-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_14/scaffold_14_16273930-16476736

-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_14-snap.3441-T1
Valid prediction for snap_scaffold_14-snap.3442-T1
Valid prediction for snap_scaffold_14-snap.3450-T1
Valid prediction for GeneMark_model.62164_t
Valid prediction for snap_scaffold_14-snap.3432-T1
Valid prediction for GeneMark_model.62145_t
Valid prediction for GeneMark_model.62172_t
Valid prediction for snap_scaffold_14-snap.3447-T1
Valid prediction for GeneMark_model.62135_t
Valid prediction for GeneMark_model.62130_t
Valid prediction for GeneMark_model.62110_t
Couldn't classify 201338, 201520
Sorry, prediction GeneMark_model.62176_t fails validation.
(ATG)	 GG	197365-197475	GT	AGG
(GGA)	 AG	197536-197585	GT	AAG
(GGT)	 AG	197609-197620	GT	AAG
(GTG)	 AG	197644-197655	GT	AAG
(GAG)	 AG	200607-200642	GT	ATG
(AGA)	 AG	201247-201272	GT	GAG
(GGA)	 AG	201293-201314	GT	GAG
(GGA)	 AG	201338-201520	GT	GAG
-recovered GeneMark_model.62176_t, initial, 197365, 197475
-recovered GeneMark_model.62176_t, terminal, 201247, 201272
-recovered GeneMark_model.62176_t, internal, 197536, 197585
-recovered GeneMark_model.62176_t, internal, 197609, 197620
-recovered GeneMark_model.62176_t, internal, 197644, 197655
-recovered GeneMark_model.62176_t, internal, 200607, 200642
-recovered GeneMark_model.62176_t, internal, 201247, 201272
-recovered GeneMark_model.62176_t, internal, 201293, 201314
-recovered GeneMark_model.62176_t, internal, 201338, 201520
Valid prediction for GeneMark_model.62153_t
Valid prediction for GeneMark_model.62109_t
Valid prediction for GeneMark_model.62099_t
Valid prediction for GeneMark_model.62166_t
Valid prediction for GeneMark_model.62147_t
Valid prediction for GlimmerHMM_glimmerT_36162-T1
Valid prediction for GeneMark_model.62149_t
Valid prediction for snap_scaffold_14-snap.3455-T1
Valid prediction for GeneMark_model.62168_t
Couldn't classify 75832, 75861
Sorry, prediction GeneMark_model.62132_t fails validation.
(ATG)	 TC	74701-74780	GT	GAG
(ACA)	 AG	74920-74928	GT	CAG
(AGA)	 AG	74958-75096	GT	AAG
(AAA)	 AG	75262-75408	GT	CAG
(CCA)	 AG	75695-75804	GT	CTG
(GGA)	 AG	75832-75861	GT	GGG
-recovered GeneMark_model.62132_t, initial, 74701, 74780
-recovered GeneMark_model.62132_t, internal, 74920, 74928
-recovered GeneMark_model.62132_t, internal, 74958, 75096
-recovered GeneMark_model.62132_t, internal, 75262, 75408
-recovered GeneMark_model.62132_t, internal, 75695, 75804
-recovered GeneMark_model.62132_t, internal, 75832, 75861
Valid prediction for snap_scaffold_14-snap.3443-T1
Valid prediction for GeneMark_model.62104_t
Valid prediction for GeneMark_model.62170_t
Valid prediction for GeneMark_model.62101_t
Valid prediction for GeneMark_model.62118_t
Valid prediction for GeneMark_model.62128_t
Valid prediction for snap_scaffold_14-snap.3434-T1
Valid prediction for GlimmerHMM_glimmerT_36166-T1
Valid prediction for snap_scaffold_14-snap.3452-T1
Valid prediction for GeneMark_model.62103_t
Valid prediction for GeneMark_model.62107_t
Valid prediction for GeneMark_model.62134_t
Valid prediction for snap_scaffold_14-snap.3423-T1
Valid prediction for snap_scaffold_14-snap.3449-T1
Valid prediction for snap_scaffold_14-snap.3425-T1
Valid prediction for GeneMark_model.62162_t
Valid prediction for snap_scaffold_14-snap.3433-T1
Valid prediction for snap_scaffold_14-snap.3437-T1
Valid prediction for GeneMark_model.62138_t
Valid prediction for GeneMark_model.62143_t
Valid prediction for GeneMark_model.62097_t
Valid prediction for snap_scaffold_14-snap.3430-T1
Valid prediction for GeneMark_model.62141_t
Valid prediction for GeneMark_model.62112_t
Valid prediction for GeneMark_model.62137_t
Valid prediction for GeneMark_model.62119_t
Valid prediction for GeneMark_model.62114_t
Valid prediction for GeneMark_model.62156_t
Valid prediction for GeneMark_model.62125_t
Valid prediction for snap_scaffold_14-snap.3429-T1
Valid prediction for GeneMark_model.62151_t
Valid prediction for GeneMark_model.62160_t
Valid prediction for GeneMark_model.62158_t
Valid prediction for snap_scaffold_14-snap.3428-T1
Valid prediction for GeneMark_model.62174_t
Valid prediction for GeneMark_model.62111_t
Valid prediction for GeneMark_model.62123_t
Valid prediction for snap_scaffold_14-snap.3427-T1
Valid prediction for snap_scaffold_14-snap.3431-T1
Valid prediction for GeneMark_model.62106_t
Valid prediction for snap_scaffold_14-snap.3445-T1
Valid prediction for GeneMark_model.62116_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.62155_t
Valid prediction for GeneMark_model.62140_t
Valid prediction for GeneMark_model.62108_t
Valid prediction for snap_scaffold_14-snap.3435-T1
Valid prediction for GlimmerHMM_glimmerT_36168-T1
Valid prediction for snap_scaffold_14-snap.3426-T1
Valid prediction for snap_scaffold_14-snap.3436-T1
Valid prediction for GeneMark_model.62098_t
Valid prediction for GeneMark_model.62169_t
Valid prediction for GeneMark_model.62136_t
Valid prediction for GeneMark_model.62146_t
Valid prediction for GeneMark_model.62154_t
Valid prediction for GeneMark_model.62139_t
Valid prediction for GlimmerHMM_glimmerT_36159-T1
Valid prediction for GeneMark_model.62122_t
Valid prediction for snap_scaffold_14-snap.3451-T1
Valid prediction for GeneMark_model.62163_t
Valid prediction for GeneMark_model.62171_t
Valid prediction for GlimmerHMM_glimmerT_36167-T1
Valid prediction for GeneMark_model.62129_t
Valid prediction for snap_scaffold_14-snap.3454-T1
Valid prediction for GeneMark_model.62161_t
Valid prediction for GeneMark_model.62167_t
Couldn't classify 117824, 117852
Sorry, prediction GeneMark_model.62133_t fails validation.
(ATG)	 AC	116713-116745	GT	CCG
(ACC)	 AG	117629-117798	GT	GGG
(GGT)	 AG	117824-117852	GT	GGG
-recovered GeneMark_model.62133_t, initial, 116713, 116745
-recovered GeneMark_model.62133_t, internal, 117629, 117798
-recovered GeneMark_model.62133_t, internal, 117824, 117852
Valid prediction for snap_scaffold_14-snap.3446-T1
Valid prediction for snap_scaffold_14-snap.3448-T1
Valid prediction for snap_scaffold_14-snap.3440-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GeneMark_model.62115_t
Valid prediction for GeneMark_model.62148_t
Valid prediction for GeneMark_model.62124_t
Valid prediction for GeneMark_model.62117_t
Valid prediction for GeneMark_model.62113_t
Valid prediction for GeneMark_model.62144_t
Valid prediction for GlimmerHMM_glimmerT_36161-T1
Valid prediction for GlimmerHMM_glimmerT_36165-T1
Valid prediction for snap_scaffold_14-snap.3444-T1
Valid prediction for snap_scaffold_14-snap.3438-T1
Valid prediction for snap_scaffold_14-snap.3424-T1
Valid prediction for snap_scaffold_14-snap.3439-T1
Valid prediction for GlimmerHMM_glimmerT_36169-T1
Valid prediction for GlimmerHMM_glimmerT_36160-T1
Valid prediction for GlimmerHMM_glimmerT_36163-T1
Valid prediction for GeneMark_model.62102_t
Valid prediction for GeneMark_model.62131_t
Valid prediction for GeneMark_model.62126_t
Valid prediction for GeneMark_model.62142_t
Valid prediction for snap_scaffold_14-snap.3453-T1
Valid prediction for GlimmerHMM_glimmerT_36164-T1
Valid prediction for GeneMark_model.62152_t
Valid prediction for GeneMark_model.62159_t
Valid prediction for GeneMark_model.62120_t
Valid prediction for GeneMark_model.62105_t
Valid prediction for GeneMark_model.62175_t
Valid prediction for GeneMark_model.62157_t
Valid prediction for GeneMark_model.62173_t
Valid prediction for GeneMark_model.62121_t
Valid prediction for GeneMark_model.62165_t
Valid prediction for GeneMark_model.62127_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 4694, rend_intergenic: 4117  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 7158, rend_intergenic: 5399  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47276, rend_intergenic: 8070  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54471, rend_intergenic: 47299  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55259, rend_intergenic: 54988  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87364, rend_intergenic: 55259  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120498, rend_intergenic: 88580  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127798, rend_intergenic: 121801  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134862, rend_intergenic: 127839  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142821, rend_intergenic: 135699  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153180, rend_intergenic: 143589  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176204, rend_intergenic: 154858  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185401, rend_intergenic: 176825  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188067, rend_intergenic: 185801  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 197985, rend_intergenic: 188088  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 201836, rend_intergenic: 199720  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 49072, rend_intergenic: 49069  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 202807
-exon list size: 866


building trellis

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82.0    
82.1    
82.3    
82.4    
82.5    
82.6    
82.7    
82.8    
82.9    
83.1    
83.2    
83.3    
83.4    
83.5    
83.6    
83.8    
83.9    
84.0    
84.1    
84.2    
84.3    
84.4    
84.6    
84.7    
84.8    
84.9    
85.0    
85.1    
85.3    
85.4    
85.5    
85.6    
85.7    
85.8    
85.9    
86.1    
86.2    
86.3    
86.4    
86.5    
86.6    
86.8    
86.9    
87.0    
87.1    
87.2    
87.3    
87.4    
87.6    
87.7    
87.8    
87.9    
88.0    
88.1    
88.2    
88.4    
88.5    
88.6    
88.7    
88.8    
88.9    
89.1    
89.2    
89.3    
89.4    
89.5    
89.6    
89.7    
89.9    
90.0    
90.1    
90.2    
90.3    
90.4    
90.6    
90.7    
90.8    
90.9    
91.0    
91.1    
91.2    
91.4    
91.5    
91.6    
91.7    
91.8    
91.9    
92.1    
92.2    
92.3    
92.4    
92.5    
92.6    
92.7    
92.9    
93.0    
93.1    
93.2    
93.3    
93.4    
93.5    
93.7    
93.8    
93.9    
94.0    
94.1    
94.2    
94.4    
94.5    
94.6    
94.7    
94.8    
94.9    
95.0    
95.2    
95.3    
95.4    
95.5    
95.6    
95.7    
95.9    
96.0    
96.1    
96.2    
96.3    
96.4    
96.5    
96.7    
96.8    
96.9    
97.0    
97.1    
97.2    
97.4    
97.5    
97.6    
97.7    
97.8    
97.9    
98.0    
98.2    
98.3    
98.4    
98.5    
98.6    
98.7    
98.8    
99.0    
99.1    
99.2    
99.3    
99.4    
99.5    
99.7    
99.8    
99.9    
-found 56 predictions from path traversal
Error with prediction: snap lend_intergenic: 4694, rend_intergenic: 4117  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 7158, rend_intergenic: 5399  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47276, rend_intergenic: 8070  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54471, rend_intergenic: 47299  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55259, rend_intergenic: 54988  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87364, rend_intergenic: 55259  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120498, rend_intergenic: 88580  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127798, rend_intergenic: 121801  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134862, rend_intergenic: 127839  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142821, rend_intergenic: 135699  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153180, rend_intergenic: 143589  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176204, rend_intergenic: 154858  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185401, rend_intergenic: 176825  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188067, rend_intergenic: 185801  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 197985, rend_intergenic: 188088  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 201836, rend_intergenic: 199720  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 49072, rend_intergenic: 49069  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 7 predictions persist after filtering for low support