-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_7/scaffold_7_15580305-15746731

-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.32068_t
Couldn't classify 66869, 67190
Couldn't classify 73078, 73197
Sorry, prediction pasa_asmbl_51336.p1 fails validation.
(GTT)	 GT	66869-67190	GT	GTG
(ACG)	 AG	67805-67916	GT	AGG
(GGC)	 AG	69060-69249	GT	AGG
(ATG)	 AG	71359-71424	GT	AGG
(CTG)	 AG	71573-71674	GT	AGG
(AGA)	 AG	73078-73197	GT	CAG
-recovered pasa_asmbl_51336.p1, initial, 71359, 71424
-recovered pasa_asmbl_51336.p1, internal, 67805, 67916
-recovered pasa_asmbl_51336.p1, internal, 69060, 69249
-recovered pasa_asmbl_51336.p1, internal, 71359, 71424
-recovered pasa_asmbl_51336.p1, internal, 71573, 71674
-recovered pasa_asmbl_51336.p1, internal, 73078, 73197
Couldn't classify 73078, 73197
Sorry, prediction pasa_asmbl_51339.p1 fails validation.
(ATG)	 GG	67816-67916	GT	AGG
(GGC)	 AG	69060-69249	GT	AGG
(ATG)	 AG	71359-71424	GT	AGG
(CTG)	 AG	71573-71674	GT	AGG
(AGA)	 AG	73078-73197	GT	CAG
-recovered pasa_asmbl_51339.p1, initial, 67816, 67916
-recovered pasa_asmbl_51339.p1, initial, 71359, 71424
-recovered pasa_asmbl_51339.p1, internal, 69060, 69249
-recovered pasa_asmbl_51339.p1, internal, 71359, 71424
-recovered pasa_asmbl_51339.p1, internal, 71573, 71674
-recovered pasa_asmbl_51339.p1, internal, 73078, 73197
Valid prediction for Augustus_model.g12892.t1
Valid prediction for Augustus_model.g12897.t1
Valid prediction for GeneMark_model.32050_t
Valid prediction for snap_scaffold_7-snap.2973-T1
Valid prediction for snap_scaffold_7-snap.2971-T1
Couldn't classify 81823, 82554
Sorry, prediction pasa_asmbl_51342.p1 fails validation.
(TGT)	 TT	81823-82554	AC	GAA
Valid prediction for GeneMark_model.32046_t
Valid prediction for GeneMark_model.32077_t
Valid prediction for snap_scaffold_7-snap.2994-T1
Valid prediction for GeneMark_model.32080_t
Couldn't classify 19895, 20111
Sorry, prediction CodingQuarry_transcript_57585-T1 fails validation.
(ATG)	 AG	19895-20111	CT	CTC
(ACC)	 AG	20430-20452	CC	GAC
-recovered CodingQuarry_transcript_57585-T1, terminal, 20430, 20452
Valid prediction for Augustus_model.g12893.t1
Valid prediction for GeneMark_model.32060_t
Valid prediction for GeneMark_model.32057_t
Valid prediction for GlimmerHMM_glimmerT_19058-T1
Couldn't classify 16737, 16796
Sorry, prediction pasa_asmbl_51331.p1 fails validation.
(ATG)	 AG	15647-15789	GT	AGG
(CTC)	 AG	16103-16247	GT	ATG
(GAG)	 AG	16737-16796	CT	AGC
-recovered pasa_asmbl_51331.p1, initial, 15647, 15789
-recovered pasa_asmbl_51331.p1, internal, 15647, 15789
-recovered pasa_asmbl_51331.p1, internal, 16103, 16247
Valid prediction for snap_scaffold_7-snap.2985-T1
Valid prediction for GlimmerHMM_glimmerT_19047-T1
Valid prediction for GeneMark_model.32034_t
Valid prediction for snap_scaffold_7-snap.2969-T1
Valid prediction for GeneMark_model.32052_t
Valid prediction for snap_scaffold_7-snap.2979-T1
Valid prediction for GeneMark_model.32067_t
Valid prediction for snap_scaffold_7-snap.2954-T1
Valid prediction for snap_scaffold_7-snap.2992-T1
Valid prediction for GeneMark_model.32037_t
Valid prediction for GeneMark_model.32075_t
Valid prediction for snap_scaffold_7-snap.2959-T1
Valid prediction for GeneMark_model.32044_t
Valid prediction for snap_scaffold_7-snap.2980-T1
Valid prediction for GeneMark_model.32073_t
Valid prediction for snap_scaffold_7-snap.2963-T1
Valid prediction for GeneMark_model.32064_t
Valid prediction for snap_scaffold_7-snap.2966-T1
Sorry, intron length (7) is less than minimum required (10)
Couldn't classify 17806, 17920
Sorry, prediction pasa_asmbl_51333.p1 fails validation.
(CCC)	 CT	17806-17920	GT	AGG
(ACG)	 AG	18091-18236	GT	AGG
(TCC)	 AG	19420-19536	TT	AAT
-recovered pasa_asmbl_51333.p1, terminal, 19420, 19536
-recovered pasa_asmbl_51333.p1, internal, 18091, 18236
Valid prediction for snap_scaffold_7-snap.2990-T1
Valid prediction for snap_scaffold_7-snap.2987-T1
Valid prediction for snap_scaffold_7-snap.2982-T1
Valid prediction for HiQ_model.g12886.t1
Valid prediction for GlimmerHMM_glimmerT_19056-T1
Valid prediction for GlimmerHMM_glimmerT_19057-T1
Valid prediction for GeneMark_model.32048_t
Valid prediction for Augustus_model.g12890.t1
Valid prediction for snap_scaffold_7-snap.2989-T1
Valid prediction for GeneMark_model.32079_t
Valid prediction for GeneMark_model.32071_t
Valid prediction for GlimmerHMM_glimmerT_19051-T1
Valid prediction for GeneMark_model.32042_t
Valid prediction for snap_scaffold_7-snap.2956-T1
Valid prediction for GeneMark_model.32053_t
Valid prediction for Augustus_model.g12891.t1
Valid prediction for GeneMark_model.32058_t
Couldn't classify 16851, 16882
Couldn't classify 17739, 17802
Sorry, prediction pasa_asmbl_51463.p1 fails validation.
(CAG)	 GT	16851-16882	GT	CGG
(GAT)	 AG	17112-17270	GT	GAG
(GCT)	 AG	17491-17643	GT	CTG
(GGA)	 AG	17739-17802	TC	TGT
-recovered pasa_asmbl_51463.p1, internal, 17112, 17270
-recovered pasa_asmbl_51463.p1, internal, 17491, 17643
Valid prediction for GlimmerHMM_glimmerT_19050-T1
Valid prediction for GeneMark_model.32062_t
Valid prediction for snap_scaffold_7-snap.2968-T1
Valid prediction for Augustus_model.g12884.t1
Valid prediction for GeneMark_model.32054_t

-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.32070_t
Valid prediction for GeneMark_model.32047_t
Valid prediction for GlimmerHMM_glimmerT_19054-T1
Valid prediction for GeneMark_model.32056_t
Valid prediction for GeneMark_model.32041_t
Valid prediction for GlimmerHMM_glimmerT_19065-T1
Valid prediction for GeneMark_model.32035_t
Valid prediction for GeneMark_model.32069_t
Valid prediction for GlimmerHMM_glimmerT_19049-T1
Valid prediction for GeneMark_model.32074_t
Valid prediction for GeneMark_model.32049_t
Valid prediction for snap_scaffold_7-snap.2976-T1
Valid prediction for snap_scaffold_7-snap.2988-T1
Valid prediction for snap_scaffold_7-snap.2965-T1
Valid prediction for GlimmerHMM_glimmerT_19062-T1
Valid prediction for snap_scaffold_7-snap.2957-T1
Valid prediction for GlimmerHMM_glimmerT_19063-T1
Valid prediction for GeneMark_model.32033_t
Valid prediction for GlimmerHMM_glimmerT_19055-T1
Valid prediction for GlimmerHMM_glimmerT_19048-T1
Valid prediction for GeneMark_model.32038_t
Valid prediction for GeneMark_model.32043_t
Valid prediction for GeneMark_model.32051_t
Valid prediction for snap_scaffold_7-snap.2967-T1
Valid prediction for snap_scaffold_7-snap.2977-T1
Valid prediction for snap_scaffold_7-snap.2993-T1
Valid prediction for Augustus_model.g12894.t1
Valid prediction for GeneMark_model.32072_t
Valid prediction for HiQ_model.g12885.t1
Valid prediction for Augustus_model.g12899.t1
Valid prediction for GlimmerHMM_glimmerT_19060-T1
Valid prediction for snap_scaffold_7-snap.2955-T1
Valid prediction for snap_scaffold_7-snap.2991-T1
Valid prediction for snap_scaffold_7-snap.2978-T1
Valid prediction for Augustus_model.g12898.t1
Valid prediction for snap_scaffold_7-snap.2961-T1
Valid prediction for GlimmerHMM_glimmerT_19061-T1
Valid prediction for Augustus_model.g12895.t1
Valid prediction for GeneMark_model.32078_t
Valid prediction for GeneMark_model.32040_t
Valid prediction for GlimmerHMM_glimmerT_19046-T1
Valid prediction for Augustus_model.g12896.t1
Valid prediction for GeneMark_model.32063_t
Valid prediction for snap_scaffold_7-snap.2974-T1
Valid prediction for snap_scaffold_7-snap.2960-T1
Valid prediction for GeneMark_model.32066_t
Valid prediction for snap_scaffold_7-snap.2962-T1
Valid prediction for snap_scaffold_7-snap.2986-T1
Valid prediction for GeneMark_model.32045_t
Valid prediction for snap_scaffold_7-snap.2958-T1
Valid prediction for snap_scaffold_7-snap.2970-T1
Valid prediction for snap_scaffold_7-snap.2984-T1
Valid prediction for snap_scaffold_7-snap.2983-T1
Valid prediction for Augustus_model.g12887.t1
Valid prediction for GeneMark_model.32036_t
Valid prediction for Augustus_model.g12889.t1
Valid prediction for snap_scaffold_7-snap.2972-T1
Valid prediction for Augustus_model.g12883.t1
Valid prediction for GeneMark_model.32055_t
Valid prediction for snap_scaffold_7-snap.2964-T1
Valid prediction for snap_scaffold_7-snap.2981-T1
Valid prediction for GlimmerHMM_glimmerT_19059-T1
Valid prediction for GeneMark_model.32065_t
Valid prediction for GeneMark_model.32076_t
Couldn't classify 152272, 152335
Sorry, prediction pasa_asmbl_50205.p1 fails validation.
(AGT)	 GC	152272-152335	GT	ACG
(GTT)	 AG	152569-152808	GT	AGG
(GAG)	 AG	152916-153033	GT	AGG
(GCT)	 AG	153126-153213	GT	GGG
(GTC)	 AG	153379-153557	GT	GGG
(ATA)	 AG	153670-153862	GT	CGG
(GTG)	 AG	154078-154206	GT	TGG
(GCT)	 AG	154805-154930	GT	AGG
(GGT)	 AG	155015-155100	GT	AGG
(TTC)	 AG	155176-155285	GT	CAG
(GTG)	 AG	155640-155871	GT	TGG
(GTC)	 AG	156198-156265	GT	GGG
(GGG)	 AG	156488-156696	GT	AGG
(GAT)	 AG	156842-157063	TG	GAT
-recovered pasa_asmbl_50205.p1, terminal, 156842, 157063
-recovered pasa_asmbl_50205.p1, internal, 152569, 152808
-recovered pasa_asmbl_50205.p1, internal, 152916, 153033
-recovered pasa_asmbl_50205.p1, internal, 153126, 153213
-recovered pasa_asmbl_50205.p1, internal, 153379, 153557
-recovered pasa_asmbl_50205.p1, internal, 153670, 153862
-recovered pasa_asmbl_50205.p1, internal, 154078, 154206
-recovered pasa_asmbl_50205.p1, internal, 154805, 154930
-recovered pasa_asmbl_50205.p1, internal, 155015, 155100
-recovered pasa_asmbl_50205.p1, internal, 155176, 155285
-recovered pasa_asmbl_50205.p1, internal, 155640, 155871
-recovered pasa_asmbl_50205.p1, internal, 156198, 156265
-recovered pasa_asmbl_50205.p1, internal, 156488, 156696
Valid prediction for GlimmerHMM_glimmerT_19066-T1
Valid prediction for GlimmerHMM_glimmerT_19052-T1
Valid prediction for snap_scaffold_7-snap.2975-T1
Valid prediction for GeneMark_model.32061_t
Valid prediction for Augustus_model.g12888.t1
Valid prediction for GeneMark_model.32059_t
Valid prediction for GlimmerHMM_glimmerT_19064-T1
Valid prediction for GlimmerHMM_glimmerT_19053-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 4787, rend_intergenic: 2256  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21898, rend_intergenic: 15695  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29026, rend_intergenic: 28863  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33954, rend_intergenic: 29953  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42321, rend_intergenic: 40600  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44516, rend_intergenic: 42502  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55127, rend_intergenic: 51772  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57469, rend_intergenic: 55157  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60881, rend_intergenic: 57542  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84729, rend_intergenic: 65612  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93557, rend_intergenic: 91642  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107229, rend_intergenic: 104484  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118613, rend_intergenic: 116963  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123038, rend_intergenic: 121872  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134651, rend_intergenic: 132415  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137077, rend_intergenic: 134667  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159813, rend_intergenic: 156560  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161188, rend_intergenic: 160176  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 166427
-exon list size: 585


building trellis

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84.8    
85.0    
85.2    
85.3    
85.5    
85.7    
85.9    
86.0    
86.2    
86.4    
86.5    
86.7    
86.9    
87.1    
87.2    
87.4    
87.6    
87.7    
87.9    
88.1    
88.2    
88.4    
88.6    
88.8    
88.9    
89.1    
89.3    
89.4    
89.6    
89.8    
89.9    
90.1    
90.3    
90.5    
90.6    
90.8    
91.0    
91.1    
91.3    
91.5    
91.7    
91.8    
92.0    
92.2    
92.3    
92.5    
92.7    
92.8    
93.0    
93.2    
93.4    
93.5    
93.7    
93.9    
94.0    
94.2    
94.4    
94.5    
94.7    
94.9    
95.1    
95.2    
95.4    
95.6    
95.7    
95.9    
96.1    
96.3    
96.4    
96.6    
96.8    
96.9    
97.1    
97.3    
97.4    
97.6    
97.8    
98.0    
98.1    
98.3    
98.5    
98.6    
98.8    
99.0    
99.1    
99.3    
99.5    
99.7    
99.8    
-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 4787, rend_intergenic: 2256  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21898, rend_intergenic: 15695  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29026, rend_intergenic: 28863  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33954, rend_intergenic: 29953  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42321, rend_intergenic: 40600  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44516, rend_intergenic: 42502  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55127, rend_intergenic: 51772  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57469, rend_intergenic: 55157  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60881, rend_intergenic: 57542  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84729, rend_intergenic: 65612  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93557, rend_intergenic: 91642  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107229, rend_intergenic: 104484  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118613, rend_intergenic: 116963  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123038, rend_intergenic: 121872  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134651, rend_intergenic: 132415  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137077, rend_intergenic: 134667  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159813, rend_intergenic: 156560  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161188, rend_intergenic: 160176  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