-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_5/scaffold_5_18577792-18758034

-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_5-snap.3471-T1
Valid prediction for GlimmerHMM_glimmerT_13687-T1
Valid prediction for snap_scaffold_5-snap.3476-T1
Valid prediction for GlimmerHMM_glimmerT_13692-T1
Valid prediction for Augustus_model.g9089.t1
Valid prediction for snap_scaffold_5-snap.3507-T1
Valid prediction for GlimmerHMM_glimmerT_13715-T1
Valid prediction for GlimmerHMM_glimmerT_13714-T1
Valid prediction for Augustus_model.g9107.t1
Valid prediction for Augustus_model.g9083.t1
Valid prediction for GlimmerHMM_glimmerT_13707-T1
Valid prediction for snap_scaffold_5-snap.3481-T1
Valid prediction for Augustus_model.g9095.t1
Valid prediction for snap_scaffold_5-snap.3483-T1
Valid prediction for snap_scaffold_5-snap.3473-T1
Valid prediction for snap_scaffold_5-snap.3478-T1
Valid prediction for GlimmerHMM_glimmerT_13694-T1
Valid prediction for Augustus_model.g9087.t1
Valid prediction for GlimmerHMM_glimmerT_13700-T1
Valid prediction for GlimmerHMM_glimmerT_13716-T1
Valid prediction for Augustus_model.g9100.t1
Valid prediction for snap_scaffold_5-snap.3492-T1
Valid prediction for Augustus_model.g9090.t1
Couldn't classify 10345, 10800
Sorry, prediction pasa_asmbl_46277.p1 fails validation.
(ATC)	 AC	10345-10800	CT	GAC
Valid prediction for GlimmerHMM_glimmerT_13699-T1
Valid prediction for Augustus_model.g9086.t1
Valid prediction for GlimmerHMM_glimmerT_13690-T1
Valid prediction for snap_scaffold_5-snap.3490-T1
Valid prediction for GlimmerHMM_glimmerT_13693-T1
Valid prediction for GlimmerHMM_glimmerT_13689-T1
Valid prediction for snap_scaffold_5-snap.3485-T1
Valid prediction for snap_scaffold_5-snap.3474-T1
Valid prediction for snap_scaffold_5-snap.3504-T1
Valid prediction for GlimmerHMM_glimmerT_13717-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 CodingQuarry_transcript_52470-T1
Valid prediction for GlimmerHMM_glimmerT_13705-T1
Valid prediction for pasa_asmbl_44852.p1
Valid prediction for GlimmerHMM_glimmerT_13702-T1
Valid prediction for snap_scaffold_5-snap.3489-T1
Valid prediction for snap_scaffold_5-snap.3498-T1
Valid prediction for HiQ_model.g9103.t1
Valid prediction for snap_scaffold_5-snap.3502-T1
Valid prediction for snap_scaffold_5-snap.3500-T1
Valid prediction for CodingQuarry_transcript_52469-T1
Valid prediction for GlimmerHMM_glimmerT_13701-T1
Valid prediction for snap_scaffold_5-snap.3482-T1
Valid prediction for HiQ_model.g9093.t1
Valid prediction for Augustus_model.g9085.t1
Valid prediction for snap_scaffold_5-snap.3470-T1
Valid prediction for Augustus_model.g9096.t1
Valid prediction for HiQ_model.g9091.t1
Valid prediction for snap_scaffold_5-snap.3475-T1
Valid prediction for snap_scaffold_5-snap.3488-T1
Valid prediction for GlimmerHMM_glimmerT_13686-T1
Valid prediction for GlimmerHMM_glimmerT_13697-T1
Valid prediction for CodingQuarry_transcript_52471-T1
Valid prediction for snap_scaffold_5-snap.3472-T1
Valid prediction for GlimmerHMM_glimmerT_13706-T1
Valid prediction for snap_scaffold_5-snap.3494-T1
Valid prediction for snap_scaffold_5-snap.3499-T1
Valid prediction for GlimmerHMM_glimmerT_13713-T1
Valid prediction for snap_scaffold_5-snap.3501-T1
Valid prediction for HiQ_model.g9101.t1
Valid prediction for CodingQuarry_transcript_52466-T1
Valid prediction for CodingQuarry_transcript_52472-T1
Valid prediction for GlimmerHMM_glimmerT_13704-T1
Couldn't classify 33265, 33360
Sorry, prediction pasa_asmbl_44872.p1 fails validation.
(ATG)	 AG	26786-26924	GT	GGG
(GAG)	 AG	28555-28627	GT	GAG
(AGA)	 AG	30135-30189	GT	AGG
(ACC)	 AG	30304-30423	GT	CCG
(GAG)	 AG	33265-33360	TA	AGT
-recovered pasa_asmbl_44872.p1, initial, 26786, 26924
-recovered pasa_asmbl_44872.p1, internal, 26786, 26924
-recovered pasa_asmbl_44872.p1, internal, 28555, 28627
-recovered pasa_asmbl_44872.p1, internal, 30135, 30189
-recovered pasa_asmbl_44872.p1, internal, 30304, 30423
Valid prediction for snap_scaffold_5-snap.3487-T1
Valid prediction for GlimmerHMM_glimmerT_13712-T1
Valid prediction for pasa_asmbl_44858.p2
Valid prediction for pasa_asmbl_44863.p1
Valid prediction for Augustus_model.g9084.t1
Valid prediction for snap_scaffold_5-snap.3497-T1
Valid prediction for snap_scaffold_5-snap.3493-T1
Valid prediction for GlimmerHMM_glimmerT_13695-T1
Valid prediction for Augustus_model.g9098.t1
Valid prediction for snap_scaffold_5-snap.3479-T1
Valid prediction for Augustus_model.g9094.t1
Valid prediction for Augustus_model.g9082.t1
Valid prediction for snap_scaffold_5-snap.3491-T1
Valid prediction for GlimmerHMM_glimmerT_13710-T1
Valid prediction for pasa_asmbl_44864.p1
Valid prediction for GlimmerHMM_glimmerT_13688-T1
Valid prediction for Augustus_model.g9104.t1
Valid prediction for Augustus_model.g9106.t1
Valid prediction for CodingQuarry_transcript_52467-T1
Valid prediction for CodingQuarry_transcript_52468-T1
Valid prediction for GlimmerHMM_glimmerT_13691-T1
Couldn't classify 38757, 38870
Sorry, prediction pasa_asmbl_44871.p1 fails validation.
(ATG)	 GA	36510-36556	GT	TGG
(CTT)	 AG	37338-37392	GT	AGG
(GAT)	 AG	37578-37651	GT	CAG
(CAT)	 AG	37868-37926	GT	CGG
(ACG)	 AG	38095-38215	GT	AGG
(GTG)	 AG	38304-38434	GT	TGG
(CGT)	 AG	38571-38638	GT	TGG
(AGG)	 AG	38757-38870	CG	AGC
-recovered pasa_asmbl_44871.p1, initial, 36510, 36556
-recovered pasa_asmbl_44871.p1, internal, 37338, 37392
-recovered pasa_asmbl_44871.p1, internal, 37578, 37651
-recovered pasa_asmbl_44871.p1, internal, 37868, 37926
-recovered pasa_asmbl_44871.p1, internal, 38095, 38215
-recovered pasa_asmbl_44871.p1, internal, 38304, 38434
-recovered pasa_asmbl_44871.p1, internal, 38571, 38638
Valid prediction for snap_scaffold_5-snap.3495-T1
Valid prediction for HiQ_model.g9102.t1
Valid prediction for snap_scaffold_5-snap.3506-T1
Valid prediction for GlimmerHMM_glimmerT_13708-T1
Valid prediction for snap_scaffold_5-snap.3496-T1
Valid prediction for GlimmerHMM_glimmerT_13703-T1
Valid prediction for snap_scaffold_5-snap.3486-T1
Valid prediction for snap_scaffold_5-snap.3503-T1
Valid prediction for HiQ_model.g9099.t1
Valid prediction for snap_scaffold_5-snap.3477-T1
Valid prediction for snap_scaffold_5-snap.3505-T1
Valid prediction for snap_scaffold_5-snap.3480-T1
Couldn't classify 96802, 96896
Couldn't classify 97008, 97257
Sorry, prediction pasa_asmbl_45055.p1 fails validation.
(AGT)	 GC	96802-96896	GT	AGG
(CTT)	 AG	97008-97257	AA	ACA
Valid prediction for pasa_asmbl_44848.p1
Valid prediction for CodingQuarry_transcript_52465-T1
Valid prediction for CodingQuarry_transcript_52473-T1
Valid prediction for snap_scaffold_5-snap.3484-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g9097.t1
Valid prediction for Augustus_model.g9088.t1
Valid prediction for GlimmerHMM_glimmerT_13711-T1
Valid prediction for GlimmerHMM_glimmerT_13696-T1
Valid prediction for GlimmerHMM_glimmerT_13698-T1
Valid prediction for HiQ_model.g9105.t1
Valid prediction for Augustus_model.g9092.t1
Valid prediction for GlimmerHMM_glimmerT_13709-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 14091, rend_intergenic: 11369  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24393, rend_intergenic: 16222  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48471, rend_intergenic: 34617  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59648, rend_intergenic: 56183  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74934, rend_intergenic: 64359  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79159, rend_intergenic: 76591  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107168, rend_intergenic: 104728  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148355, rend_intergenic: 147965  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151725, rend_intergenic: 148949  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162496, rend_intergenic: 158518  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 180243
-exon list size: 494


building trellis

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-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 14091, rend_intergenic: 11369  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24393, rend_intergenic: 16222  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48471, rend_intergenic: 34617  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59648, rend_intergenic: 56183  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74934, rend_intergenic: 64359  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79159, rend_intergenic: 76591  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107168, rend_intergenic: 104728  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148355, rend_intergenic: 147965  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151725, rend_intergenic: 148949  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162496, rend_intergenic: 158518  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 24 predictions persist after filtering for low support