-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_10/scaffold_10_1549172-1745629

-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_10-snap.350-T1
Valid prediction for Augustus_model.g16547.t1
Valid prediction for GlimmerHMM_glimmerT_24691-T1
Valid prediction for GlimmerHMM_glimmerT_24667-T1
Valid prediction for GlimmerHMM_glimmerT_24674-T1
Valid prediction for Augustus_model.g16548.t1
Valid prediction for snap_scaffold_10-snap.335-T1
Valid prediction for GlimmerHMM_glimmerT_24679-T1
Valid prediction for snap_scaffold_10-snap.351-T1
Valid prediction for GeneMark_model.42125_t
Valid prediction for GlimmerHMM_glimmerT_24675-T1
Valid prediction for GeneMark_model.42140_t
Valid prediction for snap_scaffold_10-snap.342-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_10-snap.355-T1
Valid prediction for GlimmerHMM_glimmerT_24672-T1
Valid prediction for snap_scaffold_10-snap.337-T1
Valid prediction for GlimmerHMM_glimmerT_24683-T1
Valid prediction for GeneMark_model.42132_t
Valid prediction for GlimmerHMM_glimmerT_24689-T1
Valid prediction for GeneMark_model.42118_t
Valid prediction for Augustus_model.g16539.t1
Valid prediction for snap_scaffold_10-snap.341-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GeneMark_model.42097_t
Valid prediction for GlimmerHMM_glimmerT_24668-T1
Valid prediction for GeneMark_model.42146_t
Valid prediction for GeneMark_model.42126_t
Valid prediction for HiQ_model.g16545.t1
Valid prediction for GlimmerHMM_glimmerT_24666-T1
Valid prediction for GeneMark_model.42144_t
Valid prediction for GeneMark_model.42102_t
Valid prediction for snap_scaffold_10-snap.336-T1
Valid prediction for snap_scaffold_10-snap.366-T1
Valid prediction for GeneMark_model.42096_t
Valid prediction for GeneMark_model.42103_t
Valid prediction for GeneMark_model.42124_t
Valid prediction for snap_scaffold_10-snap.365-T1
Valid prediction for GlimmerHMM_glimmerT_24677-T1
Valid prediction for snap_scaffold_10-snap.343-T1
Valid prediction for GeneMark_model.42120_t
Valid prediction for snap_scaffold_10-snap.362-T1
Valid prediction for pasa_asmbl_4234.p1
Valid prediction for GeneMark_model.42104_t
Valid prediction for GeneMark_model.42095_t
Valid prediction for snap_scaffold_10-snap.334-T1
Valid prediction for GeneMark_model.42107_t
Valid prediction for GeneMark_model.42111_t
Valid prediction for GeneMark_model.42142_t
Valid prediction for snap_scaffold_10-snap.348-T1
Valid prediction for snap_scaffold_10-snap.356-T1
Valid prediction for GeneMark_model.42122_t
Valid prediction for GeneMark_model.42116_t
Valid prediction for GeneMark_model.42099_t
Valid prediction for GeneMark_model.42138_t
Valid prediction for GeneMark_model.42113_t
Valid prediction for GeneMark_model.42134_t
Valid prediction for GeneMark_model.42109_t
Valid prediction for GeneMark_model.42110_t
Valid prediction for GlimmerHMM_glimmerT_24681-T1
Valid prediction for GeneMark_model.42145_t
Valid prediction for snap_scaffold_10-snap.364-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GeneMark_model.42136_t
Valid prediction for CodingQuarry_transcript_5280-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_24673-T1
Valid prediction for GlimmerHMM_glimmerT_24665-T1
Valid prediction for GeneMark_model.42100_t
Valid prediction for CodingQuarry_transcript_5281-T1
Valid prediction for GeneMark_model.42114_t
Valid prediction for Augustus_model.g16549.t1
Valid prediction for GlimmerHMM_glimmerT_24682-T1
Valid prediction for Augustus_model.g16540.t1
Valid prediction for GlimmerHMM_glimmerT_24680-T1
Valid prediction for snap_scaffold_10-snap.359-T1
Valid prediction for GlimmerHMM_glimmerT_24671-T1
Valid prediction for GlimmerHMM_glimmerT_24678-T1
Couldn't classify 13605, 13708
Couldn't classify 20782, 20889
Sorry, prediction pasa_asmbl_2994.p1 fails validation.
(TCT)	 TT	13605-13708	GT	AGG
(GGC)	 AG	16703-16777	GT	GGG
(CAC)	 AG	17043-17184	GT	AGG
(ACC)	 AG	18441-18593	GT	AGG
(GCA)	 AG	18839-18943	GT	AGG
(AAA)	 AG	20782-20889	AC	ACA
-recovered pasa_asmbl_2994.p1, internal, 16703, 16777
-recovered pasa_asmbl_2994.p1, internal, 17043, 17184
-recovered pasa_asmbl_2994.p1, internal, 18441, 18593
-recovered pasa_asmbl_2994.p1, internal, 18839, 18943
Valid prediction for Augustus_model.g16544.t1
Valid prediction for GeneMark_model.42139_t
Couldn't classify 115064, 115192
Sorry, prediction pasa_asmbl_2983.p1 fails validation.
(TCC)	 CT	115064-115192	GT	AGG
(ATG)	 AG	116122-116190	GC	AGG
(GGC)	 AG	116426-116539	GT	AGG
(GTG)	 AG	116660-116861	GT	GGG
(CCG)	 AG	117467-117520	GT	AGG
(ATC)	 AG	118470-118516	AG	AAA
-recovered pasa_asmbl_2983.p1, initial, 116122, 116190
-recovered pasa_asmbl_2983.p1, terminal, 118470, 118516
-recovered pasa_asmbl_2983.p1, internal, 116122, 116190
-recovered pasa_asmbl_2983.p1, internal, 116426, 116539
-recovered pasa_asmbl_2983.p1, internal, 116660, 116861
-recovered pasa_asmbl_2983.p1, internal, 117467, 117520
Valid prediction for GlimmerHMM_glimmerT_24670-T1
Valid prediction for HiQ_model.g16546.t1
Valid prediction for snap_scaffold_10-snap.370-T1
Valid prediction for GeneMark_model.42130_t
Valid prediction for Augustus_model.g16543.t1
Valid prediction for GeneMark_model.42137_t
Valid prediction for GeneMark_model.42128_t
Valid prediction for GlimmerHMM_glimmerT_24669-T1
Valid prediction for snap_scaffold_10-snap.339-T1
Valid prediction for GlimmerHMM_glimmerT_24688-T1
Valid prediction for HiQ_model.g16550.t1
Valid prediction for GeneMark_model.42098_t
Valid prediction for GeneMark_model.42123_t
Valid prediction for GeneMark_model.42133_t
Valid prediction for snap_scaffold_10-snap.347-T1
Valid prediction for Augustus_model.g16541.t1
Valid prediction for GeneMark_model.42135_t
Valid prediction for GeneMark_model.42141_t
Valid prediction for GlimmerHMM_glimmerT_24690-T1
Valid prediction for GeneMark_model.42112_t
Valid prediction for GeneMark_model.42119_t
Valid prediction for GlimmerHMM_glimmerT_24687-T1
Valid prediction for snap_scaffold_10-snap.340-T1
Valid prediction for GeneMark_model.42131_t
Valid prediction for snap_scaffold_10-snap.345-T1
Valid prediction for snap_scaffold_10-snap.363-T1
Valid prediction for GeneMark_model.42105_t
Valid prediction for GlimmerHMM_glimmerT_24676-T1
Valid prediction for snap_scaffold_10-snap.344-T1
Valid prediction for snap_scaffold_10-snap.352-T1
Valid prediction for GeneMark_model.42101_t
Valid prediction for Augustus_model.g16552.t1
Valid prediction for GeneMark_model.42108_t
Valid prediction for snap_scaffold_10-snap.354-T1
Valid prediction for GeneMark_model.42129_t
Valid prediction for GeneMark_model.42117_t
Valid prediction for snap_scaffold_10-snap.360-T1
Valid prediction for snap_scaffold_10-snap.358-T1
Valid prediction for Augustus_model.g16551.t1
Valid prediction for GeneMark_model.42143_t
Valid prediction for CodingQuarry_transcript_5282-T1
Valid prediction for snap_scaffold_10-snap.361-T1
Valid prediction for GeneMark_model.42121_t
Valid prediction for snap_scaffold_10-snap.368-T1
Valid prediction for GeneMark_model.42115_t
Valid prediction for snap_scaffold_10-snap.369-T1
Valid prediction for snap_scaffold_10-snap.346-T1
Valid prediction for GeneMark_model.42127_t
Valid prediction for GlimmerHMM_glimmerT_24686-T1
Valid prediction for snap_scaffold_10-snap.333-T1
Couldn't classify 33692, 33716
Couldn't classify 35302, 35566
Sorry, prediction pasa_asmbl_2993.p1 fails validation.
(AGT)	 AG	33692-33716	GT	CAG
(GTG)	 AG	35106-35148	GT	GAG
(CAG)	 AG	35302-35566	GT	GTG
-recovered pasa_asmbl_2993.p1, internal, 33692, 33716
-recovered pasa_asmbl_2993.p1, internal, 35106, 35148
-recovered pasa_asmbl_2993.p1, internal, 35302, 35566
Valid prediction for snap_scaffold_10-snap.367-T1
Valid prediction for snap_scaffold_10-snap.357-T1
Valid prediction for snap_scaffold_10-snap.349-T1
Valid prediction for GlimmerHMM_glimmerT_24684-T1
Valid prediction for snap_scaffold_10-snap.353-T1
Valid prediction for Augustus_model.g16542.t1
Valid prediction for snap_scaffold_10-snap.338-T1
Valid prediction for GlimmerHMM_glimmerT_24685-T1
Valid prediction for GeneMark_model.42106_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 7020, rend_intergenic: 5458  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19309, rend_intergenic: 16176  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47197, rend_intergenic: 35198  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52789, rend_intergenic: 47762  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100495, rend_intergenic: 93690  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116891, rend_intergenic: 112177  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156072, rend_intergenic: 152196  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174645, rend_intergenic: 160736  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178054, rend_intergenic: 177116  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 196458
-exon list size: 619


building trellis

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92.3    
92.4    
92.6    
92.8    
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93.1    
93.2    
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93.6    
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93.9    
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94.2    
94.4    
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94.8    
95.0    
95.2    
95.3    
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95.8    
96.0    
96.1    
96.3    
96.5    
96.6    
96.8    
96.9    
97.1    
97.3    
97.4    
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98.1    
98.2    
98.4    
98.6    
98.7    
98.9    
99.0    
99.2    
99.4    
99.5    
99.7    
99.8    
-found 32 predictions from path traversal
Error with prediction: snap lend_intergenic: 7020, rend_intergenic: 5458  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 19309, rend_intergenic: 16176  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47197, rend_intergenic: 35198  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52789, rend_intergenic: 47762  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100495, rend_intergenic: 93690  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116891, rend_intergenic: 112177  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156072, rend_intergenic: 152196  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174645, rend_intergenic: 160736  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 178054, rend_intergenic: 177116  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support