-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_17/scaffold_17_5739293-5966411

-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_17-snap.1201-T1
Valid prediction for Augustus_model.g27644.t1
Couldn't classify 9643, 9690
Sorry, prediction pasa_asmbl_17958.p1 fails validation.
(CGC)	 TG	9643-9690	GT	GGG
(TGT)	 AG	10660-10805	GT	GGG
(TCT)	 AG	11006-11064	GT	TGG
(ACG)	 AG	11215-11336	GT	AGG
(TAT)	 AG	11434-11537	GT	AGG
(AAA)	 AG	11674-11822	GT	AGG
(CAC)	 AG	12109-12246	GT	AGG
(AGG)	 AG	12399-12536	GT	TGG
(ATT)	 AG	12844-12981	GT	CAG
(ATC)	 AG	13242-14116	GA	GAG
add_exon() Sorry, pasa_asmbl_17958.p1 11434-11537-terminal-2 is invalid.
-recovered pasa_asmbl_17958.p1, terminal, 11434, 11537
-recovered pasa_asmbl_17958.p1, terminal, 13242, 14116
-recovered pasa_asmbl_17958.p1, internal, 10660, 10805
-recovered pasa_asmbl_17958.p1, internal, 11006, 11064
-recovered pasa_asmbl_17958.p1, internal, 11215, 11336
-recovered pasa_asmbl_17958.p1, internal, 11434, 11537
-recovered pasa_asmbl_17958.p1, internal, 11674, 11822
-recovered pasa_asmbl_17958.p1, internal, 12109, 12246
-recovered pasa_asmbl_17958.p1, internal, 12399, 12536
-recovered pasa_asmbl_17958.p1, internal, 12844, 12981
Valid prediction for GeneMark_model.71099_t
Valid prediction for Augustus_model.g27643.t1
Valid prediction for snap_scaffold_17-snap.1179-T1
Valid prediction for pasa_asmbl_17960.p1
Valid prediction for GlimmerHMM_glimmerT_41282-T1
Valid prediction for GlimmerHMM_glimmerT_41284-T1
Valid prediction for snap_scaffold_17-snap.1197-T1
Valid prediction for Augustus_model.g27642.t1
Valid prediction for GeneMark_model.71093_t
Valid prediction for GlimmerHMM_glimmerT_41279-T1
Valid prediction for GeneMark_model.71083_t
Valid prediction for snap_scaffold_17-snap.1190-T1
Valid prediction for GlimmerHMM_glimmerT_41286-T1
Valid prediction for GlimmerHMM_glimmerT_41262-T1
Valid prediction for GeneMark_model.71094_t
Valid prediction for GeneMark_model.71071_t
Valid prediction for GlimmerHMM_glimmerT_41269-T1
Valid prediction for snap_scaffold_17-snap.1182-T1
Valid prediction for GeneMark_model.71091_t
Valid prediction for CodingQuarry_transcript_21949-T1
Valid prediction for snap_scaffold_17-snap.1207-T1
Valid prediction for snap_scaffold_17-snap.1198-T1
Valid prediction for GeneMark_model.71089_t
Valid prediction for HiQ_model.g27637.t1
Valid prediction for GeneMark_model.71085_t
Valid prediction for GeneMark_model.71064_t
Valid prediction for GlimmerHMM_glimmerT_41274-T1
Valid prediction for GlimmerHMM_glimmerT_41290-T1
Valid prediction for GeneMark_model.71102_t
Valid prediction for GeneMark_model.71084_t
Valid prediction for snap_scaffold_17-snap.1212-T1
Couldn't classify 111003, 111095
Sorry, prediction pasa_asmbl_17959.p1 fails validation.
(GGC)	 CG	111003-111095	GT	GGG
(CCC)	 AG	112439-112564	GT	GGG
(ATT)	 AG	113723-113880	GT	CTG
(GAA)	 AG	114767-114902	GT	TGG
(GAG)	 AG	115097-115159	CA	AGC
-recovered pasa_asmbl_17959.p1, terminal, 115097, 115159
-recovered pasa_asmbl_17959.p1, internal, 112439, 112564
-recovered pasa_asmbl_17959.p1, internal, 113723, 113880
-recovered pasa_asmbl_17959.p1, internal, 114767, 114902
Valid prediction for GlimmerHMM_glimmerT_41278-T1
Valid prediction for snap_scaffold_17-snap.1203-T1
Valid prediction for GlimmerHMM_glimmerT_41277-T1
Valid prediction for snap_scaffold_17-snap.1189-T1
Valid prediction for snap_scaffold_17-snap.1194-T1
Valid prediction for Augustus_model.g27639.t1
Couldn't classify 105118, 105154
Couldn't classify 109823, 109972
Sorry, prediction pasa_asmbl_18556.p1 fails validation.
(GGG)	 AG	105118-105154	GT	AGG
(GTC)	 AG	107236-107333	GT	GGG
(ATG)	 AG	107839-107955	GT	GGG
(AGA)	 AG	108239-108393	GT	AGG
(TAT)	 AG	108513-108648	GT	AGG
(GAA)	 AG	109823-109972	GT	AGG
-recovered pasa_asmbl_18556.p1, initial, 107839, 107955
-recovered pasa_asmbl_18556.p1, internal, 105118, 105154
-recovered pasa_asmbl_18556.p1, internal, 107236, 107333
-recovered pasa_asmbl_18556.p1, internal, 107839, 107955
-recovered pasa_asmbl_18556.p1, internal, 108239, 108393
-recovered pasa_asmbl_18556.p1, internal, 108513, 108648
-recovered pasa_asmbl_18556.p1, internal, 109823, 109972
Valid prediction for snap_scaffold_17-snap.1186-T1
Valid prediction for snap_scaffold_17-snap.1204-T1
Valid prediction for Augustus_model.g27645.t1
Valid prediction for GeneMark_model.71082_t
Valid prediction for GeneMark_model.71080_t
Valid prediction for GeneMark_model.71073_t
Valid prediction for GeneMark_model.71100_t
Valid prediction for Augustus_model.g27638.t1
Valid prediction for GeneMark_model.71087_t
Valid prediction for snap_scaffold_17-snap.1199-T1
Valid prediction for Augustus_model.g27640.t1
Valid prediction for GlimmerHMM_glimmerT_41280-T1
Valid prediction for snap_scaffold_17-snap.1193-T1
Valid prediction for snap_scaffold_17-snap.1205-T1
Valid prediction for HiQ_model.g27648.t1
Valid prediction for GeneMark_model.71068_t
Valid prediction for GeneMark_model.71077_t
Valid prediction for snap_scaffold_17-snap.1188-T1
Valid prediction for snap_scaffold_17-snap.1184-T1
Valid prediction for snap_scaffold_17-snap.1213-T1
Valid prediction for GlimmerHMM_glimmerT_41281-T1
Valid prediction for GlimmerHMM_glimmerT_41275-T1
Valid prediction for snap_scaffold_17-snap.1195-T1
Valid prediction for snap_scaffold_17-snap.1183-T1
Valid prediction for snap_scaffold_17-snap.1191-T1
Valid prediction for GlimmerHMM_glimmerT_41270-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_17-snap.1211-T1
Valid prediction for GlimmerHMM_glimmerT_41289-T1
Valid prediction for GeneMark_model.71086_t
Valid prediction for snap_scaffold_17-snap.1214-T1
Valid prediction for snap_scaffold_17-snap.1177-T1
Valid prediction for GeneMark_model.71088_t
Valid prediction for GlimmerHMM_glimmerT_41261-T1
Valid prediction for GeneMark_model.71101_t
Valid prediction for snap_scaffold_17-snap.1187-T1
Valid prediction for Augustus_model.g27641.t1
Valid prediction for GlimmerHMM_glimmerT_41276-T1
Valid prediction for GlimmerHMM_glimmerT_41263-T1
Valid prediction for GeneMark_model.71096_t
Valid prediction for GeneMark_model.71066_t
Valid prediction for snap_scaffold_17-snap.1185-T1
Valid prediction for snap_scaffold_17-snap.1210-T1
Valid prediction for GeneMark_model.71075_t
Valid prediction for GeneMark_model.71074_t
Valid prediction for snap_scaffold_17-snap.1208-T1
Valid prediction for GeneMark_model.71097_t
Valid prediction for GeneMark_model.71095_t
Valid prediction for GlimmerHMM_glimmerT_41266-T1
Valid prediction for GlimmerHMM_glimmerT_41287-T1
Valid prediction for GeneMark_model.71072_t
Valid prediction for snap_scaffold_17-snap.1196-T1
Valid prediction for snap_scaffold_17-snap.1180-T1
Valid prediction for Augustus_model.g27636.t1
Valid prediction for snap_scaffold_17-snap.1178-T1
Valid prediction for GlimmerHMM_glimmerT_41267-T1
Valid prediction for GeneMark_model.71065_t
Valid prediction for GlimmerHMM_glimmerT_41268-T1
Valid prediction for GeneMark_model.71070_t
Valid prediction for GeneMark_model.71079_t
Valid prediction for CodingQuarry_transcript_21948-T1
Valid prediction for GeneMark_model.71098_t
Valid prediction for snap_scaffold_17-snap.1209-T1
Valid prediction for GeneMark_model.71069_t
Valid prediction for GeneMark_model.71067_t
Valid prediction for GeneMark_model.71090_t
Valid prediction for GeneMark_model.71063_t
Valid prediction for GlimmerHMM_glimmerT_41272-T1
Valid prediction for GlimmerHMM_glimmerT_41288-T1
Valid prediction for GlimmerHMM_glimmerT_41264-T1
Valid prediction for snap_scaffold_17-snap.1192-T1
Valid prediction for GeneMark_model.71092_t
Valid prediction for GlimmerHMM_glimmerT_41273-T1
Valid prediction for Augustus_model.g27646.t1
Valid prediction for Augustus_model.g27647.t1
Valid prediction for GeneMark_model.71078_t
Valid prediction for GlimmerHMM_glimmerT_41265-T1
Valid prediction for GlimmerHMM_glimmerT_41271-T1
Valid prediction for snap_scaffold_17-snap.1200-T1
Valid prediction for GeneMark_model.71081_t
Valid prediction for pasa_asmbl_18997.p1
Valid prediction for snap_scaffold_17-snap.1202-T1
Valid prediction for snap_scaffold_17-snap.1206-T1
Valid prediction for GlimmerHMM_glimmerT_41285-T1
Valid prediction for GlimmerHMM_glimmerT_41283-T1
Valid prediction for GeneMark_model.71076_t
Valid prediction for snap_scaffold_17-snap.1181-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 31575, rend_intergenic: 24994  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40947, rend_intergenic: 37340  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49682, rend_intergenic: 45565  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72487, rend_intergenic: 67366  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85890, rend_intergenic: 84415  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98515, rend_intergenic: 97823  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111161, rend_intergenic: 104510  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 217441, rend_intergenic: 214823  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 227119
-exon list size: 514


building trellis

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78.9    
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96.1    
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96.9    
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98.1    
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98.4    
98.6    
98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 24 predictions from path traversal
Error with prediction: snap lend_intergenic: 31575, rend_intergenic: 24994  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40947, rend_intergenic: 37340  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49682, rend_intergenic: 45565  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72487, rend_intergenic: 67366  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85890, rend_intergenic: 84415  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98515, rend_intergenic: 97823  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111161, rend_intergenic: 104510  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 217441, rend_intergenic: 214823  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 15 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 212893 - 227119
-exon list size: 23


building trellis

4.0    
8.0    
12.0    
16.0    
20.0    
24.0    
28.0    
32.0    
36.0    
40.0    
44.0    
48.0    
52.0    
56.0    
60.0    
64.0    
68.0    
72.0    
76.0    
80.0    
84.0    
88.0    
92.0    
96.0    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support