-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_13/scaffold_13_7448541-7653614

-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.55660_t
Valid prediction for CodingQuarry_transcript_13078-T1
Valid prediction for GeneMark_model.55679_t
Valid prediction for snap_scaffold_13-snap.1351-T1
Valid prediction for snap_scaffold_13-snap.1369-T1
Valid prediction for GeneMark_model.55661_t
Valid prediction for GeneMark_model.55666_t
Valid prediction for GeneMark_model.55674_t
Valid prediction for pasa_asmbl_11041.p1
Valid prediction for snap_scaffold_13-snap.1345-T1
Valid prediction for Augustus_model.g21852.t1
Valid prediction for GlimmerHMM_glimmerT_32601-T1
Valid prediction for GeneMark_model.55673_t
Valid prediction for GlimmerHMM_glimmerT_32599-T1
Valid prediction for snap_scaffold_13-snap.1344-T1
Valid prediction for GeneMark_model.55682_t
Valid prediction for Augustus_model.g21858.t1
Valid prediction for GlimmerHMM_glimmerT_32602-T1
Valid prediction for GeneMark_model.55662_t
Valid prediction for CodingQuarry_transcript_13081-T1
Valid prediction for snap_scaffold_13-snap.1353-T1
Valid prediction for snap_scaffold_13-snap.1374-T1
Valid prediction for Augustus_model.g21868.t1
Valid prediction for snap_scaffold_13-snap.1372-T1
Valid prediction for GeneMark_model.55685_t
Valid prediction for Augustus_model.g21867.t1
Valid prediction for GeneMark_model.55686_t
Valid prediction for GeneMark_model.55692_t
Valid prediction for snap_scaffold_13-snap.1342-T1
Valid prediction for Augustus_model.g21864.t1
Valid prediction for GlimmerHMM_glimmerT_32604-T1
Valid prediction for GlimmerHMM_glimmerT_32597-T1
Valid prediction for HiQ_model.g21848.t1
Valid prediction for pasa_asmbl_11044.p2
Valid prediction for GeneMark_model.55676_t
Valid prediction for CodingQuarry_transcript_13079-T1
Valid prediction for GeneMark_model.55671_t
Valid prediction for GeneMark_model.55680_t
Valid prediction for GlimmerHMM_glimmerT_32609-T1
Valid prediction for GeneMark_model.55696_t
Valid prediction for pasa_asmbl_11043.p1
Valid prediction for GeneMark_model.55663_t
Valid prediction for GlimmerHMM_glimmerT_32598-T1
Valid prediction for snap_scaffold_13-snap.1356-T1
Valid prediction for GeneMark_model.55683_t
Valid prediction for GeneMark_model.55669_t
Valid prediction for GlimmerHMM_glimmerT_32607-T1
Valid prediction for GlimmerHMM_glimmerT_32613-T1
Valid prediction for Augustus_model.g21849.t1
Couldn't classify 922, 1024
Sorry, prediction pasa_asmbl_11038.p1 fails validation.
(CAG)	 AA	922-1024	GT	GGG
(GCA)	 AG	2402-2662	GT	AGG
(ACA)	 AG	3169-3350	AG	GAA
-recovered pasa_asmbl_11038.p1, terminal, 3169, 3350
-recovered pasa_asmbl_11038.p1, internal, 2402, 2662
Valid prediction for GeneMark_model.55665_t
Valid prediction for GeneMark_model.55695_t
Valid prediction for snap_scaffold_13-snap.1375-T1
Valid prediction for GlimmerHMM_glimmerT_32596-T1
Valid prediction for GeneMark_model.55693_t
Valid prediction for GlimmerHMM_glimmerT_32615-T1
Valid prediction for GeneMark_model.55667_t
Valid prediction for snap_scaffold_13-snap.1366-T1
Valid prediction for Augustus_model.g21857.t1
Valid prediction for GeneMark_model.55697_t
Valid prediction for snap_scaffold_13-snap.1359-T1
Valid prediction for GlimmerHMM_glimmerT_32617-T1
Valid prediction for snap_scaffold_13-snap.1348-T1
Valid prediction for GeneMark_model.55689_t
Valid prediction for Augustus_model.g21850.t1
Valid prediction for snap_scaffold_13-snap.1373-T1
Valid prediction for CodingQuarry_transcript_13080-T1
Valid prediction for snap_scaffold_13-snap.1343-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_13-snap.1355-T1
Valid prediction for GlimmerHMM_glimmerT_32614-T1
Valid prediction for snap_scaffold_13-snap.1347-T1
Valid prediction for Augustus_model.g21856.t1
Valid prediction for GeneMark_model.55691_t
Valid prediction for CodingQuarry_transcript_13086-T1
Valid prediction for snap_scaffold_13-snap.1354-T1
Valid prediction for GeneMark_model.55687_t
Valid prediction for Augustus_model.g21865.t1
Valid prediction for Augustus_model.g21854.t1
Valid prediction for snap_scaffold_13-snap.1367-T1
Couldn't classify 134676, 134834
Couldn't classify 141932, 142137
Sorry, prediction pasa_asmbl_9856.p1 fails validation.
(ACT)	 CG	134676-134834	GT	AGG
(GGG)	 AG	135903-136046	GT	AGG
(AAG)	 AG	138253-138357	GT	AGG
(AAT)	 AG	138539-138581	GT	GGG
(CTG)	 AG	138692-138767	GT	AGG
(GTA)	 AG	139217-139435	GT	AAG
(GGG)	 AG	139642-139729	GT	AGG
(GAT)	 AG	140403-140555	GT	AGG
(TTT)	 AG	140679-140776	GT	AGG
(GTT)	 AG	140885-141060	GT	AGG
(CCC)	 AG	141932-142137	GT	AGG
add_exon() Sorry, pasa_asmbl_9856.p1 138692-138767-terminal-3 is invalid.
-recovered pasa_asmbl_9856.p1, terminal, 138692, 138767
-recovered pasa_asmbl_9856.p1, internal, 135903, 136046
-recovered pasa_asmbl_9856.p1, internal, 138253, 138357
-recovered pasa_asmbl_9856.p1, internal, 138539, 138581
-recovered pasa_asmbl_9856.p1, internal, 138692, 138767
-recovered pasa_asmbl_9856.p1, internal, 139217, 139435
-recovered pasa_asmbl_9856.p1, internal, 139642, 139729
-recovered pasa_asmbl_9856.p1, internal, 140403, 140555
-recovered pasa_asmbl_9856.p1, internal, 140679, 140776
-recovered pasa_asmbl_9856.p1, internal, 140885, 141060
-recovered pasa_asmbl_9856.p1, internal, 141932, 142137
Valid prediction for snap_scaffold_13-snap.1350-T1
Valid prediction for GeneMark_model.55672_t
Valid prediction for GlimmerHMM_glimmerT_32616-T1
Valid prediction for GeneMark_model.55670_t
Valid prediction for GeneMark_model.55675_t
Valid prediction for snap_scaffold_13-snap.1376-T1
Valid prediction for snap_scaffold_13-snap.1349-T1
Valid prediction for GeneMark_model.55699_t
Valid prediction for snap_scaffold_13-snap.1361-T1
Valid prediction for snap_scaffold_13-snap.1370-T1
Valid prediction for GlimmerHMM_glimmerT_32610-T1
Valid prediction for Augustus_model.g21855.t1
Valid prediction for GlimmerHMM_glimmerT_32606-T1
Valid prediction for Augustus_model.g21853.t1
Valid prediction for Augustus_model.g21859.t1
Valid prediction for GlimmerHMM_glimmerT_32611-T1
Valid prediction for GeneMark_model.55688_t
Valid prediction for GlimmerHMM_glimmerT_32600-T1
Valid prediction for Augustus_model.g21861.t1
Valid prediction for CodingQuarry_transcript_13085-T1
Valid prediction for snap_scaffold_13-snap.1358-T1
Valid prediction for GlimmerHMM_glimmerT_32612-T1
Valid prediction for Augustus_model.g21866.t1
Valid prediction for CodingQuarry_transcript_13084-T1
Valid prediction for snap_scaffold_13-snap.1363-T1
Valid prediction for snap_scaffold_13-snap.1346-T1
Valid prediction for Augustus_model.g21869.t1
Valid prediction for GlimmerHMM_glimmerT_32608-T1
Valid prediction for GeneMark_model.55694_t
Valid prediction for GeneMark_model.55684_t
Valid prediction for Augustus_model.g21863.t1
Valid prediction for GeneMark_model.55664_t
Valid prediction for snap_scaffold_13-snap.1368-T1
Valid prediction for GeneMark_model.55681_t
Valid prediction for CodingQuarry_transcript_13083-T1
Valid prediction for GeneMark_model.55677_t
Valid prediction for pasa_asmbl_9846.p1
Valid prediction for GlimmerHMM_glimmerT_32605-T1
Valid prediction for GeneMark_model.55690_t
Valid prediction for snap_scaffold_13-snap.1360-T1
Valid prediction for snap_scaffold_13-snap.1362-T1
Valid prediction for snap_scaffold_13-snap.1357-T1
Valid prediction for GlimmerHMM_glimmerT_32603-T1
Valid prediction for Augustus_model.g21860.t1
Valid prediction for snap_scaffold_13-snap.1365-T1
Valid prediction for Augustus_model.g21851.t1
Valid prediction for snap_scaffold_13-snap.1364-T1
Valid prediction for snap_scaffold_13-snap.1371-T1
Valid prediction for Augustus_model.g21862.t1
Valid prediction for snap_scaffold_13-snap.1352-T1
Valid prediction for GlimmerHMM_glimmerT_32618-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 57640, rend_intergenic: 52931  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70405, rend_intergenic: 66930  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105525, rend_intergenic: 95607  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 205074
-exon list size: 450


building trellis

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98.2    
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99.1    
99.3    
99.6    
99.8    
-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 57640, rend_intergenic: 52931  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70405, rend_intergenic: 66930  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105525, rend_intergenic: 95607  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 25 predictions persist after filtering for low support