-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_17/scaffold_17_5956760-6175218

-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_41297-T1
Valid prediction for snap_scaffold_17-snap.1225-T1
Valid prediction for snap_scaffold_17-snap.1237-T1
Valid prediction for CodingQuarry_transcript_21950-T1
Valid prediction for GeneMark_model.71114_t
Valid prediction for GlimmerHMM_glimmerT_41312-T1
Valid prediction for Augustus_model.g27664.t1
Valid prediction for snap_scaffold_17-snap.1229-T1
Valid prediction for GlimmerHMM_glimmerT_41313-T1
Valid prediction for Augustus_model.g27652.t1
Valid prediction for GeneMark_model.71127_t
Valid prediction for GlimmerHMM_glimmerT_41301-T1
Valid prediction for snap_scaffold_17-snap.1239-T1
Valid prediction for GlimmerHMM_glimmerT_41318-T1
Valid prediction for snap_scaffold_17-snap.1219-T1
Valid prediction for snap_scaffold_17-snap.1220-T1
Valid prediction for snap_scaffold_17-snap.1226-T1
Valid prediction for snap_scaffold_17-snap.1224-T1
Valid prediction for snap_scaffold_17-snap.1249-T1
Valid prediction for GlimmerHMM_glimmerT_41294-T1
Couldn't classify 39877, 40051
Couldn't classify 44067, 44374
Sorry, prediction pasa_asmbl_17966.p1 fails validation.
(GGC)	 CA	39877-40051	GT	AGG
(TTT)	 AG	40205-40285	GT	TGG
(AGA)	 AG	40397-40850	GC	AGG
(GAG)	 AG	40905-41746	GT	AGG
(CTG)	 AG	44067-44374	AA	CCA
-recovered pasa_asmbl_17966.p1, internal, 40205, 40285
-recovered pasa_asmbl_17966.p1, internal, 40397, 40850
-recovered pasa_asmbl_17966.p1, internal, 40905, 41746
Valid prediction for Augustus_model.g27650.t1
Valid prediction for GeneMark_model.71116_t
Valid prediction for GeneMark_model.71137_t
Valid prediction for snap_scaffold_17-snap.1246-T1
Valid prediction for GlimmerHMM_glimmerT_41315-T1
Valid prediction for GlimmerHMM_glimmerT_41292-T1
Valid prediction for GlimmerHMM_glimmerT_41317-T1
Valid prediction for GeneMark_model.71109_t
Valid prediction for snap_scaffold_17-snap.1248-T1
Valid prediction for GlimmerHMM_glimmerT_41316-T1
Valid prediction for GlimmerHMM_glimmerT_41296-T1
Valid prediction for GlimmerHMM_glimmerT_41299-T1
Valid prediction for snap_scaffold_17-snap.1217-T1
Valid prediction for snap_scaffold_17-snap.1215-T1
Couldn't classify 44441, 44631
Sorry, prediction pasa_asmbl_17967.p1 fails validation.
(CCC)	 CA	44441-44631	GT	CTG
(ACC)	 AG	44997-45262	GT	CAG
(GCG)	 AG	45398-45572	GT	CGG
(GCG)	 AG	45763-45818	GT	AGG
(TGA)	 AG	46398-46456	GT	AGG
(CTG)	 AG	46694-46831	GT	AGG
(GCG)	 AG	47205-47281	GT	AGG
(GTT)	 AG	47378-47393	CT	AGC
-recovered pasa_asmbl_17967.p1, terminal, 47378, 47393
-recovered pasa_asmbl_17967.p1, internal, 44997, 45262
-recovered pasa_asmbl_17967.p1, internal, 45398, 45572
-recovered pasa_asmbl_17967.p1, internal, 45763, 45818
-recovered pasa_asmbl_17967.p1, internal, 46398, 46456
-recovered pasa_asmbl_17967.p1, internal, 46694, 46831
-recovered pasa_asmbl_17967.p1, internal, 47205, 47281
Valid prediction for GeneMark_model.71125_t
Valid prediction for GeneMark_model.71115_t
Valid prediction for snap_scaffold_17-snap.1240-T1
Valid prediction for Augustus_model.g27651.t1
Valid prediction for Augustus_model.g27655.t1
Valid prediction for snap_scaffold_17-snap.1216-T1
Valid prediction for GeneMark_model.71104_t
Valid prediction for Augustus_model.g27649.t1
Valid prediction for GeneMark_model.71134_t
Valid prediction for GlimmerHMM_glimmerT_41304-T1
Valid prediction for GlimmerHMM_glimmerT_41303-T1
Valid prediction for GlimmerHMM_glimmerT_41310-T1
Valid prediction for snap_scaffold_17-snap.1233-T1
Valid prediction for GeneMark_model.71139_t
Valid prediction for GeneMark_model.71103_t
Valid prediction for GeneMark_model.71107_t
Valid prediction for HiQ_model.g27668.t1
Valid prediction for GeneMark_model.71131_t
Valid prediction for GeneMark_model.71138_t
Valid prediction for GeneMark_model.71105_t
Valid prediction for GeneMark_model.71118_t
Valid prediction for GeneMark_model.71135_t
Valid prediction for GeneMark_model.71130_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.71128_t
Couldn't classify 73543, 73594
Couldn't classify 73728, 73830
Sorry, prediction CodingQuarry_transcript_21951-T1 fails validation.
(ATG)	 CC	70859-71106	GT	GAG
(CTG)	 AG	71430-71590	GT	TGG
(ATA)	 AG	72511-72663	GT	GGG
(AGC)	 AG	73222-73359	GT	GCG
(GGT)	 AG	73543-73594	AT	AGA
(TGC)	 AC	73728-73830	GT	ATG
(ATC)	 AG	73932-74044	GT	AGG
(TTT)	 AG	74261-74372	GG	GAG
-recovered CodingQuarry_transcript_21951-T1, initial, 70859, 71106
-recovered CodingQuarry_transcript_21951-T1, terminal, 74261, 74372
-recovered CodingQuarry_transcript_21951-T1, internal, 71430, 71590
-recovered CodingQuarry_transcript_21951-T1, internal, 72511, 72663
-recovered CodingQuarry_transcript_21951-T1, internal, 73222, 73359
-recovered CodingQuarry_transcript_21951-T1, internal, 73932, 74044
Valid prediction for Augustus_model.g27667.t1
Valid prediction for Augustus_model.g27661.t1
Valid prediction for GlimmerHMM_glimmerT_41309-T1
Valid prediction for GlimmerHMM_glimmerT_41293-T1
Valid prediction for GlimmerHMM_glimmerT_41308-T1
Valid prediction for snap_scaffold_17-snap.1235-T1
Couldn't classify 58586, 58723
Couldn't classify 58856, 59827
Sorry, prediction pasa_asmbl_19005.p1 fails validation.
(CCC)	 CC	58586-58723	GT	AGG
(CTT)	 AG	58856-59827	GA	ACG
Valid prediction for snap_scaffold_17-snap.1241-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_17-snap.1228-T1
Valid prediction for GeneMark_model.71132_t
Valid prediction for Augustus_model.g27666.t1
Valid prediction for GlimmerHMM_glimmerT_41307-T1
Valid prediction for HiQ_model.g27653.t1
Valid prediction for GeneMark_model.71117_t
Valid prediction for GeneMark_model.71111_t
Valid prediction for GlimmerHMM_glimmerT_41300-T1
Valid prediction for Augustus_model.g27659.t1
Valid prediction for GlimmerHMM_glimmerT_41305-T1
Valid prediction for snap_scaffold_17-snap.1244-T1
Valid prediction for snap_scaffold_17-snap.1232-T1
Couldn't classify 56118, 56218
Sorry, prediction pasa_asmbl_19007.p1 fails validation.
(ATG)	 GC	53223-53331	GT	TGG
(GCA)	 AG	53458-53558	GT	AGG
(AAG)	 AG	53655-53864	GT	AGG
(GTG)	 AG	54080-54284	GT	AGG
(CTG)	 AG	56118-56218	CA	CCC
-recovered pasa_asmbl_19007.p1, initial, 53223, 53331
-recovered pasa_asmbl_19007.p1, internal, 53458, 53558
-recovered pasa_asmbl_19007.p1, internal, 53655, 53864
-recovered pasa_asmbl_19007.p1, internal, 54080, 54284
Valid prediction for GeneMark_model.71126_t
Valid prediction for GeneMark_model.71136_t
Valid prediction for GeneMark_model.71112_t
Valid prediction for Augustus_model.g27658.t1
Valid prediction for GeneMark_model.71106_t
Valid prediction for snap_scaffold_17-snap.1227-T1
Valid prediction for GeneMark_model.71121_t
Valid prediction for GeneMark_model.71113_t
Valid prediction for pasa_asmbl_19004.p1
Valid prediction for Augustus_model.g27663.t1
Valid prediction for Augustus_model.g27662.t1
Valid prediction for snap_scaffold_17-snap.1221-T1
Valid prediction for GlimmerHMM_glimmerT_41302-T1
Valid prediction for GeneMark_model.71123_t
Valid prediction for GeneMark_model.71120_t
Valid prediction for snap_scaffold_17-snap.1245-T1
Valid prediction for Augustus_model.g27665.t1
Couldn't classify 73543, 73594
Couldn't classify 73728, 73830
Sorry, prediction pasa_asmbl_19003.p1 fails validation.
(ATG)	 GT	70847-71106	GT	GAG
(CTG)	 AG	71430-71590	GT	TGG
(ATA)	 AG	72511-72663	GT	GGG
(AGC)	 AG	73222-73359	GT	GCG
(GGT)	 AG	73543-73594	AT	AGA
(TGC)	 AC	73728-73830	GT	ATG
(ATC)	 AG	73932-74044	GT	AGG
(TTT)	 AG	74261-74372	GG	GAG
-recovered pasa_asmbl_19003.p1, initial, 70847, 71106
-recovered pasa_asmbl_19003.p1, terminal, 74261, 74372
-recovered pasa_asmbl_19003.p1, internal, 71430, 71590
-recovered pasa_asmbl_19003.p1, internal, 72511, 72663
-recovered pasa_asmbl_19003.p1, internal, 73222, 73359
-recovered pasa_asmbl_19003.p1, internal, 73932, 74044
Valid prediction for GlimmerHMM_glimmerT_41295-T1
Valid prediction for snap_scaffold_17-snap.1223-T1
Valid prediction for snap_scaffold_17-snap.1230-T1
Valid prediction for GeneMark_model.71124_t
Valid prediction for Augustus_model.g27656.t1
Valid prediction for snap_scaffold_17-snap.1247-T1
Valid prediction for GlimmerHMM_glimmerT_41311-T1
Valid prediction for Augustus_model.g27657.t1
Valid prediction for GeneMark_model.71119_t
Valid prediction for GlimmerHMM_glimmerT_41306-T1
Valid prediction for snap_scaffold_17-snap.1234-T1
Valid prediction for GeneMark_model.71133_t
Valid prediction for snap_scaffold_17-snap.1238-T1
Valid prediction for snap_scaffold_17-snap.1222-T1
Valid prediction for Augustus_model.g27660.t1
Valid prediction for snap_scaffold_17-snap.1218-T1
Valid prediction for snap_scaffold_17-snap.1242-T1
Valid prediction for Augustus_model.g27654.t1
Valid prediction for snap_scaffold_17-snap.1236-T1
Valid prediction for GlimmerHMM_glimmerT_41298-T1
Valid prediction for GeneMark_model.71122_t
Valid prediction for GeneMark_model.71129_t
Valid prediction for snap_scaffold_17-snap.1243-T1
Valid prediction for snap_scaffold_17-snap.1231-T1
Couldn't classify 95174, 95593
Sorry, prediction pasa_asmbl_19000.p1 fails validation.
(CGC)	 TC	95174-95593	GC	GAG
Valid prediction for GlimmerHMM_glimmerT_41314-T1
Valid prediction for GeneMark_model.71108_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 23295, rend_intergenic: 22909  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48726, rend_intergenic: 37388  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111149, rend_intergenic: 110231  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166948, rend_intergenic: 166947  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168660, rend_intergenic: 167480  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181926, rend_intergenic: 169927  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 212836, rend_intergenic: 209118  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 218459
-exon list size: 562


building trellis

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29.1    
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29.6    
29.8    
30.0    
30.1    
30.3    
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30.9    
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31.9    
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32.3    
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35.1    
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98.0    
98.2    
98.4    
98.6    
98.8    
98.9    
99.1    
99.3    
99.5    
99.6    
99.8    
-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 23295, rend_intergenic: 22909  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48726, rend_intergenic: 37388  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111149, rend_intergenic: 110231  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166948, rend_intergenic: 166947  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168660, rend_intergenic: 167480  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181926, rend_intergenic: 169927  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 212836, rend_intergenic: 209118  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 18 predictions persist after filtering for low support