-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_15/scaffold_15_6757730-6993986

-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_36364-T1
Valid prediction for snap_scaffold_15-snap.1470-T1
Valid prediction for GlimmerHMM_glimmerT_36376-T1
Valid prediction for Augustus_model.g24236.t1
Valid prediction for snap_scaffold_15-snap.1454-T1
Valid prediction for Augustus_model.g24237.t1
Valid prediction for snap_scaffold_15-snap.1432-T1
Couldn't classify 208502, 208594
Sorry, prediction pasa_asmbl_15270.p1 fails validation.
(ATG)	 AC	205147-205236	GT	AGG
(GTT)	 AG	205365-205415	GT	AGG
(AGA)	 AG	205526-205613	GT	TGG
(GTC)	 AG	205757-205876	GT	GGG
(ACA)	 AG	206011-206096	GT	AGG
(CTG)	 AG	206197-206329	GT	AGG
(ACG)	 AG	206437-206592	GT	AGG
(GGC)	 AG	207035-207108	GT	AGG
(GTG)	 AG	207350-207458	GT	AGG
(GAA)	 AG	207881-207999	GT	AAG
(CTC)	 AG	208502-208594	GG	GAG
-recovered pasa_asmbl_15270.p1, initial, 205147, 205236
add_exon() Sorry, pasa_asmbl_15270.p1 206437-206592-terminal-1 is invalid.
-recovered pasa_asmbl_15270.p1, terminal, 206437, 206592
-recovered pasa_asmbl_15270.p1, internal, 205365, 205415
-recovered pasa_asmbl_15270.p1, internal, 205526, 205613
-recovered pasa_asmbl_15270.p1, internal, 205757, 205876
-recovered pasa_asmbl_15270.p1, internal, 206011, 206096
-recovered pasa_asmbl_15270.p1, internal, 206197, 206329
-recovered pasa_asmbl_15270.p1, internal, 206437, 206592
-recovered pasa_asmbl_15270.p1, internal, 207035, 207108
-recovered pasa_asmbl_15270.p1, internal, 207350, 207458
-recovered pasa_asmbl_15270.p1, internal, 207881, 207999
Valid prediction for GlimmerHMM_glimmerT_36384-T1
Valid prediction for snap_scaffold_15-snap.1468-T1
Valid prediction for CodingQuarry_transcript_18030-T1
Valid prediction for GlimmerHMM_glimmerT_36362-T1
Valid prediction for CodingQuarry_transcript_18028-T1
Valid prediction for Augustus_model.g24235.t1
Valid prediction for GlimmerHMM_glimmerT_36367-T1
Valid prediction for GlimmerHMM_glimmerT_36356-T1
Valid prediction for GlimmerHMM_glimmerT_36352-T1
Valid prediction for pasa_asmbl_15262.p1
Valid prediction for GlimmerHMM_glimmerT_36382-T1
Valid prediction for GlimmerHMM_glimmerT_36381-T1
Valid prediction for Augustus_model.g24220.t1
Valid prediction for Augustus_model.g24222.t1
Valid prediction for snap_scaffold_15-snap.1467-T1
Valid prediction for GlimmerHMM_glimmerT_36361-T1
Valid prediction for snap_scaffold_15-snap.1431-T1
Valid prediction for snap_scaffold_15-snap.1435-T1
Valid prediction for snap_scaffold_15-snap.1455-T1
Valid prediction for Augustus_model.g24224.t1
Valid prediction for HiQ_model.g24216.t1
Valid prediction for snap_scaffold_15-snap.1446-T1
Valid prediction for snap_scaffold_15-snap.1441-T1
Valid prediction for snap_scaffold_15-snap.1440-T1
Valid prediction for snap_scaffold_15-snap.1442-T1
Valid prediction for GlimmerHMM_glimmerT_36358-T1
Valid prediction for snap_scaffold_15-snap.1451-T1
Valid prediction for snap_scaffold_15-snap.1471-T1
Valid prediction for pasa_asmbl_15260.p1
Valid prediction for HiQ_model.g24234.t1
Valid prediction for snap_scaffold_15-snap.1464-T1
Valid prediction for Augustus_model.g24221.t1
Valid prediction for GlimmerHMM_glimmerT_36380-T1
Valid prediction for snap_scaffold_15-snap.1448-T1
Valid prediction for snap_scaffold_15-snap.1444-T1
Valid prediction for snap_scaffold_15-snap.1443-T1
Valid prediction for snap_scaffold_15-snap.1458-T1
Valid prediction for snap_scaffold_15-snap.1460-T1
Valid prediction for GlimmerHMM_glimmerT_36371-T1
Valid prediction for CodingQuarry_transcript_18035-T1
Valid prediction for snap_scaffold_15-snap.1474-T1
Valid prediction for GlimmerHMM_glimmerT_36360-T1
Valid prediction for snap_scaffold_15-snap.1449-T1
Valid prediction for GlimmerHMM_glimmerT_36374-T1
Valid prediction for snap_scaffold_15-snap.1438-T1
Valid prediction for Augustus_model.g24232.t1
Valid prediction for snap_scaffold_15-snap.1475-T1
Valid prediction for Augustus_model.g24223.t1
Valid prediction for HiQ_model.g24213.t1
Valid prediction for snap_scaffold_15-snap.1469-T1
Valid prediction for GlimmerHMM_glimmerT_36383-T1
Valid prediction for GlimmerHMM_glimmerT_36366-T1
Valid prediction for snap_scaffold_15-snap.1445-T1
Valid prediction for snap_scaffold_15-snap.1427-T1
Valid prediction for Augustus_model.g24230.t1
Valid prediction for GlimmerHMM_glimmerT_36373-T1
Valid prediction for snap_scaffold_15-snap.1473-T1
Couldn't classify 202031, 202117
Sorry, prediction pasa_asmbl_15268.p1 fails validation.
(GAG)	 CA	202031-202117	GT	AGG
(GCT)	 AG	202221-202292	GT	AAG
(GAA)	 AG	202681-202824	GT	AGG
(AGG)	 AG	203285-203349	GT	AGG
(CCG)	 AG	203879-204029	GT	AAG
(GTT)	 AG	204440-204517	AG	AAA
-recovered pasa_asmbl_15268.p1, terminal, 204440, 204517
-recovered pasa_asmbl_15268.p1, internal, 202221, 202292
-recovered pasa_asmbl_15268.p1, internal, 202681, 202824
-recovered pasa_asmbl_15268.p1, internal, 203285, 203349
-recovered pasa_asmbl_15268.p1, internal, 203879, 204029

-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_36357-T1
Valid prediction for HiQ_model.g24212.t1
Valid prediction for snap_scaffold_15-snap.1433-T1
Valid prediction for snap_scaffold_15-snap.1462-T1
Valid prediction for GlimmerHMM_glimmerT_36353-T1
Valid prediction for Augustus_model.g24219.t1
Valid prediction for Augustus_model.g24218.t1
Valid prediction for snap_scaffold_15-snap.1461-T1
Valid prediction for Augustus_model.g24231.t1
Valid prediction for GlimmerHMM_glimmerT_36370-T1
Valid prediction for snap_scaffold_15-snap.1452-T1
Valid prediction for Augustus_model.g24229.t1
Valid prediction for GlimmerHMM_glimmerT_36359-T1
Valid prediction for GlimmerHMM_glimmerT_36354-T1
Valid prediction for HiQ_model.g24226.t1
Valid prediction for snap_scaffold_15-snap.1429-T1
Valid prediction for GlimmerHMM_glimmerT_36368-T1
Valid prediction for GlimmerHMM_glimmerT_36369-T1
Valid prediction for CodingQuarry_transcript_18034-T1
Valid prediction for snap_scaffold_15-snap.1439-T1
Couldn't classify 211466, 211605
Sorry, prediction pasa_asmbl_14251.p1 fails validation.
(ATC)	 TC	211466-211605	GT	AGG
(GTT)	 AG	211724-211799	GT	AGG
(GTG)	 AG	211906-212055	GT	TGG
(GCA)	 AG	212157-212221	GT	TGG
(GTA)	 AG	212339-212517	GT	GGG
(GTG)	 AG	213022-213252	GT	ATG
(TGG)	 AG	213338-213522	CA	AAC
-recovered pasa_asmbl_14251.p1, terminal, 213338, 213522
-recovered pasa_asmbl_14251.p1, internal, 211724, 211799
-recovered pasa_asmbl_14251.p1, internal, 211906, 212055
-recovered pasa_asmbl_14251.p1, internal, 212157, 212221
-recovered pasa_asmbl_14251.p1, internal, 212339, 212517
-recovered pasa_asmbl_14251.p1, internal, 213022, 213252
Valid prediction for snap_scaffold_15-snap.1437-T1
Valid prediction for snap_scaffold_15-snap.1476-T1
Valid prediction for GlimmerHMM_glimmerT_36377-T1
Valid prediction for snap_scaffold_15-snap.1459-T1
Valid prediction for GlimmerHMM_glimmerT_36375-T1
Valid prediction for pasa_asmbl_14265.p1
Couldn't classify 110358, 110431
Sorry, prediction pasa_asmbl_14261.p1 fails validation.
(CTC)	 GC	110358-110431	GT	GAG
(CCT)	 AG	110805-110888	GT	AGG
(GAG)	 AG	111086-111317	GT	GAG
-recovered pasa_asmbl_14261.p1, terminal, 111086, 111317
-recovered pasa_asmbl_14261.p1, internal, 110805, 110888
-recovered pasa_asmbl_14261.p1, internal, 111086, 111317
Valid prediction for CodingQuarry_transcript_18032-T1
Valid prediction for snap_scaffold_15-snap.1453-T1
Couldn't classify 211108, 211145
Sorry, prediction pasa_asmbl_14253.p1 fails validation.
(ATG)	 AT	208948-209707	GT	CCG
(AGC)	 AG	209848-210045	GT	GGG
(CTG)	 AG	210416-210544	GT	GGG
(CCT)	 AG	210649-210796	GT	ATG
(GAT)	 AG	210902-211011	GT	AGG
(ACA)	 AG	211108-211145	CT	GGC
-recovered pasa_asmbl_14253.p1, initial, 208948, 209707
-recovered pasa_asmbl_14253.p1, internal, 209848, 210045
-recovered pasa_asmbl_14253.p1, internal, 210416, 210544
-recovered pasa_asmbl_14253.p1, internal, 210649, 210796
-recovered pasa_asmbl_14253.p1, internal, 210902, 211011
Valid prediction for GlimmerHMM_glimmerT_36365-T1
Valid prediction for GlimmerHMM_glimmerT_36355-T1
Valid prediction for GlimmerHMM_glimmerT_36378-T1
Valid prediction for CodingQuarry_transcript_18031-T1
Valid prediction for pasa_asmbl_14255.p1
Valid prediction for snap_scaffold_15-snap.1430-T1
Valid prediction for HiQ_model.g24214.t1
Valid prediction for GlimmerHMM_glimmerT_36363-T1
Valid prediction for CodingQuarry_transcript_18033-T1
Valid prediction for Augustus_model.g24211.t1
Valid prediction for snap_scaffold_15-snap.1472-T1
Valid prediction for snap_scaffold_15-snap.1465-T1
Valid prediction for pasa_asmbl_14273.p1
Valid prediction for GlimmerHMM_glimmerT_36372-T1
Valid prediction for Augustus_model.g24225.t1
Valid prediction for HiQ_model.g24233.t1
Valid prediction for HiQ_model.g24215.t1
Valid prediction for snap_scaffold_15-snap.1434-T1
Valid prediction for snap_scaffold_15-snap.1436-T1
Valid prediction for Augustus_model.g24217.t1
Valid prediction for snap_scaffold_15-snap.1463-T1
Valid prediction for snap_scaffold_15-snap.1456-T1
Valid prediction for snap_scaffold_15-snap.1447-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_36379-T1
Valid prediction for snap_scaffold_15-snap.1428-T1
Valid prediction for snap_scaffold_15-snap.1466-T1
Valid prediction for snap_scaffold_15-snap.1457-T1
Valid prediction for CodingQuarry_transcript_18029-T1
Valid prediction for Augustus_model.g24227.t1
Valid prediction for snap_scaffold_15-snap.1450-T1
Valid prediction for Augustus_model.g24228.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 12767, rend_intergenic: 8081  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58174, rend_intergenic: 50035  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99030, rend_intergenic: 97976  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103156, rend_intergenic: 99299  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127023, rend_intergenic: 123307  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154285, rend_intergenic: 138919  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164837, rend_intergenic: 154425  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174333, rend_intergenic: 171743  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178819, rend_intergenic: 174394  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181025, rend_intergenic: 178897  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192361, rend_intergenic: 190277  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 196656, rend_intergenic: 194104  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 221998, rend_intergenic: 217188  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 232000, rend_intergenic: 231298  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 236257
-exon list size: 458


building trellis

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-found 35 predictions from path traversal
Error with prediction: snap lend_intergenic: 12767, rend_intergenic: 8081  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58174, rend_intergenic: 50035  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99030, rend_intergenic: 97976  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103156, rend_intergenic: 99299  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127023, rend_intergenic: 123307  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154285, rend_intergenic: 138919  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164837, rend_intergenic: 154425  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174333, rend_intergenic: 171743  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178819, rend_intergenic: 174394  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181025, rend_intergenic: 178897  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192361, rend_intergenic: 190277  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 196656, rend_intergenic: 194104  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 221998, rend_intergenic: 217188  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 232000, rend_intergenic: 231298  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 25 predictions persist after filtering for low support