-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_6624072-6795317

-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.1328-T1
Valid prediction for Augustus_model.g35119.t1
Valid prediction for GlimmerHMM_glimmerT_52701-T1
Valid prediction for snap_scaffold_24-snap.1354-T1
Valid prediction for Augustus_model.g35111.t1
Valid prediction for Augustus_model.g35107.t1
Valid prediction for GlimmerHMM_glimmerT_52699-T1
Valid prediction for snap_scaffold_24-snap.1364-T1
Valid prediction for snap_scaffold_24-snap.1343-T1
Valid prediction for GlimmerHMM_glimmerT_52693-T1
Couldn't classify 152193, 152262
Sorry, prediction pasa_asmbl_32342.p1 fails validation.
(ACT)	 AC	152193-152262	GT	AGG
(GTA)	 AG	152830-152979	GT	AGG
(CTG)	 AG	153110-153230	GT	AAG
(GGA)	 AG	153363-153499	GT	AGG
(GCT)	 AG	153721-153855	GT	AGG
(GGT)	 AG	153956-154131	CT	AGC
add_exon() Sorry, pasa_asmbl_32342.p1 153363-153499-terminal-2 is invalid.
-recovered pasa_asmbl_32342.p1, terminal, 153363, 153499
-recovered pasa_asmbl_32342.p1, terminal, 153956, 154131
-recovered pasa_asmbl_32342.p1, internal, 152830, 152979
-recovered pasa_asmbl_32342.p1, internal, 153110, 153230
-recovered pasa_asmbl_32342.p1, internal, 153363, 153499
-recovered pasa_asmbl_32342.p1, internal, 153721, 153855
Valid prediction for Augustus_model.g35108.t1
Couldn't classify 95070, 95180
Couldn't classify 95647, 95746
Sorry, prediction pasa_asmbl_32336.p1 fails validation.
(TAC)	 CC	95070-95180	GT	ACG
(GTG)	 AG	95272-95394	GT	AGG
(CCT)	 AG	95469-95527	GT	AGG
(GGT)	 AG	95647-95746	CG	CCC
-recovered pasa_asmbl_32336.p1, internal, 95272, 95394
-recovered pasa_asmbl_32336.p1, internal, 95469, 95527
Valid prediction for GlimmerHMM_glimmerT_52710-T1
Valid prediction for snap_scaffold_24-snap.1338-T1
Valid prediction for snap_scaffold_24-snap.1367-T1
Valid prediction for Augustus_model.g35116.t1
Valid prediction for snap_scaffold_24-snap.1358-T1
Valid prediction for GlimmerHMM_glimmerT_52704-T1
Valid prediction for snap_scaffold_24-snap.1345-T1
Valid prediction for GlimmerHMM_glimmerT_52703-T1
Valid prediction for Augustus_model.g35106.t1
Valid prediction for Augustus_model.g35115.t1
Valid prediction for snap_scaffold_24-snap.1340-T1
Valid prediction for CodingQuarry_transcript_37339-T1
Valid prediction for snap_scaffold_24-snap.1348-T1
Couldn't classify 116458, 116518
Couldn't classify 118763, 118792
Sorry, prediction pasa_asmbl_32338.p1 fails validation.
(GTA)	 GT	116458-116518	GT	AGG
(CTG)	 AG	116677-116882	GT	AGG
(ATG)	 AG	117627-117787	GT	GAG
(TGT)	 AG	118085-118431	GT	AGG
(ACG)	 AG	118545-118678	GT	AGG
(GCG)	 AG	118763-118792	GA	TAG
-recovered pasa_asmbl_32338.p1, initial, 117627, 117787
-recovered pasa_asmbl_32338.p1, internal, 116677, 116882
-recovered pasa_asmbl_32338.p1, internal, 117627, 117787
-recovered pasa_asmbl_32338.p1, internal, 118085, 118431
-recovered pasa_asmbl_32338.p1, internal, 118545, 118678
Valid prediction for Augustus_model.g35114.t1
Valid prediction for GlimmerHMM_glimmerT_52706-T1
Valid prediction for snap_scaffold_24-snap.1336-T1
Valid prediction for snap_scaffold_24-snap.1330-T1
Valid prediction for Augustus_model.g35109.t1
Valid prediction for GlimmerHMM_glimmerT_52700-T1
Valid prediction for snap_scaffold_24-snap.1333-T1
Valid prediction for snap_scaffold_24-snap.1350-T1
Valid prediction for GlimmerHMM_glimmerT_52696-T1
Valid prediction for GlimmerHMM_glimmerT_52711-T1
Valid prediction for snap_scaffold_24-snap.1361-T1
Couldn't classify 167366, 167704
Sorry, prediction pasa_asmbl_32978.p1 fails validation.
(AGC)	 CC	167366-167704	GA	CGG
Valid prediction for snap_scaffold_24-snap.1332-T1
Valid prediction for Augustus_model.g35113.t1
Valid prediction for pasa_asmbl_32334.p1
Valid prediction for GlimmerHMM_glimmerT_52707-T1
Valid prediction for Augustus_model.g35118.t1
Valid prediction for Augustus_model.g35104.t1
Valid prediction for snap_scaffold_24-snap.1344-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_24-snap.1335-T1
Valid prediction for CodingQuarry_transcript_37341-T1
Valid prediction for HiQ_model.g35112.t1
Couldn't classify 11454, 11735
Sorry, prediction pasa_asmbl_32976.p1 fails validation.
(TCT)	 CT	11454-11735	GT	AGG
(GTG)	 AG	11836-11985	GT	TGG
(GGG)	 AG	12231-12319	GT	AGG
(ACC)	 AG	12903-13035	GT	AGG
(GTG)	 AG	13755-13962	GT	AGG
(CCA)	 AG	14045-14210	GT	AGG
(CAT)	 AG	14300-14433	GT	TGG
(TGG)	 AG	14609-14637	GA	AAG
-recovered pasa_asmbl_32976.p1, terminal, 14609, 14637
-recovered pasa_asmbl_32976.p1, internal, 11836, 11985
-recovered pasa_asmbl_32976.p1, internal, 12231, 12319
-recovered pasa_asmbl_32976.p1, internal, 12903, 13035
-recovered pasa_asmbl_32976.p1, internal, 13755, 13962
-recovered pasa_asmbl_32976.p1, internal, 14045, 14210
-recovered pasa_asmbl_32976.p1, internal, 14300, 14433
Valid prediction for Augustus_model.g35103.t1
Valid prediction for snap_scaffold_24-snap.1352-T1
Valid prediction for snap_scaffold_24-snap.1347-T1
Valid prediction for GlimmerHMM_glimmerT_52702-T1
Valid prediction for snap_scaffold_24-snap.1357-T1
Valid prediction for snap_scaffold_24-snap.1327-T1
Valid prediction for snap_scaffold_24-snap.1365-T1
Valid prediction for snap_scaffold_24-snap.1353-T1
Valid prediction for snap_scaffold_24-snap.1329-T1
Valid prediction for GlimmerHMM_glimmerT_52712-T1
Valid prediction for Augustus_model.g35110.t1
Couldn't classify 8731, 9150
Sorry, prediction pasa_asmbl_32977.p1 fails validation.
(AGG)	 TC	8731-9150	CC	CCC
Valid prediction for GlimmerHMM_glimmerT_52698-T1
Valid prediction for Augustus_model.g35120.t1
Valid prediction for snap_scaffold_24-snap.1346-T1
Valid prediction for snap_scaffold_24-snap.1369-T1
Valid prediction for snap_scaffold_24-snap.1337-T1
Valid prediction for GlimmerHMM_glimmerT_52697-T1
Valid prediction for snap_scaffold_24-snap.1362-T1
Valid prediction for GlimmerHMM_glimmerT_52709-T1
Valid prediction for snap_scaffold_24-snap.1356-T1
Valid prediction for snap_scaffold_24-snap.1360-T1
Valid prediction for Augustus_model.g35117.t1
Valid prediction for snap_scaffold_24-snap.1366-T1
Valid prediction for GlimmerHMM_glimmerT_52708-T1
Valid prediction for snap_scaffold_24-snap.1370-T1
Valid prediction for pasa_asmbl_32965.p1
Valid prediction for GlimmerHMM_glimmerT_52705-T1
Valid prediction for snap_scaffold_24-snap.1351-T1
Valid prediction for snap_scaffold_24-snap.1359-T1
Valid prediction for snap_scaffold_24-snap.1334-T1
Valid prediction for HiQ_model.g35105.t1
Valid prediction for snap_scaffold_24-snap.1349-T1
Valid prediction for CodingQuarry_transcript_37340-T1
Valid prediction for GlimmerHMM_glimmerT_52694-T1
Valid prediction for snap_scaffold_24-snap.1363-T1
Valid prediction for snap_scaffold_24-snap.1355-T1
Valid prediction for snap_scaffold_24-snap.1339-T1
Valid prediction for snap_scaffold_24-snap.1331-T1
Valid prediction for GlimmerHMM_glimmerT_52695-T1
Valid prediction for snap_scaffold_24-snap.1342-T1
Valid prediction for snap_scaffold_24-snap.1341-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 5544, rend_intergenic: 5215  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 8999, rend_intergenic: 5814  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20366, rend_intergenic: 9021  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25707, rend_intergenic: 21301  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31473, rend_intergenic: 26806  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34581, rend_intergenic: 31656  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41592, rend_intergenic: 39735  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57896, rend_intergenic: 52112  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65615, rend_intergenic: 58646  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73343, rend_intergenic: 72296  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74752, rend_intergenic: 74108  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96455, rend_intergenic: 83804  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123136, rend_intergenic: 110466  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139812, rend_intergenic: 127666  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147843, rend_intergenic: 142102  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149031, rend_intergenic: 148497  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154131, rend_intergenic: 150276  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163556, rend_intergenic: 156815  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 171246
-exon list size: 480


building trellis

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30.9    
31.1    
31.3    
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32.8    
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33.2    
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33.8    
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34.6    
34.9    
35.1    
35.3    
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35.9    
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85.3    
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86.3    
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97.9    
98.1    
98.3    
98.5    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 24 predictions from path traversal
Error with prediction: snap lend_intergenic: 5544, rend_intergenic: 5215  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 8999, rend_intergenic: 5814  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20366, rend_intergenic: 9021  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25707, rend_intergenic: 21301  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31473, rend_intergenic: 26806  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34581, rend_intergenic: 31656  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41592, rend_intergenic: 39735  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57896, rend_intergenic: 52112  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65615, rend_intergenic: 58646  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73343, rend_intergenic: 72296  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74752, rend_intergenic: 74108  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96455, rend_intergenic: 83804  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123136, rend_intergenic: 110466  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139812, rend_intergenic: 127666  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147843, rend_intergenic: 142102  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149031, rend_intergenic: 148497  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154131, rend_intergenic: 150276  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163556, rend_intergenic: 156815  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support