-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_7/scaffold_7_12796878-12981357

-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 GlimmerHMM_glimmerT_18295-T1
Valid prediction for snap_scaffold_7-snap.2394-T1
Valid prediction for snap_scaffold_7-snap.2392-T1
Valid prediction for snap_scaffold_7-snap.2423-T1
Valid prediction for GlimmerHMM_glimmerT_18320-T1
Valid prediction for Augustus_model.g12336.t1
Valid prediction for GlimmerHMM_glimmerT_18300-T1
Valid prediction for snap_scaffold_7-snap.2425-T1
Valid prediction for GlimmerHMM_glimmerT_18311-T1
Valid prediction for GlimmerHMM_glimmerT_18314-T1
Valid prediction for Augustus_model.g12341.t1
Valid prediction for GlimmerHMM_glimmerT_18309-T1
Valid prediction for snap_scaffold_7-snap.2398-T1
Valid prediction for GlimmerHMM_glimmerT_18305-T1
Valid prediction for snap_scaffold_7-snap.2401-T1
Valid prediction for snap_scaffold_7-snap.2400-T1
Valid prediction for snap_scaffold_7-snap.2417-T1
Valid prediction for GlimmerHMM_glimmerT_18315-T1
Couldn't classify 33066, 33157
Couldn't classify 33556, 33764
Sorry, prediction pasa_asmbl_50301.p1 fails validation.
(TTT)	 AG	33066-33157	GT	AGG
(AGT)	 AG	33298-33392	GT	AGG
(GGA)	 AG	33556-33764	CA	CCC
-recovered pasa_asmbl_50301.p1, internal, 33066, 33157
-recovered pasa_asmbl_50301.p1, internal, 33298, 33392
Valid prediction for GlimmerHMM_glimmerT_18321-T1
Valid prediction for Augustus_model.g12343.t1
Valid prediction for GlimmerHMM_glimmerT_18319-T1
Valid prediction for snap_scaffold_7-snap.2408-T1
Valid prediction for snap_scaffold_7-snap.2415-T1
Valid prediction for snap_scaffold_7-snap.2421-T1
Valid prediction for snap_scaffold_7-snap.2391-T1
Valid prediction for GlimmerHMM_glimmerT_18297-T1
Valid prediction for GlimmerHMM_glimmerT_18318-T1
Valid prediction for snap_scaffold_7-snap.2399-T1
Valid prediction for Augustus_model.g12329.t1
Valid prediction for snap_scaffold_7-snap.2429-T1
Valid prediction for Augustus_model.g12339.t1
Valid prediction for GlimmerHMM_glimmerT_18307-T1
Valid prediction for Augustus_model.g12342.t1
Valid prediction for GlimmerHMM_glimmerT_18301-T1
Valid prediction for Augustus_model.g12340.t1
Valid prediction for GlimmerHMM_glimmerT_18322-T1
Valid prediction for snap_scaffold_7-snap.2411-T1
Valid prediction for Augustus_model.g12333.t1
Valid prediction for GlimmerHMM_glimmerT_18306-T1
Valid prediction for GlimmerHMM_glimmerT_18303-T1
Valid prediction for Augustus_model.g12330.t1
Valid prediction for snap_scaffold_7-snap.2414-T1
Valid prediction for snap_scaffold_7-snap.2428-T1
Valid prediction for snap_scaffold_7-snap.2430-T1
Valid prediction for snap_scaffold_7-snap.2422-T1
Valid prediction for snap_scaffold_7-snap.2393-T1
Valid prediction for snap_scaffold_7-snap.2426-T1
Valid prediction for snap_scaffold_7-snap.2419-T1
Valid prediction for snap_scaffold_7-snap.2405-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_7-snap.2416-T1
Valid prediction for snap_scaffold_7-snap.2397-T1
Valid prediction for GlimmerHMM_glimmerT_18317-T1
Valid prediction for snap_scaffold_7-snap.2402-T1
Valid prediction for pasa_asmbl_51268.p1
Valid prediction for GlimmerHMM_glimmerT_18323-T1
Valid prediction for snap_scaffold_7-snap.2396-T1
Valid prediction for GlimmerHMM_glimmerT_18294-T1
Valid prediction for CodingQuarry_transcript_57683-T1
Valid prediction for snap_scaffold_7-snap.2390-T1
Valid prediction for GlimmerHMM_glimmerT_18316-T1
Valid prediction for Augustus_model.g12335.t1
Valid prediction for snap_scaffold_7-snap.2427-T1
Valid prediction for GlimmerHMM_glimmerT_18312-T1
Valid prediction for Augustus_model.g12345.t1
Valid prediction for GlimmerHMM_glimmerT_18299-T1
Valid prediction for Augustus_model.g12344.t1
Valid prediction for snap_scaffold_7-snap.2418-T1
Valid prediction for GlimmerHMM_glimmerT_18302-T1
Valid prediction for GlimmerHMM_glimmerT_18298-T1
Valid prediction for snap_scaffold_7-snap.2412-T1
Valid prediction for snap_scaffold_7-snap.2424-T1
Valid prediction for snap_scaffold_7-snap.2406-T1
Couldn't classify 40665, 40849
Couldn't classify 41974, 42053
Sorry, prediction pasa_asmbl_51276.p1 fails validation.
(GTG)	 CT	40665-40849	GT	CGG
(GCT)	 AG	41190-41277	GT	AGG
(CTG)	 AG	41499-41601	GT	ATG
(TTG)	 AG	41974-42053	GA	GGG
-recovered pasa_asmbl_51276.p1, internal, 41190, 41277
-recovered pasa_asmbl_51276.p1, internal, 41499, 41601
Valid prediction for snap_scaffold_7-snap.2409-T1
Valid prediction for GlimmerHMM_glimmerT_18296-T1
Valid prediction for GlimmerHMM_glimmerT_18310-T1
Valid prediction for snap_scaffold_7-snap.2395-T1
Valid prediction for Augustus_model.g12334.t1
Valid prediction for Augustus_model.g12328.t1
Valid prediction for snap_scaffold_7-snap.2410-T1
Valid prediction for GlimmerHMM_glimmerT_18313-T1
Valid prediction for Augustus_model.g12332.t1
Couldn't classify 35589, 35702
Sorry, prediction pasa_asmbl_51277.p1 fails validation.
(ATG)	 AG	32079-32198	GT	AGG
(ACT)	 AG	32545-32676	GT	AGG
(GAT)	 AG	33006-33071	GT	CTG
(TCA)	 AG	33724-33792	GT	AGG
(CTG)	 AG	35589-35702	GA	GGG
-recovered pasa_asmbl_51277.p1, initial, 32079, 32198
-recovered pasa_asmbl_51277.p1, internal, 32079, 32198
-recovered pasa_asmbl_51277.p1, internal, 32545, 32676
-recovered pasa_asmbl_51277.p1, internal, 33006, 33071
-recovered pasa_asmbl_51277.p1, internal, 33724, 33792
Valid prediction for pasa_asmbl_51273.p1
Valid prediction for snap_scaffold_7-snap.2404-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for snap_scaffold_7-snap.2407-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_18304-T1
Valid prediction for snap_scaffold_7-snap.2420-T1
Valid prediction for snap_scaffold_7-snap.2413-T1
Valid prediction for GlimmerHMM_glimmerT_18308-T1
Valid prediction for snap_scaffold_7-snap.2403-T1
Valid prediction for Augustus_model.g12331.t1
Valid prediction for CodingQuarry_transcript_57684-T1
Valid prediction for HiQ_model.g12338.t1
Valid prediction for Augustus_model.g12337.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 20137, rend_intergenic: 5814  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35416, rend_intergenic: 28871  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70052, rend_intergenic: 62095  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82767, rend_intergenic: 80035  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98532, rend_intergenic: 94963  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118907, rend_intergenic: 108597  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119732, rend_intergenic: 119043  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129674, rend_intergenic: 126935  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137183, rend_intergenic: 131128  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155594, rend_intergenic: 142318  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164982, rend_intergenic: 156707  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169996, rend_intergenic: 165096  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181821, rend_intergenic: 170134  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 184480
-exon list size: 432


building trellis

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98.2    
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98.6    
98.8    
99.1    
99.3    
99.5    
99.8    
-found 36 predictions from path traversal
Error with prediction: snap lend_intergenic: 20137, rend_intergenic: 5814  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35416, rend_intergenic: 28871  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70052, rend_intergenic: 62095  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82767, rend_intergenic: 80035  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98532, rend_intergenic: 94963  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118907, rend_intergenic: 108597  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119732, rend_intergenic: 119043  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 129674, rend_intergenic: 126935  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137183, rend_intergenic: 131128  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155594, rend_intergenic: 142318  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164982, rend_intergenic: 156707  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169996, rend_intergenic: 165096  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181821, rend_intergenic: 170134  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 22 predictions persist after filtering for low support