-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_18/scaffold_18_12923307-13225855

-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: +)Couldn't classify 6784, 7461
Sorry, prediction pasa_asmbl_20978.p1 fails validation.
(GGC)	 AA	6784-7461	TC	TGT
Valid prediction for Augustus_model.g28833.t1
Valid prediction for Augustus_model.g28832.t1
Valid prediction for Augustus_model.g28844.t1
Valid prediction for GlimmerHMM_glimmerT_43331-T1
Valid prediction for GlimmerHMM_glimmerT_43342-T1
Valid prediction for Augustus_model.g28837.t1
Valid prediction for snap_scaffold_18-snap.2764-T1
Valid prediction for snap_scaffold_18-snap.2778-T1
Valid prediction for snap_scaffold_18-snap.2760-T1
Valid prediction for snap_scaffold_18-snap.2771-T1
Valid prediction for Augustus_model.g28830.t1
Valid prediction for Augustus_model.g28835.t1
Valid prediction for GlimmerHMM_glimmerT_43317-T1
Valid prediction for GlimmerHMM_glimmerT_43324-T1
Valid prediction for GlimmerHMM_glimmerT_43318-T1
Valid prediction for GlimmerHMM_glimmerT_43330-T1
Valid prediction for GlimmerHMM_glimmerT_43336-T1
Valid prediction for snap_scaffold_18-snap.2743-T1
Valid prediction for snap_scaffold_18-snap.2769-T1
Valid prediction for snap_scaffold_18-snap.2775-T1
Valid prediction for GlimmerHMM_glimmerT_43320-T1
Valid prediction for Augustus_model.g28843.t1
Valid prediction for GlimmerHMM_glimmerT_43341-T1
Valid prediction for snap_scaffold_18-snap.2746-T1
Valid prediction for snap_scaffold_18-snap.2780-T1
Valid prediction for Augustus_model.g28834.t1
Valid prediction for GlimmerHMM_glimmerT_43323-T1
Valid prediction for GlimmerHMM_glimmerT_43337-T1
Valid prediction for snap_scaffold_18-snap.2782-T1
Valid prediction for snap_scaffold_18-snap.2756-T1
Valid prediction for Augustus_model.g28840.t1
Valid prediction for snap_scaffold_18-snap.2768-T1
Couldn't classify 7873, 10113
Sorry, prediction pasa_asmbl_20979.p1 fails validation.
(CCA)	 CG	7873-10113	TT	GAT
Valid prediction for snap_scaffold_18-snap.2763-T1
Valid prediction for GlimmerHMM_glimmerT_43327-T1
Valid prediction for pasa_asmbl_20993.p1
Valid prediction for snap_scaffold_18-snap.2753-T1
Valid prediction for snap_scaffold_18-snap.2776-T1
Valid prediction for snap_scaffold_18-snap.2759-T1
Valid prediction for GlimmerHMM_glimmerT_43321-T1
Couldn't classify 19820, 19931
Sorry, prediction pasa_asmbl_20985.p2 fails validation.
(ATG)	 AT	18760-18891	GT	AGG
(GGG)	 AG	19051-19133	GT	AGG
(TGA)	 AG	19820-19931	TG	GGT
-recovered pasa_asmbl_20985.p2, initial, 18760, 18891
-recovered pasa_asmbl_20985.p2, internal, 19051, 19133
Valid prediction for snap_scaffold_18-snap.2748-T1
Valid prediction for snap_scaffold_18-snap.2766-T1
Valid prediction for Augustus_model.g28842.t1
Valid prediction for CodingQuarry_transcript_23919-T1
Valid prediction for CodingQuarry_transcript_23918-T1
Valid prediction for snap_scaffold_18-snap.2786-T1
Valid prediction for snap_scaffold_18-snap.2790-T1
Valid prediction for GlimmerHMM_glimmerT_43347-T1
Valid prediction for snap_scaffold_18-snap.2751-T1
Valid prediction for GlimmerHMM_glimmerT_43340-T1
Valid prediction for snap_scaffold_18-snap.2785-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_18-snap.2758-T1
Valid prediction for snap_scaffold_18-snap.2744-T1
Valid prediction for GlimmerHMM_glimmerT_43328-T1
Couldn't classify 219947, 219981
Sorry, prediction pasa_asmbl_20996.p1 fails validation.
(ATG)	 TC	215933-215987	GT	AGG
(CCC)	 AG	217188-217268	GT	AGG
(AGA)	 AG	218529-218659	GT	ACG
(TCC)	 AG	218980-219073	GT	TGG
(CTA)	 AG	219947-219981	GA	ATG
-recovered pasa_asmbl_20996.p1, initial, 215933, 215987
add_exon() Sorry, pasa_asmbl_20996.p1 217188-217268-terminal-1 is invalid.
-recovered pasa_asmbl_20996.p1, terminal, 217188, 217268
-recovered pasa_asmbl_20996.p1, internal, 217188, 217268
-recovered pasa_asmbl_20996.p1, internal, 218529, 218659
-recovered pasa_asmbl_20996.p1, internal, 218980, 219073
Valid prediction for snap_scaffold_18-snap.2787-T1
Valid prediction for snap_scaffold_18-snap.2783-T1
Valid prediction for GlimmerHMM_glimmerT_43326-T1
Valid prediction for snap_scaffold_18-snap.2749-T1
Valid prediction for snap_scaffold_18-snap.2754-T1
Valid prediction for GlimmerHMM_glimmerT_43339-T1
Valid prediction for Augustus_model.g28841.t1
Valid prediction for GlimmerHMM_glimmerT_43345-T1
Valid prediction for GlimmerHMM_glimmerT_43322-T1
Valid prediction for GlimmerHMM_glimmerT_43335-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_43338-T1
Valid prediction for GlimmerHMM_glimmerT_43346-T1
Valid prediction for GlimmerHMM_glimmerT_43332-T1
Valid prediction for GlimmerHMM_glimmerT_43344-T1
Valid prediction for snap_scaffold_18-snap.2788-T1
Valid prediction for snap_scaffold_18-snap.2767-T1
Valid prediction for snap_scaffold_18-snap.2781-T1
Valid prediction for GlimmerHMM_glimmerT_43325-T1
Couldn't classify 168887, 169073
Sorry, prediction pasa_asmbl_20164.p1 fails validation.
(GAG)	 AG	168887-169073	GT	AGG
(GGT)	 AG	169412-169507	GT	AGG
(GAG)	 AG	169665-169834	GT	AGG
(GTG)	 AG	170097-170261	GT	AGG
(ATG)	 AG	170607-170714	GT	AGG
(GTG)	 AG	172088-172312	GC	AGG
-recovered pasa_asmbl_20164.p1, initial, 170607, 170714
add_exon() Sorry, pasa_asmbl_20164.p1 169412-169507-terminal-1 is invalid.
-recovered pasa_asmbl_20164.p1, terminal, 169412, 169507
-recovered pasa_asmbl_20164.p1, terminal, 172088, 172312
-recovered pasa_asmbl_20164.p1, internal, 168887, 169073
-recovered pasa_asmbl_20164.p1, internal, 169412, 169507
-recovered pasa_asmbl_20164.p1, internal, 169665, 169834
-recovered pasa_asmbl_20164.p1, internal, 170097, 170261
-recovered pasa_asmbl_20164.p1, internal, 170607, 170714
-recovered pasa_asmbl_20164.p1, internal, 172088, 172312
Valid prediction for snap_scaffold_18-snap.2777-T1
Valid prediction for snap_scaffold_18-snap.2772-T1
Valid prediction for CodingQuarry_transcript_23920-T1
Valid prediction for pasa_asmbl_20169.p1
Valid prediction for snap_scaffold_18-snap.2762-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for Augustus_model.g28846.t1
Valid prediction for Augustus_model.g28839.t1
Valid prediction for snap_scaffold_18-snap.2750-T1
Valid prediction for snap_scaffold_18-snap.2789-T1
Valid prediction for snap_scaffold_18-snap.2779-T1
Valid prediction for HiQ_model.g28836.t1
Valid prediction for snap_scaffold_18-snap.2770-T1
Valid prediction for CodingQuarry_transcript_23916-T1
Valid prediction for snap_scaffold_18-snap.2747-T1
Couldn't classify 287366, 287583
Sorry, prediction pasa_asmbl_20163.p1 fails validation.
(CCC)	 CT	287366-287583	GT	ATG
(CTT)	 AG	288565-288734	GT	AGG
(ATG)	 AG	288978-289053	GT	AGG
(GTA)	 AG	289242-289479	TG	GAT
-recovered pasa_asmbl_20163.p1, initial, 288978, 289053
-recovered pasa_asmbl_20163.p1, terminal, 289242, 289479
-recovered pasa_asmbl_20163.p1, internal, 288565, 288734
-recovered pasa_asmbl_20163.p1, internal, 288978, 289053
Valid prediction for snap_scaffold_18-snap.2765-T1
Valid prediction for snap_scaffold_18-snap.2755-T1
Valid prediction for GlimmerHMM_glimmerT_43333-T1
Valid prediction for HiQ_model.g28845.t1
Valid prediction for Augustus_model.g28831.t1
Valid prediction for GlimmerHMM_glimmerT_43343-T1
Valid prediction for Augustus_model.g28838.t1
Valid prediction for snap_scaffold_18-snap.2745-T1
Valid prediction for snap_scaffold_18-snap.2784-T1
Valid prediction for GlimmerHMM_glimmerT_43329-T1
Valid prediction for snap_scaffold_18-snap.2752-T1
Valid prediction for snap_scaffold_18-snap.2761-T1
Valid prediction for GlimmerHMM_glimmerT_43319-T1
Valid prediction for snap_scaffold_18-snap.2774-T1
Valid prediction for snap_scaffold_18-snap.2773-T1
Valid prediction for snap_scaffold_18-snap.2757-T1
Valid prediction for GlimmerHMM_glimmerT_43334-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 16183, rend_intergenic: 13071  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23829, rend_intergenic: 20191  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36605, rend_intergenic: 23922  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42387, rend_intergenic: 36636  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50297, rend_intergenic: 43844  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56308, rend_intergenic: 55194  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63018, rend_intergenic: 59119  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89650, rend_intergenic: 63041  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106415, rend_intergenic: 99913  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129627, rend_intergenic: 114104  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142336, rend_intergenic: 130251  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174428, rend_intergenic: 144924  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177688, rend_intergenic: 174472  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181549, rend_intergenic: 177703  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185886, rend_intergenic: 181919  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 204258, rend_intergenic: 188604  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 208485, rend_intergenic: 204521  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 220509, rend_intergenic: 209153  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 235027, rend_intergenic: 228381  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 249712, rend_intergenic: 237304  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 253997, rend_intergenic: 249730  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 285242, rend_intergenic: 254142  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 295241, rend_intergenic: 285964  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 300615, rend_intergenic: 297687  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 302549
-exon list size: 482


building trellis

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-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 16183, rend_intergenic: 13071  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23829, rend_intergenic: 20191  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36605, rend_intergenic: 23922  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42387, rend_intergenic: 36636  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50297, rend_intergenic: 43844  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56308, rend_intergenic: 55194  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63018, rend_intergenic: 59119  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89650, rend_intergenic: 63041  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106415, rend_intergenic: 99913  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129627, rend_intergenic: 114104  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142336, rend_intergenic: 130251  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174428, rend_intergenic: 144924  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177688, rend_intergenic: 174472  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181549, rend_intergenic: 177703  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185886, rend_intergenic: 181919  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 204258, rend_intergenic: 188604  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 208485, rend_intergenic: 204521  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 220509, rend_intergenic: 209153  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 235027, rend_intergenic: 228381  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 249712, rend_intergenic: 237304  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 253997, rend_intergenic: 249730  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 285242, rend_intergenic: 254142  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 295241, rend_intergenic: 285964  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 300615, rend_intergenic: 297687  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support