-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_6/scaffold_6_18856869-19002375

-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_6-snap.4062-T1
Valid prediction for snap_scaffold_6-snap.4049-T1
Valid prediction for GeneMark_model.28635_t
Valid prediction for GeneMark_model.28650_t
Valid prediction for snap_scaffold_6-snap.4056-T1
Valid prediction for GlimmerHMM_glimmerT_17047-T1
Valid prediction for snap_scaffold_6-snap.4051-T1
Valid prediction for snap_scaffold_6-snap.4045-T1
Valid prediction for snap_scaffold_6-snap.4040-T1
Valid prediction for GeneMark_model.28639_t
Valid prediction for CodingQuarry_transcript_55293-T1
Valid prediction for GlimmerHMM_glimmerT_17039-T1
Valid prediction for Augustus_model.g11444.t1
Valid prediction for GlimmerHMM_glimmerT_17036-T1
Valid prediction for GeneMark_model.28628_t
Valid prediction for GeneMark_model.28646_t
Valid prediction for snap_scaffold_6-snap.4071-T1
Valid prediction for GeneMark_model.28651_t
Valid prediction for GlimmerHMM_glimmerT_17054-T1
Valid prediction for GlimmerHMM_glimmerT_17037-T1
Valid prediction for GeneMark_model.28619_t
Valid prediction for snap_scaffold_6-snap.4035-T1
Valid prediction for Augustus_model.g11447.t1
Valid prediction for GeneMark_model.28624_t
Valid prediction for snap_scaffold_6-snap.4068-T1
Valid prediction for snap_scaffold_6-snap.4032-T1
Valid prediction for GlimmerHMM_glimmerT_17045-T1
Valid prediction for GeneMark_model.28630_t
Valid prediction for GeneMark_model.28625_t
Valid prediction for HiQ_model.g11443.t1
Valid prediction for pasa_asmbl_47804.p1
Valid prediction for snap_scaffold_6-snap.4046-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for Augustus_model.g11460.t1
Valid prediction for GeneMark_model.28633_t
Valid prediction for snap_scaffold_6-snap.4066-T1
Valid prediction for snap_scaffold_6-snap.4060-T1
Valid prediction for snap_scaffold_6-snap.4054-T1
Valid prediction for GlimmerHMM_glimmerT_17041-T1
Valid prediction for GeneMark_model.28643_t
Valid prediction for GlimmerHMM_glimmerT_17050-T1
Valid prediction for snap_scaffold_6-snap.4042-T1
Valid prediction for snap_scaffold_6-snap.4038-T1
Valid prediction for GeneMark_model.28621_t
Valid prediction for snap_scaffold_6-snap.4070-T1
Valid prediction for Augustus_model.g11454.t1
Valid prediction for Augustus_model.g11459.t1
Valid prediction for GeneMark_model.28653_t
Valid prediction for GeneMark_model.28645_t
Valid prediction for snap_scaffold_6-snap.4037-T1
Valid prediction for snap_scaffold_6-snap.4069-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 GlimmerHMM_glimmerT_17051-T1
Valid prediction for pasa_asmbl_49225.p1
Valid prediction for GeneMark_model.28620_t
Valid prediction for GeneMark_model.28640_t
Valid prediction for snap_scaffold_6-snap.4047-T1
Valid prediction for pasa_asmbl_49219.p1
Valid prediction for CodingQuarry_transcript_55294-T1
Valid prediction for GlimmerHMM_glimmerT_17055-T1
Valid prediction for GeneMark_model.28644_t
Valid prediction for GeneMark_model.28636_t
Valid prediction for pasa_asmbl_49224.p1
Valid prediction for GeneMark_model.28632_t
Valid prediction for snap_scaffold_6-snap.4058-T1
Valid prediction for Augustus_model.g11456.t1
Valid prediction for GeneMark_model.28641_t
Valid prediction for GeneMark_model.28647_t
Valid prediction for GeneMark_model.28652_t
Valid prediction for CodingQuarry_transcript_55296-T1
Valid prediction for HiQ_model.g11449.t1
Valid prediction for snap_scaffold_6-snap.4057-T1
Valid prediction for CodingQuarry_transcript_55295-T1
Valid prediction for GeneMark_model.28638_t
Valid prediction for GeneMark_model.28648_t
Valid prediction for snap_scaffold_6-snap.4065-T1
Valid prediction for snap_scaffold_6-snap.4064-T1
Valid prediction for GeneMark_model.28634_t
Couldn't classify 69200, 69302
Sorry, prediction pasa_asmbl_49229.p1 fails validation.
(ATG)	 TC	67483-67700	GT	ATG
(CTA)	 AG	68265-68570	GT	AGG
(AGT)	 AG	68778-69029	GT	CGG
(GGC)	 AG	69200-69302	GA	AGG
-recovered pasa_asmbl_49229.p1, initial, 67483, 67700
-recovered pasa_asmbl_49229.p1, internal, 68265, 68570
-recovered pasa_asmbl_49229.p1, internal, 68778, 69029
Valid prediction for snap_scaffold_6-snap.4043-T1
Valid prediction for snap_scaffold_6-snap.4034-T1
Valid prediction for GeneMark_model.28631_t
Valid prediction for GeneMark_model.28637_t
Valid prediction for CodingQuarry_transcript_55299-T1
Valid prediction for snap_scaffold_6-snap.4041-T1
Valid prediction for snap_scaffold_6-snap.4063-T1
Valid prediction for GlimmerHMM_glimmerT_17046-T1
Valid prediction for snap_scaffold_6-snap.4039-T1
Valid prediction for Augustus_model.g11457.t1
Valid prediction for GeneMark_model.28642_t
Valid prediction for snap_scaffold_6-snap.4044-T1
Valid prediction for HiQ_model.g11448.t1
Couldn't classify 75484, 75649
Sorry, prediction pasa_asmbl_49228.p2 fails validation.
(GAG)	 TG	75484-75649	GT	AGG
(AGT)	 AG	75948-76120	CA	AAC
-recovered pasa_asmbl_49228.p2, terminal, 75948, 76120
Valid prediction for CodingQuarry_transcript_55301-T1
Valid prediction for CodingQuarry_transcript_55300-T1
Valid prediction for GlimmerHMM_glimmerT_17052-T1
Valid prediction for Augustus_model.g11458.t1
Valid prediction for GeneMark_model.28618_t
Valid prediction for GlimmerHMM_glimmerT_17040-T1
Valid prediction for Augustus_model.g11445.t1
Valid prediction for HiQ_model.g11450.t1
Valid prediction for GeneMark_model.28623_t
Valid prediction for CodingQuarry_transcript_55298-T1
Valid prediction for snap_scaffold_6-snap.4059-T1
Valid prediction for GlimmerHMM_glimmerT_17038-T1
Couldn't classify 44755, 45043
Sorry, prediction pasa_asmbl_49231.p1 fails validation.
(TCA)	 CG	44755-45043	GT	CGG
(ACA)	 AG	46756-46886	GT	AGG
(GAC)	 AG	47334-47435	GT	AGG
(GTT)	 AG	47886-48032	GT	AGG
(TCA)	 AG	48455-48609	GT	AGG
(GGG)	 AG	49103-49185	GT	AGG
(GAG)	 AG	49429-49600	GT	AGG
(GTT)	 AG	49843-49964	GT	GGG
(GTG)	 AG	50686-50837	AG	AGA
-recovered pasa_asmbl_49231.p1, terminal, 50686, 50837
-recovered pasa_asmbl_49231.p1, internal, 46756, 46886
-recovered pasa_asmbl_49231.p1, internal, 47334, 47435
-recovered pasa_asmbl_49231.p1, internal, 47886, 48032
-recovered pasa_asmbl_49231.p1, internal, 48455, 48609
-recovered pasa_asmbl_49231.p1, internal, 49103, 49185
-recovered pasa_asmbl_49231.p1, internal, 49429, 49600
-recovered pasa_asmbl_49231.p1, internal, 49843, 49964
Valid prediction for snap_scaffold_6-snap.4055-T1
Valid prediction for CodingQuarry_transcript_55297-T1
Valid prediction for snap_scaffold_6-snap.4048-T1
Valid prediction for GlimmerHMM_glimmerT_17053-T1
Couldn't classify 116199, 117014
Sorry, prediction pasa_asmbl_49218.p1 fails validation.
(ATG)	 TC	116199-117014	AC	TCA
Valid prediction for GlimmerHMM_glimmerT_17042-T1
Valid prediction for snap_scaffold_6-snap.4036-T1
Valid prediction for snap_scaffold_6-snap.4052-T1
Valid prediction for GlimmerHMM_glimmerT_17044-T1
Valid prediction for snap_scaffold_6-snap.4033-T1
Valid prediction for HiQ_model.g11451.t1
Valid prediction for GlimmerHMM_glimmerT_17049-T1
Valid prediction for GeneMark_model.28629_t
Valid prediction for GeneMark_model.28622_t
Couldn't classify 117089, 117400
Sorry, prediction pasa_asmbl_49217.p1 fails validation.
(CCG)	 CC	117089-117400	TC	GAT
Valid prediction for Augustus_model.g11455.t1
Valid prediction for snap_scaffold_6-snap.4031-T1
Valid prediction for snap_scaffold_6-snap.4061-T1
Valid prediction for snap_scaffold_6-snap.4067-T1
Valid prediction for GlimmerHMM_glimmerT_17043-T1
Valid prediction for snap_scaffold_6-snap.4053-T1
Valid prediction for HiQ_model.g11453.t1
Valid prediction for snap_scaffold_6-snap.4050-T1
Valid prediction for GeneMark_model.28626_t
Valid prediction for Augustus_model.g11452.t1
Valid prediction for GlimmerHMM_glimmerT_17048-T1
Valid prediction for GeneMark_model.28649_t
Valid prediction for GeneMark_model.28627_t
Valid prediction for Augustus_model.g11446.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 18700, rend_intergenic: 10846  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26333, rend_intergenic: 20310  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36695, rend_intergenic: 34860  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53526, rend_intergenic: 44388  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55294, rend_intergenic: 53926  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63722, rend_intergenic: 58276  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67788, rend_intergenic: 65016  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78882, rend_intergenic: 74536  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88201, rend_intergenic: 80005  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97326, rend_intergenic: 95630  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100684, rend_intergenic: 97567  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111898, rend_intergenic: 108571  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115012, rend_intergenic: 112703  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142843, rend_intergenic: 128370  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 145507
-exon list size: 580


building trellis

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-found 25 predictions from path traversal
Error with prediction: snap lend_intergenic: 18700, rend_intergenic: 10846  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26333, rend_intergenic: 20310  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36695, rend_intergenic: 34860  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53526, rend_intergenic: 44388  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55294, rend_intergenic: 53926  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63722, rend_intergenic: 58276  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67788, rend_intergenic: 65016  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78882, rend_intergenic: 74536  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88201, rend_intergenic: 80005  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97326, rend_intergenic: 95630  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100684, rend_intergenic: 97567  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111898, rend_intergenic: 108571  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115012, rend_intergenic: 112703  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142843, rend_intergenic: 128370  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

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