-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_2/scaffold_2_4115999-4293385

-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_3739-T1
Valid prediction for GeneMark_model.6093_t
Valid prediction for snap_scaffold_2-snap.978-T1
Valid prediction for pasa_asmbl_24364.p1
Valid prediction for GeneMark_model.6106_t
Valid prediction for GlimmerHMM_glimmerT_3728-T1
Valid prediction for GlimmerHMM_glimmerT_3725-T1
Valid prediction for GeneMark_model.6091_t
Valid prediction for snap_scaffold_2-snap.976-T1
Couldn't classify 49622, 49849
Sorry, prediction pasa_asmbl_24362.p2 fails validation.
(GCA)	 AG	49622-49849	GT	GGG
(CTG)	 AG	51905-53170	GT	AGG
(GCT)	 AG	55092-55109	TC	AGT
-recovered pasa_asmbl_24362.p2, terminal, 55092, 55109
-recovered pasa_asmbl_24362.p2, internal, 49622, 49849
-recovered pasa_asmbl_24362.p2, internal, 51905, 53170
Valid prediction for GlimmerHMM_glimmerT_3734-T1
Valid prediction for GeneMark_model.6085_t
Valid prediction for GlimmerHMM_glimmerT_3740-T1
Valid prediction for Augustus_model.g2483.t1
Valid prediction for GeneMark_model.6110_t
Valid prediction for GlimmerHMM_glimmerT_3737-T1
Valid prediction for GlimmerHMM_glimmerT_3732-T1
Valid prediction for Augustus_model.g2480.t1
Valid prediction for Augustus_model.g2487.t1
Valid prediction for snap_scaffold_2-snap.958-T1
Valid prediction for snap_scaffold_2-snap.974-T1
Valid prediction for CodingQuarry_transcript_28468-T1
Valid prediction for GeneMark_model.6087_t
Valid prediction for snap_scaffold_2-snap.979-T1
Valid prediction for GeneMark_model.6108_t
Valid prediction for GeneMark_model.6084_t
Valid prediction for snap_scaffold_2-snap.960-T1
Valid prediction for CodingQuarry_transcript_28467-T1
Valid prediction for snap_scaffold_2-snap.962-T1
Valid prediction for snap_scaffold_2-snap.969-T1
Valid prediction for snap_scaffold_2-snap.966-T1
Valid prediction for snap_scaffold_2-snap.992-T1
Valid prediction for GlimmerHMM_glimmerT_3724-T1
Valid prediction for GlimmerHMM_glimmerT_3741-T1
Valid prediction for HiQ_model.g2481.t1
Valid prediction for snap_scaffold_2-snap.988-T1
Valid prediction for Augustus_model.g2486.t1
Valid prediction for GlimmerHMM_glimmerT_3729-T1
Valid prediction for GlimmerHMM_glimmerT_3723-T1
Valid prediction for snap_scaffold_2-snap.963-T1
Valid prediction for GlimmerHMM_glimmerT_3727-T1
Valid prediction for Augustus_model.g2485.t1
Valid prediction for GeneMark_model.6101_t
Valid prediction for GeneMark_model.6104_t
Valid prediction for Augustus_model.g2479.t1
Valid prediction for pasa_asmbl_24357.p1
Valid prediction for GeneMark_model.6103_t
Valid prediction for snap_scaffold_2-snap.984-T1
Valid prediction for snap_scaffold_2-snap.980-T1
Valid prediction for GeneMark_model.6117_t
Valid prediction for snap_scaffold_2-snap.965-T1
Valid prediction for snap_scaffold_2-snap.959-T1
Valid prediction for GeneMark_model.6098_t
Valid prediction for GeneMark_model.6102_t
Valid prediction for GeneMark_model.6089_t
Valid prediction for snap_scaffold_2-snap.967-T1
Valid prediction for GlimmerHMM_glimmerT_3736-T1
Valid prediction for snap_scaffold_2-snap.968-T1
Valid prediction for Augustus_model.g2478.t1
Valid prediction for GeneMark_model.6113_t
Valid prediction for GlimmerHMM_glimmerT_3730-T1
Valid prediction for snap_scaffold_2-snap.977-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_2-snap.981-T1
Valid prediction for snap_scaffold_2-snap.991-T1
Valid prediction for GeneMark_model.6112_t
Valid prediction for snap_scaffold_2-snap.985-T1
Valid prediction for snap_scaffold_2-snap.972-T1
Valid prediction for Augustus_model.g2490.t1
Valid prediction for HiQ_model.g2477.t1
Valid prediction for snap_scaffold_2-snap.971-T1
Valid prediction for GeneMark_model.6118_t
Valid prediction for snap_scaffold_2-snap.973-T1
Valid prediction for GeneMark_model.6095_t
Valid prediction for CodingQuarry_transcript_28469-T1
Valid prediction for snap_scaffold_2-snap.982-T1
Valid prediction for Augustus_model.g2484.t1
Valid prediction for Augustus_model.g2489.t1
Valid prediction for GeneMark_model.6111_t
Valid prediction for snap_scaffold_2-snap.983-T1
Valid prediction for GeneMark_model.6114_t
Valid prediction for GeneMark_model.6116_t
Couldn't classify 47589, 47672
Sorry, prediction pasa_asmbl_23081.p1 fails validation.
(GTA)	 CA	47589-47672	GT	TGG
(ATA)	 AG	48005-48164	GT	AGG
(AAT)	 AG	49248-49302	GT	CGG
(GTA)	 AG	49810-49925	GT	TAG
(TCA)	 AG	50188-50263	GT	GAG
(CTG)	 AG	50466-50620	GT	CAG
(GAA)	 AG	51011-51108	GT	ACG
(TTA)	 AG	51419-51533	GT	TGG
(ATA)	 AG	51899-51971	GT	AAG
(GTT)	 AG	52599-52701	GT	AAG
(TAC)	 AG	54564-54714	GT	CAG
(CTT)	 AG	54940-55032	GT	AAG
(TGT)	 AG	55400-55539	GT	CTG
(TTC)	 AG	58025-58120	TT	GAT
-recovered pasa_asmbl_23081.p1, terminal, 58025, 58120
-recovered pasa_asmbl_23081.p1, internal, 48005, 48164
-recovered pasa_asmbl_23081.p1, internal, 49248, 49302
-recovered pasa_asmbl_23081.p1, internal, 49810, 49925
-recovered pasa_asmbl_23081.p1, internal, 50188, 50263
-recovered pasa_asmbl_23081.p1, internal, 50466, 50620
-recovered pasa_asmbl_23081.p1, internal, 51011, 51108
-recovered pasa_asmbl_23081.p1, internal, 51419, 51533
-recovered pasa_asmbl_23081.p1, internal, 51899, 51971
-recovered pasa_asmbl_23081.p1, internal, 52599, 52701
-recovered pasa_asmbl_23081.p1, internal, 54564, 54714
-recovered pasa_asmbl_23081.p1, internal, 54940, 55032
-recovered pasa_asmbl_23081.p1, internal, 55400, 55539
Valid prediction for CodingQuarry_transcript_28471-T1
Valid prediction for GeneMark_model.6086_t
Valid prediction for GeneMark_model.6100_t
Valid prediction for GlimmerHMM_glimmerT_3738-T1
Valid prediction for snap_scaffold_2-snap.964-T1
Valid prediction for snap_scaffold_2-snap.961-T1
Valid prediction for GlimmerHMM_glimmerT_3733-T1
Valid prediction for CodingQuarry_transcript_28470-T1
Valid prediction for GlimmerHMM_glimmerT_3731-T1
Valid prediction for GeneMark_model.6109_t
Valid prediction for snap_scaffold_2-snap.986-T1
Valid prediction for GeneMark_model.6097_t
Valid prediction for snap_scaffold_2-snap.987-T1
Valid prediction for GlimmerHMM_glimmerT_3722-T1
Valid prediction for GeneMark_model.6115_t
Valid prediction for GeneMark_model.6099_t
Valid prediction for Augustus_model.g2482.t1
Valid prediction for GlimmerHMM_glimmerT_3735-T1
Couldn't classify 25013, 25076
Sorry, prediction pasa_asmbl_23086.p1 fails validation.
(GTA)	 AG	25013-25076	GT	CGG
(ATG)	 AG	27001-27052	GT	CAG
(TGC)	 AG	27237-27300	GT	AGG
(GTG)	 AG	28181-28387	GT	CTG
(ATT)	 AG	28624-28703	GT	TGG
(GAA)	 AG	29202-29280	GT	AGG
(GTT)	 AG	29672-29743	GT	CTG
(AAT)	 AG	30226-30288	GT	AGG
(ACT)	 AG	30580-30720	AA	AAA
-recovered pasa_asmbl_23086.p1, initial, 27001, 27052
-recovered pasa_asmbl_23086.p1, terminal, 30580, 30720
-recovered pasa_asmbl_23086.p1, internal, 25013, 25076
-recovered pasa_asmbl_23086.p1, internal, 27001, 27052
-recovered pasa_asmbl_23086.p1, internal, 27237, 27300
-recovered pasa_asmbl_23086.p1, internal, 28181, 28387
-recovered pasa_asmbl_23086.p1, internal, 28624, 28703
-recovered pasa_asmbl_23086.p1, internal, 29202, 29280
-recovered pasa_asmbl_23086.p1, internal, 29672, 29743
-recovered pasa_asmbl_23086.p1, internal, 30226, 30288
Valid prediction for GlimmerHMM_glimmerT_3726-T1
Valid prediction for snap_scaffold_2-snap.989-T1
Valid prediction for GeneMark_model.6088_t
Valid prediction for HiQ_model.g2488.t1
Valid prediction for snap_scaffold_2-snap.975-T1
Valid prediction for GeneMark_model.6090_t
Valid prediction for GeneMark_model.6107_t
Valid prediction for GeneMark_model.6092_t
Valid prediction for GeneMark_model.6096_t
Valid prediction for GeneMark_model.6105_t
Valid prediction for snap_scaffold_2-snap.970-T1
Valid prediction for GeneMark_model.6094_t
Valid prediction for snap_scaffold_2-snap.990-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 28755, rend_intergenic: 27168  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70849, rend_intergenic: 69010  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91532, rend_intergenic: 84642  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104121, rend_intergenic: 100438  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122812, rend_intergenic: 121075  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144075, rend_intergenic: 139548  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174618, rend_intergenic: 170029  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 177387
-exon list size: 487


building trellis

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-found 20 predictions from path traversal
Error with prediction: snap lend_intergenic: 28755, rend_intergenic: 27168  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70849, rend_intergenic: 69010  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91532, rend_intergenic: 84642  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104121, rend_intergenic: 100438  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122812, rend_intergenic: 121075  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144075, rend_intergenic: 139548  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174618, rend_intergenic: 170029  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