-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_12/scaffold_12_9401326-9575779

-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_29817-T1
Couldn't classify 104783, 104899
Sorry, prediction pasa_asmbl_7865.p1 fails validation.
(CCC)	 TC	104783-104899	GT	AGG
(GTG)	 AG	105045-105171	GT	GGG
(GTG)	 AG	105290-105870	GT	AAG
-recovered pasa_asmbl_7865.p1, terminal, 105290, 105870
-recovered pasa_asmbl_7865.p1, internal, 105045, 105171
-recovered pasa_asmbl_7865.p1, internal, 105290, 105870
Valid prediction for GlimmerHMM_glimmerT_29820-T1
Valid prediction for snap_scaffold_12-snap.1783-T1
Valid prediction for GlimmerHMM_glimmerT_29819-T1
Valid prediction for snap_scaffold_12-snap.1778-T1
Valid prediction for GlimmerHMM_glimmerT_29815-T1
Valid prediction for GlimmerHMM_glimmerT_29807-T1
Valid prediction for snap_scaffold_12-snap.1787-T1
Valid prediction for snap_scaffold_12-snap.1794-T1
Valid prediction for snap_scaffold_12-snap.1790-T1
Valid prediction for snap_scaffold_12-snap.1761-T1
Valid prediction for snap_scaffold_12-snap.1781-T1
Valid prediction for GlimmerHMM_glimmerT_29831-T1
Valid prediction for GlimmerHMM_glimmerT_29813-T1
Valid prediction for snap_scaffold_12-snap.1796-T1
Valid prediction for GlimmerHMM_glimmerT_29829-T1
Valid prediction for snap_scaffold_12-snap.1769-T1
Valid prediction for GlimmerHMM_glimmerT_29821-T1
Valid prediction for snap_scaffold_12-snap.1765-T1
Valid prediction for snap_scaffold_12-snap.1775-T1
Valid prediction for GlimmerHMM_glimmerT_29812-T1
Valid prediction for snap_scaffold_12-snap.1763-T1
Valid prediction for GlimmerHMM_glimmerT_29806-T1
Valid prediction for snap_scaffold_12-snap.1760-T1
Couldn't classify 103422, 103634
Couldn't classify 104547, 104686
Sorry, prediction pasa_asmbl_7863.p1 fails validation.
(TAT)	 GC	103422-103634	GT	CGG
(ATG)	 AG	103711-103735	GT	AGG
(ATG)	 AG	103974-104087	GT	AGG
(AGA)	 AG	104274-104408	GT	AGG
(TGG)	 AG	104547-104686	CC	CCC
-recovered pasa_asmbl_7863.p1, initial, 103711, 103735
add_exon() Sorry, pasa_asmbl_7863.p1 103974-104087-initial-1 is invalid.
-recovered pasa_asmbl_7863.p1, initial, 103974, 104087
-recovered pasa_asmbl_7863.p1, terminal, 103974, 104087
-recovered pasa_asmbl_7863.p1, internal, 103711, 103735
-recovered pasa_asmbl_7863.p1, internal, 103974, 104087
-recovered pasa_asmbl_7863.p1, internal, 104274, 104408
Valid prediction for snap_scaffold_12-snap.1774-T1
Valid prediction for Augustus_model.g19718.t1
Valid prediction for snap_scaffold_12-snap.1777-T1
Valid prediction for snap_scaffold_12-snap.1766-T1
Valid prediction for snap_scaffold_12-snap.1792-T1
Valid prediction for snap_scaffold_12-snap.1773-T1
Valid prediction for snap_scaffold_12-snap.1780-T1
Valid prediction for HiQ_model.g19716.t1
Valid prediction for snap_scaffold_12-snap.1771-T1
Valid prediction for snap_scaffold_12-snap.1772-T1
Valid prediction for snap_scaffold_12-snap.1791-T1
Valid prediction for snap_scaffold_12-snap.1786-T1
Valid prediction for Augustus_model.g19714.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.g19722.t1
Valid prediction for snap_scaffold_12-snap.1785-T1
Valid prediction for snap_scaffold_12-snap.1776-T1
Valid prediction for Augustus_model.g19721.t1
Valid prediction for GlimmerHMM_glimmerT_29832-T1
Valid prediction for GlimmerHMM_glimmerT_29808-T1
Valid prediction for GlimmerHMM_glimmerT_29830-T1
Valid prediction for GlimmerHMM_glimmerT_29826-T1
Valid prediction for Augustus_model.g19723.t1
Valid prediction for snap_scaffold_12-snap.1793-T1
Valid prediction for GlimmerHMM_glimmerT_29823-T1
Valid prediction for Augustus_model.g19719.t1
Valid prediction for snap_scaffold_12-snap.1768-T1
Valid prediction for GlimmerHMM_glimmerT_29818-T1
Valid prediction for GlimmerHMM_glimmerT_29811-T1
Valid prediction for Augustus_model.g19717.t1
Valid prediction for snap_scaffold_12-snap.1767-T1
Valid prediction for snap_scaffold_12-snap.1779-T1
Valid prediction for Augustus_model.g19709.t1
Valid prediction for Augustus_model.g19724.t1
Valid prediction for Augustus_model.g19708.t1
Valid prediction for snap_scaffold_12-snap.1770-T1
Couldn't classify 36307, 36392
Couldn't classify 36878, 36948
Sorry, prediction pasa_asmbl_8679.p1 fails validation.
(GTG)	 AC	36307-36392	GT	AAG
(GTA)	 AG	36541-36612	GT	GTG
(GTA)	 AG	36711-36784	GT	AGG
(GTG)	 AG	36878-36948	AG	AGA
-recovered pasa_asmbl_8679.p1, internal, 36541, 36612
-recovered pasa_asmbl_8679.p1, internal, 36711, 36784
Valid prediction for Augustus_model.g19711.t1
Couldn't classify 61577, 61600
Sorry, prediction pasa_asmbl_8674.p1 fails validation.
(TTC)	 AG	61577-61600	GT	AGG
(GAG)	 AG	61695-61787	GT	AGG
(GAG)	 AG	62036-62161	GT	AGG
(GGA)	 AG	62298-62519	GT	AGG
(ATG)	 AG	63010-63102	GT	AGG
(GCT)	 AG	63293-63371	GT	AGG
(ACG)	 AG	63514-63577	GT	AGG
(CAA)	 AG	64865-64965	GT	GAG
(GCT)	 AG	65169-65281	GT	TGG
(TCA)	 AG	65789-65901	GT	TGG
(GCT)	 AG	66048-66151	GT	AGG
(ATC)	 AG	66417-66457	TG	AGT
-recovered pasa_asmbl_8674.p1, initial, 63010, 63102
-recovered pasa_asmbl_8674.p1, terminal, 66417, 66457
-recovered pasa_asmbl_8674.p1, internal, 61577, 61600
-recovered pasa_asmbl_8674.p1, internal, 61695, 61787
-recovered pasa_asmbl_8674.p1, internal, 62036, 62161
-recovered pasa_asmbl_8674.p1, internal, 62298, 62519
-recovered pasa_asmbl_8674.p1, internal, 63010, 63102
-recovered pasa_asmbl_8674.p1, internal, 63293, 63371
-recovered pasa_asmbl_8674.p1, internal, 63514, 63577
-recovered pasa_asmbl_8674.p1, internal, 64865, 64965
-recovered pasa_asmbl_8674.p1, internal, 65169, 65281
-recovered pasa_asmbl_8674.p1, internal, 65789, 65901
-recovered pasa_asmbl_8674.p1, internal, 66048, 66151
Valid prediction for GlimmerHMM_glimmerT_29827-T1
Valid prediction for snap_scaffold_12-snap.1789-T1
Valid prediction for snap_scaffold_12-snap.1762-T1
Couldn't classify 158562, 158760
Sorry, prediction pasa_asmbl_8672.p2 fails validation.
(GAA)	 AG	158562-158760	GT	AGG
(TGG)	 AG	161589-161725	CC	AGC
-recovered pasa_asmbl_8672.p2, terminal, 161589, 161725
-recovered pasa_asmbl_8672.p2, internal, 158562, 158760
Valid prediction for GlimmerHMM_glimmerT_29825-T1
Valid prediction for snap_scaffold_12-snap.1784-T1
Valid prediction for Augustus_model.g19712.t1
Valid prediction for Augustus_model.g19720.t1
Valid prediction for GlimmerHMM_glimmerT_29822-T1
Valid prediction for Augustus_model.g19710.t1
Valid prediction for Augustus_model.g19715.t1
Valid prediction for snap_scaffold_12-snap.1764-T1
Valid prediction for GlimmerHMM_glimmerT_29828-T1
Valid prediction for GlimmerHMM_glimmerT_29824-T1
Valid prediction for snap_scaffold_12-snap.1782-T1
Valid prediction for Augustus_model.g19713.t1
Valid prediction for GlimmerHMM_glimmerT_29810-T1
Valid prediction for GlimmerHMM_glimmerT_29809-T1
Valid prediction for GlimmerHMM_glimmerT_29816-T1
Valid prediction for snap_scaffold_12-snap.1795-T1
Valid prediction for GlimmerHMM_glimmerT_29814-T1
Couldn't classify 53679, 53747
Couldn't classify 61300, 61369
Sorry, prediction pasa_asmbl_8675.p1 fails validation.
(TTT)	 AA	53679-53747	GT	CGG
(GCC)	 AG	55522-55641	GT	CCG
(GTG)	 AG	56071-56187	GT	CGG
(GCC)	 AG	56416-56565	GT	AGG
(GAG)	 AG	56809-56924	GT	AGG
(GCT)	 AG	57092-57206	GT	AGG
(ATG)	 AG	57321-57440	GT	AGG
(GAG)	 AG	57660-57851	GT	AGG
(GCT)	 AG	57958-58149	GT	AGG
(GCT)	 AG	58345-58516	GT	TGG
(GCG)	 AG	59927-60006	GT	AGG
(ATT)	 AG	60144-60229	GT	CGG
(CCG)	 AG	60375-60441	GT	TGG
(GGC)	 AG	60552-60667	GT	AGG
(GGT)	 AG	61300-61369	GT	GGG
-recovered pasa_asmbl_8675.p1, initial, 57321, 57440
-recovered pasa_asmbl_8675.p1, internal, 55522, 55641
-recovered pasa_asmbl_8675.p1, internal, 56071, 56187
-recovered pasa_asmbl_8675.p1, internal, 56416, 56565
-recovered pasa_asmbl_8675.p1, internal, 56809, 56924
-recovered pasa_asmbl_8675.p1, internal, 57092, 57206
-recovered pasa_asmbl_8675.p1, internal, 57321, 57440
-recovered pasa_asmbl_8675.p1, internal, 57660, 57851
-recovered pasa_asmbl_8675.p1, internal, 57958, 58149
-recovered pasa_asmbl_8675.p1, internal, 58345, 58516
-recovered pasa_asmbl_8675.p1, internal, 59927, 60006
-recovered pasa_asmbl_8675.p1, internal, 60144, 60229
-recovered pasa_asmbl_8675.p1, internal, 60375, 60441
-recovered pasa_asmbl_8675.p1, internal, 60552, 60667
-recovered pasa_asmbl_8675.p1, internal, 61300, 61369
Valid prediction for Augustus_model.g19707.t1
Couldn't classify 37159, 37295
Couldn't classify 37936, 37981
Sorry, prediction pasa_asmbl_8677.p1 fails validation.
(GAG)	 TG	37159-37295	GT	AGG
(GCT)	 AG	37481-37747	GT	AGG
(GAG)	 AG	37936-37981	GC	GGG
-recovered pasa_asmbl_8677.p1, internal, 37481, 37747
-recovered pasa_asmbl_8677.p1, internal, 37936, 37981
Valid prediction for snap_scaffold_12-snap.1788-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 108001, rend_intergenic: 107998  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17371, rend_intergenic: 12730  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24781, rend_intergenic: 19866  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29906, rend_intergenic: 25390  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48972, rend_intergenic: 44257  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60294, rend_intergenic: 49308  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82728, rend_intergenic: 77896  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87779, rend_intergenic: 83594  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105714, rend_intergenic: 103362  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109266, rend_intergenic: 107202  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110409, rend_intergenic: 110362  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115700, rend_intergenic: 110441  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127743, rend_intergenic: 122580  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149677, rend_intergenic: 134221  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156893, rend_intergenic: 150044  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157790, rend_intergenic: 157640  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168303, rend_intergenic: 158931  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 174454
-exon list size: 402


building trellis

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-found 26 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 108001, rend_intergenic: 107998  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 17371, rend_intergenic: 12730  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24781, rend_intergenic: 19866  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29906, rend_intergenic: 25390  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48972, rend_intergenic: 44257  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60294, rend_intergenic: 49308  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82728, rend_intergenic: 77896  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87779, rend_intergenic: 83594  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105714, rend_intergenic: 103362  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109266, rend_intergenic: 107202  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110409, rend_intergenic: 110362  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115700, rend_intergenic: 110441  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127743, rend_intergenic: 122580  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149677, rend_intergenic: 134221  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156893, rend_intergenic: 150044  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157790, rend_intergenic: 157640  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168303, rend_intergenic: 158931  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 13 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 158508 - 174454
-exon list size: 11


building trellis

7.7    
15.4    
23.1    
30.8    
38.5    
46.2    
53.8    
61.5    
69.2    
76.9    
84.6    
92.3    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 159001 - 174454
-exon list size: 10


building trellis

8.3    
16.7    
25.0    
33.3    
41.7    
50.0    
58.3    
66.7    
75.0    
83.3    
91.7    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 163625 - 174454
-exon list size: 8


building trellis

10.0    
20.0    
30.0    
40.0    
50.0    
60.0    
70.0    
80.0    
90.0    
-found 1 predictions from path traversal
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support