-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_7/scaffold_7_6473936-6712960

-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 GeneMark_model.30178_t
Valid prediction for GeneMark_model.30173_t
Valid prediction for snap_scaffold_7-snap.1396-T1
Valid prediction for snap_scaffold_7-snap.1383-T1
Valid prediction for GlimmerHMM_glimmerT_17994-T1
Valid prediction for Augustus_model.g12073.t1
Valid prediction for GeneMark_model.30194_t
Valid prediction for GlimmerHMM_glimmerT_17978-T1
Valid prediction for GeneMark_model.30163_t
Valid prediction for Augustus_model.g12075.t1
Valid prediction for snap_scaffold_7-snap.1358-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for HiQ_model.g12074.t1
Valid prediction for snap_scaffold_7-snap.1359-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for Augustus_model.g12084.t1
Valid prediction for GeneMark_model.30171_t
Valid prediction for GlimmerHMM_glimmerT_17993-T1
Valid prediction for snap_scaffold_7-snap.1360-T1
Valid prediction for snap_scaffold_7-snap.1372-T1
Valid prediction for GlimmerHMM_glimmerT_17987-T1
Valid prediction for GeneMark_model.30183_t
Valid prediction for GeneMark_model.30169_t
Valid prediction for GeneMark_model.30192_t
Couldn't classify 149461, 149594
Sorry, prediction pasa_asmbl_50753.p1 fails validation.
(CTC)	 CC	149461-149594	GT	GGG
(GTA)	 AG	151894-152023	GT	AGG
(GCC)	 AG	152518-152619	GT	AGG
(ATT)	 AG	152803-153000	GT	GGG
(GAG)	 AG	153122-153310	GT	TGG
(TTC)	 AG	154728-154739	CG	GAC
-recovered pasa_asmbl_50753.p1, terminal, 154728, 154739
-recovered pasa_asmbl_50753.p1, internal, 151894, 152023
-recovered pasa_asmbl_50753.p1, internal, 152518, 152619
-recovered pasa_asmbl_50753.p1, internal, 152803, 153000
-recovered pasa_asmbl_50753.p1, internal, 153122, 153310
Valid prediction for snap_scaffold_7-snap.1378-T1
Valid prediction for pasa_asmbl_50756.p1
Valid prediction for Augustus_model.g12083.t1
Valid prediction for Augustus_model.g12081.t1
Valid prediction for snap_scaffold_7-snap.1381-T1
Valid prediction for GeneMark_model.30160_t
Valid prediction for GlimmerHMM_glimmerT_17985-T1
Valid prediction for snap_scaffold_7-snap.1361-T1
Valid prediction for GeneMark_model.30175_t
Valid prediction for GlimmerHMM_glimmerT_17992-T1
Valid prediction for GlimmerHMM_glimmerT_17981-T1
Valid prediction for snap_scaffold_7-snap.1366-T1
Valid prediction for snap_scaffold_7-snap.1379-T1
Valid prediction for GeneMark_model.30157_t
Valid prediction for GeneMark_model.30185_t
Valid prediction for GlimmerHMM_glimmerT_17988-T1
Valid prediction for GlimmerHMM_glimmerT_17968-T1
Valid prediction for snap_scaffold_7-snap.1365-T1
Valid prediction for Augustus_model.g12060.t1
Valid prediction for snap_scaffold_7-snap.1380-T1
Valid prediction for GeneMark_model.30180_t
Valid prediction for snap_scaffold_7-snap.1392-T1
Valid prediction for GeneMark_model.30156_t
Valid prediction for GeneMark_model.30170_t
Valid prediction for GeneMark_model.30162_t
Valid prediction for GeneMark_model.30190_t
Valid prediction for GeneMark_model.30159_t

-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_7-snap.1389-T1
Valid prediction for snap_scaffold_7-snap.1397-T1
Valid prediction for Augustus_model.g12068.t1
Valid prediction for Augustus_model.g12078.t1
Valid prediction for GeneMark_model.30161_t
Valid prediction for GlimmerHMM_glimmerT_17989-T1
Valid prediction for snap_scaffold_7-snap.1371-T1
Valid prediction for CodingQuarry_transcript_57379-T1
Valid prediction for pasa_asmbl_49744.p1
Valid prediction for Augustus_model.g12076.t1
Valid prediction for snap_scaffold_7-snap.1376-T1
Valid prediction for GeneMark_model.30165_t
Couldn't classify 195967, 196719
Sorry, prediction pasa_asmbl_49729.p1 fails validation.
(TTC)	 AC	195967-196719	TT	TGT
Valid prediction for snap_scaffold_7-snap.1382-T1
Valid prediction for CodingQuarry_transcript_57378-T1
Valid prediction for snap_scaffold_7-snap.1374-T1
Valid prediction for GlimmerHMM_glimmerT_17977-T1
Valid prediction for Augustus_model.g12069.t1
Valid prediction for GlimmerHMM_glimmerT_17976-T1
Valid prediction for snap_scaffold_7-snap.1375-T1
Valid prediction for snap_scaffold_7-snap.1385-T1
Valid prediction for Augustus_model.g12065.t1
Valid prediction for snap_scaffold_7-snap.1370-T1
Valid prediction for Augustus_model.g12077.t1
Valid prediction for GeneMark_model.30176_t
Valid prediction for GeneMark_model.30193_t
Couldn't classify 133757, 134116
Sorry, prediction pasa_asmbl_49734.p1 fails validation.
(ATG)	 CC	133757-134116	AA	AGA
Valid prediction for GeneMark_model.30181_t
Valid prediction for snap_scaffold_7-snap.1395-T1
Valid prediction for GlimmerHMM_glimmerT_17984-T1
Couldn't classify 76761, 77003
Sorry, prediction pasa_asmbl_49737.p1 fails validation.
(ACG)	 AG	76761-77003	GT	AGG
(GTC)	 AG	78244-78348	GT	AGG
(GGA)	 AG	78522-78629	GC	GAG
-recovered pasa_asmbl_49737.p1, terminal, 78522, 78629
-recovered pasa_asmbl_49737.p1, internal, 76761, 77003
-recovered pasa_asmbl_49737.p1, internal, 78244, 78348
-recovered pasa_asmbl_49737.p1, internal, 78522, 78629
Valid prediction for CodingQuarry_transcript_57383-T1
Valid prediction for Augustus_model.g12071.t1
Valid prediction for Augustus_model.g12062.t1
Valid prediction for GlimmerHMM_glimmerT_17974-T1
Valid prediction for GeneMark_model.30179_t
Valid prediction for GlimmerHMM_glimmerT_17980-T1
Valid prediction for GeneMark_model.30187_t
Valid prediction for snap_scaffold_7-snap.1391-T1
Valid prediction for GlimmerHMM_glimmerT_17972-T1
Valid prediction for Augustus_model.g12064.t1
Valid prediction for GeneMark_model.30191_t
Valid prediction for GlimmerHMM_glimmerT_17991-T1
Valid prediction for GlimmerHMM_glimmerT_17975-T1
Valid prediction for snap_scaffold_7-snap.1387-T1
Valid prediction for GeneMark_model.30164_t
Valid prediction for GlimmerHMM_glimmerT_17986-T1
Valid prediction for snap_scaffold_7-snap.1364-T1
Valid prediction for snap_scaffold_7-snap.1390-T1
Valid prediction for snap_scaffold_7-snap.1368-T1
Valid prediction for snap_scaffold_7-snap.1394-T1
Valid prediction for snap_scaffold_7-snap.1362-T1
Valid prediction for GlimmerHMM_glimmerT_17971-T1
Valid prediction for GeneMark_model.30195_t
Valid prediction for GlimmerHMM_glimmerT_17983-T1
Valid prediction for GeneMark_model.30188_t
Valid prediction for GeneMark_model.30177_t
Valid prediction for snap_scaffold_7-snap.1388-T1
Couldn't classify 135476, 135660
Sorry, prediction pasa_asmbl_49732.p1 fails validation.
(GCC)	 AG	135476-135660	GT	TGG
(GAT)	 AG	135800-135926	GT	TTG
(CTT)	 AG	136480-136536	GT	TTG
(GGT)	 AG	136772-136888	GT	AGG
(GCA)	 AG	137125-137202	CT	GAC
-recovered pasa_asmbl_49732.p1, terminal, 137125, 137202
-recovered pasa_asmbl_49732.p1, internal, 135476, 135660
-recovered pasa_asmbl_49732.p1, internal, 135800, 135926
-recovered pasa_asmbl_49732.p1, internal, 136480, 136536
-recovered pasa_asmbl_49732.p1, internal, 136772, 136888
Valid prediction for Augustus_model.g12080.t1
Valid prediction for snap_scaffold_7-snap.1377-T1
Valid prediction for CodingQuarry_transcript_57381-T1
Valid prediction for snap_scaffold_7-snap.1373-T1
Valid prediction for GeneMark_model.30182_t
Valid prediction for GeneMark_model.30166_t
Valid prediction for Augustus_model.g12082.t1
Valid prediction for GlimmerHMM_glimmerT_17970-T1
Valid prediction for GeneMark_model.30172_t
Valid prediction for GeneMark_model.30186_t
Valid prediction for HiQ_model.g12079.t1
Valid prediction for snap_scaffold_7-snap.1369-T1
Valid prediction for GeneMark_model.30167_t
Valid prediction for snap_scaffold_7-snap.1386-T1
Valid prediction for Augustus_model.g12067.t1
Valid prediction for GeneMark_model.30174_t
Valid prediction for GlimmerHMM_glimmerT_17979-T1
Valid prediction for GlimmerHMM_glimmerT_17990-T1
Couldn't classify 68320, 68505
Couldn't classify 70972, 71106
Sorry, prediction pasa_asmbl_49739.p2 fails validation.
(ATC)	 AG	68320-68505	GT	AGG
(CAC)	 AG	70972-71106	TA	GGT
-recovered pasa_asmbl_49739.p2, internal, 68320, 68505
Valid prediction for GeneMark_model.30189_t
Valid prediction for snap_scaffold_7-snap.1367-T1
Valid prediction for GlimmerHMM_glimmerT_17969-T1
Valid prediction for Augustus_model.g12066.t1
Valid prediction for Augustus_model.g12061.t1
Valid prediction for Augustus_model.g12063.t1
Valid prediction for GeneMark_model.30184_t
Valid prediction for pasa_asmbl_49730.p1
Couldn't classify 134468, 135253
Sorry, prediction pasa_asmbl_49733.p1 fails validation.
(GAC)	 AG	134468-135253	GC	CCG
-recovered pasa_asmbl_49733.p1, internal, 134468, 135253
Valid prediction for GlimmerHMM_glimmerT_17973-T1
Valid prediction for HiQ_model.g12070.t1
Valid prediction for GlimmerHMM_glimmerT_17982-T1
Valid prediction for Augustus_model.g12072.t1
Valid prediction for GeneMark_model.30168_t
Valid prediction for snap_scaffold_7-snap.1363-T1
Valid prediction for snap_scaffold_7-snap.1384-T1
Valid prediction for GeneMark_model.30158_t
Valid prediction for snap_scaffold_7-snap.1393-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 153627, rend_intergenic: 148626  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158914, rend_intergenic: 155007  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 221758, rend_intergenic: 193585  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 232328, rend_intergenic: 225678  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 239025
-exon list size: 566


building trellis

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92.6    
92.8    
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93.8    
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95.8    
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96.1    
96.3    
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96.8    
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97.9    
98.1    
98.2    
98.4    
98.6    
98.8    
98.9    
99.1    
99.3    
99.5    
99.6    
99.8    
-found 40 predictions from path traversal
Error with prediction: snap lend_intergenic: 153627, rend_intergenic: 148626  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158914, rend_intergenic: 155007  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 221758, rend_intergenic: 193585  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 232328, rend_intergenic: 225678  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 31 predictions persist after filtering for low support