-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_17/scaffold_17_13879640-14119193

-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_17-snap.2870-T1
Valid prediction for snap_scaffold_17-snap.2875-T1
Valid prediction for snap_scaffold_17-snap.2872-T1
Valid prediction for Augustus_model.g27605.t1
Valid prediction for snap_scaffold_17-snap.2892-T1
Valid prediction for snap_scaffold_17-snap.2899-T1
Valid prediction for CodingQuarry_transcript_22255-T1
Couldn't classify 37306, 37366
Sorry, prediction pasa_asmbl_19358.p1 fails validation.
(GCC)	 GC	37306-37366	GT	AGG
(CTG)	 AG	37786-38045	CC	AGC
-recovered pasa_asmbl_19358.p1, terminal, 37786, 38045
Valid prediction for Augustus_model.g27615.t1
Valid prediction for snap_scaffold_17-snap.2913-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_17-snap.2877-T1
Valid prediction for GlimmerHMM_glimmerT_41417-T1
Valid prediction for pasa_asmbl_19377.p1
Valid prediction for snap_scaffold_17-snap.2882-T1
Valid prediction for snap_scaffold_17-snap.2909-T1
Valid prediction for snap_scaffold_17-snap.2890-T1
Valid prediction for CodingQuarry_transcript_22251-T1
Valid prediction for snap_scaffold_17-snap.2869-T1
Valid prediction for CodingQuarry_transcript_22249-T1
Valid prediction for snap_scaffold_17-snap.2905-T1
Valid prediction for snap_scaffold_17-snap.2901-T1
Valid prediction for GlimmerHMM_glimmerT_41421-T1
Valid prediction for Augustus_model.g27614.t1
Valid prediction for GlimmerHMM_glimmerT_41420-T1
Valid prediction for GlimmerHMM_glimmerT_41436-T1
Valid prediction for GlimmerHMM_glimmerT_41442-T1
Valid prediction for GlimmerHMM_glimmerT_41426-T1
Valid prediction for Augustus_model.g27613.t1
Valid prediction for GlimmerHMM_glimmerT_41423-T1
Valid prediction for GlimmerHMM_glimmerT_41446-T1
Valid prediction for pasa_asmbl_19373.p1
Valid prediction for pasa_asmbl_19368.p1
Valid prediction for snap_scaffold_17-snap.2895-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for HiQ_model.g27611.t1
Valid prediction for GlimmerHMM_glimmerT_41439-T1
Valid prediction for snap_scaffold_17-snap.2879-T1
Valid prediction for GlimmerHMM_glimmerT_41438-T1
Valid prediction for snap_scaffold_17-snap.2898-T1
Valid prediction for Augustus_model.g27617.t1
Valid prediction for snap_scaffold_17-snap.2884-T1
Valid prediction for Augustus_model.g27600.t1
Valid prediction for GlimmerHMM_glimmerT_41433-T1
Valid prediction for GlimmerHMM_glimmerT_41424-T1
Valid prediction for snap_scaffold_17-snap.2866-T1
Valid prediction for GlimmerHMM_glimmerT_41430-T1
Valid prediction for GlimmerHMM_glimmerT_41428-T1
Valid prediction for Augustus_model.g27616.t1
Couldn't classify 176692, 176748
Couldn't classify 180684, 181258
Sorry, prediction pasa_asmbl_19382.p1 fails validation.
(GAT)	 CA	176692-176748	GT	CTG
(ACG)	 AG	177687-177819	GT	CAG
(TTC)	 AG	180684-181258	CC	AAC
-recovered pasa_asmbl_19382.p1, internal, 177687, 177819
Valid prediction for snap_scaffold_17-snap.2894-T1
Couldn't classify 202268, 202593
Sorry, prediction pasa_asmbl_19387.p1 fails validation.
(GAT)	 GG	202268-202593	GT	AGG
(GTT)	 AG	202859-202988	TG	AAT
-recovered pasa_asmbl_19387.p1, terminal, 202859, 202988
Valid prediction for Augustus_model.g27607.t1
Valid prediction for GlimmerHMM_glimmerT_41425-T1
Valid prediction for Augustus_model.g27621.t1
Valid prediction for Augustus_model.g27606.t1
Valid prediction for GlimmerHMM_glimmerT_41434-T1
Valid prediction for Augustus_model.g27603.t1
Valid prediction for snap_scaffold_17-snap.2873-T1
Valid prediction for HiQ_model.g27609.t1
Valid prediction for Augustus_model.g27602.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_17-snap.2912-T1
Valid prediction for snap_scaffold_17-snap.2888-T1
Valid prediction for CodingQuarry_transcript_22246-T1
Valid prediction for pasa_asmbl_18404.p1
Valid prediction for GlimmerHMM_glimmerT_41435-T1
Valid prediction for HiQ_model.g27608.t1
Valid prediction for Augustus_model.g27618.t1
Valid prediction for GlimmerHMM_glimmerT_41422-T1
Valid prediction for snap_scaffold_17-snap.2878-T1
Valid prediction for HiQ_model.g27610.t1
Valid prediction for snap_scaffold_17-snap.2891-T1
Valid prediction for CodingQuarry_transcript_22252-T1
Valid prediction for CodingQuarry_transcript_22253-T1
Valid prediction for GlimmerHMM_glimmerT_41437-T1
Valid prediction for Augustus_model.g27619.t1
Valid prediction for pasa_asmbl_18395.p1
Valid prediction for pasa_asmbl_18384.p1
Couldn't classify 165219, 165310
Sorry, prediction pasa_asmbl_18388.p2 fails validation.
(TCA)	 AA	165219-165310	GT	TGG
(GAA)	 AG	165674-165732	GT	AGG
(TGG)	 AG	165959-166053	GT	CTG
(AGT)	 AG	166529-166657	GT	AGG
(ATT)	 AG	167101-167190	AG	GAA
-recovered pasa_asmbl_18388.p2, terminal, 167101, 167190
-recovered pasa_asmbl_18388.p2, internal, 165674, 165732
-recovered pasa_asmbl_18388.p2, internal, 165959, 166053
-recovered pasa_asmbl_18388.p2, internal, 166529, 166657
Valid prediction for HiQ_model.g27601.t1
Valid prediction for Augustus_model.g27622.t1
Valid prediction for CodingQuarry_transcript_22248-T1
Valid prediction for snap_scaffold_17-snap.2897-T1
Valid prediction for snap_scaffold_17-snap.2867-T1
Valid prediction for GlimmerHMM_glimmerT_41445-T1
Valid prediction for snap_scaffold_17-snap.2883-T1
Valid prediction for snap_scaffold_17-snap.2885-T1
Valid prediction for snap_scaffold_17-snap.2880-T1
Valid prediction for CodingQuarry_transcript_22254-T1
Valid prediction for snap_scaffold_17-snap.2906-T1
Valid prediction for snap_scaffold_17-snap.2874-T1
Valid prediction for Augustus_model.g27620.t1
Valid prediction for snap_scaffold_17-snap.2910-T1
Valid prediction for snap_scaffold_17-snap.2903-T1
Valid prediction for GlimmerHMM_glimmerT_41418-T1
Valid prediction for snap_scaffold_17-snap.2886-T1
Valid prediction for snap_scaffold_17-snap.2871-T1
Couldn't classify 3419, 3631
Sorry, prediction pasa_asmbl_18408.p2 fails validation.
(GCC)	 AG	3419-3631	GT	AGG
(ACT)	 AG	3823-3900	GT	TCG
(AGC)	 AG	4102-4263	GT	CGG
(GGC)	 AG	4356-4460	GT	AGG
(GCT)	 AG	4890-5111	GT	CGG
(GAG)	 AG	5344-5496	GT	AGG
(ATC)	 AG	5634-5788	GT	GAG
(GCT)	 AG	6251-6377	GT	TGG
(TTC)	 AG	6845-7028	GT	AGG
(GTG)	 AG	7263-7420	GT	CGG
(AAA)	 AG	7687-7865	GT	AAG
(ACT)	 AG	8094-8232	GT	AGG
(AGC)	 AG	8417-8857	GC	AAG
-recovered pasa_asmbl_18408.p2, terminal, 8417, 8857
-recovered pasa_asmbl_18408.p2, internal, 3419, 3631
-recovered pasa_asmbl_18408.p2, internal, 3823, 3900
-recovered pasa_asmbl_18408.p2, internal, 4102, 4263
-recovered pasa_asmbl_18408.p2, internal, 4356, 4460
-recovered pasa_asmbl_18408.p2, internal, 4890, 5111
-recovered pasa_asmbl_18408.p2, internal, 5344, 5496
-recovered pasa_asmbl_18408.p2, internal, 5634, 5788
-recovered pasa_asmbl_18408.p2, internal, 6251, 6377
-recovered pasa_asmbl_18408.p2, internal, 6845, 7028
-recovered pasa_asmbl_18408.p2, internal, 7263, 7420
-recovered pasa_asmbl_18408.p2, internal, 7687, 7865
-recovered pasa_asmbl_18408.p2, internal, 8094, 8232
-recovered pasa_asmbl_18408.p2, internal, 8417, 8857
Valid prediction for Augustus_model.g27604.t1
Valid prediction for GlimmerHMM_glimmerT_41427-T1
Valid prediction for snap_scaffold_17-snap.2904-T1
Couldn't classify 199127, 199162
Sorry, prediction pasa_asmbl_18387.p1 fails validation.
(GCT)	 CA	199127-199162	GT	ATG
(TCA)	 AG	199256-199425	GT	AGG
(CTG)	 AG	200241-200323	GT	AGG
(CTT)	 AG	200564-200706	TG	AAT
-recovered pasa_asmbl_18387.p1, terminal, 200564, 200706
-recovered pasa_asmbl_18387.p1, internal, 199256, 199425
-recovered pasa_asmbl_18387.p1, internal, 200241, 200323
Valid prediction for GlimmerHMM_glimmerT_41443-T1
Valid prediction for GlimmerHMM_glimmerT_41441-T1
Valid prediction for snap_scaffold_17-snap.2907-T1
Valid prediction for snap_scaffold_17-snap.2914-T1
Valid prediction for snap_scaffold_17-snap.2876-T1
Valid prediction for GlimmerHMM_glimmerT_41429-T1
Valid prediction for GlimmerHMM_glimmerT_41431-T1
Valid prediction for GlimmerHMM_glimmerT_41444-T1
Valid prediction for snap_scaffold_17-snap.2887-T1
Couldn't classify 35222, 35776
Sorry, prediction pasa_asmbl_18406.p1 fails validation.
(GTT)	 AC	35222-35776	GC	AAG
Valid prediction for GlimmerHMM_glimmerT_41440-T1
Valid prediction for CodingQuarry_transcript_22247-T1
Valid prediction for snap_scaffold_17-snap.2881-T1
Valid prediction for snap_scaffold_17-snap.2889-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_17-snap.2902-T1
Valid prediction for snap_scaffold_17-snap.2911-T1
Valid prediction for pasa_asmbl_18396.p1
Valid prediction for snap_scaffold_17-snap.2900-T1
Valid prediction for CodingQuarry_transcript_22250-T1
Valid prediction for CodingQuarry_transcript_22244-T1
Valid prediction for GlimmerHMM_glimmerT_41419-T1
Valid prediction for snap_scaffold_17-snap.2908-T1
Valid prediction for snap_scaffold_17-snap.2896-T1
Valid prediction for CodingQuarry_transcript_22245-T1
Valid prediction for HiQ_model.g27612.t1
Valid prediction for snap_scaffold_17-snap.2893-T1
Valid prediction for snap_scaffold_17-snap.2868-T1
Valid prediction for GlimmerHMM_glimmerT_41432-T1
Valid prediction for GlimmerHMM_glimmerT_41447-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 17413, rend_intergenic: 16482  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34246, rend_intergenic: 31406  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54996, rend_intergenic: 47251  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64395, rend_intergenic: 61126  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67141, rend_intergenic: 65619  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128678, rend_intergenic: 126202  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138957, rend_intergenic: 137635  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156809, rend_intergenic: 144044  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170247, rend_intergenic: 167672  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179691, rend_intergenic: 170647  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 236599, rend_intergenic: 232184  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 239554
-exon list size: 448


building trellis

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-found 40 predictions from path traversal
Error with prediction: snap lend_intergenic: 17413, rend_intergenic: 16482  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34246, rend_intergenic: 31406  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54996, rend_intergenic: 47251  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64395, rend_intergenic: 61126  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67141, rend_intergenic: 65619  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128678, rend_intergenic: 126202  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138957, rend_intergenic: 137635  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156809, rend_intergenic: 144044  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170247, rend_intergenic: 167672  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179691, rend_intergenic: 170647  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 236599, rend_intergenic: 232184  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 38 predictions persist after filtering for low support