-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_28/scaffold_28_7666190-7846432

-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_28-snap.1753-T1
Valid prediction for snap_scaffold_28-snap.1752-T1
Valid prediction for HiQ_model.g39208.t1
Valid prediction for snap_scaffold_28-snap.1771-T1
Valid prediction for pasa_asmbl_37711.p1
Valid prediction for CodingQuarry_transcript_43727-T1
Valid prediction for GlimmerHMM_glimmerT_59154-T1
Valid prediction for GlimmerHMM_glimmerT_59171-T1
Valid prediction for Augustus_model.g39201.t1
Valid prediction for GlimmerHMM_glimmerT_59168-T1
Valid prediction for Augustus_model.g39202.t1
Couldn't classify 24207, 24230
Couldn't classify 26370, 26417
Sorry, prediction pasa_asmbl_37846.p2 fails validation.
(GCC)	 GA	24207-24230	GT	AGG
(AAT)	 AG	24314-24412	GT	AGG
(GAC)	 AG	24546-24644	GT	AGG
(AAC)	 AG	25127-25324	GT	TGG
(AAC)	 AG	25736-25834	GT	AGG
(TCT)	 AG	26370-26417	AT	ACA
-recovered pasa_asmbl_37846.p2, internal, 24314, 24412
-recovered pasa_asmbl_37846.p2, internal, 24546, 24644
-recovered pasa_asmbl_37846.p2, internal, 25127, 25324
-recovered pasa_asmbl_37846.p2, internal, 25736, 25834
Couldn't classify 51136, 51401
Couldn't classify 51695, 52088
Sorry, prediction pasa_asmbl_37702.p1 fails validation.
(ACG)	 CC	51136-51401	GT	AGG
(GTC)	 AG	51695-52088	GT	AGG
-recovered pasa_asmbl_37702.p1, internal, 51695, 52088
Valid prediction for snap_scaffold_28-snap.1765-T1
Valid prediction for GlimmerHMM_glimmerT_59153-T1
Valid prediction for GlimmerHMM_glimmerT_59162-T1
Valid prediction for snap_scaffold_28-snap.1764-T1
Valid prediction for snap_scaffold_28-snap.1733-T1
Valid prediction for CodingQuarry_transcript_43721-T1
Valid prediction for pasa_asmbl_37703.p2
Valid prediction for pasa_asmbl_37828.p1
Valid prediction for CodingQuarry_transcript_43720-T1
Valid prediction for GlimmerHMM_glimmerT_59170-T1
Couldn't classify 53335, 53435
Couldn't classify 53457, 53592
Sorry, prediction CodingQuarry_transcript_43719-T1 fails validation.
(ATG)	 AA	53335-53435	AG	GGA
(GGG)	 GA	53457-53592	GA	GAG
Valid prediction for snap_scaffold_28-snap.1746-T1
Valid prediction for snap_scaffold_28-snap.1766-T1
Valid prediction for snap_scaffold_28-snap.1740-T1
Valid prediction for GlimmerHMM_glimmerT_59166-T1
Couldn't classify 34813, 34841
Couldn't classify 37094, 37329
Sorry, prediction pasa_asmbl_37700.p1 fails validation.
(CTG)	 CT	34813-34841	GT	GCG
(GAA)	 AG	35063-35141	GT	AGG
(TCT)	 AG	35366-35499	GT	GGG
(CTT)	 AG	35699-35923	GT	GGG
(GCC)	 AG	36640-36794	GT	AGG
(ACC)	 AG	37094-37329	GA	CGG
-recovered pasa_asmbl_37700.p1, internal, 35063, 35141
-recovered pasa_asmbl_37700.p1, internal, 35366, 35499
-recovered pasa_asmbl_37700.p1, internal, 35699, 35923
-recovered pasa_asmbl_37700.p1, internal, 36640, 36794
Valid prediction for snap_scaffold_28-snap.1757-T1
Valid prediction for snap_scaffold_28-snap.1742-T1
Valid prediction for snap_scaffold_28-snap.1762-T1
Valid prediction for Augustus_model.g39204.t1
Valid prediction for CodingQuarry_transcript_43724-T1
Valid prediction for GlimmerHMM_glimmerT_59149-T1
Valid prediction for Augustus_model.g39203.t1
Valid prediction for snap_scaffold_28-snap.1759-T1
Valid prediction for snap_scaffold_28-snap.1760-T1
Valid prediction for snap_scaffold_28-snap.1756-T1
Valid prediction for pasa_asmbl_37706.p3
Valid prediction for HiQ_model.g39205.t1
Valid prediction for snap_scaffold_28-snap.1748-T1
Valid prediction for GlimmerHMM_glimmerT_59164-T1
Valid prediction for snap_scaffold_28-snap.1761-T1
Valid prediction for GlimmerHMM_glimmerT_59158-T1
Valid prediction for GlimmerHMM_glimmerT_59151-T1
Valid prediction for GlimmerHMM_glimmerT_59150-T1
Valid prediction for GlimmerHMM_glimmerT_59147-T1
Valid prediction for snap_scaffold_28-snap.1754-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_28-snap.1768-T1
Valid prediction for CodingQuarry_transcript_43723-T1
Valid prediction for GlimmerHMM_glimmerT_59163-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_59148-T1
Valid prediction for GlimmerHMM_glimmerT_59159-T1
Valid prediction for snap_scaffold_28-snap.1769-T1
Couldn't classify 78763, 79036
Sorry, prediction pasa_asmbl_38416.p1 fails validation.
(CTC)	 CT	78763-79036	GT	CGG
(GGA)	 AG	80043-80185	CT	AAC
-recovered pasa_asmbl_38416.p1, terminal, 80043, 80185
Valid prediction for GlimmerHMM_glimmerT_59172-T1
Valid prediction for snap_scaffold_28-snap.1735-T1
Valid prediction for snap_scaffold_28-snap.1743-T1
Valid prediction for snap_scaffold_28-snap.1736-T1
Valid prediction for snap_scaffold_28-snap.1758-T1
Couldn't classify 7764, 7952
Sorry, prediction pasa_asmbl_38422.p1 fails validation.
(ATG)	 AG	4026-4062	GT	AGG
(GAG)	 AG	6593-6698	GT	AGG
(CGC)	 AG	6937-7072	GT	AAG
(GAC)	 AG	7281-7526	GT	TGG
(GTG)	 AG	7764-7952	AG	AGA
-recovered pasa_asmbl_38422.p1, initial, 4026, 4062
-recovered pasa_asmbl_38422.p1, internal, 4026, 4062
-recovered pasa_asmbl_38422.p1, internal, 6593, 6698
-recovered pasa_asmbl_38422.p1, internal, 6937, 7072
-recovered pasa_asmbl_38422.p1, internal, 7281, 7526
Valid prediction for GlimmerHMM_glimmerT_59155-T1
Valid prediction for snap_scaffold_28-snap.1739-T1
Valid prediction for GlimmerHMM_glimmerT_59167-T1
Valid prediction for snap_scaffold_28-snap.1744-T1
Valid prediction for Augustus_model.g39212.t1
Valid prediction for snap_scaffold_28-snap.1767-T1
Valid prediction for snap_scaffold_28-snap.1745-T1
Valid prediction for Augustus_model.g39214.t1
Valid prediction for GlimmerHMM_glimmerT_59157-T1
Valid prediction for snap_scaffold_28-snap.1741-T1
Valid prediction for snap_scaffold_28-snap.1755-T1
Valid prediction for snap_scaffold_28-snap.1750-T1
Valid prediction for GlimmerHMM_glimmerT_59160-T1
Valid prediction for pasa_asmbl_38414.p1
Valid prediction for GlimmerHMM_glimmerT_59156-T1
Valid prediction for snap_scaffold_28-snap.1749-T1
Valid prediction for GlimmerHMM_glimmerT_59165-T1
Valid prediction for GlimmerHMM_glimmerT_59161-T1
Couldn't classify 7941, 7954
Couldn't classify 21177, 21331
Sorry, prediction pasa_asmbl_38421.p1 fails validation.
(CGC)	 AC	7941-7954	GT	AGG
(CAT)	 AG	8041-8262	GT	AGG
(GCC)	 AG	8746-8866	GT	AGG
(GTG)	 AG	9037-9132	GT	AGG
(CAA)	 AG	9362-9477	GT	AAG
(GTA)	 AG	11926-12091	GT	AGG
(GTT)	 AG	12235-12333	GT	AGG
(GAC)	 AG	12806-13065	GT	TCG
(TGG)	 AG	14448-14658	GT	TGG
(CTT)	 AG	15957-15986	GT	CGG
(ATG)	 AG	16320-16457	GT	CAG
(GTG)	 AG	16786-16931	GT	AGG
(TTT)	 AG	17123-17252	GT	AGG
(GTG)	 AG	20193-20277	GT	GGG
(ATC)	 AG	20751-20837	GT	AGG
(ATG)	 AG	21177-21331	GT	CGG
-recovered pasa_asmbl_38421.p1, initial, 16320, 16457
add_exon() Sorry, pasa_asmbl_38421.p1 21177-21331-initial-1 is invalid.
-recovered pasa_asmbl_38421.p1, initial, 21177, 21331
-recovered pasa_asmbl_38421.p1, internal, 8041, 8262
-recovered pasa_asmbl_38421.p1, internal, 8746, 8866
-recovered pasa_asmbl_38421.p1, internal, 9037, 9132
-recovered pasa_asmbl_38421.p1, internal, 9362, 9477
-recovered pasa_asmbl_38421.p1, internal, 11926, 12091
-recovered pasa_asmbl_38421.p1, internal, 12235, 12333
-recovered pasa_asmbl_38421.p1, internal, 12806, 13065
-recovered pasa_asmbl_38421.p1, internal, 14448, 14658
-recovered pasa_asmbl_38421.p1, internal, 15957, 15986
-recovered pasa_asmbl_38421.p1, internal, 16320, 16457
-recovered pasa_asmbl_38421.p1, internal, 16786, 16931
-recovered pasa_asmbl_38421.p1, internal, 17123, 17252
-recovered pasa_asmbl_38421.p1, internal, 20193, 20277
-recovered pasa_asmbl_38421.p1, internal, 20751, 20837
-recovered pasa_asmbl_38421.p1, internal, 21177, 21331
Valid prediction for Augustus_model.g39213.t1
Valid prediction for CodingQuarry_transcript_43725-T1
Valid prediction for GlimmerHMM_glimmerT_59169-T1
Valid prediction for Augustus_model.g39209.t1
Valid prediction for snap_scaffold_28-snap.1738-T1
Valid prediction for snap_scaffold_28-snap.1770-T1
Valid prediction for pasa_asmbl_38410.p1
Valid prediction for snap_scaffold_28-snap.1763-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_28-snap.1732-T1
Valid prediction for CodingQuarry_transcript_43726-T1
Valid prediction for snap_scaffold_28-snap.1734-T1
Valid prediction for HiQ_model.g39215.t1
Valid prediction for Augustus_model.g39211.t1
Valid prediction for HiQ_model.g39210.t1
Valid prediction for snap_scaffold_28-snap.1751-T1
Valid prediction for Augustus_model.g39207.t1
Valid prediction for GlimmerHMM_glimmerT_59146-T1
Valid prediction for snap_scaffold_28-snap.1737-T1
Valid prediction for GlimmerHMM_glimmerT_59152-T1
Valid prediction for Augustus_model.g39206.t1
Valid prediction for snap_scaffold_28-snap.1747-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 16857, rend_intergenic: 3431  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41104, rend_intergenic: 16995  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44713, rend_intergenic: 41909  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59424, rend_intergenic: 47142  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62617, rend_intergenic: 59749  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66662, rend_intergenic: 64972  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81519, rend_intergenic: 76951  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91890, rend_intergenic: 86439  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95165, rend_intergenic: 91892  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134122, rend_intergenic: 99776  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149940, rend_intergenic: 134879  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155149, rend_intergenic: 154838  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170933, rend_intergenic: 156420  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176218, rend_intergenic: 173984  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 180243
-exon list size: 477


building trellis

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-found 25 predictions from path traversal
Error with prediction: snap lend_intergenic: 16857, rend_intergenic: 3431  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41104, rend_intergenic: 16995  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44713, rend_intergenic: 41909  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59424, rend_intergenic: 47142  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62617, rend_intergenic: 59749  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66662, rend_intergenic: 64972  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81519, rend_intergenic: 76951  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91890, rend_intergenic: 86439  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95165, rend_intergenic: 91892  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134122, rend_intergenic: 99776  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149940, rend_intergenic: 134879  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155149, rend_intergenic: 154838  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170933, rend_intergenic: 156420  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176218, rend_intergenic: 173984  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 18 predictions persist after filtering for low support