-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_3/scaffold_3_18468589-18642026

-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_3-snap.3637-T1
Valid prediction for Augustus_model.g5682.t1
Valid prediction for GlimmerHMM_glimmerT_8534-T1
Valid prediction for snap_scaffold_3-snap.3653-T1
Valid prediction for snap_scaffold_3-snap.3650-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for GeneMark_model.13860_t
Valid prediction for GeneMark_model.13893_t
Valid prediction for GeneMark_model.13867_t
Valid prediction for snap_scaffold_3-snap.3664-T1
Valid prediction for snap_scaffold_3-snap.3632-T1
Valid prediction for Augustus_model.g5667.t1
Valid prediction for Augustus_model.g5673.t1
Valid prediction for GlimmerHMM_glimmerT_8535-T1
Valid prediction for snap_scaffold_3-snap.3665-T1
Valid prediction for Augustus_model.g5666.t1
Valid prediction for snap_scaffold_3-snap.3640-T1
Valid prediction for GeneMark_model.13879_t
Valid prediction for GlimmerHMM_glimmerT_8553-T1
Valid prediction for GeneMark_model.13877_t
Valid prediction for GlimmerHMM_glimmerT_8548-T1
Valid prediction for snap_scaffold_3-snap.3634-T1
Valid prediction for GeneMark_model.13871_t
Valid prediction for GeneMark_model.13864_t
Valid prediction for snap_scaffold_3-snap.3657-T1
Valid prediction for snap_scaffold_3-snap.3662-T1
Valid prediction for GeneMark_model.13891_t
Valid prediction for GeneMark_model.13883_t
Valid prediction for snap_scaffold_3-snap.3635-T1
Valid prediction for CodingQuarry_transcript_46364-T1
Valid prediction for GeneMark_model.13896_t
Valid prediction for GeneMark_model.13885_t
Valid prediction for Augustus_model.g5672.t1
Valid prediction for GeneMark_model.13874_t
Valid prediction for GlimmerHMM_glimmerT_8540-T1
Valid prediction for snap_scaffold_3-snap.3645-T1
Valid prediction for GeneMark_model.13857_t
Valid prediction for GlimmerHMM_glimmerT_8554-T1
Valid prediction for snap_scaffold_3-snap.3647-T1
Valid prediction for GlimmerHMM_glimmerT_8544-T1
Valid prediction for snap_scaffold_3-snap.3641-T1
Valid prediction for snap_scaffold_3-snap.3658-T1
Valid prediction for GeneMark_model.13872_t
Valid prediction for snap_scaffold_3-snap.3663-T1
Valid prediction for GeneMark_model.13876_t
Valid prediction for snap_scaffold_3-snap.3633-T1
Valid prediction for GlimmerHMM_glimmerT_8543-T1
Valid prediction for snap_scaffold_3-snap.3668-T1
Valid prediction for snap_scaffold_3-snap.3639-T1
Valid prediction for GlimmerHMM_glimmerT_8536-T1
Valid prediction for snap_scaffold_3-snap.3652-T1
Valid prediction for Augustus_model.g5668.t1
Valid prediction for Augustus_model.g5683.t1
Valid prediction for GlimmerHMM_glimmerT_8537-T1
Valid prediction for GeneMark_model.13859_t
Valid prediction for snap_scaffold_3-snap.3670-T1
Valid prediction for snap_scaffold_3-snap.3666-T1
Valid prediction for pasa_asmbl_40696.p1
Valid prediction for GeneMark_model.13887_t
Valid prediction for GeneMark_model.13889_t
Valid prediction for GlimmerHMM_glimmerT_8552-T1
Valid prediction for Augustus_model.g5674.t1
Valid prediction for snap_scaffold_3-snap.3649-T1
Valid prediction for Augustus_model.g5679.t1
Valid prediction for GlimmerHMM_glimmerT_8542-T1
Valid prediction for GeneMark_model.13862_t
Valid prediction for snap_scaffold_3-snap.3644-T1
Valid prediction for GeneMark_model.13869_t

-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.13866_t
Valid prediction for GeneMark_model.13882_t
Valid prediction for snap_scaffold_3-snap.3667-T1
Valid prediction for snap_scaffold_3-snap.3638-T1
Valid prediction for GeneMark_model.13890_t
Valid prediction for GlimmerHMM_glimmerT_8545-T1
Valid prediction for Augustus_model.g5681.t1
Valid prediction for CodingQuarry_transcript_46365-T1
Valid prediction for snap_scaffold_3-snap.3654-T1
Valid prediction for snap_scaffold_3-snap.3660-T1
Valid prediction for Augustus_model.g5671.t1
Valid prediction for GeneMark_model.13897_t
Valid prediction for GlimmerHMM_glimmerT_8539-T1
Valid prediction for GeneMark_model.13878_t
Valid prediction for Augustus_model.g5675.t1
Valid prediction for Augustus_model.g5678.t1
Valid prediction for snap_scaffold_3-snap.3648-T1
Valid prediction for GeneMark_model.13863_t
Valid prediction for GeneMark_model.13858_t
Valid prediction for GlimmerHMM_glimmerT_8551-T1
Valid prediction for Augustus_model.g5680.t1
Couldn't classify 49219, 56575
Couldn't classify 56621, 58851
Sorry, prediction CodingQuarry_transcript_46367-T1 fails validation.
(ATG)	 TC	47004-47129	GT	AGG
(GAA)	 AG	48458-48547	GT	TGG
(GTC)	 AG	48711-48768	GT	AGG
(AGG)	 AG	48880-48968	GT	AGG
(ATG)	 AG	49219-56575	CA	GGC
(AAG)	 GG	56621-58851	TG	GAT
-recovered CodingQuarry_transcript_46367-T1, initial, 47004, 47129
-recovered CodingQuarry_transcript_46367-T1, internal, 48458, 48547
-recovered CodingQuarry_transcript_46367-T1, internal, 48711, 48768
-recovered CodingQuarry_transcript_46367-T1, internal, 48880, 48968
Valid prediction for GeneMark_model.13870_t
Valid prediction for GeneMark_model.13865_t
Couldn't classify 49219, 55272
Sorry, prediction pasa_asmbl_39579.p1 fails validation.
(ATG)	 CC	46743-46835	GT	GCG
(GTC)	 AG	47001-47129	GT	AGG
(GAA)	 AG	48458-48547	GT	TGG
(GTC)	 AG	48711-48768	GT	AGG
(AGG)	 AG	48880-48968	GT	AGG
(ATG)	 AG	49219-55272	AA	CCA
-recovered pasa_asmbl_39579.p1, initial, 46743, 46835
-recovered pasa_asmbl_39579.p1, internal, 47001, 47129
-recovered pasa_asmbl_39579.p1, internal, 48458, 48547
-recovered pasa_asmbl_39579.p1, internal, 48711, 48768
-recovered pasa_asmbl_39579.p1, internal, 48880, 48968
Valid prediction for snap_scaffold_3-snap.3646-T1
Valid prediction for snap_scaffold_3-snap.3642-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for Augustus_model.g5670.t1
Valid prediction for snap_scaffold_3-snap.3659-T1
Valid prediction for snap_scaffold_3-snap.3669-T1
Valid prediction for snap_scaffold_3-snap.3655-T1
Valid prediction for snap_scaffold_3-snap.3636-T1
Valid prediction for GeneMark_model.13888_t
Valid prediction for snap_scaffold_3-snap.3651-T1
Valid prediction for GeneMark_model.13868_t
Valid prediction for snap_scaffold_3-snap.3656-T1
Valid prediction for GeneMark_model.13875_t
Valid prediction for GlimmerHMM_glimmerT_8547-T1
Valid prediction for Augustus_model.g5676.t1
Valid prediction for snap_scaffold_3-snap.3661-T1
Valid prediction for HiQ_model.g5677.t1
Valid prediction for GeneMark_model.13886_t
Valid prediction for GlimmerHMM_glimmerT_8550-T1
Couldn't classify 145650, 145805
Sorry, prediction pasa_asmbl_39575.p2 fails validation.
(ATT)	 GG	145650-145805	GT	AGG
(GCA)	 AG	146128-146151	GT	ACG
(GTG)	 AG	147338-147505	CC	GAC
-recovered pasa_asmbl_39575.p2, terminal, 147338, 147505
-recovered pasa_asmbl_39575.p2, internal, 146128, 146151
Valid prediction for GeneMark_model.13892_t
Valid prediction for GeneMark_model.13894_t
Valid prediction for GlimmerHMM_glimmerT_8546-T1
Valid prediction for GlimmerHMM_glimmerT_8549-T1
Valid prediction for Augustus_model.g5669.t1
Couldn't classify 49219, 55272
Couldn't classify 55377, 55385
Sorry, prediction CodingQuarry_transcript_46368-T1 fails validation.
(ATG)	 TC	47004-47129	GT	AGG
(GAA)	 AG	48458-48547	GT	TGG
(GTC)	 AG	48711-48768	GT	AGG
(AGG)	 AG	48880-48968	GT	AGG
(ATG)	 AG	49219-55272	AA	CCA
(TTC)	 CC	55377-55385	AG	AAA
-recovered CodingQuarry_transcript_46368-T1, initial, 47004, 47129
-recovered CodingQuarry_transcript_46368-T1, internal, 48458, 48547
-recovered CodingQuarry_transcript_46368-T1, internal, 48711, 48768
-recovered CodingQuarry_transcript_46368-T1, internal, 48880, 48968
Couldn't classify 49219, 56575
Couldn't classify 56621, 58834
Sorry, prediction CodingQuarry_transcript_46366-T1 fails validation.
(ATG)	 AC	48545-48547	GT	TGG
(GTC)	 AG	48711-48768	GT	AGG
(AGG)	 AG	48880-48968	GT	AGG
(ATG)	 AG	49219-56575	CA	GGC
(AAG)	 GG	56621-58834	GT	CGG
(GTT)	 AG	59244-59335	AT	AAA
-recovered CodingQuarry_transcript_46366-T1, initial, 48545, 48547
-recovered CodingQuarry_transcript_46366-T1, terminal, 59244, 59335
-recovered CodingQuarry_transcript_46366-T1, internal, 48711, 48768
-recovered CodingQuarry_transcript_46366-T1, internal, 48880, 48968
Valid prediction for GlimmerHMM_glimmerT_8541-T1
Couldn't classify 133822, 133953
Sorry, prediction pasa_asmbl_39576.p2 fails validation.
(ATG)	 AG	131605-131774	GT	AGG
(GTT)	 AG	133299-133404	GT	AGG
(CAC)	 AG	133822-133953	TA	TGT
-recovered pasa_asmbl_39576.p2, initial, 131605, 131774
-recovered pasa_asmbl_39576.p2, internal, 131605, 131774
-recovered pasa_asmbl_39576.p2, internal, 133299, 133404
Valid prediction for GeneMark_model.13895_t
Valid prediction for GeneMark_model.13884_t
Valid prediction for GeneMark_model.13861_t
Valid prediction for GlimmerHMM_glimmerT_8538-T1
Valid prediction for snap_scaffold_3-snap.3643-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 27714, rend_intergenic: 25934  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32534, rend_intergenic: 27735  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36151, rend_intergenic: 33762  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52235, rend_intergenic: 48019  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62163, rend_intergenic: 52395  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62764, rend_intergenic: 62548  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66481, rend_intergenic: 63558  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128987, rend_intergenic: 124910  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134305, rend_intergenic: 130450  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143738, rend_intergenic: 139558  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162085, rend_intergenic: 158819  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170148, rend_intergenic: 167349  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 173438
-exon list size: 573


building trellis

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98.3    
98.4    
98.6    
98.8    
99.0    
99.1    
99.3    
99.5    
99.7    
99.8    
-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 27714, rend_intergenic: 25934  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32534, rend_intergenic: 27735  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36151, rend_intergenic: 33762  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52235, rend_intergenic: 48019  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62163, rend_intergenic: 52395  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62764, rend_intergenic: 62548  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66481, rend_intergenic: 63558  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128987, rend_intergenic: 124910  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134305, rend_intergenic: 130450  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143738, rend_intergenic: 139558  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162085, rend_intergenic: 158819  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170148, rend_intergenic: 167349  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 18 predictions persist after filtering for low support