-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_21/scaffold_21_2817941-3052160

-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_21-snap.531-T1
Valid prediction for GlimmerHMM_glimmerT_47333-T1
Valid prediction for snap_scaffold_21-snap.513-T1
Valid prediction for GlimmerHMM_glimmerT_47321-T1
Valid prediction for CodingQuarry_transcript_32473-T1
Valid prediction for Augustus_model.g31508.t1
Valid prediction for pasa_asmbl_28440.p1
Valid prediction for snap_scaffold_21-snap.510-T1
Valid prediction for Augustus_model.g31506.t1
Couldn't classify 211034, 211228
Couldn't classify 212678, 212770
Sorry, prediction pasa_asmbl_28438.p1 fails validation.
(TGT)	 AG	211034-211228	GT	ATG
(GTG)	 AG	212088-212182	GT	AGG
(TAT)	 AG	212418-212547	GT	CTG
(AGT)	 AG	212678-212770	GT	AAG
-recovered pasa_asmbl_28438.p1, internal, 211034, 211228
-recovered pasa_asmbl_28438.p1, internal, 212088, 212182
-recovered pasa_asmbl_28438.p1, internal, 212418, 212547
-recovered pasa_asmbl_28438.p1, internal, 212678, 212770
Valid prediction for snap_scaffold_21-snap.526-T1
Valid prediction for Augustus_model.g31521.t1
Valid prediction for snap_scaffold_21-snap.538-T1
Couldn't classify 60056, 60139
Couldn't classify 60472, 60637
Sorry, prediction pasa_asmbl_28987.p1 fails validation.
(AGC)	 CC	60056-60139	GT	CGG
(GAT)	 AG	60305-60381	GT	AAG
(GTA)	 AG	60472-60637	AC	ACA
-recovered pasa_asmbl_28987.p1, internal, 60305, 60381
Valid prediction for Augustus_model.g31513.t1
Valid prediction for GlimmerHMM_glimmerT_47309-T1
Valid prediction for CodingQuarry_transcript_32470-T1
Valid prediction for snap_scaffold_21-snap.530-T1
Valid prediction for pasa_asmbl_28437.p1
Valid prediction for GlimmerHMM_glimmerT_47313-T1
Valid prediction for GlimmerHMM_glimmerT_47310-T1
Valid prediction for snap_scaffold_21-snap.540-T1
Valid prediction for snap_scaffold_21-snap.557-T1
Valid prediction for snap_scaffold_21-snap.520-T1
Valid prediction for Augustus_model.g31529.t1
Valid prediction for snap_scaffold_21-snap.518-T1
Valid prediction for snap_scaffold_21-snap.517-T1
Valid prediction for snap_scaffold_21-snap.551-T1
Valid prediction for GlimmerHMM_glimmerT_47320-T1
Valid prediction for GlimmerHMM_glimmerT_47330-T1
Valid prediction for CodingQuarry_transcript_32471-T1
Valid prediction for snap_scaffold_21-snap.525-T1
Valid prediction for Augustus_model.g31511.t1
Valid prediction for GlimmerHMM_glimmerT_47306-T1
Valid prediction for snap_scaffold_21-snap.552-T1
Valid prediction for snap_scaffold_21-snap.555-T1
Valid prediction for HiQ_model.g31535.t1
Valid prediction for GlimmerHMM_glimmerT_47328-T1
Valid prediction for GlimmerHMM_glimmerT_47317-T1
Valid prediction for pasa_asmbl_28428.p1
Valid prediction for HiQ_model.g31527.t1
Valid prediction for snap_scaffold_21-snap.539-T1
Valid prediction for snap_scaffold_21-snap.534-T1
Valid prediction for Augustus_model.g31533.t1
Valid prediction for snap_scaffold_21-snap.514-T1
Valid prediction for snap_scaffold_21-snap.521-T1
Valid prediction for GlimmerHMM_glimmerT_47329-T1
Valid prediction for snap_scaffold_21-snap.535-T1
Valid prediction for Augustus_model.g31518.t1
Valid prediction for HiQ_model.g31530.t1
Valid prediction for GlimmerHMM_glimmerT_47302-T1
Valid prediction for snap_scaffold_21-snap.523-T1
Valid prediction for CodingQuarry_transcript_32472-T1
Valid prediction for Augustus_model.g31512.t1
Valid prediction for Augustus_model.g31531.t1
Valid prediction for HiQ_model.g31520.t1
Valid prediction for snap_scaffold_21-snap.524-T1
Valid prediction for Augustus_model.g31509.t1
Valid prediction for GlimmerHMM_glimmerT_47318-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 snap_scaffold_21-snap.550-T1
Valid prediction for snap_scaffold_21-snap.541-T1
Valid prediction for GlimmerHMM_glimmerT_47324-T1
Valid prediction for snap_scaffold_21-snap.547-T1
Valid prediction for GlimmerHMM_glimmerT_47325-T1
Valid prediction for GlimmerHMM_glimmerT_47327-T1
Valid prediction for GlimmerHMM_glimmerT_47322-T1
Valid prediction for snap_scaffold_21-snap.548-T1
Valid prediction for Augustus_model.g31532.t1
Valid prediction for snap_scaffold_21-snap.511-T1
Valid prediction for Augustus_model.g31515.t1
Valid prediction for Augustus_model.g31523.t1
Valid prediction for GlimmerHMM_glimmerT_47303-T1
Valid prediction for snap_scaffold_21-snap.553-T1
Valid prediction for snap_scaffold_21-snap.527-T1
Valid prediction for snap_scaffold_21-snap.549-T1
Valid prediction for Augustus_model.g31514.t1
Valid prediction for GlimmerHMM_glimmerT_47305-T1
Valid prediction for GlimmerHMM_glimmerT_47326-T1
Valid prediction for Augustus_model.g31534.t1
Valid prediction for snap_scaffold_21-snap.529-T1
Couldn't classify 217407, 218537
Sorry, prediction pasa_asmbl_27490.p1 fails validation.
(CCA)	 GA	217407-218537	AA	GAA
Valid prediction for GlimmerHMM_glimmerT_47304-T1
Valid prediction for GlimmerHMM_glimmerT_47307-T1
Valid prediction for snap_scaffold_21-snap.543-T1
Valid prediction for GlimmerHMM_glimmerT_47323-T1
Valid prediction for snap_scaffold_21-snap.537-T1
Valid prediction for GlimmerHMM_glimmerT_47312-T1
Valid prediction for snap_scaffold_21-snap.522-T1
Valid prediction for GlimmerHMM_glimmerT_47315-T1
Valid prediction for snap_scaffold_21-snap.542-T1
Valid prediction for GlimmerHMM_glimmerT_47308-T1
Valid prediction for snap_scaffold_21-snap.515-T1
Valid prediction for snap_scaffold_21-snap.536-T1
Valid prediction for snap_scaffold_21-snap.545-T1
Valid prediction for snap_scaffold_21-snap.512-T1
Valid prediction for GlimmerHMM_glimmerT_47311-T1
Valid prediction for Augustus_model.g31524.t1
Couldn't classify 47609, 47779
Couldn't classify 48219, 48275
Sorry, prediction pasa_asmbl_27501.p1 fails validation.
(CGT)	 GC	47609-47779	GT	AGG
(GAC)	 AG	47967-48107	GT	AGG
(AAC)	 AG	48219-48275	TG	GCT
-recovered pasa_asmbl_27501.p1, internal, 47967, 48107
Valid prediction for Augustus_model.g31516.t1
Couldn't classify 50681, 50692
Sorry, prediction pasa_asmbl_27500.p1 fails validation.
(AGG)	 GG	50681-50692	GT	GGG
(ACT)	 AG	50783-51109	GT	GGG
(GGG)	 AG	51211-51324	CT	GAC
-recovered pasa_asmbl_27500.p1, terminal, 51211, 51324
-recovered pasa_asmbl_27500.p1, internal, 50783, 51109
Valid prediction for GlimmerHMM_glimmerT_47316-T1
Valid prediction for snap_scaffold_21-snap.532-T1
Valid prediction for snap_scaffold_21-snap.546-T1
Valid prediction for Augustus_model.g31507.t1
Valid prediction for Augustus_model.g31517.t1
Valid prediction for GlimmerHMM_glimmerT_47331-T1
Valid prediction for snap_scaffold_21-snap.556-T1
Valid prediction for Augustus_model.g31522.t1
Valid prediction for Augustus_model.g31526.t1
Valid prediction for Augustus_model.g31528.t1
Couldn't classify 58576, 58710
Couldn't classify 59332, 59475
Sorry, prediction pasa_asmbl_27498.p1 fails validation.
(AAC)	 AG	58576-58710	GT	AGG
(GTC)	 AG	59064-59162	GT	AGG
(GAT)	 AG	59332-59475	GA	TGG
-recovered pasa_asmbl_27498.p1, internal, 58576, 58710
-recovered pasa_asmbl_27498.p1, internal, 59064, 59162
Valid prediction for HiQ_model.g31510.t1
Valid prediction for Augustus_model.g31525.t1
Valid prediction for GlimmerHMM_glimmerT_47319-T1
Valid prediction for snap_scaffold_21-snap.533-T1
Valid prediction for GlimmerHMM_glimmerT_47314-T1
Valid prediction for snap_scaffold_21-snap.544-T1
Valid prediction for pasa_asmbl_27493.p1
Valid prediction for snap_scaffold_21-snap.516-T1
Couldn't classify 56142, 56262
Sorry, prediction pasa_asmbl_27499.p1 fails validation.
(ATG)	 CG	54053-54089	GT	AGG
(GGG)	 AG	54264-54369	GT	AGG
(CTC)	 AG	54536-54671	GC	AGG
(GAC)	 AG	54941-55186	GT	TGG
(GTG)	 AG	55822-56012	GT	AGG
(CAT)	 AG	56142-56262	CT	CCC
-recovered pasa_asmbl_27499.p1, initial, 54053, 54089
-recovered pasa_asmbl_27499.p1, internal, 54264, 54369
-recovered pasa_asmbl_27499.p1, internal, 54536, 54671
-recovered pasa_asmbl_27499.p1, internal, 54941, 55186
-recovered pasa_asmbl_27499.p1, internal, 55822, 56012
Valid prediction for snap_scaffold_21-snap.528-T1
Couldn't classify 65456, 65485
Sorry, prediction pasa_asmbl_27497.p1 fails validation.
(CTG)	 AC	65456-65485	GT	CAG
(GTG)	 AG	66017-66169	GT	CTG
(GTG)	 AG	67640-67785	GT	AGG
(CTT)	 AG	68060-68189	GT	AGG
(GTG)	 AG	71017-71101	GT	GGG
(AGC)	 AG	71239-71325	GT	AGG
(ACA)	 AG	73559-73713	GT	CGG
(CTT)	 AG	75650-75724	GC	GAG
-recovered pasa_asmbl_27497.p1, terminal, 67640, 67785
-recovered pasa_asmbl_27497.p1, terminal, 75650, 75724
-recovered pasa_asmbl_27497.p1, internal, 66017, 66169
-recovered pasa_asmbl_27497.p1, internal, 67640, 67785
-recovered pasa_asmbl_27497.p1, internal, 68060, 68189
-recovered pasa_asmbl_27497.p1, internal, 71017, 71101
-recovered pasa_asmbl_27497.p1, internal, 71239, 71325
-recovered pasa_asmbl_27497.p1, internal, 73559, 73713
-recovered pasa_asmbl_27497.p1, internal, 75650, 75724
Valid prediction for HiQ_model.g31519.t1
Valid prediction for snap_scaffold_21-snap.519-T1
Valid prediction for snap_scaffold_21-snap.554-T1
Valid prediction for GlimmerHMM_glimmerT_47332-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 22596, rend_intergenic: 19876  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33306, rend_intergenic: 31528  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93083, rend_intergenic: 89140  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127230, rend_intergenic: 119788  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 234220
-exon list size: 529


building trellis

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-found 37 predictions from path traversal
Error with prediction: snap lend_intergenic: 22596, rend_intergenic: 19876  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33306, rend_intergenic: 31528  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93083, rend_intergenic: 89140  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127230, rend_intergenic: 119788  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 33 predictions persist after filtering for low support