-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_13/scaffold_13_15246087-15402570

-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_32893-T1
Valid prediction for GlimmerHMM_glimmerT_32904-T1
Valid prediction for snap_scaffold_13-snap.2967-T1
Valid prediction for pasa_asmbl_11500.p1
Valid prediction for snap_scaffold_13-snap.2974-T1
Valid prediction for snap_scaffold_13-snap.2953-T1
Valid prediction for snap_scaffold_13-snap.2979-T1
Valid prediction for Augustus_model.g21942.t1
Valid prediction for GlimmerHMM_glimmerT_32902-T1
Couldn't classify 120858, 121228
Sorry, prediction pasa_asmbl_11495.p1 fails validation.
(ATG)	 CC	118654-118808	GT	AGG
(GAC)	 AG	119459-119548	GT	TGG
(GGG)	 AG	120221-120279	GT	AGG
(ATA)	 AG	120858-121228	AA	GGA
-recovered pasa_asmbl_11495.p1, initial, 118654, 118808
-recovered pasa_asmbl_11495.p1, internal, 119459, 119548
-recovered pasa_asmbl_11495.p1, internal, 120221, 120279
Valid prediction for GlimmerHMM_glimmerT_32908-T1
Valid prediction for GlimmerHMM_glimmerT_32890-T1
Valid prediction for snap_scaffold_13-snap.2957-T1
Valid prediction for snap_scaffold_13-snap.2980-T1
Valid prediction for snap_scaffold_13-snap.2982-T1
Couldn't classify 123466, 123801
Sorry, prediction pasa_asmbl_11497.p1 fails validation.
(TGG)	 GA	123466-123801	GC	GAG
Valid prediction for Augustus_model.g21950.t1
Couldn't classify 146086, 146242
Couldn't classify 146774, 146889
Sorry, prediction pasa_asmbl_11504.p1 fails validation.
(CTG)	 CG	146086-146242	GT	GGG
(GAA)	 AG	146483-146560	GT	AGG
(GAG)	 AG	146774-146889	GT	AGG
-recovered pasa_asmbl_11504.p1, internal, 146483, 146560
-recovered pasa_asmbl_11504.p1, internal, 146774, 146889
Valid prediction for GlimmerHMM_glimmerT_32896-T1
Valid prediction for Augustus_model.g21941.t1
Valid prediction for snap_scaffold_13-snap.2987-T1
Valid prediction for snap_scaffold_13-snap.2968-T1
Valid prediction for GlimmerHMM_glimmerT_32895-T1
Valid prediction for GlimmerHMM_glimmerT_32899-T1
Valid prediction for snap_scaffold_13-snap.2972-T1
Valid prediction for snap_scaffold_13-snap.2984-T1
Valid prediction for snap_scaffold_13-snap.2971-T1
Valid prediction for Augustus_model.g21938.t1
Valid prediction for snap_scaffold_13-snap.2978-T1
Valid prediction for Augustus_model.g21945.t1
Valid prediction for snap_scaffold_13-snap.2961-T1
Valid prediction for snap_scaffold_13-snap.2960-T1
Valid prediction for HiQ_model.g21949.t1
Valid prediction for CodingQuarry_transcript_13330-T1
Valid prediction for snap_scaffold_13-snap.2950-T1
Valid prediction for CodingQuarry_transcript_13331-T1
Valid prediction for Augustus_model.g21951.t1
Valid prediction for Augustus_model.g21943.t1
Valid prediction for GlimmerHMM_glimmerT_32900-T1
Valid prediction for GlimmerHMM_glimmerT_32912-T1
Valid prediction for GlimmerHMM_glimmerT_32898-T1
Valid prediction for GlimmerHMM_glimmerT_32910-T1
Valid prediction for snap_scaffold_13-snap.2965-T1
Valid prediction for GlimmerHMM_glimmerT_32907-T1
Valid prediction for snap_scaffold_13-snap.2955-T1
Couldn't classify 129454, 129747
Couldn't classify 131175, 131225
Sorry, prediction pasa_asmbl_11692.p1 fails validation.
(ACA)	 TG	129454-129747	GT	AGG
(GAG)	 AG	130245-130448	GT	AGG
(GAG)	 AG	131175-131225	AA	GGA
-recovered pasa_asmbl_11692.p1, internal, 130245, 130448
Valid prediction for snap_scaffold_13-snap.2975-T1
Valid prediction for HiQ_model.g21952.t1
Valid prediction for Augustus_model.g21948.t1
Couldn't classify 154422, 154745
Sorry, prediction pasa_asmbl_11505.p3 fails validation.
(ATG)	 TC	154422-154745	TG	TAT
Valid prediction for GlimmerHMM_glimmerT_32906-T1
Valid prediction for GlimmerHMM_glimmerT_32892-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_13-snap.2988-T1
Couldn't classify 60558, 60710
Couldn't classify 61917, 62066
Sorry, prediction pasa_asmbl_10349.p1 fails validation.
(GGG)	 CA	60558-60710	GT	ATG
(GTG)	 AG	61130-61256	GT	GGG
(GTG)	 AG	61352-61425	GT	AGG
(CTG)	 AG	61554-61640	GT	AGG
(GAC)	 AG	61917-62066	GC	GGG
-recovered pasa_asmbl_10349.p1, internal, 61130, 61256
-recovered pasa_asmbl_10349.p1, internal, 61352, 61425
-recovered pasa_asmbl_10349.p1, internal, 61554, 61640
-recovered pasa_asmbl_10349.p1, internal, 61917, 62066
Valid prediction for snap_scaffold_13-snap.2986-T1
Valid prediction for CodingQuarry_transcript_13328-T1
Valid prediction for snap_scaffold_13-snap.2973-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for Augustus_model.g21944.t1
Valid prediction for snap_scaffold_13-snap.2954-T1
Valid prediction for snap_scaffold_13-snap.2958-T1
Valid prediction for snap_scaffold_13-snap.2951-T1
Valid prediction for snap_scaffold_13-snap.2959-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_32894-T1
Valid prediction for snap_scaffold_13-snap.2969-T1
Couldn't classify 118150, 118263
Sorry, prediction pasa_asmbl_10237.p1 fails validation.
(AAG)	 TG	118150-118263	GT	CTG
(ATG)	 AG	118620-118724	GT	AGG
(GTC)	 AG	118880-118936	GT	AGG
(TTC)	 AG	119384-119461	AA	AAA
-recovered pasa_asmbl_10237.p1, initial, 118620, 118724
-recovered pasa_asmbl_10237.p1, terminal, 119384, 119461
-recovered pasa_asmbl_10237.p1, internal, 118620, 118724
-recovered pasa_asmbl_10237.p1, internal, 118880, 118936
Valid prediction for GlimmerHMM_glimmerT_32897-T1
Valid prediction for CodingQuarry_transcript_13329-T1
Valid prediction for snap_scaffold_13-snap.2976-T1
Valid prediction for Augustus_model.g21940.t1
Valid prediction for snap_scaffold_13-snap.2962-T1
Valid prediction for Augustus_model.g21946.t1
Valid prediction for GlimmerHMM_glimmerT_32905-T1
Valid prediction for GlimmerHMM_glimmerT_32891-T1
Valid prediction for snap_scaffold_13-snap.2956-T1
Valid prediction for HiQ_model.g21937.t1
Couldn't classify 71436, 71508
Sorry, prediction pasa_asmbl_10239.p1 fails validation.
(GAT)	 AG	71436-71508	GT	GGG
(TGT)	 AG	72244-72362	GT	TGG
(GAT)	 AG	72835-72901	GT	AGG
(AGG)	 AG	73325-73497	CT	AAC
add_exon() Sorry, pasa_asmbl_10239.p1 72835-72901-terminal-3 is invalid.
-recovered pasa_asmbl_10239.p1, terminal, 72835, 72901
-recovered pasa_asmbl_10239.p1, terminal, 73325, 73497
-recovered pasa_asmbl_10239.p1, internal, 71436, 71508
-recovered pasa_asmbl_10239.p1, internal, 72244, 72362
-recovered pasa_asmbl_10239.p1, internal, 72835, 72901
Valid prediction for GlimmerHMM_glimmerT_32903-T1
Valid prediction for snap_scaffold_13-snap.2964-T1
Valid prediction for snap_scaffold_13-snap.2985-T1
Valid prediction for snap_scaffold_13-snap.2963-T1
Valid prediction for GlimmerHMM_glimmerT_32909-T1
Valid prediction for GlimmerHMM_glimmerT_32911-T1
Valid prediction for snap_scaffold_13-snap.2952-T1
Couldn't classify 107819, 107939
Sorry, prediction pasa_asmbl_10238.p2 fails validation.
(ATG)	 CC	105173-105183	GT	AGG
(CGG)	 AG	105658-105727	GT	GGG
(ATC)	 AG	107560-107657	GT	CAG
(GGG)	 AG	107819-107939	AA	GCA
-recovered pasa_asmbl_10238.p2, initial, 105173, 105183
-recovered pasa_asmbl_10238.p2, internal, 105658, 105727
-recovered pasa_asmbl_10238.p2, internal, 107560, 107657
Valid prediction for snap_scaffold_13-snap.2977-T1
Valid prediction for Augustus_model.g21939.t1
Valid prediction for GlimmerHMM_glimmerT_32901-T1
Valid prediction for snap_scaffold_13-snap.2966-T1
Couldn't classify 146723, 146883
Sorry, prediction pasa_asmbl_10235.p1 fails validation.
(GCG)	 GA	146723-146883	GT	AGG
(AAT)	 AG	147585-147686	GT	GTG
(CGA)	 AG	147831-148044	GT	CTG
(AAC)	 AG	148559-148672	GA	GAG
-recovered pasa_asmbl_10235.p1, terminal, 148559, 148672
-recovered pasa_asmbl_10235.p1, internal, 147585, 147686
-recovered pasa_asmbl_10235.p1, internal, 147831, 148044
Valid prediction for snap_scaffold_13-snap.2983-T1
Valid prediction for Augustus_model.g21947.t1
Couldn't classify 57823, 57902
Couldn't classify 59634, 59773
Sorry, prediction pasa_asmbl_10427.p1 fails validation.
(GTT)	 GT	57823-57902	GT	GGG
(GTT)	 AG	58445-58507	GT	AGG
(TGC)	 AG	59052-59164	GT	TGG
(ACT)	 AG	59634-59773	GA	AGG
-recovered pasa_asmbl_10427.p1, internal, 58445, 58507
-recovered pasa_asmbl_10427.p1, internal, 59052, 59164
Valid prediction for snap_scaffold_13-snap.2970-T1
Valid prediction for snap_scaffold_13-snap.2981-T1
Valid prediction for snap_scaffold_13-snap.2989-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 6451, rend_intergenic: 1989  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13994, rend_intergenic: 11740  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33092, rend_intergenic: 15366  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34564, rend_intergenic: 33271  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46031, rend_intergenic: 37024  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59063, rend_intergenic: 47909  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73697, rend_intergenic: 59674  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79012, rend_intergenic: 73980  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79375, rend_intergenic: 79094  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82904, rend_intergenic: 79410  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85888, rend_intergenic: 82988  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90352, rend_intergenic: 88998  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95015, rend_intergenic: 94392  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98105, rend_intergenic: 95255  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101791, rend_intergenic: 98552  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112252, rend_intergenic: 103942  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117419, rend_intergenic: 114545  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121286, rend_intergenic: 118036  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125193, rend_intergenic: 123615  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138286, rend_intergenic: 129519  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153598, rend_intergenic: 142875  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 156484
-exon list size: 384


building trellis

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-found 25 predictions from path traversal
Error with prediction: snap lend_intergenic: 6451, rend_intergenic: 1989  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13994, rend_intergenic: 11740  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33092, rend_intergenic: 15366  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34564, rend_intergenic: 33271  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46031, rend_intergenic: 37024  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59063, rend_intergenic: 47909  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73697, rend_intergenic: 59674  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79012, rend_intergenic: 73980  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79375, rend_intergenic: 79094  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82904, rend_intergenic: 79410  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85888, rend_intergenic: 82988  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90352, rend_intergenic: 88998  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95015, rend_intergenic: 94392  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98105, rend_intergenic: 95255  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101791, rend_intergenic: 98552  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112252, rend_intergenic: 103942  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117419, rend_intergenic: 114545  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121286, rend_intergenic: 118036  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125193, rend_intergenic: 123615  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138286, rend_intergenic: 129519  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153598, rend_intergenic: 142875  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support