-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_21/scaffold_21_6877400-7070836

-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_21-snap.1418-T1
Valid prediction for snap_scaffold_21-snap.1415-T1
Valid prediction for snap_scaffold_21-snap.1448-T1
Valid prediction for snap_scaffold_21-snap.1423-T1
Valid prediction for GlimmerHMM_glimmerT_47951-T1
Valid prediction for GlimmerHMM_glimmerT_47955-T1
Valid prediction for GlimmerHMM_glimmerT_47980-T1
Valid prediction for snap_scaffold_21-snap.1420-T1
Valid prediction for GlimmerHMM_glimmerT_47977-T1
Couldn't classify 115047, 115127
Couldn't classify 115374, 115889
Sorry, prediction pasa_asmbl_28707.p1 fails validation.
(AAG)	 TA	115047-115127	GT	AGG
(ATC)	 AG	115374-115889	CC	CCC
Valid prediction for GlimmerHMM_glimmerT_47968-T1
Valid prediction for Augustus_model.g32016.t1
Valid prediction for GlimmerHMM_glimmerT_47966-T1
Valid prediction for GlimmerHMM_glimmerT_47970-T1
Valid prediction for Augustus_model.g32019.t1
Valid prediction for GlimmerHMM_glimmerT_47973-T1
Valid prediction for snap_scaffold_21-snap.1442-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_47953-T1
Valid prediction for GlimmerHMM_glimmerT_47969-T1
Valid prediction for Augustus_model.g32014.t1
Valid prediction for snap_scaffold_21-snap.1451-T1
Valid prediction for snap_scaffold_21-snap.1446-T1
Valid prediction for snap_scaffold_21-snap.1433-T1
Valid prediction for Augustus_model.g32024.t1
Valid prediction for GlimmerHMM_glimmerT_47974-T1
Valid prediction for snap_scaffold_21-snap.1456-T1
Valid prediction for GlimmerHMM_glimmerT_47948-T1
Valid prediction for snap_scaffold_21-snap.1439-T1
Valid prediction for Augustus_model.g32020.t1
Valid prediction for snap_scaffold_21-snap.1455-T1
Valid prediction for Augustus_model.g32004.t1
Valid prediction for snap_scaffold_21-snap.1424-T1
Valid prediction for snap_scaffold_21-snap.1419-T1
Valid prediction for snap_scaffold_21-snap.1449-T1
Valid prediction for snap_scaffold_21-snap.1447-T1
Valid prediction for snap_scaffold_21-snap.1445-T1
Valid prediction for GlimmerHMM_glimmerT_47981-T1
Valid prediction for Augustus_model.g32021.t1
Valid prediction for snap_scaffold_21-snap.1438-T1
Valid prediction for pasa_asmbl_28708.p1
Valid prediction for GlimmerHMM_glimmerT_47958-T1
Valid prediction for GlimmerHMM_glimmerT_47964-T1
Valid prediction for GlimmerHMM_glimmerT_47957-T1
Valid prediction for GlimmerHMM_glimmerT_47976-T1
Valid prediction for snap_scaffold_21-snap.1452-T1
Valid prediction for GlimmerHMM_glimmerT_47962-T1
Valid prediction for Augustus_model.g32022.t1
Valid prediction for snap_scaffold_21-snap.1413-T1
Valid prediction for snap_scaffold_21-snap.1435-T1
Valid prediction for GlimmerHMM_glimmerT_47978-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: -)Couldn't classify 136968, 137184
Sorry, prediction pasa_asmbl_27752.p1 fails validation.
(CAC)	 CC	136968-137184	GT	AGG
(TGC)	 AG	137620-137783	GT	CTG
(TGT)	 AG	137996-138101	GT	ATG
(ACC)	 AG	139611-139703	GT	AGG
(ACA)	 AG	139856-139972	GT	GGG
(AGT)	 AG	140546-140701	GT	AGG
(CTT)	 AG	140918-141031	GT	GGG
(AGA)	 AG	141158-141226	GT	TGG
(TGA)	 AG	141434-141520	GT	ACG
(CGG)	 AG	141678-141806	GT	GGG
(ATG)	 AG	142011-142142	GT	AGG
(ACA)	 AG	142251-142379	GT	AGG
(ATA)	 AG	142485-142604	GT	CGG
(ACG)	 AG	143458-143580	GT	GGG
(ACA)	 AG	143913-144035	GC	AGG
(ATA)	 AG	144195-144314	GT	AGG
(ACA)	 AG	144504-144632	GT	GGG
(CGA)	 AG	144790-144960	GT	GGG
(CTG)	 AG	145200-145283	GT	AGG
(ACA)	 AG	145658-145786	GT	TGG
(ATG)	 AG	145879-146016	GT	AGG
(GCG)	 AG	146213-146353	GT	GGG
(ATG)	 AG	146826-146954	GT	CGG
(ACC)	 AG	147910-148077	GT	AGG
(TGA)	 AG	148637-148726	GT	AGG
(AAG)	 AG	148944-149075	GT	AGG
(ATG)	 AG	149319-149470	CA	AAC
-recovered pasa_asmbl_27752.p1, initial, 142011, 142142
add_exon() Sorry, pasa_asmbl_27752.p1 145879-146016-initial-1 is invalid.
-recovered pasa_asmbl_27752.p1, initial, 145879, 146016
add_exon() Sorry, pasa_asmbl_27752.p1 146826-146954-initial-1 is invalid.
-recovered pasa_asmbl_27752.p1, initial, 146826, 146954
-recovered pasa_asmbl_27752.p1, terminal, 149319, 149470
-recovered pasa_asmbl_27752.p1, internal, 137620, 137783
-recovered pasa_asmbl_27752.p1, internal, 137996, 138101
-recovered pasa_asmbl_27752.p1, internal, 139611, 139703
-recovered pasa_asmbl_27752.p1, internal, 139856, 139972
-recovered pasa_asmbl_27752.p1, internal, 140546, 140701
-recovered pasa_asmbl_27752.p1, internal, 140918, 141031
-recovered pasa_asmbl_27752.p1, internal, 141158, 141226
-recovered pasa_asmbl_27752.p1, internal, 141434, 141520
-recovered pasa_asmbl_27752.p1, internal, 141678, 141806
-recovered pasa_asmbl_27752.p1, internal, 142011, 142142
-recovered pasa_asmbl_27752.p1, internal, 142251, 142379
-recovered pasa_asmbl_27752.p1, internal, 142485, 142604
-recovered pasa_asmbl_27752.p1, internal, 143458, 143580
-recovered pasa_asmbl_27752.p1, internal, 143913, 144035
-recovered pasa_asmbl_27752.p1, internal, 144195, 144314
-recovered pasa_asmbl_27752.p1, internal, 144504, 144632
-recovered pasa_asmbl_27752.p1, internal, 144790, 144960
-recovered pasa_asmbl_27752.p1, internal, 145200, 145283
-recovered pasa_asmbl_27752.p1, internal, 145658, 145786
-recovered pasa_asmbl_27752.p1, internal, 145879, 146016
-recovered pasa_asmbl_27752.p1, internal, 146213, 146353
-recovered pasa_asmbl_27752.p1, internal, 146826, 146954
-recovered pasa_asmbl_27752.p1, internal, 147910, 148077
-recovered pasa_asmbl_27752.p1, internal, 148637, 148726
-recovered pasa_asmbl_27752.p1, internal, 148944, 149075
Valid prediction for GlimmerHMM_glimmerT_47959-T1
Valid prediction for snap_scaffold_21-snap.1428-T1
Valid prediction for Augustus_model.g32010.t1
Valid prediction for pasa_asmbl_27772.p1
Valid prediction for snap_scaffold_21-snap.1434-T1
Valid prediction for snap_scaffold_21-snap.1427-T1
Valid prediction for GlimmerHMM_glimmerT_47945-T1
Valid prediction for snap_scaffold_21-snap.1444-T1
Valid prediction for snap_scaffold_21-snap.1421-T1
Valid prediction for Augustus_model.g32006.t1
Valid prediction for snap_scaffold_21-snap.1437-T1
Valid prediction for snap_scaffold_21-snap.1441-T1
Valid prediction for HiQ_model.g32007.t1
Valid prediction for GlimmerHMM_glimmerT_47965-T1
Valid prediction for HiQ_model.g32018.t1
Valid prediction for HiQ_model.g32009.t1
Valid prediction for GlimmerHMM_glimmerT_47979-T1
Valid prediction for snap_scaffold_21-snap.1426-T1
Valid prediction for Augustus_model.g32011.t1
Valid prediction for GlimmerHMM_glimmerT_47954-T1
Valid prediction for GlimmerHMM_glimmerT_47947-T1
Valid prediction for snap_scaffold_21-snap.1430-T1
Valid prediction for snap_scaffold_21-snap.1443-T1
Valid prediction for GlimmerHMM_glimmerT_47956-T1
Couldn't classify 105019, 105466
Couldn't classify 105800, 105804
Sorry, prediction CodingQuarry_transcript_32602-T1 fails validation.
(ATG)	 TG	105019-105466	CT	ACC
(CTT)	 AC	105800-105804	GG	GAG
Valid prediction for snap_scaffold_21-snap.1457-T1
Couldn't classify 16298, 16437
Sorry, prediction pasa_asmbl_27780.p1 fails validation.
(ATG)	 AG	13846-14056	GT	TGG
(ACT)	 AG	16298-16437	GG	CAG
-recovered pasa_asmbl_27780.p1, initial, 13846, 14056
-recovered pasa_asmbl_27780.p1, internal, 13846, 14056
Valid prediction for snap_scaffold_21-snap.1436-T1
Valid prediction for GlimmerHMM_glimmerT_47967-T1
Valid prediction for snap_scaffold_21-snap.1422-T1
Valid prediction for Augustus_model.g32003.t1
Valid prediction for GlimmerHMM_glimmerT_47960-T1
Valid prediction for snap_scaffold_21-snap.1432-T1
Valid prediction for snap_scaffold_21-snap.1425-T1
Sorry, intron length (6) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_47949-T1
Valid prediction for GlimmerHMM_glimmerT_47971-T1
Couldn't classify 121355, 121586
Couldn't classify 121728, 122278
Sorry, prediction pasa_asmbl_27758.p1 fails validation.
(AGT)	 CC	121355-121586	GT	AGG
(ATG)	 AG	121728-122278	GA	GGG
Valid prediction for Augustus_model.g32025.t1
Valid prediction for snap_scaffold_21-snap.1453-T1
Valid prediction for Augustus_model.g32013.t1
Valid prediction for Augustus_model.g32023.t1
Valid prediction for snap_scaffold_21-snap.1416-T1
Valid prediction for GlimmerHMM_glimmerT_47961-T1
Valid prediction for GlimmerHMM_glimmerT_47972-T1
Couldn't classify 122339, 122692
Sorry, prediction pasa_asmbl_27757.p1 fails validation.
(AAG)	 GC	122339-122692	GT	GAG
Valid prediction for CodingQuarry_transcript_32604-T1
Valid prediction for snap_scaffold_21-snap.1417-T1
Valid prediction for pasa_asmbl_27751.p2
Valid prediction for snap_scaffold_21-snap.1450-T1
Valid prediction for CodingQuarry_transcript_32603-T1
Valid prediction for GlimmerHMM_glimmerT_47950-T1
Valid prediction for Augustus_model.g32015.t1
Valid prediction for Augustus_model.g32008.t1
Couldn't classify 91909, 91982
Couldn't classify 100706, 100821
Sorry, prediction pasa_asmbl_27765.p1 fails validation.
(AGC)	 GC	91909-91982	GT	GGG
(ATC)	 AG	93525-93666	GT	AGG
(GGA)	 AG	95164-95296	GT	AGG
(GTG)	 AG	96543-96739	GT	GGG
(GTC)	 AG	97055-97850	GT	AGG
(CCA)	 AG	100706-100821	AC	GTA
add_exon() Sorry, pasa_asmbl_27765.p1 97055-97850-terminal-3 is invalid.
-recovered pasa_asmbl_27765.p1, terminal, 97055, 97850
-recovered pasa_asmbl_27765.p1, internal, 93525, 93666
-recovered pasa_asmbl_27765.p1, internal, 95164, 95296
-recovered pasa_asmbl_27765.p1, internal, 96543, 96739
-recovered pasa_asmbl_27765.p1, internal, 97055, 97850
Valid prediction for snap_scaffold_21-snap.1454-T1
Valid prediction for GlimmerHMM_glimmerT_47963-T1
Valid prediction for HiQ_model.g32017.t1
Valid prediction for GlimmerHMM_glimmerT_47946-T1
Valid prediction for pasa_asmbl_27770.p1
Valid prediction for snap_scaffold_21-snap.1429-T1
Valid prediction for snap_scaffold_21-snap.1440-T1
Valid prediction for snap_scaffold_21-snap.1431-T1
Valid prediction for snap_scaffold_21-snap.1414-T1
Valid prediction for CodingQuarry_transcript_32600-T1
Valid prediction for GlimmerHMM_glimmerT_47952-T1
Valid prediction for GlimmerHMM_glimmerT_47975-T1
Valid prediction for Augustus_model.g32005.t1
Valid prediction for Augustus_model.g32012.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 9137, rend_intergenic: 8682  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 11642, rend_intergenic: 9413  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14233, rend_intergenic: 12736  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28131, rend_intergenic: 18118  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42745, rend_intergenic: 39490  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66328, rend_intergenic: 43558  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94455, rend_intergenic: 91046  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103485, rend_intergenic: 101386  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149838, rend_intergenic: 137655  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169713, rend_intergenic: 167172  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177207, rend_intergenic: 174697  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192294, rend_intergenic: 191221  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 193437
-exon list size: 498


building trellis

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99.8    
-found 39 predictions from path traversal
Error with prediction: snap lend_intergenic: 9137, rend_intergenic: 8682  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 11642, rend_intergenic: 9413  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14233, rend_intergenic: 12736  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28131, rend_intergenic: 18118  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42745, rend_intergenic: 39490  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66328, rend_intergenic: 43558  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94455, rend_intergenic: 91046  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103485, rend_intergenic: 101386  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149838, rend_intergenic: 137655  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169713, rend_intergenic: 167172  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 177207, rend_intergenic: 174697  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192294, rend_intergenic: 191221  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 29 predictions persist after filtering for low support