-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_12960355-13098819

-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 HiQ_model.g15427.t1
Valid prediction for GlimmerHMM_glimmerT_23129-T1
Valid prediction for Augustus_model.g15428.t1
Couldn't classify 76745, 76769
Couldn't classify 79910, 79940
Sorry, prediction pasa_asmbl_54480.p1 fails validation.
(GGC)	 AA	76745-76769	GT	AGG
(CTA)	 AG	77223-77570	GT	AGG
(CCC)	 AG	77831-77952	GT	AGG
(GTT)	 AG	78134-78259	GT	AGG
(AGG)	 AG	78438-78515	GC	AGG
(ATA)	 AG	78816-78911	GT	AAG
(ATG)	 AG	79036-79113	GT	CGG
(TCT)	 AG	79446-79684	GT	CTG
(GGA)	 AG	79910-79940	GG	AGG
-recovered pasa_asmbl_54480.p1, initial, 79036, 79113
-recovered pasa_asmbl_54480.p1, internal, 77223, 77570
-recovered pasa_asmbl_54480.p1, internal, 77831, 77952
-recovered pasa_asmbl_54480.p1, internal, 78134, 78259
-recovered pasa_asmbl_54480.p1, internal, 78438, 78515
-recovered pasa_asmbl_54480.p1, internal, 78816, 78911
-recovered pasa_asmbl_54480.p1, internal, 79036, 79113
-recovered pasa_asmbl_54480.p1, internal, 79446, 79684
Valid prediction for GlimmerHMM_glimmerT_23127-T1
Valid prediction for Augustus_model.g15429.t1
Valid prediction for GlimmerHMM_glimmerT_23125-T1
Valid prediction for snap_scaffold_9-snap.2564-T1
Valid prediction for snap_scaffold_9-snap.2578-T1
Couldn't classify 80342, 80526
Couldn't classify 80554, 80557
Sorry, prediction CodingQuarry_transcript_62388-T1 fails validation.
(ATG)	 AG	79996-80046	GT	AGG
(GTG)	 AG	80342-80526	AT	ACA
(ATG)	 AC	80554-80557	CC	GAC
-recovered CodingQuarry_transcript_62388-T1, initial, 79996, 80046
-recovered CodingQuarry_transcript_62388-T1, internal, 79996, 80046
Valid prediction for snap_scaffold_9-snap.2582-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_9-snap.2576-T1
Valid prediction for Augustus_model.g15424.t1
Valid prediction for snap_scaffold_9-snap.2584-T1
Valid prediction for Augustus_model.g15422.t1
Valid prediction for snap_scaffold_9-snap.2585-T1
Valid prediction for GlimmerHMM_glimmerT_23130-T1
Valid prediction for GlimmerHMM_glimmerT_23139-T1
Valid prediction for snap_scaffold_9-snap.2568-T1
Valid prediction for snap_scaffold_9-snap.2559-T1
Valid prediction for GlimmerHMM_glimmerT_23121-T1
Valid prediction for snap_scaffold_9-snap.2583-T1
Valid prediction for GlimmerHMM_glimmerT_23132-T1
Valid prediction for GlimmerHMM_glimmerT_23131-T1
Valid prediction for snap_scaffold_9-snap.2560-T1
Valid prediction for GlimmerHMM_glimmerT_23134-T1
Valid prediction for CodingQuarry_transcript_62387-T1
Valid prediction for snap_scaffold_9-snap.2587-T1
Valid prediction for snap_scaffold_9-snap.2566-T1
Valid prediction for snap_scaffold_9-snap.2577-T1
Valid prediction for snap_scaffold_9-snap.2570-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for snap_scaffold_9-snap.2574-T1
Valid prediction for GlimmerHMM_glimmerT_23137-T1
Valid prediction for Augustus_model.g15426.t1
Valid prediction for snap_scaffold_9-snap.2586-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_9-snap.2579-T1
Couldn't classify 37604, 37636
Couldn't classify 38907, 38980
Sorry, prediction pasa_asmbl_55760.p1 fails validation.
(AAC)	 TC	37604-37636	GT	AGG
(AAC)	 AG	37812-38027	GT	AGG
(GCG)	 AG	38164-38221	GT	AGG
(GCT)	 AG	38907-38980	CT	CCC
-recovered pasa_asmbl_55760.p1, internal, 37812, 38027
-recovered pasa_asmbl_55760.p1, internal, 38164, 38221
Valid prediction for GlimmerHMM_glimmerT_23128-T1
Valid prediction for snap_scaffold_9-snap.2571-T1
Valid prediction for GlimmerHMM_glimmerT_23123-T1
Valid prediction for snap_scaffold_9-snap.2573-T1
Valid prediction for Augustus_model.g15425.t1
Valid prediction for GlimmerHMM_glimmerT_23135-T1
Couldn't classify 45123, 45158
Sorry, prediction pasa_asmbl_55417.p1 fails validation.
(ATG)	 CC	40014-40055	GT	AGG
(GAC)	 AG	40788-40910	GT	AGG
(AGG)	 AG	41256-41369	GT	AGG
(GGC)	 AG	42321-42467	GT	AGG
(GTG)	 AG	42690-42900	GT	CAG
(CGA)	 AG	43724-43914	GC	AGG
(GTT)	 AG	44093-44193	GT	AGG
(GCA)	 AG	44534-44672	GT	AGG
(ATC)	 AG	45123-45158	AG	ACA
-recovered pasa_asmbl_55417.p1, initial, 40014, 40055
-recovered pasa_asmbl_55417.p1, internal, 40788, 40910
-recovered pasa_asmbl_55417.p1, internal, 41256, 41369
-recovered pasa_asmbl_55417.p1, internal, 42321, 42467
-recovered pasa_asmbl_55417.p1, internal, 42690, 42900
-recovered pasa_asmbl_55417.p1, internal, 43724, 43914
-recovered pasa_asmbl_55417.p1, internal, 44093, 44193
-recovered pasa_asmbl_55417.p1, internal, 44534, 44672
Valid prediction for Augustus_model.g15420.t1
Valid prediction for GlimmerHMM_glimmerT_23140-T1
Valid prediction for Augustus_model.g15421.t1
Valid prediction for Augustus_model.g15431.t1
Valid prediction for GlimmerHMM_glimmerT_23136-T1
Valid prediction for snap_scaffold_9-snap.2572-T1
Valid prediction for snap_scaffold_9-snap.2561-T1
Valid prediction for GlimmerHMM_glimmerT_23126-T1
Valid prediction for GlimmerHMM_glimmerT_23122-T1
Valid prediction for snap_scaffold_9-snap.2569-T1
Valid prediction for snap_scaffold_9-snap.2565-T1
Valid prediction for Augustus_model.g15430.t1
Couldn't classify 64827, 64856
Couldn't classify 68061, 68204
Sorry, prediction pasa_asmbl_55413.p1 fails validation.
(GTT)	 GT	64827-64856	GT	GGG
(GCT)	 AG	64956-65097	GT	TGG
(GTT)	 AG	65191-65305	GT	AGG
(GAG)	 AG	65627-65812	GT	AAG
(GCA)	 AG	66003-66174	GT	AGG
(GTT)	 AG	66344-66424	GT	GGG
(GTG)	 AG	66522-66651	GT	AGG
(GAG)	 AG	66855-66955	GT	GGG
(ACA)	 AG	67195-67365	GT	AGG
(ATC)	 AG	67909-67968	GT	AGG
(GCC)	 AG	68061-68204	AC	GGA
add_exon() Sorry, pasa_asmbl_55413.p1 65191-65305-terminal-3 is invalid.
-recovered pasa_asmbl_55413.p1, terminal, 65191, 65305
-recovered pasa_asmbl_55413.p1, internal, 64956, 65097
-recovered pasa_asmbl_55413.p1, internal, 65191, 65305
-recovered pasa_asmbl_55413.p1, internal, 65627, 65812
-recovered pasa_asmbl_55413.p1, internal, 66003, 66174
-recovered pasa_asmbl_55413.p1, internal, 66344, 66424
-recovered pasa_asmbl_55413.p1, internal, 66522, 66651
-recovered pasa_asmbl_55413.p1, internal, 66855, 66955
-recovered pasa_asmbl_55413.p1, internal, 67195, 67365
-recovered pasa_asmbl_55413.p1, internal, 67909, 67968
Valid prediction for GlimmerHMM_glimmerT_23133-T1
Valid prediction for GlimmerHMM_glimmerT_23120-T1
Valid prediction for snap_scaffold_9-snap.2562-T1
Valid prediction for Augustus_model.g15419.t1
Valid prediction for snap_scaffold_9-snap.2563-T1
Valid prediction for snap_scaffold_9-snap.2567-T1
Couldn't classify 68349, 68442
Sorry, prediction pasa_asmbl_55781.p1 fails validation.
(GGC)	 CA	68349-68442	GT	GGG
(CCT)	 AG	68619-68683	GT	ATG
(ATT)	 AG	69052-69113	GT	AGG
(GGA)	 AG	69319-69400	GT	AGG
(GAG)	 AG	69486-69533	CT	AGC
-recovered pasa_asmbl_55781.p1, terminal, 69486, 69533
-recovered pasa_asmbl_55781.p1, internal, 68619, 68683
-recovered pasa_asmbl_55781.p1, internal, 69052, 69113
-recovered pasa_asmbl_55781.p1, internal, 69319, 69400
Valid prediction for snap_scaffold_9-snap.2580-T1
Valid prediction for Augustus_model.g15423.t1
Valid prediction for snap_scaffold_9-snap.2589-T1
Valid prediction for GlimmerHMM_glimmerT_23124-T1
Valid prediction for GlimmerHMM_glimmerT_23138-T1
Valid prediction for snap_scaffold_9-snap.2575-T1
Valid prediction for snap_scaffold_9-snap.2588-T1
Valid prediction for GlimmerHMM_glimmerT_23141-T1
Valid prediction for CodingQuarry_transcript_62386-T1
Valid prediction for snap_scaffold_9-snap.2581-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 22220, rend_intergenic: 15233  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33721, rend_intergenic: 31068  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36744, rend_intergenic: 34713  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41158, rend_intergenic: 36945  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46999, rend_intergenic: 46024  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51432, rend_intergenic: 51281  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68238, rend_intergenic: 53616  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74841, rend_intergenic: 69199  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80239, rend_intergenic: 76653  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86124, rend_intergenic: 82880  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128371, rend_intergenic: 92948  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136202, rend_intergenic: 128732  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 138465
-exon list size: 398


building trellis

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-found 18 predictions from path traversal
Error with prediction: snap lend_intergenic: 22220, rend_intergenic: 15233  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33721, rend_intergenic: 31068  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36744, rend_intergenic: 34713  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41158, rend_intergenic: 36945  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46999, rend_intergenic: 46024  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51432, rend_intergenic: 51281  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68238, rend_intergenic: 53616  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74841, rend_intergenic: 69199  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80239, rend_intergenic: 76653  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86124, rend_intergenic: 82880  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128371, rend_intergenic: 92948  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136202, rend_intergenic: 128732  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

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