-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_5/scaffold_5_5326663-5575609

-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 snap_scaffold_5-snap.1089-T1
Valid prediction for GlimmerHMM_glimmerT_11927-T1
Valid prediction for snap_scaffold_5-snap.1080-T1
Valid prediction for snap_scaffold_5-snap.1046-T1
Valid prediction for snap_scaffold_5-snap.1066-T1
Valid prediction for snap_scaffold_5-snap.1084-T1
Valid prediction for GlimmerHMM_glimmerT_11934-T1
Valid prediction for snap_scaffold_5-snap.1049-T1
Valid prediction for Augustus_model.g7804.t1
Valid prediction for GlimmerHMM_glimmerT_11936-T1
Valid prediction for GlimmerHMM_glimmerT_11928-T1
Valid prediction for snap_scaffold_5-snap.1067-T1
Valid prediction for snap_scaffold_5-snap.1064-T1
Valid prediction for snap_scaffold_5-snap.1082-T1
Valid prediction for GlimmerHMM_glimmerT_11930-T1
Valid prediction for snap_scaffold_5-snap.1051-T1
Valid prediction for snap_scaffold_5-snap.1079-T1
Valid prediction for GlimmerHMM_glimmerT_11940-T1
Valid prediction for snap_scaffold_5-snap.1048-T1
Valid prediction for snap_scaffold_5-snap.1062-T1
Valid prediction for snap_scaffold_5-snap.1053-T1
Valid prediction for snap_scaffold_5-snap.1071-T1
Valid prediction for HiQ_model.g7822.t1
Valid prediction for snap_scaffold_5-snap.1073-T1
Valid prediction for snap_scaffold_5-snap.1091-T1
Valid prediction for CodingQuarry_transcript_52057-T1
Valid prediction for snap_scaffold_5-snap.1074-T1
Valid prediction for snap_scaffold_5-snap.1056-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_11943-T1
Valid prediction for snap_scaffold_5-snap.1087-T1
Valid prediction for snap_scaffold_5-snap.1069-T1
Valid prediction for GlimmerHMM_glimmerT_11926-T1
Valid prediction for snap_scaffold_5-snap.1063-T1
Couldn't classify 183803, 183844
Sorry, prediction pasa_asmbl_45347.p1 fails validation.
(AAG)	 CC	183803-183844	GT	AGG
(GTC)	 AG	184725-184788	GT	TGG
(ATG)	 AG	184948-184999	GT	CAG
(CTC)	 AG	185328-185391	GT	AGG
(GTG)	 AG	185569-185775	GT	CGG
(GTA)	 AG	186171-186250	GT	TGG
(GAA)	 AG	186351-186429	GT	AGG
(GTT)	 AG	186568-186639	GT	CTG
(AAT)	 AG	186893-186955	GT	AGG
(ATG)	 AG	187084-187224	CT	AGC
-recovered pasa_asmbl_45347.p1, initial, 184948, 184999
-recovered pasa_asmbl_45347.p1, terminal, 187084, 187224
-recovered pasa_asmbl_45347.p1, internal, 184725, 184788
-recovered pasa_asmbl_45347.p1, internal, 184948, 184999
-recovered pasa_asmbl_45347.p1, internal, 185328, 185391
-recovered pasa_asmbl_45347.p1, internal, 185569, 185775
-recovered pasa_asmbl_45347.p1, internal, 186171, 186250
-recovered pasa_asmbl_45347.p1, internal, 186351, 186429
-recovered pasa_asmbl_45347.p1, internal, 186568, 186639
-recovered pasa_asmbl_45347.p1, internal, 186893, 186955
Valid prediction for snap_scaffold_5-snap.1047-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 CodingQuarry_transcript_52059-T1
Valid prediction for Augustus_model.g7805.t1
Valid prediction for GlimmerHMM_glimmerT_11941-T1
Valid prediction for GlimmerHMM_glimmerT_11944-T1
Valid prediction for GlimmerHMM_glimmerT_11942-T1
Valid prediction for snap_scaffold_5-snap.1057-T1
Valid prediction for snap_scaffold_5-snap.1081-T1
Valid prediction for Augustus_model.g7815.t1
Valid prediction for snap_scaffold_5-snap.1054-T1
Valid prediction for Augustus_model.g7819.t1
Valid prediction for GlimmerHMM_glimmerT_11925-T1
Valid prediction for pasa_asmbl_44036.p1
Valid prediction for Augustus_model.g7818.t1
Valid prediction for snap_scaffold_5-snap.1075-T1
Couldn't classify 39219, 39272
Sorry, prediction pasa_asmbl_44042.p1 fails validation.
(AAG)	 GC	39219-39272	GT	AGG
(GTG)	 AG	39399-39524	GT	AGG
(AGA)	 AG	39706-39794	GT	AAG
(GTT)	 AG	39987-40105	GT	AGG
(TGG)	 AG	40253-40314	GG	AAG
-recovered pasa_asmbl_44042.p1, terminal, 40253, 40314
-recovered pasa_asmbl_44042.p1, internal, 39399, 39524
-recovered pasa_asmbl_44042.p1, internal, 39706, 39794
-recovered pasa_asmbl_44042.p1, internal, 39987, 40105
Valid prediction for Augustus_model.g7812.t1
Valid prediction for snap_scaffold_5-snap.1072-T1
Valid prediction for snap_scaffold_5-snap.1070-T1
Valid prediction for CodingQuarry_transcript_52058-T1
Valid prediction for Augustus_model.g7803.t1
Valid prediction for Augustus_model.g7809.t1
Valid prediction for snap_scaffold_5-snap.1083-T1
Valid prediction for snap_scaffold_5-snap.1058-T1
Valid prediction for HiQ_model.g7820.t1
Valid prediction for Augustus_model.g7816.t1
Valid prediction for Augustus_model.g7810.t1
Valid prediction for Augustus_model.g7802.t1
Valid prediction for GlimmerHMM_glimmerT_11945-T1
Valid prediction for Augustus_model.g7807.t1
Valid prediction for Augustus_model.g7817.t1
Valid prediction for snap_scaffold_5-snap.1068-T1
Valid prediction for GlimmerHMM_glimmerT_11931-T1
Valid prediction for Augustus_model.g7823.t1
Valid prediction for snap_scaffold_5-snap.1078-T1
Valid prediction for Augustus_model.g7808.t1
Valid prediction for GlimmerHMM_glimmerT_11933-T1
Valid prediction for snap_scaffold_5-snap.1086-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for Augustus_model.g7814.t1
Valid prediction for GlimmerHMM_glimmerT_11935-T1
Valid prediction for Augustus_model.g7806.t1
Valid prediction for snap_scaffold_5-snap.1052-T1
Valid prediction for snap_scaffold_5-snap.1045-T1
Valid prediction for Augustus_model.g7811.t1
Valid prediction for Augustus_model.g7813.t1
Valid prediction for GlimmerHMM_glimmerT_11937-T1
Valid prediction for snap_scaffold_5-snap.1060-T1
Valid prediction for Augustus_model.g7821.t1
Couldn't classify 8675, 8873
Sorry, prediction pasa_asmbl_44045.p1 fails validation.
(CGT)	 CC	8675-8873	GT	CAG
(GCA)	 AG	11126-11403	GT	CGG
(GCG)	 AG	12000-12264	GT	AGG
(GTT)	 AG	14626-14855	GG	GAG
-recovered pasa_asmbl_44045.p1, terminal, 14626, 14855
-recovered pasa_asmbl_44045.p1, internal, 11126, 11403
-recovered pasa_asmbl_44045.p1, internal, 12000, 12264
Valid prediction for snap_scaffold_5-snap.1088-T1
Valid prediction for snap_scaffold_5-snap.1055-T1
Valid prediction for GlimmerHMM_glimmerT_11938-T1
Valid prediction for Augustus_model.g7825.t1
Valid prediction for CodingQuarry_transcript_52056-T1
Couldn't classify 69649, 69848
Sorry, prediction pasa_asmbl_44039.p1 fails validation.
(ATG)	 AG	66535-66565	GT	TGG
(GTA)	 AG	66649-67368	GT	AGG
(GTG)	 AG	67484-68191	GT	AGG
(GGG)	 AG	68320-68438	GT	GGG
(GAA)	 AG	68667-69324	GT	CAG
(TGA)	 AG	69649-69848	GA	TTG
-recovered pasa_asmbl_44039.p1, initial, 66535, 66565
-recovered pasa_asmbl_44039.p1, internal, 66535, 66565
-recovered pasa_asmbl_44039.p1, internal, 66649, 67368
-recovered pasa_asmbl_44039.p1, internal, 67484, 68191
-recovered pasa_asmbl_44039.p1, internal, 68320, 68438
-recovered pasa_asmbl_44039.p1, internal, 68667, 69324
Valid prediction for snap_scaffold_5-snap.1059-T1
Valid prediction for snap_scaffold_5-snap.1077-T1
Valid prediction for snap_scaffold_5-snap.1065-T1
Valid prediction for snap_scaffold_5-snap.1061-T1
Couldn't classify 54050, 54295
Couldn't classify 56971, 57648
Sorry, prediction pasa_asmbl_44041.p1 fails validation.
(GAG)	 AG	54050-54295	GT	GGG
(GTG)	 AG	55149-55256	GT	AGG
(CTG)	 AG	56971-57648	CC	ACC
-recovered pasa_asmbl_44041.p1, internal, 54050, 54295
-recovered pasa_asmbl_44041.p1, internal, 55149, 55256
Valid prediction for Augustus_model.g7824.t1
Couldn't classify 35528, 35663
Sorry, prediction pasa_asmbl_44044.p1 fails validation.
(ATG)	 GG	34546-34757	GT	AGG
(CAT)	 AG	35027-35161	GT	CAG
(GGC)	 AG	35528-35663	AT	CCA
-recovered pasa_asmbl_44044.p1, initial, 34546, 34757
-recovered pasa_asmbl_44044.p1, internal, 35027, 35161
Valid prediction for snap_scaffold_5-snap.1085-T1
Valid prediction for Augustus_model.g7826.t1
Valid prediction for GlimmerHMM_glimmerT_11939-T1
Valid prediction for GlimmerHMM_glimmerT_11932-T1
Couldn't classify 38559, 38660
Couldn't classify 39204, 39227
Sorry, prediction pasa_asmbl_44043.p1 fails validation.
(TTG)	 TC	38559-38660	GT	AGG
(GGT)	 AG	38859-39050	GT	AGG
(GTG)	 AG	39204-39227	AG	TCA
-recovered pasa_asmbl_44043.p1, internal, 38859, 39050
Valid prediction for snap_scaffold_5-snap.1090-T1
Valid prediction for snap_scaffold_5-snap.1076-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_11929-T1
Valid prediction for snap_scaffold_5-snap.1050-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 8381, rend_intergenic: 1959  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17336, rend_intergenic: 15341  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31328, rend_intergenic: 19808  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49237, rend_intergenic: 33189  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95153, rend_intergenic: 50324  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115777, rend_intergenic: 104234  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116887, rend_intergenic: 116441  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137882, rend_intergenic: 116938  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142799, rend_intergenic: 137994  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143989, rend_intergenic: 143149  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149871, rend_intergenic: 148250  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163523, rend_intergenic: 151719  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188036, rend_intergenic: 184917  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200773, rend_intergenic: 190673  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 215244, rend_intergenic: 210203  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 225137, rend_intergenic: 218024  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 232986, rend_intergenic: 227660  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 234240, rend_intergenic: 234093  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 244645, rend_intergenic: 234256  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 248947
-exon list size: 477


building trellis

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-found 32 predictions from path traversal
Error with prediction: snap lend_intergenic: 8381, rend_intergenic: 1959  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17336, rend_intergenic: 15341  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31328, rend_intergenic: 19808  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49237, rend_intergenic: 33189  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95153, rend_intergenic: 50324  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115777, rend_intergenic: 104234  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116887, rend_intergenic: 116441  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137882, rend_intergenic: 116938  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142799, rend_intergenic: 137994  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143989, rend_intergenic: 143149  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149871, rend_intergenic: 148250  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163523, rend_intergenic: 151719  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188036, rend_intergenic: 184917  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200773, rend_intergenic: 190673  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 215244, rend_intergenic: 210203  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 225137, rend_intergenic: 218024  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 232986, rend_intergenic: 227660  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 234240, rend_intergenic: 234093  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 244645, rend_intergenic: 234256  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 11 predictions persist after filtering for low support