-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_9/scaffold_9_3936006-4199318

-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 Augustus_model.g14598.t1
Valid prediction for snap_scaffold_9-snap.896-T1
Valid prediction for Augustus_model.g14607.t1
Valid prediction for GlimmerHMM_glimmerT_21959-T1
Valid prediction for GlimmerHMM_glimmerT_21975-T1
Valid prediction for snap_scaffold_9-snap.882-T1
Valid prediction for GlimmerHMM_glimmerT_21952-T1
Valid prediction for snap_scaffold_9-snap.895-T1
Valid prediction for GlimmerHMM_glimmerT_21958-T1
Valid prediction for Augustus_model.g14599.t1
Valid prediction for snap_scaffold_9-snap.887-T1
Valid prediction for snap_scaffold_9-snap.886-T1
Valid prediction for GlimmerHMM_glimmerT_21960-T1
Valid prediction for snap_scaffold_9-snap.890-T1
Valid prediction for snap_scaffold_9-snap.878-T1
Valid prediction for Augustus_model.g14597.t1
Valid prediction for snap_scaffold_9-snap.876-T1
Valid prediction for GlimmerHMM_glimmerT_21954-T1
Valid prediction for snap_scaffold_9-snap.872-T1
Valid prediction for Augustus_model.g14611.t1
Valid prediction for Augustus_model.g14600.t1
Valid prediction for Augustus_model.g14601.t1
Valid prediction for snap_scaffold_9-snap.863-T1
Valid prediction for snap_scaffold_9-snap.879-T1
Valid prediction for snap_scaffold_9-snap.873-T1
Valid prediction for GlimmerHMM_glimmerT_21969-T1
Valid prediction for GlimmerHMM_glimmerT_21965-T1
Valid prediction for Augustus_model.g14608.t1
Valid prediction for snap_scaffold_9-snap.857-T1
Valid prediction for snap_scaffold_9-snap.865-T1
Valid prediction for GlimmerHMM_glimmerT_21957-T1
Valid prediction for snap_scaffold_9-snap.874-T1
Valid prediction for GlimmerHMM_glimmerT_21972-T1
Valid prediction for snap_scaffold_9-snap.885-T1
Valid prediction for snap_scaffold_9-snap.898-T1
Valid prediction for snap_scaffold_9-snap.880-T1
Valid prediction for snap_scaffold_9-snap.859-T1
Valid prediction for GlimmerHMM_glimmerT_21976-T1
Valid prediction for GlimmerHMM_glimmerT_21970-T1
Valid prediction for GlimmerHMM_glimmerT_21951-T1
Valid prediction for snap_scaffold_9-snap.893-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_21956-T1
Valid prediction for Augustus_model.g14612.t1
Valid prediction for snap_scaffold_9-snap.892-T1
Valid prediction for snap_scaffold_9-snap.900-T1
Valid prediction for Augustus_model.g14606.t1
Valid prediction for snap_scaffold_9-snap.884-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_21964-T1
Valid prediction for GlimmerHMM_glimmerT_21968-T1
Valid prediction for snap_scaffold_9-snap.862-T1
Valid prediction for snap_scaffold_9-snap.870-T1
Valid prediction for GlimmerHMM_glimmerT_21966-T1
Valid prediction for pasa_asmbl_54961.p1
Valid prediction for GlimmerHMM_glimmerT_21961-T1
Valid prediction for Augustus_model.g14603.t1
Valid prediction for snap_scaffold_9-snap.866-T1
Couldn't classify 53185, 53390
Couldn't classify 53604, 53715
Sorry, prediction pasa_asmbl_55754.p2 fails validation.
(GTG)	 AG	53185-53390	GT	AAG
(GCT)	 AG	53604-53715	GA	ACG
-recovered pasa_asmbl_55754.p2, internal, 53185, 53390
Valid prediction for snap_scaffold_9-snap.894-T1
Valid prediction for snap_scaffold_9-snap.877-T1
Valid prediction for GlimmerHMM_glimmerT_21973-T1
Valid prediction for CodingQuarry_transcript_62151-T1
Valid prediction for snap_scaffold_9-snap.861-T1
Valid prediction for snap_scaffold_9-snap.867-T1
Valid prediction for snap_scaffold_9-snap.897-T1
Valid prediction for snap_scaffold_9-snap.881-T1
Valid prediction for snap_scaffold_9-snap.899-T1
Valid prediction for Augustus_model.g14609.t1
Valid prediction for snap_scaffold_9-snap.888-T1
Valid prediction for snap_scaffold_9-snap.889-T1
Valid prediction for GlimmerHMM_glimmerT_21950-T1
Valid prediction for Augustus_model.g14602.t1
Valid prediction for snap_scaffold_9-snap.860-T1
Valid prediction for snap_scaffold_9-snap.875-T1
Valid prediction for GlimmerHMM_glimmerT_21967-T1
Valid prediction for HiQ_model.g14610.t1
Valid prediction for GlimmerHMM_glimmerT_21962-T1
Valid prediction for Augustus_model.g14605.t1
Valid prediction for GlimmerHMM_glimmerT_21963-T1
Valid prediction for snap_scaffold_9-snap.883-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_21974-T1
Valid prediction for CodingQuarry_transcript_62150-T1
Valid prediction for GlimmerHMM_glimmerT_21953-T1
Valid prediction for snap_scaffold_9-snap.901-T1
Valid prediction for snap_scaffold_9-snap.869-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for snap_scaffold_9-snap.891-T1
Couldn't classify 55933, 56044
Sorry, prediction pasa_asmbl_54955.p1 fails validation.
(GCA)	 CT	55933-56044	GT	AGG
(CTT)	 AG	56403-56539	GT	AGG
(ATC)	 AG	56874-57056	AG	GAA
-recovered pasa_asmbl_54955.p1, terminal, 56874, 57056
-recovered pasa_asmbl_54955.p1, internal, 56403, 56539
Valid prediction for snap_scaffold_9-snap.858-T1
Valid prediction for snap_scaffold_9-snap.864-T1
Valid prediction for snap_scaffold_9-snap.871-T1
Valid prediction for snap_scaffold_9-snap.902-T1
Valid prediction for GlimmerHMM_glimmerT_21971-T1
Couldn't classify 38179, 38237
Sorry, prediction pasa_asmbl_54957.p1 fails validation.
(GCC)	 CC	38179-38237	GT	CAG
(GTG)	 AG	38361-38469	GT	GGG
(GAC)	 AG	38673-38777	GT	AGG
(CAA)	 AG	38908-39010	GT	TTG
(GGC)	 AG	39432-39487	CA	AGC
-recovered pasa_asmbl_54957.p1, terminal, 39432, 39487
-recovered pasa_asmbl_54957.p1, internal, 38361, 38469
-recovered pasa_asmbl_54957.p1, internal, 38673, 38777
-recovered pasa_asmbl_54957.p1, internal, 38908, 39010
Valid prediction for snap_scaffold_9-snap.868-T1
Valid prediction for GlimmerHMM_glimmerT_21955-T1
Valid prediction for Augustus_model.g14604.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 8182, rend_intergenic: 2793  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22413, rend_intergenic: 8467  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61702, rend_intergenic: 22505  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63467, rend_intergenic: 61717  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65758, rend_intergenic: 63499  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74189, rend_intergenic: 66295  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112470, rend_intergenic: 76093  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115386, rend_intergenic: 112472  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129339, rend_intergenic: 126767  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132483, rend_intergenic: 130078  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142756, rend_intergenic: 135000  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149037, rend_intergenic: 143579  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155413, rend_intergenic: 152221  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165054, rend_intergenic: 155741  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 204879, rend_intergenic: 170522  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 219640, rend_intergenic: 206258  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 223125, rend_intergenic: 220831  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 225070, rend_intergenic: 223614  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 237709, rend_intergenic: 232160  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 240679, rend_intergenic: 237759  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 243811, rend_intergenic: 242300  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 245632, rend_intergenic: 243820  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 251571, rend_intergenic: 246352  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 261110, rend_intergenic: 255227  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 263313
-exon list size: 504


building trellis

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98.2    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 8182, rend_intergenic: 2793  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22413, rend_intergenic: 8467  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61702, rend_intergenic: 22505  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63467, rend_intergenic: 61717  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65758, rend_intergenic: 63499  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74189, rend_intergenic: 66295  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112470, rend_intergenic: 76093  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115386, rend_intergenic: 112472  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129339, rend_intergenic: 126767  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132483, rend_intergenic: 130078  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142756, rend_intergenic: 135000  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149037, rend_intergenic: 143579  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155413, rend_intergenic: 152221  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165054, rend_intergenic: 155741  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 204879, rend_intergenic: 170522  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 219640, rend_intergenic: 206258  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 223125, rend_intergenic: 220831  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 225070, rend_intergenic: 223614  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 237709, rend_intergenic: 232160  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 240679, rend_intergenic: 237759  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 243811, rend_intergenic: 242300  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 245632, rend_intergenic: 243820  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 251571, rend_intergenic: 246352  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 261110, rend_intergenic: 255227  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 14 predictions persist after filtering for low support