-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_20/scaffold_20_7068967-7301976

-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_20-snap.1567-T1
Valid prediction for CodingQuarry_transcript_30549-T1
Valid prediction for GlimmerHMM_glimmerT_46268-T1
Valid prediction for CodingQuarry_transcript_30551-T1
Couldn't classify 203921, 203939
Couldn't classify 205896, 206099
Sorry, prediction pasa_asmbl_27146.p1 fails validation.
(CTC)	 TC	203921-203939	GT	CGG
(ATG)	 AG	204309-204671	GT	AGG
(ATG)	 AG	205533-205636	GT	ACG
(GAT)	 AG	205896-206099	NN	NNN
add_exon() Sorry, pasa_asmbl_27146.p1 204309-204671-initial-1 is invalid.
-recovered pasa_asmbl_27146.p1, initial, 204309, 204671
add_exon() Sorry, pasa_asmbl_27146.p1 205533-205636-initial-1 is invalid.
-recovered pasa_asmbl_27146.p1, initial, 205533, 205636
-recovered pasa_asmbl_27146.p1, internal, 204309, 204671
-recovered pasa_asmbl_27146.p1, internal, 205533, 205636
Valid prediction for snap_scaffold_20-snap.1546-T1
Valid prediction for Augustus_model.g30715.t1
Valid prediction for pasa_asmbl_26697.p1
Valid prediction for snap_scaffold_20-snap.1537-T1
Valid prediction for Augustus_model.g30712.t1
Valid prediction for Augustus_model.g30716.t1
Valid prediction for snap_scaffold_20-snap.1569-T1
Valid prediction for snap_scaffold_20-snap.1557-T1
Valid prediction for snap_scaffold_20-snap.1556-T1
Valid prediction for GlimmerHMM_glimmerT_46266-T1
Valid prediction for CodingQuarry_transcript_30550-T1
Valid prediction for GlimmerHMM_glimmerT_46265-T1
Valid prediction for snap_scaffold_20-snap.1560-T1
Valid prediction for GlimmerHMM_glimmerT_46262-T1
Valid prediction for snap_scaffold_20-snap.1545-T1
Valid prediction for Augustus_model.g30714.t1
Valid prediction for GlimmerHMM_glimmerT_46254-T1
Valid prediction for snap_scaffold_20-snap.1553-T1
Valid prediction for Augustus_model.g30702.t1
Valid prediction for snap_scaffold_20-snap.1533-T1
Valid prediction for GlimmerHMM_glimmerT_46264-T1
Valid prediction for snap_scaffold_20-snap.1572-T1
Valid prediction for Augustus_model.g30706.t1
Valid prediction for snap_scaffold_20-snap.1559-T1
Valid prediction for GlimmerHMM_glimmerT_46250-T1
Valid prediction for pasa_asmbl_26717.p1
Couldn't classify 147924, 147983
Sorry, prediction pasa_asmbl_26714.p1 fails validation.
(ATG)	 AG	144723-144759	GT	GCG
(CCA)	 AG	145653-145711	GT	TGG
(GTT)	 AG	145881-145962	GT	AGG
(AGG)	 AG	146114-146157	GT	AGG
(GCA)	 AG	146276-146329	GT	AGG
(GTT)	 AG	146519-146571	GT	AGG
(GGT)	 AG	146701-146809	GT	AGG
(TGT)	 AG	147924-147983	CT	TCC
-recovered pasa_asmbl_26714.p1, initial, 144723, 144759
-recovered pasa_asmbl_26714.p1, internal, 144723, 144759
-recovered pasa_asmbl_26714.p1, internal, 145653, 145711
-recovered pasa_asmbl_26714.p1, internal, 145881, 145962
-recovered pasa_asmbl_26714.p1, internal, 146114, 146157
-recovered pasa_asmbl_26714.p1, internal, 146276, 146329
-recovered pasa_asmbl_26714.p1, internal, 146519, 146571
-recovered pasa_asmbl_26714.p1, internal, 146701, 146809
Valid prediction for GlimmerHMM_glimmerT_46260-T1
Valid prediction for snap_scaffold_20-snap.1577-T1
Valid prediction for HiQ_model.g30719.t1
Valid prediction for snap_scaffold_20-snap.1573-T1
Valid prediction for snap_scaffold_20-snap.1541-T1
Valid prediction for snap_scaffold_20-snap.1571-T1
Valid prediction for CodingQuarry_transcript_30544-T1
Valid prediction for snap_scaffold_20-snap.1578-T1
Valid prediction for GlimmerHMM_glimmerT_46261-T1
Valid prediction for HiQ_model.g30698.t1
Valid prediction for pasa_asmbl_26706.p1
Valid prediction for snap_scaffold_20-snap.1562-T1
Valid prediction for pasa_asmbl_26705.p2
Valid prediction for Augustus_model.g30717.t1
Valid prediction for GlimmerHMM_glimmerT_46251-T1
Valid prediction for pasa_asmbl_26708.p1
Valid prediction for Augustus_model.g30703.t1
Valid prediction for snap_scaffold_20-snap.1563-T1
Valid prediction for snap_scaffold_20-snap.1574-T1
Valid prediction for Augustus_model.g30713.t1
Valid prediction for Augustus_model.g30720.t1
Valid prediction for GlimmerHMM_glimmerT_46258-T1
Valid prediction for Augustus_model.g30718.t1
Couldn't classify 142418, 142744
Sorry, prediction pasa_asmbl_26713.p1 fails validation.
(CCT)	 CT	142418-142744	GT	AGG
(GAA)	 AG	142922-142996	GT	AGG
(ATT)	 AG	143091-143217	GT	GGG
(ACT)	 AG	143486-144030	AC	AAA
-recovered pasa_asmbl_26713.p1, terminal, 143486, 144030
-recovered pasa_asmbl_26713.p1, internal, 142922, 142996
-recovered pasa_asmbl_26713.p1, internal, 143091, 143217
Valid prediction for Augustus_model.g30709.t1
Valid prediction for GlimmerHMM_glimmerT_46249-T1
Valid prediction for CodingQuarry_transcript_30552-T1
Valid prediction for snap_scaffold_20-snap.1544-T1
Valid prediction for snap_scaffold_20-snap.1551-T1
Valid prediction for snap_scaffold_20-snap.1558-T1
Valid prediction for snap_scaffold_20-snap.1561-T1
Valid prediction for GlimmerHMM_glimmerT_46243-T1
Valid prediction for Augustus_model.g30708.t1
Valid prediction for GlimmerHMM_glimmerT_46267-T1
Valid prediction for GlimmerHMM_glimmerT_46257-T1
Valid prediction for HiQ_model.g30711.t1
Valid prediction for snap_scaffold_20-snap.1564-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_20-snap.1555-T1
Valid prediction for snap_scaffold_20-snap.1536-T1
Valid prediction for snap_scaffold_20-snap.1554-T1
Couldn't classify 224187, 225011
Sorry, prediction pasa_asmbl_25870.p1 fails validation.
(AAA)	 CC	224187-225011	AC	GCA
Valid prediction for CodingQuarry_transcript_30545-T1
Valid prediction for snap_scaffold_20-snap.1543-T1
Valid prediction for HiQ_model.g30700.t1
Valid prediction for GlimmerHMM_glimmerT_46248-T1
Valid prediction for Augustus_model.g30721.t1
Valid prediction for GlimmerHMM_glimmerT_46256-T1
Valid prediction for snap_scaffold_20-snap.1538-T1
Valid prediction for snap_scaffold_20-snap.1576-T1
Valid prediction for snap_scaffold_20-snap.1532-T1
Valid prediction for Augustus_model.g30705.t1
Valid prediction for GlimmerHMM_glimmerT_46255-T1
Couldn't classify 10643, 10790
Couldn't classify 11141, 11325
Sorry, prediction pasa_asmbl_26321.p1 fails validation.
(GGA)	 CT	10643-10790	GT	CGG
(GTG)	 AG	11141-11325	CC	GGC
Valid prediction for GlimmerHMM_glimmerT_46253-T1
Valid prediction for Augustus_model.g30707.t1
Valid prediction for GlimmerHMM_glimmerT_46242-T1
Couldn't classify 6121, 6294
Couldn't classify 6948, 7096
Sorry, prediction pasa_asmbl_25896.p1 fails validation.
(CTC)	 CA	6121-6294	GT	AGG
(GGG)	 AG	6420-6497	GT	CGG
(AGG)	 AG	6583-6640	GT	GAG
(CCG)	 AG	6948-7096	GT	AGG
add_exon() Sorry, pasa_asmbl_25896.p1 6583-6640-terminal-3 is invalid.
-recovered pasa_asmbl_25896.p1, terminal, 6583, 6640
-recovered pasa_asmbl_25896.p1, internal, 6420, 6497
-recovered pasa_asmbl_25896.p1, internal, 6583, 6640
-recovered pasa_asmbl_25896.p1, internal, 6948, 7096
Valid prediction for snap_scaffold_20-snap.1575-T1
Valid prediction for snap_scaffold_20-snap.1550-T1
Valid prediction for snap_scaffold_20-snap.1549-T1
Valid prediction for snap_scaffold_20-snap.1540-T1
Valid prediction for snap_scaffold_20-snap.1570-T1
Valid prediction for GlimmerHMM_glimmerT_46263-T1
Valid prediction for GlimmerHMM_glimmerT_46252-T1
Valid prediction for snap_scaffold_20-snap.1548-T1
Valid prediction for snap_scaffold_20-snap.1539-T1
Valid prediction for GlimmerHMM_glimmerT_46269-T1
Valid prediction for snap_scaffold_20-snap.1535-T1
Valid prediction for Augustus_model.g30704.t1
Valid prediction for snap_scaffold_20-snap.1531-T1
Couldn't classify 204503, 204571
Sorry, prediction pasa_asmbl_26226.p1 fails validation.
(CAC)	 AG	204503-204571	GT	AGG
(GCC)	 AG	204800-204882	GT	AAG
(GAC)	 AG	204994-205103	GT	CGG
(GCG)	 AG	205203-205285	GT	AGG
(GCC)	 AG	205395-205535	GT	AGG
(GCG)	 AG	207883-207981	GT	CGG
(AAG)	 AG	208125-208189	GT	AGG
(CTA)	 AG	208345-208498	GT	AGG
(AGT)	 AG	208599-208693	GT	AGG
(GTG)	 AG	208932-209061	GT	AGG
(GAC)	 AG	209360-209435	GT	AGG
(ACA)	 AG	209660-209712	GT	CGG
(CCG)	 AG	210661-210888	AT	AAA
add_exon() Sorry, pasa_asmbl_26226.p1 208125-208189-terminal-2 is invalid.
-recovered pasa_asmbl_26226.p1, terminal, 208125, 208189
add_exon() Sorry, pasa_asmbl_26226.p1 208599-208693-terminal-2 is invalid.
-recovered pasa_asmbl_26226.p1, terminal, 208599, 208693
add_exon() Sorry, pasa_asmbl_26226.p1 209360-209435-terminal-3 is invalid.
-recovered pasa_asmbl_26226.p1, terminal, 209360, 209435
-recovered pasa_asmbl_26226.p1, terminal, 210661, 210888
-recovered pasa_asmbl_26226.p1, internal, 204503, 204571
-recovered pasa_asmbl_26226.p1, internal, 204800, 204882
-recovered pasa_asmbl_26226.p1, internal, 204994, 205103
-recovered pasa_asmbl_26226.p1, internal, 205203, 205285
-recovered pasa_asmbl_26226.p1, internal, 205395, 205535
-recovered pasa_asmbl_26226.p1, internal, 207883, 207981
-recovered pasa_asmbl_26226.p1, internal, 208125, 208189
-recovered pasa_asmbl_26226.p1, internal, 208345, 208498
-recovered pasa_asmbl_26226.p1, internal, 208599, 208693
-recovered pasa_asmbl_26226.p1, internal, 208932, 209061
-recovered pasa_asmbl_26226.p1, internal, 209360, 209435
-recovered pasa_asmbl_26226.p1, internal, 209660, 209712
Valid prediction for snap_scaffold_20-snap.1547-T1
Valid prediction for pasa_asmbl_25885.p1
Valid prediction for pasa_asmbl_25874.p1
Valid prediction for HiQ_model.g30710.t1
Valid prediction for GlimmerHMM_glimmerT_46259-T1
Valid prediction for GlimmerHMM_glimmerT_46244-T1
Couldn't classify 18679, 19059
Sorry, prediction pasa_asmbl_25892.p1 fails validation.
(CTG)	 GC	18679-19059	TC	AGT
Valid prediction for snap_scaffold_20-snap.1566-T1
Valid prediction for snap_scaffold_20-snap.1542-T1
Valid prediction for snap_scaffold_20-snap.1534-T1
Valid prediction for pasa_asmbl_25889.p1
Valid prediction for pasa_asmbl_25876.p1
Valid prediction for snap_scaffold_20-snap.1552-T1
Valid prediction for Augustus_model.g30699.t1
Valid prediction for GlimmerHMM_glimmerT_46245-T1
Valid prediction for GlimmerHMM_glimmerT_46247-T1
Valid prediction for Augustus_model.g30701.t1
Valid prediction for snap_scaffold_20-snap.1568-T1
Valid prediction for snap_scaffold_20-snap.1565-T1
Valid prediction for GlimmerHMM_glimmerT_46246-T1
Valid prediction for CodingQuarry_transcript_30546-T1
Couldn't classify 17508, 17834
Sorry, prediction pasa_asmbl_25894.p1 fails validation.
(GCT)	 CT	17508-17834	AC	ACA

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 29220, rend_intergenic: 25580  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45204, rend_intergenic: 42486  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61617, rend_intergenic: 45221  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78790, rend_intergenic: 61925  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93829, rend_intergenic: 83748  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99057, rend_intergenic: 95618  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104222, rend_intergenic: 100665  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121753, rend_intergenic: 117311  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161720, rend_intergenic: 158561  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163819, rend_intergenic: 162141  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180499, rend_intergenic: 165508  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 193159, rend_intergenic: 180924  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 231560, rend_intergenic: 220593  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 233010
-exon list size: 556


building trellis

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88.0    
88.2    
88.4    
88.5    
88.7    
88.9    
89.1    
89.2    
89.4    
89.6    
89.8    
90.0    
90.1    
90.3    
90.5    
90.7    
90.9    
91.0    
91.2    
91.4    
91.6    
91.8    
91.9    
92.1    
92.3    
92.5    
92.7    
92.8    
93.0    
93.2    
93.4    
93.5    
93.7    
93.9    
94.1    
94.3    
94.4    
94.6    
94.8    
95.0    
95.2    
95.3    
95.5    
95.7    
95.9    
96.1    
96.2    
96.4    
96.6    
96.8    
97.0    
97.1    
97.3    
97.5    
97.7    
97.8    
98.0    
98.2    
98.4    
98.6    
98.7    
98.9    
99.1    
99.3    
99.5    
99.6    
99.8    
-found 37 predictions from path traversal
Error with prediction: snap lend_intergenic: 29220, rend_intergenic: 25580  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45204, rend_intergenic: 42486  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61617, rend_intergenic: 45221  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78790, rend_intergenic: 61925  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93829, rend_intergenic: 83748  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99057, rend_intergenic: 95618  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104222, rend_intergenic: 100665  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121753, rend_intergenic: 117311  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161720, rend_intergenic: 158561  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163819, rend_intergenic: 162141  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180499, rend_intergenic: 165508  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 193159, rend_intergenic: 180924  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 231560, rend_intergenic: 220593  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 28 predictions persist after filtering for low support