-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_18/scaffold_18_1933688-2146435

-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_18-snap.436-T1
Valid prediction for Augustus_model.g27879.t1
Valid prediction for GlimmerHMM_glimmerT_41856-T1
Valid prediction for snap_scaffold_18-snap.441-T1
Valid prediction for Augustus_model.g27884.t1
Valid prediction for pasa_asmbl_20402.p2
Valid prediction for snap_scaffold_18-snap.421-T1
Valid prediction for snap_scaffold_18-snap.425-T1
Valid prediction for GlimmerHMM_glimmerT_41864-T1
Valid prediction for CodingQuarry_transcript_23682-T1
Valid prediction for Augustus_model.g27877.t1
Valid prediction for HiQ_model.g27864.t1
Valid prediction for snap_scaffold_18-snap.420-T1
Valid prediction for snap_scaffold_18-snap.443-T1
Valid prediction for Augustus_model.g27885.t1
Valid prediction for GlimmerHMM_glimmerT_41865-T1
Valid prediction for GlimmerHMM_glimmerT_41876-T1
Valid prediction for snap_scaffold_18-snap.439-T1
Valid prediction for CodingQuarry_transcript_23686-T1
Valid prediction for pasa_asmbl_20397.p1
Couldn't classify 173081, 173141
Couldn't classify 174021, 174164
Sorry, prediction pasa_asmbl_21142.p1 fails validation.
(GGT)	 TT	173081-173141	GT	CAG
(ATA)	 AG	173625-173722	GT	GGG
(GAG)	 AG	174021-174164	GG	GGG
-recovered pasa_asmbl_21142.p1, internal, 173625, 173722
Valid prediction for snap_scaffold_18-snap.418-T1
Valid prediction for snap_scaffold_18-snap.407-T1
Valid prediction for snap_scaffold_18-snap.423-T1
Valid prediction for HiQ_model.g27868.t1
Valid prediction for GlimmerHMM_glimmerT_41862-T1
Valid prediction for snap_scaffold_18-snap.434-T1
Valid prediction for snap_scaffold_18-snap.437-T1
Valid prediction for HiQ_model.g27863.t1
Valid prediction for snap_scaffold_18-snap.438-T1
Valid prediction for Augustus_model.g27874.t1
Valid prediction for GlimmerHMM_glimmerT_41859-T1
Valid prediction for snap_scaffold_18-snap.415-T1
Valid prediction for snap_scaffold_18-snap.433-T1
Valid prediction for GlimmerHMM_glimmerT_41861-T1
Valid prediction for snap_scaffold_18-snap.448-T1
Valid prediction for CodingQuarry_transcript_23683-T1
Valid prediction for snap_scaffold_18-snap.427-T1
Valid prediction for Augustus_model.g27870.t1
Valid prediction for GlimmerHMM_glimmerT_41853-T1
Valid prediction for CodingQuarry_transcript_23689-T1
Valid prediction for snap_scaffold_18-snap.446-T1
Valid prediction for snap_scaffold_18-snap.445-T1
Valid prediction for GlimmerHMM_glimmerT_41867-T1
Valid prediction for pasa_asmbl_20394.p1
Valid prediction for snap_scaffold_18-snap.430-T1
Valid prediction for GlimmerHMM_glimmerT_41854-T1
Valid prediction for Augustus_model.g27872.t1
Valid prediction for snap_scaffold_18-snap.431-T1
Valid prediction for GlimmerHMM_glimmerT_41870-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 pasa_asmbl_19681.p1
Valid prediction for HiQ_model.g27865.t1
Couldn't classify 139797, 140003
Sorry, prediction pasa_asmbl_19687.p4 fails validation.
(ATC)	 AC	139797-140003	GT	GCG
(TCG)	 AG	140119-140256	GA	GAG
-recovered pasa_asmbl_19687.p4, terminal, 140119, 140256
Valid prediction for Augustus_model.g27876.t1
Valid prediction for GlimmerHMM_glimmerT_41871-T1
Couldn't classify 93003, 93017
Couldn't classify 93795, 94139
Sorry, prediction pasa_asmbl_19694.p1 fails validation.
(CCC)	 CA	93003-93017	GT	AGG
(GTG)	 AG	93131-93390	GT	TGG
(GAC)	 AG	93507-93678	GT	CGG
(CCA)	 AG	93795-94139	CA	CCC
-recovered pasa_asmbl_19694.p1, internal, 93131, 93390
-recovered pasa_asmbl_19694.p1, internal, 93507, 93678
Valid prediction for Augustus_model.g27869.t1
Valid prediction for Augustus_model.g27866.t1
Valid prediction for CodingQuarry_transcript_23687-T1
Valid prediction for GlimmerHMM_glimmerT_41860-T1
Valid prediction for snap_scaffold_18-snap.422-T1
Valid prediction for Augustus_model.g27880.t1
Valid prediction for Augustus_model.g27873.t1
Valid prediction for snap_scaffold_18-snap.414-T1
Valid prediction for snap_scaffold_18-snap.444-T1
Valid prediction for snap_scaffold_18-snap.442-T1
Valid prediction for GlimmerHMM_glimmerT_41874-T1
Valid prediction for snap_scaffold_18-snap.406-T1
Valid prediction for Augustus_model.g27878.t1
Couldn't classify 129715, 130620
Sorry, prediction pasa_asmbl_19688.p1 fails validation.
(ATG)	 AG	129715-130620	CG	AGC
Couldn't classify 171189, 171288
Sorry, prediction pasa_asmbl_19680.p1 fails validation.
(GAT)	 AT	171189-171288	GT	AGG
(ATT)	 AG	173352-173500	GT	TGG
(GAC)	 AG	174983-175150	GC	GAG
-recovered pasa_asmbl_19680.p1, terminal, 174983, 175150
-recovered pasa_asmbl_19680.p1, internal, 173352, 173500
-recovered pasa_asmbl_19680.p1, internal, 174983, 175150
Valid prediction for snap_scaffold_18-snap.426-T1
Valid prediction for GlimmerHMM_glimmerT_41873-T1
Valid prediction for snap_scaffold_18-snap.411-T1
Valid prediction for snap_scaffold_18-snap.428-T1
Valid prediction for GlimmerHMM_glimmerT_41863-T1
Couldn't classify 83748, 83944
Couldn't classify 85942, 86019
Sorry, prediction pasa_asmbl_19700.p1 fails validation.
(ACC)	 CC	83748-83944	GT	AGG
(TGT)	 AG	84065-84204	GT	TGG
(ACG)	 AG	84743-84924	GT	AGG
(GCA)	 AG	85079-85117	GT	AGG
(GGT)	 AG	85548-85748	GT	AGG
(AGT)	 AG	85942-86019	GG	GGG
-recovered pasa_asmbl_19700.p1, internal, 84065, 84204
-recovered pasa_asmbl_19700.p1, internal, 84743, 84924
-recovered pasa_asmbl_19700.p1, internal, 85079, 85117
-recovered pasa_asmbl_19700.p1, internal, 85548, 85748
Couldn't classify 35254, 35344
Sorry, prediction pasa_asmbl_19707.p1 fails validation.
(ATG)	 TG	33783-33943	GT	CAG
(GAT)	 AG	34285-34414	GT	AGG
(ACG)	 AG	34568-34695	GT	AAG
(GTT)	 AG	35254-35344	CT	TCC
-recovered pasa_asmbl_19707.p1, initial, 33783, 33943
-recovered pasa_asmbl_19707.p1, internal, 34285, 34414
-recovered pasa_asmbl_19707.p1, internal, 34568, 34695
Valid prediction for Augustus_model.g27867.t1
Valid prediction for snap_scaffold_18-snap.435-T1
Valid prediction for Augustus_model.g27861.t1
Valid prediction for Augustus_model.g27862.t1
Valid prediction for pasa_asmbl_19682.p1
Valid prediction for CodingQuarry_transcript_23688-T1
Valid prediction for snap_scaffold_18-snap.429-T1
Valid prediction for snap_scaffold_18-snap.408-T1
Valid prediction for snap_scaffold_18-snap.424-T1
Valid prediction for GlimmerHMM_glimmerT_41872-T1
Valid prediction for GlimmerHMM_glimmerT_41852-T1
Valid prediction for snap_scaffold_18-snap.409-T1
Couldn't classify 201542, 201695
Sorry, prediction pasa_asmbl_19673.p1 fails validation.
(GAG)	 CA	201542-201695	GT	AAG
(CAA)	 AG	201792-201935	GT	GGG
(CTC)	 AG	202070-202197	GT	GAG
-recovered pasa_asmbl_19673.p1, terminal, 202070, 202197
-recovered pasa_asmbl_19673.p1, internal, 201792, 201935
-recovered pasa_asmbl_19673.p1, internal, 202070, 202197
Valid prediction for snap_scaffold_18-snap.410-T1
Valid prediction for GlimmerHMM_glimmerT_41858-T1
Valid prediction for snap_scaffold_18-snap.413-T1
Valid prediction for GlimmerHMM_glimmerT_41851-T1
Couldn't classify 91851, 91866
Couldn't classify 92481, 92819
Sorry, prediction pasa_asmbl_19695.p1 fails validation.
(GGC)	 AC	91851-91866	GT	AGG
(AGT)	 AG	91983-92209	GT	AGG
(AGT)	 AG	92325-92381	GT	AGG
(GCT)	 AG	92481-92819	CC	TGC
-recovered pasa_asmbl_19695.p1, internal, 91983, 92209
-recovered pasa_asmbl_19695.p1, internal, 92325, 92381
Valid prediction for GlimmerHMM_glimmerT_41857-T1
Valid prediction for CodingQuarry_transcript_23681-T1
Valid prediction for snap_scaffold_18-snap.432-T1
Valid prediction for Augustus_model.g27871.t1
Valid prediction for snap_scaffold_18-snap.419-T1
Couldn't classify 86346, 86357
Couldn't classify 90815, 90943
Sorry, prediction pasa_asmbl_19698.p1 fails validation.
(CCC)	 CC	86346-86357	GT	AGG
(GTG)	 AG	86516-86625	GT	TGG
(TAA)	 AG	86721-86970	GT	AGG
(GAT)	 AG	88031-88129	GT	TGG
(ACG)	 AG	90477-90656	GT	AGG
(CCC)	 AG	90815-90943	AC	GCA
-recovered pasa_asmbl_19698.p1, internal, 86516, 86625
-recovered pasa_asmbl_19698.p1, internal, 86721, 86970
-recovered pasa_asmbl_19698.p1, internal, 88031, 88129
-recovered pasa_asmbl_19698.p1, internal, 90477, 90656
Valid prediction for snap_scaffold_18-snap.447-T1
Valid prediction for GlimmerHMM_glimmerT_41866-T1
Valid prediction for Augustus_model.g27875.t1
Valid prediction for Augustus_model.g27883.t1
Couldn't classify 58349, 58504
Couldn't classify 60252, 60642
Sorry, prediction pasa_asmbl_19704.p1 fails validation.
(CTG)	 CT	58349-58504	GT	AGG
(GAC)	 AG	58809-58933	GT	CAG
(GGA)	 AG	59200-59366	GT	CCG
(GAG)	 AG	59582-59676	GT	AGG
(CAA)	 AG	59817-59983	GT	CGG
(AGA)	 AG	60252-60642	AC	CCA
-recovered pasa_asmbl_19704.p1, internal, 58809, 58933
-recovered pasa_asmbl_19704.p1, internal, 59200, 59366
-recovered pasa_asmbl_19704.p1, internal, 59582, 59676
-recovered pasa_asmbl_19704.p1, internal, 59817, 59983
Valid prediction for GlimmerHMM_glimmerT_41855-T1
Valid prediction for snap_scaffold_18-snap.440-T1
Valid prediction for GlimmerHMM_glimmerT_41869-T1
Valid prediction for CodingQuarry_transcript_23684-T1
Valid prediction for CodingQuarry_transcript_23685-T1
Valid prediction for snap_scaffold_18-snap.412-T1
Valid prediction for Augustus_model.g27881.t1
Valid prediction for snap_scaffold_18-snap.405-T1
Couldn't classify 91359, 91613
Couldn't classify 91716, 91790
Sorry, prediction pasa_asmbl_19696.p1 fails validation.
(GCC)	 GC	91359-91613	GT	AGG
(CGC)	 AG	91716-91790	CC	CCC
Couldn't classify 178705, 178748
Sorry, prediction pasa_asmbl_19676.p1 fails validation.
(GCG)	 TA	178705-178748	GT	CAG
(TGG)	 AG	179142-179179	GT	AGG
(GTC)	 AG	179378-179499	GT	ATG
(ACA)	 AG	179806-179883	GT	GAG
(GGC)	 AG	180022-180132	GT	AGG
(GTA)	 AG	180311-180745	AG	AGA
-recovered pasa_asmbl_19676.p1, terminal, 180311, 180745
-recovered pasa_asmbl_19676.p1, internal, 179142, 179179
-recovered pasa_asmbl_19676.p1, internal, 179378, 179499
-recovered pasa_asmbl_19676.p1, internal, 179806, 179883
-recovered pasa_asmbl_19676.p1, internal, 180022, 180132
Valid prediction for snap_scaffold_18-snap.417-T1
Valid prediction for Augustus_model.g27882.t1
Valid prediction for GlimmerHMM_glimmerT_41875-T1
Valid prediction for GlimmerHMM_glimmerT_41868-T1
Valid prediction for snap_scaffold_18-snap.416-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 75691, rend_intergenic: 74071  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79917, rend_intergenic: 75775  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84886, rend_intergenic: 80803  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102583, rend_intergenic: 98364  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113138, rend_intergenic: 109250  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133853, rend_intergenic: 120933  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140344, rend_intergenic: 134448  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167997, rend_intergenic: 151711  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185138, rend_intergenic: 183721  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 191426, rend_intergenic: 185927  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 198606, rend_intergenic: 194590  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 206326, rend_intergenic: 198640  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 212748
-exon list size: 469


building trellis

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-found 38 predictions from path traversal
Error with prediction: snap lend_intergenic: 75691, rend_intergenic: 74071  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79917, rend_intergenic: 75775  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84886, rend_intergenic: 80803  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102583, rend_intergenic: 98364  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113138, rend_intergenic: 109250  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133853, rend_intergenic: 120933  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140344, rend_intergenic: 134448  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167997, rend_intergenic: 151711  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185138, rend_intergenic: 183721  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 191426, rend_intergenic: 185927  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 198606, rend_intergenic: 194590  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 206326, rend_intergenic: 198640  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 32 predictions persist after filtering for low support