-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_25/scaffold_25_6709797-6868305

-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.97134_t
Valid prediction for GeneMark_model.97145_t
Valid prediction for GlimmerHMM_glimmerT_55686-T1
Valid prediction for snap_scaffold_25-snap.1466-T1
Valid prediction for Augustus_model.g37153.t1
Valid prediction for GeneMark_model.97123_t
Valid prediction for snap_scaffold_25-snap.1479-T1
Valid prediction for snap_scaffold_25-snap.1456-T1
Valid prediction for Augustus_model.g37162.t1
Valid prediction for GlimmerHMM_glimmerT_55689-T1
Valid prediction for GeneMark_model.97147_t
Valid prediction for Augustus_model.g37150.t1
Valid prediction for Augustus_model.g37154.t1
Valid prediction for snap_scaffold_25-snap.1452-T1
Valid prediction for pasa_asmbl_33647.p1
Valid prediction for snap_scaffold_25-snap.1465-T1
Valid prediction for GeneMark_model.97124_t
Valid prediction for GeneMark_model.97140_t
Valid prediction for snap_scaffold_25-snap.1467-T1
Couldn't classify 51984, 52077
Couldn't classify 54356, 54542
Sorry, prediction pasa_asmbl_33643.p2 fails validation.
(TTC)	 GG	51984-52077	GT	AGG
(AAA)	 AG	53416-53479	GT	AGG
(CCT)	 AG	54139-54234	GT	AGG
(GCT)	 AG	54356-54542	GT	TGG
-recovered pasa_asmbl_33643.p2, internal, 53416, 53479
-recovered pasa_asmbl_33643.p2, internal, 54139, 54234
-recovered pasa_asmbl_33643.p2, internal, 54356, 54542
Valid prediction for snap_scaffold_25-snap.1473-T1
Valid prediction for pasa_asmbl_33648.p1
Valid prediction for snap_scaffold_25-snap.1478-T1
Valid prediction for snap_scaffold_25-snap.1480-T1
Valid prediction for GlimmerHMM_glimmerT_55690-T1
Valid prediction for snap_scaffold_25-snap.1477-T1
Valid prediction for GlimmerHMM_glimmerT_55706-T1
Valid prediction for snap_scaffold_25-snap.1487-T1
Valid prediction for GeneMark_model.97151_t
Valid prediction for snap_scaffold_25-snap.1471-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_25-snap.1482-T1
Valid prediction for GlimmerHMM_glimmerT_55694-T1
Valid prediction for GeneMark_model.97157_t
Couldn't classify 32320, 32538
Couldn't classify 32680, 32775
Sorry, prediction pasa_asmbl_33636.p2 fails validation.
(GAG)	 CC	32320-32538	GT	AGG
(GAG)	 AG	32680-32775	GG	AAG
Valid prediction for snap_scaffold_25-snap.1469-T1
Valid prediction for GeneMark_model.97136_t
Valid prediction for snap_scaffold_25-snap.1474-T1
Valid prediction for snap_scaffold_25-snap.1449-T1
Valid prediction for GlimmerHMM_glimmerT_55692-T1
Valid prediction for CodingQuarry_transcript_38681-T1
Couldn't classify 29889, 30013
Couldn't classify 30814, 30835
Sorry, prediction pasa_asmbl_33932.p1 fails validation.
(GAC)	 AC	29889-30013	GT	AAG
(ATT)	 AG	30188-30302	GT	CAG
(GAT)	 AG	30487-30680	GT	TGG
(GTA)	 AG	30814-30835	GG	ACG
-recovered pasa_asmbl_33932.p1, internal, 30188, 30302
-recovered pasa_asmbl_33932.p1, internal, 30487, 30680
Valid prediction for Augustus_model.g37155.t1
Couldn't classify 59738, 59884
Sorry, prediction pasa_asmbl_33644.p3 fails validation.
(CGG)	 AG	59738-59884	GT	GGG
(AAT)	 AG	61543-61689	GT	AGG
(TCG)	 AG	64029-64133	TC	GAT
-recovered pasa_asmbl_33644.p3, terminal, 64029, 64133
-recovered pasa_asmbl_33644.p3, internal, 59738, 59884
-recovered pasa_asmbl_33644.p3, internal, 61543, 61689
Valid prediction for GeneMark_model.97127_t
Valid prediction for snap_scaffold_25-snap.1450-T1
Valid prediction for snap_scaffold_25-snap.1463-T1
Valid prediction for snap_scaffold_25-snap.1485-T1
Valid prediction for GeneMark_model.97155_t
Valid prediction for GlimmerHMM_glimmerT_55703-T1
Valid prediction for GlimmerHMM_glimmerT_55697-T1
Valid prediction for Augustus_model.g37149.t1
Valid prediction for GlimmerHMM_glimmerT_55693-T1
Valid prediction for snap_scaffold_25-snap.1460-T1
Valid prediction for GlimmerHMM_glimmerT_55684-T1
Valid prediction for Augustus_model.g37164.t1
Valid prediction for GlimmerHMM_glimmerT_55695-T1
Valid prediction for GlimmerHMM_glimmerT_55687-T1
Valid prediction for GeneMark_model.97146_t
Valid prediction for GeneMark_model.97129_t
Valid prediction for snap_scaffold_25-snap.1459-T1
Valid prediction for Augustus_model.g37152.t1
Valid prediction for snap_scaffold_25-snap.1470-T1
Valid prediction for GeneMark_model.97130_t
Valid prediction for GeneMark_model.97153_t
Valid prediction for Augustus_model.g37159.t1
Valid prediction for GlimmerHMM_glimmerT_55702-T1
Valid prediction for GlimmerHMM_glimmerT_55699-T1
Valid prediction for GeneMark_model.97142_t
Valid prediction for GlimmerHMM_glimmerT_55688-T1
Couldn't classify 35850, 35951
Sorry, prediction pasa_asmbl_33881.p1 fails validation.
(CCC)	 AC	35850-35951	GT	AGG
(CGC)	 AG	37743-37913	GT	TGG
(AGC)	 AG	38058-38177	GT	TGG
(ATG)	 AG	38316-38408	GT	TGG
(TCC)	 AG	38525-38665	CC	AGC
-recovered pasa_asmbl_33881.p1, initial, 38316, 38408
-recovered pasa_asmbl_33881.p1, terminal, 38525, 38665
-recovered pasa_asmbl_33881.p1, internal, 37743, 37913
-recovered pasa_asmbl_33881.p1, internal, 38058, 38177
-recovered pasa_asmbl_33881.p1, internal, 38316, 38408
Valid prediction for GlimmerHMM_glimmerT_55709-T1
Valid prediction for Augustus_model.g37151.t1
Valid prediction for snap_scaffold_25-snap.1472-T1
Valid prediction for Augustus_model.g37163.t1
Valid prediction for snap_scaffold_25-snap.1468-T1
Valid prediction for GeneMark_model.97137_t
Valid prediction for Augustus_model.g37157.t1
Valid prediction for snap_scaffold_25-snap.1454-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.97154_t
Valid prediction for GlimmerHMM_glimmerT_55685-T1
Valid prediction for GeneMark_model.97139_t
Valid prediction for GeneMark_model.97138_t
Valid prediction for snap_scaffold_25-snap.1458-T1
Couldn't classify 56585, 56777
Couldn't classify 56924, 57030
Sorry, prediction pasa_asmbl_34342.p1 fails validation.
(CAA)	 AC	56585-56777	GT	AAG
(AGA)	 AG	56924-57030	AT	ACA
Valid prediction for Augustus_model.g37161.t1
Valid prediction for GlimmerHMM_glimmerT_55698-T1
Valid prediction for GlimmerHMM_glimmerT_55707-T1
Valid prediction for GeneMark_model.97158_t
Valid prediction for snap_scaffold_25-snap.1464-T1
Couldn't classify 57280, 57421
Couldn't classify 58157, 58370
Sorry, prediction pasa_asmbl_34341.p1 fails validation.
(GTG)	 CT	57280-57421	GT	AGG
(AGT)	 AG	57538-57636	GT	AGG
(AAC)	 AG	57758-57886	GT	GGG
(CCA)	 AG	57977-58049	GT	AGG
(TTC)	 AG	58157-58370	AT	ACA
-recovered pasa_asmbl_34341.p1, internal, 57538, 57636
-recovered pasa_asmbl_34341.p1, internal, 57758, 57886
-recovered pasa_asmbl_34341.p1, internal, 57977, 58049
Couldn't classify 31374, 31454
Sorry, prediction pasa_asmbl_34345.p2 fails validation.
(ATT)	 AG	31374-31454	GT	GGG
(GTG)	 AG	32723-32989	CT	GAC
-recovered pasa_asmbl_34345.p2, terminal, 32723, 32989
-recovered pasa_asmbl_34345.p2, internal, 31374, 31454
Valid prediction for Augustus_model.g37165.t1
Valid prediction for GlimmerHMM_glimmerT_55708-T1
Valid prediction for Augustus_model.g37156.t1
Valid prediction for snap_scaffold_25-snap.1453-T1
Valid prediction for GlimmerHMM_glimmerT_55700-T1
Valid prediction for GeneMark_model.97125_t
Valid prediction for GeneMark_model.97149_t
Valid prediction for snap_scaffold_25-snap.1451-T1
Valid prediction for snap_scaffold_25-snap.1462-T1
Valid prediction for snap_scaffold_25-snap.1481-T1
Valid prediction for GeneMark_model.97156_t
Valid prediction for Augustus_model.g37158.t1
Valid prediction for snap_scaffold_25-snap.1475-T1
Valid prediction for snap_scaffold_25-snap.1484-T1
Valid prediction for GlimmerHMM_glimmerT_55704-T1
Valid prediction for GlimmerHMM_glimmerT_55691-T1
Valid prediction for snap_scaffold_25-snap.1476-T1
Valid prediction for GeneMark_model.97150_t
Valid prediction for GeneMark_model.97133_t
Valid prediction for Augustus_model.g37160.t1
Valid prediction for Augustus_model.g37166.t1
Valid prediction for snap_scaffold_25-snap.1455-T1
Valid prediction for snap_scaffold_25-snap.1486-T1
Valid prediction for GlimmerHMM_glimmerT_55701-T1
Valid prediction for GeneMark_model.97143_t
Valid prediction for GeneMark_model.97128_t
Valid prediction for GeneMark_model.97131_t
Valid prediction for GeneMark_model.97132_t
Valid prediction for GlimmerHMM_glimmerT_55705-T1
Valid prediction for snap_scaffold_25-snap.1461-T1
Valid prediction for snap_scaffold_25-snap.1488-T1
Valid prediction for GeneMark_model.97144_t
Valid prediction for GlimmerHMM_glimmerT_55710-T1
Valid prediction for snap_scaffold_25-snap.1457-T1
Valid prediction for GlimmerHMM_glimmerT_55696-T1
Valid prediction for GeneMark_model.97148_t
Valid prediction for GeneMark_model.97135_t
Valid prediction for GeneMark_model.97152_t
Valid prediction for GeneMark_model.97126_t
Couldn't classify 55298, 55436
Couldn't classify 55985, 56509
Sorry, prediction pasa_asmbl_34343.p1 fails validation.
(GAA)	 TT	55298-55436	GT	TGG
(ACC)	 AG	55566-55652	GT	AGG
(GAA)	 AG	55756-55820	GT	AAG
(CTG)	 AG	55985-56509	GA	AGG
-recovered pasa_asmbl_34343.p1, internal, 55566, 55652
-recovered pasa_asmbl_34343.p1, internal, 55756, 55820
Valid prediction for snap_scaffold_25-snap.1483-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 13094, rend_intergenic: 8075  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16470, rend_intergenic: 14650  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23258, rend_intergenic: 17560  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25261, rend_intergenic: 24161  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38665, rend_intergenic: 31538  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50217, rend_intergenic: 48725  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119833, rend_intergenic: 114669  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132473, rend_intergenic: 132001  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136843, rend_intergenic: 132502  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 158509
-exon list size: 699


building trellis

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91.9    
92.0    
92.2    
92.3    
92.4    
92.6    
92.7    
92.9    
93.0    
93.2    
93.3    
93.4    
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    
95.6    
95.7    
95.9    
96.0    
96.1    
96.3    
96.4    
96.6    
96.7    
96.9    
97.0    
97.1    
97.3    
97.4    
97.6    
97.7    
97.9    
98.0    
98.1    
98.3    
98.4    
98.6    
98.7    
98.9    
99.0    
99.1    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 35 predictions from path traversal
Error with prediction: snap lend_intergenic: 13094, rend_intergenic: 8075  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16470, rend_intergenic: 14650  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23258, rend_intergenic: 17560  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25261, rend_intergenic: 24161  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38665, rend_intergenic: 31538  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50217, rend_intergenic: 48725  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119833, rend_intergenic: 114669  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132473, rend_intergenic: 132001  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136843, rend_intergenic: 132502  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 24 predictions persist after filtering for low support