-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_5/scaffold_5_9350981-9600225

-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_12699-T1
Valid prediction for GlimmerHMM_glimmerT_12687-T1
Valid prediction for GlimmerHMM_glimmerT_12681-T1
Valid prediction for GeneMark_model.21490_t
Valid prediction for snap_scaffold_5-snap.1791-T1
Valid prediction for GlimmerHMM_glimmerT_12688-T1
Valid prediction for Augustus_model.g8416.t1
Valid prediction for Augustus_model.g8412.t1
Valid prediction for HiQ_model.g8425.t1
Valid prediction for snap_scaffold_5-snap.1808-T1
Valid prediction for Augustus_model.g8405.t1
Valid prediction for snap_scaffold_5-snap.1784-T1
Valid prediction for Augustus_model.g8415.t1
Couldn't classify 229409, 229467
Sorry, prediction pasa_asmbl_44285.p1 fails validation.
(GTA)	 CG	229409-229467	GT	AGG
(CCC)	 AG	229625-229699	GT	ATG
(AGA)	 AG	229826-229899	GT	AGG
(ACG)	 AG	229980-230091	GT	TGG
(TGG)	 AG	230214-230314	GT	GGG
(CTG)	 AG	230461-230634	GT	AGG
(GGA)	 AG	230735-230792	GT	AGG
(AGG)	 AG	230898-231048	GC	GAG
-recovered pasa_asmbl_44285.p1, terminal, 230898, 231048
-recovered pasa_asmbl_44285.p1, internal, 229625, 229699
-recovered pasa_asmbl_44285.p1, internal, 229826, 229899
-recovered pasa_asmbl_44285.p1, internal, 229980, 230091
-recovered pasa_asmbl_44285.p1, internal, 230214, 230314
-recovered pasa_asmbl_44285.p1, internal, 230461, 230634
-recovered pasa_asmbl_44285.p1, internal, 230735, 230792
-recovered pasa_asmbl_44285.p1, internal, 230898, 231048
Valid prediction for snap_scaffold_5-snap.1794-T1
Valid prediction for GeneMark_model.21501_t
Valid prediction for GlimmerHMM_glimmerT_12689-T1
Valid prediction for Augustus_model.g8414.t1
Valid prediction for snap_scaffold_5-snap.1775-T1
Valid prediction for HiQ_model.g8404.t1
Valid prediction for snap_scaffold_5-snap.1806-T1
Valid prediction for snap_scaffold_5-snap.1811-T1
Couldn't classify 33813, 33846
Sorry, prediction GeneMark_model.21479_t fails validation.
(GAC)	 AG	33813-33846	GT	GAG
(AGA)	 AG	33868-33882	GT	GGG
(AGA)	 AG	34642-34656	GT	GAG
(TGG)	 AG	34810-34863	GT	CAG
(GTG)	 AG	35045-35092	GT	CAG
(CAA)	 AG	36048-36062	GT	AGG
(CCA)	 AG	36341-36416	AG	AGA
-recovered GeneMark_model.21479_t, terminal, 36341, 36416
-recovered GeneMark_model.21479_t, internal, 33813, 33846
-recovered GeneMark_model.21479_t, internal, 33868, 33882
-recovered GeneMark_model.21479_t, internal, 34642, 34656
-recovered GeneMark_model.21479_t, internal, 34810, 34863
-recovered GeneMark_model.21479_t, internal, 35045, 35092
-recovered GeneMark_model.21479_t, internal, 36048, 36062
Valid prediction for GeneMark_model.21482_t
Valid prediction for snap_scaffold_5-snap.1774-T1
Valid prediction for Augustus_model.g8413.t1
Valid prediction for GlimmerHMM_glimmerT_12691-T1
Valid prediction for snap_scaffold_5-snap.1793-T1
Valid prediction for GlimmerHMM_glimmerT_12672-T1
Valid prediction for Augustus_model.g8410.t1
Valid prediction for snap_scaffold_5-snap.1781-T1
Valid prediction for GlimmerHMM_glimmerT_12676-T1
Valid prediction for GlimmerHMM_glimmerT_12670-T1
Valid prediction for GeneMark_model.21493_t
Valid prediction for GlimmerHMM_glimmerT_12685-T1
Valid prediction for GeneMark_model.21496_t
Valid prediction for GeneMark_model.21502_t
Valid prediction for snap_scaffold_5-snap.1783-T1
Valid prediction for GlimmerHMM_glimmerT_12675-T1
Valid prediction for GeneMark_model.21477_t
Valid prediction for GeneMark_model.21480_t
Valid prediction for GeneMark_model.21506_t
Valid prediction for snap_scaffold_5-snap.1802-T1
Valid prediction for snap_scaffold_5-snap.1787-T1
Valid prediction for GlimmerHMM_glimmerT_12682-T1
Valid prediction for snap_scaffold_5-snap.1795-T1
Valid prediction for snap_scaffold_5-snap.1777-T1
Valid prediction for GeneMark_model.21488_t
Valid prediction for Augustus_model.g8427.t1
Valid prediction for GeneMark_model.21475_t
Valid prediction for GeneMark_model.21487_t
Valid prediction for GeneMark_model.21494_t
Valid prediction for CodingQuarry_transcript_52054-T1
Valid prediction for GlimmerHMM_glimmerT_12667-T1
Valid prediction for GlimmerHMM_glimmerT_12669-T1
Valid prediction for pasa_asmbl_44283.p1
Valid prediction for GeneMark_model.21509_t
Valid prediction for GeneMark_model.21495_t
Valid prediction for snap_scaffold_5-snap.1779-T1
Valid prediction for GeneMark_model.21476_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 GlimmerHMM_glimmerT_12677-T1
Valid prediction for Augustus_model.g8407.t1
Valid prediction for GeneMark_model.21486_t
Valid prediction for snap_scaffold_5-snap.1789-T1
Couldn't classify 151525, 152136
Sorry, prediction pasa_asmbl_45661.p1 fails validation.
(GTG)	 GT	151525-152136	GT	AGG
(AAC)	 AG	152283-152327	GT	AGG
(GAG)	 AG	153071-153097	AA	AGA
-recovered pasa_asmbl_45661.p1, terminal, 153071, 153097
-recovered pasa_asmbl_45661.p1, internal, 152283, 152327
Valid prediction for GeneMark_model.21491_t
Valid prediction for snap_scaffold_5-snap.1804-T1
Valid prediction for Augustus_model.g8424.t1
Valid prediction for GeneMark_model.21484_t
Valid prediction for GeneMark_model.21498_t
Valid prediction for GeneMark_model.21503_t
Valid prediction for Augustus_model.g8403.t1
Valid prediction for snap_scaffold_5-snap.1799-T1
Valid prediction for snap_scaffold_5-snap.1790-T1
Valid prediction for GlimmerHMM_glimmerT_12666-T1
Valid prediction for GlimmerHMM_glimmerT_12668-T1
Valid prediction for snap_scaffold_5-snap.1810-T1
Valid prediction for GlimmerHMM_glimmerT_12694-T1
Couldn't classify 53448, 53603
Sorry, prediction pasa_asmbl_45668.p1 fails validation.
(CTC)	 AG	53448-53603	GT	GTG
(GAT)	 AG	53689-53787	GT	GGG
(GTG)	 AG	53891-53987	GT	TGG
(ATG)	 AG	55107-55120	AC	AGA
-recovered pasa_asmbl_45668.p1, terminal, 55107, 55120
-recovered pasa_asmbl_45668.p1, internal, 53448, 53603
-recovered pasa_asmbl_45668.p1, internal, 53689, 53787
-recovered pasa_asmbl_45668.p1, internal, 53891, 53987
Valid prediction for GlimmerHMM_glimmerT_12679-T1
Valid prediction for GlimmerHMM_glimmerT_12673-T1
Valid prediction for GeneMark_model.21492_t
Valid prediction for snap_scaffold_5-snap.1776-T1
Valid prediction for GlimmerHMM_glimmerT_12697-T1
Valid prediction for pasa_asmbl_45663.p1
Valid prediction for GlimmerHMM_glimmerT_12702-T1
Valid prediction for GeneMark_model.21507_t
Valid prediction for GlimmerHMM_glimmerT_12700-T1
Valid prediction for snap_scaffold_5-snap.1786-T1
Valid prediction for Augustus_model.g8411.t1
Valid prediction for Augustus_model.g8422.t1
Valid prediction for Augustus_model.g8409.t1
Valid prediction for GlimmerHMM_glimmerT_12683-T1
Valid prediction for GeneMark_model.21508_t
Valid prediction for snap_scaffold_5-snap.1785-T1
Valid prediction for snap_scaffold_5-snap.1773-T1
Valid prediction for snap_scaffold_5-snap.1796-T1
Valid prediction for snap_scaffold_5-snap.1788-T1
Valid prediction for GlimmerHMM_glimmerT_12701-T1
Valid prediction for snap_scaffold_5-snap.1798-T1
Couldn't classify 217201, 217232
Sorry, prediction GeneMark_model.21478_t fails validation.
(CCT)	 AG	217201-217232	GT	CCG
(GCA)	 AG	217368-217385	GT	GAG
(AGG)	 AG	217407-217441	GT	CAG
(CTC)	 AG	218304-218432	GT	AAG
(AGC)	 AG	218573-218636	GT	GTG
(AAC)	 AG	218707-218725	CC	AAC
-recovered GeneMark_model.21478_t, terminal, 218707, 218725
-recovered GeneMark_model.21478_t, internal, 217201, 217232
-recovered GeneMark_model.21478_t, internal, 217368, 217385
-recovered GeneMark_model.21478_t, internal, 217407, 217441
-recovered GeneMark_model.21478_t, internal, 218304, 218432
-recovered GeneMark_model.21478_t, internal, 218573, 218636
Valid prediction for GlimmerHMM_glimmerT_12686-T1
Valid prediction for snap_scaffold_5-snap.1778-T1
Valid prediction for Augustus_model.g8421.t1
Valid prediction for Augustus_model.g8417.t1
Valid prediction for GeneMark_model.21485_t
Valid prediction for snap_scaffold_5-snap.1809-T1
Valid prediction for CodingQuarry_transcript_52051-T1
Valid prediction for Augustus_model.g8418.t1
Valid prediction for snap_scaffold_5-snap.1797-T1
Valid prediction for Augustus_model.g8423.t1
Valid prediction for GeneMark_model.21481_t
Valid prediction for snap_scaffold_5-snap.1782-T1
Valid prediction for snap_scaffold_5-snap.1807-T1
Valid prediction for Augustus_model.g8406.t1
Valid prediction for GeneMark_model.21505_t
Valid prediction for GlimmerHMM_glimmerT_12695-T1
Valid prediction for HiQ_model.g8426.t1
Valid prediction for GlimmerHMM_glimmerT_12693-T1
Valid prediction for GlimmerHMM_glimmerT_12665-T1
Valid prediction for snap_scaffold_5-snap.1801-T1
Valid prediction for pasa_asmbl_45672.p1
Valid prediction for HiQ_model.g8408.t1
Valid prediction for GlimmerHMM_glimmerT_12674-T1
Valid prediction for GlimmerHMM_glimmerT_12698-T1
Valid prediction for GlimmerHMM_glimmerT_12684-T1
Valid prediction for snap_scaffold_5-snap.1800-T1
Valid prediction for GlimmerHMM_glimmerT_12671-T1
Valid prediction for Augustus_model.g8419.t1
Valid prediction for GeneMark_model.21510_t
Valid prediction for GeneMark_model.21489_t
Valid prediction for CodingQuarry_transcript_52052-T1
Valid prediction for GlimmerHMM_glimmerT_12678-T1
Valid prediction for pasa_asmbl_45676.p1
Valid prediction for CodingQuarry_transcript_52053-T1
Valid prediction for HiQ_model.g8420.t1
Valid prediction for snap_scaffold_5-snap.1780-T1
Valid prediction for GlimmerHMM_glimmerT_12680-T1
Couldn't classify 150496, 151329
Sorry, prediction pasa_asmbl_45662.p1 fails validation.
(ATG)	 TA	149563-149589	GT	AGG
(ACG)	 AG	149910-149934	GT	AGG
(TCT)	 AG	150306-150400	GT	AGG
(AAC)	 AG	150496-151329	CC	CTC
-recovered pasa_asmbl_45662.p1, initial, 149563, 149589
-recovered pasa_asmbl_45662.p1, internal, 149910, 149934
-recovered pasa_asmbl_45662.p1, internal, 150306, 150400
Couldn't classify 73698, 74030
Sorry, prediction pasa_asmbl_45667.p1 fails validation.
(CCT)	 TG	73698-74030	AT	GCA
Valid prediction for snap_scaffold_5-snap.1803-T1
Valid prediction for GeneMark_model.21500_t
Valid prediction for snap_scaffold_5-snap.1792-T1
Valid prediction for GlimmerHMM_glimmerT_12690-T1
Valid prediction for GlimmerHMM_glimmerT_12692-T1
Valid prediction for GeneMark_model.21504_t
Valid prediction for snap_scaffold_5-snap.1805-T1
Valid prediction for GlimmerHMM_glimmerT_12696-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 174663, rend_intergenic: 174660  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33596, rend_intergenic: 31993  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46974, rend_intergenic: 37691  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59653, rend_intergenic: 56142  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76297, rend_intergenic: 65311  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189053, rend_intergenic: 184390  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 225610, rend_intergenic: 221161  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 249245
-exon list size: 654


building trellis

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87.8    
88.0    
88.1    
88.3    
88.4    
88.6    
88.7    
88.9    
89.0    
89.2    
89.3    
89.5    
89.6    
89.8    
89.9    
90.1    
90.2    
90.4    
90.5    
90.7    
90.9    
91.0    
91.2    
91.3    
91.5    
91.6    
91.8    
91.9    
92.1    
92.2    
92.4    
92.5    
92.7    
92.8    
93.0    
93.1    
93.3    
93.4    
93.6    
93.8    
93.9    
94.1    
94.2    
94.4    
94.5    
94.7    
94.8    
95.0    
95.1    
95.3    
95.4    
95.6    
95.7    
95.9    
96.0    
96.2    
96.3    
96.5    
96.6    
96.8    
97.0    
97.1    
97.3    
97.4    
97.6    
97.7    
97.9    
98.0    
98.2    
98.3    
98.5    
98.6    
98.8    
98.9    
99.1    
99.2    
99.4    
99.5    
99.7    
99.8    
-found 36 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 174663, rend_intergenic: 174660  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33596, rend_intergenic: 31993  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46974, rend_intergenic: 37691  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59653, rend_intergenic: 56142  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76297, rend_intergenic: 65311  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 189053, rend_intergenic: 184390  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 225610, rend_intergenic: 221161  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 27 predictions persist after filtering for low support