-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_10/scaffold_10_5250355-5504242

-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 snap_scaffold_10-snap.1164-T1
Valid prediction for CodingQuarry_transcript_5400-T1
Valid prediction for HiQ_model.g16949.t1
Valid prediction for GlimmerHMM_glimmerT_25262-T1
Valid prediction for snap_scaffold_10-snap.1160-T1
Couldn't classify 199565, 199600
Sorry, prediction pasa_asmbl_4449.p2 fails validation.
(CGT)	 AA	199565-199600	GT	CTG
(TTA)	 AG	200718-200818	GT	TGG
(TGC)	 AG	201093-201138	GT	AGG
(AAG)	 AG	201466-201717	AT	AGA
-recovered pasa_asmbl_4449.p2, terminal, 201466, 201717
-recovered pasa_asmbl_4449.p2, internal, 200718, 200818
-recovered pasa_asmbl_4449.p2, internal, 201093, 201138
Valid prediction for GeneMark_model.43195_t
Valid prediction for snap_scaffold_10-snap.1173-T1
Valid prediction for snap_scaffold_10-snap.1183-T1
Valid prediction for snap_scaffold_10-snap.1168-T1
Valid prediction for GlimmerHMM_glimmerT_25260-T1
Valid prediction for GeneMark_model.43180_t
Couldn't classify 135881, 135948
Couldn't classify 139311, 139369
Sorry, prediction pasa_asmbl_4443.p1 fails validation.
(GAA)	 CA	135881-135948	GT	AGG
(AAA)	 AG	136966-137059	GT	AGG
(GAT)	 AG	137283-137380	GT	TAG
(TTG)	 AG	137487-137627	GT	AGG
(ATA)	 AG	138588-138703	GT	GGG
(GCT)	 AG	139311-139369	GT	CGG
add_exon() Sorry, pasa_asmbl_4443.p1 137487-137627-terminal-1 is invalid.
-recovered pasa_asmbl_4443.p1, terminal, 137487, 137627
-recovered pasa_asmbl_4443.p1, internal, 136966, 137059
-recovered pasa_asmbl_4443.p1, internal, 137283, 137380
-recovered pasa_asmbl_4443.p1, internal, 137487, 137627
-recovered pasa_asmbl_4443.p1, internal, 138588, 138703
-recovered pasa_asmbl_4443.p1, internal, 139311, 139369
Valid prediction for Augustus_model.g16933.t1
Valid prediction for GlimmerHMM_glimmerT_25261-T1
Valid prediction for Augustus_model.g16946.t1
Valid prediction for GeneMark_model.43188_t
Valid prediction for Augustus_model.g16938.t1
Valid prediction for GeneMark_model.43178_t
Valid prediction for GeneMark_model.43198_t
Valid prediction for CodingQuarry_transcript_5398-T1
Valid prediction for GlimmerHMM_glimmerT_25259-T1
Valid prediction for GlimmerHMM_glimmerT_25266-T1
Valid prediction for GeneMark_model.43176_t
Valid prediction for pasa_asmbl_4451.p1
Valid prediction for GeneMark_model.43184_t
Valid prediction for GlimmerHMM_glimmerT_25272-T1
Valid prediction for GlimmerHMM_glimmerT_25253-T1
Valid prediction for GlimmerHMM_glimmerT_25250-T1
Valid prediction for CodingQuarry_transcript_5399-T1
Couldn't classify 13004, 13026
Sorry, prediction pasa_asmbl_4439.p1 fails validation.
(CAA)	 GT	13004-13026	GT	TTG
(GCC)	 AG	14465-14750	AG	AGA
-recovered pasa_asmbl_4439.p1, terminal, 14465, 14750
Valid prediction for GlimmerHMM_glimmerT_25264-T1
Valid prediction for snap_scaffold_10-snap.1162-T1
Valid prediction for CodingQuarry_transcript_5393-T1
Valid prediction for Augustus_model.g16941.t1
Couldn't classify 243261, 243584
Sorry, prediction pasa_asmbl_4454.p1 fails validation.
(CCT)	 TC	243261-243584	GA	GAG
Valid prediction for HiQ_model.g16944.t1
Valid prediction for snap_scaffold_10-snap.1171-T1
Valid prediction for snap_scaffold_10-snap.1181-T1
Valid prediction for GeneMark_model.43174_t
Valid prediction for GlimmerHMM_glimmerT_25247-T1
Valid prediction for snap_scaffold_10-snap.1176-T1
Valid prediction for snap_scaffold_10-snap.1167-T1
Valid prediction for snap_scaffold_10-snap.1159-T1
Couldn't classify 11403, 11595
Couldn't classify 11811, 12028
Sorry, prediction pasa_asmbl_4438.p1 fails validation.
(GCC)	 CA	11403-11595	GT	AGG
(AAA)	 AG	11811-12028	AG	GCA
Valid prediction for Augustus_model.g16942.t1
Valid prediction for snap_scaffold_10-snap.1170-T1
Valid prediction for Augustus_model.g16936.t1
Couldn't classify 60883, 60930
Couldn't classify 63657, 63683
Sorry, prediction pasa_asmbl_4441.p1 fails validation.
(CAC)	 GT	60883-60930	GT	AGG
(ATC)	 AG	61203-61340	GT	AGG
(TAC)	 AG	62541-62756	GT	TGG
(GAC)	 AG	62876-62950	GT	AGG
(AGT)	 AG	63390-63482	GT	TGG
(CCA)	 AG	63657-63683	GC	GAG
-recovered pasa_asmbl_4441.p1, internal, 61203, 61340
-recovered pasa_asmbl_4441.p1, internal, 62541, 62756
-recovered pasa_asmbl_4441.p1, internal, 62876, 62950
-recovered pasa_asmbl_4441.p1, internal, 63390, 63482
-recovered pasa_asmbl_4441.p1, internal, 63657, 63683
Valid prediction for Augustus_model.g16940.t1
Valid prediction for GlimmerHMM_glimmerT_25269-T1
Valid prediction for snap_scaffold_10-snap.1177-T1
Valid prediction for GeneMark_model.43187_t
Valid prediction for GeneMark_model.43190_t
Valid prediction for GeneMark_model.43182_t
Valid prediction for snap_scaffold_10-snap.1155-T1
Valid prediction for GeneMark_model.43196_t
Valid prediction for GeneMark_model.43189_t
Valid prediction for Augustus_model.g16939.t1
Valid prediction for snap_scaffold_10-snap.1188-T1
Valid prediction for GeneMark_model.43186_t
Valid prediction for snap_scaffold_10-snap.1179-T1
Valid prediction for GeneMark_model.43172_t
Valid prediction for snap_scaffold_10-snap.1157-T1
Valid prediction for snap_scaffold_10-snap.1184-T1
Valid prediction for GlimmerHMM_glimmerT_25256-T1
Valid prediction for GeneMark_model.43171_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 snap_scaffold_10-snap.1175-T1
Couldn't classify 3009, 3167
Sorry, prediction pasa_asmbl_3281.p1 fails validation.
(CTT)	 CT	3009-3167	GT	AGG
(GAT)	 AG	3765-3893	GT	GGG
(GTT)	 AG	4338-4391	GT	AGG
(GGA)	 AG	4475-4539	GT	AGG
(TTC)	 AG	4710-4824	GT	AGG
(GAT)	 AG	5237-5314	GT	AGG
(GTG)	 AG	5572-5633	GT	AGG
(GAG)	 AG	7051-7153	GT	AGG
(CCA)	 AG	7432-7509	GT	GGG
(TGT)	 AG	7969-8116	GT	TGG
(AAG)	 AG	8300-8383	GT	AGG
(GAC)	 AG	9009-9159	GT	GGG
(TGG)	 AG	9420-9495	GT	TGG
(CCT)	 AG	9937-10003	GT	AGG
(ACC)	 AG	10331-10707	AA	AAA
-recovered pasa_asmbl_3281.p1, terminal, 4475, 4539
-recovered pasa_asmbl_3281.p1, terminal, 10331, 10707
-recovered pasa_asmbl_3281.p1, internal, 3765, 3893
-recovered pasa_asmbl_3281.p1, internal, 4338, 4391
-recovered pasa_asmbl_3281.p1, internal, 4475, 4539
-recovered pasa_asmbl_3281.p1, internal, 4710, 4824
-recovered pasa_asmbl_3281.p1, internal, 5237, 5314
-recovered pasa_asmbl_3281.p1, internal, 5572, 5633
-recovered pasa_asmbl_3281.p1, internal, 7051, 7153
-recovered pasa_asmbl_3281.p1, internal, 7432, 7509
-recovered pasa_asmbl_3281.p1, internal, 7969, 8116
-recovered pasa_asmbl_3281.p1, internal, 8300, 8383
-recovered pasa_asmbl_3281.p1, internal, 9009, 9159
-recovered pasa_asmbl_3281.p1, internal, 9420, 9495
-recovered pasa_asmbl_3281.p1, internal, 9937, 10003
Valid prediction for snap_scaffold_10-snap.1174-T1
Valid prediction for Augustus_model.g16945.t1
Valid prediction for GlimmerHMM_glimmerT_25258-T1
Valid prediction for GeneMark_model.43199_t
Valid prediction for GeneMark_model.43200_t
Valid prediction for GlimmerHMM_glimmerT_25263-T1
Valid prediction for GlimmerHMM_glimmerT_25265-T1
Valid prediction for GlimmerHMM_glimmerT_25254-T1
Valid prediction for snap_scaffold_10-snap.1182-T1
Valid prediction for GlimmerHMM_glimmerT_25248-T1
Valid prediction for GlimmerHMM_glimmerT_25252-T1
Valid prediction for snap_scaffold_10-snap.1161-T1
Valid prediction for GeneMark_model.43173_t
Valid prediction for snap_scaffold_10-snap.1156-T1
Valid prediction for Augustus_model.g16937.t1
Valid prediction for GeneMark_model.43170_t
Valid prediction for GeneMark_model.43185_t
Valid prediction for GlimmerHMM_glimmerT_25257-T1
Valid prediction for GlimmerHMM_glimmerT_25270-T1
Valid prediction for snap_scaffold_10-snap.1180-T1
Valid prediction for pasa_asmbl_3273.p1
Valid prediction for GeneMark_model.43192_t
Valid prediction for snap_scaffold_10-snap.1172-T1
Valid prediction for snap_scaffold_10-snap.1187-T1
Valid prediction for snap_scaffold_10-snap.1185-T1
Valid prediction for GlimmerHMM_glimmerT_25267-T1
Valid prediction for GeneMark_model.43201_t
Valid prediction for snap_scaffold_10-snap.1152-T1
Valid prediction for snap_scaffold_10-snap.1154-T1
Valid prediction for GeneMark_model.43181_t
Valid prediction for GlimmerHMM_glimmerT_25271-T1
Valid prediction for HiQ_model.g16931.t1
Valid prediction for GeneMark_model.43179_t
Valid prediction for GlimmerHMM_glimmerT_25274-T1
Valid prediction for snap_scaffold_10-snap.1163-T1
Valid prediction for Augustus_model.g16934.t1
Valid prediction for GlimmerHMM_glimmerT_25273-T1
Valid prediction for HiQ_model.g16950.t1
Valid prediction for Augustus_model.g16935.t1
Valid prediction for GlimmerHMM_glimmerT_25268-T1
Valid prediction for GeneMark_model.43177_t
Valid prediction for Augustus_model.g16947.t1
Valid prediction for GlimmerHMM_glimmerT_25255-T1
Valid prediction for CodingQuarry_transcript_5397-T1
Valid prediction for GeneMark_model.43191_t
Valid prediction for snap_scaffold_10-snap.1166-T1
Valid prediction for snap_scaffold_10-snap.1186-T1
Couldn't classify 16706, 16755
Sorry, prediction pasa_asmbl_3279.p1 fails validation.
(CAA)	 CA	16706-16755	GT	AAG
(GCC)	 AG	16898-17011	GT	GGG
(TGA)	 AG	17312-17393	GT	GGG
(TTC)	 AG	17550-17640	GT	AGG
(CTA)	 AG	18246-18412	GT	AGG
(ATC)	 AG	18614-18785	GT	GGG
(GTG)	 AG	18932-19080	GT	AGG
(GTC)	 AG	19184-19549	AT	GAA
-recovered pasa_asmbl_3279.p1, terminal, 19184, 19549
-recovered pasa_asmbl_3279.p1, internal, 16898, 17011
-recovered pasa_asmbl_3279.p1, internal, 17312, 17393
-recovered pasa_asmbl_3279.p1, internal, 17550, 17640
-recovered pasa_asmbl_3279.p1, internal, 18246, 18412
-recovered pasa_asmbl_3279.p1, internal, 18614, 18785
-recovered pasa_asmbl_3279.p1, internal, 18932, 19080
Valid prediction for GeneMark_model.43193_t
Valid prediction for snap_scaffold_10-snap.1165-T1
Valid prediction for CodingQuarry_transcript_5394-T1
Valid prediction for snap_scaffold_10-snap.1158-T1
Valid prediction for snap_scaffold_10-snap.1178-T1
Valid prediction for HiQ_model.g16932.t1
Valid prediction for snap_scaffold_10-snap.1189-T1
Valid prediction for HiQ_model.g16948.t1
Valid prediction for GeneMark_model.43175_t
Valid prediction for GlimmerHMM_glimmerT_25251-T1
Valid prediction for pasa_asmbl_3268.p1
Valid prediction for snap_scaffold_10-snap.1153-T1
Valid prediction for GeneMark_model.43197_t
Valid prediction for snap_scaffold_10-snap.1169-T1
Valid prediction for GlimmerHMM_glimmerT_25249-T1
Couldn't classify 12019, 12130
Sorry, prediction pasa_asmbl_3280.p1 fails validation.
(CGT)	 GA	12019-12130	GT	AAG
(CGG)	 AG	12373-13052	TA	AAT
-recovered pasa_asmbl_3280.p1, terminal, 12373, 13052
Valid prediction for Augustus_model.g16943.t1
Valid prediction for GeneMark_model.43194_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 25436, rend_intergenic: 21028  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28570, rend_intergenic: 26000  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31555, rend_intergenic: 28778  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52007, rend_intergenic: 41886  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195798, rend_intergenic: 190112  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 205243, rend_intergenic: 202789  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 253888
-exon list size: 517


building trellis

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-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 25436, rend_intergenic: 21028  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28570, rend_intergenic: 26000  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31555, rend_intergenic: 28778  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52007, rend_intergenic: 41886  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195798, rend_intergenic: 190112  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 205243, rend_intergenic: 202789  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 27 predictions persist after filtering for low support