-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_4/scaffold_4_5513372-5738334

-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 GlimmerHMM_glimmerT_9601-T1
Valid prediction for pasa_asmbl_42694.p1
Valid prediction for Augustus_model.g6266.t1
Valid prediction for Augustus_model.g6257.t1
Valid prediction for Augustus_model.g6253.t1
Valid prediction for snap_scaffold_4-snap.1210-T1
Valid prediction for GeneMark_model.15693_t
Valid prediction for snap_scaffold_4-snap.1231-T1
Valid prediction for GlimmerHMM_glimmerT_9600-T1
Valid prediction for snap_scaffold_4-snap.1245-T1
Valid prediction for Augustus_model.g6245.t1
Valid prediction for Augustus_model.g6246.t1
Valid prediction for GeneMark_model.15679_t
Valid prediction for GeneMark_model.15696_t
Valid prediction for HiQ_model.g6276.t1
Couldn't classify 194218, 194520
Couldn't classify 197081, 197215
Sorry, prediction pasa_asmbl_42697.p1 fails validation.
(AAC)	 GG	194218-194520	GT	AGG
(GCT)	 AG	196294-196468	GT	TGG
(GAA)	 AG	196556-196713	GT	AAG
(CAC)	 AG	196837-196944	GT	AGG
(GTC)	 AG	197081-197215	AA	CCA
-recovered pasa_asmbl_42697.p1, internal, 196294, 196468
-recovered pasa_asmbl_42697.p1, internal, 196556, 196713
-recovered pasa_asmbl_42697.p1, internal, 196837, 196944
Valid prediction for GlimmerHMM_glimmerT_9621-T1
Valid prediction for GeneMark_model.15676_t
Valid prediction for GlimmerHMM_glimmerT_9612-T1
Valid prediction for GeneMark_model.15721_t
Valid prediction for GeneMark_model.15708_t
Valid prediction for snap_scaffold_4-snap.1248-T1
Valid prediction for GeneMark_model.15700_t
Valid prediction for CodingQuarry_transcript_48901-T1
Valid prediction for snap_scaffold_4-snap.1225-T1
Valid prediction for GeneMark_model.15719_t
Valid prediction for Augustus_model.g6262.t1
Valid prediction for pasa_asmbl_42696.p1
Valid prediction for GlimmerHMM_glimmerT_9588-T1
Valid prediction for Augustus_model.g6259.t1
Valid prediction for GeneMark_model.15694_t
Valid prediction for GeneMark_model.15692_t
Valid prediction for GlimmerHMM_glimmerT_9619-T1
Valid prediction for snap_scaffold_4-snap.1212-T1
Valid prediction for snap_scaffold_4-snap.1233-T1
Valid prediction for snap_scaffold_4-snap.1226-T1
Valid prediction for GeneMark_model.15705_t
Couldn't classify 209926, 210053
Sorry, prediction pasa_asmbl_42700.p1 fails validation.
(GTA)	 AC	209926-210053	GT	AGG
(ATT)	 AG	210177-210291	GT	AGG
(GTG)	 AG	210826-210927	CC	GAC
-recovered pasa_asmbl_42700.p1, terminal, 210826, 210927
-recovered pasa_asmbl_42700.p1, internal, 210177, 210291
Valid prediction for HiQ_model.g6267.t1
Valid prediction for GeneMark_model.15686_t
Valid prediction for snap_scaffold_4-snap.1234-T1
Valid prediction for GlimmerHMM_glimmerT_9620-T1
Valid prediction for snap_scaffold_4-snap.1252-T1
Valid prediction for GeneMark_model.15680_t
Valid prediction for Augustus_model.g6273.t1
Valid prediction for GlimmerHMM_glimmerT_9587-T1
Valid prediction for Augustus_model.g6270.t1
Valid prediction for snap_scaffold_4-snap.1214-T1
Valid prediction for Augustus_model.g6252.t1
Valid prediction for GlimmerHMM_glimmerT_9604-T1
Valid prediction for GeneMark_model.15674_t
Valid prediction for GlimmerHMM_glimmerT_9616-T1
Valid prediction for CodingQuarry_transcript_48899-T1
Valid prediction for snap_scaffold_4-snap.1208-T1
Valid prediction for Augustus_model.g6277.t1
Valid prediction for GeneMark_model.15704_t
Valid prediction for GlimmerHMM_glimmerT_9615-T1
Valid prediction for GeneMark_model.15677_t
Valid prediction for snap_scaffold_4-snap.1223-T1
Valid prediction for snap_scaffold_4-snap.1251-T1
Valid prediction for GeneMark_model.15689_t
Valid prediction for GlimmerHMM_glimmerT_9595-T1
Valid prediction for snap_scaffold_4-snap.1241-T1
Valid prediction for GeneMark_model.15682_t
Valid prediction for snap_scaffold_4-snap.1220-T1
Valid prediction for snap_scaffold_4-snap.1217-T1
Valid prediction for GlimmerHMM_glimmerT_9589-T1
Valid prediction for GlimmerHMM_glimmerT_9610-T1
Valid prediction for GeneMark_model.15701_t
Valid prediction for GeneMark_model.15716_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.15710_t
Valid prediction for snap_scaffold_4-snap.1224-T1
Valid prediction for snap_scaffold_4-snap.1238-T1
Valid prediction for Augustus_model.g6263.t1
Valid prediction for GeneMark_model.15690_t
Valid prediction for GlimmerHMM_glimmerT_9611-T1
Valid prediction for GlimmerHMM_glimmerT_9614-T1
Valid prediction for pasa_asmbl_41355.p6
Valid prediction for snap_scaffold_4-snap.1213-T1
Valid prediction for GeneMark_model.15709_t
Valid prediction for GlimmerHMM_glimmerT_9613-T1
Valid prediction for snap_scaffold_4-snap.1242-T1
Valid prediction for snap_scaffold_4-snap.1246-T1
Valid prediction for GlimmerHMM_glimmerT_9603-T1
Valid prediction for GeneMark_model.15702_t
Valid prediction for GlimmerHMM_glimmerT_9606-T1
Valid prediction for GeneMark_model.15717_t
Valid prediction for GlimmerHMM_glimmerT_9591-T1
Valid prediction for Augustus_model.g6275.t1
Valid prediction for snap_scaffold_4-snap.1218-T1
Valid prediction for GeneMark_model.15687_t
Valid prediction for GeneMark_model.15678_t
Valid prediction for GeneMark_model.15684_t
Valid prediction for Augustus_model.g6272.t1
Valid prediction for snap_scaffold_4-snap.1221-T1
Valid prediction for GeneMark_model.15688_t
Valid prediction for GlimmerHMM_glimmerT_9593-T1
Valid prediction for Augustus_model.g6264.t1
Valid prediction for GlimmerHMM_glimmerT_9590-T1
Valid prediction for GlimmerHMM_glimmerT_9609-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_4-snap.1239-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_4-snap.1209-T1
Valid prediction for Augustus_model.g6265.t1
Valid prediction for Augustus_model.g6261.t1
Valid prediction for GlimmerHMM_glimmerT_9594-T1
Valid prediction for GeneMark_model.15718_t
Valid prediction for HiQ_model.g6250.t1
Valid prediction for snap_scaffold_4-snap.1228-T1
Valid prediction for CodingQuarry_transcript_48896-T1
Couldn't classify 157814, 157876
Sorry, prediction pasa_asmbl_41348.p1 fails validation.
(AAT)	 AG	157814-157876	GT	AGG
(GCC)	 AG	158057-158117	GT	AGG
(ACG)	 AG	158327-158524	GT	CAG
(CTG)	 AG	158779-158834	GT	AAG
-recovered pasa_asmbl_41348.p1, terminal, 158779, 158834
-recovered pasa_asmbl_41348.p1, internal, 157814, 157876
-recovered pasa_asmbl_41348.p1, internal, 158057, 158117
-recovered pasa_asmbl_41348.p1, internal, 158327, 158524
-recovered pasa_asmbl_41348.p1, internal, 158779, 158834
Valid prediction for GeneMark_model.15706_t
Valid prediction for snap_scaffold_4-snap.1254-T1
Valid prediction for GlimmerHMM_glimmerT_9598-T1
Valid prediction for snap_scaffold_4-snap.1247-T1
Valid prediction for Augustus_model.g6254.t1
Valid prediction for snap_scaffold_4-snap.1250-T1
Valid prediction for GeneMark_model.15712_t
Valid prediction for Augustus_model.g6255.t1
Valid prediction for GlimmerHMM_glimmerT_9596-T1
Valid prediction for GeneMark_model.15713_t
Valid prediction for GeneMark_model.15722_t
Valid prediction for snap_scaffold_4-snap.1232-T1
Valid prediction for Augustus_model.g6269.t1
Valid prediction for pasa_asmbl_41365.p1
Valid prediction for GlimmerHMM_glimmerT_9607-T1
Valid prediction for GlimmerHMM_glimmerT_9605-T1
Valid prediction for snap_scaffold_4-snap.1227-T1
Valid prediction for Augustus_model.g6268.t1
Valid prediction for GeneMark_model.15698_t
Valid prediction for CodingQuarry_transcript_48894-T1
Valid prediction for snap_scaffold_4-snap.1240-T1
Valid prediction for snap_scaffold_4-snap.1216-T1
Valid prediction for GeneMark_model.15715_t
Valid prediction for Augustus_model.g6251.t1
Valid prediction for snap_scaffold_4-snap.1236-T1
Valid prediction for GlimmerHMM_glimmerT_9608-T1
Valid prediction for GlimmerHMM_glimmerT_9617-T1
Valid prediction for Augustus_model.g6274.t1
Valid prediction for GeneMark_model.15697_t
Valid prediction for snap_scaffold_4-snap.1237-T1
Couldn't classify 131278, 132273
Sorry, prediction pasa_asmbl_41351.p1 fails validation.
(GGG)	 TG	131278-132273	TG	AGT
Valid prediction for snap_scaffold_4-snap.1229-T1
Valid prediction for snap_scaffold_4-snap.1235-T1
Valid prediction for CodingQuarry_transcript_48898-T1
Valid prediction for Augustus_model.g6248.t1
Valid prediction for GeneMark_model.15711_t
Valid prediction for GlimmerHMM_glimmerT_9602-T1
Valid prediction for HiQ_model.g6260.t1
Valid prediction for snap_scaffold_4-snap.1249-T1
Valid prediction for GlimmerHMM_glimmerT_9599-T1
Valid prediction for GeneMark_model.15720_t
Valid prediction for snap_scaffold_4-snap.1215-T1
Valid prediction for Augustus_model.g6271.t1
Valid prediction for GeneMark_model.15685_t
Valid prediction for GeneMark_model.15707_t
Valid prediction for GeneMark_model.15699_t
Valid prediction for CodingQuarry_transcript_48895-T1
Valid prediction for snap_scaffold_4-snap.1230-T1
Valid prediction for GeneMark_model.15714_t
Valid prediction for GeneMark_model.15675_t
Valid prediction for GeneMark_model.15691_t
Valid prediction for GeneMark_model.15681_t
Valid prediction for Augustus_model.g6256.t1
Valid prediction for pasa_asmbl_41346.p1
Valid prediction for CodingQuarry_transcript_48897-T1
Valid prediction for Augustus_model.g6249.t1
Valid prediction for Augustus_model.g6258.t1
Valid prediction for snap_scaffold_4-snap.1222-T1
Valid prediction for GlimmerHMM_glimmerT_9592-T1
Valid prediction for snap_scaffold_4-snap.1219-T1
Valid prediction for snap_scaffold_4-snap.1243-T1
Valid prediction for GlimmerHMM_glimmerT_9618-T1
Valid prediction for snap_scaffold_4-snap.1211-T1
Valid prediction for snap_scaffold_4-snap.1244-T1
Valid prediction for GeneMark_model.15683_t
Valid prediction for Augustus_model.g6247.t1
Valid prediction for GlimmerHMM_glimmerT_9597-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 10172, rend_intergenic: 2028  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38732, rend_intergenic: 17106  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45570, rend_intergenic: 40480  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55425, rend_intergenic: 49336  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73826, rend_intergenic: 68953  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81600, rend_intergenic: 76220  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95552, rend_intergenic: 91662  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105903, rend_intergenic: 98511  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116305, rend_intergenic: 107148  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141108, rend_intergenic: 136793  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 132010, rend_intergenic: 132007  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 224963
-exon list size: 672


building trellis

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90.5    
90.7    
90.8    
90.9    
91.1    
91.2    
91.4    
91.5    
91.7    
91.8    
92.0    
92.1    
92.3    
92.4    
92.6    
92.7    
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    
95.5    
95.7    
95.8    
96.0    
96.1    
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 43 predictions from path traversal
Error with prediction: snap lend_intergenic: 10172, rend_intergenic: 2028  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38732, rend_intergenic: 17106  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45570, rend_intergenic: 40480  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55425, rend_intergenic: 49336  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73826, rend_intergenic: 68953  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81600, rend_intergenic: 76220  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95552, rend_intergenic: 91662  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105903, rend_intergenic: 98511  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116305, rend_intergenic: 107148  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141108, rend_intergenic: 136793  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 132010, rend_intergenic: 132007  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 38 predictions persist after filtering for low support