-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_6/scaffold_6_17600984-17839023

-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_6-snap.3751-T1
Valid prediction for HiQ_model.g11043.t1
Valid prediction for GlimmerHMM_glimmerT_16459-T1
Valid prediction for CodingQuarry_transcript_55414-T1
Valid prediction for snap_scaffold_6-snap.3781-T1
Valid prediction for GlimmerHMM_glimmerT_16485-T1
Valid prediction for snap_scaffold_6-snap.3784-T1
Valid prediction for snap_scaffold_6-snap.3783-T1
Valid prediction for GlimmerHMM_glimmerT_16474-T1
Valid prediction for snap_scaffold_6-snap.3759-T1
Valid prediction for GlimmerHMM_glimmerT_16451-T1
Valid prediction for Augustus_model.g11033.t1
Valid prediction for GlimmerHMM_glimmerT_16472-T1
Valid prediction for GlimmerHMM_glimmerT_16445-T1
Valid prediction for snap_scaffold_6-snap.3769-T1
Valid prediction for snap_scaffold_6-snap.3778-T1
Sorry, intron length (8) is less than minimum required (10)
Couldn't classify 109927, 111039
Sorry, prediction pasa_asmbl_47781.p1 fails validation.
(CAC)	 CC	109927-111039	GC	CAG
Valid prediction for snap_scaffold_6-snap.3737-T1
Valid prediction for Augustus_model.g11034.t1
Valid prediction for GlimmerHMM_glimmerT_16457-T1
Valid prediction for GlimmerHMM_glimmerT_16475-T1
Valid prediction for snap_scaffold_6-snap.3755-T1
Valid prediction for GlimmerHMM_glimmerT_16482-T1
Valid prediction for snap_scaffold_6-snap.3765-T1
Valid prediction for CodingQuarry_transcript_55411-T1
Valid prediction for snap_scaffold_6-snap.3740-T1
Couldn't classify 228823, 228841
Sorry, prediction pasa_asmbl_47789.p2 fails validation.
(TGG)	 GG	228823-228841	GT	TAG
(ACA)	 AG	229390-229472	GT	AGG
(AAC)	 AG	229964-230173	CC	GAC
-recovered pasa_asmbl_47789.p2, terminal, 229964, 230173
-recovered pasa_asmbl_47789.p2, internal, 229390, 229472
Valid prediction for snap_scaffold_6-snap.3738-T1
Valid prediction for GlimmerHMM_glimmerT_16461-T1
Valid prediction for snap_scaffold_6-snap.3753-T1
Valid prediction for snap_scaffold_6-snap.3748-T1
Couldn't classify 109317, 109571
Sorry, prediction pasa_asmbl_47779.p2 fails validation.
(ATG)	 AT	109096-109197	GT	AGG
(GGG)	 AG	109317-109571	AA	CCA
-recovered pasa_asmbl_47779.p2, initial, 109096, 109197
Valid prediction for pasa_asmbl_47771.p1
Valid prediction for snap_scaffold_6-snap.3773-T1
Valid prediction for CodingQuarry_transcript_55417-T1
Valid prediction for Augustus_model.g11015.t1
Couldn't classify 226055, 226645
Sorry, prediction pasa_asmbl_47785.p1 fails validation.
(CCC)	 GG	226055-226645	GT	GAG
Valid prediction for HiQ_model.g11024.t1
Valid prediction for CodingQuarry_transcript_55415-T1
Valid prediction for snap_scaffold_6-snap.3741-T1
Valid prediction for snap_scaffold_6-snap.3736-T1
Valid prediction for Augustus_model.g11032.t1
Valid prediction for GlimmerHMM_glimmerT_16478-T1
Valid prediction for Augustus_model.g11041.t1
Valid prediction for GlimmerHMM_glimmerT_16469-T1
Valid prediction for snap_scaffold_6-snap.3758-T1
Valid prediction for snap_scaffold_6-snap.3770-T1
Valid prediction for CodingQuarry_transcript_55416-T1
Valid prediction for GlimmerHMM_glimmerT_16467-T1
Valid prediction for GlimmerHMM_glimmerT_16466-T1
Couldn't classify 209007, 209066
Couldn't classify 212081, 212125
Sorry, prediction pasa_asmbl_47783.p1 fails validation.
(CTC)	 AC	209007-209066	GT	AGG
(ATG)	 AG	210333-210473	GT	AAG
(GCT)	 AG	210709-210846	GT	GAG
(TCT)	 AG	212081-212125	GG	AGG
-recovered pasa_asmbl_47783.p1, initial, 210333, 210473
-recovered pasa_asmbl_47783.p1, internal, 210333, 210473
-recovered pasa_asmbl_47783.p1, internal, 210709, 210846
Valid prediction for Augustus_model.g11036.t1
Valid prediction for Augustus_model.g11039.t1
Valid prediction for snap_scaffold_6-snap.3762-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for Augustus_model.g11029.t1
Valid prediction for snap_scaffold_6-snap.3761-T1
Valid prediction for snap_scaffold_6-snap.3750-T1
Valid prediction for snap_scaffold_6-snap.3734-T1
Valid prediction for GlimmerHMM_glimmerT_16448-T1
Valid prediction for GlimmerHMM_glimmerT_16473-T1
Couldn't classify 223491, 223580
Couldn't classify 225783, 225841
Sorry, prediction pasa_asmbl_47979.p2 fails validation.
(AAG)	 TG	223491-223580	GT	AGG
(GTG)	 AG	224234-224432	GT	GGG
(ATG)	 AG	225269-225349	GT	AAG
(TGG)	 AG	225783-225841	CT	CCC
-recovered pasa_asmbl_47979.p2, initial, 225269, 225349
-recovered pasa_asmbl_47979.p2, internal, 224234, 224432
-recovered pasa_asmbl_47979.p2, internal, 225269, 225349
Valid prediction for GlimmerHMM_glimmerT_16481-T1
Valid prediction for Augustus_model.g11014.t1
Valid prediction for HiQ_model.g11040.t1
Valid prediction for snap_scaffold_6-snap.3782-T1
Valid prediction for GlimmerHMM_glimmerT_16453-T1
Valid prediction for GlimmerHMM_glimmerT_16455-T1
Valid prediction for Augustus_model.g11042.t1
Couldn't classify 23430, 24809
Sorry, prediction pasa_asmbl_47769.p1 fails validation.
(TGC)	 AA	23430-24809	AA	AAA
Valid prediction for snap_scaffold_6-snap.3735-T1
Valid prediction for GlimmerHMM_glimmerT_16483-T1
Valid prediction for Augustus_model.g11035.t1
Valid prediction for snap_scaffold_6-snap.3767-T1
Valid prediction for GlimmerHMM_glimmerT_16447-T1
Valid prediction for snap_scaffold_6-snap.3771-T1
Valid prediction for snap_scaffold_6-snap.3780-T1
Valid prediction for Augustus_model.g11025.t1
Valid prediction for GlimmerHMM_glimmerT_16484-T1
Valid prediction for GlimmerHMM_glimmerT_16463-T1
Valid prediction for snap_scaffold_6-snap.3775-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_16479-T1
Couldn't classify 39152, 39344
Sorry, prediction pasa_asmbl_49198.p1 fails validation.
(TCT)	 AG	39152-39344	GT	AAG
(AGG)	 AG	39573-39741	GT	TGG
(GTA)	 AG	40174-40309	GT	AGG
(ATG)	 AG	40802-40988	GT	AGG
(GTG)	 AG	41485-41645	GT	AGG
(ATC)	 AG	41759-41860	GT	TGG
(GGA)	 AG	42128-42223	GT	AGG
(TCT)	 AG	42313-42432	GT	TGG
(GGA)	 AG	42911-42955	GA	AAG
-recovered pasa_asmbl_49198.p1, initial, 40802, 40988
-recovered pasa_asmbl_49198.p1, terminal, 42911, 42955
-recovered pasa_asmbl_49198.p1, internal, 39152, 39344
-recovered pasa_asmbl_49198.p1, internal, 39573, 39741
-recovered pasa_asmbl_49198.p1, internal, 40174, 40309
-recovered pasa_asmbl_49198.p1, internal, 40802, 40988
-recovered pasa_asmbl_49198.p1, internal, 41485, 41645
-recovered pasa_asmbl_49198.p1, internal, 41759, 41860
-recovered pasa_asmbl_49198.p1, internal, 42128, 42223
-recovered pasa_asmbl_49198.p1, internal, 42313, 42432
Couldn't classify 191500, 191601
Sorry, prediction pasa_asmbl_49195.p1 fails validation.
(GCC)	 TC	191500-191601	GT	TGG
(AAA)	 AG	193459-193679	GT	GAG
(CAT)	 AG	193855-193960	GG	AAG
-recovered pasa_asmbl_49195.p1, terminal, 193855, 193960
-recovered pasa_asmbl_49195.p1, internal, 193459, 193679
Valid prediction for snap_scaffold_6-snap.3760-T1
Valid prediction for CodingQuarry_transcript_55413-T1
Valid prediction for snap_scaffold_6-snap.3746-T1
Valid prediction for GlimmerHMM_glimmerT_16450-T1
Valid prediction for Augustus_model.g11023.t1
Valid prediction for Augustus_model.g11019.t1
Valid prediction for GlimmerHMM_glimmerT_16480-T1
Valid prediction for snap_scaffold_6-snap.3743-T1
Valid prediction for GlimmerHMM_glimmerT_16477-T1
Valid prediction for Augustus_model.g11026.t1
Valid prediction for snap_scaffold_6-snap.3752-T1
Valid prediction for Augustus_model.g11017.t1
Valid prediction for pasa_asmbl_49202.p1
Valid prediction for GlimmerHMM_glimmerT_16460-T1
Couldn't classify 189951, 190436
Sorry, prediction pasa_asmbl_49196.p1 fails validation.
(CAG)	 GA	189951-190436	GA	GTG
Valid prediction for GlimmerHMM_glimmerT_16464-T1
Valid prediction for snap_scaffold_6-snap.3774-T1
Valid prediction for HiQ_model.g11044.t1
Valid prediction for GlimmerHMM_glimmerT_16468-T1
Valid prediction for snap_scaffold_6-snap.3747-T1
Valid prediction for Augustus_model.g11016.t1
Valid prediction for snap_scaffold_6-snap.3739-T1
Valid prediction for GlimmerHMM_glimmerT_16449-T1
Valid prediction for GlimmerHMM_glimmerT_16465-T1
Valid prediction for GlimmerHMM_glimmerT_16476-T1
Valid prediction for snap_scaffold_6-snap.3756-T1
Valid prediction for Augustus_model.g11037.t1
Valid prediction for GlimmerHMM_glimmerT_16456-T1
Valid prediction for CodingQuarry_transcript_55412-T1
Valid prediction for Augustus_model.g11018.t1
Valid prediction for GlimmerHMM_glimmerT_16452-T1
Valid prediction for snap_scaffold_6-snap.3742-T1
Valid prediction for GlimmerHMM_glimmerT_16446-T1
Valid prediction for snap_scaffold_6-snap.3744-T1
Valid prediction for snap_scaffold_6-snap.3766-T1
Valid prediction for snap_scaffold_6-snap.3776-T1
Valid prediction for Augustus_model.g11031.t1
Valid prediction for snap_scaffold_6-snap.3754-T1
Valid prediction for Augustus_model.g11020.t1
Valid prediction for snap_scaffold_6-snap.3777-T1
Valid prediction for snap_scaffold_6-snap.3749-T1
Valid prediction for Augustus_model.g11028.t1
Couldn't classify 94656, 94709
Sorry, prediction GlimmerHMM_glimmerT_16471-T1 fails validation.
(ATG)	 AG	79550-79583	GT	AGG
(TGA)	 AG	83961-84122	GT	AAG
(ACA)	 AG	88105-88277	GT	AGG
(AGT)	 AG	94656-94709	NN	ANN
-recovered GlimmerHMM_glimmerT_16471-T1, initial, 79550, 79583
-recovered GlimmerHMM_glimmerT_16471-T1, internal, 79550, 79583
-recovered GlimmerHMM_glimmerT_16471-T1, internal, 83961, 84122
-recovered GlimmerHMM_glimmerT_16471-T1, internal, 88105, 88277
Valid prediction for GlimmerHMM_glimmerT_16470-T1
Valid prediction for Augustus_model.g11022.t1
Valid prediction for snap_scaffold_6-snap.3745-T1
Valid prediction for snap_scaffold_6-snap.3768-T1
Valid prediction for snap_scaffold_6-snap.3779-T1
Valid prediction for GlimmerHMM_glimmerT_16458-T1
Valid prediction for snap_scaffold_6-snap.3772-T1
Valid prediction for snap_scaffold_6-snap.3757-T1
Valid prediction for Augustus_model.g11038.t1
Valid prediction for Augustus_model.g11027.t1
Valid prediction for GlimmerHMM_glimmerT_16462-T1
Valid prediction for snap_scaffold_6-snap.3763-T1
Valid prediction for GlimmerHMM_glimmerT_16454-T1
Valid prediction for snap_scaffold_6-snap.3764-T1
Valid prediction for Augustus_model.g11021.t1
Valid prediction for Augustus_model.g11030.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 16343, rend_intergenic: 13832  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60856, rend_intergenic: 54548  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79884, rend_intergenic: 75056  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84831, rend_intergenic: 82141  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93182, rend_intergenic: 85605  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120779, rend_intergenic: 113712  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142813, rend_intergenic: 123511  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157562, rend_intergenic: 149728  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158603, rend_intergenic: 157992  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166264, rend_intergenic: 161146  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181910, rend_intergenic: 167468  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184475, rend_intergenic: 182853  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192044, rend_intergenic: 189463  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 193001, rend_intergenic: 192300  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 207858, rend_intergenic: 201133  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 214455, rend_intergenic: 209521  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 238040
-exon list size: 464


building trellis

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-found 47 predictions from path traversal
Error with prediction: snap lend_intergenic: 16343, rend_intergenic: 13832  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60856, rend_intergenic: 54548  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79884, rend_intergenic: 75056  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84831, rend_intergenic: 82141  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93182, rend_intergenic: 85605  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120779, rend_intergenic: 113712  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 142813, rend_intergenic: 123511  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157562, rend_intergenic: 149728  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158603, rend_intergenic: 157992  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 166264, rend_intergenic: 161146  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181910, rend_intergenic: 167468  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 184475, rend_intergenic: 182853  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192044, rend_intergenic: 189463  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 193001, rend_intergenic: 192300  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 207858, rend_intergenic: 201133  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 214455, rend_intergenic: 209521  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 38 predictions persist after filtering for low support