-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_16/scaffold_16_4165957-4355114

-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_39047-T1
Valid prediction for Augustus_model.g26232.t1
Valid prediction for snap_scaffold_16-snap.836-T1
Valid prediction for GeneMark_model.66836_t
Valid prediction for GlimmerHMM_glimmerT_39039-T1
Valid prediction for Augustus_model.g26218.t1
Valid prediction for snap_scaffold_16-snap.833-T1
Valid prediction for GeneMark_model.66833_t
Valid prediction for GlimmerHMM_glimmerT_39042-T1
Valid prediction for GlimmerHMM_glimmerT_39035-T1
Valid prediction for snap_scaffold_16-snap.824-T1
Valid prediction for GeneMark_model.66864_t
Valid prediction for GlimmerHMM_glimmerT_39032-T1
Valid prediction for GlimmerHMM_glimmerT_39033-T1
Valid prediction for Augustus_model.g26225.t1
Valid prediction for snap_scaffold_16-snap.816-T1
Valid prediction for Augustus_model.g26222.t1
Valid prediction for GlimmerHMM_glimmerT_39034-T1
Valid prediction for GeneMark_model.66856_t
Valid prediction for GeneMark_model.66860_t
Valid prediction for snap_scaffold_16-snap.847-T1
Valid prediction for GeneMark_model.66839_t
Valid prediction for GeneMark_model.66857_t
Valid prediction for GeneMark_model.66851_t
Valid prediction for snap_scaffold_16-snap.817-T1
Valid prediction for GeneMark_model.66837_t
Valid prediction for GlimmerHMM_glimmerT_39030-T1
Valid prediction for Augustus_model.g26224.t1
Valid prediction for Augustus_model.g26221.t1
Valid prediction for snap_scaffold_16-snap.840-T1
Valid prediction for snap_scaffold_16-snap.819-T1
Valid prediction for GeneMark_model.66853_t
Valid prediction for snap_scaffold_16-snap.842-T1
Valid prediction for Augustus_model.g26223.t1
Valid prediction for snap_scaffold_16-snap.839-T1
Valid prediction for GlimmerHMM_glimmerT_39041-T1
Valid prediction for snap_scaffold_16-snap.813-T1
Valid prediction for GeneMark_model.66858_t
Valid prediction for GlimmerHMM_glimmerT_39040-T1
Valid prediction for snap_scaffold_16-snap.831-T1
Valid prediction for GeneMark_model.66862_t
Valid prediction for snap_scaffold_16-snap.848-T1
Valid prediction for snap_scaffold_16-snap.828-T1
Valid prediction for GeneMark_model.66834_t
Valid prediction for GlimmerHMM_glimmerT_39038-T1
Valid prediction for GeneMark_model.66840_t
Valid prediction for snap_scaffold_16-snap.823-T1
Valid prediction for snap_scaffold_16-snap.825-T1
Valid prediction for GeneMark_model.66831_t
Valid prediction for GlimmerHMM_glimmerT_39031-T1
Valid prediction for GlimmerHMM_glimmerT_39029-T1
Valid prediction for Augustus_model.g26217.t1
Valid prediction for GeneMark_model.66848_t
Valid prediction for Augustus_model.g26228.t1
Valid prediction for Augustus_model.g26229.t1
Valid prediction for GeneMark_model.66842_t
Valid prediction for GeneMark_model.66846_t
Valid prediction for Augustus_model.g26216.t1
Valid prediction for GlimmerHMM_glimmerT_39044-T1
Valid prediction for snap_scaffold_16-snap.830-T1
Valid prediction for snap_scaffold_16-snap.821-T1
Valid prediction for GeneMark_model.66844_t
Valid prediction for snap_scaffold_16-snap.829-T1
Valid prediction for GeneMark_model.66830_t
Valid prediction for GeneMark_model.66854_t
Valid prediction for Augustus_model.g26219.t1
Valid prediction for snap_scaffold_16-snap.826-T1
Valid prediction for Augustus_model.g26230.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_16-snap.841-T1
Valid prediction for GeneMark_model.66843_t
Valid prediction for GeneMark_model.66852_t
Valid prediction for Augustus_model.g26234.t1
Valid prediction for snap_scaffold_16-snap.822-T1
Valid prediction for GlimmerHMM_glimmerT_39046-T1
Valid prediction for GlimmerHMM_glimmerT_39049-T1
Valid prediction for GlimmerHMM_glimmerT_39037-T1
Valid prediction for GeneMark_model.66832_t
Valid prediction for GeneMark_model.66841_t
Valid prediction for GlimmerHMM_glimmerT_39048-T1
Valid prediction for GeneMark_model.66850_t
Valid prediction for GeneMark_model.66847_t
Valid prediction for GeneMark_model.66855_t
Valid prediction for Augustus_model.g26227.t1
Valid prediction for GlimmerHMM_glimmerT_39036-T1
Valid prediction for snap_scaffold_16-snap.843-T1
Couldn't classify 3993, 4025
Couldn't classify 9523, 9825
Sorry, prediction pasa_asmbl_16751.p1 fails validation.
(GTC)	 GG	3993-4025	GT	AGG
(AAC)	 AG	4126-4190	GT	AGG
(TCC)	 AG	4291-4427	GT	AGG
(ATG)	 AG	4587-4729	GT	AGG
(TTT)	 AG	4897-5055	GT	ACG
(AAA)	 AG	5163-5241	GT	CGG
(ATA)	 AG	5379-5452	GT	TGG
(CTT)	 AG	5569-5658	GT	AGG
(ATG)	 AG	5843-5968	GT	ACG
(TAC)	 AG	6200-6241	GT	TGG
(ACG)	 AG	6370-6475	GT	AGG
(ATT)	 AG	8562-8593	GT	AGG
(GGT)	 AG	9523-9825	CC	GGC
add_exon() Sorry, pasa_asmbl_16751.p1 4587-4729-initial-1 is invalid.
-recovered pasa_asmbl_16751.p1, initial, 4587, 4729
-recovered pasa_asmbl_16751.p1, initial, 5843, 5968
-recovered pasa_asmbl_16751.p1, internal, 4126, 4190
-recovered pasa_asmbl_16751.p1, internal, 4291, 4427
-recovered pasa_asmbl_16751.p1, internal, 4587, 4729
-recovered pasa_asmbl_16751.p1, internal, 4897, 5055
-recovered pasa_asmbl_16751.p1, internal, 5163, 5241
-recovered pasa_asmbl_16751.p1, internal, 5379, 5452
-recovered pasa_asmbl_16751.p1, internal, 5569, 5658
-recovered pasa_asmbl_16751.p1, internal, 5843, 5968
-recovered pasa_asmbl_16751.p1, internal, 6200, 6241
-recovered pasa_asmbl_16751.p1, internal, 6370, 6475
-recovered pasa_asmbl_16751.p1, internal, 8562, 8593
Valid prediction for snap_scaffold_16-snap.838-T1
Valid prediction for GeneMark_model.66838_t
Valid prediction for GeneMark_model.66845_t
Couldn't classify 1990, 2128
Couldn't classify 3726, 3899
Sorry, prediction pasa_asmbl_16233.p1 fails validation.
(TCT)	 CG	1990-2128	GT	CGG
(ACT)	 AG	2231-2333	GT	GGG
(AAG)	 AG	2457-2499	GT	AGG
(GCG)	 AG	3182-3301	GT	AGG
(CGG)	 AG	3726-3899	AC	ACA
-recovered pasa_asmbl_16233.p1, internal, 2231, 2333
-recovered pasa_asmbl_16233.p1, internal, 2457, 2499
-recovered pasa_asmbl_16233.p1, internal, 3182, 3301
Valid prediction for snap_scaffold_16-snap.845-T1
Valid prediction for Augustus_model.g26220.t1
Valid prediction for snap_scaffold_16-snap.815-T1
Valid prediction for snap_scaffold_16-snap.827-T1
Valid prediction for GeneMark_model.66865_t
Valid prediction for GeneMark_model.66859_t
Valid prediction for pasa_asmbl_16230.p1
Valid prediction for GeneMark_model.66866_t
Valid prediction for Augustus_model.g26231.t1
Valid prediction for Augustus_model.g26226.t1
Valid prediction for HiQ_model.g26233.t1
Valid prediction for GlimmerHMM_glimmerT_39050-T1
Valid prediction for GlimmerHMM_glimmerT_39045-T1
Valid prediction for GlimmerHMM_glimmerT_39043-T1
Valid prediction for GeneMark_model.66835_t
Couldn't classify 9883, 11163
Sorry, prediction pasa_asmbl_16232.p1 fails validation.
(CCC)	 CC	9883-11163	AA	GAA
Valid prediction for snap_scaffold_16-snap.818-T1
Valid prediction for snap_scaffold_16-snap.820-T1
Valid prediction for CodingQuarry_transcript_19908-T1
Valid prediction for GeneMark_model.66863_t
Valid prediction for snap_scaffold_16-snap.814-T1
Valid prediction for GeneMark_model.66861_t
Valid prediction for GeneMark_model.66849_t
Valid prediction for snap_scaffold_16-snap.844-T1
Valid prediction for GeneMark_model.66867_t
Valid prediction for snap_scaffold_16-snap.834-T1
Valid prediction for snap_scaffold_16-snap.835-T1
Valid prediction for snap_scaffold_16-snap.837-T1
Valid prediction for snap_scaffold_16-snap.832-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 6983, rend_intergenic: 2629  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16114, rend_intergenic: 7389  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21581, rend_intergenic: 18587  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27775, rend_intergenic: 23938  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81563, rend_intergenic: 80947  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119191, rend_intergenic: 104509  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148379, rend_intergenic: 142199  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171472, rend_intergenic: 150140  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 189158
-exon list size: 605


building trellis

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-found 25 predictions from path traversal
Error with prediction: snap lend_intergenic: 6983, rend_intergenic: 2629  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16114, rend_intergenic: 7389  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21581, rend_intergenic: 18587  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27775, rend_intergenic: 23938  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81563, rend_intergenic: 80947  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119191, rend_intergenic: 104509  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148379, rend_intergenic: 142199  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171472, rend_intergenic: 150140  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support