-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_26/scaffold_26_2154280-2322057

-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_26-snap.475-T1
Valid prediction for snap_scaffold_26-snap.441-T1
Valid prediction for GlimmerHMM_glimmerT_56514-T1
Valid prediction for GeneMark_model.98578_t
Valid prediction for GeneMark_model.98567_t
Valid prediction for snap_scaffold_26-snap.455-T1
Valid prediction for GeneMark_model.98574_t
Valid prediction for GlimmerHMM_glimmerT_56496-T1
Valid prediction for snap_scaffold_26-snap.443-T1
Valid prediction for snap_scaffold_26-snap.464-T1
Valid prediction for GlimmerHMM_glimmerT_56519-T1
Valid prediction for snap_scaffold_26-snap.472-T1
Valid prediction for snap_scaffold_26-snap.467-T1
Valid prediction for snap_scaffold_26-snap.453-T1
Valid prediction for GlimmerHMM_glimmerT_56512-T1
Valid prediction for snap_scaffold_26-snap.473-T1
Valid prediction for GlimmerHMM_glimmerT_56524-T1
Valid prediction for CodingQuarry_transcript_40165-T1
Valid prediction for Augustus_model.g37636.t1
Valid prediction for snap_scaffold_26-snap.452-T1
Valid prediction for GeneMark_model.98561_t
Valid prediction for GeneMark_model.98571_t
Valid prediction for GeneMark_model.98545_t
Valid prediction for Augustus_model.g37626.t1
Valid prediction for GeneMark_model.98580_t
Valid prediction for Augustus_model.g37635.t1
Valid prediction for Augustus_model.g37627.t1
Valid prediction for GlimmerHMM_glimmerT_56516-T1
Valid prediction for Augustus_model.g37633.t1
Valid prediction for GlimmerHMM_glimmerT_56502-T1
Valid prediction for snap_scaffold_26-snap.447-T1
Valid prediction for snap_scaffold_26-snap.446-T1
Valid prediction for snap_scaffold_26-snap.461-T1
Couldn't classify 112601, 113175
Sorry, prediction pasa_asmbl_35274.p1 fails validation.
(AGC)	 CC	112601-113175	GT	AGG
(GTT)	 AG	113505-113946	GA	AGG
-recovered pasa_asmbl_35274.p1, terminal, 113505, 113946
Valid prediction for snap_scaffold_26-snap.451-T1
Valid prediction for GeneMark_model.98550_t
Valid prediction for pasa_asmbl_35265.p1
Valid prediction for GeneMark_model.98547_t
Valid prediction for GlimmerHMM_glimmerT_56503-T1
Valid prediction for snap_scaffold_26-snap.439-T1
Valid prediction for GeneMark_model.98557_t
Valid prediction for GlimmerHMM_glimmerT_56501-T1
Valid prediction for snap_scaffold_26-snap.471-T1
Valid prediction for GlimmerHMM_glimmerT_56500-T1
Couldn't classify 7771, 8256
Sorry, prediction pasa_asmbl_35263.p1 fails validation.
(CCC)	 AG	7771-8256	AA	ACA
Valid prediction for snap_scaffold_26-snap.465-T1
Valid prediction for GlimmerHMM_glimmerT_56521-T1
Valid prediction for snap_scaffold_26-snap.474-T1
Valid prediction for GeneMark_model.98564_t
Valid prediction for GeneMark_model.98572_t
Valid prediction for pasa_asmbl_35271.p2
Valid prediction for snap_scaffold_26-snap.460-T1
Valid prediction for snap_scaffold_26-snap.438-T1
Valid prediction for GeneMark_model.98562_t
Valid prediction for GeneMark_model.98575_t
Valid prediction for Augustus_model.g37634.t1
Valid prediction for GeneMark_model.98554_t
Valid prediction for GeneMark_model.98568_t
Valid prediction for snap_scaffold_26-snap.445-T1
Valid prediction for GlimmerHMM_glimmerT_56495-T1
Couldn't classify 125351, 125487
Couldn't classify 127289, 127335
Sorry, prediction pasa_asmbl_35278.p2 fails validation.
(ACC)	 CG	125351-125487	GT	AGG
(GTT)	 AG	126121-126239	GT	CCG
(AAT)	 AG	127289-127335	GT	GAG
-recovered pasa_asmbl_35278.p2, internal, 126121, 126239
-recovered pasa_asmbl_35278.p2, internal, 127289, 127335
Valid prediction for CodingQuarry_transcript_40164-T1
Valid prediction for GlimmerHMM_glimmerT_56510-T1
Valid prediction for Augustus_model.g37639.t1
Valid prediction for GeneMark_model.98584_t
Valid prediction for GeneMark_model.98556_t
Valid prediction for GlimmerHMM_glimmerT_56520-T1
Valid prediction for snap_scaffold_26-snap.442-T1
Valid prediction for GeneMark_model.98552_t
Valid prediction for GeneMark_model.98582_t
Valid prediction for GeneMark_model.98559_t
Couldn't classify 74841, 74921
Sorry, prediction pasa_asmbl_35869.p1 fails validation.
(ATG)	 CG	74439-74529	GT	GGG
(ATG)	 AG	74606-74745	GT	GGG
(CAC)	 AG	74841-74921	GT	AGG
-recovered pasa_asmbl_35869.p1, initial, 74439, 74529
add_exon() Sorry, pasa_asmbl_35869.p1 74606-74745-initial-1 is invalid.
-recovered pasa_asmbl_35869.p1, initial, 74606, 74745
-recovered pasa_asmbl_35869.p1, internal, 74606, 74745
-recovered pasa_asmbl_35869.p1, internal, 74841, 74921
Couldn't classify 112145, 112386
Sorry, prediction pasa_asmbl_35273.p1 fails validation.
(ATG)	 CA	110603-111146	GT	AGG
(GCA)	 AG	112145-112386	GG	CTG
-recovered pasa_asmbl_35273.p1, initial, 110603, 111146
Valid prediction for Augustus_model.g37629.t1
Valid prediction for GlimmerHMM_glimmerT_56517-T1
Valid prediction for snap_scaffold_26-snap.457-T1
Valid prediction for snap_scaffold_26-snap.469-T1
Valid prediction for Augustus_model.g37637.t1
Valid prediction for GlimmerHMM_glimmerT_56505-T1
Valid prediction for GlimmerHMM_glimmerT_56499-T1
Valid prediction for Augustus_model.g37638.t1
Valid prediction for GeneMark_model.98570_t
Valid prediction for GeneMark_model.98576_t
Valid prediction for HiQ_model.g37632.t1
Couldn't classify 127637, 127689
Couldn't classify 131143, 131250
Sorry, prediction pasa_asmbl_35279.p1 fails validation.
(AAC)	 TT	127637-127689	GT	AGG
(CTT)	 AG	128024-128156	GT	TGG
(TCC)	 AG	128918-128963	GT	TGG
(GTG)	 AG	130277-130461	GT	AGG
(TTG)	 AG	131143-131250	GG	CAG
-recovered pasa_asmbl_35279.p1, internal, 128024, 128156
-recovered pasa_asmbl_35279.p1, internal, 128918, 128963
-recovered pasa_asmbl_35279.p1, internal, 130277, 130461
Valid prediction for GlimmerHMM_glimmerT_56513-T1
Valid prediction for snap_scaffold_26-snap.462-T1
Valid prediction for GlimmerHMM_glimmerT_56508-T1
Couldn't classify 121915, 122002
Couldn't classify 122326, 122548
Sorry, prediction pasa_asmbl_35277.p1 fails validation.
(GTC)	 TG	121915-122002	GT	ATG
(TGA)	 AG	122114-122189	GT	CGG
(GTA)	 AG	122326-122548	GG	GGG
-recovered pasa_asmbl_35277.p1, internal, 122114, 122189
Valid prediction for GeneMark_model.98569_t
Valid prediction for snap_scaffold_26-snap.437-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.98563_t
Valid prediction for snap_scaffold_26-snap.468-T1
Valid prediction for GeneMark_model.98573_t
Valid prediction for HiQ_model.g37631.t1
Valid prediction for GlimmerHMM_glimmerT_56523-T1
Valid prediction for GeneMark_model.98566_t
Valid prediction for GlimmerHMM_glimmerT_56507-T1
Valid prediction for snap_scaffold_26-snap.448-T1
Valid prediction for snap_scaffold_26-snap.463-T1
Valid prediction for GlimmerHMM_glimmerT_56511-T1
Valid prediction for GeneMark_model.98579_t
Valid prediction for snap_scaffold_26-snap.458-T1
Valid prediction for GeneMark_model.98583_t
Valid prediction for GlimmerHMM_glimmerT_56522-T1
Valid prediction for GlimmerHMM_glimmerT_56504-T1
Valid prediction for snap_scaffold_26-snap.470-T1
Valid prediction for GlimmerHMM_glimmerT_56497-T1
Valid prediction for GlimmerHMM_glimmerT_56515-T1
Valid prediction for snap_scaffold_26-snap.449-T1
Valid prediction for GeneMark_model.98549_t
Valid prediction for GeneMark_model.98546_t
Valid prediction for Augustus_model.g37628.t1
Valid prediction for pasa_asmbl_34718.p1
Valid prediction for snap_scaffold_26-snap.444-T1
Valid prediction for GeneMark_model.98548_t
Valid prediction for GeneMark_model.98565_t
Valid prediction for GeneMark_model.98551_t
Couldn't classify 89814, 89934
Couldn't classify 90277, 90413
Sorry, prediction pasa_asmbl_35186.p1 fails validation.
(CTG)	 TG	89814-89934	GT	ATG
(ATC)	 AG	90037-90144	GT	CAG
(GGT)	 AG	90277-90413	GG	GAG
-recovered pasa_asmbl_35186.p1, internal, 90037, 90144
Valid prediction for snap_scaffold_26-snap.440-T1
Valid prediction for GlimmerHMM_glimmerT_56518-T1
Valid prediction for CodingQuarry_transcript_40162-T1
Couldn't classify 97701, 97811
Sorry, prediction pasa_asmbl_34713.p1 fails validation.
(ATG)	 CT	96547-96575	GT	AGG
(CAT)	 AG	96818-96908	GT	TGG
(GGT)	 AG	97029-97139	GT	AGG
(GCG)	 AG	97223-97378	GT	AGG
(CTG)	 AG	97701-97811	GT	AGG
-recovered pasa_asmbl_34713.p1, initial, 96547, 96575
-recovered pasa_asmbl_34713.p1, internal, 96818, 96908
-recovered pasa_asmbl_34713.p1, internal, 97029, 97139
-recovered pasa_asmbl_34713.p1, internal, 97223, 97378
-recovered pasa_asmbl_34713.p1, internal, 97701, 97811
Valid prediction for GlimmerHMM_glimmerT_56509-T1
Valid prediction for snap_scaffold_26-snap.454-T1
Valid prediction for GeneMark_model.98555_t
Valid prediction for snap_scaffold_26-snap.459-T1
Valid prediction for snap_scaffold_26-snap.456-T1
Valid prediction for GeneMark_model.98560_t
Valid prediction for GeneMark_model.98581_t
Valid prediction for Augustus_model.g37630.t1
Valid prediction for GlimmerHMM_glimmerT_56498-T1
Valid prediction for snap_scaffold_26-snap.450-T1
Valid prediction for snap_scaffold_26-snap.466-T1
Valid prediction for CodingQuarry_transcript_40163-T1
Valid prediction for GeneMark_model.98553_t
Valid prediction for GeneMark_model.98577_t
Valid prediction for GeneMark_model.98558_t
Valid prediction for GlimmerHMM_glimmerT_56506-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 47913, rend_intergenic: 19946  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52445, rend_intergenic: 48575  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67013, rend_intergenic: 61030  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70581, rend_intergenic: 69392  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78786, rend_intergenic: 76451  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99538, rend_intergenic: 98426  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117080, rend_intergenic: 116045  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124988, rend_intergenic: 122255  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133452, rend_intergenic: 127285  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137459, rend_intergenic: 135760  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142615, rend_intergenic: 139826  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 167778
-exon list size: 589


building trellis

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-found 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 47913, rend_intergenic: 19946  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52445, rend_intergenic: 48575  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67013, rend_intergenic: 61030  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70581, rend_intergenic: 69392  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78786, rend_intergenic: 76451  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99538, rend_intergenic: 98426  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117080, rend_intergenic: 116045  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124988, rend_intergenic: 122255  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133452, rend_intergenic: 127285  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137459, rend_intergenic: 135760  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142615, rend_intergenic: 139826  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support