-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_4/scaffold_4_874315-1115194

-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_8721-T1
Valid prediction for GlimmerHMM_glimmerT_8731-T1
Valid prediction for snap_scaffold_4-snap.235-T1
Valid prediction for Augustus_model.g5649.t1
Valid prediction for Augustus_model.g5648.t1
Valid prediction for Augustus_model.g5643.t1
Valid prediction for GlimmerHMM_glimmerT_8729-T1
Valid prediction for GlimmerHMM_glimmerT_8709-T1
Valid prediction for GlimmerHMM_glimmerT_8708-T1
Valid prediction for snap_scaffold_4-snap.224-T1
Valid prediction for snap_scaffold_4-snap.193-T1
Valid prediction for snap_scaffold_4-snap.201-T1
Valid prediction for snap_scaffold_4-snap.244-T1
Valid prediction for snap_scaffold_4-snap.251-T1
Valid prediction for snap_scaffold_4-snap.254-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_8714-T1
Valid prediction for snap_scaffold_4-snap.238-T1
Valid prediction for snap_scaffold_4-snap.205-T1
Valid prediction for snap_scaffold_4-snap.207-T1
Valid prediction for snap_scaffold_4-snap.196-T1
Valid prediction for snap_scaffold_4-snap.241-T1
Valid prediction for Augustus_model.g5636.t1
Valid prediction for Augustus_model.g5644.t1
Valid prediction for snap_scaffold_4-snap.219-T1
Valid prediction for GlimmerHMM_glimmerT_8700-T1
Valid prediction for GlimmerHMM_glimmerT_8726-T1
Valid prediction for snap_scaffold_4-snap.202-T1
Valid prediction for snap_scaffold_4-snap.237-T1
Valid prediction for snap_scaffold_4-snap.243-T1
Valid prediction for GlimmerHMM_glimmerT_8696-T1
Valid prediction for GlimmerHMM_glimmerT_8698-T1
Valid prediction for GlimmerHMM_glimmerT_8717-T1
Valid prediction for GlimmerHMM_glimmerT_8724-T1
Valid prediction for Augustus_model.g5642.t1
Valid prediction for snap_scaffold_4-snap.200-T1
Valid prediction for snap_scaffold_4-snap.199-T1
Valid prediction for GlimmerHMM_glimmerT_8730-T1
Valid prediction for GlimmerHMM_glimmerT_8693-T1
Valid prediction for snap_scaffold_4-snap.206-T1
Couldn't classify 134151, 134331
Couldn't classify 134424, 134584
Sorry, prediction pasa_asmbl_42191.p2 fails validation.
(TTC)	 AC	134151-134331	GT	CGG
(CGG)	 AG	134424-134584	TA	GGT
Valid prediction for snap_scaffold_4-snap.250-T1
Valid prediction for GlimmerHMM_glimmerT_8697-T1
Valid prediction for GlimmerHMM_glimmerT_8725-T1
Valid prediction for GlimmerHMM_glimmerT_8694-T1
Valid prediction for snap_scaffold_4-snap.222-T1
Valid prediction for snap_scaffold_4-snap.194-T1
Valid prediction for snap_scaffold_4-snap.229-T1
Valid prediction for GlimmerHMM_glimmerT_8723-T1
Valid prediction for snap_scaffold_4-snap.215-T1
Valid prediction for GlimmerHMM_glimmerT_8716-T1
Valid prediction for Augustus_model.g5646.t1
Valid prediction for snap_scaffold_4-snap.256-T1
Valid prediction for GlimmerHMM_glimmerT_8690-T1
Valid prediction for GlimmerHMM_glimmerT_8705-T1
Valid prediction for snap_scaffold_4-snap.210-T1
Valid prediction for snap_scaffold_4-snap.209-T1
Valid prediction for snap_scaffold_4-snap.245-T1
Valid prediction for GlimmerHMM_glimmerT_8712-T1
Valid prediction for snap_scaffold_4-snap.234-T1
Valid prediction for snap_scaffold_4-snap.218-T1
Valid prediction for snap_scaffold_4-snap.248-T1
Valid prediction for GlimmerHMM_glimmerT_8702-T1
Valid prediction for snap_scaffold_4-snap.212-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_4-snap.228-T1
Valid prediction for snap_scaffold_4-snap.227-T1
Valid prediction for Augustus_model.g5633.t1
Valid prediction for pasa_asmbl_42358.p1
Valid prediction for Augustus_model.g5638.t1
Valid prediction for GlimmerHMM_glimmerT_8707-T1
Valid prediction for snap_scaffold_4-snap.221-T1
Valid prediction for Augustus_model.g5650.t1
Valid prediction for snap_scaffold_4-snap.249-T1
Valid prediction for snap_scaffold_4-snap.242-T1
Valid prediction for snap_scaffold_4-snap.197-T1
Valid prediction for Augustus_model.g5635.t1
Valid prediction for GlimmerHMM_glimmerT_8718-T1
Valid prediction for GlimmerHMM_glimmerT_8720-T1
Valid prediction for snap_scaffold_4-snap.216-T1
Valid prediction for snap_scaffold_4-snap.213-T1
Valid prediction for snap_scaffold_4-snap.217-T1
Valid prediction for snap_scaffold_4-snap.195-T1
Valid prediction for GlimmerHMM_glimmerT_8706-T1
Valid prediction for snap_scaffold_4-snap.223-T1
Valid prediction for CodingQuarry_transcript_48873-T1
Valid prediction for snap_scaffold_4-snap.230-T1
Valid prediction for GlimmerHMM_glimmerT_8703-T1
Valid prediction for Augustus_model.g5651.t1
Valid prediction for Augustus_model.g5634.t1
Valid prediction for GlimmerHMM_glimmerT_8732-T1
Valid prediction for Augustus_model.g5637.t1
Valid prediction for snap_scaffold_4-snap.240-T1
Valid prediction for GlimmerHMM_glimmerT_8701-T1
Valid prediction for snap_scaffold_4-snap.214-T1
Valid prediction for snap_scaffold_4-snap.232-T1
Valid prediction for Augustus_model.g5632.t1
Valid prediction for snap_scaffold_4-snap.231-T1
Valid prediction for GlimmerHMM_glimmerT_8710-T1
Valid prediction for snap_scaffold_4-snap.233-T1
Valid prediction for snap_scaffold_4-snap.239-T1
Valid prediction for GlimmerHMM_glimmerT_8728-T1
Valid prediction for snap_scaffold_4-snap.252-T1
Valid prediction for GlimmerHMM_glimmerT_8692-T1
Valid prediction for GlimmerHMM_glimmerT_8722-T1
Valid prediction for snap_scaffold_4-snap.220-T1
Valid prediction for GlimmerHMM_glimmerT_8695-T1
Valid prediction for CodingQuarry_transcript_48872-T1
Valid prediction for GlimmerHMM_glimmerT_8715-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for snap_scaffold_4-snap.198-T1
Valid prediction for snap_scaffold_4-snap.203-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g5645.t1
Valid prediction for snap_scaffold_4-snap.253-T1
Valid prediction for HiQ_model.g5641.t1
Valid prediction for GlimmerHMM_glimmerT_8727-T1
Valid prediction for snap_scaffold_4-snap.211-T1
Valid prediction for snap_scaffold_4-snap.225-T1
Valid prediction for HiQ_model.g5640.t1
Valid prediction for snap_scaffold_4-snap.236-T1
Valid prediction for GlimmerHMM_glimmerT_8719-T1
Valid prediction for snap_scaffold_4-snap.204-T1
Valid prediction for GlimmerHMM_glimmerT_8713-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for snap_scaffold_4-snap.246-T1
Valid prediction for GlimmerHMM_glimmerT_8699-T1
Couldn't classify 134731, 134803
Sorry, prediction pasa_asmbl_42354.p2 fails validation.
(GGG)	 GA	134731-134803	GT	AGG
(GTC)	 AG	136948-137051	GT	AGG
(AGG)	 AG	138823-138969	AA	GAA
-recovered pasa_asmbl_42354.p2, terminal, 138823, 138969
-recovered pasa_asmbl_42354.p2, internal, 136948, 137051
Valid prediction for Augustus_model.g5639.t1
Valid prediction for GlimmerHMM_glimmerT_8691-T1
Valid prediction for Augustus_model.g5647.t1
Valid prediction for snap_scaffold_4-snap.255-T1
Couldn't classify 53924, 54000
Sorry, prediction pasa_asmbl_42361.p2 fails validation.
(ATG)	 GC	52399-52447	GT	GAG
(TGC)	 AG	53322-53507	GT	TGG
(GTA)	 AG	53924-54000	AG	ACA
-recovered pasa_asmbl_42361.p2, initial, 52399, 52447
-recovered pasa_asmbl_42361.p2, internal, 53322, 53507
Valid prediction for GlimmerHMM_glimmerT_8704-T1
Couldn't classify 54324, 54555
Sorry, prediction pasa_asmbl_42360.p2 fails validation.
(CAT)	 TG	54324-54555	GT	AGG
(AGC)	 AG	55270-55366	GT	AGG
(GAG)	 AG	56577-56640	CC	AGC
-recovered pasa_asmbl_42360.p2, terminal, 56577, 56640
-recovered pasa_asmbl_42360.p2, internal, 55270, 55366
Valid prediction for GlimmerHMM_glimmerT_8711-T1
Valid prediction for snap_scaffold_4-snap.208-T1
Valid prediction for snap_scaffold_4-snap.226-T1
Valid prediction for snap_scaffold_4-snap.247-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 107632, rend_intergenic: 107629  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13974, rend_intergenic: 6295  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15651, rend_intergenic: 14002  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24127, rend_intergenic: 15680  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35747, rend_intergenic: 24140  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45375, rend_intergenic: 43306  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54495, rend_intergenic: 45996  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69658, rend_intergenic: 55496  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72446, rend_intergenic: 71770  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75776, rend_intergenic: 73149  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83240, rend_intergenic: 76431  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85774, rend_intergenic: 85008  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102139, rend_intergenic: 85860  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122144, rend_intergenic: 118168  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127958, rend_intergenic: 124774  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138228, rend_intergenic: 128015  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146847, rend_intergenic: 142535  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166791, rend_intergenic: 146860  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 183871, rend_intergenic: 180045  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186970, rend_intergenic: 184800  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192110, rend_intergenic: 187405  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199547, rend_intergenic: 196259  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 203007, rend_intergenic: 200176  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 207439, rend_intergenic: 204947  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 221259, rend_intergenic: 213240  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 230433, rend_intergenic: 222327  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 235407, rend_intergenic: 230487  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 240239, rend_intergenic: 236339  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 240880
-exon list size: 537


building trellis

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-found 44 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 107632, rend_intergenic: 107629  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13974, rend_intergenic: 6295  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15651, rend_intergenic: 14002  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24127, rend_intergenic: 15680  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35747, rend_intergenic: 24140  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45375, rend_intergenic: 43306  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54495, rend_intergenic: 45996  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69658, rend_intergenic: 55496  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72446, rend_intergenic: 71770  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75776, rend_intergenic: 73149  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83240, rend_intergenic: 76431  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85774, rend_intergenic: 85008  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102139, rend_intergenic: 85860  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122144, rend_intergenic: 118168  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127958, rend_intergenic: 124774  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138228, rend_intergenic: 128015  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146847, rend_intergenic: 142535  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166791, rend_intergenic: 146860  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 183871, rend_intergenic: 180045  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186970, rend_intergenic: 184800  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192110, rend_intergenic: 187405  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199547, rend_intergenic: 196259  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 203007, rend_intergenic: 200176  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 207439, rend_intergenic: 204947  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 221259, rend_intergenic: 213240  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 230433, rend_intergenic: 222327  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 235407, rend_intergenic: 230487  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 240239, rend_intergenic: 236339  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 30 predictions persist after filtering for low support