-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_11/scaffold_11_7267314-7469021

-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_27948-T1
Valid prediction for GeneMark_model.48342_t
Valid prediction for GlimmerHMM_glimmerT_27957-T1
Valid prediction for GeneMark_model.48338_t
Valid prediction for GeneMark_model.48343_t
Valid prediction for GlimmerHMM_glimmerT_27949-T1
Valid prediction for GeneMark_model.48314_t
Valid prediction for Augustus_model.g18636.t1
Valid prediction for GeneMark_model.48316_t
Valid prediction for GeneMark_model.48327_t
Valid prediction for GeneMark_model.48308_t
Valid prediction for snap_scaffold_11-snap.1723-T1
Valid prediction for snap_scaffold_11-snap.1696-T1
Valid prediction for GeneMark_model.48321_t
Valid prediction for GeneMark_model.48300_t
Valid prediction for snap_scaffold_11-snap.1719-T1
Valid prediction for snap_scaffold_11-snap.1725-T1
Valid prediction for GeneMark_model.48311_t
Valid prediction for snap_scaffold_11-snap.1702-T1
Sorry, intron length (3) is less than minimum required (10)
Couldn't classify 137565, 137630
Sorry, prediction pasa_asmbl_5634.p1 fails validation.
(ATG)	 AC	134415-134490	GT	AGG
(CTG)	 AG	135786-135887	GT	CAG
(AAC)	 AG	136439-136873	GT	TGG
(AGT)	 AG	137053-137186	GT	AGG
(ATA)	 AG	137565-137630	AT	GGA
-recovered pasa_asmbl_5634.p1, initial, 134415, 134490
-recovered pasa_asmbl_5634.p1, internal, 135786, 135887
-recovered pasa_asmbl_5634.p1, internal, 136439, 136873
-recovered pasa_asmbl_5634.p1, internal, 137053, 137186
Valid prediction for snap_scaffold_11-snap.1708-T1
Valid prediction for GeneMark_model.48295_t
Valid prediction for snap_scaffold_11-snap.1734-T1
Valid prediction for snap_scaffold_11-snap.1707-T1
Valid prediction for GeneMark_model.48325_t
Valid prediction for Augustus_model.g18631.t1
Valid prediction for GeneMark_model.48347_t
Valid prediction for GeneMark_model.48319_t
Valid prediction for GeneMark_model.48330_t
Valid prediction for GeneMark_model.48290_t
Valid prediction for snap_scaffold_11-snap.1722-T1
Valid prediction for pasa_asmbl_5632.p1
Valid prediction for GeneMark_model.48288_t
Valid prediction for GeneMark_model.48349_t
Valid prediction for GlimmerHMM_glimmerT_27940-T1
Valid prediction for snap_scaffold_11-snap.1738-T1
Valid prediction for GeneMark_model.48340_t
Valid prediction for GeneMark_model.48323_t
Valid prediction for CodingQuarry_transcript_8082-T1
Valid prediction for snap_scaffold_11-snap.1735-T1
Valid prediction for GeneMark_model.48346_t
Valid prediction for snap_scaffold_11-snap.1729-T1
Valid prediction for snap_scaffold_11-snap.1736-T1
Valid prediction for Augustus_model.g18635.t1
Valid prediction for snap_scaffold_11-snap.1710-T1
Valid prediction for GeneMark_model.48303_t
Valid prediction for snap_scaffold_11-snap.1717-T1
Valid prediction for snap_scaffold_11-snap.1701-T1
Valid prediction for snap_scaffold_11-snap.1737-T1
Valid prediction for snap_scaffold_11-snap.1728-T1
Valid prediction for snap_scaffold_11-snap.1709-T1
Valid prediction for GlimmerHMM_glimmerT_27943-T1
Valid prediction for GlimmerHMM_glimmerT_27944-T1
Valid prediction for snap_scaffold_11-snap.1721-T1
Valid prediction for CodingQuarry_transcript_8083-T1
Valid prediction for snap_scaffold_11-snap.1714-T1
Valid prediction for GeneMark_model.48297_t
Valid prediction for snap_scaffold_11-snap.1705-T1
Valid prediction for GlimmerHMM_glimmerT_27952-T1
Valid prediction for GeneMark_model.48305_t
Valid prediction for snap_scaffold_11-snap.1732-T1
Valid prediction for GeneMark_model.48312_t
Valid prediction for snap_scaffold_11-snap.1698-T1
Valid prediction for GeneMark_model.48318_t
Valid prediction for GlimmerHMM_glimmerT_27954-T1
Valid prediction for GeneMark_model.48299_t
Valid prediction for GeneMark_model.48310_t
Valid prediction for GlimmerHMM_glimmerT_27950-T1
Valid prediction for GeneMark_model.48291_t
Valid prediction for GeneMark_model.48329_t
Valid prediction for HiQ_model.g18633.t1
Valid prediction for snap_scaffold_11-snap.1713-T1
Valid prediction for GeneMark_model.48345_t
Valid prediction for GlimmerHMM_glimmerT_27955-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 snap_scaffold_11-snap.1727-T1
Valid prediction for snap_scaffold_11-snap.1724-T1
Valid prediction for GlimmerHMM_glimmerT_27961-T1
Valid prediction for Augustus_model.g18638.t1
Valid prediction for GeneMark_model.48334_t
Valid prediction for GlimmerHMM_glimmerT_27960-T1
Valid prediction for snap_scaffold_11-snap.1706-T1
Valid prediction for snap_scaffold_11-snap.1733-T1
Valid prediction for GeneMark_model.48296_t
Valid prediction for snap_scaffold_11-snap.1699-T1
Valid prediction for snap_scaffold_11-snap.1731-T1
Valid prediction for GeneMark_model.48350_t
Valid prediction for GeneMark_model.48293_t
Valid prediction for GeneMark_model.48301_t
Valid prediction for GeneMark_model.48304_t
Valid prediction for GeneMark_model.48292_t
Valid prediction for GeneMark_model.48315_t
Valid prediction for GeneMark_model.48339_t
Valid prediction for GeneMark_model.48344_t
Valid prediction for Augustus_model.g18637.t1
Valid prediction for GeneMark_model.48326_t
Valid prediction for Augustus_model.g18639.t1
Valid prediction for GlimmerHMM_glimmerT_27945-T1
Valid prediction for GeneMark_model.48341_t
Valid prediction for GeneMark_model.48351_t
Valid prediction for GlimmerHMM_glimmerT_27958-T1
Valid prediction for snap_scaffold_11-snap.1695-T1
Valid prediction for GeneMark_model.48320_t
Valid prediction for GeneMark_model.48337_t
Valid prediction for GeneMark_model.48328_t
Valid prediction for Augustus_model.g18630.t1
Valid prediction for GeneMark_model.48294_t
Valid prediction for GeneMark_model.48289_t
Valid prediction for GlimmerHMM_glimmerT_27941-T1
Valid prediction for snap_scaffold_11-snap.1697-T1
Valid prediction for GlimmerHMM_glimmerT_27959-T1
Valid prediction for GeneMark_model.48348_t
Valid prediction for GeneMark_model.48317_t
Valid prediction for snap_scaffold_11-snap.1711-T1
Valid prediction for snap_scaffold_11-snap.1715-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_27962-T1
Valid prediction for Augustus_model.g18628.t1
Valid prediction for snap_scaffold_11-snap.1703-T1
Valid prediction for GlimmerHMM_glimmerT_27956-T1
Valid prediction for GeneMark_model.48335_t
Valid prediction for snap_scaffold_11-snap.1720-T1
Valid prediction for GeneMark_model.48324_t
Valid prediction for GeneMark_model.48306_t
Valid prediction for snap_scaffold_11-snap.1730-T1
Valid prediction for snap_scaffold_11-snap.1726-T1
Valid prediction for GeneMark_model.48298_t
Valid prediction for GeneMark_model.48307_t
Valid prediction for GlimmerHMM_glimmerT_27963-T1
Valid prediction for Augustus_model.g18629.t1
Valid prediction for Augustus_model.g18634.t1
Valid prediction for GeneMark_model.48322_t
Valid prediction for GlimmerHMM_glimmerT_27946-T1
Valid prediction for GlimmerHMM_glimmerT_27965-T1
Valid prediction for GeneMark_model.48333_t
Valid prediction for GlimmerHMM_glimmerT_27964-T1
Valid prediction for snap_scaffold_11-snap.1739-T1
Valid prediction for snap_scaffold_11-snap.1704-T1
Valid prediction for Augustus_model.g18641.t1
Valid prediction for GeneMark_model.48302_t
Valid prediction for GlimmerHMM_glimmerT_27942-T1
Valid prediction for snap_scaffold_11-snap.1718-T1
Valid prediction for GlimmerHMM_glimmerT_27947-T1
Valid prediction for snap_scaffold_11-snap.1712-T1
Valid prediction for snap_scaffold_11-snap.1716-T1
Valid prediction for GeneMark_model.48313_t
Valid prediction for GlimmerHMM_glimmerT_27951-T1
Valid prediction for GlimmerHMM_glimmerT_27939-T1
Valid prediction for Augustus_model.g18640.t1
Valid prediction for GeneMark_model.48309_t
Valid prediction for GlimmerHMM_glimmerT_27953-T1
Valid prediction for GeneMark_model.48331_t
Valid prediction for GeneMark_model.48336_t
Valid prediction for snap_scaffold_11-snap.1700-T1
Valid prediction for Augustus_model.g18632.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 14864, rend_intergenic: 4818  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17764, rend_intergenic: 15175  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33160, rend_intergenic: 19618  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39407, rend_intergenic: 33871  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40222, rend_intergenic: 39491  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41236, rend_intergenic: 41018  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61341, rend_intergenic: 41241  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86859, rend_intergenic: 83127  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90299, rend_intergenic: 88708  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91441, rend_intergenic: 90325  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102845, rend_intergenic: 91626  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127635, rend_intergenic: 104781  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155329, rend_intergenic: 152005  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158647, rend_intergenic: 155678  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187266, rend_intergenic: 161559  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199494, rend_intergenic: 191558  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 201708
-exon list size: 828


building trellis

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84.7    
84.8    
84.9    
85.1    
85.2    
85.3    
85.4    
85.5    
85.7    
85.8    
85.9    
86.0    
86.1    
86.3    
86.4    
86.5    
86.6    
86.7    
86.9    
87.0    
87.1    
87.2    
87.3    
87.5    
87.6    
87.7    
87.8    
88.0    
88.1    
88.2    
88.3    
88.4    
88.6    
88.7    
88.8    
88.9    
89.0    
89.2    
89.3    
89.4    
89.5    
89.6    
89.8    
89.9    
90.0    
90.1    
90.2    
90.4    
90.5    
90.6    
90.7    
90.8    
91.0    
91.1    
91.2    
91.3    
91.4    
91.6    
91.7    
91.8    
91.9    
92.0    
92.2    
92.3    
92.4    
92.5    
92.7    
92.8    
92.9    
93.0    
93.1    
93.3    
93.4    
93.5    
93.6    
93.7    
93.9    
94.0    
94.1    
94.2    
94.3    
94.5    
94.6    
94.7    
94.8    
94.9    
95.1    
95.2    
95.3    
95.4    
95.5    
95.7    
95.8    
95.9    
96.0    
96.1    
96.3    
96.4    
96.5    
96.6    
96.7    
96.9    
97.0    
97.1    
97.2    
97.3    
97.5    
97.6    
97.7    
97.8    
98.0    
98.1    
98.2    
98.3    
98.4    
98.6    
98.7    
98.8    
98.9    
99.0    
99.2    
99.3    
99.4    
99.5    
99.6    
99.8    
99.9    
-found 43 predictions from path traversal
Error with prediction: snap lend_intergenic: 14864, rend_intergenic: 4818  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17764, rend_intergenic: 15175  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33160, rend_intergenic: 19618  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39407, rend_intergenic: 33871  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40222, rend_intergenic: 39491  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41236, rend_intergenic: 41018  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61341, rend_intergenic: 41241  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86859, rend_intergenic: 83127  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90299, rend_intergenic: 88708  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91441, rend_intergenic: 90325  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102845, rend_intergenic: 91626  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127635, rend_intergenic: 104781  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155329, rend_intergenic: 152005  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158647, rend_intergenic: 155678  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187266, rend_intergenic: 161559  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199494, rend_intergenic: 191558  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support