-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_11/scaffold_11_2868938-3084297

-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_26782-T1
Valid prediction for GlimmerHMM_glimmerT_26771-T1
Valid prediction for GlimmerHMM_glimmerT_26766-T1
Valid prediction for snap_scaffold_11-snap.771-T1
Valid prediction for Augustus_model.g17711.t1
Valid prediction for GlimmerHMM_glimmerT_26773-T1
Valid prediction for GlimmerHMM_glimmerT_26783-T1
Valid prediction for snap_scaffold_11-snap.777-T1
Valid prediction for snap_scaffold_11-snap.751-T1
Valid prediction for snap_scaffold_11-snap.742-T1
Valid prediction for snap_scaffold_11-snap.755-T1
Valid prediction for Augustus_model.g17716.t1
Valid prediction for Augustus_model.g17702.t1
Valid prediction for snap_scaffold_11-snap.731-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_26747-T1
Valid prediction for GlimmerHMM_glimmerT_26781-T1
Valid prediction for GlimmerHMM_glimmerT_26778-T1
Valid prediction for snap_scaffold_11-snap.763-T1
Valid prediction for Augustus_model.g17705.t1
Valid prediction for snap_scaffold_11-snap.775-T1
Valid prediction for snap_scaffold_11-snap.759-T1
Valid prediction for snap_scaffold_11-snap.756-T1
Couldn't classify 123133, 123181
Couldn't classify 128879, 128988
Sorry, prediction pasa_asmbl_5392.p1 fails validation.
(CCA)	 GT	123133-123181	GT	CAG
(TTT)	 AG	123558-123598	GT	AGG
(ATG)	 AG	124115-124280	GT	AGG
(ACA)	 AG	126463-126530	GT	CTG
(AGA)	 AG	126747-126909	GT	AGG
(GTT)	 AG	128879-128988	GC	CAG
-recovered pasa_asmbl_5392.p1, initial, 124115, 124280
-recovered pasa_asmbl_5392.p1, internal, 123558, 123598
-recovered pasa_asmbl_5392.p1, internal, 124115, 124280
-recovered pasa_asmbl_5392.p1, internal, 126463, 126530
-recovered pasa_asmbl_5392.p1, internal, 126747, 126909
-recovered pasa_asmbl_5392.p1, internal, 128879, 128988
Valid prediction for GlimmerHMM_glimmerT_26745-T1
Valid prediction for snap_scaffold_11-snap.739-T1
Valid prediction for HiQ_model.g17710.t1
Valid prediction for snap_scaffold_11-snap.753-T1
Valid prediction for snap_scaffold_11-snap.741-T1
Valid prediction for GlimmerHMM_glimmerT_26776-T1
Valid prediction for Augustus_model.g17706.t1
Valid prediction for snap_scaffold_11-snap.733-T1
Valid prediction for snap_scaffold_11-snap.736-T1
Valid prediction for snap_scaffold_11-snap.730-T1
Valid prediction for snap_scaffold_11-snap.732-T1
Valid prediction for snap_scaffold_11-snap.728-T1
Valid prediction for GlimmerHMM_glimmerT_26765-T1
Valid prediction for snap_scaffold_11-snap.738-T1
Valid prediction for GlimmerHMM_glimmerT_26779-T1
Valid prediction for snap_scaffold_11-snap.764-T1
Valid prediction for Augustus_model.g17714.t1
Valid prediction for Augustus_model.g17707.t1
Valid prediction for GlimmerHMM_glimmerT_26780-T1
Valid prediction for Augustus_model.g17703.t1
Couldn't classify 152623, 152687
Sorry, prediction pasa_asmbl_5395.p1 fails validation.
(CCA)	 CC	152623-152687	GT	GTG
(GCT)	 AG	154054-154126	GT	ATG
(GTG)	 AG	154264-154340	GT	TGG
(GAT)	 AG	154433-154553	GT	AGG
(GAC)	 AG	154973-155086	GT	AGG
(AGT)	 AG	155355-155523	GT	GGG
(CCT)	 AG	157509-157519	AA	AGA
-recovered pasa_asmbl_5395.p1, terminal, 157509, 157519
-recovered pasa_asmbl_5395.p1, internal, 154054, 154126
-recovered pasa_asmbl_5395.p1, internal, 154264, 154340
-recovered pasa_asmbl_5395.p1, internal, 154433, 154553
-recovered pasa_asmbl_5395.p1, internal, 154973, 155086
-recovered pasa_asmbl_5395.p1, internal, 155355, 155523
Valid prediction for snap_scaffold_11-snap.744-T1
Valid prediction for Augustus_model.g17717.t1
Valid prediction for snap_scaffold_11-snap.770-T1
Valid prediction for CodingQuarry_transcript_8010-T1
Valid prediction for snap_scaffold_11-snap.750-T1
Valid prediction for snap_scaffold_11-snap.754-T1
Valid prediction for GlimmerHMM_glimmerT_26763-T1
Valid prediction for pasa_asmbl_5394.p1
Valid prediction for GlimmerHMM_glimmerT_26758-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_26748-T1
Valid prediction for CodingQuarry_transcript_8009-T1
Valid prediction for GlimmerHMM_glimmerT_26759-T1
Valid prediction for snap_scaffold_11-snap.735-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: -)Couldn't classify 80349, 80402
Couldn't classify 81238, 81467
Sorry, prediction pasa_asmbl_6521.p1 fails validation.
(GGC)	 AC	80349-80402	GT	CGG
(GTG)	 AG	80513-80615	GT	TGG
(AGA)	 AG	80880-81029	GT	TGG
(GAG)	 AG	81238-81467	TG	GGT
-recovered pasa_asmbl_6521.p1, internal, 80513, 80615
-recovered pasa_asmbl_6521.p1, internal, 80880, 81029
Valid prediction for snap_scaffold_11-snap.768-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_11-snap.727-T1
Valid prediction for GlimmerHMM_glimmerT_26749-T1
Couldn't classify 157559, 157765
Sorry, prediction pasa_asmbl_6519.p1 fails validation.
(AAG)	 GG	157559-157765	GT	GGG
(CAA)	 AG	159304-159411	GA	GAG
-recovered pasa_asmbl_6519.p1, terminal, 159304, 159411
Valid prediction for GlimmerHMM_glimmerT_26762-T1
Valid prediction for GlimmerHMM_glimmerT_26761-T1
Valid prediction for GlimmerHMM_glimmerT_26752-T1
Valid prediction for GlimmerHMM_glimmerT_26770-T1
Valid prediction for snap_scaffold_11-snap.760-T1
Valid prediction for snap_scaffold_11-snap.749-T1
Valid prediction for snap_scaffold_11-snap.765-T1
Valid prediction for snap_scaffold_11-snap.766-T1
Valid prediction for snap_scaffold_11-snap.774-T1
Valid prediction for snap_scaffold_11-snap.757-T1
Valid prediction for GlimmerHMM_glimmerT_26754-T1
Valid prediction for snap_scaffold_11-snap.776-T1
Valid prediction for GlimmerHMM_glimmerT_26772-T1
Valid prediction for Augustus_model.g17704.t1
Valid prediction for GlimmerHMM_glimmerT_26774-T1
Valid prediction for snap_scaffold_11-snap.746-T1
Valid prediction for snap_scaffold_11-snap.734-T1
Valid prediction for GlimmerHMM_glimmerT_26775-T1
Valid prediction for GlimmerHMM_glimmerT_26755-T1
Valid prediction for snap_scaffold_11-snap.772-T1
Valid prediction for Augustus_model.g17708.t1
Valid prediction for snap_scaffold_11-snap.729-T1
Couldn't classify 82061, 82111
Sorry, prediction pasa_asmbl_6520.p1 fails validation.
(GGG)	 CG	82061-82111	GT	AGG
(CTG)	 AG	82253-82359	GT	AGG
(GTA)	 AG	82541-82715	CA	AAC
-recovered pasa_asmbl_6520.p1, terminal, 82541, 82715
-recovered pasa_asmbl_6520.p1, internal, 82253, 82359
Valid prediction for snap_scaffold_11-snap.773-T1
Valid prediction for GlimmerHMM_glimmerT_26768-T1
Valid prediction for snap_scaffold_11-snap.745-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_11-snap.740-T1
Valid prediction for snap_scaffold_11-snap.737-T1
Valid prediction for snap_scaffold_11-snap.747-T1
Valid prediction for snap_scaffold_11-snap.767-T1
Valid prediction for HiQ_model.g17712.t1
Valid prediction for Augustus_model.g17715.t1
Valid prediction for snap_scaffold_11-snap.743-T1
Valid prediction for snap_scaffold_11-snap.748-T1
Valid prediction for GlimmerHMM_glimmerT_26764-T1
Valid prediction for GlimmerHMM_glimmerT_26753-T1
Valid prediction for snap_scaffold_11-snap.769-T1
Valid prediction for CodingQuarry_transcript_8011-T1
Valid prediction for snap_scaffold_11-snap.761-T1
Valid prediction for GlimmerHMM_glimmerT_26756-T1
Valid prediction for Augustus_model.g17713.t1
Valid prediction for GlimmerHMM_glimmerT_26751-T1
Valid prediction for snap_scaffold_11-snap.762-T1
Valid prediction for GlimmerHMM_glimmerT_26777-T1
Valid prediction for GlimmerHMM_glimmerT_26757-T1
Valid prediction for HiQ_model.g17701.t1
Valid prediction for Augustus_model.g17700.t1
Couldn't classify 52141, 52279
Sorry, prediction pasa_asmbl_6524.p1 fails validation.
(ATC)	 AG	52141-52279	GT	AGG
(GCA)	 AG	52474-52586	GT	CTG
(AGT)	 AG	52807-52963	GT	AGG
(TGG)	 AG	53446-53603	AC	GAA
-recovered pasa_asmbl_6524.p1, terminal, 53446, 53603
-recovered pasa_asmbl_6524.p1, internal, 52141, 52279
-recovered pasa_asmbl_6524.p1, internal, 52474, 52586
-recovered pasa_asmbl_6524.p1, internal, 52807, 52963
Valid prediction for GlimmerHMM_glimmerT_26767-T1
Valid prediction for CodingQuarry_transcript_8008-T1
Valid prediction for GlimmerHMM_glimmerT_26750-T1
Valid prediction for GlimmerHMM_glimmerT_26769-T1
Valid prediction for snap_scaffold_11-snap.758-T1
Valid prediction for snap_scaffold_11-snap.752-T1
Valid prediction for Augustus_model.g17709.t1
Valid prediction for GlimmerHMM_glimmerT_26746-T1
Valid prediction for GlimmerHMM_glimmerT_26760-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 5705, rend_intergenic: 4886  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25520, rend_intergenic: 6054  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26276, rend_intergenic: 25950  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34704, rend_intergenic: 27670  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51584, rend_intergenic: 34895  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57667, rend_intergenic: 55996  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67742, rend_intergenic: 60806  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83881, rend_intergenic: 69101  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96837, rend_intergenic: 93887  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105997, rend_intergenic: 104668  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118052, rend_intergenic: 105999  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123817, rend_intergenic: 120761  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126475, rend_intergenic: 124115  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192812, rend_intergenic: 180332  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 201462, rend_intergenic: 198245  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 215360
-exon list size: 513


building trellis

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-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 5705, rend_intergenic: 4886  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25520, rend_intergenic: 6054  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26276, rend_intergenic: 25950  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34704, rend_intergenic: 27670  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51584, rend_intergenic: 34895  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57667, rend_intergenic: 55996  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67742, rend_intergenic: 60806  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83881, rend_intergenic: 69101  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96837, rend_intergenic: 93887  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105997, rend_intergenic: 104668  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118052, rend_intergenic: 105999  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123817, rend_intergenic: 120761  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126475, rend_intergenic: 124115  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192812, rend_intergenic: 180332  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 201462, rend_intergenic: 198245  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 26 predictions persist after filtering for low support