-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_25/scaffold_25_4197241-4433156

-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_25-snap.877-T1
Valid prediction for GlimmerHMM_glimmerT_53983-T1
Valid prediction for Augustus_model.g35834.t1
Valid prediction for snap_scaffold_25-snap.865-T1
Valid prediction for snap_scaffold_25-snap.880-T1
Valid prediction for Augustus_model.g35827.t1
Valid prediction for snap_scaffold_25-snap.866-T1
Valid prediction for snap_scaffold_25-snap.868-T1
Valid prediction for GlimmerHMM_glimmerT_53978-T1
Valid prediction for GlimmerHMM_glimmerT_53995-T1
Valid prediction for CodingQuarry_transcript_38698-T1
Valid prediction for Augustus_model.g35818.t1
Valid prediction for CodingQuarry_transcript_38697-T1
Valid prediction for Augustus_model.g35817.t1
Valid prediction for snap_scaffold_25-snap.910-T1
Valid prediction for GlimmerHMM_glimmerT_53996-T1
Valid prediction for snap_scaffold_25-snap.900-T1
Valid prediction for GlimmerHMM_glimmerT_53994-T1
Valid prediction for snap_scaffold_25-snap.899-T1
Valid prediction for snap_scaffold_25-snap.896-T1
Valid prediction for snap_scaffold_25-snap.871-T1
Valid prediction for GlimmerHMM_glimmerT_53971-T1
Valid prediction for snap_scaffold_25-snap.867-T1
Couldn't classify 26251, 26313
Sorry, prediction pasa_asmbl_33481.p1 fails validation.
(CTT)	 GG	26251-26313	GT	CGG
(TTT)	 AG	27212-27417	GT	AAG
(ACA)	 AG	27715-27748	CT	AGC
-recovered pasa_asmbl_33481.p1, terminal, 27715, 27748
-recovered pasa_asmbl_33481.p1, internal, 27212, 27417
Valid prediction for GlimmerHMM_glimmerT_53979-T1
Valid prediction for Augustus_model.g35822.t1
Valid prediction for snap_scaffold_25-snap.906-T1
Valid prediction for snap_scaffold_25-snap.864-T1
Valid prediction for snap_scaffold_25-snap.883-T1
Valid prediction for snap_scaffold_25-snap.908-T1
Valid prediction for HiQ_model.g35829.t1
Valid prediction for snap_scaffold_25-snap.894-T1
Valid prediction for snap_scaffold_25-snap.869-T1
Couldn't classify 95263, 95647
Sorry, prediction Augustus_model.g35826.t1 fails validation.
(GCC)	 AG	95263-95647	GT	AGG
(CCC)	 AG	96306-96364	GT	CGG
(CGA)	 AG	96812-96854	GT	CGG
(GAA)	 AG	97329-97436	GA	GAG
-recovered Augustus_model.g35826.t1, terminal, 97329, 97436
-recovered Augustus_model.g35826.t1, internal, 95263, 95647
-recovered Augustus_model.g35826.t1, internal, 96306, 96364
-recovered Augustus_model.g35826.t1, internal, 96812, 96854
Valid prediction for snap_scaffold_25-snap.870-T1
Valid prediction for snap_scaffold_25-snap.874-T1
Valid prediction for pasa_asmbl_33487.p1
Valid prediction for GlimmerHMM_glimmerT_53972-T1
Valid prediction for snap_scaffold_25-snap.887-T1
Valid prediction for Augustus_model.g35819.t1
Valid prediction for snap_scaffold_25-snap.873-T1
Valid prediction for snap_scaffold_25-snap.879-T1
Valid prediction for GlimmerHMM_glimmerT_53985-T1
Valid prediction for Augustus_model.g35824.t1
Valid prediction for GlimmerHMM_glimmerT_53986-T1
Valid prediction for CodingQuarry_transcript_38699-T1
Valid prediction for snap_scaffold_25-snap.890-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_53989-T1
Valid prediction for Augustus_model.g35835.t1
Valid prediction for GlimmerHMM_glimmerT_53975-T1
Valid prediction for snap_scaffold_25-snap.888-T1
Valid prediction for Augustus_model.g35830.t1
Valid prediction for Augustus_model.g35839.t1
Valid prediction for snap_scaffold_25-snap.882-T1
Valid prediction for GlimmerHMM_glimmerT_53976-T1
Valid prediction for snap_scaffold_25-snap.893-T1
Valid prediction for GlimmerHMM_glimmerT_53991-T1
Valid prediction for GlimmerHMM_glimmerT_53974-T1
Valid prediction for snap_scaffold_25-snap.901-T1
Valid prediction for Augustus_model.g35816.t1
Valid prediction for GlimmerHMM_glimmerT_53980-T1
Valid prediction for snap_scaffold_25-snap.903-T1
Valid prediction for snap_scaffold_25-snap.904-T1
Valid prediction for snap_scaffold_25-snap.892-T1
Valid prediction for GlimmerHMM_glimmerT_53970-T1
Valid prediction for GlimmerHMM_glimmerT_54001-T1
Valid prediction for GlimmerHMM_glimmerT_53999-T1
Valid prediction for Augustus_model.g35823.t1
Valid prediction for snap_scaffold_25-snap.886-T1
Valid prediction for GlimmerHMM_glimmerT_53982-T1
Valid prediction for Augustus_model.g35837.t1
Valid prediction for snap_scaffold_25-snap.907-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_25-snap.863-T1
Couldn't classify 44809, 44838
Couldn't classify 48254, 48267
Sorry, prediction pasa_asmbl_34185.p1 fails validation.
(GGT)	 CT	44809-44838	GT	AGG
(GTC)	 AG	44943-45028	GT	CAG
(GGA)	 AG	45196-45277	GT	AGG
(AAA)	 AG	45398-45504	GT	CGG
(GGC)	 AG	45718-45816	GT	AGG
(ATA)	 AG	45953-46097	GT	CGG
(CTG)	 AG	46555-46669	GT	AGG
(CCT)	 AG	46831-47000	GT	AGG
(TCA)	 AG	47241-47386	GT	AGG
(CAC)	 AG	47578-47724	GT	AGG
(GCT)	 AG	47936-48084	GT	CAG
(AAC)	 AG	48254-48267	AG	AGA
-recovered pasa_asmbl_34185.p1, internal, 44943, 45028
-recovered pasa_asmbl_34185.p1, internal, 45196, 45277
-recovered pasa_asmbl_34185.p1, internal, 45398, 45504
-recovered pasa_asmbl_34185.p1, internal, 45718, 45816
-recovered pasa_asmbl_34185.p1, internal, 45953, 46097
-recovered pasa_asmbl_34185.p1, internal, 46555, 46669
-recovered pasa_asmbl_34185.p1, internal, 46831, 47000
-recovered pasa_asmbl_34185.p1, internal, 47241, 47386
-recovered pasa_asmbl_34185.p1, internal, 47578, 47724
-recovered pasa_asmbl_34185.p1, internal, 47936, 48084
Valid prediction for CodingQuarry_transcript_38695-T1
Valid prediction for GlimmerHMM_glimmerT_54000-T1
Valid prediction for snap_scaffold_25-snap.895-T1
Valid prediction for snap_scaffold_25-snap.876-T1
Valid prediction for snap_scaffold_25-snap.905-T1
Valid prediction for snap_scaffold_25-snap.891-T1
Valid prediction for HiQ_model.g35831.t1
Valid prediction for GlimmerHMM_glimmerT_53987-T1
Valid prediction for snap_scaffold_25-snap.878-T1
Valid prediction for snap_scaffold_25-snap.872-T1
Couldn't classify 42979, 43057
Couldn't classify 44484, 44522
Sorry, prediction pasa_asmbl_34186.p2 fails validation.
(ATC)	 AG	42979-43057	GT	CTG
(TGC)	 AG	43730-43926	GT	AGG
(GCT)	 AG	44091-44171	GT	AGG
(AGA)	 AG	44277-44363	GT	AGG
(GAA)	 AG	44484-44522	GA	TCG
-recovered pasa_asmbl_34186.p2, internal, 42979, 43057
-recovered pasa_asmbl_34186.p2, internal, 43730, 43926
-recovered pasa_asmbl_34186.p2, internal, 44091, 44171
-recovered pasa_asmbl_34186.p2, internal, 44277, 44363
Valid prediction for Augustus_model.g35820.t1
Valid prediction for Augustus_model.g35833.t1
Valid prediction for snap_scaffold_25-snap.862-T1
Valid prediction for GlimmerHMM_glimmerT_53973-T1
Valid prediction for GlimmerHMM_glimmerT_53997-T1
Valid prediction for GlimmerHMM_glimmerT_53998-T1
Valid prediction for Augustus_model.g35836.t1
Valid prediction for GlimmerHMM_glimmerT_53984-T1
Valid prediction for GlimmerHMM_glimmerT_53993-T1
Valid prediction for snap_scaffold_25-snap.875-T1
Valid prediction for GlimmerHMM_glimmerT_53977-T1
Valid prediction for snap_scaffold_25-snap.897-T1
Valid prediction for GlimmerHMM_glimmerT_53990-T1
Valid prediction for snap_scaffold_25-snap.884-T1
Valid prediction for snap_scaffold_25-snap.881-T1
Valid prediction for Augustus_model.g35825.t1
Valid prediction for snap_scaffold_25-snap.889-T1
Valid prediction for GlimmerHMM_glimmerT_53992-T1
Valid prediction for snap_scaffold_25-snap.909-T1
Valid prediction for Augustus_model.g35838.t1
Valid prediction for snap_scaffold_25-snap.885-T1
Valid prediction for GlimmerHMM_glimmerT_53981-T1
Valid prediction for HiQ_model.g35828.t1
Valid prediction for snap_scaffold_25-snap.898-T1
Valid prediction for Augustus_model.g35821.t1
Couldn't classify 100212, 100325
Sorry, prediction pasa_asmbl_34181.p1 fails validation.
(ATG)	 CC	97334-97447	GT	TGG
(CTT)	 AG	98814-98888	GT	ATG
(TTG)	 AG	100212-100325	GC	ACG
-recovered pasa_asmbl_34181.p1, initial, 97334, 97447
-recovered pasa_asmbl_34181.p1, internal, 98814, 98888
-recovered pasa_asmbl_34181.p1, internal, 100212, 100325
Couldn't classify 104905, 105000
Sorry, prediction pasa_asmbl_34180.p1 fails validation.
(ATG)	 GC	101092-101185	GT	CGG
(ATG)	 AG	101403-101521	GT	AGG
(GCC)	 AG	103729-103841	GT	AGG
(TGA)	 AG	104012-104163	GT	CAG
(GCA)	 AG	104257-104354	GT	AGG
(GCG)	 AG	104637-104786	GT	AAG
(GAG)	 AG	104905-105000	CA	ACC
-recovered pasa_asmbl_34180.p1, initial, 101092, 101185
add_exon() Sorry, pasa_asmbl_34180.p1 101403-101521-initial-1 is invalid.
-recovered pasa_asmbl_34180.p1, initial, 101403, 101521
-recovered pasa_asmbl_34180.p1, internal, 101403, 101521
-recovered pasa_asmbl_34180.p1, internal, 103729, 103841
-recovered pasa_asmbl_34180.p1, internal, 104012, 104163
-recovered pasa_asmbl_34180.p1, internal, 104257, 104354
-recovered pasa_asmbl_34180.p1, internal, 104637, 104786
Valid prediction for snap_scaffold_25-snap.902-T1
Valid prediction for GlimmerHMM_glimmerT_53988-T1
Valid prediction for Augustus_model.g35832.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 70153, rend_intergenic: 67411  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91074, rend_intergenic: 89336  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138766, rend_intergenic: 132153  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142138, rend_intergenic: 139190  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158495, rend_intergenic: 154775  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175669, rend_intergenic: 168007  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 213483, rend_intergenic: 204160  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 219633, rend_intergenic: 213566  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 220482, rend_intergenic: 219846  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 221687, rend_intergenic: 220586  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 230439, rend_intergenic: 225048  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 235916
-exon list size: 536


building trellis

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-found 42 predictions from path traversal
Error with prediction: snap lend_intergenic: 70153, rend_intergenic: 67411  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91074, rend_intergenic: 89336  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138766, rend_intergenic: 132153  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142138, rend_intergenic: 139190  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158495, rend_intergenic: 154775  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175669, rend_intergenic: 168007  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 213483, rend_intergenic: 204160  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 219633, rend_intergenic: 213566  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 220482, rend_intergenic: 219846  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 221687, rend_intergenic: 220586  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 230439, rend_intergenic: 225048  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 34 predictions persist after filtering for low support