-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_2/scaffold_2_5297792-5477426

-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 Augustus_model.g2601.t1
Valid prediction for Augustus_model.g2609.t1
Valid prediction for snap_scaffold_2-snap.1225-T1
Valid prediction for GlimmerHMM_glimmerT_3909-T1
Valid prediction for snap_scaffold_2-snap.1232-T1
Valid prediction for snap_scaffold_2-snap.1212-T1
Valid prediction for GlimmerHMM_glimmerT_3901-T1
Valid prediction for GlimmerHMM_glimmerT_3891-T1
Valid prediction for Augustus_model.g2598.t1
Valid prediction for GeneMark_model.6399_t
Valid prediction for Augustus_model.g2606.t1
Valid prediction for GlimmerHMM_glimmerT_3916-T1
Valid prediction for GeneMark_model.6406_t
Valid prediction for snap_scaffold_2-snap.1231-T1
Valid prediction for snap_scaffold_2-snap.1244-T1
Valid prediction for snap_scaffold_2-snap.1243-T1
Valid prediction for GeneMark_model.6414_t
Couldn't classify 149896, 150069
Sorry, prediction pasa_asmbl_24444.p1 fails validation.
(ATG)	 GA	142772-144010	GT	AGG
(ATC)	 AG	144819-144968	GT	AGG
(GAG)	 AG	145638-145789	GT	AGG
(AGG)	 AG	145909-146003	GT	AGG
(GTG)	 AG	148258-148429	GT	AAG
(AGA)	 AG	149285-149342	GT	AGG
(GTG)	 AG	149896-150069	GG	TGG
-recovered pasa_asmbl_24444.p1, initial, 142772, 144010
-recovered pasa_asmbl_24444.p1, internal, 144819, 144968
-recovered pasa_asmbl_24444.p1, internal, 145638, 145789
-recovered pasa_asmbl_24444.p1, internal, 145909, 146003
-recovered pasa_asmbl_24444.p1, internal, 148258, 148429
-recovered pasa_asmbl_24444.p1, internal, 149285, 149342
Valid prediction for snap_scaffold_2-snap.1208-T1
Valid prediction for GeneMark_model.6401_t
Valid prediction for snap_scaffold_2-snap.1206-T1
Valid prediction for snap_scaffold_2-snap.1235-T1
Valid prediction for snap_scaffold_2-snap.1219-T1
Valid prediction for GlimmerHMM_glimmerT_3902-T1
Valid prediction for snap_scaffold_2-snap.1216-T1
Valid prediction for snap_scaffold_2-snap.1228-T1
Valid prediction for GlimmerHMM_glimmerT_3896-T1
Valid prediction for GlimmerHMM_glimmerT_3904-T1
Valid prediction for GlimmerHMM_glimmerT_3898-T1
Valid prediction for Augustus_model.g2612.t1
Valid prediction for GlimmerHMM_glimmerT_3915-T1
Valid prediction for Augustus_model.g2607.t1
Valid prediction for snap_scaffold_2-snap.1215-T1
Valid prediction for GlimmerHMM_glimmerT_3900-T1
Valid prediction for GeneMark_model.6412_t
Valid prediction for pasa_asmbl_24441.p1
Valid prediction for GlimmerHMM_glimmerT_3910-T1
Valid prediction for snap_scaffold_2-snap.1218-T1
Valid prediction for GlimmerHMM_glimmerT_3908-T1
Valid prediction for GeneMark_model.6397_t
Valid prediction for GlimmerHMM_glimmerT_3892-T1
Valid prediction for GlimmerHMM_glimmerT_3894-T1
Valid prediction for Augustus_model.g2600.t1
Valid prediction for snap_scaffold_2-snap.1210-T1
Valid prediction for Augustus_model.g2608.t1
Valid prediction for GeneMark_model.6398_t
Valid prediction for GlimmerHMM_glimmerT_3917-T1
Valid prediction for Augustus_model.g2595.t1
Valid prediction for Augustus_model.g2596.t1
Valid prediction for GlimmerHMM_glimmerT_3893-T1
Valid prediction for GeneMark_model.6395_t
Couldn't classify 158693, 158894
Sorry, prediction pasa_asmbl_24449.p1 fails validation.
(CAG)	 TG	158693-158894	GT	GGG
(AGG)	 AG	160162-160442	AC	GAA
-recovered pasa_asmbl_24449.p1, terminal, 160162, 160442
Valid prediction for GeneMark_model.6404_t
Valid prediction for snap_scaffold_2-snap.1224-T1
Valid prediction for GlimmerHMM_glimmerT_3914-T1
Valid prediction for GeneMark_model.6405_t
Valid prediction for GeneMark_model.6413_t
Valid prediction for GlimmerHMM_glimmerT_3895-T1
Valid prediction for GeneMark_model.6408_t
Valid prediction for snap_scaffold_2-snap.1237-T1
Valid prediction for GeneMark_model.6415_t
Valid prediction for snap_scaffold_2-snap.1238-T1
Couldn't classify 91511, 91551
Sorry, prediction pasa_asmbl_24443.p1 fails validation.
(CAG)	 TA	91511-91551	GT	TTG
(AAT)	 AG	91760-91927	GT	AGG
(ATA)	 AG	92328-92468	GT	GAG
(GTA)	 AG	92878-92959	GT	AGG
(CTG)	 AG	93410-93559	AG	GAA
-recovered pasa_asmbl_24443.p1, terminal, 93410, 93559
-recovered pasa_asmbl_24443.p1, internal, 91760, 91927
-recovered pasa_asmbl_24443.p1, internal, 92328, 92468
-recovered pasa_asmbl_24443.p1, internal, 92878, 92959
Valid prediction for GeneMark_model.6402_t
Valid prediction for snap_scaffold_2-snap.1217-T1
Valid prediction for GlimmerHMM_glimmerT_3913-T1
Valid prediction for snap_scaffold_2-snap.1241-T1
Valid prediction for GeneMark_model.6392_t
Valid prediction for GlimmerHMM_glimmerT_3899-T1
Valid prediction for snap_scaffold_2-snap.1209-T1
Valid prediction for GlimmerHMM_glimmerT_3912-T1
Valid prediction for snap_scaffold_2-snap.1242-T1
Valid prediction for snap_scaffold_2-snap.1240-T1
Valid prediction for pasa_asmbl_24442.p1
Valid prediction for Augustus_model.g2613.t1
Valid prediction for snap_scaffold_2-snap.1213-T1
Valid prediction for snap_scaffold_2-snap.1214-T1
Valid prediction for Augustus_model.g2610.t1
Valid prediction for HiQ_model.g2597.t1
Valid prediction for snap_scaffold_2-snap.1223-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.6396_t
Valid prediction for snap_scaffold_2-snap.1211-T1
Valid prediction for snap_scaffold_2-snap.1229-T1
Couldn't classify 83975, 84144
Sorry, prediction pasa_asmbl_23173.p1 fails validation.
(AGC)	 GA	83975-84144	GT	CGG
(AGG)	 AG	84510-84585	GT	AGG
(GTG)	 AG	84706-84838	GT	CAG
(AAG)	 AG	84936-85142	GT	CTG
(ACT)	 AG	85271-85437	GT	GGG
(GAT)	 AG	85575-85583	GG	AAG
-recovered pasa_asmbl_23173.p1, terminal, 85575, 85583
-recovered pasa_asmbl_23173.p1, internal, 84510, 84585
-recovered pasa_asmbl_23173.p1, internal, 84706, 84838
-recovered pasa_asmbl_23173.p1, internal, 84936, 85142
-recovered pasa_asmbl_23173.p1, internal, 85271, 85437
Valid prediction for snap_scaffold_2-snap.1226-T1
Valid prediction for Augustus_model.g2593.t1
Valid prediction for CodingQuarry_transcript_28499-T1
Valid prediction for pasa_asmbl_23170.p1
Valid prediction for GeneMark_model.6420_t
Valid prediction for GeneMark_model.6407_t
Valid prediction for GeneMark_model.6410_t
Valid prediction for HiQ_model.g2602.t1
Valid prediction for GlimmerHMM_glimmerT_3897-T1
Valid prediction for GeneMark_model.6403_t
Valid prediction for GeneMark_model.6417_t
Valid prediction for snap_scaffold_2-snap.1205-T1
Valid prediction for GlimmerHMM_glimmerT_3907-T1
Valid prediction for GlimmerHMM_glimmerT_3890-T1
Valid prediction for CodingQuarry_transcript_28500-T1
Valid prediction for snap_scaffold_2-snap.1230-T1
Valid prediction for CodingQuarry_transcript_28497-T1
Valid prediction for GeneMark_model.6400_t
Valid prediction for snap_scaffold_2-snap.1239-T1
Valid prediction for GeneMark_model.6393_t
Couldn't classify 70087, 70461
Sorry, prediction pasa_asmbl_23178.p4 fails validation.
(ATG)	 AC	70087-70461	GG	AAG
Valid prediction for GeneMark_model.6394_t
Valid prediction for GlimmerHMM_glimmerT_3911-T1
Valid prediction for snap_scaffold_2-snap.1222-T1
Valid prediction for snap_scaffold_2-snap.1236-T1
Valid prediction for HiQ_model.g2599.t1
Couldn't classify 71290, 71685
Sorry, prediction pasa_asmbl_23177.p3 fails validation.
(TTG)	 CT	71290-71685	CG	AAC
Valid prediction for GlimmerHMM_glimmerT_3905-T1
Valid prediction for snap_scaffold_2-snap.1233-T1
Valid prediction for snap_scaffold_2-snap.1207-T1
Valid prediction for snap_scaffold_2-snap.1234-T1
Valid prediction for Augustus_model.g2611.t1
Valid prediction for GlimmerHMM_glimmerT_3906-T1
Valid prediction for snap_scaffold_2-snap.1204-T1
Valid prediction for GlimmerHMM_glimmerT_3903-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for Augustus_model.g2604.t1
Valid prediction for snap_scaffold_2-snap.1220-T1
Valid prediction for GeneMark_model.6391_t
Valid prediction for Augustus_model.g2594.t1
Valid prediction for GeneMark_model.6409_t
Valid prediction for snap_scaffold_2-snap.1227-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GeneMark_model.6411_t
Valid prediction for GlimmerHMM_glimmerT_3889-T1
Valid prediction for snap_scaffold_2-snap.1221-T1
Valid prediction for Augustus_model.g2603.t1
Valid prediction for CodingQuarry_transcript_28498-T1
Valid prediction for GeneMark_model.6418_t
Valid prediction for GeneMark_model.6416_t
Valid prediction for Augustus_model.g2605.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 4721, rend_intergenic: 3498  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15070, rend_intergenic: 8090  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18545, rend_intergenic: 16983  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44270, rend_intergenic: 18551  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65885, rend_intergenic: 64359  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139559, rend_intergenic: 138644  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141008, rend_intergenic: 139977  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147362, rend_intergenic: 145407  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 179635
-exon list size: 602


building trellis

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-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 4721, rend_intergenic: 3498  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15070, rend_intergenic: 8090  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18545, rend_intergenic: 16983  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44270, rend_intergenic: 18551  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65885, rend_intergenic: 64359  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139559, rend_intergenic: 138644  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141008, rend_intergenic: 139977  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147362, rend_intergenic: 145407  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

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

-building DP trellis

-building trellis in range 169519 - 179635
-exon list size: 5


building trellis

14.3    
28.6    
42.9    
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71.4    
85.7    
-found 1 predictions from path traversal

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