-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_14/scaffold_14_3287958-3504354

-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_33510-T1
Valid prediction for GlimmerHMM_glimmerT_33502-T1
Valid prediction for snap_scaffold_14-snap.553-T1
Valid prediction for snap_scaffold_14-snap.545-T1
Valid prediction for snap_scaffold_14-snap.588-T1
Valid prediction for Augustus_model.g22407.t1
Valid prediction for GlimmerHMM_glimmerT_33499-T1
Valid prediction for snap_scaffold_14-snap.577-T1
Valid prediction for GlimmerHMM_glimmerT_33515-T1
Valid prediction for snap_scaffold_14-snap.563-T1
Valid prediction for snap_scaffold_14-snap.567-T1
Valid prediction for Augustus_model.g22413.t1
Valid prediction for Augustus_model.g22412.t1
Valid prediction for GlimmerHMM_glimmerT_33506-T1
Valid prediction for snap_scaffold_14-snap.565-T1
Valid prediction for snap_scaffold_14-snap.580-T1
Valid prediction for GlimmerHMM_glimmerT_33513-T1
Valid prediction for snap_scaffold_14-snap.561-T1
Valid prediction for Augustus_model.g22419.t1
Valid prediction for Augustus_model.g22411.t1
Valid prediction for snap_scaffold_14-snap.578-T1
Valid prediction for GlimmerHMM_glimmerT_33494-T1
Valid prediction for Augustus_model.g22408.t1
Valid prediction for snap_scaffold_14-snap.582-T1
Valid prediction for snap_scaffold_14-snap.574-T1
Valid prediction for snap_scaffold_14-snap.543-T1
Valid prediction for snap_scaffold_14-snap.586-T1
Valid prediction for GlimmerHMM_glimmerT_33498-T1
Valid prediction for Augustus_model.g22415.t1
Valid prediction for Augustus_model.g22420.t1
Valid prediction for snap_scaffold_14-snap.557-T1
Valid prediction for snap_scaffold_14-snap.560-T1
Valid prediction for snap_scaffold_14-snap.547-T1
Valid prediction for snap_scaffold_14-snap.583-T1
Valid prediction for snap_scaffold_14-snap.558-T1
Valid prediction for snap_scaffold_14-snap.546-T1
Valid prediction for GlimmerHMM_glimmerT_33512-T1
Valid prediction for snap_scaffold_14-snap.544-T1
Valid prediction for snap_scaffold_14-snap.569-T1
Valid prediction for snap_scaffold_14-snap.576-T1
Valid prediction for snap_scaffold_14-snap.587-T1
Valid prediction for GlimmerHMM_glimmerT_33501-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 GlimmerHMM_glimmerT_33511-T1
Valid prediction for GlimmerHMM_glimmerT_33507-T1
Valid prediction for GlimmerHMM_glimmerT_33495-T1
Valid prediction for snap_scaffold_14-snap.556-T1
Valid prediction for GlimmerHMM_glimmerT_33497-T1
Valid prediction for GlimmerHMM_glimmerT_33503-T1
Valid prediction for pasa_asmbl_13004.p1
Valid prediction for snap_scaffold_14-snap.568-T1
Valid prediction for snap_scaffold_14-snap.584-T1
Valid prediction for Augustus_model.g22416.t1
Valid prediction for snap_scaffold_14-snap.555-T1
Valid prediction for snap_scaffold_14-snap.549-T1
Valid prediction for GlimmerHMM_glimmerT_33514-T1
Couldn't classify 58751, 58858
Couldn't classify 59584, 59661
Sorry, prediction pasa_asmbl_13833.p1 fails validation.
(TTC)	 TG	58751-58858	GT	AGG
(TCT)	 AG	59080-59241	GT	AGG
(AAC)	 AG	59584-59661	AC	AGA
-recovered pasa_asmbl_13833.p1, internal, 59080, 59241
Valid prediction for snap_scaffold_14-snap.562-T1
Valid prediction for snap_scaffold_14-snap.552-T1
Valid prediction for Augustus_model.g22414.t1
Valid prediction for snap_scaffold_14-snap.550-T1
Valid prediction for snap_scaffold_14-snap.575-T1
Valid prediction for snap_scaffold_14-snap.559-T1
Couldn't classify 50884, 51057
Couldn't classify 52225, 52281
Sorry, prediction pasa_asmbl_13790.p2 fails validation.
(GCC)	 AA	50884-51057	GT	CGG
(GTT)	 AG	51538-51663	GT	TGG
(CTG)	 AG	52225-52281	GT	GGG
-recovered pasa_asmbl_13790.p2, internal, 51538, 51663
-recovered pasa_asmbl_13790.p2, internal, 52225, 52281
Valid prediction for Augustus_model.g22409.t1
Valid prediction for snap_scaffold_14-snap.572-T1
Couldn't classify 125593, 126009
Sorry, prediction pasa_asmbl_13010.p1 fails validation.
(GAC)	 GA	125593-126009	TT	AAT
Valid prediction for snap_scaffold_14-snap.581-T1
Valid prediction for CodingQuarry_transcript_15613-T1
Couldn't classify 72498, 72664
Sorry, prediction pasa_asmbl_13012.p1 fails validation.
(CGC)	 AG	72498-72664	GT	AGG
(ATG)	 AG	72909-73035	GT	AGG
(GTG)	 AG	73302-73403	GT	AGG
(GCA)	 AG	73978-74124	GT	AGG
(ATT)	 AG	74338-74496	GT	AGG
(GAG)	 AG	74597-74763	GT	AGG
(TGT)	 AG	74928-75122	GT	AGG
(AGT)	 AG	75883-75994	CT	AGC
-recovered pasa_asmbl_13012.p1, initial, 72909, 73035
add_exon() Sorry, pasa_asmbl_13012.p1 74928-75122-terminal-1 is invalid.
-recovered pasa_asmbl_13012.p1, terminal, 74928, 75122
-recovered pasa_asmbl_13012.p1, terminal, 75883, 75994
-recovered pasa_asmbl_13012.p1, internal, 72498, 72664
-recovered pasa_asmbl_13012.p1, internal, 72909, 73035
-recovered pasa_asmbl_13012.p1, internal, 73302, 73403
-recovered pasa_asmbl_13012.p1, internal, 73978, 74124
-recovered pasa_asmbl_13012.p1, internal, 74338, 74496
-recovered pasa_asmbl_13012.p1, internal, 74597, 74763
-recovered pasa_asmbl_13012.p1, internal, 74928, 75122
Valid prediction for snap_scaffold_14-snap.570-T1
Valid prediction for GlimmerHMM_glimmerT_33504-T1
Valid prediction for snap_scaffold_14-snap.554-T1
Couldn't classify 65287, 65310
Couldn't classify 68251, 68403
Sorry, prediction pasa_asmbl_13014.p1 fails validation.
(CCC)	 GC	65287-65310	GT	AGG
(ACG)	 AG	65880-66063	GT	CGG
(AGG)	 AG	67670-67775	GT	AGG
(GCA)	 AG	67947-68103	GT	GGG
(GTG)	 AG	68251-68403	CA	CGC
-recovered pasa_asmbl_13014.p1, internal, 65880, 66063
-recovered pasa_asmbl_13014.p1, internal, 67670, 67775
-recovered pasa_asmbl_13014.p1, internal, 67947, 68103
Valid prediction for GlimmerHMM_glimmerT_33508-T1
Valid prediction for snap_scaffold_14-snap.551-T1
Valid prediction for Augustus_model.g22418.t1
Valid prediction for CodingQuarry_transcript_15616-T1
Valid prediction for GlimmerHMM_glimmerT_33500-T1
Valid prediction for Augustus_model.g22417.t1
Valid prediction for snap_scaffold_14-snap.571-T1
Valid prediction for GlimmerHMM_glimmerT_33509-T1
Valid prediction for snap_scaffold_14-snap.548-T1
Valid prediction for GlimmerHMM_glimmerT_33496-T1
Valid prediction for snap_scaffold_14-snap.585-T1
Valid prediction for snap_scaffold_14-snap.579-T1
Valid prediction for Augustus_model.g22410.t1
Valid prediction for GlimmerHMM_glimmerT_33505-T1
Valid prediction for snap_scaffold_14-snap.573-T1
Valid prediction for snap_scaffold_14-snap.566-T1
Valid prediction for snap_scaffold_14-snap.564-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 69844, rend_intergenic: 69230  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85340, rend_intergenic: 78505  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98301, rend_intergenic: 88243  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108165, rend_intergenic: 105012  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114435, rend_intergenic: 113285  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115826, rend_intergenic: 114687  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130632, rend_intergenic: 116262  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144089, rend_intergenic: 140444  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154304, rend_intergenic: 145713  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159311, rend_intergenic: 154677  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170024, rend_intergenic: 161627  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175231, rend_intergenic: 171823  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 191853, rend_intergenic: 184100  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195253, rend_intergenic: 192004  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 216397
-exon list size: 403


building trellis

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-found 30 predictions from path traversal
Error with prediction: snap lend_intergenic: 69844, rend_intergenic: 69230  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85340, rend_intergenic: 78505  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98301, rend_intergenic: 88243  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108165, rend_intergenic: 105012  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114435, rend_intergenic: 113285  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115826, rend_intergenic: 114687  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130632, rend_intergenic: 116262  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144089, rend_intergenic: 140444  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154304, rend_intergenic: 145713  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159311, rend_intergenic: 154677  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170024, rend_intergenic: 161627  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175231, rend_intergenic: 171823  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 191853, rend_intergenic: 184100  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195253, rend_intergenic: 192004  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support