-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_13/scaffold_13_4891426-5135812

-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_13-snap.969-T1
Valid prediction for Augustus_model.g21033.t1
Valid prediction for snap_scaffold_13-snap.955-T1
Valid prediction for GlimmerHMM_glimmerT_31613-T1
Valid prediction for snap_scaffold_13-snap.950-T1
Valid prediction for GlimmerHMM_glimmerT_31609-T1
Couldn't classify 234216, 234499
Couldn't classify 234653, 234686
Sorry, prediction pasa_asmbl_11628.p1 fails validation.
(GAT)	 CG	234216-234499	GT	AGG
(AAT)	 AG	234653-234686	AT	GGA
Valid prediction for snap_scaffold_13-snap.935-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for pasa_asmbl_10825.p1
Valid prediction for snap_scaffold_13-snap.949-T1
Valid prediction for Augustus_model.g21020.t1
Valid prediction for GlimmerHMM_glimmerT_31601-T1
Valid prediction for snap_scaffold_13-snap.933-T1
Valid prediction for snap_scaffold_13-snap.936-T1
Valid prediction for snap_scaffold_13-snap.957-T1
Valid prediction for GlimmerHMM_glimmerT_31614-T1
Valid prediction for snap_scaffold_13-snap.944-T1
Valid prediction for snap_scaffold_13-snap.952-T1
Valid prediction for GlimmerHMM_glimmerT_31619-T1
Valid prediction for GlimmerHMM_glimmerT_31605-T1
Valid prediction for GlimmerHMM_glimmerT_31606-T1
Valid prediction for snap_scaffold_13-snap.958-T1
Valid prediction for snap_scaffold_13-snap.929-T1
Valid prediction for GlimmerHMM_glimmerT_31623-T1
Valid prediction for GlimmerHMM_glimmerT_31618-T1
Valid prediction for snap_scaffold_13-snap.938-T1
Couldn't classify 234010, 234067
Sorry, prediction pasa_asmbl_11635.p1 fails validation.
(ATG)	 AA	231543-231647	GT	GGG
(GCA)	 AG	231771-231849	GT	AGG
(AAG)	 AG	231967-232070	GT	GGG
(GAA)	 AG	232191-232492	GT	AGG
(GTT)	 AG	232790-232870	GT	AGG
(CGA)	 AG	233186-233272	GT	AAG
(GCT)	 AG	233472-233557	GT	CGG
(GTG)	 AG	233687-233783	GT	AGG
(AGA)	 AG	234010-234067	GT	TGG
-recovered pasa_asmbl_11635.p1, initial, 231543, 231647
-recovered pasa_asmbl_11635.p1, internal, 231771, 231849
-recovered pasa_asmbl_11635.p1, internal, 231967, 232070
-recovered pasa_asmbl_11635.p1, internal, 232191, 232492
-recovered pasa_asmbl_11635.p1, internal, 232790, 232870
-recovered pasa_asmbl_11635.p1, internal, 233186, 233272
-recovered pasa_asmbl_11635.p1, internal, 233472, 233557
-recovered pasa_asmbl_11635.p1, internal, 233687, 233783
-recovered pasa_asmbl_11635.p1, internal, 234010, 234067
Valid prediction for snap_scaffold_13-snap.939-T1
Valid prediction for snap_scaffold_13-snap.931-T1
Valid prediction for GlimmerHMM_glimmerT_31602-T1
Valid prediction for Augustus_model.g21030.t1
Valid prediction for GlimmerHMM_glimmerT_31621-T1
Valid prediction for HiQ_model.g21039.t1
Valid prediction for GlimmerHMM_glimmerT_31604-T1
Valid prediction for snap_scaffold_13-snap.976-T1
Valid prediction for GlimmerHMM_glimmerT_31612-T1
Valid prediction for snap_scaffold_13-snap.966-T1
Valid prediction for snap_scaffold_13-snap.974-T1
Valid prediction for CodingQuarry_transcript_13017-T1
Valid prediction for GlimmerHMM_glimmerT_31629-T1
Valid prediction for snap_scaffold_13-snap.971-T1
Valid prediction for snap_scaffold_13-snap.943-T1
Valid prediction for snap_scaffold_13-snap.977-T1
Valid prediction for snap_scaffold_13-snap.964-T1
Valid prediction for snap_scaffold_13-snap.942-T1
Valid prediction for Augustus_model.g21026.t1
Valid prediction for GlimmerHMM_glimmerT_31625-T1
Valid prediction for snap_scaffold_13-snap.945-T1
Valid prediction for Augustus_model.g21027.t1
Valid prediction for snap_scaffold_13-snap.962-T1
Valid prediction for snap_scaffold_13-snap.954-T1
Valid prediction for snap_scaffold_13-snap.927-T1
Valid prediction for snap_scaffold_13-snap.940-T1
Valid prediction for Augustus_model.g21022.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_13-snap.965-T1
Valid prediction for snap_scaffold_13-snap.932-T1
Valid prediction for GlimmerHMM_glimmerT_31611-T1
Valid prediction for Augustus_model.g21023.t1
Valid prediction for snap_scaffold_13-snap.973-T1
Valid prediction for GlimmerHMM_glimmerT_31616-T1
Valid prediction for snap_scaffold_13-snap.961-T1
Valid prediction for snap_scaffold_13-snap.960-T1
Valid prediction for snap_scaffold_13-snap.972-T1
Couldn't classify 50408, 51175
Couldn't classify 51413, 51520
Sorry, prediction pasa_asmbl_9670.p1 fails validation.
(GAT)	 TA	50408-51175	GT	GTG
(TGT)	 AG	51413-51520	AA	ACA
Valid prediction for snap_scaffold_13-snap.948-T1
Valid prediction for snap_scaffold_13-snap.963-T1
Valid prediction for snap_scaffold_13-snap.937-T1
Valid prediction for Augustus_model.g21029.t1
Valid prediction for snap_scaffold_13-snap.975-T1
Valid prediction for CodingQuarry_transcript_13016-T1
Valid prediction for snap_scaffold_13-snap.967-T1
Valid prediction for Augustus_model.g21035.t1
Valid prediction for GlimmerHMM_glimmerT_31610-T1
Valid prediction for snap_scaffold_13-snap.928-T1
Valid prediction for GlimmerHMM_glimmerT_31615-T1
Valid prediction for snap_scaffold_13-snap.934-T1
Valid prediction for snap_scaffold_13-snap.951-T1
Valid prediction for GlimmerHMM_glimmerT_31628-T1
Valid prediction for GlimmerHMM_glimmerT_31626-T1
Valid prediction for GlimmerHMM_glimmerT_31627-T1
Valid prediction for GlimmerHMM_glimmerT_31607-T1
Valid prediction for snap_scaffold_13-snap.968-T1
Couldn't classify 147747, 147852
Sorry, prediction pasa_asmbl_9668.p1 fails validation.
(CGG)	 GT	147747-147852	GT	CGG
(ACG)	 AG	148115-148245	GT	AGG
(GTG)	 AG	149235-149366	GT	TGG
(GTT)	 AG	149581-149717	GT	AGG
(ATA)	 AG	149866-150041	GT	AAG
(GTG)	 AG	150843-151048	TT	AAT
-recovered pasa_asmbl_9668.p1, terminal, 150843, 151048
-recovered pasa_asmbl_9668.p1, internal, 148115, 148245
-recovered pasa_asmbl_9668.p1, internal, 149235, 149366
-recovered pasa_asmbl_9668.p1, internal, 149581, 149717
-recovered pasa_asmbl_9668.p1, internal, 149866, 150041
Valid prediction for GlimmerHMM_glimmerT_31620-T1
Valid prediction for snap_scaffold_13-snap.953-T1
Valid prediction for Augustus_model.g21034.t1
Valid prediction for Augustus_model.g21021.t1
Valid prediction for GlimmerHMM_glimmerT_31608-T1
Valid prediction for Augustus_model.g21028.t1
Couldn't classify 60079, 60299
Couldn't classify 62002, 62122
Sorry, prediction pasa_asmbl_10335.p1 fails validation.
(GTG)	 AG	60079-60299	GT	AGG
(CTC)	 AG	61031-61090	GT	AGG
(GGA)	 AG	62002-62122	AG	AGA
add_exon() Sorry, pasa_asmbl_10335.p1 61031-61090-terminal-1 is invalid.
-recovered pasa_asmbl_10335.p1, terminal, 61031, 61090
-recovered pasa_asmbl_10335.p1, internal, 60079, 60299
-recovered pasa_asmbl_10335.p1, internal, 61031, 61090
Valid prediction for snap_scaffold_13-snap.970-T1
Valid prediction for snap_scaffold_13-snap.947-T1
Valid prediction for GlimmerHMM_glimmerT_31603-T1
Valid prediction for snap_scaffold_13-snap.946-T1
Valid prediction for snap_scaffold_13-snap.959-T1
Valid prediction for GlimmerHMM_glimmerT_31622-T1
Valid prediction for snap_scaffold_13-snap.941-T1
Valid prediction for snap_scaffold_13-snap.930-T1
Valid prediction for Augustus_model.g21031.t1
Valid prediction for snap_scaffold_13-snap.926-T1
Valid prediction for Augustus_model.g21037.t1
Valid prediction for GlimmerHMM_glimmerT_31600-T1
Valid prediction for GlimmerHMM_glimmerT_31617-T1
Valid prediction for Augustus_model.g21032.t1
Valid prediction for pasa_asmbl_9673.p1
Valid prediction for Augustus_model.g21036.t1
Valid prediction for Augustus_model.g21024.t1
Valid prediction for Augustus_model.g21038.t1
Valid prediction for snap_scaffold_13-snap.956-T1
Valid prediction for Augustus_model.g21025.t1
Valid prediction for GlimmerHMM_glimmerT_31624-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 7163, rend_intergenic: 3686  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 9989, rend_intergenic: 7617  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14052, rend_intergenic: 10676  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24318, rend_intergenic: 19998  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26093, rend_intergenic: 25260  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39339, rend_intergenic: 31730  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43685, rend_intergenic: 41108  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51678, rend_intergenic: 44408  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67702, rend_intergenic: 54482  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75200, rend_intergenic: 67706  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87354, rend_intergenic: 84489  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101533, rend_intergenic: 95918  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119281, rend_intergenic: 105495  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136360, rend_intergenic: 121918  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150645, rend_intergenic: 146360  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156509, rend_intergenic: 152552  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169917, rend_intergenic: 162743  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172256, rend_intergenic: 169957  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175152, rend_intergenic: 174043  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179076, rend_intergenic: 175893  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187886, rend_intergenic: 181422  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195854, rend_intergenic: 189292  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 197544, rend_intergenic: 196052  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200589, rend_intergenic: 198294  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 244387
-exon list size: 448


building trellis

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-found 39 predictions from path traversal
Error with prediction: snap lend_intergenic: 7163, rend_intergenic: 3686  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 9989, rend_intergenic: 7617  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14052, rend_intergenic: 10676  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24318, rend_intergenic: 19998  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26093, rend_intergenic: 25260  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39339, rend_intergenic: 31730  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43685, rend_intergenic: 41108  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51678, rend_intergenic: 44408  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67702, rend_intergenic: 54482  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75200, rend_intergenic: 67706  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87354, rend_intergenic: 84489  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101533, rend_intergenic: 95918  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119281, rend_intergenic: 105495  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136360, rend_intergenic: 121918  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150645, rend_intergenic: 146360  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156509, rend_intergenic: 152552  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169917, rend_intergenic: 162743  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172256, rend_intergenic: 169957  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175152, rend_intergenic: 174043  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179076, rend_intergenic: 175893  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 187886, rend_intergenic: 181422  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195854, rend_intergenic: 189292  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 197544, rend_intergenic: 196052  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 200589, rend_intergenic: 198294  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 23 predictions persist after filtering for low support