-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_27/scaffold_27_5232085-5459714

-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_27-snap.1261-T1
Valid prediction for snap_scaffold_27-snap.1219-T1
Valid prediction for snap_scaffold_27-snap.1257-T1
Valid prediction for snap_scaffold_27-snap.1246-T1
Valid prediction for snap_scaffold_27-snap.1266-T1
Valid prediction for snap_scaffold_27-snap.1226-T1
Valid prediction for snap_scaffold_27-snap.1222-T1
Valid prediction for snap_scaffold_27-snap.1240-T1
Valid prediction for snap_scaffold_27-snap.1224-T1
Valid prediction for Augustus_model.g37992.t1
Valid prediction for GlimmerHMM_glimmerT_57312-T1
Valid prediction for snap_scaffold_27-snap.1258-T1
Valid prediction for snap_scaffold_27-snap.1249-T1
Valid prediction for snap_scaffold_27-snap.1263-T1
Valid prediction for GlimmerHMM_glimmerT_57309-T1
Valid prediction for snap_scaffold_27-snap.1281-T1
Valid prediction for GlimmerHMM_glimmerT_57328-T1
Couldn't classify 189642, 189738
Sorry, prediction pasa_asmbl_36570.p1 fails validation.
(GCG)	 GG	189642-189738	GT	AGG
(GTG)	 AG	189855-190470	GT	TGG
(CGC)	 AG	190702-190786	GT	AGG
(ACG)	 AG	190940-191104	CT	AAC
-recovered pasa_asmbl_36570.p1, terminal, 190940, 191104
-recovered pasa_asmbl_36570.p1, internal, 189855, 190470
-recovered pasa_asmbl_36570.p1, internal, 190702, 190786
Valid prediction for GlimmerHMM_glimmerT_57303-T1
Valid prediction for GlimmerHMM_glimmerT_57314-T1
Valid prediction for snap_scaffold_27-snap.1270-T1
Valid prediction for snap_scaffold_27-snap.1239-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_57310-T1
Valid prediction for snap_scaffold_27-snap.1251-T1
Valid prediction for Augustus_model.g37985.t1
Valid prediction for snap_scaffold_27-snap.1276-T1
Valid prediction for snap_scaffold_27-snap.1225-T1
Valid prediction for GlimmerHMM_glimmerT_57333-T1
Valid prediction for GlimmerHMM_glimmerT_57304-T1
Valid prediction for snap_scaffold_27-snap.1230-T1
Valid prediction for Augustus_model.g37989.t1
Valid prediction for Augustus_model.g37979.t1
Valid prediction for snap_scaffold_27-snap.1252-T1
Valid prediction for GlimmerHMM_glimmerT_57313-T1
Valid prediction for Augustus_model.g37982.t1
Valid prediction for GlimmerHMM_glimmerT_57325-T1
Valid prediction for snap_scaffold_27-snap.1278-T1
Valid prediction for snap_scaffold_27-snap.1264-T1
Valid prediction for snap_scaffold_27-snap.1256-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_57337-T1
Couldn't classify 188146, 188171
Couldn't classify 189169, 189207
Sorry, prediction pasa_asmbl_36563.p1 fails validation.
(CTG)	 AG	188146-188171	GT	AGG
(AGA)	 AG	188357-188476	GT	TGG
(TTA)	 AG	188679-188889	GT	TGG
(GCC)	 AG	189169-189207	GT	GCG
-recovered pasa_asmbl_36563.p1, internal, 188146, 188171
-recovered pasa_asmbl_36563.p1, internal, 188357, 188476
-recovered pasa_asmbl_36563.p1, internal, 188679, 188889
-recovered pasa_asmbl_36563.p1, internal, 189169, 189207
Valid prediction for snap_scaffold_27-snap.1243-T1
Valid prediction for Augustus_model.g37986.t1
Valid prediction for GlimmerHMM_glimmerT_57332-T1
Valid prediction for GlimmerHMM_glimmerT_57311-T1
Valid prediction for Augustus_model.g37996.t1
Valid prediction for snap_scaffold_27-snap.1220-T1
Valid prediction for Augustus_model.g37980.t1
Valid prediction for snap_scaffold_27-snap.1273-T1
Valid prediction for snap_scaffold_27-snap.1277-T1
Valid prediction for GlimmerHMM_glimmerT_57305-T1
Couldn't classify 207118, 207740
Sorry, prediction pasa_asmbl_36342.p1 fails validation.
(ATG)	 AC	206684-206966	GT	AGG
(GTG)	 AG	207118-207740	GG	GAG
-recovered pasa_asmbl_36342.p1, initial, 206684, 206966
Valid prediction for snap_scaffold_27-snap.1228-T1
Valid prediction for snap_scaffold_27-snap.1244-T1
Valid prediction for snap_scaffold_27-snap.1247-T1
Valid prediction for GlimmerHMM_glimmerT_57322-T1
Valid prediction for GlimmerHMM_glimmerT_57338-T1
Valid prediction for GlimmerHMM_glimmerT_57308-T1
Valid prediction for snap_scaffold_27-snap.1233-T1
Valid prediction for GlimmerHMM_glimmerT_57319-T1
Valid prediction for GlimmerHMM_glimmerT_57318-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for Augustus_model.g37990.t1
Valid prediction for GlimmerHMM_glimmerT_57335-T1
Valid prediction for snap_scaffold_27-snap.1237-T1
Valid prediction for snap_scaffold_27-snap.1232-T1
Valid prediction for snap_scaffold_27-snap.1223-T1
Valid prediction for snap_scaffold_27-snap.1280-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_27-snap.1234-T1
Valid prediction for snap_scaffold_27-snap.1238-T1
Valid prediction for snap_scaffold_27-snap.1218-T1
Valid prediction for GlimmerHMM_glimmerT_57334-T1
Valid prediction for pasa_asmbl_37008.p1
Valid prediction for Augustus_model.g37984.t1
Valid prediction for Augustus_model.g37997.t1
Valid prediction for snap_scaffold_27-snap.1259-T1
Valid prediction for Augustus_model.g37995.t1
Valid prediction for snap_scaffold_27-snap.1248-T1
Valid prediction for Augustus_model.g37981.t1
Valid prediction for snap_scaffold_27-snap.1274-T1
Valid prediction for GlimmerHMM_glimmerT_57336-T1
Valid prediction for GlimmerHMM_glimmerT_57327-T1
Valid prediction for Augustus_model.g37987.t1
Valid prediction for snap_scaffold_27-snap.1229-T1
Valid prediction for snap_scaffold_27-snap.1221-T1
Valid prediction for snap_scaffold_27-snap.1275-T1
Valid prediction for snap_scaffold_27-snap.1282-T1
Valid prediction for snap_scaffold_27-snap.1268-T1
Valid prediction for GlimmerHMM_glimmerT_57329-T1
Couldn't classify 138687, 139028
Sorry, prediction pasa_asmbl_37002.p1 fails validation.
(CTC)	 GA	138687-139028	TC	CCT
Valid prediction for GlimmerHMM_glimmerT_57320-T1
Valid prediction for HiQ_model.g37994.t1
Valid prediction for GlimmerHMM_glimmerT_57306-T1
Valid prediction for snap_scaffold_27-snap.1227-T1
Valid prediction for snap_scaffold_27-snap.1253-T1
Valid prediction for GlimmerHMM_glimmerT_57307-T1
Valid prediction for GlimmerHMM_glimmerT_57324-T1
Valid prediction for snap_scaffold_27-snap.1231-T1
Valid prediction for GlimmerHMM_glimmerT_57315-T1
Valid prediction for snap_scaffold_27-snap.1241-T1
Valid prediction for snap_scaffold_27-snap.1255-T1
Valid prediction for snap_scaffold_27-snap.1265-T1
Valid prediction for snap_scaffold_27-snap.1254-T1
Valid prediction for CodingQuarry_transcript_41895-T1
Valid prediction for snap_scaffold_27-snap.1271-T1
Valid prediction for GlimmerHMM_glimmerT_57316-T1
Valid prediction for snap_scaffold_27-snap.1242-T1
Valid prediction for Augustus_model.g37991.t1
Valid prediction for snap_scaffold_27-snap.1267-T1
Valid prediction for snap_scaffold_27-snap.1235-T1
Valid prediction for snap_scaffold_27-snap.1262-T1
Valid prediction for snap_scaffold_27-snap.1272-T1
Valid prediction for snap_scaffold_27-snap.1217-T1
Valid prediction for Augustus_model.g37983.t1
Valid prediction for GlimmerHMM_glimmerT_57339-T1
Valid prediction for GlimmerHMM_glimmerT_57326-T1
Valid prediction for HiQ_model.g37993.t1
Valid prediction for Augustus_model.g37988.t1
Valid prediction for snap_scaffold_27-snap.1236-T1
Valid prediction for snap_scaffold_27-snap.1250-T1
Valid prediction for GlimmerHMM_glimmerT_57331-T1
Valid prediction for snap_scaffold_27-snap.1269-T1
Valid prediction for GlimmerHMM_glimmerT_57321-T1
Valid prediction for snap_scaffold_27-snap.1245-T1
Valid prediction for snap_scaffold_27-snap.1260-T1
Valid prediction for GlimmerHMM_glimmerT_57323-T1
Valid prediction for GlimmerHMM_glimmerT_57330-T1
Valid prediction for snap_scaffold_27-snap.1279-T1
Valid prediction for GlimmerHMM_glimmerT_57317-T1
Valid prediction for pasa_asmbl_37006.p1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 13920, rend_intergenic: 9064  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18076, rend_intergenic: 14862  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37174, rend_intergenic: 23726  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40196, rend_intergenic: 39653  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44163, rend_intergenic: 40288  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53029, rend_intergenic: 45675  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55973, rend_intergenic: 53200  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69410, rend_intergenic: 65613  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81815, rend_intergenic: 70198  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85890, rend_intergenic: 82461  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100254, rend_intergenic: 86108  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101167, rend_intergenic: 100834  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104685, rend_intergenic: 101270  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107946, rend_intergenic: 107101  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112637, rend_intergenic: 108334  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120733, rend_intergenic: 117818  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138346, rend_intergenic: 130459  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146830, rend_intergenic: 140654  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154365, rend_intergenic: 151076  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156759, rend_intergenic: 155678  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160514, rend_intergenic: 157945  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173028, rend_intergenic: 161579  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 190474, rend_intergenic: 180043  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 197710, rend_intergenic: 195205  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 205242, rend_intergenic: 201700  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 213740, rend_intergenic: 213038  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 222750, rend_intergenic: 214954  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 227630
-exon list size: 513


building trellis

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-found 46 predictions from path traversal
Error with prediction: snap lend_intergenic: 13920, rend_intergenic: 9064  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18076, rend_intergenic: 14862  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37174, rend_intergenic: 23726  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40196, rend_intergenic: 39653  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44163, rend_intergenic: 40288  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53029, rend_intergenic: 45675  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55973, rend_intergenic: 53200  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69410, rend_intergenic: 65613  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81815, rend_intergenic: 70198  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85890, rend_intergenic: 82461  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100254, rend_intergenic: 86108  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101167, rend_intergenic: 100834  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104685, rend_intergenic: 101270  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107946, rend_intergenic: 107101  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112637, rend_intergenic: 108334  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120733, rend_intergenic: 117818  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138346, rend_intergenic: 130459  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146830, rend_intergenic: 140654  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154365, rend_intergenic: 151076  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156759, rend_intergenic: 155678  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160514, rend_intergenic: 157945  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173028, rend_intergenic: 161579  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 190474, rend_intergenic: 180043  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 197710, rend_intergenic: 195205  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 205242, rend_intergenic: 201700  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 213740, rend_intergenic: 213038  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 222750, rend_intergenic: 214954  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 22 predictions persist after filtering for low support