-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_4/scaffold_4_4236294-4394639

-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 GeneMark_model.15450_t
Valid prediction for snap_scaffold_4-snap.985-T1
Valid prediction for GlimmerHMM_glimmerT_9391-T1
Valid prediction for GeneMark_model.15446_t
Valid prediction for GlimmerHMM_glimmerT_9404-T1
Valid prediction for snap_scaffold_4-snap.998-T1
Valid prediction for GlimmerHMM_glimmerT_9414-T1
Valid prediction for GlimmerHMM_glimmerT_9412-T1
Valid prediction for GlimmerHMM_glimmerT_9394-T1
Valid prediction for Augustus_model.g6115.t1
Valid prediction for Augustus_model.g6122.t1
Valid prediction for GlimmerHMM_glimmerT_9395-T1
Valid prediction for GeneMark_model.15474_t
Valid prediction for snap_scaffold_4-snap.967-T1
Valid prediction for Augustus_model.g6112.t1
Valid prediction for GeneMark_model.15457_t
Valid prediction for GlimmerHMM_glimmerT_9390-T1
Valid prediction for snap_scaffold_4-snap.992-T1
Valid prediction for GlimmerHMM_glimmerT_9389-T1
Valid prediction for GlimmerHMM_glimmerT_9399-T1
Valid prediction for GeneMark_model.15476_t
Valid prediction for snap_scaffold_4-snap.975-T1
Valid prediction for GlimmerHMM_glimmerT_9411-T1
Valid prediction for snap_scaffold_4-snap.969-T1
Valid prediction for GeneMark_model.15470_t
Valid prediction for snap_scaffold_4-snap.984-T1
Valid prediction for snap_scaffold_4-snap.988-T1
Valid prediction for snap_scaffold_4-snap.997-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for GeneMark_model.15443_t
Valid prediction for GeneMark_model.15451_t
Valid prediction for GlimmerHMM_glimmerT_9410-T1
Valid prediction for GeneMark_model.15437_t
Valid prediction for Augustus_model.g6121.t1
Valid prediction for GlimmerHMM_glimmerT_9407-T1
Valid prediction for Augustus_model.g6104.t1
Valid prediction for snap_scaffold_4-snap.990-T1
Valid prediction for snap_scaffold_4-snap.966-T1
Valid prediction for GeneMark_model.15448_t
Valid prediction for GeneMark_model.15477_t
Valid prediction for Augustus_model.g6105.t1
Valid prediction for Augustus_model.g6113.t1
Valid prediction for GeneMark_model.15460_t
Valid prediction for Augustus_model.g6114.t1
Valid prediction for GeneMark_model.15471_t
Valid prediction for snap_scaffold_4-snap.999-T1
Valid prediction for Augustus_model.g6102.t1
Valid prediction for Augustus_model.g6117.t1
Valid prediction for Augustus_model.g6116.t1
Valid prediction for GeneMark_model.15464_t
Valid prediction for Augustus_model.g6106.t1
Valid prediction for GlimmerHMM_glimmerT_9416-T1
Valid prediction for snap_scaffold_4-snap.994-T1
Valid prediction for GeneMark_model.15458_t
Valid prediction for GlimmerHMM_glimmerT_9392-T1
Valid prediction for GlimmerHMM_glimmerT_9409-T1
Valid prediction for GeneMark_model.15466_t
Valid prediction for GlimmerHMM_glimmerT_9408-T1
Valid prediction for GeneMark_model.15454_t
Valid prediction for GeneMark_model.15463_t
Valid prediction for GeneMark_model.15482_t
Valid prediction for GeneMark_model.15480_t
Valid prediction for snap_scaffold_4-snap.983-T1
Valid prediction for pasa_asmbl_42566.p1
Valid prediction for GlimmerHMM_glimmerT_9396-T1
Valid prediction for Augustus_model.g6107.t1
Valid prediction for HiQ_model.g6118.t1
Valid prediction for GeneMark_model.15445_t
Valid prediction for GeneMark_model.15462_t
Valid prediction for GeneMark_model.15441_t
Valid prediction for snap_scaffold_4-snap.974-T1
Valid prediction for snap_scaffold_4-snap.980-T1
Valid prediction for CodingQuarry_transcript_48841-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 GeneMark_model.15449_t
Valid prediction for snap_scaffold_4-snap.987-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GeneMark_model.15439_t
Valid prediction for GlimmerHMM_glimmerT_9397-T1
Valid prediction for snap_scaffold_4-snap.982-T1
Valid prediction for CodingQuarry_transcript_48842-T1
Valid prediction for GeneMark_model.15453_t
Valid prediction for snap_scaffold_4-snap.996-T1
Valid prediction for Augustus_model.g6109.t1
Valid prediction for snap_scaffold_4-snap.977-T1
Valid prediction for GeneMark_model.15461_t
Valid prediction for GeneMark_model.15444_t
Valid prediction for Augustus_model.g6120.t1
Valid prediction for snap_scaffold_4-snap.978-T1
Valid prediction for GeneMark_model.15468_t
Valid prediction for GeneMark_model.15459_t
Valid prediction for snap_scaffold_4-snap.981-T1
Valid prediction for GlimmerHMM_glimmerT_9403-T1
Valid prediction for snap_scaffold_4-snap.968-T1
Valid prediction for GeneMark_model.15452_t
Valid prediction for GlimmerHMM_glimmerT_9405-T1
Valid prediction for GeneMark_model.15440_t
Valid prediction for Augustus_model.g6101.t1
Valid prediction for HiQ_model.g6119.t1
Valid prediction for snap_scaffold_4-snap.976-T1
Valid prediction for GlimmerHMM_glimmerT_9406-T1
Valid prediction for GeneMark_model.15465_t
Valid prediction for snap_scaffold_4-snap.973-T1
Valid prediction for GlimmerHMM_glimmerT_9413-T1
Valid prediction for GlimmerHMM_glimmerT_9401-T1
Valid prediction for GeneMark_model.15438_t
Valid prediction for GlimmerHMM_glimmerT_9402-T1
Valid prediction for GeneMark_model.15455_t
Valid prediction for Augustus_model.g6108.t1
Valid prediction for GeneMark_model.15478_t
Valid prediction for snap_scaffold_4-snap.991-T1
Valid prediction for GlimmerHMM_glimmerT_9400-T1
Valid prediction for GeneMark_model.15467_t
Valid prediction for GeneMark_model.15442_t
Couldn't classify 13331, 13385
Sorry, prediction pasa_asmbl_41246.p1 fails validation.
(GCA)	 CA	13331-13385	GT	AGG
(CTA)	 AG	13904-13936	GT	AGG
(AAG)	 AG	14083-14112	GT	CAG
(GGA)	 AG	15342-15416	GT	ACG
(ATC)	 AG	15579-15647	GT	GGG
(CAG)	 AG	16172-16217	GT	GGG
(GAT)	 AG	18331-18376	CC	AAC
-recovered pasa_asmbl_41246.p1, terminal, 18331, 18376
-recovered pasa_asmbl_41246.p1, internal, 13904, 13936
-recovered pasa_asmbl_41246.p1, internal, 14083, 14112
-recovered pasa_asmbl_41246.p1, internal, 15342, 15416
-recovered pasa_asmbl_41246.p1, internal, 15579, 15647
-recovered pasa_asmbl_41246.p1, internal, 16172, 16217
Valid prediction for snap_scaffold_4-snap.972-T1
Valid prediction for GeneMark_model.15483_t
Valid prediction for Augustus_model.g6111.t1
Valid prediction for GeneMark_model.15472_t
Valid prediction for GlimmerHMM_glimmerT_9415-T1
Valid prediction for GeneMark_model.15479_t
Valid prediction for snap_scaffold_4-snap.970-T1
Valid prediction for snap_scaffold_4-snap.986-T1
Valid prediction for GlimmerHMM_glimmerT_9393-T1
Valid prediction for snap_scaffold_4-snap.979-T1
Valid prediction for GeneMark_model.15456_t
Valid prediction for snap_scaffold_4-snap.989-T1
Valid prediction for GlimmerHMM_glimmerT_9398-T1
Valid prediction for GeneMark_model.15484_t
Valid prediction for CodingQuarry_transcript_48843-T1
Valid prediction for snap_scaffold_4-snap.971-T1
Valid prediction for Augustus_model.g6103.t1
Valid prediction for GeneMark_model.15447_t
Valid prediction for GeneMark_model.15473_t
Valid prediction for snap_scaffold_4-snap.995-T1
Valid prediction for Augustus_model.g6110.t1
Valid prediction for GeneMark_model.15469_t
Valid prediction for GeneMark_model.15481_t
Valid prediction for snap_scaffold_4-snap.993-T1
Valid prediction for GlimmerHMM_glimmerT_9388-T1
Valid prediction for GeneMark_model.15475_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 16642, rend_intergenic: 13019  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22233, rend_intergenic: 16674  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49035, rend_intergenic: 46748  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71300, rend_intergenic: 65259  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74093, rend_intergenic: 73248  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81323, rend_intergenic: 74721  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87863, rend_intergenic: 85371  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104361, rend_intergenic: 97144  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111046, rend_intergenic: 108507  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118136, rend_intergenic: 111395  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126017, rend_intergenic: 123351  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 158346
-exon list size: 717


building trellis

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-found 36 predictions from path traversal
Error with prediction: snap lend_intergenic: 16642, rend_intergenic: 13019  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22233, rend_intergenic: 16674  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49035, rend_intergenic: 46748  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71300, rend_intergenic: 65259  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74093, rend_intergenic: 73248  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81323, rend_intergenic: 74721  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87863, rend_intergenic: 85371  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104361, rend_intergenic: 97144  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111046, rend_intergenic: 108507  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118136, rend_intergenic: 111395  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126017, rend_intergenic: 123351  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