-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_10/scaffold_10_12888355-13052548

-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 Augustus_model.g17058.t1
Valid prediction for snap_scaffold_10-snap.2573-T1
Valid prediction for HiQ_model.g17056.t1
Couldn't classify 146722, 146844
Couldn't classify 147649, 147690
Sorry, prediction pasa_asmbl_3578.p1 fails validation.
(GTG)	 TG	146722-146844	GT	AGG
(CTG)	 AG	147067-147180	GT	TGG
(AGA)	 AG	147444-147527	GT	AGG
(GTG)	 AG	147649-147690	AC	ACA
-recovered pasa_asmbl_3578.p1, internal, 147067, 147180
-recovered pasa_asmbl_3578.p1, internal, 147444, 147527
Valid prediction for snap_scaffold_10-snap.2553-T1
Valid prediction for snap_scaffold_10-snap.2533-T1
Valid prediction for Augustus_model.g17050.t1
Valid prediction for GlimmerHMM_glimmerT_25650-T1
Valid prediction for GlimmerHMM_glimmerT_25648-T1
Valid prediction for GlimmerHMM_glimmerT_25645-T1
Valid prediction for Augustus_model.g17043.t1
Valid prediction for CodingQuarry_transcript_5612-T1
Valid prediction for snap_scaffold_10-snap.2546-T1
Valid prediction for pasa_asmbl_3559.p1
Valid prediction for GlimmerHMM_glimmerT_25654-T1
Valid prediction for GlimmerHMM_glimmerT_25656-T1
Valid prediction for snap_scaffold_10-snap.2569-T1
Valid prediction for HiQ_model.g17069.t1
Valid prediction for Augustus_model.g17045.t1
Valid prediction for snap_scaffold_10-snap.2561-T1
Valid prediction for Augustus_model.g17052.t1
Valid prediction for Augustus_model.g17057.t1
Valid prediction for HiQ_model.g17054.t1
Valid prediction for snap_scaffold_10-snap.2534-T1
Valid prediction for Augustus_model.g17041.t1
Valid prediction for GlimmerHMM_glimmerT_25640-T1
Couldn't classify 71201, 71985
Sorry, prediction pasa_asmbl_3901.p1 fails validation.
(ATG)	 CA	70063-70354	GT	AGG
(GTG)	 AG	70436-70581	GT	AGG
(TCT)	 AG	70760-70879	GT	AGG
(CTG)	 AG	71001-71121	GT	AAG
(CTG)	 AG	71201-71985	GG	GGG
-recovered pasa_asmbl_3901.p1, initial, 70063, 70354
-recovered pasa_asmbl_3901.p1, internal, 70436, 70581
-recovered pasa_asmbl_3901.p1, internal, 70760, 70879
-recovered pasa_asmbl_3901.p1, internal, 71001, 71121
Valid prediction for pasa_asmbl_3562.p1
Valid prediction for Augustus_model.g17066.t1
Valid prediction for GlimmerHMM_glimmerT_25659-T1
Couldn't classify 21734, 22675
Sorry, prediction pasa_asmbl_3558.p1 fails validation.
(GGT)	 CA	21734-22675	CG	CCC
Valid prediction for GlimmerHMM_glimmerT_25642-T1
Valid prediction for GlimmerHMM_glimmerT_25636-T1
Valid prediction for CodingQuarry_transcript_5615-T1
Valid prediction for pasa_asmbl_3564.p1
Valid prediction for Augustus_model.g17065.t1
Valid prediction for GlimmerHMM_glimmerT_25647-T1
Valid prediction for snap_scaffold_10-snap.2548-T1
Valid prediction for Augustus_model.g17067.t1
Valid prediction for pasa_asmbl_3566.p1
Valid prediction for CodingQuarry_transcript_5620-T1
Valid prediction for GlimmerHMM_glimmerT_25660-T1
Valid prediction for snap_scaffold_10-snap.2547-T1
Valid prediction for snap_scaffold_10-snap.2536-T1
Valid prediction for snap_scaffold_10-snap.2557-T1
Valid prediction for GlimmerHMM_glimmerT_25641-T1
Valid prediction for HiQ_model.g17051.t1
Valid prediction for snap_scaffold_10-snap.2554-T1
Valid prediction for GlimmerHMM_glimmerT_25635-T1
Valid prediction for pasa_asmbl_3565.p1
Valid prediction for GlimmerHMM_glimmerT_25649-T1
Valid prediction for pasa_asmbl_3570.p1
Valid prediction for GlimmerHMM_glimmerT_25655-T1
Valid prediction for Augustus_model.g17059.t1
Valid prediction for Augustus_model.g17046.t1
Valid prediction for Augustus_model.g17070.t1
Valid prediction for GlimmerHMM_glimmerT_25644-T1
Valid prediction for GlimmerHMM_glimmerT_25633-T1
Valid prediction for HiQ_model.g17064.t1
Valid prediction for snap_scaffold_10-snap.2551-T1
Valid prediction for HiQ_model.g17055.t1
Valid prediction for pasa_asmbl_3560.p1
Valid prediction for snap_scaffold_10-snap.2568-T1
Valid prediction for CodingQuarry_transcript_5614-T1
Valid prediction for GlimmerHMM_glimmerT_25658-T1
Valid prediction for snap_scaffold_10-snap.2542-T1
Valid prediction for snap_scaffold_10-snap.2538-T1
Couldn't classify 139362, 139431
Sorry, prediction pasa_asmbl_3575.p1 fails validation.
(TAC)	 AG	139362-139431	GT	TGG
(CTC)	 AG	139556-139729	GT	AGG
(GCG)	 AG	139814-139896	GT	AGG
(GTG)	 AG	140089-140194	GT	AGG
(AAC)	 AG	140331-140428	AG	AGA
-recovered pasa_asmbl_3575.p1, terminal, 140331, 140428
-recovered pasa_asmbl_3575.p1, internal, 139362, 139431
-recovered pasa_asmbl_3575.p1, internal, 139556, 139729
-recovered pasa_asmbl_3575.p1, internal, 139814, 139896
-recovered pasa_asmbl_3575.p1, internal, 140089, 140194
Couldn't classify 77350, 77359
Sorry, prediction pasa_asmbl_3567.p1 fails validation.
(AAA)	 GC	77350-77359	GT	GGG
(GAT)	 AG	77787-78481	GC	GAG
-recovered pasa_asmbl_3567.p1, terminal, 77787, 78481
-recovered pasa_asmbl_3567.p1, internal, 77787, 78481
Valid prediction for snap_scaffold_10-snap.2563-T1
Valid prediction for Augustus_model.g17044.t1
Valid prediction for GlimmerHMM_glimmerT_25643-T1
Valid prediction for snap_scaffold_10-snap.2552-T1
Valid prediction for GlimmerHMM_glimmerT_25638-T1
Valid prediction for CodingQuarry_transcript_5616-T1
Valid prediction for snap_scaffold_10-snap.2571-T1
Valid prediction for CodingQuarry_transcript_5622-T1
Valid prediction for snap_scaffold_10-snap.2550-T1
Valid prediction for CodingQuarry_transcript_5613-T1
Valid prediction for snap_scaffold_10-snap.2567-T1
Valid prediction for Augustus_model.g17053.t1
Valid prediction for snap_scaffold_10-snap.2549-T1
Valid prediction for snap_scaffold_10-snap.2574-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for pasa_asmbl_3571.p1
Valid prediction for snap_scaffold_10-snap.2545-T1
Valid prediction for GlimmerHMM_glimmerT_25646-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_10-snap.2564-T1
Valid prediction for pasa_asmbl_4845.p1
Valid prediction for GlimmerHMM_glimmerT_25637-T1
Valid prediction for HiQ_model.g17063.t1
Valid prediction for HiQ_model.g17049.t1
Valid prediction for CodingQuarry_transcript_5619-T1
Valid prediction for GlimmerHMM_glimmerT_25639-T1
Valid prediction for snap_scaffold_10-snap.2541-T1
Valid prediction for snap_scaffold_10-snap.2540-T1
Valid prediction for CodingQuarry_transcript_5611-T1
Valid prediction for snap_scaffold_10-snap.2544-T1
Valid prediction for HiQ_model.g17042.t1
Valid prediction for snap_scaffold_10-snap.2565-T1
Valid prediction for snap_scaffold_10-snap.2537-T1
Valid prediction for HiQ_model.g17062.t1
Valid prediction for Augustus_model.g17068.t1
Valid prediction for snap_scaffold_10-snap.2560-T1
Valid prediction for snap_scaffold_10-snap.2535-T1
Valid prediction for snap_scaffold_10-snap.2572-T1
Valid prediction for Augustus_model.g17047.t1
Valid prediction for snap_scaffold_10-snap.2562-T1
Valid prediction for pasa_asmbl_4852.p1
Valid prediction for GlimmerHMM_glimmerT_25651-T1
Valid prediction for snap_scaffold_10-snap.2543-T1
Valid prediction for GlimmerHMM_glimmerT_25657-T1
Valid prediction for snap_scaffold_10-snap.2575-T1
Valid prediction for snap_scaffold_10-snap.2539-T1
Valid prediction for snap_scaffold_10-snap.2555-T1
Valid prediction for snap_scaffold_10-snap.2566-T1
Valid prediction for Augustus_model.g17060.t1
Valid prediction for GlimmerHMM_glimmerT_25661-T1
Valid prediction for pasa_asmbl_4844.p1
Valid prediction for Augustus_model.g17061.t1
Valid prediction for snap_scaffold_10-snap.2558-T1
Couldn't classify 113643, 113701
Sorry, prediction pasa_asmbl_4843.p1 fails validation.
(ATG)	 CC	111441-111504	GT	AGG
(TTC)	 AG	111820-111855	GT	AGG
(TGG)	 AG	111990-112103	GT	TGG
(ACA)	 AG	112422-112451	GT	AGG
(TCC)	 AG	112699-112790	GT	AGG
(GAT)	 AG	113038-113163	GT	AGG
(AAT)	 AG	113364-113463	GT	TCG
(TGG)	 AG	113643-113701	AG	CCA
-recovered pasa_asmbl_4843.p1, initial, 111441, 111504
-recovered pasa_asmbl_4843.p1, internal, 111820, 111855
-recovered pasa_asmbl_4843.p1, internal, 111990, 112103
-recovered pasa_asmbl_4843.p1, internal, 112422, 112451
-recovered pasa_asmbl_4843.p1, internal, 112699, 112790
-recovered pasa_asmbl_4843.p1, internal, 113038, 113163
-recovered pasa_asmbl_4843.p1, internal, 113364, 113463
Valid prediction for GlimmerHMM_glimmerT_25634-T1
Valid prediction for Augustus_model.g17048.t1
Valid prediction for GlimmerHMM_glimmerT_25652-T1
Valid prediction for snap_scaffold_10-snap.2556-T1
Valid prediction for snap_scaffold_10-snap.2559-T1
Valid prediction for CodingQuarry_transcript_5618-T1
Valid prediction for snap_scaffold_10-snap.2570-T1
Valid prediction for pasa_asmbl_4837.p1
Valid prediction for Augustus_model.g17071.t1
Valid prediction for GlimmerHMM_glimmerT_25662-T1
Valid prediction for GlimmerHMM_glimmerT_25653-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 9077, rend_intergenic: 5255  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21480, rend_intergenic: 17880  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30236, rend_intergenic: 22351  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87584, rend_intergenic: 83784  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94642, rend_intergenic: 91105  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101373, rend_intergenic: 94824  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109229, rend_intergenic: 105127  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134169, rend_intergenic: 129275  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140428, rend_intergenic: 137254  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144285, rend_intergenic: 142980  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149498, rend_intergenic: 144366  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158607, rend_intergenic: 150183  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 164194
-exon list size: 460


building trellis

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-found 35 predictions from path traversal
Error with prediction: snap lend_intergenic: 9077, rend_intergenic: 5255  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21480, rend_intergenic: 17880  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30236, rend_intergenic: 22351  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87584, rend_intergenic: 83784  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94642, rend_intergenic: 91105  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101373, rend_intergenic: 94824  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109229, rend_intergenic: 105127  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134169, rend_intergenic: 129275  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140428, rend_intergenic: 137254  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144285, rend_intergenic: 142980  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149498, rend_intergenic: 144366  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158607, rend_intergenic: 150183  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 34 predictions persist after filtering for low support