_39367-T1
Couldn't classify 82678, 83010
Sorry, prediction pasa_asmbl_17118.p1 fails validation.
(CAC)	 AC	82678-83010	CC	CCC
Valid prediction for snap_scaffold_16-snap.1310-T1
Valid prediction for GeneMark_model.67373_t
Valid prediction for GeneMark_model.67368_t
Valid prediction for snap_scaffold_16-snap.1321-T1
Valid prediction for snap_scaffold_16-snap.1298-T1
Valid prediction for GeneMark_model.67356_t
Valid prediction for snap_scaffold_16-snap.1300-T1
Valid prediction for GlimmerHMM_glimmerT_39347-T1
Couldn't classify 40465, 40503
Sorry, prediction pasa_asmbl_17112.p1 fails validation.
(CCG)	 TA	40465-40503	GT	CGG
(GAG)	 AG	41860-42019	GT	GCG
(CTT)	 AG	42668-42813	GT	AGG
(GCG)	 AG	43112-43318	GT	AGG
(AAC)	 AG	43467-43615	GT	AGG
(GAA)	 AG	44421-44574	GT	AGG
(CCG)	 AG	45173-45331	GT	AGG
(GTC)	 AG	45507-45596	GT	CTG
(TCT)	 AG	45836-45984	GT	AGG
(GGT)	 AG	46445-46869	GT	CGG
(TTT)	 AG	49501-49625	GT	AGG
(ATC)	 AG	49756-49897	GT	AGG
(GTG)	 AG	50097-50421	GT	AGG
(GGA)	 AG	50633-50705	TG	AGT
-recovered pasa_asmbl_17112.p1, terminal, 50633, 50705
-recovered pasa_asmbl_17112.p1, internal, 41860, 42019
-recovered pasa_asmbl_17112.p1, internal, 42668, 42813
-recovered pasa_asmbl_17112.p1, internal, 43112, 43318
-recovered pasa_asmbl_17112.p1, internal, 43467, 43615
-recovered pasa_asmbl_17112.p1, internal, 44421, 44574
-recovered pasa_asmbl_17112.p1, internal, 45173, 45331
-recovered pasa_asmbl_17112.p1, internal, 45507, 45596
-recovered pasa_asmbl_17112.p1, internal, 45836, 45984
-recovered pasa_asmbl_17112.p1, internal, 46445, 46869
-recovered pasa_asmbl_17112.p1, internal, 49501, 49625
-recovered pasa_asmbl_17112.p1, internal, 49756, 49897
-recovered pasa_asmbl_17112.p1, internal, 50097, 50421
Couldn't classify 71150, 71218
Couldn't classify 74787, 74882
Sorry, prediction pasa_asmbl_17116.p1 fails validation.
(GAT)	 AG	71150-71218	GT	AGG
(CTG)	 AG	71522-71728	GT	CGG
(AGC)	 AG	71883-72026	GT	AGG
(CAA)	 AG	72230-72418	GT	AGG
(CAC)	 AG	72619-72736	GT	GGG
(AGA)	 AG	72977-73032	GT	AAG
(GAT)	 AG	73176-73285	GT	GAG
(TCT)	 AG	73515-73616	GT	ACG
(GGT)	 AG	73710-73770	GT	TGG
(GCC)	 AG	73862-73933	GT	AGG
(AGT)	 AG	74787-74882	CA	TCC
-recovered pasa_asmbl_17116.p1, internal, 71150, 71218
-recovered pasa_asmbl_17116.p1, internal, 71522, 71728
-recovered pasa_asmbl_17116.p1, internal, 71883, 72026
-recovered pasa_asmbl_17116.p1, internal, 72230, 72418
-recovered pasa_asmbl_17116.p1, internal, 72619, 72736
-recovered pasa_asmbl_17116.p1, internal, 72977, 73032
-recovered pasa_asmbl_17116.p1, internal, 73176, 73285
-recovered pasa_asmbl_17116.p1, internal, 73515, 73616
-recovered pasa_asmbl_17116.p1, internal, 73710, 73770
-recovered pasa_asmbl_17116.p1, internal, 73862, 73933
Valid prediction for Augustus_model.g26437.t1
Valid prediction for snap_scaffold_16-snap.1320-T1
Valid prediction for snap_scaffold_16-snap.1297-T1
Valid prediction for GlimmerHMM_glimmerT_39360-T1
Valid prediction for GeneMark_model.67378_t
Valid prediction for snap_scaffold_16-snap.1304-T1
Valid prediction for GeneMark_model.67371_t
Valid prediction for GlimmerHMM_glimmerT_39344-T1
Valid prediction for Augustus_model.g26436.t1
Valid prediction for snap_scaffold_16-snap.1314-T1
Couldn't classify 204789, 205381
Couldn't classify 205642, 205735
Sorry, prediction pasa_asmbl_17125.p1 fails validation.
(GTT)	 GG	204789-205381	GT	AGG
(AGA)	 AG	205642-205735	CC	CCC
Valid prediction for Augustus_model.g26439.t1
Valid prediction for GlimmerHMM_glimmerT_39349-T1
Valid prediction for GeneMark_model.67360_t
Valid prediction for GlimmerHMM_glimmerT_39353-T1
Valid prediction for GeneMark_model.67376_t
Valid prediction for snap_scaffold_16-snap.1295-T1
Valid prediction for Augustus_model.g26433.t1
Valid prediction for GeneMark_model.67380_t
Valid prediction for GeneMark_model.67390_t
Valid prediction for snap_scaffold_16-snap.1317-T1
Valid prediction for GeneMark_model.67348_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 GlimmerHMM_glimmerT_39356-T1
Valid prediction for GlimmerHMM_glimmerT_39366-T1
Valid prediction for GeneMark_model.67387_t
Valid prediction for snap_scaffold_16-snap.1307-T1
Valid prediction for snap_scaffold_16-snap.1318-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_39362-T1
Valid prediction for snap_scaffold_16-snap.1311-T1
Valid prediction for GeneMark_model.67381_t
Valid prediction for GlimmerHMM_glimmerT_39352-T1
Valid prediction for GeneMark_model.67391_t
Valid prediction for GlimmerHMM_glimmerT_39369-T1
Valid prediction for GlimmerHMM_glimmerT_39350-T1
Valid prediction for GeneMark_model.67383_t
Valid prediction for GlimmerHMM_glimmerT_39346-T1
Valid prediction for Augustus_model.g26443.t1
Valid prediction for GeneMark_model.67357_t
Valid prediction for GlimmerHMM_glimmerT_39355-T1
Valid prediction for Augustus_model.g26435.t1
Valid prediction for Augustus_model.g26445.t1
Valid prediction for snap_scaffold_16-snap.1299-T1
Valid prediction for GlimmerHMM_glimmerT_39365-T1
Valid prediction for GeneMark_model.67384_t
Valid prediction for snap_scaffold_16-snap.1326-T1
Valid prediction for snap_scaffold_16-snap.1315-T1
Valid prediction for GlimmerHMM_glimmerT_39358-T1
Valid prediction for Augustus_model.g26447.t1
Valid prediction for GeneMark_model.67374_t
Couldn't classify 79959, 80342
Couldn't classify 83140, 83570
Sorry, prediction pasa_asmbl_16342.p1 fails validation.
(GAC)	 TG	79959-80342	GT	AGG
(GAG)	 AG	81773-81953	GT	AGG
(GGA)	 AG	83140-83570	AA	TGA
-recovered pasa_asmbl_16342.p1, internal, 81773, 81953
Valid prediction for GeneMark_model.67369_t
Valid prediction for GeneMark_model.67388_t
Couldn't classify 83664, 83966
Sorry, prediction pasa_asmbl_16339.p1 fails validation.
(GGG)	 AG	83664-83966	GT	AGG
(GTA)	 AG	84102-84407	AC	GAA
-recovered pasa_asmbl_16339.p1, terminal, 84102, 84407
-recovered pasa_asmbl_16339.p1, internal, 83664, 83966
Valid prediction for GeneMark_model.67351_t
Valid prediction for GeneMark_model.67372_t
Valid prediction for GeneMark_model.67363_t
Valid prediction for GlimmerHMM_glimmerT_39363-T1
Valid prediction for GeneMark_model.67355_t
Valid prediction for snap_scaffold_16-snap.1305-T1
Valid prediction for GeneMark_model.67379_t
Valid prediction for GeneMark_model.67377_t
Valid prediction for GlimmerHMM_glimmerT_39351-T1
Valid prediction for snap_scaffold_16-snap.1324-T1
Valid prediction for GeneMark_model.67367_t
Valid prediction for snap_scaffold_16-snap.1323-T1
Valid prediction for GeneMark_model.67349_t
Valid prediction for snap_scaffold_16-snap.1306-T1
Valid prediction for snap_scaffold_16-snap.1312-T1
Valid prediction for Augustus_model.g26442.t1
Valid prediction for GlimmerHMM_glimmerT_39354-T1
Valid prediction for snap_scaffold_16-snap.1309-T1
Valid prediction for GlimmerHMM_glimmerT_39364-T1
Valid prediction for GeneMark_model.67375_t
Valid prediction for GeneMark_model.67370_t
Valid prediction for GeneMark_model.67365_t
Valid prediction for GlimmerHMM_glimmerT_39359-T1
Valid prediction for GeneMark_model.67386_t
Valid prediction for snap_scaffold_16-snap.1313-T1
Valid prediction for snap_scaffold_16-snap.1302-T1
Valid prediction for GeneMark_model.67359_t
Valid prediction for snap_scaffold_16-snap.1327-T1
Valid prediction for GeneMark_model.67385_t
Valid prediction for GeneMark_model.67358_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 72852, rend_intergenic: 72346  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74313, rend_intergenic: 72991  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97641, rend_intergenic: 84406  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104500, rend_intergenic: 99537  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113976, rend_intergenic: 109849  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125714, rend_intergenic: 120799  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142351, rend_intergenic: 138302  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153408, rend_intergenic: 147220  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159559, rend_intergenic: 153565  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160962, rend_intergenic: 159676  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195859, rend_intergenic: 193464  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 206266, rend_intergenic: 196000  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 212368
-exon list size: 587


building trellis

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99.8    
-found 32 predictions from path traversal
Error with prediction: snap lend_intergenic: 72852, rend_intergenic: 72346  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74313, rend_intergenic: 72991  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97641, rend_intergenic: 84406  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104500, rend_intergenic: 99537  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113976, rend_intergenic: 109849  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125714, rend_intergenic: 120799  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142351, rend_intergenic: 138302  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153408, rend_intergenic: 147220  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159559, rend_intergenic: 153565  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160962, rend_intergenic: 159676  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195859, rend_intergenic: 193464  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 206266, rend_intergenic: 196000  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 24448
-exon list size: 10


building trellis

8.3    
16.7    
25.0    
33.3    
41.7    
50.0    
58.3    
66.7    
75.0    
83.3    
91.7    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 19099
-exon list size: 6


building trellis

12.5    
25.0    
37.5    
50.0    
62.5    
75.0    
87.5    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 13932
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 10360
-exon list size: 1


building trellis

33.3    
66.7    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support