-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_16/scaffold_16_7698717-7952362

-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 Augustus_model.g25765.t1
Valid prediction for snap_scaffold_16-snap.1446-T1
Valid prediction for snap_scaffold_16-snap.1415-T1
Valid prediction for Augustus_model.g25756.t1
Valid prediction for GlimmerHMM_glimmerT_38598-T1
Valid prediction for GlimmerHMM_glimmerT_38623-T1
Valid prediction for GlimmerHMM_glimmerT_38620-T1
Valid prediction for Augustus_model.g25767.t1
Valid prediction for GlimmerHMM_glimmerT_38605-T1
Valid prediction for GlimmerHMM_glimmerT_38604-T1
Valid prediction for Augustus_model.g25769.t1
Valid prediction for snap_scaffold_16-snap.1421-T1
Valid prediction for snap_scaffold_16-snap.1433-T1
Valid prediction for GlimmerHMM_glimmerT_38600-T1
Couldn't classify 128722, 128865
Sorry, prediction pasa_asmbl_16357.p1 fails validation.
(ATG)	 TC	126594-126745	GT	AAG
(GGG)	 AG	126952-127033	GT	AGG
(AAC)	 AG	127128-127247	GT	AGG
(GGA)	 AG	127432-127576	GT	AGG
(GGC)	 AG	127785-127930	GT	CGG
(GCT)	 AG	128520-128645	GT	AGG
(GAG)	 AG	128722-128865	AC	ACA
-recovered pasa_asmbl_16357.p1, initial, 126594, 126745
-recovered pasa_asmbl_16357.p1, internal, 126952, 127033
-recovered pasa_asmbl_16357.p1, internal, 127128, 127247
-recovered pasa_asmbl_16357.p1, internal, 127432, 127576
-recovered pasa_asmbl_16357.p1, internal, 127785, 127930
-recovered pasa_asmbl_16357.p1, internal, 128520, 128645
Valid prediction for GlimmerHMM_glimmerT_38612-T1
Valid prediction for snap_scaffold_16-snap.1414-T1
Valid prediction for snap_scaffold_16-snap.1425-T1
Valid prediction for GlimmerHMM_glimmerT_38607-T1
Valid prediction for snap_scaffold_16-snap.1427-T1
Valid prediction for GlimmerHMM_glimmerT_38618-T1
Valid prediction for CodingQuarry_transcript_20012-T1
Valid prediction for snap_scaffold_16-snap.1408-T1
Valid prediction for snap_scaffold_16-snap.1409-T1
Valid prediction for snap_scaffold_16-snap.1447-T1
Valid prediction for snap_scaffold_16-snap.1431-T1
Valid prediction for Augustus_model.g25757.t1
Valid prediction for snap_scaffold_16-snap.1422-T1
Valid prediction for snap_scaffold_16-snap.1406-T1
Valid prediction for snap_scaffold_16-snap.1416-T1
Valid prediction for snap_scaffold_16-snap.1445-T1
Valid prediction for GlimmerHMM_glimmerT_38591-T1
Valid prediction for snap_scaffold_16-snap.1418-T1
Valid prediction for GlimmerHMM_glimmerT_38592-T1
Valid prediction for snap_scaffold_16-snap.1450-T1
Valid prediction for pasa_asmbl_16360.p1
Valid prediction for snap_scaffold_16-snap.1434-T1
Valid prediction for snap_scaffold_16-snap.1426-T1
Valid prediction for snap_scaffold_16-snap.1452-T1
Couldn't classify 9088, 9865
Sorry, prediction pasa_asmbl_16355.p1 fails validation.
(GGA)	 CA	9088-9865	GT	TAG
(ATT)	 AG	10251-10276	CT	GAC
-recovered pasa_asmbl_16355.p1, terminal, 10251, 10276
Valid prediction for HiQ_model.g25774.t1
Couldn't classify 246048, 246306
Couldn't classify 247556, 247627
Sorry, prediction pasa_asmbl_16363.p1 fails validation.
(ACT)	 CG	246048-246306	GT	GGG
(ATC)	 AG	246538-246611	GT	AGG
(GGC)	 AG	246777-246951	GT	AGG
(ACT)	 AG	247076-247177	GT	AGG
(ATC)	 AG	247249-247424	GT	AGG
(CCT)	 AG	247556-247627	GT	AGG
-recovered pasa_asmbl_16363.p1, internal, 246538, 246611
-recovered pasa_asmbl_16363.p1, internal, 246777, 246951
-recovered pasa_asmbl_16363.p1, internal, 247076, 247177
-recovered pasa_asmbl_16363.p1, internal, 247249, 247424
-recovered pasa_asmbl_16363.p1, internal, 247556, 247627
Valid prediction for snap_scaffold_16-snap.1424-T1
Valid prediction for GlimmerHMM_glimmerT_38611-T1
Valid prediction for GlimmerHMM_glimmerT_38625-T1
Valid prediction for Augustus_model.g25777.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 GlimmerHMM_glimmerT_38621-T1
Valid prediction for Augustus_model.g25764.t1
Valid prediction for Augustus_model.g25762.t1
Valid prediction for GlimmerHMM_glimmerT_38606-T1
Valid prediction for snap_scaffold_16-snap.1423-T1
Valid prediction for snap_scaffold_16-snap.1444-T1
Valid prediction for Augustus_model.g25760.t1
Valid prediction for GlimmerHMM_glimmerT_38624-T1
Valid prediction for GlimmerHMM_glimmerT_38590-T1
Valid prediction for snap_scaffold_16-snap.1428-T1
Valid prediction for GlimmerHMM_glimmerT_38613-T1
Valid prediction for GlimmerHMM_glimmerT_38602-T1
Valid prediction for snap_scaffold_16-snap.1443-T1
Valid prediction for GlimmerHMM_glimmerT_38617-T1
Valid prediction for snap_scaffold_16-snap.1439-T1
Valid prediction for snap_scaffold_16-snap.1410-T1
Valid prediction for snap_scaffold_16-snap.1437-T1
Valid prediction for CodingQuarry_transcript_20013-T1
Valid prediction for Augustus_model.g25768.t1
Valid prediction for snap_scaffold_16-snap.1419-T1
Valid prediction for Augustus_model.g25761.t1
Valid prediction for snap_scaffold_16-snap.1449-T1
Valid prediction for snap_scaffold_16-snap.1432-T1
Valid prediction for GlimmerHMM_glimmerT_38597-T1
Valid prediction for Augustus_model.g25766.t1
Valid prediction for GlimmerHMM_glimmerT_38595-T1
Valid prediction for Augustus_model.g25775.t1
Valid prediction for GlimmerHMM_glimmerT_38593-T1
Valid prediction for snap_scaffold_16-snap.1435-T1
Valid prediction for Augustus_model.g25758.t1
Valid prediction for Augustus_model.g25776.t1
Couldn't classify 34197, 34284
Sorry, prediction pasa_asmbl_17206.p1 fails validation.
(GTG)	 CA	34197-34284	GT	AGG
(ATG)	 AG	34448-35491	GT	GGG
(GGC)	 AG	35675-36160	GT	AGG
(GTT)	 AG	36322-36458	GT	AGG
(AAA)	 AG	36672-36781	GT	ACG
(GAA)	 AG	36963-37108	GT	CTG
(ACC)	 AG	37261-37310	GT	GAG
add_exon() Sorry, pasa_asmbl_17206.p1 34448-35491-initial-1 is invalid.
-recovered pasa_asmbl_17206.p1, initial, 34448, 35491
-recovered pasa_asmbl_17206.p1, terminal, 37261, 37310
-recovered pasa_asmbl_17206.p1, internal, 34448, 35491
-recovered pasa_asmbl_17206.p1, internal, 35675, 36160
-recovered pasa_asmbl_17206.p1, internal, 36322, 36458
-recovered pasa_asmbl_17206.p1, internal, 36672, 36781
-recovered pasa_asmbl_17206.p1, internal, 36963, 37108
-recovered pasa_asmbl_17206.p1, internal, 37261, 37310
Valid prediction for Augustus_model.g25772.t1
Valid prediction for snap_scaffold_16-snap.1451-T1
Valid prediction for snap_scaffold_16-snap.1436-T1
Valid prediction for GlimmerHMM_glimmerT_38626-T1
Valid prediction for GlimmerHMM_glimmerT_38599-T1
Valid prediction for snap_scaffold_16-snap.1448-T1
Valid prediction for GlimmerHMM_glimmerT_38619-T1
Valid prediction for pasa_asmbl_17208.p1
Valid prediction for Augustus_model.g25763.t1
Couldn't classify 247877, 247937
Sorry, prediction pasa_asmbl_17189.p1 fails validation.
(ACA)	 GA	247877-247937	GT	AGG
(ACT)	 AG	248349-248391	GT	TGG
(CGT)	 AG	248492-248531	GT	AGG
(TTG)	 AG	248633-248763	GT	CTG
(CCA)	 AG	248917-249008	GT	TGG
(AGT)	 AG	249193-249314	GT	AAG
(GTA)	 AG	249514-249672	GT	AGG
(AAG)	 AG	250083-250259	CT	GAC
-recovered pasa_asmbl_17189.p1, terminal, 250083, 250259
-recovered pasa_asmbl_17189.p1, internal, 248349, 248391
-recovered pasa_asmbl_17189.p1, internal, 248492, 248531
-recovered pasa_asmbl_17189.p1, internal, 248633, 248763
-recovered pasa_asmbl_17189.p1, internal, 248917, 249008
-recovered pasa_asmbl_17189.p1, internal, 249193, 249314
-recovered pasa_asmbl_17189.p1, internal, 249514, 249672
Valid prediction for snap_scaffold_16-snap.1438-T1
Valid prediction for Augustus_model.g25773.t1
Valid prediction for snap_scaffold_16-snap.1407-T1
Valid prediction for GlimmerHMM_glimmerT_38609-T1
Valid prediction for GlimmerHMM_glimmerT_38596-T1
Valid prediction for snap_scaffold_16-snap.1405-T1
Valid prediction for snap_scaffold_16-snap.1430-T1
Valid prediction for snap_scaffold_16-snap.1412-T1
Couldn't classify 118733, 118822
Sorry, prediction pasa_asmbl_17200.p1 fails validation.
(CAG)	 TT	118733-118822	GT	CTG
(GAG)	 AG	119467-119649	GT	AGG
(GGC)	 AG	120894-121610	CA	GAC
-recovered pasa_asmbl_17200.p1, terminal, 120894, 121610
-recovered pasa_asmbl_17200.p1, internal, 119467, 119649
Valid prediction for GlimmerHMM_glimmerT_38622-T1
Valid prediction for GlimmerHMM_glimmerT_38610-T1
Valid prediction for snap_scaffold_16-snap.1441-T1
Valid prediction for HiQ_model.g25778.t1
Valid prediction for GlimmerHMM_glimmerT_38615-T1
Valid prediction for snap_scaffold_16-snap.1429-T1
Couldn't classify 112813, 112849
Couldn't classify 117678, 117772
Sorry, prediction pasa_asmbl_17201.p1 fails validation.
(GTT)	 TC	112813-112849	GT	TGG
(CTA)	 AG	113366-113499	GT	AGG
(ACG)	 AG	115751-115831	GT	AGG
(GTG)	 AG	115978-116036	GT	AGG
(GAT)	 AG	116512-116621	GT	AGG
(CTG)	 AG	117678-117772	CT	AGC
add_exon() Sorry, pasa_asmbl_17201.p1 116512-116621-terminal-2 is invalid.
-recovered pasa_asmbl_17201.p1, terminal, 116512, 116621
-recovered pasa_asmbl_17201.p1, internal, 113366, 113499
-recovered pasa_asmbl_17201.p1, internal, 115751, 115831
-recovered pasa_asmbl_17201.p1, internal, 115978, 116036
-recovered pasa_asmbl_17201.p1, internal, 116512, 116621
Valid prediction for Augustus_model.g25770.t1
Valid prediction for snap_scaffold_16-snap.1420-T1
Valid prediction for GlimmerHMM_glimmerT_38608-T1
Valid prediction for Augustus_model.g25771.t1
Valid prediction for snap_scaffold_16-snap.1411-T1
Valid prediction for snap_scaffold_16-snap.1442-T1
Valid prediction for snap_scaffold_16-snap.1413-T1
Couldn't classify 57985, 58015
Couldn't classify 59708, 59853
Sorry, prediction pasa_asmbl_17205.p1 fails validation.
(CAA)	 AG	57985-58015	GT	CTG
(TGG)	 AG	58396-58553	GT	AGG
(GAT)	 AG	58828-58944	GT	CTG
(GGT)	 AG	59130-59245	GT	AGG
(ATA)	 AG	59362-59510	GT	AGG
(ACA)	 AG	59708-59853	CT	CCC
add_exon() Sorry, pasa_asmbl_17205.p1 59130-59245-terminal-2 is invalid.
-recovered pasa_asmbl_17205.p1, terminal, 59130, 59245
-recovered pasa_asmbl_17205.p1, internal, 57985, 58015
-recovered pasa_asmbl_17205.p1, internal, 58396, 58553
-recovered pasa_asmbl_17205.p1, internal, 58828, 58944
-recovered pasa_asmbl_17205.p1, internal, 59130, 59245
-recovered pasa_asmbl_17205.p1, internal, 59362, 59510
Valid prediction for GlimmerHMM_glimmerT_38616-T1
Valid prediction for GlimmerHMM_glimmerT_38594-T1
Valid prediction for GlimmerHMM_glimmerT_38601-T1
Valid prediction for GlimmerHMM_glimmerT_38614-T1
Valid prediction for snap_scaffold_16-snap.1453-T1
Valid prediction for Augustus_model.g25759.t1
Valid prediction for snap_scaffold_16-snap.1417-T1
Valid prediction for snap_scaffold_16-snap.1440-T1
Valid prediction for GlimmerHMM_glimmerT_38603-T1
Valid prediction for HiQ_model.g25755.t1
Valid prediction for pasa_asmbl_17204.p1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 27072, rend_intergenic: 14686  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54669, rend_intergenic: 49703  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82526, rend_intergenic: 75711  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105694, rend_intergenic: 98954  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119465, rend_intergenic: 117469  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134285, rend_intergenic: 132037  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151568, rend_intergenic: 147467  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163944, rend_intergenic: 156821  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170061, rend_intergenic: 166706  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 205947, rend_intergenic: 205702  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 238989, rend_intergenic: 235803  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 253646
-exon list size: 501


building trellis

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95.8    
96.0    
96.2    
96.4    
96.6    
96.8    
97.0    
97.2    
97.4    
97.6    
97.8    
98.0    
98.2    
98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 37 predictions from path traversal
Error with prediction: snap lend_intergenic: 27072, rend_intergenic: 14686  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54669, rend_intergenic: 49703  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82526, rend_intergenic: 75711  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105694, rend_intergenic: 98954  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119465, rend_intergenic: 117469  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134285, rend_intergenic: 132037  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151568, rend_intergenic: 147467  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163944, rend_intergenic: 156821  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170061, rend_intergenic: 166706  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 205947, rend_intergenic: 205702  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 238989, rend_intergenic: 235803  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