-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_21/scaffold_21_3187877-3362471

-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 GlimmerHMM_glimmerT_48532-T1
Valid prediction for GlimmerHMM_glimmerT_48539-T1
Valid prediction for Augustus_model.g32486.t1
Valid prediction for Augustus_model.g32475.t1
Valid prediction for GlimmerHMM_glimmerT_48546-T1
Valid prediction for Augustus_model.g32472.t1
Valid prediction for snap_scaffold_21-snap.627-T1
Valid prediction for GeneMark_model.84298_t
Valid prediction for snap_scaffold_21-snap.600-T1
Valid prediction for GeneMark_model.84294_t
Valid prediction for GeneMark_model.84308_t
Valid prediction for GeneMark_model.84296_t
Valid prediction for GeneMark_model.84266_t
Valid prediction for GeneMark_model.84283_t
Valid prediction for GlimmerHMM_glimmerT_48548-T1
Valid prediction for snap_scaffold_21-snap.592-T1
Valid prediction for GlimmerHMM_glimmerT_48540-T1
Valid prediction for Augustus_model.g32466.t1
Valid prediction for GlimmerHMM_glimmerT_48536-T1
Couldn't classify 136006, 136371
Sorry, prediction pasa_asmbl_28506.p1 fails validation.
(CCC)	 TA	136006-136371	CC	CGC
Couldn't classify 125702, 125750
Couldn't classify 132700, 132765
Sorry, prediction pasa_asmbl_28505.p1 fails validation.
(ATC)	 AG	125702-125750	GT	AGG
(AGC)	 AG	126617-126766	GT	GGG
(CTG)	 AG	128452-128524	GT	TGG
(GAT)	 AG	129223-129417	GT	TGG
(GTC)	 AG	130217-130298	GT	AGG
(CAC)	 AG	132700-132765	GA	CTG
add_exon() Sorry, pasa_asmbl_28505.p1 125702-125750-terminal-3 is invalid.
-recovered pasa_asmbl_28505.p1, terminal, 125702, 125750
-recovered pasa_asmbl_28505.p1, internal, 125702, 125750
-recovered pasa_asmbl_28505.p1, internal, 126617, 126766
-recovered pasa_asmbl_28505.p1, internal, 128452, 128524
-recovered pasa_asmbl_28505.p1, internal, 129223, 129417
-recovered pasa_asmbl_28505.p1, internal, 130217, 130298
Valid prediction for snap_scaffold_21-snap.611-T1
Valid prediction for snap_scaffold_21-snap.591-T1
Valid prediction for GlimmerHMM_glimmerT_48537-T1
Valid prediction for snap_scaffold_21-snap.624-T1
Valid prediction for GeneMark_model.84265_t
Valid prediction for GlimmerHMM_glimmerT_48544-T1
Valid prediction for GlimmerHMM_glimmerT_48551-T1
Valid prediction for snap_scaffold_21-snap.588-T1
Valid prediction for snap_scaffold_21-snap.594-T1
Valid prediction for snap_scaffold_21-snap.614-T1
Valid prediction for GlimmerHMM_glimmerT_48538-T1
Valid prediction for GlimmerHMM_glimmerT_48531-T1
Valid prediction for snap_scaffold_21-snap.587-T1
Valid prediction for snap_scaffold_21-snap.608-T1
Valid prediction for GeneMark_model.84306_t
Valid prediction for GeneMark_model.84285_t
Valid prediction for Augustus_model.g32484.t1
Valid prediction for GeneMark_model.84292_t
Valid prediction for snap_scaffold_21-snap.598-T1
Valid prediction for Augustus_model.g32470.t1
Valid prediction for snap_scaffold_21-snap.586-T1
Valid prediction for GeneMark_model.84286_t
Valid prediction for GeneMark_model.84278_t
Valid prediction for snap_scaffold_21-snap.606-T1
Valid prediction for GlimmerHMM_glimmerT_48554-T1
Valid prediction for GlimmerHMM_glimmerT_48541-T1
Valid prediction for GlimmerHMM_glimmerT_48555-T1
Valid prediction for Augustus_model.g32467.t1
Valid prediction for GlimmerHMM_glimmerT_48557-T1
Valid prediction for Augustus_model.g32481.t1
Valid prediction for snap_scaffold_21-snap.593-T1
Valid prediction for GeneMark_model.84300_t
Valid prediction for snap_scaffold_21-snap.596-T1
Valid prediction for GeneMark_model.84275_t
Valid prediction for GeneMark_model.84270_t
Valid prediction for GeneMark_model.84281_t
Valid prediction for GeneMark_model.84279_t
Valid prediction for HiQ_model.g32474.t1
Valid prediction for Augustus_model.g32485.t1
Valid prediction for snap_scaffold_21-snap.605-T1
Valid prediction for GlimmerHMM_glimmerT_48543-T1
Valid prediction for GeneMark_model.84260_t
Valid prediction for GeneMark_model.84277_t
Valid prediction for GeneMark_model.84271_t
Couldn't classify 56826, 56914
Sorry, prediction pasa_asmbl_28502.p1 fails validation.
(AGC)	 AG	56826-56914	GT	AAG
(GCA)	 AG	57745-57929	GT	CGG
(TGG)	 AG	59503-59667	GT	AGG
(GTG)	 AG	60097-60158	GT	AGG
(CTG)	 AG	60470-60550	GT	AGG
(GAA)	 AG	61557-61625	GT	AGG
(CTC)	 AG	62344-62464	GT	AGG
(GTA)	 AG	63420-63576	GT	AGG
(TGG)	 AG	63811-63952	GT	TGG
(ACC)	 AG	64609-64779	GT	CGG
(GCT)	 AG	67153-67332	GT	AGG
(CTG)	 AG	68420-68594	GT	CGG
(GTC)	 AG	70490-70584	AG	AAA
add_exon() Sorry, pasa_asmbl_28502.p1 56826-56914-terminal-2 is invalid.
-recovered pasa_asmbl_28502.p1, terminal, 56826, 56914
-recovered pasa_asmbl_28502.p1, terminal, 70490, 70584
-recovered pasa_asmbl_28502.p1, internal, 56826, 56914
-recovered pasa_asmbl_28502.p1, internal, 57745, 57929
-recovered pasa_asmbl_28502.p1, internal, 59503, 59667
-recovered pasa_asmbl_28502.p1, internal, 60097, 60158
-recovered pasa_asmbl_28502.p1, internal, 60470, 60550
-recovered pasa_asmbl_28502.p1, internal, 61557, 61625
-recovered pasa_asmbl_28502.p1, internal, 62344, 62464
-recovered pasa_asmbl_28502.p1, internal, 63420, 63576
-recovered pasa_asmbl_28502.p1, internal, 63811, 63952
-recovered pasa_asmbl_28502.p1, internal, 64609, 64779
-recovered pasa_asmbl_28502.p1, internal, 67153, 67332
-recovered pasa_asmbl_28502.p1, internal, 68420, 68594
Valid prediction for GeneMark_model.84302_t
Valid prediction for GeneMark_model.84273_t
Valid prediction for GeneMark_model.84268_t
Valid prediction for snap_scaffold_21-snap.604-T1
Valid prediction for GlimmerHMM_glimmerT_48552-T1
Valid prediction for snap_scaffold_21-snap.617-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_21-snap.597-T1
Valid prediction for snap_scaffold_21-snap.601-T1
Valid prediction for GeneMark_model.84262_t
Valid prediction for GeneMark_model.84290_t
Couldn't classify 139914, 140047
Couldn't classify 141831, 141959
Sorry, prediction pasa_asmbl_28507.p1 fails validation.
(CAG)	 TT	139914-140047	GC	AGG
(GCG)	 AG	140642-140765	GT	ACG
(AAT)	 AG	141215-141394	GT	AGG
(GTC)	 AG	141596-141688	GT	AGG
(GAG)	 AG	141831-141959	GG	GAG
-recovered pasa_asmbl_28507.p1, internal, 140642, 140765
-recovered pasa_asmbl_28507.p1, internal, 141215, 141394
-recovered pasa_asmbl_28507.p1, internal, 141596, 141688
Valid prediction for Augustus_model.g32471.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 GeneMark_model.84293_t
Valid prediction for GeneMark_model.84299_t
Couldn't classify 22667, 22772
Couldn't classify 25262, 25308
Sorry, prediction pasa_asmbl_28248.p1 fails validation.
(CTG)	 TG	22667-22772	GT	AGG
(GAT)	 AG	22917-23018	GT	AGG
(AGG)	 AG	24428-24545	GT	AGG
(GTA)	 AG	24736-24947	GT	CAG
(AAG)	 AG	25262-25308	GT	TTG
-recovered pasa_asmbl_28248.p1, internal, 22917, 23018
-recovered pasa_asmbl_28248.p1, internal, 24428, 24545
-recovered pasa_asmbl_28248.p1, internal, 24736, 24947
-recovered pasa_asmbl_28248.p1, internal, 25262, 25308
Couldn't classify 26299, 26613
Sorry, prediction pasa_asmbl_27552.p1 fails validation.
(AGC)	 TC	26299-26613	AG	TGA
Valid prediction for snap_scaffold_21-snap.609-T1
Valid prediction for GeneMark_model.84303_t
Valid prediction for GlimmerHMM_glimmerT_48547-T1
Valid prediction for Augustus_model.g32480.t1
Valid prediction for GeneMark_model.84304_t
Valid prediction for snap_scaffold_21-snap.621-T1
Valid prediction for GlimmerHMM_glimmerT_48550-T1
Valid prediction for Augustus_model.g32476.t1
Valid prediction for snap_scaffold_21-snap.599-T1
Valid prediction for GlimmerHMM_glimmerT_48545-T1
Valid prediction for GeneMark_model.84287_t
Valid prediction for Augustus_model.g32488.t1
Valid prediction for GlimmerHMM_glimmerT_48549-T1
Valid prediction for GeneMark_model.84305_t
Valid prediction for Augustus_model.g32489.t1
Valid prediction for GeneMark_model.84276_t
Valid prediction for GeneMark_model.84261_t
Valid prediction for GeneMark_model.84284_t
Valid prediction for Augustus_model.g32469.t1
Valid prediction for GeneMark_model.84272_t
Valid prediction for GeneMark_model.84307_t
Valid prediction for Augustus_model.g32482.t1
Valid prediction for snap_scaffold_21-snap.615-T1
Valid prediction for snap_scaffold_21-snap.622-T1
Valid prediction for GlimmerHMM_glimmerT_48534-T1
Valid prediction for Augustus_model.g32483.t1
Valid prediction for GeneMark_model.84267_t
Valid prediction for snap_scaffold_21-snap.610-T1
Valid prediction for snap_scaffold_21-snap.603-T1
Valid prediction for snap_scaffold_21-snap.626-T1
Valid prediction for GeneMark_model.84274_t
Valid prediction for GeneMark_model.84301_t
Valid prediction for Augustus_model.g32477.t1
Valid prediction for GeneMark_model.84288_t
Valid prediction for GlimmerHMM_glimmerT_48535-T1
Valid prediction for GeneMark_model.84263_t
Valid prediction for Augustus_model.g32468.t1
Valid prediction for GeneMark_model.84295_t
Valid prediction for GeneMark_model.84269_t
Valid prediction for snap_scaffold_21-snap.602-T1
Valid prediction for snap_scaffold_21-snap.589-T1
Valid prediction for GeneMark_model.84291_t
Valid prediction for GeneMark_model.84264_t
Valid prediction for snap_scaffold_21-snap.623-T1
Valid prediction for snap_scaffold_21-snap.613-T1
Valid prediction for snap_scaffold_21-snap.619-T1
Valid prediction for snap_scaffold_21-snap.612-T1
Valid prediction for snap_scaffold_21-snap.590-T1
Valid prediction for snap_scaffold_21-snap.620-T1
Valid prediction for snap_scaffold_21-snap.607-T1
Valid prediction for snap_scaffold_21-snap.618-T1
Valid prediction for Augustus_model.g32487.t1
Valid prediction for Augustus_model.g32479.t1
Valid prediction for GlimmerHMM_glimmerT_48559-T1
Valid prediction for snap_scaffold_21-snap.625-T1
Valid prediction for Augustus_model.g32478.t1
Valid prediction for snap_scaffold_21-snap.595-T1
Valid prediction for GeneMark_model.84297_t
Valid prediction for GeneMark_model.84280_t
Valid prediction for GlimmerHMM_glimmerT_48558-T1
Valid prediction for GlimmerHMM_glimmerT_48533-T1
Valid prediction for GlimmerHMM_glimmerT_48542-T1
Valid prediction for GeneMark_model.84289_t
Valid prediction for Augustus_model.g32473.t1
Valid prediction for GlimmerHMM_glimmerT_48556-T1
Valid prediction for snap_scaffold_21-snap.616-T1
Valid prediction for GeneMark_model.84282_t
Couldn't classify 26935, 27366
Sorry, prediction pasa_asmbl_27551.p2 fails validation.
(CCC)	 AC	26935-27366	TT	AGT
Valid prediction for GlimmerHMM_glimmerT_48553-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 41323, rend_intergenic: 37730  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57967, rend_intergenic: 56706  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70915, rend_intergenic: 58073  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87731, rend_intergenic: 76409  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91454, rend_intergenic: 88017  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93858, rend_intergenic: 92244  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98235, rend_intergenic: 94499  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123337, rend_intergenic: 117876  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143458, rend_intergenic: 124746  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165258, rend_intergenic: 161842  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172171, rend_intergenic: 171608  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 174595
-exon list size: 713


building trellis

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76.4    
76.5    
76.6    
76.8    
76.9    
77.1    
77.2    
77.3    
77.5    
77.6    
77.8    
77.9    
78.0    
78.2    
78.3    
78.5    
78.6    
78.7    
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    
81.3    
81.4    
81.5    
81.7    
81.8    
82.0    
82.1    
82.2    
82.4    
82.5    
82.7    
82.8    
82.9    
83.1    
83.2    
83.4    
83.5    
83.6    
83.8    
83.9    
84.1    
84.2    
84.3    
84.5    
84.6    
84.8    
84.9    
85.0    
85.2    
85.3    
85.5    
85.6    
85.7    
85.9    
86.0    
86.2    
86.3    
86.4    
86.6    
86.7    
86.9    
87.0    
87.1    
87.3    
87.4    
87.6    
87.7    
87.8    
88.0    
88.1    
88.3    
88.4    
88.5    
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    
91.5    
91.6    
91.7    
91.9    
92.0    
92.2    
92.3    
92.4    
92.6    
92.7    
92.9    
93.0    
93.1    
93.3    
93.4    
93.6    
93.7    
93.8    
94.0    
94.1    
94.3    
94.4    
94.5    
94.7    
94.8    
95.0    
95.1    
95.2    
95.4    
95.5    
95.7    
95.8    
95.9    
96.1    
96.2    
96.4    
96.5    
96.6    
96.8    
96.9    
97.1    
97.2    
97.3    
97.5    
97.6    
97.8    
97.9    
98.0    
98.2    
98.3    
98.5    
98.6    
98.7    
98.9    
99.0    
99.2    
99.3    
99.4    
99.6    
99.7    
99.9    
-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 41323, rend_intergenic: 37730  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57967, rend_intergenic: 56706  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70915, rend_intergenic: 58073  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87731, rend_intergenic: 76409  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91454, rend_intergenic: 88017  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93858, rend_intergenic: 92244  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98235, rend_intergenic: 94499  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123337, rend_intergenic: 117876  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143458, rend_intergenic: 124746  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165258, rend_intergenic: 161842  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172171, rend_intergenic: 171608  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support