-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_12/scaffold_12_2333640-2590321

-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.51054_t
Valid prediction for GlimmerHMM_glimmerT_29557-T1
Valid prediction for GeneMark_model.51046_t
Valid prediction for snap_scaffold_12-snap.512-T1
Valid prediction for GeneMark_model.51056_t
Valid prediction for GeneMark_model.51060_t
Valid prediction for Augustus_model.g19671.t1
Valid prediction for snap_scaffold_12-snap.484-T1
Valid prediction for snap_scaffold_12-snap.487-T1
Valid prediction for GeneMark_model.51066_t
Valid prediction for GeneMark_model.51089_t
Valid prediction for snap_scaffold_12-snap.478-T1
Valid prediction for HiQ_model.g19681.t1
Valid prediction for snap_scaffold_12-snap.494-T1
Valid prediction for GeneMark_model.51072_t
Valid prediction for snap_scaffold_12-snap.518-T1
Valid prediction for GeneMark_model.51062_t
Valid prediction for GeneMark_model.51099_t
Valid prediction for GeneMark_model.51074_t
Valid prediction for GlimmerHMM_glimmerT_29559-T1
Valid prediction for GlimmerHMM_glimmerT_29566-T1
Valid prediction for GeneMark_model.51050_t
Valid prediction for snap_scaffold_12-snap.471-T1
Valid prediction for GlimmerHMM_glimmerT_29556-T1
Valid prediction for GeneMark_model.51075_t
Valid prediction for GlimmerHMM_glimmerT_29568-T1
Couldn't classify 88822, 88985
Couldn't classify 91080, 91155
Sorry, prediction pasa_asmbl_8455.p1 fails validation.
(GCC)	 CG	88822-88985	GT	AGG
(GTA)	 AG	89358-89741	GT	AGG
(CGG)	 AG	91080-91155	GG	TTG
-recovered pasa_asmbl_8455.p1, internal, 89358, 89741
Valid prediction for Augustus_model.g19672.t1
Valid prediction for GeneMark_model.51079_t
Valid prediction for GeneMark_model.51052_t
Valid prediction for GlimmerHMM_glimmerT_29550-T1
Valid prediction for snap_scaffold_12-snap.509-T1
Valid prediction for Augustus_model.g19666.t1
Valid prediction for GeneMark_model.51064_t
Valid prediction for GeneMark_model.51048_t
Valid prediction for snap_scaffold_12-snap.521-T1
Valid prediction for GlimmerHMM_glimmerT_29573-T1
Valid prediction for snap_scaffold_12-snap.470-T1
Couldn't classify 99532, 99707
Couldn't classify 101154, 101793
Sorry, prediction pasa_asmbl_8458.p1 fails validation.
(CCA)	 TC	99532-99707	GT	GGG
(AGG)	 AG	101154-101793	TT	GGT
Valid prediction for GeneMark_model.51092_t
Valid prediction for GeneMark_model.51087_t
Couldn't classify 94624, 94721
Sorry, prediction pasa_asmbl_8456.p1 fails validation.
(ATG)	 AC	91954-91982	GT	AGG
(GTC)	 AG	94093-94316	GT	CTG
(TGC)	 AG	94624-94721	GC	AGG
-recovered pasa_asmbl_8456.p1, initial, 91954, 91982
-recovered pasa_asmbl_8456.p1, internal, 94093, 94316
-recovered pasa_asmbl_8456.p1, internal, 94624, 94721
Valid prediction for snap_scaffold_12-snap.524-T1
Valid prediction for snap_scaffold_12-snap.474-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GeneMark_model.51080_t
Valid prediction for snap_scaffold_12-snap.493-T1
Valid prediction for snap_scaffold_12-snap.488-T1
Valid prediction for GeneMark_model.51045_t
Valid prediction for Augustus_model.g19667.t1
Couldn't classify 87140, 87296
Sorry, prediction pasa_asmbl_8453.p1 fails validation.
(ATG)	 AC	81222-81314	GT	AGG
(CTG)	 AG	82718-82876	GT	AGG
(TTT)	 AG	83257-83409	GT	AGG
(GGG)	 AG	83553-83717	GT	AGG
(GTT)	 AG	84309-84416	GT	AGG
(AAA)	 AG	84688-84891	GT	AGG
(ATC)	 AG	86038-86146	GT	AGG
(TGT)	 AG	86609-86882	GT	AAG
(CGA)	 AG	87140-87296	GG	CAG
-recovered pasa_asmbl_8453.p1, initial, 81222, 81314
add_exon() Sorry, pasa_asmbl_8453.p1 86038-86146-terminal-3 is invalid.
-recovered pasa_asmbl_8453.p1, terminal, 86038, 86146
-recovered pasa_asmbl_8453.p1, internal, 82718, 82876
-recovered pasa_asmbl_8453.p1, internal, 83257, 83409
-recovered pasa_asmbl_8453.p1, internal, 83553, 83717
-recovered pasa_asmbl_8453.p1, internal, 84309, 84416
-recovered pasa_asmbl_8453.p1, internal, 84688, 84891
-recovered pasa_asmbl_8453.p1, internal, 86038, 86146
-recovered pasa_asmbl_8453.p1, internal, 86609, 86882
Valid prediction for snap_scaffold_12-snap.489-T1
Valid prediction for GlimmerHMM_glimmerT_29554-T1
Valid prediction for GeneMark_model.51083_t
Valid prediction for snap_scaffold_12-snap.496-T1
Valid prediction for snap_scaffold_12-snap.481-T1
Valid prediction for snap_scaffold_12-snap.505-T1
Valid prediction for GeneMark_model.51082_t
Valid prediction for Augustus_model.g19676.t1
Valid prediction for GlimmerHMM_glimmerT_29563-T1
Valid prediction for GlimmerHMM_glimmerT_29551-T1
Valid prediction for snap_scaffold_12-snap.503-T1
Valid prediction for Augustus_model.g19669.t1
Valid prediction for Augustus_model.g19668.t1
Valid prediction for GeneMark_model.51090_t
Valid prediction for GlimmerHMM_glimmerT_29561-T1
Couldn't classify 247307, 247416
Sorry, prediction pasa_asmbl_8462.p1 fails validation.
(ATG)	 TC	244162-244245	GT	GGG
(TGG)	 AG	244543-244635	GT	AGG
(GTG)	 AG	244991-245087	GT	AGG
(ATT)	 AG	245313-245453	GT	TGG
(GGA)	 AG	247307-247416	TG	CGT
-recovered pasa_asmbl_8462.p1, initial, 244162, 244245
-recovered pasa_asmbl_8462.p1, internal, 244543, 244635
-recovered pasa_asmbl_8462.p1, internal, 244991, 245087
-recovered pasa_asmbl_8462.p1, internal, 245313, 245453
Valid prediction for GeneMark_model.51070_t
Valid prediction for snap_scaffold_12-snap.516-T1
Valid prediction for GeneMark_model.51085_t
Valid prediction for GeneMark_model.51078_t
Valid prediction for snap_scaffold_12-snap.485-T1
Valid prediction for GeneMark_model.51068_t
Valid prediction for Augustus_model.g19665.t1
Valid prediction for snap_scaffold_12-snap.522-T1
Valid prediction for snap_scaffold_12-snap.473-T1
Valid prediction for GlimmerHMM_glimmerT_29562-T1
Valid prediction for Augustus_model.g19670.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_29570-T1
Valid prediction for snap_scaffold_12-snap.499-T1
Valid prediction for GlimmerHMM_glimmerT_29552-T1
Valid prediction for snap_scaffold_12-snap.504-T1
Valid prediction for snap_scaffold_12-snap.523-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for Augustus_model.g19664.t1
Valid prediction for GeneMark_model.51061_t
Valid prediction for GeneMark_model.51051_t
Valid prediction for snap_scaffold_12-snap.468-T1
Valid prediction for Augustus_model.g19675.t1
Valid prediction for snap_scaffold_12-snap.476-T1
Valid prediction for snap_scaffold_12-snap.502-T1
Valid prediction for GlimmerHMM_glimmerT_29567-T1
Valid prediction for Augustus_model.g19678.t1
Valid prediction for GeneMark_model.51073_t
Valid prediction for GeneMark_model.51044_t
Valid prediction for GeneMark_model.51053_t
Valid prediction for snap_scaffold_12-snap.477-T1
Valid prediction for GeneMark_model.51096_t
Valid prediction for GlimmerHMM_glimmerT_29564-T1
Valid prediction for GlimmerHMM_glimmerT_29558-T1
Valid prediction for GeneMark_model.51098_t
Valid prediction for Augustus_model.g19674.t1
Valid prediction for snap_scaffold_12-snap.475-T1
Valid prediction for GeneMark_model.51088_t
Valid prediction for HiQ_model.g19663.t1
Valid prediction for GlimmerHMM_glimmerT_29560-T1
Valid prediction for GeneMark_model.51071_t
Valid prediction for GeneMark_model.51065_t
Valid prediction for GlimmerHMM_glimmerT_29572-T1
Valid prediction for snap_scaffold_12-snap.491-T1
Valid prediction for snap_scaffold_12-snap.498-T1
Valid prediction for snap_scaffold_12-snap.511-T1
Valid prediction for GeneMark_model.51086_t
Valid prediction for GeneMark_model.51095_t
Valid prediction for snap_scaffold_12-snap.472-T1
Valid prediction for GeneMark_model.51055_t
Valid prediction for snap_scaffold_12-snap.507-T1
Valid prediction for GeneMark_model.51091_t
Valid prediction for GlimmerHMM_glimmerT_29569-T1
Valid prediction for GeneMark_model.51093_t
Valid prediction for GlimmerHMM_glimmerT_29549-T1
Valid prediction for GlimmerHMM_glimmerT_29571-T1
Valid prediction for snap_scaffold_12-snap.501-T1
Valid prediction for GeneMark_model.51067_t
Valid prediction for Augustus_model.g19673.t1
Valid prediction for snap_scaffold_12-snap.482-T1
Valid prediction for snap_scaffold_12-snap.514-T1
Valid prediction for snap_scaffold_12-snap.517-T1
Valid prediction for GeneMark_model.51076_t
Valid prediction for pasa_asmbl_7460.p1
Valid prediction for Augustus_model.g19677.t1
Valid prediction for snap_scaffold_12-snap.515-T1
Valid prediction for snap_scaffold_12-snap.490-T1
Valid prediction for GeneMark_model.51069_t
Valid prediction for snap_scaffold_12-snap.497-T1
Valid prediction for snap_scaffold_12-snap.486-T1
Valid prediction for GeneMark_model.51057_t
Valid prediction for snap_scaffold_12-snap.479-T1
Valid prediction for GlimmerHMM_glimmerT_29555-T1
Valid prediction for Augustus_model.g19680.t1
Valid prediction for GlimmerHMM_glimmerT_29553-T1
Valid prediction for snap_scaffold_12-snap.469-T1
Valid prediction for snap_scaffold_12-snap.483-T1
Valid prediction for snap_scaffold_12-snap.513-T1
Valid prediction for GeneMark_model.51094_t
Valid prediction for snap_scaffold_12-snap.508-T1
Valid prediction for GeneMark_model.51058_t
Valid prediction for GeneMark_model.51077_t
Valid prediction for snap_scaffold_12-snap.510-T1
Valid prediction for GlimmerHMM_glimmerT_29565-T1
Valid prediction for GeneMark_model.51047_t
Valid prediction for snap_scaffold_12-snap.519-T1
Valid prediction for snap_scaffold_12-snap.492-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for snap_scaffold_12-snap.480-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GeneMark_model.51059_t
Valid prediction for snap_scaffold_12-snap.495-T1
Valid prediction for snap_scaffold_12-snap.506-T1
Valid prediction for snap_scaffold_12-snap.500-T1
Valid prediction for GeneMark_model.51097_t
Valid prediction for GeneMark_model.51049_t
Valid prediction for GeneMark_model.51081_t
Valid prediction for GeneMark_model.51063_t
Valid prediction for snap_scaffold_12-snap.520-T1
Valid prediction for Augustus_model.g19679.t1
Valid prediction for GeneMark_model.51084_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 26285, rend_intergenic: 25099  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51163, rend_intergenic: 32056  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66732, rend_intergenic: 56492  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71620, rend_intergenic: 68916  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77756, rend_intergenic: 73550  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81720, rend_intergenic: 77994  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85169, rend_intergenic: 82356  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97920, rend_intergenic: 91076  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100569, rend_intergenic: 98232  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153890, rend_intergenic: 152376  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171548, rend_intergenic: 168659  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182348, rend_intergenic: 179915  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 201002, rend_intergenic: 196579  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 203437, rend_intergenic: 201349  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 256682
-exon list size: 723


building trellis

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77.4    
77.5    
77.7    
77.8    
77.9    
78.1    
78.2    
78.3    
78.5    
78.6    
78.8    
78.9    
79.0    
79.2    
79.3    
79.4    
79.6    
79.7    
79.9    
80.0    
80.1    
80.3    
80.4    
80.6    
80.7    
80.8    
81.0    
81.1    
81.2    
81.4    
81.5    
81.7    
81.8    
81.9    
82.1    
82.2    
82.3    
82.5    
82.6    
82.8    
82.9    
83.0    
83.2    
83.3    
83.4    
83.6    
83.7    
83.9    
84.0    
84.1    
84.3    
84.4    
84.6    
84.7    
84.8    
85.0    
85.1    
85.2    
85.4    
85.5    
85.7    
85.8    
85.9    
86.1    
86.2    
86.3    
86.5    
86.6    
86.8    
86.9    
87.0    
87.2    
87.3    
87.4    
87.6    
87.7    
87.9    
88.0    
88.1    
88.3    
88.4    
88.6    
88.7    
88.8    
89.0    
89.1    
89.2    
89.4    
89.5    
89.7    
89.8    
89.9    
90.1    
90.2    
90.3    
90.5    
90.6    
90.8    
90.9    
91.0    
91.2    
91.3    
91.4    
91.6    
91.7    
91.9    
92.0    
92.1    
92.3    
92.4    
92.6    
92.7    
92.8    
93.0    
93.1    
93.2    
93.4    
93.5    
93.7    
93.8    
93.9    
94.1    
94.2    
94.3    
94.5    
94.6    
94.8    
94.9    
95.0    
95.2    
95.3    
95.4    
95.6    
95.7    
95.9    
96.0    
96.1    
96.3    
96.4    
96.6    
96.7    
96.8    
97.0    
97.1    
97.2    
97.4    
97.5    
97.7    
97.8    
97.9    
98.1    
98.2    
98.3    
98.5    
98.6    
98.8    
98.9    
99.0    
99.2    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 38 predictions from path traversal
Error with prediction: snap lend_intergenic: 26285, rend_intergenic: 25099  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51163, rend_intergenic: 32056  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66732, rend_intergenic: 56492  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71620, rend_intergenic: 68916  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77756, rend_intergenic: 73550  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81720, rend_intergenic: 77994  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85169, rend_intergenic: 82356  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97920, rend_intergenic: 91076  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100569, rend_intergenic: 98232  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153890, rend_intergenic: 152376  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171548, rend_intergenic: 168659  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182348, rend_intergenic: 179915  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 201002, rend_intergenic: 196579  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 203437, rend_intergenic: 201349  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 24 predictions persist after filtering for low support