-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_6/scaffold_6_5227614-5412146

-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_14633-T1
Valid prediction for GlimmerHMM_glimmerT_14658-T1
Valid prediction for snap_scaffold_6-snap.1246-T1
Valid prediction for GlimmerHMM_glimmerT_14657-T1
Valid prediction for snap_scaffold_6-snap.1260-T1
Valid prediction for snap_scaffold_6-snap.1250-T1
Valid prediction for snap_scaffold_6-snap.1238-T1
Valid prediction for snap_scaffold_6-snap.1248-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_6-snap.1236-T1
Valid prediction for snap_scaffold_6-snap.1244-T1
Valid prediction for Augustus_model.g9699.t1
Valid prediction for snap_scaffold_6-snap.1267-T1
Couldn't classify 17411, 17594
Couldn't classify 21804, 21838
Sorry, prediction pasa_asmbl_46931.p1 fails validation.
(GGC)	 TA	17411-17594	GT	GGG
(GGT)	 AG	18894-19051	GT	AGG
(GAA)	 AG	21530-21653	GT	CTG
(ACC)	 AG	21804-21838	GA	AGG
-recovered pasa_asmbl_46931.p1, internal, 18894, 19051
-recovered pasa_asmbl_46931.p1, internal, 21530, 21653
Valid prediction for GlimmerHMM_glimmerT_14639-T1
Valid prediction for snap_scaffold_6-snap.1257-T1
Valid prediction for GlimmerHMM_glimmerT_14655-T1
Valid prediction for GlimmerHMM_glimmerT_14629-T1
Valid prediction for Augustus_model.g9706.t1
Valid prediction for snap_scaffold_6-snap.1271-T1
Valid prediction for GlimmerHMM_glimmerT_14646-T1
Valid prediction for GlimmerHMM_glimmerT_14654-T1
Couldn't classify 54357, 54368
Couldn't classify 56013, 56016
Sorry, prediction pasa_asmbl_46941.p1 fails validation.
(GTT)	 GT	54357-54368	GT	GGG
(TAC)	 AG	54520-54593	GT	GGG
(GTG)	 AG	54753-54836	GT	CCG
(GCT)	 AG	54930-55073	GT	AGG
(GCT)	 AG	55414-55525	GT	AGG
(TCC)	 AG	55838-55914	GT	AGG
(GAC)	 AG	56013-56016	AG	CCA
-recovered pasa_asmbl_46941.p1, internal, 54520, 54593
-recovered pasa_asmbl_46941.p1, internal, 54753, 54836
-recovered pasa_asmbl_46941.p1, internal, 54930, 55073
-recovered pasa_asmbl_46941.p1, internal, 55414, 55525
-recovered pasa_asmbl_46941.p1, internal, 55838, 55914
Valid prediction for snap_scaffold_6-snap.1239-T1
Valid prediction for snap_scaffold_6-snap.1240-T1
Valid prediction for snap_scaffold_6-snap.1270-T1
Valid prediction for Augustus_model.g9703.t1
Valid prediction for GlimmerHMM_glimmerT_14652-T1
Valid prediction for GlimmerHMM_glimmerT_14641-T1
Valid prediction for GlimmerHMM_glimmerT_14650-T1
Valid prediction for snap_scaffold_6-snap.1273-T1
Valid prediction for GlimmerHMM_glimmerT_14630-T1
Valid prediction for pasa_asmbl_46943.p1
Valid prediction for snap_scaffold_6-snap.1268-T1
Valid prediction for GlimmerHMM_glimmerT_14634-T1
Valid prediction for pasa_asmbl_46942.p1
Valid prediction for GlimmerHMM_glimmerT_14631-T1
Valid prediction for snap_scaffold_6-snap.1255-T1
Couldn't classify 25801, 25986
Sorry, prediction pasa_asmbl_46932.p1 fails validation.
(GTG)	 GG	25801-25986	GT	TAG
(AGC)	 AG	26087-26278	GT	AGG
(CTG)	 AG	27657-27821	AA	GAA
-recovered pasa_asmbl_46932.p1, terminal, 27657, 27821
-recovered pasa_asmbl_46932.p1, internal, 26087, 26278
Valid prediction for snap_scaffold_6-snap.1231-T1
Valid prediction for CodingQuarry_transcript_55048-T1
Valid prediction for snap_scaffold_6-snap.1245-T1
Couldn't classify 44121, 44186
Couldn't classify 44818, 44919
Sorry, prediction pasa_asmbl_47977.p1 fails validation.
(TTG)	 AG	44121-44186	GT	AAG
(GCC)	 AG	44341-44452	GT	AGG
(AAC)	 AG	44563-44708	GT	AGG
(GTT)	 AG	44818-44919	GG	CTG
-recovered pasa_asmbl_47977.p1, internal, 44121, 44186
-recovered pasa_asmbl_47977.p1, internal, 44341, 44452
-recovered pasa_asmbl_47977.p1, internal, 44563, 44708
Valid prediction for snap_scaffold_6-snap.1251-T1
Valid prediction for Augustus_model.g9696.t1
Valid prediction for GlimmerHMM_glimmerT_14642-T1
Valid prediction for snap_scaffold_6-snap.1256-T1
Valid prediction for Augustus_model.g9698.t1
Valid prediction for GlimmerHMM_glimmerT_14645-T1
Valid prediction for GlimmerHMM_glimmerT_14653-T1
Valid prediction for CodingQuarry_transcript_55050-T1
Valid prediction for Augustus_model.g9692.t1
Valid prediction for Augustus_model.g9708.t1
Valid prediction for GlimmerHMM_glimmerT_14637-T1
Valid prediction for snap_scaffold_6-snap.1264-T1
Valid prediction for snap_scaffold_6-snap.1249-T1
Valid prediction for snap_scaffold_6-snap.1252-T1
Valid prediction for Augustus_model.g9709.t1
Valid prediction for pasa_asmbl_46934.p1
Valid prediction for snap_scaffold_6-snap.1263-T1
Valid prediction for Augustus_model.g9702.t1
Valid prediction for GlimmerHMM_glimmerT_14638-T1
Valid prediction for HiQ_model.g9695.t1
Valid prediction for Augustus_model.g9693.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_14643-T1
Valid prediction for GlimmerHMM_glimmerT_14651-T1
Valid prediction for snap_scaffold_6-snap.1234-T1
Valid prediction for snap_scaffold_6-snap.1235-T1
Valid prediction for snap_scaffold_6-snap.1262-T1
Valid prediction for snap_scaffold_6-snap.1253-T1
Valid prediction for Augustus_model.g9704.t1
Valid prediction for CodingQuarry_transcript_55049-T1
Valid prediction for snap_scaffold_6-snap.1247-T1
Valid prediction for GlimmerHMM_glimmerT_14656-T1
Valid prediction for snap_scaffold_6-snap.1242-T1
Valid prediction for snap_scaffold_6-snap.1259-T1
Valid prediction for Augustus_model.g9710.t1
Valid prediction for snap_scaffold_6-snap.1266-T1
Valid prediction for snap_scaffold_6-snap.1233-T1
Valid prediction for Augustus_model.g9700.t1
Couldn't classify 5651, 5975
Sorry, prediction pasa_asmbl_48419.p1 fails validation.
(ATG)	 TC	3623-3649	GT	AGG
(CTG)	 AG	3796-3882	GT	AAG
(GAC)	 AG	4795-4938	GT	AGG
(AGG)	 AG	5115-5245	GT	CGG
(AAC)	 AG	5651-5975	GA	GGG
-recovered pasa_asmbl_48419.p1, initial, 3623, 3649
-recovered pasa_asmbl_48419.p1, internal, 3796, 3882
-recovered pasa_asmbl_48419.p1, internal, 4795, 4938
-recovered pasa_asmbl_48419.p1, internal, 5115, 5245
Valid prediction for GlimmerHMM_glimmerT_14632-T1
Valid prediction for snap_scaffold_6-snap.1265-T1
Valid prediction for snap_scaffold_6-snap.1232-T1
Valid prediction for snap_scaffold_6-snap.1261-T1
Valid prediction for Augustus_model.g9701.t1
Valid prediction for GlimmerHMM_glimmerT_14635-T1
Valid prediction for GlimmerHMM_glimmerT_14640-T1
Valid prediction for GlimmerHMM_glimmerT_14649-T1
Valid prediction for GlimmerHMM_glimmerT_14636-T1
Valid prediction for GlimmerHMM_glimmerT_14659-T1
Valid prediction for snap_scaffold_6-snap.1241-T1
Couldn't classify 134068, 134112
Sorry, prediction pasa_asmbl_48412.p1 fails validation.
(TCC)	 TT	134068-134112	GT	AAG
(ACG)	 AG	134681-134717	GT	CAG
(ATT)	 AG	134904-134990	GT	AGG
(ACG)	 AG	135219-135328	GT	AGG
(AAA)	 AG	135413-135509	GT	AAG
(CGA)	 AG	135805-135904	GT	ACG
(GAA)	 AG	136058-136259	GT	AGG
(ATT)	 AG	136456-136512	AG	GAA
-recovered pasa_asmbl_48412.p1, terminal, 136456, 136512
-recovered pasa_asmbl_48412.p1, internal, 134681, 134717
-recovered pasa_asmbl_48412.p1, internal, 134904, 134990
-recovered pasa_asmbl_48412.p1, internal, 135219, 135328
-recovered pasa_asmbl_48412.p1, internal, 135413, 135509
-recovered pasa_asmbl_48412.p1, internal, 135805, 135904
-recovered pasa_asmbl_48412.p1, internal, 136058, 136259
Valid prediction for GlimmerHMM_glimmerT_14647-T1
Valid prediction for HiQ_model.g9707.t1
Valid prediction for HiQ_model.g9697.t1
Couldn't classify 8094, 9581
Sorry, prediction pasa_asmbl_48417.p1 fails validation.
(CGC)	 CC	8094-9581	GG	GAG
Valid prediction for CodingQuarry_transcript_55047-T1
Valid prediction for HiQ_model.g9694.t1
Valid prediction for pasa_asmbl_48413.p1
Valid prediction for snap_scaffold_6-snap.1237-T1
Valid prediction for GlimmerHMM_glimmerT_14648-T1
Valid prediction for snap_scaffold_6-snap.1258-T1
Valid prediction for snap_scaffold_6-snap.1243-T1
Valid prediction for GlimmerHMM_glimmerT_14644-T1
Valid prediction for pasa_asmbl_48409.p1
Valid prediction for snap_scaffold_6-snap.1254-T1
Valid prediction for snap_scaffold_6-snap.1269-T1
Couldn't classify 6045, 7823
Sorry, prediction pasa_asmbl_48418.p1 fails validation.
(TCC)	 GC	6045-7823	TC	ACT
Valid prediction for Augustus_model.g9705.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 26554, rend_intergenic: 5266  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29816, rend_intergenic: 29677  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36113, rend_intergenic: 30057  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67849, rend_intergenic: 65980  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91840, rend_intergenic: 68726  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97006, rend_intergenic: 92828  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106786, rend_intergenic: 99716  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117646, rend_intergenic: 114953  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126477, rend_intergenic: 118177  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141444, rend_intergenic: 133714  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167888, rend_intergenic: 165921  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 31211, rend_intergenic: 31208  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 184533
-exon list size: 457


building trellis

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-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 26554, rend_intergenic: 5266  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29816, rend_intergenic: 29677  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36113, rend_intergenic: 30057  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67849, rend_intergenic: 65980  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91840, rend_intergenic: 68726  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97006, rend_intergenic: 92828  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106786, rend_intergenic: 99716  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117646, rend_intergenic: 114953  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126477, rend_intergenic: 118177  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141444, rend_intergenic: 133714  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167888, rend_intergenic: 165921  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 31211, rend_intergenic: 31208  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support