-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_10/scaffold_10_3173589-3363472

-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.g16257.t1
Valid prediction for snap_scaffold_10-snap.700-T1
Valid prediction for GlimmerHMM_glimmerT_24390-T1
Valid prediction for snap_scaffold_10-snap.701-T1
Valid prediction for snap_scaffold_10-snap.699-T1
Valid prediction for snap_scaffold_10-snap.686-T1
Valid prediction for Augustus_model.g16248.t1
Valid prediction for GlimmerHMM_glimmerT_24395-T1
Valid prediction for GlimmerHMM_glimmerT_24393-T1
Valid prediction for snap_scaffold_10-snap.728-T1
Valid prediction for snap_scaffold_10-snap.693-T1
Valid prediction for GlimmerHMM_glimmerT_24391-T1
Valid prediction for snap_scaffold_10-snap.710-T1
Valid prediction for GlimmerHMM_glimmerT_24404-T1
Valid prediction for GlimmerHMM_glimmerT_24407-T1
Valid prediction for snap_scaffold_10-snap.714-T1
Valid prediction for snap_scaffold_10-snap.690-T1
Valid prediction for GlimmerHMM_glimmerT_24394-T1
Valid prediction for GlimmerHMM_glimmerT_24410-T1
Valid prediction for snap_scaffold_10-snap.717-T1
Valid prediction for snap_scaffold_10-snap.697-T1
Valid prediction for GlimmerHMM_glimmerT_24417-T1
Valid prediction for Augustus_model.g16246.t1
Valid prediction for snap_scaffold_10-snap.691-T1
Valid prediction for Augustus_model.g16261.t1
Valid prediction for snap_scaffold_10-snap.719-T1
Valid prediction for GlimmerHMM_glimmerT_24389-T1
Valid prediction for snap_scaffold_10-snap.720-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g16243.t1
Valid prediction for GlimmerHMM_glimmerT_24388-T1
Valid prediction for snap_scaffold_10-snap.695-T1
Valid prediction for GlimmerHMM_glimmerT_24385-T1
Valid prediction for snap_scaffold_10-snap.704-T1
Valid prediction for snap_scaffold_10-snap.723-T1
Valid prediction for snap_scaffold_10-snap.687-T1
Valid prediction for snap_scaffold_10-snap.726-T1
Valid prediction for GlimmerHMM_glimmerT_24392-T1
Valid prediction for snap_scaffold_10-snap.716-T1
Valid prediction for GlimmerHMM_glimmerT_24412-T1
Valid prediction for Augustus_model.g16247.t1
Valid prediction for GlimmerHMM_glimmerT_24406-T1
Valid prediction for snap_scaffold_10-snap.703-T1
Valid prediction for Augustus_model.g16254.t1
Valid prediction for snap_scaffold_10-snap.694-T1
Valid prediction for GlimmerHMM_glimmerT_24405-T1
Valid prediction for Augustus_model.g16245.t1
Valid prediction for Augustus_model.g16253.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_10-snap.698-T1
Valid prediction for snap_scaffold_10-snap.725-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_24402-T1
Valid prediction for snap_scaffold_10-snap.692-T1
Valid prediction for snap_scaffold_10-snap.724-T1
Couldn't classify 11518, 11663
Sorry, prediction pasa_asmbl_4196.p1 fails validation.
(GAA)	 TG	11518-11663	GT	CGG
(GGA)	 AG	12139-12195	GT	GGG
(ATT)	 AG	12477-12534	GT	AGG
(AGC)	 AG	12841-13416	GT	GAG
-recovered pasa_asmbl_4196.p1, terminal, 12841, 13416
-recovered pasa_asmbl_4196.p1, internal, 12139, 12195
-recovered pasa_asmbl_4196.p1, internal, 12477, 12534
-recovered pasa_asmbl_4196.p1, internal, 12841, 13416
Valid prediction for GlimmerHMM_glimmerT_24411-T1
Valid prediction for GlimmerHMM_glimmerT_24387-T1
Valid prediction for snap_scaffold_10-snap.711-T1
Couldn't classify 48644, 48745
Couldn't classify 48930, 49107
Sorry, prediction CodingQuarry_transcript_5329-T1 fails validation.
(ATG)	 GG	45238-45253	GT	AGG
(GTG)	 AG	47888-48055	GT	TGG
(ACC)	 AG	48275-48414	GT	TGG
(ATC)	 AG	48644-48745	AT	TAA
(GAC)	 AC	48930-49107	GT	TGG
(AGC)	 AG	49283-49565	GT	CGG
(GTT)	 AG	49790-50051	TG	GAT
-recovered CodingQuarry_transcript_5329-T1, initial, 45238, 45253
-recovered CodingQuarry_transcript_5329-T1, terminal, 49790, 50051
-recovered CodingQuarry_transcript_5329-T1, internal, 47888, 48055
-recovered CodingQuarry_transcript_5329-T1, internal, 48275, 48414
-recovered CodingQuarry_transcript_5329-T1, internal, 49283, 49565
Valid prediction for snap_scaffold_10-snap.705-T1
Valid prediction for GlimmerHMM_glimmerT_24401-T1
Valid prediction for GlimmerHMM_glimmerT_24415-T1
Valid prediction for HiQ_model.g16242.t1
Valid prediction for snap_scaffold_10-snap.702-T1
Valid prediction for HiQ_model.g16260.t1
Couldn't classify 165756, 165809
Sorry, prediction pasa_asmbl_4179.p1 fails validation.
(CCC)	 CC	165756-165809	GT	AGG
(GAG)	 AG	166131-166204	GT	AAG
(AGA)	 AG	166843-166989	GT	GGG
(GAT)	 AG	167183-167231	CA	AAC
-recovered pasa_asmbl_4179.p1, terminal, 167183, 167231
-recovered pasa_asmbl_4179.p1, internal, 166131, 166204
-recovered pasa_asmbl_4179.p1, internal, 166843, 166989
Valid prediction for GlimmerHMM_glimmerT_24414-T1
Valid prediction for Augustus_model.g16255.t1
Couldn't classify 128398, 128709
Sorry, prediction pasa_asmbl_3034.p1 fails validation.
(TTC)	 TG	128398-128709	AT	AAA
Valid prediction for snap_scaffold_10-snap.708-T1
Valid prediction for Augustus_model.g16250.t1
Valid prediction for GlimmerHMM_glimmerT_24416-T1
Valid prediction for GlimmerHMM_glimmerT_24408-T1
Valid prediction for Augustus_model.g16258.t1
Valid prediction for CodingQuarry_transcript_5330-T1
Valid prediction for snap_scaffold_10-snap.685-T1
Valid prediction for snap_scaffold_10-snap.696-T1
Valid prediction for snap_scaffold_10-snap.715-T1
Valid prediction for GlimmerHMM_glimmerT_24409-T1
Valid prediction for snap_scaffold_10-snap.706-T1
Valid prediction for HiQ_model.g16251.t1
Valid prediction for Augustus_model.g16259.t1
Valid prediction for snap_scaffold_10-snap.689-T1
Valid prediction for pasa_asmbl_4178.p1
Valid prediction for snap_scaffold_10-snap.721-T1
Valid prediction for GlimmerHMM_glimmerT_24403-T1
Valid prediction for GlimmerHMM_glimmerT_24386-T1
Valid prediction for Augustus_model.g16249.t1
Couldn't classify 71869, 71912
Sorry, prediction pasa_asmbl_4183.p1 fails validation.
(TAC)	 AG	71869-71912	GT	CGG
(GAT)	 AG	74175-74247	GT	AGG
(TAC)	 AG	74362-74475	GT	AGG
(AAC)	 AG	74607-74735	GT	AGG
(GCA)	 AG	75031-75341	GT	GGG
(AGG)	 AG	75600-75653	GT	AAG
(TGA)	 AG	76044-76083	GT	TGG
(AGT)	 AG	76656-76671	GT	TGG
(ACA)	 AG	76897-76929	GT	GGG
(GTG)	 AG	77080-77147	GT	ACG
(CTG)	 AG	77268-77437	GC	AGG
(TGT)	 AG	77859-77889	AG	AGA
-recovered pasa_asmbl_4183.p1, terminal, 77859, 77889
-recovered pasa_asmbl_4183.p1, internal, 71869, 71912
-recovered pasa_asmbl_4183.p1, internal, 74175, 74247
-recovered pasa_asmbl_4183.p1, internal, 74362, 74475
-recovered pasa_asmbl_4183.p1, internal, 74607, 74735
-recovered pasa_asmbl_4183.p1, internal, 75031, 75341
-recovered pasa_asmbl_4183.p1, internal, 75600, 75653
-recovered pasa_asmbl_4183.p1, internal, 76044, 76083
-recovered pasa_asmbl_4183.p1, internal, 76656, 76671
-recovered pasa_asmbl_4183.p1, internal, 76897, 76929
-recovered pasa_asmbl_4183.p1, internal, 77080, 77147
-recovered pasa_asmbl_4183.p1, internal, 77268, 77437
Valid prediction for snap_scaffold_10-snap.713-T1
Valid prediction for CodingQuarry_transcript_5328-T1
Valid prediction for GlimmerHMM_glimmerT_24384-T1
Valid prediction for snap_scaffold_10-snap.707-T1
Valid prediction for Augustus_model.g16252.t1
Valid prediction for GlimmerHMM_glimmerT_24398-T1
Valid prediction for Augustus_model.g16244.t1
Valid prediction for snap_scaffold_10-snap.709-T1
Valid prediction for GlimmerHMM_glimmerT_24400-T1
Valid prediction for snap_scaffold_10-snap.688-T1
Valid prediction for snap_scaffold_10-snap.718-T1
Valid prediction for CodingQuarry_transcript_5326-T1
Valid prediction for CodingQuarry_transcript_5327-T1
Valid prediction for GlimmerHMM_glimmerT_24396-T1
Couldn't classify 21832, 21920
Couldn't classify 23312, 23360
Sorry, prediction pasa_asmbl_4192.p1 fails validation.
(ATC)	 TC	21832-21920	GT	AGG
(CGG)	 AG	22243-22351	GT	TGG
(GCC)	 AG	22469-22548	GT	TGG
(CCT)	 AG	22986-23093	GT	TGG
(GTC)	 AG	23312-23360	GA	CAG
-recovered pasa_asmbl_4192.p1, internal, 22243, 22351
-recovered pasa_asmbl_4192.p1, internal, 22469, 22548
-recovered pasa_asmbl_4192.p1, internal, 22986, 23093
Valid prediction for pasa_asmbl_4181.p1
Valid prediction for GlimmerHMM_glimmerT_24413-T1
Valid prediction for snap_scaffold_10-snap.727-T1
Valid prediction for snap_scaffold_10-snap.712-T1
Valid prediction for Augustus_model.g16256.t1
Valid prediction for GlimmerHMM_glimmerT_24397-T1
Valid prediction for snap_scaffold_10-snap.722-T1
Valid prediction for GlimmerHMM_glimmerT_24399-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 15262, rend_intergenic: 5684  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23441, rend_intergenic: 15808  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25667, rend_intergenic: 24005  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37489, rend_intergenic: 28580  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40039, rend_intergenic: 37748  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44480, rend_intergenic: 43094  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46168, rend_intergenic: 45239  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50809, rend_intergenic: 46256  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60877, rend_intergenic: 58391  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64689, rend_intergenic: 63498  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90162, rend_intergenic: 67910  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98042, rend_intergenic: 91279  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118022, rend_intergenic: 115262  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133306, rend_intergenic: 131097  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142966, rend_intergenic: 139834  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159098, rend_intergenic: 151457  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172884, rend_intergenic: 164679  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 189884
-exon list size: 496


building trellis

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-found 32 predictions from path traversal
Error with prediction: snap lend_intergenic: 15262, rend_intergenic: 5684  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23441, rend_intergenic: 15808  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25667, rend_intergenic: 24005  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37489, rend_intergenic: 28580  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40039, rend_intergenic: 37748  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44480, rend_intergenic: 43094  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46168, rend_intergenic: 45239  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50809, rend_intergenic: 46256  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60877, rend_intergenic: 58391  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64689, rend_intergenic: 63498  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90162, rend_intergenic: 67910  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98042, rend_intergenic: 91279  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118022, rend_intergenic: 115262  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133306, rend_intergenic: 131097  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142966, rend_intergenic: 139834  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159098, rend_intergenic: 151457  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172884, rend_intergenic: 164679  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 27 predictions persist after filtering for low support