-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_24/scaffold_24_9898181-10049135

-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.95071_t
Valid prediction for snap_scaffold_24-snap.2112-T1
Valid prediction for GeneMark_model.95044_t
Valid prediction for snap_scaffold_24-snap.2115-T1
Valid prediction for Augustus_model.g36501.t1
Valid prediction for snap_scaffold_24-snap.2107-T1
Valid prediction for GlimmerHMM_glimmerT_54536-T1
Valid prediction for GeneMark_model.95036_t
Valid prediction for Augustus_model.g36506.t1
Valid prediction for GeneMark_model.95040_t
Valid prediction for GeneMark_model.95067_t
Valid prediction for snap_scaffold_24-snap.2121-T1
Valid prediction for GeneMark_model.95063_t
Valid prediction for GeneMark_model.95047_t
Valid prediction for pasa_asmbl_32538.p1
Valid prediction for snap_scaffold_24-snap.2113-T1
Valid prediction for GeneMark_model.95054_t
Valid prediction for GeneMark_model.95059_t
Valid prediction for snap_scaffold_24-snap.2109-T1
Valid prediction for GeneMark_model.95034_t
Valid prediction for GeneMark_model.95061_t
Valid prediction for snap_scaffold_24-snap.2119-T1
Valid prediction for Augustus_model.g36507.t1
Valid prediction for GlimmerHMM_glimmerT_54541-T1
Valid prediction for snap_scaffold_24-snap.2104-T1
Valid prediction for snap_scaffold_24-snap.2100-T1
Valid prediction for GlimmerHMM_glimmerT_54544-T1
Valid prediction for CodingQuarry_transcript_37342-T1
Valid prediction for GeneMark_model.95049_t
Valid prediction for snap_scaffold_24-snap.2092-T1
Valid prediction for snap_scaffold_24-snap.2124-T1
Valid prediction for snap_scaffold_24-snap.2096-T1
Valid prediction for snap_scaffold_24-snap.2114-T1
Valid prediction for GlimmerHMM_glimmerT_54534-T1
Valid prediction for GlimmerHMM_glimmerT_54553-T1
Valid prediction for snap_scaffold_24-snap.2099-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GeneMark_model.95037_t
Valid prediction for snap_scaffold_24-snap.2093-T1
Valid prediction for snap_scaffold_24-snap.2123-T1
Valid prediction for GeneMark_model.95069_t
Valid prediction for HiQ_model.g36496.t1
Valid prediction for GeneMark_model.95057_t
Valid prediction for GeneMark_model.95064_t
Valid prediction for GeneMark_model.95051_t
Valid prediction for GlimmerHMM_glimmerT_54532-T1
Valid prediction for GeneMark_model.95039_t
Valid prediction for snap_scaffold_24-snap.2120-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 GeneMark_model.95058_t
Valid prediction for GeneMark_model.95056_t
Valid prediction for snap_scaffold_24-snap.2094-T1
Valid prediction for Augustus_model.g36500.t1
Valid prediction for GlimmerHMM_glimmerT_54540-T1
Valid prediction for GlimmerHMM_glimmerT_54539-T1
Valid prediction for GeneMark_model.95062_t
Valid prediction for pasa_asmbl_33144.p1
Valid prediction for snap_scaffold_24-snap.2098-T1
Valid prediction for GlimmerHMM_glimmerT_54552-T1
Valid prediction for snap_scaffold_24-snap.2106-T1
Couldn't classify 97524, 97970
Sorry, prediction pasa_asmbl_33145.p1 fails validation.
(AGC)	 GG	97524-97970	AT	GAA
Couldn't classify 95775, 95979
Couldn't classify 96116, 96244
Sorry, prediction CodingQuarry_transcript_37348-T1 fails validation.
(ATG)	 AA	91674-91807	GT	AGG
(GAA)	 AG	92005-92129	GT	AGG
(AGC)	 AG	92285-92487	GT	CGG
(GCA)	 AG	92992-93076	GT	AGG
(CTG)	 AG	93267-93396	GT	ACG
(GCG)	 AG	93916-94071	GT	AGG
(TAA)	 AG	94175-94246	GT	TGG
(TGT)	 AG	94432-94551	GT	TTG
(GTA)	 AG	94642-94764	GT	CAG
(GCT)	 AG	95775-95979	CA	CAC
(TCC)	 CA	96116-96244	GA	AGG
-recovered CodingQuarry_transcript_37348-T1, initial, 91674, 91807
-recovered CodingQuarry_transcript_37348-T1, internal, 92005, 92129
-recovered CodingQuarry_transcript_37348-T1, internal, 92285, 92487
-recovered CodingQuarry_transcript_37348-T1, internal, 92992, 93076
-recovered CodingQuarry_transcript_37348-T1, internal, 93267, 93396
-recovered CodingQuarry_transcript_37348-T1, internal, 93916, 94071
-recovered CodingQuarry_transcript_37348-T1, internal, 94175, 94246
-recovered CodingQuarry_transcript_37348-T1, internal, 94432, 94551
-recovered CodingQuarry_transcript_37348-T1, internal, 94642, 94764
Valid prediction for GlimmerHMM_glimmerT_54546-T1
Valid prediction for GeneMark_model.95035_t
Valid prediction for GeneMark_model.95043_t
Valid prediction for GlimmerHMM_glimmerT_54547-T1
Valid prediction for GeneMark_model.95068_t
Valid prediction for GlimmerHMM_glimmerT_54542-T1
Valid prediction for GlimmerHMM_glimmerT_54537-T1
Valid prediction for GeneMark_model.95066_t
Valid prediction for GlimmerHMM_glimmerT_54531-T1
Valid prediction for GeneMark_model.95052_t
Valid prediction for CodingQuarry_transcript_37346-T1
Valid prediction for GlimmerHMM_glimmerT_54545-T1
Valid prediction for snap_scaffold_24-snap.2101-T1
Valid prediction for GlimmerHMM_glimmerT_54535-T1
Valid prediction for GeneMark_model.95053_t
Valid prediction for CodingQuarry_transcript_37349-T1
Valid prediction for Augustus_model.g36505.t1
Valid prediction for Augustus_model.g36495.t1
Valid prediction for Augustus_model.g36502.t1
Valid prediction for Augustus_model.g36494.t1
Valid prediction for snap_scaffold_24-snap.2091-T1
Couldn't classify 95775, 95979
Couldn't classify 96116, 96244
Sorry, prediction CodingQuarry_transcript_37345-T1 fails validation.
(ATG)	 AA	91674-91807	GT	AGG
(GAA)	 AG	92005-92129	GT	AGG
(AGC)	 AG	92285-92487	GT	CGG
(GCA)	 AG	92992-93076	GT	AGG
(CTG)	 AG	93267-93396	GT	ACG
(GCG)	 AG	93916-94071	GT	AGG
(TAA)	 AG	94175-94246	GT	TGG
(TGT)	 AG	94432-94551	GT	TTG
(GTA)	 AG	95492-95614	GT	CAG
(GCT)	 AG	95775-95979	CA	CAC
(TCC)	 CA	96116-96244	GA	AGG
-recovered CodingQuarry_transcript_37345-T1, initial, 91674, 91807
-recovered CodingQuarry_transcript_37345-T1, internal, 92005, 92129
-recovered CodingQuarry_transcript_37345-T1, internal, 92285, 92487
-recovered CodingQuarry_transcript_37345-T1, internal, 92992, 93076
-recovered CodingQuarry_transcript_37345-T1, internal, 93267, 93396
-recovered CodingQuarry_transcript_37345-T1, internal, 93916, 94071
-recovered CodingQuarry_transcript_37345-T1, internal, 94175, 94246
-recovered CodingQuarry_transcript_37345-T1, internal, 94432, 94551
-recovered CodingQuarry_transcript_37345-T1, internal, 95492, 95614
Valid prediction for GeneMark_model.95060_t
Valid prediction for CodingQuarry_transcript_37347-T1
Valid prediction for GeneMark_model.95070_t
Valid prediction for snap_scaffold_24-snap.2095-T1
Valid prediction for GlimmerHMM_glimmerT_54543-T1
Valid prediction for GlimmerHMM_glimmerT_54551-T1
Valid prediction for GlimmerHMM_glimmerT_54548-T1
Valid prediction for snap_scaffold_24-snap.2090-T1
Valid prediction for snap_scaffold_24-snap.2105-T1
Valid prediction for GeneMark_model.95048_t
Valid prediction for snap_scaffold_24-snap.2108-T1
Valid prediction for snap_scaffold_24-snap.2122-T1
Valid prediction for GeneMark_model.95050_t
Valid prediction for snap_scaffold_24-snap.2118-T1
Valid prediction for snap_scaffold_24-snap.2102-T1
Valid prediction for GeneMark_model.95045_t
Valid prediction for CodingQuarry_transcript_37344-T1
Valid prediction for GlimmerHMM_glimmerT_54533-T1
Valid prediction for snap_scaffold_24-snap.2117-T1
Valid prediction for GlimmerHMM_glimmerT_54529-T1
Valid prediction for GlimmerHMM_glimmerT_54530-T1
Valid prediction for GeneMark_model.95065_t
Valid prediction for snap_scaffold_24-snap.2103-T1
Valid prediction for snap_scaffold_24-snap.2110-T1
Valid prediction for GeneMark_model.95055_t
Couldn't classify 109802, 109894
Sorry, prediction CodingQuarry_transcript_37343-T1 fails validation.
(ATG)	 AT	105875-105925	GT	AGG
(GGG)	 AG	107108-107160	GT	AAG
(TTG)	 AG	107324-107417	GT	AGG
(ATC)	 AG	107778-107849	GT	ACG
(TTT)	 AG	108078-108226	GT	GCG
(GTG)	 AG	108373-108466	GT	TGG
(TCC)	 AG	108725-108841	GT	AGG
(AGT)	 AG	108969-109139	GT	AGG
(AAT)	 AG	109275-109353	GT	TGG
(GCA)	 AG	109457-109566	GT	AAG
(ACG)	 CG	109802-109894	GT	ACG
(GAA)	 AG	109983-110202	GT	CGG
(GCA)	 AG	110316-110531	GT	TGG
(CGG)	 AG	110666-110866	GT	GGG
(ACG)	 AG	111263-111340	GT	AGG
(TTA)	 AG	111752-111837	GT	TGG
(GGC)	 AG	111996-112160	TC	AAT
-recovered CodingQuarry_transcript_37343-T1, initial, 105875, 105925
-recovered CodingQuarry_transcript_37343-T1, terminal, 111996, 112160
-recovered CodingQuarry_transcript_37343-T1, internal, 107108, 107160
-recovered CodingQuarry_transcript_37343-T1, internal, 107324, 107417
-recovered CodingQuarry_transcript_37343-T1, internal, 107778, 107849
-recovered CodingQuarry_transcript_37343-T1, internal, 108078, 108226
-recovered CodingQuarry_transcript_37343-T1, internal, 108373, 108466
-recovered CodingQuarry_transcript_37343-T1, internal, 108725, 108841
-recovered CodingQuarry_transcript_37343-T1, internal, 108969, 109139
-recovered CodingQuarry_transcript_37343-T1, internal, 109275, 109353
-recovered CodingQuarry_transcript_37343-T1, internal, 109457, 109566
-recovered CodingQuarry_transcript_37343-T1, internal, 109983, 110202
-recovered CodingQuarry_transcript_37343-T1, internal, 110316, 110531
-recovered CodingQuarry_transcript_37343-T1, internal, 110666, 110866
-recovered CodingQuarry_transcript_37343-T1, internal, 111263, 111340
-recovered CodingQuarry_transcript_37343-T1, internal, 111752, 111837
Couldn't classify 97025, 97262
Sorry, prediction pasa_asmbl_33150.p2 fails validation.
(ATG)	 TG	96404-96436	GT	CGG
(AAA)	 AG	96725-96834	GT	AGG
(GAT)	 AG	97025-97262	AC	ACA
-recovered pasa_asmbl_33150.p2, initial, 96404, 96436
-recovered pasa_asmbl_33150.p2, internal, 96725, 96834
Valid prediction for snap_scaffold_24-snap.2111-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for HiQ_model.g36497.t1
Valid prediction for Augustus_model.g36504.t1
Valid prediction for snap_scaffold_24-snap.2116-T1
Valid prediction for CodingQuarry_transcript_37350-T1
Valid prediction for GeneMark_model.95072_t
Valid prediction for GlimmerHMM_glimmerT_54538-T1
Valid prediction for GeneMark_model.95038_t
Valid prediction for HiQ_model.g36498.t1
Couldn't classify 95775, 95976
Sorry, prediction pasa_asmbl_33154.p1 fails validation.
(ATG)	 AA	91674-91807	GT	AGG
(GAA)	 AG	92005-92129	GT	AGG
(AGC)	 AG	92285-92487	GT	CGG
(GCA)	 AG	92992-93076	GT	AGG
(CTG)	 AG	93267-93396	GT	ACG
(GCG)	 AG	93916-94071	GT	AGG
(TAA)	 AG	94175-94246	GT	TGG
(TGT)	 AG	94432-94551	GT	TTG
(GTA)	 AG	94642-94764	GT	CAG
(GCT)	 AG	95775-95976	AC	ACA
-recovered pasa_asmbl_33154.p1, initial, 91674, 91807
-recovered pasa_asmbl_33154.p1, internal, 92005, 92129
-recovered pasa_asmbl_33154.p1, internal, 92285, 92487
-recovered pasa_asmbl_33154.p1, internal, 92992, 93076
-recovered pasa_asmbl_33154.p1, internal, 93267, 93396
-recovered pasa_asmbl_33154.p1, internal, 93916, 94071
-recovered pasa_asmbl_33154.p1, internal, 94175, 94246
-recovered pasa_asmbl_33154.p1, internal, 94432, 94551
-recovered pasa_asmbl_33154.p1, internal, 94642, 94764
Valid prediction for snap_scaffold_24-snap.2097-T1
Valid prediction for snap_scaffold_24-snap.2089-T1
Valid prediction for Augustus_model.g36499.t1
Valid prediction for GeneMark_model.95041_t
Valid prediction for Augustus_model.g36503.t1
Valid prediction for GlimmerHMM_glimmerT_54550-T1
Valid prediction for GlimmerHMM_glimmerT_54549-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 18783, rend_intergenic: 12022  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25874, rend_intergenic: 20351  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59282, rend_intergenic: 56608  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85786, rend_intergenic: 79359  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96099, rend_intergenic: 92326  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106070, rend_intergenic: 100719  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117877, rend_intergenic: 108095  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127691, rend_intergenic: 121967  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137778, rend_intergenic: 127821  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150059, rend_intergenic: 138110  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 150955
-exon list size: 578


building trellis

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80.5    
80.7    
80.9    
81.0    
81.2    
81.4    
81.6    
81.7    
81.9    
82.1    
82.2    
82.4    
82.6    
82.8    
82.9    
83.1    
83.3    
83.4    
83.6    
83.8    
84.0    
84.1    
84.3    
84.5    
84.7    
84.8    
85.0    
85.2    
85.3    
85.5    
85.7    
85.9    
86.0    
86.2    
86.4    
86.6    
86.7    
86.9    
87.1    
87.2    
87.4    
87.6    
87.8    
87.9    
88.1    
88.3    
88.4    
88.6    
88.8    
89.0    
89.1    
89.3    
89.5    
89.7    
89.8    
90.0    
90.2    
90.3    
90.5    
90.7    
90.9    
91.0    
91.2    
91.4    
91.6    
91.7    
91.9    
92.1    
92.2    
92.4    
92.6    
92.8    
92.9    
93.1    
93.3    
93.4    
93.6    
93.8    
94.0    
94.1    
94.3    
94.5    
94.7    
94.8    
95.0    
95.2    
95.3    
95.5    
95.7    
95.9    
96.0    
96.2    
96.4    
96.6    
96.7    
96.9    
97.1    
97.2    
97.4    
97.6    
97.8    
97.9    
98.1    
98.3    
98.4    
98.6    
98.8    
99.0    
99.1    
99.3    
99.5    
99.7    
99.8    
-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 18783, rend_intergenic: 12022  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25874, rend_intergenic: 20351  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59282, rend_intergenic: 56608  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85786, rend_intergenic: 79359  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96099, rend_intergenic: 92326  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 106070, rend_intergenic: 100719  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117877, rend_intergenic: 108095  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127691, rend_intergenic: 121967  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137778, rend_intergenic: 127821  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150059, rend_intergenic: 138110  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support