-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_23/scaffold_23_6879954-7049172

-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 HiQ_model.g35287.t1
Valid prediction for snap_scaffold_23-snap.1283-T1
Valid prediction for snap_scaffold_23-snap.1271-T1
Valid prediction for GeneMark_model.90980_t
Valid prediction for GlimmerHMM_glimmerT_52461-T1
Valid prediction for GlimmerHMM_glimmerT_52472-T1
Valid prediction for GeneMark_model.90973_t
Valid prediction for snap_scaffold_23-snap.1263-T1
Valid prediction for GeneMark_model.90962_t
Valid prediction for snap_scaffold_23-snap.1259-T1
Valid prediction for GlimmerHMM_glimmerT_52467-T1
Valid prediction for GeneMark_model.90956_t
Valid prediction for GeneMark_model.90964_t
Couldn't classify 140193, 140249
Sorry, prediction pasa_asmbl_30960.p1 fails validation.
(CAG)	 TC	140193-140249	GT	AGG
(GAG)	 AG	140877-141016	GT	AGG
(TTC)	 AG	141817-141976	GT	GGG
(GTC)	 AG	142409-142519	GT	AGG
(GAA)	 AG	142681-142761	GT	AGG
(GAC)	 AG	143114-143302	AG	AGA
-recovered pasa_asmbl_30960.p1, terminal, 143114, 143302
-recovered pasa_asmbl_30960.p1, internal, 140877, 141016
-recovered pasa_asmbl_30960.p1, internal, 141817, 141976
-recovered pasa_asmbl_30960.p1, internal, 142409, 142519
-recovered pasa_asmbl_30960.p1, internal, 142681, 142761
Valid prediction for snap_scaffold_23-snap.1270-T1
Valid prediction for GlimmerHMM_glimmerT_52478-T1
Valid prediction for GlimmerHMM_glimmerT_52465-T1
Valid prediction for GeneMark_model.90958_t
Valid prediction for GeneMark_model.90971_t
Valid prediction for GeneMark_model.90949_t
Valid prediction for snap_scaffold_23-snap.1252-T1
Valid prediction for GeneMark_model.90952_t
Valid prediction for snap_scaffold_23-snap.1267-T1
Valid prediction for snap_scaffold_23-snap.1281-T1
Valid prediction for snap_scaffold_23-snap.1261-T1
Valid prediction for GeneMark_model.90975_t
Valid prediction for GlimmerHMM_glimmerT_52471-T1
Valid prediction for snap_scaffold_23-snap.1253-T1
Valid prediction for GeneMark_model.90982_t
Valid prediction for GeneMark_model.90960_t
Valid prediction for GeneMark_model.90945_t
Valid prediction for GeneMark_model.90943_t
Valid prediction for snap_scaffold_23-snap.1279-T1
Valid prediction for snap_scaffold_23-snap.1268-T1
Valid prediction for snap_scaffold_23-snap.1275-T1
Valid prediction for GeneMark_model.90938_t
Valid prediction for snap_scaffold_23-snap.1257-T1
Valid prediction for Augustus_model.g35286.t1
Valid prediction for GeneMark_model.90954_t
Valid prediction for GeneMark_model.90967_t
Valid prediction for snap_scaffold_23-snap.1248-T1
Valid prediction for Augustus_model.g35276.t1
Valid prediction for GeneMark_model.90951_t
Valid prediction for GeneMark_model.90985_t
Valid prediction for snap_scaffold_23-snap.1273-T1
Valid prediction for GeneMark_model.90947_t
Valid prediction for GeneMark_model.90965_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_52477-T1
Valid prediction for pasa_asmbl_31725.p1
Valid prediction for GeneMark_model.90983_t
Valid prediction for GlimmerHMM_glimmerT_52476-T1
Valid prediction for GeneMark_model.90963_t
Valid prediction for HiQ_model.g35285.t1
Valid prediction for GeneMark_model.90988_t
Valid prediction for GeneMark_model.90950_t
Valid prediction for Augustus_model.g35281.t1
Valid prediction for pasa_asmbl_31717.p1
Valid prediction for HiQ_model.g35282.t1
Valid prediction for snap_scaffold_23-snap.1286-T1
Valid prediction for GeneMark_model.90942_t
Valid prediction for snap_scaffold_23-snap.1280-T1
Valid prediction for Augustus_model.g35284.t1
Valid prediction for pasa_asmbl_31715.p1
Valid prediction for snap_scaffold_23-snap.1258-T1
Valid prediction for GeneMark_model.90939_t
Valid prediction for snap_scaffold_23-snap.1250-T1
Valid prediction for GlimmerHMM_glimmerT_52468-T1
Valid prediction for GlimmerHMM_glimmerT_52470-T1
Valid prediction for pasa_asmbl_31727.p1
Valid prediction for GeneMark_model.90970_t
Valid prediction for CodingQuarry_transcript_35633-T1
Valid prediction for GlimmerHMM_glimmerT_52460-T1
Valid prediction for GeneMark_model.90974_t
Valid prediction for snap_scaffold_23-snap.1276-T1
Valid prediction for HiQ_model.g35278.t1
Valid prediction for snap_scaffold_23-snap.1272-T1
Valid prediction for snap_scaffold_23-snap.1284-T1
Valid prediction for GeneMark_model.90966_t
Valid prediction for GeneMark_model.90955_t
Valid prediction for GlimmerHMM_glimmerT_52479-T1
Valid prediction for Augustus_model.g35280.t1
Valid prediction for GeneMark_model.90957_t
Valid prediction for GlimmerHMM_glimmerT_52480-T1
Valid prediction for CodingQuarry_transcript_35634-T1
Valid prediction for snap_scaffold_23-snap.1277-T1
Valid prediction for HiQ_model.g35279.t1
Valid prediction for HiQ_model.g35283.t1
Valid prediction for HiQ_model.g35290.t1
Valid prediction for GeneMark_model.90977_t
Valid prediction for GlimmerHMM_glimmerT_52469-T1
Valid prediction for GlimmerHMM_glimmerT_52466-T1
Valid prediction for GeneMark_model.90959_t
Valid prediction for pasa_asmbl_31723.p1
Valid prediction for CodingQuarry_transcript_35638-T1
Valid prediction for GlimmerHMM_glimmerT_52463-T1
Couldn't classify 21021, 21141
Sorry, prediction pasa_asmbl_31728.p1 fails validation.
(GCG)	 AA	21021-21141	GT	AGG
(CGA)	 AG	21600-21919	TA	AGT
-recovered pasa_asmbl_31728.p1, terminal, 21600, 21919
Valid prediction for GeneMark_model.90976_t
Valid prediction for GlimmerHMM_glimmerT_52459-T1
Valid prediction for GeneMark_model.90946_t
Valid prediction for GeneMark_model.90961_t
Valid prediction for CodingQuarry_transcript_35636-T1
Valid prediction for snap_scaffold_23-snap.1251-T1
Valid prediction for GeneMark_model.90981_t
Valid prediction for snap_scaffold_23-snap.1269-T1
Valid prediction for GeneMark_model.90978_t
Valid prediction for snap_scaffold_23-snap.1260-T1
Valid prediction for Augustus_model.g35288.t1
Valid prediction for snap_scaffold_23-snap.1264-T1
Valid prediction for GeneMark_model.90944_t
Valid prediction for GeneMark_model.90986_t
Valid prediction for snap_scaffold_23-snap.1256-T1
Couldn't classify 18154, 18244
Couldn't classify 20631, 20813
Sorry, prediction pasa_asmbl_31729.p1 fails validation.
(GAG)	 AC	18154-18244	GT	AGG
(CTG)	 AG	18939-19108	GT	AGG
(ATG)	 AG	19360-19525	GT	TGG
(AGC)	 AG	19865-20052	GT	AGG
(GAA)	 AG	20209-20283	GT	AGG
(GGA)	 AG	20376-20465	GT	AGG
(CAC)	 AG	20631-20813	GG	GGG
-recovered pasa_asmbl_31729.p1, initial, 19360, 19525
-recovered pasa_asmbl_31729.p1, internal, 18939, 19108
-recovered pasa_asmbl_31729.p1, internal, 19360, 19525
-recovered pasa_asmbl_31729.p1, internal, 19865, 20052
-recovered pasa_asmbl_31729.p1, internal, 20209, 20283
-recovered pasa_asmbl_31729.p1, internal, 20376, 20465
Valid prediction for pasa_asmbl_31730.p1
Valid prediction for GeneMark_model.90953_t
Valid prediction for GeneMark_model.90984_t
Valid prediction for GlimmerHMM_glimmerT_52462-T1
Valid prediction for GlimmerHMM_glimmerT_52482-T1
Valid prediction for snap_scaffold_23-snap.1266-T1
Valid prediction for CodingQuarry_transcript_35637-T1
Valid prediction for pasa_asmbl_31711.p1
Valid prediction for Augustus_model.g35277.t1
Valid prediction for GlimmerHMM_glimmerT_52475-T1
Valid prediction for snap_scaffold_23-snap.1265-T1
Valid prediction for snap_scaffold_23-snap.1282-T1
Valid prediction for GeneMark_model.90969_t
Valid prediction for snap_scaffold_23-snap.1249-T1
Valid prediction for GlimmerHMM_glimmerT_52481-T1
Valid prediction for snap_scaffold_23-snap.1285-T1
Valid prediction for CodingQuarry_transcript_35635-T1
Valid prediction for GlimmerHMM_glimmerT_52474-T1
Valid prediction for GeneMark_model.90941_t
Valid prediction for GeneMark_model.90948_t
Valid prediction for snap_scaffold_23-snap.1262-T1
Valid prediction for GeneMark_model.90968_t
Valid prediction for snap_scaffold_23-snap.1254-T1
Valid prediction for snap_scaffold_23-snap.1247-T1
Couldn't classify 1721, 1807
Sorry, prediction pasa_asmbl_31731.p1 fails validation.
(TCA)	 AC	1721-1807	GT	AGG
(AAT)	 AG	2065-2197	GT	TGG
(TGC)	 AG	2399-2511	GT	CAG
(GGA)	 AG	2803-2994	GT	AGG
(TAC)	 AG	3104-3251	GT	AGG
(GAG)	 AG	3393-3575	GT	TGG
(CTC)	 AG	3894-4122	GT	AGG
(GGC)	 AG	4299-4476	GC	AAG
-recovered pasa_asmbl_31731.p1, terminal, 4299, 4476
-recovered pasa_asmbl_31731.p1, internal, 2065, 2197
-recovered pasa_asmbl_31731.p1, internal, 2399, 2511
-recovered pasa_asmbl_31731.p1, internal, 2803, 2994
-recovered pasa_asmbl_31731.p1, internal, 3104, 3251
-recovered pasa_asmbl_31731.p1, internal, 3393, 3575
-recovered pasa_asmbl_31731.p1, internal, 3894, 4122
-recovered pasa_asmbl_31731.p1, internal, 4299, 4476
Valid prediction for snap_scaffold_23-snap.1278-T1
Valid prediction for GeneMark_model.90940_t
Valid prediction for snap_scaffold_23-snap.1274-T1
Valid prediction for Augustus_model.g35289.t1
Valid prediction for snap_scaffold_23-snap.1255-T1
Valid prediction for GeneMark_model.90987_t
Valid prediction for GlimmerHMM_glimmerT_52464-T1
Couldn't classify 110620, 110931
Sorry, prediction pasa_asmbl_31211.p1 fails validation.
(CTC)	 CC	110620-110931	TC	AAT
Valid prediction for GlimmerHMM_glimmerT_52473-T1
Valid prediction for GeneMark_model.90979_t
Valid prediction for GeneMark_model.90972_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 52891, rend_intergenic: 48371  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62816, rend_intergenic: 53770  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66004, rend_intergenic: 64339  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75952, rend_intergenic: 66252  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82746, rend_intergenic: 76801  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95838, rend_intergenic: 83991  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96745, rend_intergenic: 96347  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99710, rend_intergenic: 96812  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101646, rend_intergenic: 99758  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106381, rend_intergenic: 101664  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115260, rend_intergenic: 112678  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143302, rend_intergenic: 136976  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151205, rend_intergenic: 147301  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154110, rend_intergenic: 151482  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160702, rend_intergenic: 154714  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 169219
-exon list size: 652


building trellis

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91.0    
91.1    
91.3    
91.4    
91.6    
91.7    
91.9    
92.0    
92.2    
92.4    
92.5    
92.7    
92.8    
93.0    
93.1    
93.3    
93.4    
93.6    
93.7    
93.9    
94.0    
94.2    
94.3    
94.5    
94.6    
94.8    
95.0    
95.1    
95.3    
95.4    
95.6    
95.7    
95.9    
96.0    
96.2    
96.3    
96.5    
96.6    
96.8    
96.9    
97.1    
97.2    
97.4    
97.6    
97.7    
97.9    
98.0    
98.2    
98.3    
98.5    
98.6    
98.8    
98.9    
99.1    
99.2    
99.4    
99.5    
99.7    
99.8    
-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 52891, rend_intergenic: 48371  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62816, rend_intergenic: 53770  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66004, rend_intergenic: 64339  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75952, rend_intergenic: 66252  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82746, rend_intergenic: 76801  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95838, rend_intergenic: 83991  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96745, rend_intergenic: 96347  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99710, rend_intergenic: 96812  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101646, rend_intergenic: 99758  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106381, rend_intergenic: 101664  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115260, rend_intergenic: 112678  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143302, rend_intergenic: 136976  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151205, rend_intergenic: 147301  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154110, rend_intergenic: 151482  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160702, rend_intergenic: 154714  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