-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_12/scaffold_12_2758356-2976135

-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 snap_scaffold_12-snap.590-T1
Valid prediction for GlimmerHMM_glimmerT_29608-T1
Valid prediction for GeneMark_model.51167_t
Valid prediction for CodingQuarry_transcript_10117-T1
Valid prediction for GlimmerHMM_glimmerT_29601-T1
Valid prediction for snap_scaffold_12-snap.582-T1
Valid prediction for pasa_asmbl_8492.p1
Valid prediction for snap_scaffold_12-snap.563-T1
Valid prediction for GeneMark_model.51147_t
Valid prediction for snap_scaffold_12-snap.565-T1
Valid prediction for GeneMark_model.51156_t
Valid prediction for snap_scaffold_12-snap.594-T1
Valid prediction for GeneMark_model.51151_t
Valid prediction for GeneMark_model.51152_t
Valid prediction for GlimmerHMM_glimmerT_29619-T1
Valid prediction for GlimmerHMM_glimmerT_29620-T1
Valid prediction for Augustus_model.g19710.t1
Valid prediction for GlimmerHMM_glimmerT_29604-T1
Valid prediction for snap_scaffold_12-snap.572-T1
Valid prediction for Augustus_model.g19703.t1
Valid prediction for GeneMark_model.51161_t
Valid prediction for CodingQuarry_transcript_10118-T1
Valid prediction for GlimmerHMM_glimmerT_29617-T1
Valid prediction for GlimmerHMM_glimmerT_29594-T1
Valid prediction for HiQ_model.g19709.t1
Valid prediction for GlimmerHMM_glimmerT_29612-T1
Valid prediction for GlimmerHMM_glimmerT_29602-T1
Valid prediction for snap_scaffold_12-snap.592-T1
Valid prediction for snap_scaffold_12-snap.595-T1
Valid prediction for snap_scaffold_12-snap.577-T1
Couldn't classify 3910, 3917
Sorry, prediction pasa_asmbl_8487.p1 fails validation.
(TGT)	 TA	3910-3917	GT	GTG
(CGC)	 AG	4006-4162	GT	TGG
(GTG)	 AG	4416-4523	GT	AGG
(GTG)	 AG	4701-4822	GT	AAG
(GAG)	 AG	4944-5013	GT	AGG
(TAT)	 AG	5223-5438	GT	AGG
(GGC)	 AG	6180-6277	GT	TGG
(TGC)	 AG	6376-6439	GT	AGG
(GTG)	 AG	6567-6677	GT	TGG
(CTG)	 AG	7111-7175	GT	AGG
(ACT)	 AG	7265-7327	GT	TGG
(GGC)	 AG	7558-7632	GT	AGG
(ACT)	 AG	7854-7957	GT	CAG
(GTG)	 AG	8084-8206	GT	TGG
(ACG)	 AG	8390-8492	GT	AAG
(GTT)	 AG	8702-8795	GT	AGG
(ATG)	 AG	9141-9244	GT	AGG
(GTT)	 AG	9692-9809	GT	AGG
(AAG)	 AG	10119-10259	GT	AGG
(CGC)	 AG	10428-10541	GT	TGG
(CAT)	 AG	10882-10995	GC	GAG
-recovered pasa_asmbl_8487.p1, initial, 9141, 9244
-recovered pasa_asmbl_8487.p1, terminal, 10882, 10995
-recovered pasa_asmbl_8487.p1, internal, 4006, 4162
-recovered pasa_asmbl_8487.p1, internal, 4416, 4523
-recovered pasa_asmbl_8487.p1, internal, 4701, 4822
-recovered pasa_asmbl_8487.p1, internal, 4944, 5013
-recovered pasa_asmbl_8487.p1, internal, 5223, 5438
-recovered pasa_asmbl_8487.p1, internal, 6180, 6277
-recovered pasa_asmbl_8487.p1, internal, 6376, 6439
-recovered pasa_asmbl_8487.p1, internal, 6567, 6677
-recovered pasa_asmbl_8487.p1, internal, 7111, 7175
-recovered pasa_asmbl_8487.p1, internal, 7265, 7327
-recovered pasa_asmbl_8487.p1, internal, 7558, 7632
-recovered pasa_asmbl_8487.p1, internal, 7854, 7957
-recovered pasa_asmbl_8487.p1, internal, 8084, 8206
-recovered pasa_asmbl_8487.p1, internal, 8390, 8492
-recovered pasa_asmbl_8487.p1, internal, 8702, 8795
-recovered pasa_asmbl_8487.p1, internal, 9141, 9244
-recovered pasa_asmbl_8487.p1, internal, 9692, 9809
-recovered pasa_asmbl_8487.p1, internal, 10119, 10259
-recovered pasa_asmbl_8487.p1, internal, 10428, 10541
-recovered pasa_asmbl_8487.p1, internal, 10882, 10995
Valid prediction for GlimmerHMM_glimmerT_29593-T1
Valid prediction for GlimmerHMM_glimmerT_29607-T1
Valid prediction for GlimmerHMM_glimmerT_29610-T1
Valid prediction for pasa_asmbl_9164.p1
Valid prediction for snap_scaffold_12-snap.584-T1
Valid prediction for snap_scaffold_12-snap.567-T1
Valid prediction for Augustus_model.g19706.t1
Valid prediction for GeneMark_model.51159_t
Valid prediction for GlimmerHMM_glimmerT_29618-T1
Valid prediction for snap_scaffold_12-snap.574-T1
Valid prediction for Augustus_model.g19700.t1
Valid prediction for snap_scaffold_12-snap.575-T1
Valid prediction for snap_scaffold_12-snap.579-T1
Valid prediction for Augustus_model.g19702.t1
Valid prediction for snap_scaffold_12-snap.597-T1
Valid prediction for GeneMark_model.51137_t
Valid prediction for GeneMark_model.51169_t
Valid prediction for GeneMark_model.51143_t
Valid prediction for GeneMark_model.51153_t
Couldn't classify 197361, 197829
Sorry, prediction pasa_asmbl_8494.p1 fails validation.
(AGA)	 CG	197361-197829	GT	AGG
(CAC)	 AG	199847-199956	GT	AGG
(ATC)	 AG	202472-202576	GT	TGG
(ATC)	 AG	203387-203513	GT	AGG
(TGA)	 AG	204515-204537	GC	GAG
-recovered pasa_asmbl_8494.p1, terminal, 204515, 204537
-recovered pasa_asmbl_8494.p1, internal, 199847, 199956
-recovered pasa_asmbl_8494.p1, internal, 202472, 202576
-recovered pasa_asmbl_8494.p1, internal, 203387, 203513
-recovered pasa_asmbl_8494.p1, internal, 204515, 204537
Valid prediction for GeneMark_model.51141_t
Valid prediction for GeneMark_model.51139_t
Valid prediction for GeneMark_model.51158_t
Valid prediction for snap_scaffold_12-snap.589-T1
Valid prediction for GlimmerHMM_glimmerT_29599-T1
Valid prediction for snap_scaffold_12-snap.588-T1
Valid prediction for GeneMark_model.51172_t
Valid prediction for GeneMark_model.51170_t
Valid prediction for snap_scaffold_12-snap.564-T1
Valid prediction for GlimmerHMM_glimmerT_29613-T1
Valid prediction for GeneMark_model.51154_t
Valid prediction for Augustus_model.g19711.t1
Valid prediction for GeneMark_model.51165_t
Valid prediction for snap_scaffold_12-snap.591-T1
Valid prediction for GeneMark_model.51149_t
Valid prediction for GlimmerHMM_glimmerT_29616-T1
Valid prediction for GeneMark_model.51163_t
Valid prediction for GlimmerHMM_glimmerT_29605-T1
Valid prediction for HiQ_model.g19698.t1
Valid prediction for HiQ_model.g19712.t1
Valid prediction for GlimmerHMM_glimmerT_29595-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 Augustus_model.g19701.t1
Valid prediction for GlimmerHMM_glimmerT_29606-T1
Valid prediction for GlimmerHMM_glimmerT_29611-T1
Valid prediction for GeneMark_model.51140_t
Couldn't classify 203255, 203407
Couldn't classify 203934, 204077
Sorry, prediction pasa_asmbl_8308.p1 fails validation.
(GAT)	 AG	203255-203407	GT	TGG
(GTG)	 AG	203934-204077	AT	TTA
-recovered pasa_asmbl_8308.p1, internal, 203255, 203407
Valid prediction for GlimmerHMM_glimmerT_29614-T1
Valid prediction for snap_scaffold_12-snap.578-T1
Sorry, intron length (4) is less than minimum required (10)
Couldn't classify 7290, 7452
Sorry, prediction pasa_asmbl_7472.p1 fails validation.
(AGG)	 CC	7290-7452	GT	AGG
(GGA)	 AG	7747-7843	GT	AGG
(GTC)	 AG	7960-8054	GT	GGG
(GGA)	 AG	8387-8637	GT	GGG
(GTC)	 AG	9283-9372	GT	AGG
(GAC)	 AG	9638-9745	GT	AGG
(GTG)	 AG	10097-10210	GT	AGG
(GTG)	 AG	10300-10464	GG	GAG
-recovered pasa_asmbl_7472.p1, terminal, 10300, 10464
-recovered pasa_asmbl_7472.p1, internal, 7747, 7843
-recovered pasa_asmbl_7472.p1, internal, 7960, 8054
-recovered pasa_asmbl_7472.p1, internal, 8387, 8637
-recovered pasa_asmbl_7472.p1, internal, 9283, 9372
-recovered pasa_asmbl_7472.p1, internal, 9638, 9745
-recovered pasa_asmbl_7472.p1, internal, 10097, 10210
Valid prediction for GeneMark_model.51160_t
Valid prediction for HiQ_model.g19708.t1
Valid prediction for CodingQuarry_transcript_10112-T1
Valid prediction for GeneMark_model.51138_t
Valid prediction for snap_scaffold_12-snap.573-T1
Valid prediction for snap_scaffold_12-snap.571-T1
Valid prediction for snap_scaffold_12-snap.583-T1
Valid prediction for GlimmerHMM_glimmerT_29609-T1
Valid prediction for snap_scaffold_12-snap.593-T1
Valid prediction for GeneMark_model.51144_t
Valid prediction for CodingQuarry_transcript_10116-T1
Valid prediction for GlimmerHMM_glimmerT_29600-T1
Valid prediction for GlimmerHMM_glimmerT_29615-T1
Valid prediction for GlimmerHMM_glimmerT_29597-T1
Valid prediction for GeneMark_model.51150_t
Valid prediction for GlimmerHMM_glimmerT_29622-T1
Valid prediction for CodingQuarry_transcript_10114-T1
Valid prediction for Augustus_model.g19707.t1
Valid prediction for GeneMark_model.51166_t
Valid prediction for GeneMark_model.51146_t
Valid prediction for snap_scaffold_12-snap.587-T1
Valid prediction for GlimmerHMM_glimmerT_29621-T1
Valid prediction for Augustus_model.g19704.t1
Valid prediction for GeneMark_model.51171_t
Valid prediction for CodingQuarry_transcript_10113-T1
Valid prediction for snap_scaffold_12-snap.586-T1
Valid prediction for snap_scaffold_12-snap.568-T1
Couldn't classify 47091, 47185
Sorry, prediction pasa_asmbl_7465.p1 fails validation.
(TCA)	 CC	47091-47185	GT	CAG
(GAT)	 AG	49410-49526	GT	CAG
(TGA)	 AG	49931-49994	GT	TGG
(CAA)	 AG	50187-50415	GT	AAG
(TTG)	 AG	50676-52449	GT	CTG
(GCT)	 AG	52592-52753	GT	AGG
(GCT)	 AG	53257-53427	GT	AGG
(GTT)	 AG	53784-53957	GT	AGG
(GCT)	 AG	54335-54508	GT	AGG
(GCT)	 AG	54753-54926	GT	AAG
(TGT)	 AG	55089-55135	GT	ATG
(ATG)	 AG	55463-55998	AT	AGA
add_exon() Sorry, pasa_asmbl_7465.p1 53784-53957-terminal-1 is invalid.
-recovered pasa_asmbl_7465.p1, terminal, 53784, 53957
add_exon() Sorry, pasa_asmbl_7465.p1 54335-54508-terminal-1 is invalid.
-recovered pasa_asmbl_7465.p1, terminal, 54335, 54508
-recovered pasa_asmbl_7465.p1, terminal, 55463, 55998
-recovered pasa_asmbl_7465.p1, internal, 49410, 49526
-recovered pasa_asmbl_7465.p1, internal, 49931, 49994
-recovered pasa_asmbl_7465.p1, internal, 50187, 50415
-recovered pasa_asmbl_7465.p1, internal, 50676, 52449
-recovered pasa_asmbl_7465.p1, internal, 52592, 52753
-recovered pasa_asmbl_7465.p1, internal, 53257, 53427
-recovered pasa_asmbl_7465.p1, internal, 53784, 53957
-recovered pasa_asmbl_7465.p1, internal, 54335, 54508
-recovered pasa_asmbl_7465.p1, internal, 54753, 54926
-recovered pasa_asmbl_7465.p1, internal, 55089, 55135
Valid prediction for snap_scaffold_12-snap.570-T1
Valid prediction for GeneMark_model.51155_t
Valid prediction for snap_scaffold_12-snap.581-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_12-snap.566-T1
Valid prediction for GeneMark_model.51148_t
Valid prediction for GlimmerHMM_glimmerT_29603-T1
Valid prediction for Augustus_model.g19713.t1
Valid prediction for GeneMark_model.51157_t
Valid prediction for GeneMark_model.51164_t
Valid prediction for Augustus_model.g19705.t1
Valid prediction for GlimmerHMM_glimmerT_29596-T1
Valid prediction for GeneMark_model.51162_t
Valid prediction for CodingQuarry_transcript_10115-T1
Valid prediction for snap_scaffold_12-snap.569-T1
Couldn't classify 204566, 204659
Sorry, prediction pasa_asmbl_7463.p1 fails validation.
(TAC)	 TC	204566-204659	GT	AGG
(TTT)	 AG	205338-205603	GA	AGG
-recovered pasa_asmbl_7463.p1, terminal, 205338, 205603
Valid prediction for GeneMark_model.51168_t
Valid prediction for snap_scaffold_12-snap.585-T1
Valid prediction for snap_scaffold_12-snap.576-T1
Valid prediction for snap_scaffold_12-snap.580-T1
Valid prediction for GeneMark_model.51173_t
Couldn't classify 47091, 47185
Couldn't classify 48904, 49021
Sorry, prediction pasa_asmbl_7468.p1 fails validation.
(TCA)	 CC	47091-47185	GT	CAG
(GAT)	 AG	47576-47692	GT	CAG
(GAT)	 AG	48402-48518	GT	CAG
(GAT)	 AG	48904-49021	TA	AGT
-recovered pasa_asmbl_7468.p1, internal, 47576, 47692
-recovered pasa_asmbl_7468.p1, internal, 48402, 48518
Valid prediction for GeneMark_model.51142_t
Valid prediction for Augustus_model.g19699.t1
Valid prediction for GlimmerHMM_glimmerT_29598-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 17445, rend_intergenic: 12178  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42875, rend_intergenic: 27073  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78608, rend_intergenic: 77862  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118204, rend_intergenic: 114143  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124129, rend_intergenic: 121330  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 196678, rend_intergenic: 192221  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 217780
-exon list size: 568


building trellis

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83.0    
83.2    
83.3    
83.5    
83.7    
83.9    
84.0    
84.2    
84.4    
84.6    
84.7    
84.9    
85.1    
85.3    
85.4    
85.6    
85.8    
86.0    
86.1    
86.3    
86.5    
86.7    
86.8    
87.0    
87.2    
87.4    
87.5    
87.7    
87.9    
88.1    
88.2    
88.4    
88.6    
88.8    
88.9    
89.1    
89.3    
89.5    
89.6    
89.8    
90.0    
90.2    
90.4    
90.5    
90.7    
90.9    
91.1    
91.2    
91.4    
91.6    
91.8    
91.9    
92.1    
92.3    
92.5    
92.6    
92.8    
93.0    
93.2    
93.3    
93.5    
93.7    
93.9    
94.0    
94.2    
94.4    
94.6    
94.7    
94.9    
95.1    
95.3    
95.4    
95.6    
95.8    
96.0    
96.1    
96.3    
96.5    
96.7    
96.8    
97.0    
97.2    
97.4    
97.5    
97.7    
97.9    
98.1    
98.2    
98.4    
98.6    
98.8    
98.9    
99.1    
99.3    
99.5    
99.6    
99.8    
-found 25 predictions from path traversal
Error with prediction: snap lend_intergenic: 17445, rend_intergenic: 12178  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42875, rend_intergenic: 27073  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78608, rend_intergenic: 77862  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118204, rend_intergenic: 114143  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124129, rend_intergenic: 121330  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 196678, rend_intergenic: 192221  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support