-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_19/scaffold_19_11341461-11516992

-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 Augustus_model.g29785.t1
Valid prediction for Augustus_model.g29787.t1
Valid prediction for snap_scaffold_19-snap.2193-T1
Valid prediction for pasa_asmbl_21706.p1
Valid prediction for Augustus_model.g29775.t1
Valid prediction for GlimmerHMM_glimmerT_44903-T1
Valid prediction for snap_scaffold_19-snap.2225-T1
Valid prediction for snap_scaffold_19-snap.2221-T1
Valid prediction for Augustus_model.g29777.t1
Valid prediction for GlimmerHMM_glimmerT_44912-T1
Valid prediction for snap_scaffold_19-snap.2196-T1
Valid prediction for GlimmerHMM_glimmerT_44922-T1
Valid prediction for GlimmerHMM_glimmerT_44900-T1
Valid prediction for snap_scaffold_19-snap.2207-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_19-snap.2188-T1
Valid prediction for snap_scaffold_19-snap.2229-T1
Valid prediction for GlimmerHMM_glimmerT_44918-T1
Valid prediction for snap_scaffold_19-snap.2224-T1
Valid prediction for snap_scaffold_19-snap.2218-T1
Valid prediction for Augustus_model.g29774.t1
Valid prediction for snap_scaffold_19-snap.2205-T1
Valid prediction for snap_scaffold_19-snap.2209-T1
Valid prediction for HiQ_model.g29773.t1
Couldn't classify 145134, 145152
Sorry, prediction pasa_asmbl_21698.p1 fails validation.
(GTG)	 GA	145134-145152	GT	CTG
(GTC)	 AG	148040-148080	GT	GGG
(GGC)	 AG	148227-148311	GT	AGG
(GTG)	 AG	148488-148599	GT	AGG
(ATA)	 AG	149317-149359	AT	GAA
-recovered pasa_asmbl_21698.p1, terminal, 149317, 149359
-recovered pasa_asmbl_21698.p1, internal, 148040, 148080
-recovered pasa_asmbl_21698.p1, internal, 148227, 148311
-recovered pasa_asmbl_21698.p1, internal, 148488, 148599
Valid prediction for GlimmerHMM_glimmerT_44904-T1
Valid prediction for snap_scaffold_19-snap.2228-T1
Valid prediction for GlimmerHMM_glimmerT_44920-T1
Valid prediction for pasa_asmbl_21691.p1
Valid prediction for snap_scaffold_19-snap.2202-T1
Valid prediction for GlimmerHMM_glimmerT_44916-T1
Valid prediction for snap_scaffold_19-snap.2203-T1
Valid prediction for CodingQuarry_transcript_25804-T1
Valid prediction for snap_scaffold_19-snap.2199-T1
Valid prediction for GlimmerHMM_glimmerT_44906-T1
Valid prediction for snap_scaffold_19-snap.2200-T1
Valid prediction for snap_scaffold_19-snap.2214-T1
Valid prediction for snap_scaffold_19-snap.2191-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 CodingQuarry_transcript_25802-T1
Valid prediction for GlimmerHMM_glimmerT_44902-T1
Valid prediction for CodingQuarry_transcript_25799-T1
Valid prediction for GlimmerHMM_glimmerT_44901-T1
Valid prediction for HiQ_model.g29782.t1
Valid prediction for HiQ_model.g29780.t1
Valid prediction for GlimmerHMM_glimmerT_44905-T1
Valid prediction for GlimmerHMM_glimmerT_44909-T1
Valid prediction for snap_scaffold_19-snap.2192-T1
Valid prediction for Augustus_model.g29770.t1
Valid prediction for snap_scaffold_19-snap.2227-T1
Valid prediction for Augustus_model.g29776.t1
Valid prediction for snap_scaffold_19-snap.2197-T1
Valid prediction for Augustus_model.g29771.t1
Valid prediction for snap_scaffold_19-snap.2195-T1
Valid prediction for HiQ_model.g29784.t1
Valid prediction for GlimmerHMM_glimmerT_44919-T1
Valid prediction for snap_scaffold_19-snap.2210-T1
Valid prediction for pasa_asmbl_22393.p1
Couldn't classify 42848, 43190
Sorry, prediction pasa_asmbl_22396.p1 fails validation.
(CCC)	 CC	42848-43190	GT	AGG
(ACC)	 AG	43523-44212	GT	CGG
(CAG)	 AG	44307-44456	GT	AGG
(GTC)	 AG	44563-44763	GT	AGG
(ATG)	 AG	44992-45155	GT	AGG
(GGC)	 AG	45296-45517	GG	GAG
add_exon() Sorry, pasa_asmbl_22396.p1 44992-45155-initial-1 is invalid.
-recovered pasa_asmbl_22396.p1, initial, 44992, 45155
-recovered pasa_asmbl_22396.p1, terminal, 45296, 45517
-recovered pasa_asmbl_22396.p1, internal, 43523, 44212
-recovered pasa_asmbl_22396.p1, internal, 44307, 44456
-recovered pasa_asmbl_22396.p1, internal, 44563, 44763
-recovered pasa_asmbl_22396.p1, internal, 44992, 45155
Valid prediction for snap_scaffold_19-snap.2201-T1
Valid prediction for GlimmerHMM_glimmerT_44899-T1
Couldn't classify 39895, 40324
Couldn't classify 41913, 42364
Sorry, prediction pasa_asmbl_22398.p1 fails validation.
(CGG)	 AC	39895-40324	GT	AGG
(GCT)	 AG	40425-40643	GT	AGG
(ATC)	 AG	40793-41279	GT	AGG
(CCG)	 AG	41403-41512	GT	AAG
(TCG)	 AG	41913-42364	CC	CGC
-recovered pasa_asmbl_22398.p1, internal, 40425, 40643
-recovered pasa_asmbl_22398.p1, internal, 40793, 41279
-recovered pasa_asmbl_22398.p1, internal, 41403, 41512
Valid prediction for snap_scaffold_19-snap.2217-T1
Valid prediction for snap_scaffold_19-snap.2189-T1
Valid prediction for GlimmerHMM_glimmerT_44914-T1
Valid prediction for pasa_asmbl_22387.p1
Valid prediction for snap_scaffold_19-snap.2190-T1
Valid prediction for snap_scaffold_19-snap.2216-T1
Valid prediction for GlimmerHMM_glimmerT_44915-T1
Valid prediction for snap_scaffold_19-snap.2223-T1
Valid prediction for Augustus_model.g29778.t1
Valid prediction for GlimmerHMM_glimmerT_44917-T1
Valid prediction for snap_scaffold_19-snap.2215-T1
Valid prediction for snap_scaffold_19-snap.2208-T1
Valid prediction for snap_scaffold_19-snap.2226-T1
Valid prediction for snap_scaffold_19-snap.2194-T1
Couldn't classify 85865, 85988
Couldn't classify 86563, 86684
Sorry, prediction pasa_asmbl_22725.p1 fails validation.
(CCG)	 AC	85865-85988	GT	GGG
(GTG)	 AG	86221-86364	GT	AGG
(GCA)	 AG	86563-86684	CA	TAC
-recovered pasa_asmbl_22725.p1, internal, 86221, 86364
Couldn't classify 38585, 38646
Couldn't classify 39386, 39422
Sorry, prediction pasa_asmbl_22401.p2 fails validation.
(TCA)	 GC	38585-38646	GT	AGG
(GCC)	 AG	38787-38987	GT	AGG
(GGA)	 AG	39085-39252	GT	AGG
(GTC)	 AG	39386-39422	CC	CCC
-recovered pasa_asmbl_22401.p2, internal, 38787, 38987
-recovered pasa_asmbl_22401.p2, internal, 39085, 39252
Valid prediction for GlimmerHMM_glimmerT_44897-T1
Valid prediction for Augustus_model.g29779.t1
Valid prediction for GlimmerHMM_glimmerT_44913-T1
Valid prediction for Augustus_model.g29786.t1
Valid prediction for GlimmerHMM_glimmerT_44921-T1
Couldn't classify 87177, 87206
Sorry, prediction pasa_asmbl_22385.p2 fails validation.
(GCG)	 GC	87177-87206	GT	ATG
(ATC)	 AG	87494-87653	GT	GGG
(CCT)	 AG	87772-87911	GT	AGG
(GTG)	 AG	88370-88453	GA	AGG
-recovered pasa_asmbl_22385.p2, terminal, 88370, 88453
-recovered pasa_asmbl_22385.p2, internal, 87494, 87653
-recovered pasa_asmbl_22385.p2, internal, 87772, 87911
Valid prediction for CodingQuarry_transcript_25803-T1
Valid prediction for snap_scaffold_19-snap.2198-T1
Valid prediction for snap_scaffold_19-snap.2211-T1
Valid prediction for pasa_asmbl_22414.p1
Valid prediction for HiQ_model.g29781.t1
Valid prediction for GlimmerHMM_glimmerT_44908-T1
Valid prediction for snap_scaffold_19-snap.2213-T1
Valid prediction for snap_scaffold_19-snap.2206-T1
Valid prediction for GlimmerHMM_glimmerT_44911-T1
Valid prediction for GlimmerHMM_glimmerT_44907-T1
Valid prediction for snap_scaffold_19-snap.2204-T1
Valid prediction for CodingQuarry_transcript_25800-T1
Valid prediction for pasa_asmbl_22391.p1
Couldn't classify 37464, 37537
Couldn't classify 38213, 38370
Sorry, prediction pasa_asmbl_22402.p1 fails validation.
(AGC)	 GC	37464-37537	GT	AGG
(GTC)	 AG	37727-37841	GT	GAG
(CAG)	 AG	37973-38084	GT	AGG
(ACT)	 AG	38213-38370	AC	GCA
-recovered pasa_asmbl_22402.p1, internal, 37727, 37841
-recovered pasa_asmbl_22402.p1, internal, 37973, 38084
Valid prediction for GlimmerHMM_glimmerT_44910-T1
Valid prediction for Augustus_model.g29772.t1
Valid prediction for snap_scaffold_19-snap.2219-T1
Valid prediction for snap_scaffold_19-snap.2220-T1
Valid prediction for GlimmerHMM_glimmerT_44898-T1
Valid prediction for snap_scaffold_19-snap.2212-T1
Valid prediction for Augustus_model.g29783.t1
Valid prediction for CodingQuarry_transcript_25801-T1
Couldn't classify 98175, 98398
Couldn't classify 98891, 99075
Sorry, prediction pasa_asmbl_22383.p1 fails validation.
(CTA)	 TT	98175-98398	GT	AAG
(GTT)	 AG	98602-98708	GT	CGG
(GTA)	 AG	98891-99075	GT	GGG
-recovered pasa_asmbl_22383.p1, internal, 98602, 98708
-recovered pasa_asmbl_22383.p1, internal, 98891, 99075
Valid prediction for CodingQuarry_transcript_25798-T1
Valid prediction for snap_scaffold_19-snap.2222-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 5364, rend_intergenic: 5099  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 12612, rend_intergenic: 11464  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16324, rend_intergenic: 15291  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18271, rend_intergenic: 16567  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38879, rend_intergenic: 30546  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61522, rend_intergenic: 59355  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70524, rend_intergenic: 62567  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78540, rend_intergenic: 75094  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79323, rend_intergenic: 78815  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83177, rend_intergenic: 79644  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107765, rend_intergenic: 107416  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111207, rend_intergenic: 108087  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138458, rend_intergenic: 130016  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154897, rend_intergenic: 152559  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 175532
-exon list size: 400


building trellis

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-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 5364, rend_intergenic: 5099  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 12612, rend_intergenic: 11464  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16324, rend_intergenic: 15291  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18271, rend_intergenic: 16567  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38879, rend_intergenic: 30546  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61522, rend_intergenic: 59355  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70524, rend_intergenic: 62567  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78540, rend_intergenic: 75094  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79323, rend_intergenic: 78815  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83177, rend_intergenic: 79644  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107765, rend_intergenic: 107416  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111207, rend_intergenic: 108087  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138458, rend_intergenic: 130016  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154897, rend_intergenic: 152559  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 22 predictions persist after filtering for low support