-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_13/scaffold_13_7255916-7558795

-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_13-snap.1354-T1
Valid prediction for HiQ_model.g21235.t1
Valid prediction for pasa_asmbl_11060.p2
Valid prediction for pasa_asmbl_11050.p1
Valid prediction for CodingQuarry_transcript_13111-T1
Valid prediction for GlimmerHMM_glimmerT_31880-T1
Valid prediction for CodingQuarry_transcript_13105-T1
Valid prediction for GlimmerHMM_glimmerT_31876-T1
Valid prediction for pasa_asmbl_11039.p1
Valid prediction for snap_scaffold_13-snap.1332-T1
Valid prediction for CodingQuarry_transcript_13108-T1
Valid prediction for Augustus_model.g21230.t1
Valid prediction for HiQ_model.g21233.t1
Valid prediction for snap_scaffold_13-snap.1362-T1
Valid prediction for snap_scaffold_13-snap.1337-T1
Valid prediction for snap_scaffold_13-snap.1347-T1
Valid prediction for GlimmerHMM_glimmerT_31867-T1
Valid prediction for snap_scaffold_13-snap.1345-T1
Valid prediction for GlimmerHMM_glimmerT_31865-T1
Valid prediction for GlimmerHMM_glimmerT_31885-T1
Couldn't classify 22541, 22677
Sorry, prediction pasa_asmbl_11033.p1 fails validation.
(ATG)	 CC	20255-20332	GT	AGG
(GAG)	 AG	20466-20628	GT	TGG
(GCA)	 AG	20749-20869	GT	AAG
(AGG)	 AG	21023-21097	GT	AGG
(AAC)	 AG	21193-21245	GT	GAG
(ATG)	 AG	21342-21487	GT	CAG
(AAC)	 AG	21788-21885	GT	AGG
(GGT)	 AG	22014-22113	GC	AGG
(GTG)	 AG	22233-22359	GT	AGG
(GGG)	 AG	22541-22677	TA	CCT
-recovered pasa_asmbl_11033.p1, initial, 20255, 20332
add_exon() Sorry, pasa_asmbl_11033.p1 21342-21487-initial-1 is invalid.
-recovered pasa_asmbl_11033.p1, initial, 21342, 21487
-recovered pasa_asmbl_11033.p1, internal, 20466, 20628
-recovered pasa_asmbl_11033.p1, internal, 20749, 20869
-recovered pasa_asmbl_11033.p1, internal, 21023, 21097
-recovered pasa_asmbl_11033.p1, internal, 21193, 21245
-recovered pasa_asmbl_11033.p1, internal, 21342, 21487
-recovered pasa_asmbl_11033.p1, internal, 21788, 21885
-recovered pasa_asmbl_11033.p1, internal, 22014, 22113
-recovered pasa_asmbl_11033.p1, internal, 22233, 22359
Valid prediction for Augustus_model.g21226.t1
Valid prediction for snap_scaffold_13-snap.1342-T1
Valid prediction for GlimmerHMM_glimmerT_31884-T1
Valid prediction for GlimmerHMM_glimmerT_31871-T1
Valid prediction for GlimmerHMM_glimmerT_31872-T1
Valid prediction for pasa_asmbl_11047.p1
Valid prediction for GlimmerHMM_glimmerT_31866-T1
Valid prediction for CodingQuarry_transcript_13113-T1
Valid prediction for GlimmerHMM_glimmerT_31877-T1
Valid prediction for Augustus_model.g21236.t1
Valid prediction for snap_scaffold_13-snap.1361-T1
Valid prediction for snap_scaffold_13-snap.1329-T1
Valid prediction for snap_scaffold_13-snap.1359-T1
Valid prediction for snap_scaffold_13-snap.1343-T1
Valid prediction for snap_scaffold_13-snap.1336-T1
Valid prediction for GlimmerHMM_glimmerT_31883-T1
Valid prediction for snap_scaffold_13-snap.1339-T1
Valid prediction for snap_scaffold_13-snap.1324-T1
Valid prediction for snap_scaffold_13-snap.1341-T1
Valid prediction for snap_scaffold_13-snap.1319-T1
Valid prediction for Augustus_model.g21234.t1
Valid prediction for HiQ_model.g21228.t1
Valid prediction for pasa_asmbl_11059.p1
Valid prediction for snap_scaffold_13-snap.1322-T1
Couldn't classify 37588, 37707
Sorry, prediction pasa_asmbl_11038.p1 fails validation.
(ATG)	 AG	36419-36557	GT	GGG
(GTG)	 AG	36803-36875	GT	GAG
(AGA)	 AG	37412-37466	GT	TGG
(ACT)	 AG	37588-37707	GT	AGG
-recovered pasa_asmbl_11038.p1, initial, 36419, 36557
-recovered pasa_asmbl_11038.p1, internal, 36419, 36557
-recovered pasa_asmbl_11038.p1, internal, 36803, 36875
-recovered pasa_asmbl_11038.p1, internal, 37412, 37466
-recovered pasa_asmbl_11038.p1, internal, 37588, 37707
Valid prediction for Augustus_model.g21237.t1
Valid prediction for GlimmerHMM_glimmerT_31882-T1
Valid prediction for pasa_asmbl_11041.p1
Couldn't classify 105042, 105193
Sorry, prediction pasa_asmbl_11040.p1 fails validation.
(GAA)	 TG	105042-105193	GT	AGG
(GAA)	 AG	105316-105441	GT	GTG
(GGT)	 AG	105625-105713	GT	CAG
(AAA)	 AG	105789-105999	GT	GGG
(GAT)	 AG	106217-106469	GC	GAG
-recovered pasa_asmbl_11040.p1, terminal, 106217, 106469
-recovered pasa_asmbl_11040.p1, internal, 105316, 105441
-recovered pasa_asmbl_11040.p1, internal, 105625, 105713
-recovered pasa_asmbl_11040.p1, internal, 105789, 105999
-recovered pasa_asmbl_11040.p1, internal, 106217, 106469
Valid prediction for GlimmerHMM_glimmerT_31860-T1
Valid prediction for snap_scaffold_13-snap.1330-T1
Valid prediction for snap_scaffold_13-snap.1333-T1
Valid prediction for Augustus_model.g21223.t1
Valid prediction for Augustus_model.g21229.t1
Valid prediction for GlimmerHMM_glimmerT_31888-T1
Valid prediction for GlimmerHMM_glimmerT_31881-T1
Valid prediction for snap_scaffold_13-snap.1351-T1
Valid prediction for CodingQuarry_transcript_13114-T1
Couldn't classify 31829, 32281
Sorry, prediction pasa_asmbl_11036.p1 fails validation.
(ATG)	 AC	31829-32281	AC	AGA
Valid prediction for snap_scaffold_13-snap.1325-T1
Valid prediction for GlimmerHMM_glimmerT_31890-T1
Valid prediction for HiQ_model.g21219.t1
Valid prediction for snap_scaffold_13-snap.1344-T1
Valid prediction for snap_scaffold_13-snap.1356-T1
Valid prediction for GlimmerHMM_glimmerT_31879-T1
Valid prediction for pasa_asmbl_11057.p1
Valid prediction for Augustus_model.g21243.t1
Valid prediction for GlimmerHMM_glimmerT_31864-T1
Couldn't classify 193547, 193649
Sorry, prediction pasa_asmbl_11054.p1 fails validation.
(CAG)	 AA	193547-193649	GT	GGG
(GCA)	 AG	195027-195287	GT	AGG
(ACA)	 AG	195794-195975	AG	GAA
-recovered pasa_asmbl_11054.p1, terminal, 195794, 195975
-recovered pasa_asmbl_11054.p1, internal, 195027, 195287
Valid prediction for GlimmerHMM_glimmerT_31894-T1
Valid prediction for GlimmerHMM_glimmerT_31875-T1
Valid prediction for GlimmerHMM_glimmerT_31873-T1
Valid prediction for Augustus_model.g21221.t1
Valid prediction for GlimmerHMM_glimmerT_31868-T1
Valid prediction for snap_scaffold_13-snap.1346-T1
Valid prediction for Augustus_model.g21222.t1
Valid prediction for HiQ_model.g21232.t1
Valid prediction for snap_scaffold_13-snap.1348-T1
Valid prediction for CodingQuarry_transcript_13112-T1
Valid prediction for snap_scaffold_13-snap.1328-T1
Valid prediction for Augustus_model.g21218.t1
Valid prediction for CodingQuarry_transcript_13110-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 CodingQuarry_transcript_13103-T1
Valid prediction for Augustus_model.g21238.t1
Valid prediction for GlimmerHMM_glimmerT_31887-T1
Valid prediction for snap_scaffold_13-snap.1349-T1
Valid prediction for snap_scaffold_13-snap.1335-T1
Valid prediction for HiQ_model.g21227.t1
Valid prediction for Augustus_model.g21244.t1
Couldn't classify 39857, 40015
Couldn't classify 47113, 47318
Sorry, prediction pasa_asmbl_10378.p1 fails validation.
(ACT)	 CG	39857-40015	GT	AGG
(GGG)	 AG	41084-41227	GT	AGG
(AAG)	 AG	43434-43538	GT	AGG
(AAT)	 AG	43720-43762	GT	GGG
(CTG)	 AG	43873-43948	GT	AGG
(GTA)	 AG	44398-44616	GT	AAG
(GGG)	 AG	44823-44910	GT	AGG
(GAT)	 AG	45584-45736	GT	AGG
(TTT)	 AG	45860-45957	GT	AGG
(GTT)	 AG	46066-46241	GT	AGG
(CCC)	 AG	47113-47318	GT	AGG
add_exon() Sorry, pasa_asmbl_10378.p1 43873-43948-terminal-3 is invalid.
-recovered pasa_asmbl_10378.p1, terminal, 43873, 43948
-recovered pasa_asmbl_10378.p1, internal, 41084, 41227
-recovered pasa_asmbl_10378.p1, internal, 43434, 43538
-recovered pasa_asmbl_10378.p1, internal, 43720, 43762
-recovered pasa_asmbl_10378.p1, internal, 43873, 43948
-recovered pasa_asmbl_10378.p1, internal, 44398, 44616
-recovered pasa_asmbl_10378.p1, internal, 44823, 44910
-recovered pasa_asmbl_10378.p1, internal, 45584, 45736
-recovered pasa_asmbl_10378.p1, internal, 45860, 45957
-recovered pasa_asmbl_10378.p1, internal, 46066, 46241
-recovered pasa_asmbl_10378.p1, internal, 47113, 47318
Valid prediction for snap_scaffold_13-snap.1331-T1
Valid prediction for CodingQuarry_transcript_13118-T1
Valid prediction for pasa_asmbl_9872.p1
Valid prediction for GlimmerHMM_glimmerT_31863-T1
Couldn't classify 51347, 51529
Sorry, prediction pasa_asmbl_9892.p1 fails validation.
(ACG)	 AC	51347-51529	GT	ATG
(GAT)	 AG	52023-52085	GT	AGG
(ACA)	 AG	54450-54509	GT	CGG
(GAG)	 AG	56351-56443	GT	AGG
(GCC)	 AG	56567-56665	GT	AGG
(ACG)	 AG	56775-56855	GT	AGG
(GCT)	 AG	57215-57325	CC	GAC
-recovered pasa_asmbl_9892.p1, terminal, 57215, 57325
-recovered pasa_asmbl_9892.p1, internal, 52023, 52085
-recovered pasa_asmbl_9892.p1, internal, 54450, 54509
-recovered pasa_asmbl_9892.p1, internal, 56351, 56443
-recovered pasa_asmbl_9892.p1, internal, 56567, 56665
-recovered pasa_asmbl_9892.p1, internal, 56775, 56855
Valid prediction for Augustus_model.g21241.t1
Couldn't classify 238159, 238313
Sorry, prediction pasa_asmbl_9875.p1 fails validation.
(AAG)	 CA	238159-238313	GT	AAG
(GAC)	 AG	238502-238665	GT	AGG
(ACC)	 AG	238903-239082	GT	GAG
(AAT)	 AG	239179-239326	GC	AGG
(CTG)	 AG	239527-239692	GT	GGG
(GGA)	 AG	239793-239906	TG	AGT
-recovered pasa_asmbl_9875.p1, terminal, 239793, 239906
-recovered pasa_asmbl_9875.p1, internal, 238502, 238665
-recovered pasa_asmbl_9875.p1, internal, 238903, 239082
-recovered pasa_asmbl_9875.p1, internal, 239179, 239326
-recovered pasa_asmbl_9875.p1, internal, 239527, 239692
Valid prediction for snap_scaffold_13-snap.1350-T1
Valid prediction for snap_scaffold_13-snap.1352-T1
Valid prediction for GlimmerHMM_glimmerT_31892-T1
Valid prediction for HiQ_model.g21225.t1
Valid prediction for Augustus_model.g21224.t1
Valid prediction for GlimmerHMM_glimmerT_31870-T1
Valid prediction for Augustus_model.g21242.t1
Valid prediction for GlimmerHMM_glimmerT_31886-T1
Valid prediction for HiQ_model.g21231.t1
Valid prediction for GlimmerHMM_glimmerT_31869-T1
Valid prediction for snap_scaffold_13-snap.1338-T1
Valid prediction for snap_scaffold_13-snap.1357-T1
Valid prediction for GlimmerHMM_glimmerT_31893-T1
Valid prediction for CodingQuarry_transcript_13106-T1
Valid prediction for Augustus_model.g21220.t1
Valid prediction for Augustus_model.g21239.t1
Valid prediction for GlimmerHMM_glimmerT_31862-T1
Valid prediction for snap_scaffold_13-snap.1326-T1
Valid prediction for snap_scaffold_13-snap.1340-T1
Valid prediction for HiQ_model.g21217.t1
Valid prediction for GlimmerHMM_glimmerT_31878-T1
Valid prediction for CodingQuarry_transcript_13116-T1
Valid prediction for pasa_asmbl_9876.p1
Valid prediction for GlimmerHMM_glimmerT_31861-T1
Valid prediction for pasa_asmbl_9878.p1
Valid prediction for CodingQuarry_transcript_13104-T1
Valid prediction for GlimmerHMM_glimmerT_31874-T1
Valid prediction for pasa_asmbl_9867.p1
Valid prediction for snap_scaffold_13-snap.1355-T1
Valid prediction for snap_scaffold_13-snap.1334-T1
Valid prediction for GlimmerHMM_glimmerT_31891-T1
Valid prediction for GlimmerHMM_glimmerT_31889-T1
Valid prediction for snap_scaffold_13-snap.1323-T1
Valid prediction for CodingQuarry_transcript_13117-T1
Valid prediction for snap_scaffold_13-snap.1321-T1
Valid prediction for snap_scaffold_13-snap.1353-T1
Valid prediction for snap_scaffold_13-snap.1320-T1
Valid prediction for snap_scaffold_13-snap.1358-T1
Valid prediction for Augustus_model.g21240.t1
Valid prediction for CodingQuarry_transcript_13107-T1
Valid prediction for CodingQuarry_transcript_13109-T1
Valid prediction for HiQ_model.g21216.t1
Valid prediction for snap_scaffold_13-snap.1327-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 250265, rend_intergenic: 245556  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 263030, rend_intergenic: 259555  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 302880
-exon list size: 556


building trellis

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91.0    
91.2    
91.4    
91.6    
91.8    
91.9    
92.1    
92.3    
92.5    
92.7    
92.8    
93.0    
93.2    
93.4    
93.5    
93.7    
93.9    
94.1    
94.3    
94.4    
94.6    
94.8    
95.0    
95.2    
95.3    
95.5    
95.7    
95.9    
96.1    
96.2    
96.4    
96.6    
96.8    
97.0    
97.1    
97.3    
97.5    
97.7    
97.8    
98.0    
98.2    
98.4    
98.6    
98.7    
98.9    
99.1    
99.3    
99.5    
99.6    
99.8    
-found 41 predictions from path traversal
Error with prediction: snap lend_intergenic: 250265, rend_intergenic: 245556  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 263030, rend_intergenic: 259555  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 39 predictions persist after filtering for low support