-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_1/scaffold_1_17437399-17591140

-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_1-snap.3177-T1
Valid prediction for snap_scaffold_1-snap.3195-T1
Valid prediction for GeneMark_model.3508_t
Valid prediction for GeneMark_model.3504_t
Valid prediction for snap_scaffold_1-snap.3180-T1
Valid prediction for snap_scaffold_1-snap.3199-T1
Valid prediction for GeneMark_model.3465_t
Valid prediction for GeneMark_model.3469_t
Valid prediction for snap_scaffold_1-snap.3190-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_2400-T1
Valid prediction for Augustus_model.g1742.t1
Valid prediction for snap_scaffold_1-snap.3181-T1
Valid prediction for GeneMark_model.3491_t
Valid prediction for GeneMark_model.3487_t
Valid prediction for GlimmerHMM_glimmerT_2395-T1
Valid prediction for snap_scaffold_1-snap.3186-T1
Valid prediction for GlimmerHMM_glimmerT_2380-T1
Valid prediction for GlimmerHMM_glimmerT_2393-T1
Valid prediction for GeneMark_model.3506_t
Valid prediction for GlimmerHMM_glimmerT_2404-T1
Valid prediction for GlimmerHMM_glimmerT_2396-T1
Valid prediction for snap_scaffold_1-snap.3176-T1
Valid prediction for GlimmerHMM_glimmerT_2382-T1
Valid prediction for GeneMark_model.3512_t
Valid prediction for GeneMark_model.3499_t
Valid prediction for GeneMark_model.3516_t
Valid prediction for GeneMark_model.3489_t
Valid prediction for GeneMark_model.3494_t
Valid prediction for GeneMark_model.3484_t
Valid prediction for snap_scaffold_1-snap.3188-T1
Valid prediction for GeneMark_model.3502_t
Valid prediction for GlimmerHMM_glimmerT_2398-T1
Valid prediction for GeneMark_model.3461_t
Valid prediction for GeneMark_model.3473_t
Valid prediction for Augustus_model.g1743.t1
Valid prediction for GlimmerHMM_glimmerT_2402-T1
Valid prediction for GeneMark_model.3510_t
Valid prediction for GeneMark_model.3463_t
Valid prediction for snap_scaffold_1-snap.3189-T1
Valid prediction for GeneMark_model.3478_t
Valid prediction for GeneMark_model.3475_t
Valid prediction for GeneMark_model.3501_t
Valid prediction for GeneMark_model.3482_t
Valid prediction for GeneMark_model.3492_t
Valid prediction for GeneMark_model.3495_t
Valid prediction for GeneMark_model.3486_t
Valid prediction for snap_scaffold_1-snap.3196-T1
Valid prediction for snap_scaffold_1-snap.3174-T1
Valid prediction for GlimmerHMM_glimmerT_2392-T1
Valid prediction for snap_scaffold_1-snap.3169-T1
Valid prediction for Augustus_model.g1740.t1
Valid prediction for GlimmerHMM_glimmerT_2390-T1
Valid prediction for GlimmerHMM_glimmerT_2384-T1
Valid prediction for GeneMark_model.3467_t
Valid prediction for snap_scaffold_1-snap.3182-T1
Valid prediction for snap_scaffold_1-snap.3192-T1
Valid prediction for Augustus_model.g1737.t1
Valid prediction for snap_scaffold_1-snap.3172-T1
Valid prediction for snap_scaffold_1-snap.3168-T1
Valid prediction for Augustus_model.g1744.t1
Valid prediction for GeneMark_model.3480_t
Valid prediction for GeneMark_model.3497_t
Valid prediction for snap_scaffold_1-snap.3197-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 GeneMark_model.3509_t
Valid prediction for snap_scaffold_1-snap.3184-T1
Valid prediction for GeneMark_model.3464_t
Valid prediction for GlimmerHMM_glimmerT_2383-T1
Valid prediction for GlimmerHMM_glimmerT_2391-T1
Valid prediction for snap_scaffold_1-snap.3200-T1
Valid prediction for snap_scaffold_1-snap.3173-T1
Valid prediction for GeneMark_model.3485_t
Valid prediction for GeneMark_model.3511_t
Valid prediction for GeneMark_model.3505_t
Valid prediction for GeneMark_model.3513_t
Valid prediction for snap_scaffold_1-snap.3194-T1
Valid prediction for GeneMark_model.3488_t
Valid prediction for GlimmerHMM_glimmerT_2386-T1
Valid prediction for snap_scaffold_1-snap.3171-T1
Valid prediction for GeneMark_model.3503_t
Couldn't classify 4343, 5222
Couldn't classify 6552, 6635
Sorry, prediction pasa_asmbl_1279.p1 fails validation.
(GAG)	 AG	4343-5222	GT	AGG
(GAG)	 AG	5498-5619	GT	AGG
(TCA)	 AG	6552-6635	CC	CCC
-recovered pasa_asmbl_1279.p1, internal, 4343, 5222
-recovered pasa_asmbl_1279.p1, internal, 5498, 5619
Valid prediction for GlimmerHMM_glimmerT_2403-T1
Valid prediction for snap_scaffold_1-snap.3175-T1
Valid prediction for GlimmerHMM_glimmerT_2385-T1
Valid prediction for GlimmerHMM_glimmerT_2405-T1
Valid prediction for GeneMark_model.3466_t
Valid prediction for Augustus_model.g1738.t1
Couldn't classify 6714, 7220
Sorry, prediction pasa_asmbl_1041.p1 fails validation.
(GAT)	 CT	6714-7220	AA	GAA
Valid prediction for snap_scaffold_1-snap.3185-T1
Valid prediction for GeneMark_model.3490_t
Valid prediction for snap_scaffold_1-snap.3187-T1
Valid prediction for GeneMark_model.3498_t
Valid prediction for GeneMark_model.3481_t
Valid prediction for GeneMark_model.3479_t
Valid prediction for GeneMark_model.3474_t
Valid prediction for snap_scaffold_1-snap.3179-T1
Valid prediction for GlimmerHMM_glimmerT_2397-T1
Valid prediction for GeneMark_model.3517_t
Valid prediction for snap_scaffold_1-snap.3198-T1
Valid prediction for GlimmerHMM_glimmerT_2401-T1
Valid prediction for GlimmerHMM_glimmerT_2399-T1
Couldn't classify 30550, 30730
Couldn't classify 33136, 33243
Sorry, prediction pasa_asmbl_1373.p1 fails validation.
(CAG)	 AC	30550-30730	GT	GGG
(GCT)	 AG	31416-31490	GT	AGG
(ACA)	 AG	32432-32519	GT	CAG
(GCG)	 AG	32869-32956	GT	GGG
(GGC)	 AG	33136-33243	CC	CAC
-recovered pasa_asmbl_1373.p1, internal, 31416, 31490
-recovered pasa_asmbl_1373.p1, internal, 32432, 32519
-recovered pasa_asmbl_1373.p1, internal, 32869, 32956
Valid prediction for Augustus_model.g1746.t1
Valid prediction for GlimmerHMM_glimmerT_2394-T1
Valid prediction for Augustus_model.g1733.t1
Valid prediction for GeneMark_model.3460_t
Valid prediction for GeneMark_model.3493_t
Valid prediction for GlimmerHMM_glimmerT_2381-T1
Valid prediction for snap_scaffold_1-snap.3193-T1
Valid prediction for Augustus_model.g1739.t1
Valid prediction for GeneMark_model.3496_t
Valid prediction for Augustus_model.g1734.t1
Valid prediction for GeneMark_model.3470_t
Valid prediction for Augustus_model.g1747.t1
Valid prediction for GeneMark_model.3476_t
Valid prediction for GeneMark_model.3500_t
Valid prediction for GeneMark_model.3483_t
Valid prediction for GlimmerHMM_glimmerT_2389-T1
Valid prediction for snap_scaffold_1-snap.3178-T1
Valid prediction for snap_scaffold_1-snap.3191-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for GeneMark_model.3462_t
Valid prediction for GlimmerHMM_glimmerT_2406-T1
Valid prediction for Augustus_model.g1741.t1
Valid prediction for GeneMark_model.3507_t
Valid prediction for snap_scaffold_1-snap.3201-T1
Valid prediction for snap_scaffold_1-snap.3183-T1
Couldn't classify 3893, 4213
Sorry, prediction pasa_asmbl_1042.p1 fails validation.
(ATG)	 CG	3893-4213	TC	GGT
Valid prediction for GeneMark_model.3471_t
Valid prediction for GlimmerHMM_glimmerT_2387-T1
Valid prediction for Augustus_model.g1745.t1
Valid prediction for GeneMark_model.3472_t
Valid prediction for GlimmerHMM_glimmerT_2388-T1
Valid prediction for snap_scaffold_1-snap.3170-T1
Valid prediction for Augustus_model.g1735.t1
Valid prediction for Augustus_model.g1736.t1
Valid prediction for GeneMark_model.3514_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 12456, rend_intergenic: 8909  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15624, rend_intergenic: 14860  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18500, rend_intergenic: 15942  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28065, rend_intergenic: 23983  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43109, rend_intergenic: 40575  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54119, rend_intergenic: 44196  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68431, rend_intergenic: 60846  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75885, rend_intergenic: 72609  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85451, rend_intergenic: 76396  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94047, rend_intergenic: 87398  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101805, rend_intergenic: 96509  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104985, rend_intergenic: 102053  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138209, rend_intergenic: 113204  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144927, rend_intergenic: 140159  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 153742
-exon list size: 663


building trellis

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-found 36 predictions from path traversal
Error with prediction: snap lend_intergenic: 12456, rend_intergenic: 8909  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15624, rend_intergenic: 14860  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18500, rend_intergenic: 15942  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28065, rend_intergenic: 23983  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43109, rend_intergenic: 40575  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54119, rend_intergenic: 44196  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68431, rend_intergenic: 60846  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75885, rend_intergenic: 72609  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85451, rend_intergenic: 76396  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94047, rend_intergenic: 87398  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101805, rend_intergenic: 96509  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104985, rend_intergenic: 102053  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138209, rend_intergenic: 113204  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144927, rend_intergenic: 140159  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support