-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_6/scaffold_6_8021945-8206627

-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 Augustus_model.g9978.t1
Valid prediction for GlimmerHMM_glimmerT_15046-T1
Valid prediction for CodingQuarry_transcript_55123-T1
Valid prediction for GlimmerHMM_glimmerT_15057-T1
Valid prediction for GlimmerHMM_glimmerT_15068-T1
Couldn't classify 135132, 135194
Sorry, prediction pasa_asmbl_47104.p1 fails validation.
(GTG)	 CA	135132-135194	GT	AGG
(CAA)	 AG	135575-135703	GT	AGG
(GTG)	 AG	135795-135893	GT	AGG
(GAC)	 AG	136052-136134	GT	AGG
(CGA)	 AG	136311-136437	GT	AGG
(GTA)	 AG	136607-136702	GT	AAG
(GGT)	 AG	137250-137372	GT	AGG
(GTG)	 AG	139066-139230	GT	AGG
(GTG)	 AG	139449-139574	AC	AGA
-recovered pasa_asmbl_47104.p1, terminal, 139449, 139574
-recovered pasa_asmbl_47104.p1, internal, 135575, 135703
-recovered pasa_asmbl_47104.p1, internal, 135795, 135893
-recovered pasa_asmbl_47104.p1, internal, 136052, 136134
-recovered pasa_asmbl_47104.p1, internal, 136311, 136437
-recovered pasa_asmbl_47104.p1, internal, 136607, 136702
-recovered pasa_asmbl_47104.p1, internal, 137250, 137372
-recovered pasa_asmbl_47104.p1, internal, 139066, 139230
Valid prediction for Augustus_model.g9985.t1
Valid prediction for snap_scaffold_6-snap.1792-T1
Valid prediction for GlimmerHMM_glimmerT_15072-T1
Valid prediction for pasa_asmbl_47097.p1
Valid prediction for snap_scaffold_6-snap.1778-T1
Valid prediction for HiQ_model.g9973.t1
Valid prediction for snap_scaffold_6-snap.1783-T1
Valid prediction for CodingQuarry_transcript_55127-T1
Valid prediction for snap_scaffold_6-snap.1799-T1
Valid prediction for Augustus_model.g9977.t1
Valid prediction for GlimmerHMM_glimmerT_15051-T1
Couldn't classify 145783, 145935
Sorry, prediction pasa_asmbl_47107.p1 fails validation.
(ATG)	 AA	143474-143821	GT	AGG
(GCT)	 AG	145783-145935	AG	CCA
-recovered pasa_asmbl_47107.p1, initial, 143474, 143821
Valid prediction for CodingQuarry_transcript_55125-T1
Valid prediction for CodingQuarry_transcript_55124-T1
Valid prediction for GlimmerHMM_glimmerT_15050-T1
Valid prediction for snap_scaffold_6-snap.1803-T1
Valid prediction for Augustus_model.g9991.t1
Valid prediction for pasa_asmbl_47093.p1
Valid prediction for HiQ_model.g9990.t1
Valid prediction for HiQ_model.g9976.t1
Valid prediction for snap_scaffold_6-snap.1797-T1
Valid prediction for Augustus_model.g9992.t1
Valid prediction for GlimmerHMM_glimmerT_15043-T1
Valid prediction for CodingQuarry_transcript_55128-T1
Valid prediction for snap_scaffold_6-snap.1794-T1
Valid prediction for HiQ_model.g9987.t1
Couldn't classify 161082, 161191
Sorry, prediction pasa_asmbl_47112.p1 fails validation.
(ATG)	 AC	159917-160216	GT	AGG
(GTC)	 AG	160332-160517	GT	AGG
(AGA)	 AG	160662-160842	GT	CGG
(ACA)	 AG	161082-161191	CT	AGC
-recovered pasa_asmbl_47112.p1, initial, 159917, 160216
-recovered pasa_asmbl_47112.p1, internal, 160332, 160517
-recovered pasa_asmbl_47112.p1, internal, 160662, 160842
Valid prediction for GlimmerHMM_glimmerT_15059-T1
Valid prediction for Augustus_model.g9970.t1
Valid prediction for snap_scaffold_6-snap.1807-T1
Valid prediction for GlimmerHMM_glimmerT_15066-T1
Valid prediction for HiQ_model.g9975.t1
Valid prediction for GlimmerHMM_glimmerT_15042-T1
Couldn't classify 83764, 83872
Couldn't classify 84806, 84931
Sorry, prediction pasa_asmbl_47098.p1 fails validation.
(GGA)	 CA	83764-83872	GT	AGG
(TCC)	 AG	83969-84057	GT	GTG
(AAC)	 AG	84185-84291	GT	AGG
(GAA)	 AG	84497-84662	GT	AGG
(ACG)	 AG	84806-84931	AA	GGA
-recovered pasa_asmbl_47098.p1, internal, 83969, 84057
-recovered pasa_asmbl_47098.p1, internal, 84185, 84291
-recovered pasa_asmbl_47098.p1, internal, 84497, 84662
Valid prediction for snap_scaffold_6-snap.1812-T1
Valid prediction for snap_scaffold_6-snap.1801-T1
Valid prediction for snap_scaffold_6-snap.1788-T1
Valid prediction for GlimmerHMM_glimmerT_15061-T1
Valid prediction for Augustus_model.g9988.t1
Valid prediction for snap_scaffold_6-snap.1809-T1
Valid prediction for CodingQuarry_transcript_55126-T1
Valid prediction for GlimmerHMM_glimmerT_15067-T1
Valid prediction for snap_scaffold_6-snap.1782-T1
Valid prediction for snap_scaffold_6-snap.1790-T1
Valid prediction for snap_scaffold_6-snap.1780-T1
Valid prediction for pasa_asmbl_47102.p1
Valid prediction for GlimmerHMM_glimmerT_15055-T1
Valid prediction for Augustus_model.g9971.t1
Valid prediction for snap_scaffold_6-snap.1808-T1
Couldn't classify 118339, 119180
Sorry, prediction pasa_asmbl_47101.p1 fails validation.
(ATG)	 AA	117085-117141	GT	AGG
(TTC)	 AG	117816-117924	GT	AGG
(GTG)	 AG	118045-118155	GT	TGG
(GCC)	 AG	118339-119180	AT	CCA
-recovered pasa_asmbl_47101.p1, initial, 117085, 117141
-recovered pasa_asmbl_47101.p1, internal, 117816, 117924
-recovered pasa_asmbl_47101.p1, internal, 118045, 118155
Valid prediction for snap_scaffold_6-snap.1777-T1
Valid prediction for Augustus_model.g9980.t1
Valid prediction for GlimmerHMM_glimmerT_15048-T1
Valid prediction for GlimmerHMM_glimmerT_15065-T1
Couldn't classify 146395, 146484
Sorry, prediction pasa_asmbl_47108.p1 fails validation.
(TCA)	 GC	146395-146484	GT	AGG
(GTC)	 AG	146650-146710	GT	CTG
(GTG)	 AG	146861-146945	GT	ATG
(CTC)	 AG	147279-147390	GT	AGG
(GAA)	 AG	147635-147781	TG	GAT
-recovered pasa_asmbl_47108.p1, terminal, 147635, 147781
-recovered pasa_asmbl_47108.p1, internal, 146650, 146710
-recovered pasa_asmbl_47108.p1, internal, 146861, 146945
-recovered pasa_asmbl_47108.p1, internal, 147279, 147390
Valid prediction for snap_scaffold_6-snap.1804-T1
Valid prediction for GlimmerHMM_glimmerT_15056-T1
Valid prediction for GlimmerHMM_glimmerT_15070-T1
Valid prediction for snap_scaffold_6-snap.1787-T1
Valid prediction for snap_scaffold_6-snap.1811-T1
Valid prediction for HiQ_model.g9982.t1
Valid prediction for GlimmerHMM_glimmerT_15071-T1
Valid prediction for snap_scaffold_6-snap.1781-T1
Valid prediction for Augustus_model.g9972.t1
Valid prediction for pasa_asmbl_47111.p1
Valid prediction for GlimmerHMM_glimmerT_15060-T1
Valid prediction for HiQ_model.g9984.t1
Valid prediction for snap_scaffold_6-snap.1785-T1
Valid prediction for Augustus_model.g9968.t1
Valid prediction for snap_scaffold_6-snap.1816-T1
Valid prediction for snap_scaffold_6-snap.1813-T1
Valid prediction for pasa_asmbl_47096.p1
Valid prediction for GlimmerHMM_glimmerT_15045-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 GlimmerHMM_glimmerT_15063-T1
Valid prediction for GlimmerHMM_glimmerT_15074-T1
Valid prediction for snap_scaffold_6-snap.1789-T1
Valid prediction for snap_scaffold_6-snap.1786-T1
Valid prediction for GlimmerHMM_glimmerT_15044-T1
Valid prediction for CodingQuarry_transcript_55121-T1
Valid prediction for Augustus_model.g9974.t1
Valid prediction for GlimmerHMM_glimmerT_15064-T1
Valid prediction for Augustus_model.g9986.t1
Valid prediction for GlimmerHMM_glimmerT_15053-T1
Valid prediction for snap_scaffold_6-snap.1779-T1
Valid prediction for GlimmerHMM_glimmerT_15054-T1
Valid prediction for snap_scaffold_6-snap.1806-T1
Valid prediction for HiQ_model.g9969.t1
Valid prediction for GlimmerHMM_glimmerT_15049-T1
Valid prediction for snap_scaffold_6-snap.1814-T1
Valid prediction for GlimmerHMM_glimmerT_15062-T1
Valid prediction for Augustus_model.g9994.t1
Valid prediction for Augustus_model.g9995.t1
Valid prediction for snap_scaffold_6-snap.1795-T1
Valid prediction for GlimmerHMM_glimmerT_15073-T1
Valid prediction for Augustus_model.g9983.t1
Valid prediction for Augustus_model.g9979.t1
Valid prediction for Augustus_model.g9989.t1
Valid prediction for Augustus_model.g9981.t1
Valid prediction for pasa_asmbl_48529.p1
Valid prediction for snap_scaffold_6-snap.1796-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_6-snap.1800-T1
Couldn't classify 68932, 69000
Sorry, prediction pasa_asmbl_48531.p1 fails validation.
(TGC)	 TG	68932-69000	GT	AGG
(AAT)	 AG	69291-69386	GT	AGG
(AGT)	 AG	69460-69690	GT	AGG
(AAT)	 AG	69819-69841	GT	AGG
(AGG)	 AG	69989-70107	GT	AGG
(CCC)	 AG	70213-70760	AT	AGA
-recovered pasa_asmbl_48531.p1, terminal, 70213, 70760
-recovered pasa_asmbl_48531.p1, internal, 69291, 69386
-recovered pasa_asmbl_48531.p1, internal, 69460, 69690
-recovered pasa_asmbl_48531.p1, internal, 69819, 69841
-recovered pasa_asmbl_48531.p1, internal, 69989, 70107
Valid prediction for snap_scaffold_6-snap.1793-T1
Valid prediction for GlimmerHMM_glimmerT_15047-T1
Valid prediction for snap_scaffold_6-snap.1805-T1
Valid prediction for snap_scaffold_6-snap.1810-T1
Valid prediction for Augustus_model.g9993.t1
Valid prediction for snap_scaffold_6-snap.1791-T1
Valid prediction for GlimmerHMM_glimmerT_15069-T1
Valid prediction for GlimmerHMM_glimmerT_15058-T1
Valid prediction for pasa_asmbl_48538.p1
Valid prediction for snap_scaffold_6-snap.1784-T1
Valid prediction for snap_scaffold_6-snap.1798-T1
Valid prediction for snap_scaffold_6-snap.1802-T1
Valid prediction for snap_scaffold_6-snap.1815-T1
Valid prediction for GlimmerHMM_glimmerT_15052-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 29413, rend_intergenic: 28665  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32177, rend_intergenic: 29683  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75235, rend_intergenic: 73014  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78429, rend_intergenic: 78065  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89513, rend_intergenic: 81939  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134208, rend_intergenic: 130027  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137566, rend_intergenic: 134655  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182579, rend_intergenic: 177529  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 149609, rend_intergenic: 149606  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 184683
-exon list size: 401


building trellis

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37.0    
37.2    
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38.2    
38.5    
38.7    
39.0    
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39.5    
39.7    
40.0    
40.2    
40.4    
40.7    
40.9    
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41.9    
42.2    
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97.5    
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98.0    
98.3    
98.5    
98.8    
99.0    
99.3    
99.5    
99.8    
-found 38 predictions from path traversal
Error with prediction: snap lend_intergenic: 29413, rend_intergenic: 28665  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32177, rend_intergenic: 29683  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75235, rend_intergenic: 73014  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78429, rend_intergenic: 78065  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89513, rend_intergenic: 81939  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134208, rend_intergenic: 130027  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137566, rend_intergenic: 134655  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182579, rend_intergenic: 177529  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 149609, rend_intergenic: 149606  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 33 predictions persist after filtering for low support