-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_21/scaffold_21_3046633-3260524

-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.g31553.t1
Couldn't classify 198070, 198158
Sorry, prediction pasa_asmbl_28482.p1 fails validation.
(AGC)	 AG	198070-198158	GT	AAG
(GCA)	 AG	198989-199173	GT	CGG
(TGG)	 AG	200747-200911	GT	AGG
(GTG)	 AG	201341-201402	GT	AGG
(CTG)	 AG	201714-201794	GT	AGG
(GAA)	 AG	202801-202869	GT	AGG
(CTC)	 AG	203588-203708	GT	AGG
(GTA)	 AG	204664-204820	GT	AGG
(TGG)	 AG	205055-205196	GT	TGG
(ACC)	 AG	205853-206023	GT	CGG
(GCT)	 AG	208397-208576	GT	AGG
(CTG)	 AG	209664-209838	GT	CGG
(GTC)	 AG	211734-211828	AG	AAA
add_exon() Sorry, pasa_asmbl_28482.p1 198070-198158-terminal-2 is invalid.
-recovered pasa_asmbl_28482.p1, terminal, 198070, 198158
-recovered pasa_asmbl_28482.p1, terminal, 211734, 211828
-recovered pasa_asmbl_28482.p1, internal, 198070, 198158
-recovered pasa_asmbl_28482.p1, internal, 198989, 199173
-recovered pasa_asmbl_28482.p1, internal, 200747, 200911
-recovered pasa_asmbl_28482.p1, internal, 201341, 201402
-recovered pasa_asmbl_28482.p1, internal, 201714, 201794
-recovered pasa_asmbl_28482.p1, internal, 202801, 202869
-recovered pasa_asmbl_28482.p1, internal, 203588, 203708
-recovered pasa_asmbl_28482.p1, internal, 204664, 204820
-recovered pasa_asmbl_28482.p1, internal, 205055, 205196
-recovered pasa_asmbl_28482.p1, internal, 205853, 206023
-recovered pasa_asmbl_28482.p1, internal, 208397, 208576
-recovered pasa_asmbl_28482.p1, internal, 209664, 209838
Valid prediction for GlimmerHMM_glimmerT_47335-T1
Valid prediction for GlimmerHMM_glimmerT_47363-T1
Valid prediction for HiQ_model.g31550.t1
Valid prediction for snap_scaffold_21-snap.559-T1
Valid prediction for GlimmerHMM_glimmerT_47339-T1
Valid prediction for snap_scaffold_21-snap.579-T1
Valid prediction for HiQ_model.g31559.t1
Couldn't classify 89094, 89144
Sorry, prediction pasa_asmbl_28455.p1 fails validation.
(AGA)	 AC	89094-89144	GT	AGG
(CAA)	 AG	90195-90308	GT	GGG
(AAA)	 AG	91851-91907	GT	TGG
(CCT)	 AG	92045-92097	GT	ACG
(TAA)	 AG	93460-93526	GT	GGG
(GAG)	 AG	94878-95050	GT	AGG
(GGT)	 AG	96291-96381	GT	AGG
(AAC)	 AG	96498-96676	GT	AAG
(GTT)	 AG	97177-97240	AG	GAA
-recovered pasa_asmbl_28455.p1, terminal, 97177, 97240
-recovered pasa_asmbl_28455.p1, internal, 90195, 90308
-recovered pasa_asmbl_28455.p1, internal, 91851, 91907
-recovered pasa_asmbl_28455.p1, internal, 92045, 92097
-recovered pasa_asmbl_28455.p1, internal, 93460, 93526
-recovered pasa_asmbl_28455.p1, internal, 94878, 95050
-recovered pasa_asmbl_28455.p1, internal, 96291, 96381
-recovered pasa_asmbl_28455.p1, internal, 96498, 96676
Valid prediction for GlimmerHMM_glimmerT_47353-T1
Valid prediction for GlimmerHMM_glimmerT_47357-T1
Valid prediction for snap_scaffold_21-snap.590-T1
Couldn't classify 138466, 138559
Sorry, prediction pasa_asmbl_28478.p1 fails validation.
(AGC)	 TC	138466-138559	GT	AGG
(GTC)	 AG	139318-139414	GT	GGG
(CTG)	 AG	139763-139914	GT	TGG
(GGT)	 AG	140256-140393	GT	AGG
(GGA)	 AG	140737-140976	GT	CGG
(ACT)	 AG	141762-141961	GT	TGG
(ACC)	 AG	142060-142236	GT	GGG
(CTT)	 AG	142597-142667	GT	AGG
(TGC)	 AG	142790-142889	GT	AGG
(GTC)	 AG	143090-143143	GT	GGG
(AAA)	 AG	143852-143917	GT	ACG
(ATG)	 AG	144753-144821	GT	AGG
(GGA)	 AG	145050-145146	GT	GGG
(TGT)	 AG	145547-145617	CG	GAC
-recovered pasa_asmbl_28478.p1, initial, 144753, 144821
-recovered pasa_asmbl_28478.p1, terminal, 145547, 145617
-recovered pasa_asmbl_28478.p1, internal, 139318, 139414
-recovered pasa_asmbl_28478.p1, internal, 139763, 139914
-recovered pasa_asmbl_28478.p1, internal, 140256, 140393
-recovered pasa_asmbl_28478.p1, internal, 140737, 140976
-recovered pasa_asmbl_28478.p1, internal, 141762, 141961
-recovered pasa_asmbl_28478.p1, internal, 142060, 142236
-recovered pasa_asmbl_28478.p1, internal, 142597, 142667
-recovered pasa_asmbl_28478.p1, internal, 142790, 142889
-recovered pasa_asmbl_28478.p1, internal, 143090, 143143
-recovered pasa_asmbl_28478.p1, internal, 143852, 143917
-recovered pasa_asmbl_28478.p1, internal, 144753, 144821
-recovered pasa_asmbl_28478.p1, internal, 145050, 145146
Valid prediction for GlimmerHMM_glimmerT_47366-T1
Valid prediction for pasa_asmbl_28472.p1
Valid prediction for snap_scaffold_21-snap.587-T1
Valid prediction for snap_scaffold_21-snap.601-T1
Valid prediction for snap_scaffold_21-snap.565-T1
Valid prediction for snap_scaffold_21-snap.593-T1
Valid prediction for Augustus_model.g31551.t1
Valid prediction for GlimmerHMM_glimmerT_47349-T1
Valid prediction for snap_scaffold_21-snap.596-T1
Valid prediction for Augustus_model.g31555.t1
Valid prediction for GlimmerHMM_glimmerT_47364-T1
Valid prediction for snap_scaffold_21-snap.581-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for CodingQuarry_transcript_32482-T1
Valid prediction for snap_scaffold_21-snap.585-T1
Valid prediction for Augustus_model.g31537.t1
Valid prediction for snap_scaffold_21-snap.595-T1
Valid prediction for snap_scaffold_21-snap.588-T1
Valid prediction for Augustus_model.g31542.t1
Valid prediction for GlimmerHMM_glimmerT_47358-T1
Valid prediction for snap_scaffold_21-snap.576-T1
Valid prediction for CodingQuarry_transcript_32481-T1
Valid prediction for Augustus_model.g31552.t1
Valid prediction for snap_scaffold_21-snap.580-T1
Couldn't classify 96232, 96381
Couldn't classify 97492, 97539
Sorry, prediction pasa_asmbl_28453.p1 fails validation.
(AGA)	 GG	96232-96381	GT	AGG
(AAC)	 AG	96498-96676	GT	AAG
(GTT)	 AG	97177-97231	GT	AGG
(TGT)	 AG	97492-97539	AA	AGA
-recovered pasa_asmbl_28453.p1, internal, 96498, 96676
-recovered pasa_asmbl_28453.p1, internal, 97177, 97231
Valid prediction for snap_scaffold_21-snap.560-T1
Valid prediction for GlimmerHMM_glimmerT_47367-T1
Valid prediction for snap_scaffold_21-snap.577-T1
Valid prediction for GlimmerHMM_glimmerT_47354-T1
Valid prediction for snap_scaffold_21-snap.557-T1
Valid prediction for snap_scaffold_21-snap.599-T1
Valid prediction for snap_scaffold_21-snap.573-T1
Valid prediction for Augustus_model.g31556.t1
Valid prediction for snap_scaffold_21-snap.594-T1
Valid prediction for Augustus_model.g31549.t1
Valid prediction for snap_scaffold_21-snap.578-T1
Valid prediction for snap_scaffold_21-snap.575-T1
Valid prediction for snap_scaffold_21-snap.566-T1
Valid prediction for snap_scaffold_21-snap.563-T1
Valid prediction for GlimmerHMM_glimmerT_47352-T1
Valid prediction for CodingQuarry_transcript_32480-T1
Valid prediction for snap_scaffold_21-snap.562-T1
Valid prediction for GlimmerHMM_glimmerT_47368-T1
Valid prediction for snap_scaffold_21-snap.598-T1
Valid prediction for Augustus_model.g31539.t1
Valid prediction for pasa_asmbl_28460.p1
Valid prediction for Augustus_model.g31543.t1
Valid prediction for GlimmerHMM_glimmerT_47362-T1
Valid prediction for GlimmerHMM_glimmerT_47343-T1
Valid prediction for HiQ_model.g31547.t1
Valid prediction for Augustus_model.g31557.t1
Valid prediction for snap_scaffold_21-snap.589-T1
Valid prediction for GlimmerHMM_glimmerT_47351-T1
Valid prediction for GlimmerHMM_glimmerT_47356-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_47365-T1
Valid prediction for GlimmerHMM_glimmerT_47334-T1
Valid prediction for Augustus_model.g31558.t1
Valid prediction for snap_scaffold_21-snap.582-T1
Valid prediction for Augustus_model.g31541.t1
Valid prediction for GlimmerHMM_glimmerT_47347-T1
Valid prediction for snap_scaffold_21-snap.571-T1
Valid prediction for GlimmerHMM_glimmerT_47350-T1
Valid prediction for Augustus_model.g31540.t1
Valid prediction for snap_scaffold_21-snap.570-T1
Valid prediction for GlimmerHMM_glimmerT_47344-T1
Valid prediction for GlimmerHMM_glimmerT_47348-T1
Valid prediction for snap_scaffold_21-snap.584-T1
Valid prediction for GlimmerHMM_glimmerT_47346-T1
Valid prediction for snap_scaffold_21-snap.558-T1
Valid prediction for snap_scaffold_21-snap.592-T1
Couldn't classify 160410, 160469
Sorry, prediction pasa_asmbl_27502.p1 fails validation.
(CTG)	 CC	160410-160469	GT	AGG
(AGG)	 AG	160710-160855	GT	AGG
(AGT)	 AG	161227-161339	GT	AAG
(CCA)	 AG	161473-161609	CC	GAC
-recovered pasa_asmbl_27502.p1, terminal, 161473, 161609
-recovered pasa_asmbl_27502.p1, internal, 160710, 160855
-recovered pasa_asmbl_27502.p1, internal, 161227, 161339
Valid prediction for GlimmerHMM_glimmerT_47345-T1
Valid prediction for snap_scaffold_21-snap.569-T1
Valid prediction for Augustus_model.g31544.t1
Valid prediction for snap_scaffold_21-snap.600-T1
Valid prediction for Augustus_model.g31554.t1
Valid prediction for GlimmerHMM_glimmerT_47361-T1
Valid prediction for Augustus_model.g31545.t1
Valid prediction for HiQ_model.g31548.t1
Valid prediction for Augustus_model.g31538.t1
Valid prediction for GlimmerHMM_glimmerT_47342-T1
Valid prediction for snap_scaffold_21-snap.564-T1
Valid prediction for CodingQuarry_transcript_32479-T1
Valid prediction for snap_scaffold_21-snap.583-T1
Valid prediction for CodingQuarry_transcript_32475-T1
Valid prediction for CodingQuarry_transcript_32474-T1
Valid prediction for GlimmerHMM_glimmerT_47336-T1
Valid prediction for snap_scaffold_21-snap.572-T1
Valid prediction for snap_scaffold_21-snap.568-T1
Valid prediction for GlimmerHMM_glimmerT_47337-T1
Valid prediction for GlimmerHMM_glimmerT_47341-T1
Valid prediction for pasa_asmbl_27506.p1
Couldn't classify 157024, 157030
Couldn't classify 157902, 157991
Sorry, prediction pasa_asmbl_27504.p1 fails validation.
(TAT)	 AT	157024-157030	GT	AGG
(GCC)	 AG	157170-157307	GT	TGG
(GGG)	 AG	157487-157785	GT	GGG
(GTG)	 AG	157902-157991	CA	TTC
-recovered pasa_asmbl_27504.p1, internal, 157170, 157307
-recovered pasa_asmbl_27504.p1, internal, 157487, 157785
Valid prediction for snap_scaffold_21-snap.597-T1
Valid prediction for CodingQuarry_transcript_32476-T1
Valid prediction for snap_scaffold_21-snap.574-T1
Valid prediction for GlimmerHMM_glimmerT_47340-T1
Valid prediction for pasa_asmbl_27505.p1
Valid prediction for snap_scaffold_21-snap.586-T1
Valid prediction for GlimmerHMM_glimmerT_47359-T1
Valid prediction for GlimmerHMM_glimmerT_47360-T1
Valid prediction for HiQ_model.g31546.t1
Valid prediction for GlimmerHMM_glimmerT_47338-T1
Valid prediction for GlimmerHMM_glimmerT_47355-T1
Valid prediction for snap_scaffold_21-snap.591-T1
Valid prediction for snap_scaffold_21-snap.567-T1
Valid prediction for CodingQuarry_transcript_32477-T1
Valid prediction for snap_scaffold_21-snap.561-T1
Valid prediction for Augustus_model.g31536.t1
Valid prediction for pasa_asmbl_27513.p1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 15083, rend_intergenic: 12180  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29720, rend_intergenic: 27429  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38728, rend_intergenic: 30277  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49034, rend_intergenic: 39154  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121540, rend_intergenic: 103529  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127845, rend_intergenic: 123516  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199211, rend_intergenic: 197950  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 212159, rend_intergenic: 199317  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 213892
-exon list size: 557


building trellis

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90.5    
90.7    
90.9    
91.1    
91.2    
91.4    
91.6    
91.8    
91.9    
92.1    
92.3    
92.5    
92.7    
92.8    
93.0    
93.2    
93.4    
93.6    
93.7    
93.9    
94.1    
94.3    
94.5    
94.6    
94.8    
95.0    
95.2    
95.3    
95.5    
95.7    
95.9    
96.1    
96.2    
96.4    
96.6    
96.8    
97.0    
97.1    
97.3    
97.5    
97.7    
97.9    
98.0    
98.2    
98.4    
98.6    
98.7    
98.9    
99.1    
99.3    
99.5    
99.6    
99.8    
-found 39 predictions from path traversal
Error with prediction: snap lend_intergenic: 15083, rend_intergenic: 12180  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29720, rend_intergenic: 27429  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38728, rend_intergenic: 30277  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49034, rend_intergenic: 39154  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121540, rend_intergenic: 103529  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127845, rend_intergenic: 123516  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199211, rend_intergenic: 197950  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 212159, rend_intergenic: 199317  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

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