-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_24/scaffold_24_5252898-5454301

-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_24-snap.1077-T1
Valid prediction for Augustus_model.g34966.t1
Valid prediction for pasa_asmbl_32208.p1
Valid prediction for GlimmerHMM_glimmerT_52496-T1
Valid prediction for HiQ_model.g34975.t1
Valid prediction for Augustus_model.g34958.t1
Valid prediction for GlimmerHMM_glimmerT_52521-T1
Valid prediction for snap_scaffold_24-snap.1075-T1
Valid prediction for Augustus_model.g34973.t1
Valid prediction for GlimmerHMM_glimmerT_52520-T1
Valid prediction for GlimmerHMM_glimmerT_52506-T1
Couldn't classify 132413, 132413
Sorry, prediction CodingQuarry_transcript_37309-T1 fails validation.
(ATG)	 CC	130345-130428	GT	ATG
(GGT)	 AG	130763-130878	GT	TGG
(ATA)	 AG	132413-132413	TA	GAT
-recovered CodingQuarry_transcript_37309-T1, initial, 130345, 130428
-recovered CodingQuarry_transcript_37309-T1, internal, 130763, 130878
Valid prediction for snap_scaffold_24-snap.1079-T1
Valid prediction for Augustus_model.g34967.t1
Valid prediction for snap_scaffold_24-snap.1067-T1
Valid prediction for snap_scaffold_24-snap.1063-T1
Valid prediction for pasa_asmbl_32216.p1
Valid prediction for Augustus_model.g34974.t1
Valid prediction for GlimmerHMM_glimmerT_52508-T1
Valid prediction for snap_scaffold_24-snap.1082-T1
Valid prediction for snap_scaffold_24-snap.1060-T1
Valid prediction for snap_scaffold_24-snap.1049-T1
Valid prediction for Augustus_model.g34978.t1
Valid prediction for snap_scaffold_24-snap.1073-T1
Valid prediction for GlimmerHMM_glimmerT_52517-T1
Valid prediction for snap_scaffold_24-snap.1069-T1
Valid prediction for snap_scaffold_24-snap.1047-T1
Valid prediction for snap_scaffold_24-snap.1048-T1
Couldn't classify 173853, 173999
Sorry, prediction pasa_asmbl_32217.p1 fails validation.
(TGC)	 AC	173853-173999	GT	AGG
(GTG)	 AG	174252-174389	GT	AGG
(TAC)	 AG	174613-174751	GT	TGG
(CTG)	 AG	174924-175075	GT	CGG
(AGG)	 AG	175224-175322	GT	GGG
(GAA)	 AG	175504-175650	TA	GAT
-recovered pasa_asmbl_32217.p1, terminal, 175504, 175650
-recovered pasa_asmbl_32217.p1, internal, 174252, 174389
-recovered pasa_asmbl_32217.p1, internal, 174613, 174751
-recovered pasa_asmbl_32217.p1, internal, 174924, 175075
-recovered pasa_asmbl_32217.p1, internal, 175224, 175322
Valid prediction for Augustus_model.g34959.t1
Valid prediction for snap_scaffold_24-snap.1058-T1
Valid prediction for snap_scaffold_24-snap.1045-T1
Valid prediction for GlimmerHMM_glimmerT_52511-T1
Valid prediction for GlimmerHMM_glimmerT_52507-T1
Valid prediction for GlimmerHMM_glimmerT_52524-T1
Valid prediction for GlimmerHMM_glimmerT_52497-T1
Valid prediction for Augustus_model.g34976.t1
Valid prediction for GlimmerHMM_glimmerT_52502-T1
Valid prediction for snap_scaffold_24-snap.1072-T1
Valid prediction for CodingQuarry_transcript_37308-T1
Valid prediction for snap_scaffold_24-snap.1066-T1
Valid prediction for GlimmerHMM_glimmerT_52499-T1
Valid prediction for Augustus_model.g34970.t1
Valid prediction for GlimmerHMM_glimmerT_52510-T1
Valid prediction for GlimmerHMM_glimmerT_52498-T1
Valid prediction for Augustus_model.g34969.t1
Valid prediction for snap_scaffold_24-snap.1076-T1
Valid prediction for GlimmerHMM_glimmerT_52523-T1
Valid prediction for CodingQuarry_transcript_37306-T1
Valid prediction for Augustus_model.g34972.t1
Valid prediction for GlimmerHMM_glimmerT_52515-T1
Valid prediction for Augustus_model.g34980.t1
Valid prediction for Augustus_model.g34977.t1
Valid prediction for snap_scaffold_24-snap.1061-T1
Valid prediction for GlimmerHMM_glimmerT_52522-T1
Couldn't classify 130318, 130428
Sorry, prediction pasa_asmbl_32213.p1 fails validation.
(GGT)	 CA	130318-130428	GT	ATG
(GGT)	 AG	130763-130878	GT	TGG
(GCT)	 AG	131380-131453	GT	AGG
(ATA)	 AG	132413-132504	AC	AGA
-recovered pasa_asmbl_32213.p1, terminal, 132413, 132504
-recovered pasa_asmbl_32213.p1, internal, 130763, 130878
-recovered pasa_asmbl_32213.p1, internal, 131380, 131453
Valid prediction for GlimmerHMM_glimmerT_52519-T1
Valid prediction for GlimmerHMM_glimmerT_52518-T1
Valid prediction for snap_scaffold_24-snap.1054-T1
Valid prediction for GlimmerHMM_glimmerT_52505-T1
Valid prediction for Augustus_model.g34981.t1
Couldn't classify 121017, 121085
Couldn't classify 127161, 127260
Sorry, prediction pasa_asmbl_32630.p1 fails validation.
(AGG)	 TC	121017-121085	GT	AGG
(GGC)	 AG	121358-121473	GT	AGG
(GAC)	 AG	123242-123311	GT	GGG
(AAA)	 AG	123576-123668	GT	AGG
(GAG)	 AG	123977-124069	GC	AGG
(GAG)	 AG	124763-124888	GT	AGG
(GGG)	 AG	125148-125369	GT	AGG
(ATG)	 AG	126042-126134	GT	AGG
(GCT)	 AG	126818-126896	GT	AGG
(AAG)	 AG	126995-127049	GT	AGG
(GAA)	 AG	127161-127260	GA	GTG
-recovered pasa_asmbl_32630.p1, initial, 126042, 126134
-recovered pasa_asmbl_32630.p1, internal, 121358, 121473
-recovered pasa_asmbl_32630.p1, internal, 123242, 123311
-recovered pasa_asmbl_32630.p1, internal, 123576, 123668
-recovered pasa_asmbl_32630.p1, internal, 123977, 124069
-recovered pasa_asmbl_32630.p1, internal, 124763, 124888
-recovered pasa_asmbl_32630.p1, internal, 125148, 125369
-recovered pasa_asmbl_32630.p1, internal, 126042, 126134
-recovered pasa_asmbl_32630.p1, internal, 126818, 126896
-recovered pasa_asmbl_32630.p1, internal, 126995, 127049
Valid prediction for HiQ_model.g34964.t1
Valid prediction for GlimmerHMM_glimmerT_52512-T1
Couldn't classify 102542, 102605
Couldn't classify 111296, 111463
Sorry, prediction pasa_asmbl_32210.p1 fails validation.
(ATC)	 AG	102542-102605	GT	AGG
(GTG)	 AG	105206-105320	GT	AGG
(CCT)	 AG	106641-106731	GT	CGG
(GGG)	 AG	106982-107095	GT	AGG
(ATC)	 AG	107979-108095	GT	CTG
(GCC)	 AG	108406-108555	GT	GGG
(GAC)	 AG	109037-109161	GT	AGG
(GTT)	 AG	109770-109884	GT	AGG
(GTG)	 AG	110337-110456	GT	AGG
(AGC)	 AG	110571-110762	GT	AGG
(GTG)	 AG	110936-111127	GT	AGG
(GCC)	 AG	111296-111463	GC	CCG
-recovered pasa_asmbl_32210.p1, internal, 102542, 102605
-recovered pasa_asmbl_32210.p1, internal, 105206, 105320
-recovered pasa_asmbl_32210.p1, internal, 106641, 106731
-recovered pasa_asmbl_32210.p1, internal, 106982, 107095
-recovered pasa_asmbl_32210.p1, internal, 107979, 108095
-recovered pasa_asmbl_32210.p1, internal, 108406, 108555
-recovered pasa_asmbl_32210.p1, internal, 109037, 109161
-recovered pasa_asmbl_32210.p1, internal, 109770, 109884
-recovered pasa_asmbl_32210.p1, internal, 110337, 110456
-recovered pasa_asmbl_32210.p1, internal, 110571, 110762
-recovered pasa_asmbl_32210.p1, internal, 110936, 111127
-recovered pasa_asmbl_32210.p1, internal, 111296, 111463
Valid prediction for Augustus_model.g34960.t1
Valid prediction for snap_scaffold_24-snap.1080-T1
Valid prediction for CodingQuarry_transcript_37311-T1
Valid prediction for snap_scaffold_24-snap.1055-T1
Valid prediction for snap_scaffold_24-snap.1078-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_24-snap.1044-T1
Valid prediction for Augustus_model.g34979.t1
Valid prediction for GlimmerHMM_glimmerT_52514-T1
Couldn't classify 179381, 179689
Sorry, prediction pasa_asmbl_32220.p1 fails validation.
(ATG)	 TC	179381-179689	AC	CCA

-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_24-snap.1053-T1
Valid prediction for GlimmerHMM_glimmerT_52501-T1
Valid prediction for CodingQuarry_transcript_37304-T1
Valid prediction for HiQ_model.g34961.t1
Valid prediction for Augustus_model.g34962.t1
Valid prediction for snap_scaffold_24-snap.1065-T1
Valid prediction for GlimmerHMM_glimmerT_52504-T1
Valid prediction for pasa_asmbl_32885.p1
Valid prediction for snap_scaffold_24-snap.1068-T1
Valid prediction for GlimmerHMM_glimmerT_52513-T1
Valid prediction for pasa_asmbl_32899.p1
Valid prediction for snap_scaffold_24-snap.1050-T1
Valid prediction for CodingQuarry_transcript_37305-T1
Valid prediction for GlimmerHMM_glimmerT_52503-T1
Valid prediction for snap_scaffold_24-snap.1070-T1
Valid prediction for snap_scaffold_24-snap.1071-T1
Valid prediction for snap_scaffold_24-snap.1081-T1
Valid prediction for GlimmerHMM_glimmerT_52509-T1
Couldn't classify 134362, 134616
Sorry, prediction pasa_asmbl_32896.p1 fails validation.
(TCT)	 AC	134362-134616	GT	TGG
(GTG)	 AG	134865-134969	GT	TGG
(GCC)	 AG	135301-135393	GT	AGG
(GAA)	 AG	135522-135563	TT	GAT
-recovered pasa_asmbl_32896.p1, terminal, 135522, 135563
-recovered pasa_asmbl_32896.p1, internal, 134865, 134969
-recovered pasa_asmbl_32896.p1, internal, 135301, 135393
Valid prediction for snap_scaffold_24-snap.1052-T1
Valid prediction for GlimmerHMM_glimmerT_52500-T1
Couldn't classify 133973, 134046
Sorry, prediction pasa_asmbl_32897.p1 fails validation.
(ATG)	 CC	132031-132102	GT	TTG
(AAA)	 AG	132209-132337	GT	ACG
(GAA)	 AG	132472-132535	GT	AGG
(CGG)	 AG	132733-132863	GT	CGG
(TAC)	 AG	132962-133044	GT	AGG
(TCA)	 AG	133202-133385	GT	AGG
(GTC)	 AG	133572-133637	GT	GCG
(GGT)	 AG	133781-133883	GT	CGG
(GCG)	 AG	133973-134046	AC	GTA
-recovered pasa_asmbl_32897.p1, initial, 132031, 132102
-recovered pasa_asmbl_32897.p1, internal, 132209, 132337
-recovered pasa_asmbl_32897.p1, internal, 132472, 132535
-recovered pasa_asmbl_32897.p1, internal, 132733, 132863
-recovered pasa_asmbl_32897.p1, internal, 132962, 133044
-recovered pasa_asmbl_32897.p1, internal, 133202, 133385
-recovered pasa_asmbl_32897.p1, internal, 133572, 133637
-recovered pasa_asmbl_32897.p1, internal, 133781, 133883
Valid prediction for snap_scaffold_24-snap.1057-T1
Valid prediction for Augustus_model.g34971.t1
Couldn't classify 147907, 147965
Sorry, prediction pasa_asmbl_32887.p2 fails validation.
(GCA)	 AC	147907-147965	GT	ATG
(CTC)	 AG	148336-148468	GT	AGG
(CTG)	 AG	148610-148755	GT	AAG
(GAG)	 AG	148942-149006	GT	AGG
(ACT)	 AG	149139-149377	GT	GGG
(GTC)	 AG	149582-149643	GT	GAG
(TGT)	 AG	149802-149955	GT	TGG
(CTG)	 AG	150107-150200	GT	AGG
(AGT)	 AG	152707-152855	AG	GAA
-recovered pasa_asmbl_32887.p2, terminal, 152707, 152855
-recovered pasa_asmbl_32887.p2, internal, 148336, 148468
-recovered pasa_asmbl_32887.p2, internal, 148610, 148755
-recovered pasa_asmbl_32887.p2, internal, 148942, 149006
-recovered pasa_asmbl_32887.p2, internal, 149139, 149377
-recovered pasa_asmbl_32887.p2, internal, 149582, 149643
-recovered pasa_asmbl_32887.p2, internal, 149802, 149955
-recovered pasa_asmbl_32887.p2, internal, 150107, 150200
Valid prediction for snap_scaffold_24-snap.1059-T1
Valid prediction for GlimmerHMM_glimmerT_52516-T1
Valid prediction for snap_scaffold_24-snap.1074-T1
Couldn't classify 139140, 139247
Sorry, prediction pasa_asmbl_32895.p1 fails validation.
(ATG)	 AC	136795-136832	GT	AGG
(GCG)	 AG	138531-138684	GT	AGG
(GTG)	 AG	139140-139247	GA	GGG
-recovered pasa_asmbl_32895.p1, initial, 136795, 136832
-recovered pasa_asmbl_32895.p1, internal, 138531, 138684
Couldn't classify 141332, 141530
Sorry, prediction pasa_asmbl_32893.p1 fails validation.
(CGC)	 GC	141332-141530	GT	TGG
(AGT)	 AG	142493-142588	GT	CAG
(ATG)	 AG	142824-142939	GT	AGG
(GAG)	 AG	143161-143359	GT	CCG
(TGT)	 AG	143879-143983	GT	AGG
(ATT)	 AG	144627-144718	GG	AGG
-recovered pasa_asmbl_32893.p1, initial, 142824, 142939
-recovered pasa_asmbl_32893.p1, terminal, 144627, 144718
-recovered pasa_asmbl_32893.p1, internal, 142493, 142588
-recovered pasa_asmbl_32893.p1, internal, 142824, 142939
-recovered pasa_asmbl_32893.p1, internal, 143161, 143359
-recovered pasa_asmbl_32893.p1, internal, 143879, 143983
Valid prediction for snap_scaffold_24-snap.1062-T1
Valid prediction for snap_scaffold_24-snap.1051-T1
Valid prediction for snap_scaffold_24-snap.1056-T1
Valid prediction for HiQ_model.g34963.t1
Valid prediction for snap_scaffold_24-snap.1046-T1
Valid prediction for HiQ_model.g34965.t1
Valid prediction for Augustus_model.g34968.t1
Valid prediction for snap_scaffold_24-snap.1064-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 107265, rend_intergenic: 92658  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112129, rend_intergenic: 111247  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124165, rend_intergenic: 118604  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127927, rend_intergenic: 124766  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145658, rend_intergenic: 138679  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 194809, rend_intergenic: 191640  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 201404
-exon list size: 444


building trellis

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92.8    
93.0    
93.3    
93.5    
93.7    
93.9    
94.2    
94.4    
94.6    
94.8    
95.1    
95.3    
95.5    
95.7    
96.0    
96.2    
96.4    
96.6    
96.9    
97.1    
97.3    
97.5    
97.8    
98.0    
98.2    
98.4    
98.7    
98.9    
99.1    
99.3    
99.6    
99.8    
-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 107265, rend_intergenic: 92658  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112129, rend_intergenic: 111247  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124165, rend_intergenic: 118604  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127927, rend_intergenic: 124766  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145658, rend_intergenic: 138679  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 194809, rend_intergenic: 191640  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 28 predictions persist after filtering for low support