-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_9989198-10201268

-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_29922-T1
Valid prediction for Augustus_model.g19793.t1
Valid prediction for snap_scaffold_12-snap.1920-T1
Valid prediction for snap_scaffold_12-snap.1898-T1
Valid prediction for snap_scaffold_12-snap.1915-T1
Valid prediction for snap_scaffold_12-snap.1887-T1
Valid prediction for snap_scaffold_12-snap.1902-T1
Valid prediction for HiQ_model.g19773.t1
Valid prediction for GlimmerHMM_glimmerT_29911-T1
Valid prediction for snap_scaffold_12-snap.1904-T1
Valid prediction for Augustus_model.g19796.t1
Valid prediction for Augustus_model.g19800.t1
Valid prediction for snap_scaffold_12-snap.1909-T1
Valid prediction for GlimmerHMM_glimmerT_29903-T1
Valid prediction for snap_scaffold_12-snap.1901-T1
Valid prediction for GlimmerHMM_glimmerT_29912-T1
Valid prediction for CodingQuarry_transcript_10360-T1
Valid prediction for HiQ_model.g19798.t1
Valid prediction for Augustus_model.g19785.t1
Valid prediction for Augustus_model.g19791.t1
Valid prediction for pasa_asmbl_7908.p1
Valid prediction for Augustus_model.g19782.t1
Valid prediction for snap_scaffold_12-snap.1892-T1
Valid prediction for snap_scaffold_12-snap.1907-T1
Valid prediction for snap_scaffold_12-snap.1897-T1
Valid prediction for pasa_asmbl_7907.p1
Couldn't classify 205306, 205455
Couldn't classify 207692, 207774
Sorry, prediction pasa_asmbl_7913.p2 fails validation.
(GCG)	 AG	205306-205455	GT	AGG
(GGC)	 AG	206518-206607	GT	AGG
(CTG)	 AG	206994-207177	GT	AGG
(GAC)	 AG	207692-207774	AT	TCA
-recovered pasa_asmbl_7913.p2, internal, 205306, 205455
-recovered pasa_asmbl_7913.p2, internal, 206518, 206607
-recovered pasa_asmbl_7913.p2, internal, 206994, 207177
Valid prediction for GlimmerHMM_glimmerT_29930-T1
Valid prediction for snap_scaffold_12-snap.1912-T1
Valid prediction for HiQ_model.g19797.t1
Valid prediction for CodingQuarry_transcript_10359-T1
Valid prediction for HiQ_model.g19795.t1
Valid prediction for GlimmerHMM_glimmerT_29932-T1
Couldn't classify 3145, 3711
Sorry, prediction pasa_asmbl_7901.p1 fails validation.
(ATG)	 CA	2595-3026	GT	AGG
(AAT)	 AG	3145-3711	GC	GAG
-recovered pasa_asmbl_7901.p1, initial, 2595, 3026
-recovered pasa_asmbl_7901.p1, internal, 3145, 3711
Valid prediction for GlimmerHMM_glimmerT_29904-T1
Valid prediction for GlimmerHMM_glimmerT_29933-T1
Valid prediction for Augustus_model.g19787.t1
Valid prediction for GlimmerHMM_glimmerT_29931-T1
Valid prediction for GlimmerHMM_glimmerT_29907-T1
Valid prediction for snap_scaffold_12-snap.1910-T1
Valid prediction for snap_scaffold_12-snap.1913-T1
Valid prediction for GlimmerHMM_glimmerT_29924-T1
Valid prediction for snap_scaffold_12-snap.1905-T1
Couldn't classify 3865, 4608
Sorry, prediction pasa_asmbl_7902.p1 fails validation.
(TCA)	 TC	3865-4608	CT	AAC
Valid prediction for snap_scaffold_12-snap.1919-T1
Valid prediction for GlimmerHMM_glimmerT_29916-T1
Valid prediction for snap_scaffold_12-snap.1918-T1
Couldn't classify 172167, 172907
Sorry, prediction pasa_asmbl_7904.p1 fails validation.
(AAA)	 TA	172167-172907	CA	AGC
Valid prediction for GlimmerHMM_glimmerT_29928-T1
Valid prediction for GlimmerHMM_glimmerT_29925-T1
Valid prediction for snap_scaffold_12-snap.1916-T1
Valid prediction for CodingQuarry_transcript_10361-T1
Valid prediction for snap_scaffold_12-snap.1922-T1
Valid prediction for GlimmerHMM_glimmerT_29935-T1
Valid prediction for pasa_asmbl_7906.p1
Valid prediction for snap_scaffold_12-snap.1895-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: -)Couldn't classify 142648, 142716
Couldn't classify 144975, 145074
Sorry, prediction pasa_asmbl_8727.p1 fails validation.
(TTC)	 CC	142648-142716	GT	CGG
(GTG)	 AG	143360-143525	GT	GGG
(ATG)	 AG	144065-144195	GT	AGG
(GTG)	 AG	144295-144441	GT	TGG
(GTG)	 AG	144686-144810	GT	AGG
(GTA)	 AG	144975-145074	AT	AGA
add_exon() Sorry, pasa_asmbl_8727.p1 144065-144195-initial-1 is invalid.
-recovered pasa_asmbl_8727.p1, initial, 144065, 144195
-recovered pasa_asmbl_8727.p1, internal, 143360, 143525
-recovered pasa_asmbl_8727.p1, internal, 144065, 144195
-recovered pasa_asmbl_8727.p1, internal, 144295, 144441
-recovered pasa_asmbl_8727.p1, internal, 144686, 144810
Valid prediction for CodingQuarry_transcript_10355-T1
Valid prediction for snap_scaffold_12-snap.1923-T1
Valid prediction for snap_scaffold_12-snap.1899-T1
Valid prediction for snap_scaffold_12-snap.1900-T1
Valid prediction for GlimmerHMM_glimmerT_29926-T1
Valid prediction for CodingQuarry_transcript_10356-T1
Valid prediction for snap_scaffold_12-snap.1891-T1
Valid prediction for GlimmerHMM_glimmerT_29920-T1
Valid prediction for pasa_asmbl_8718.p1
Valid prediction for GlimmerHMM_glimmerT_29913-T1
Valid prediction for Augustus_model.g19790.t1
Valid prediction for GlimmerHMM_glimmerT_29917-T1
Valid prediction for snap_scaffold_12-snap.1921-T1
Valid prediction for GlimmerHMM_glimmerT_29914-T1
Valid prediction for snap_scaffold_12-snap.1917-T1
Valid prediction for CodingQuarry_transcript_10354-T1
Valid prediction for GlimmerHMM_glimmerT_29910-T1
Valid prediction for snap_scaffold_12-snap.1903-T1
Valid prediction for snap_scaffold_12-snap.1911-T1
Valid prediction for GlimmerHMM_glimmerT_29906-T1
Valid prediction for Augustus_model.g19786.t1
Valid prediction for GlimmerHMM_glimmerT_29918-T1
Valid prediction for GlimmerHMM_glimmerT_29921-T1
Valid prediction for snap_scaffold_12-snap.1894-T1
Valid prediction for pasa_asmbl_8716.p1
Valid prediction for GlimmerHMM_glimmerT_29905-T1
Valid prediction for GlimmerHMM_glimmerT_29934-T1
Valid prediction for Augustus_model.g19777.t1
Valid prediction for CodingQuarry_transcript_10357-T1
Valid prediction for snap_scaffold_12-snap.1893-T1
Valid prediction for CodingQuarry_transcript_10353-T1
Valid prediction for snap_scaffold_12-snap.1914-T1
Valid prediction for snap_scaffold_12-snap.1908-T1
Valid prediction for Augustus_model.g19778.t1
Valid prediction for GlimmerHMM_glimmerT_29919-T1
Valid prediction for Augustus_model.g19781.t1
Valid prediction for GlimmerHMM_glimmerT_29929-T1
Valid prediction for Augustus_model.g19784.t1
Valid prediction for snap_scaffold_12-snap.1906-T1
Valid prediction for HiQ_model.g19794.t1
Valid prediction for snap_scaffold_12-snap.1896-T1
Valid prediction for HiQ_model.g19799.t1
Valid prediction for pasa_asmbl_8731.p1
Valid prediction for snap_scaffold_12-snap.1888-T1
Valid prediction for GlimmerHMM_glimmerT_29923-T1
Valid prediction for Augustus_model.g19780.t1
Valid prediction for snap_scaffold_12-snap.1890-T1
Valid prediction for GlimmerHMM_glimmerT_29915-T1
Valid prediction for Augustus_model.g19775.t1
Valid prediction for pasa_asmbl_8725.p1
Valid prediction for GlimmerHMM_glimmerT_29909-T1
Valid prediction for Augustus_model.g19779.t1
Valid prediction for Augustus_model.g19792.t1
Valid prediction for GlimmerHMM_glimmerT_29908-T1
Valid prediction for CodingQuarry_transcript_10358-T1
Valid prediction for Augustus_model.g19774.t1
Valid prediction for Augustus_model.g19788.t1
Valid prediction for HiQ_model.g19776.t1
Valid prediction for pasa_asmbl_8730.p1
Valid prediction for snap_scaffold_12-snap.1889-T1
Valid prediction for CodingQuarry_transcript_10362-T1
Couldn't classify 196330, 196533
Sorry, prediction pasa_asmbl_8714.p1 fails validation.
(CAG)	 TG	196330-196533	GT	TGG
(GCT)	 AG	196666-196848	GT	AGG
(GCC)	 AG	197456-197701	GT	TAG
(TCC)	 AG	197825-197939	GT	AGG
(ATT)	 AG	198052-198176	GT	AGG
(GAC)	 AG	198466-198632	GT	AGG
(ATA)	 AG	198797-198941	GT	GGG
(ATC)	 AG	199147-199236	CA	AGC
-recovered pasa_asmbl_8714.p1, terminal, 199147, 199236
-recovered pasa_asmbl_8714.p1, internal, 196666, 196848
-recovered pasa_asmbl_8714.p1, internal, 197456, 197701
-recovered pasa_asmbl_8714.p1, internal, 197825, 197939
-recovered pasa_asmbl_8714.p1, internal, 198052, 198176
-recovered pasa_asmbl_8714.p1, internal, 198466, 198632
-recovered pasa_asmbl_8714.p1, internal, 198797, 198941
Valid prediction for Augustus_model.g19789.t1
Valid prediction for GlimmerHMM_glimmerT_29927-T1
Valid prediction for Augustus_model.g19783.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 51624, rend_intergenic: 48102  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54740, rend_intergenic: 52635  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69626, rend_intergenic: 65832  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80278, rend_intergenic: 70468  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103821, rend_intergenic: 97442  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107717, rend_intergenic: 104005  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109489, rend_intergenic: 108405  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112845, rend_intergenic: 112671  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115181, rend_intergenic: 112861  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118504, rend_intergenic: 115825  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140600, rend_intergenic: 119156  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149293, rend_intergenic: 141167  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153971, rend_intergenic: 152395  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163035, rend_intergenic: 161339  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 211917, rend_intergenic: 204007  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 212071
-exon list size: 387


building trellis

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99.2    
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-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 51624, rend_intergenic: 48102  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54740, rend_intergenic: 52635  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69626, rend_intergenic: 65832  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80278, rend_intergenic: 70468  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103821, rend_intergenic: 97442  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107717, rend_intergenic: 104005  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109489, rend_intergenic: 108405  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112845, rend_intergenic: 112671  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115181, rend_intergenic: 112861  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118504, rend_intergenic: 115825  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140600, rend_intergenic: 119156  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149293, rend_intergenic: 141167  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153971, rend_intergenic: 152395  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163035, rend_intergenic: 161339  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 211917, rend_intergenic: 204007  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 26 predictions persist after filtering for low support