-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_7/scaffold_7_1137900-1344549

-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_16859-T1
Valid prediction for snap_scaffold_7-snap.279-T1
Valid prediction for Augustus_model.g11258.t1
Valid prediction for pasa_asmbl_49594.p1
Valid prediction for snap_scaffold_7-snap.292-T1
Valid prediction for snap_scaffold_7-snap.287-T1
Valid prediction for GlimmerHMM_glimmerT_16867-T1
Valid prediction for snap_scaffold_7-snap.297-T1
Valid prediction for GlimmerHMM_glimmerT_16873-T1
Valid prediction for GlimmerHMM_glimmerT_16857-T1
Valid prediction for GlimmerHMM_glimmerT_16870-T1
Valid prediction for GlimmerHMM_glimmerT_16851-T1
Valid prediction for snap_scaffold_7-snap.271-T1
Valid prediction for GlimmerHMM_glimmerT_16868-T1
Valid prediction for pasa_asmbl_49577.p1
Valid prediction for GlimmerHMM_glimmerT_16874-T1
Valid prediction for CodingQuarry_transcript_57435-T1
Valid prediction for snap_scaffold_7-snap.284-T1
Valid prediction for snap_scaffold_7-snap.299-T1
Valid prediction for Augustus_model.g11246.t1
Valid prediction for snap_scaffold_7-snap.291-T1
Valid prediction for GlimmerHMM_glimmerT_16848-T1
Valid prediction for snap_scaffold_7-snap.288-T1
Valid prediction for snap_scaffold_7-snap.268-T1
Valid prediction for snap_scaffold_7-snap.294-T1
Valid prediction for GlimmerHMM_glimmerT_16872-T1
Valid prediction for Augustus_model.g11253.t1
Valid prediction for snap_scaffold_7-snap.269-T1
Valid prediction for Augustus_model.g11257.t1
Couldn't classify 44969, 44997
Couldn't classify 59134, 59223
Sorry, prediction pasa_asmbl_49579.p1 fails validation.
(CTG)	 CT	44969-44997	GT	AAG
(CCT)	 AG	47194-47250	GT	GAG
(GTC)	 AG	47664-47727	GT	TAG
(CCA)	 AG	49161-49235	GT	CAG
(GAG)	 AG	49463-49607	GT	CGG
(GTA)	 AG	50224-50342	GT	AGG
(AGC)	 AG	52007-52090	GT	AGG
(ATC)	 AG	54513-54628	GT	AGG
(ACT)	 AG	54795-54967	GT	AGG
(GCC)	 AG	57654-57793	GT	AGG
(GGA)	 AG	59134-59223	GC	CCG
-recovered pasa_asmbl_49579.p1, internal, 47194, 47250
-recovered pasa_asmbl_49579.p1, internal, 47664, 47727
-recovered pasa_asmbl_49579.p1, internal, 49161, 49235
-recovered pasa_asmbl_49579.p1, internal, 49463, 49607
-recovered pasa_asmbl_49579.p1, internal, 50224, 50342
-recovered pasa_asmbl_49579.p1, internal, 52007, 52090
-recovered pasa_asmbl_49579.p1, internal, 54513, 54628
-recovered pasa_asmbl_49579.p1, internal, 54795, 54967
-recovered pasa_asmbl_49579.p1, internal, 57654, 57793
-recovered pasa_asmbl_49579.p1, internal, 59134, 59223
Valid prediction for Augustus_model.g11254.t1
Valid prediction for snap_scaffold_7-snap.266-T1
Valid prediction for HiQ_model.g11249.t1
Valid prediction for Augustus_model.g11262.t1
Valid prediction for Augustus_model.g11255.t1
Valid prediction for GlimmerHMM_glimmerT_16855-T1
Valid prediction for snap_scaffold_7-snap.296-T1
Valid prediction for snap_scaffold_7-snap.293-T1
Valid prediction for GlimmerHMM_glimmerT_16865-T1
Valid prediction for GlimmerHMM_glimmerT_16858-T1
Valid prediction for GlimmerHMM_glimmerT_16863-T1
Valid prediction for snap_scaffold_7-snap.264-T1
Valid prediction for snap_scaffold_7-snap.304-T1
Couldn't classify 86756, 86887
Couldn't classify 88927, 89385
Sorry, prediction pasa_asmbl_49587.p1 fails validation.
(CAG)	 CT	86756-86887	GT	AGG
(AAT)	 AG	88050-88199	GT	AGG
(TGT)	 AG	88927-89385	CC	CGC
-recovered pasa_asmbl_49587.p1, internal, 88050, 88199
Valid prediction for snap_scaffold_7-snap.289-T1
Valid prediction for Augustus_model.g11260.t1
Valid prediction for snap_scaffold_7-snap.275-T1
Valid prediction for snap_scaffold_7-snap.280-T1
Valid prediction for Augustus_model.g11252.t1
Valid prediction for snap_scaffold_7-snap.311-T1
Valid prediction for snap_scaffold_7-snap.282-T1
Valid prediction for Augustus_model.g11251.t1
Valid prediction for snap_scaffold_7-snap.302-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_7-snap.301-T1
Valid prediction for snap_scaffold_7-snap.305-T1
Valid prediction for snap_scaffold_7-snap.314-T1
Valid prediction for snap_scaffold_7-snap.277-T1
Valid prediction for snap_scaffold_7-snap.306-T1
Valid prediction for snap_scaffold_7-snap.313-T1
Valid prediction for GlimmerHMM_glimmerT_16864-T1
Valid prediction for snap_scaffold_7-snap.274-T1
Valid prediction for GlimmerHMM_glimmerT_16862-T1
Valid prediction for snap_scaffold_7-snap.281-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for HiQ_model.g11248.t1
Valid prediction for snap_scaffold_7-snap.300-T1
Valid prediction for snap_scaffold_7-snap.273-T1
Valid prediction for GlimmerHMM_glimmerT_16871-T1
Valid prediction for snap_scaffold_7-snap.308-T1
Valid prediction for CodingQuarry_transcript_57433-T1
Couldn't classify 183282, 183584
Sorry, prediction pasa_asmbl_50710.p1 fails validation.
(GAC)	 CC	183282-183584	GT	GGG
(AAG)	 AG	185111-185311	GT	GGG
(GTA)	 AG	185611-185742	GT	AGG
(GTT)	 AG	186660-186813	GT	CGG
(ACC)	 AG	187162-187223	GT	GGG
(GAG)	 AG	187325-187424	GT	CTG
(ACC)	 AG	187780-187913	GT	AGG
(AAG)	 AG	188056-188115	GT	AGG
(ATC)	 AG	188897-189058	AG	AGA
-recovered pasa_asmbl_50710.p1, terminal, 188897, 189058
-recovered pasa_asmbl_50710.p1, internal, 185111, 185311
-recovered pasa_asmbl_50710.p1, internal, 185611, 185742
-recovered pasa_asmbl_50710.p1, internal, 186660, 186813
-recovered pasa_asmbl_50710.p1, internal, 187162, 187223
-recovered pasa_asmbl_50710.p1, internal, 187325, 187424
-recovered pasa_asmbl_50710.p1, internal, 187780, 187913
-recovered pasa_asmbl_50710.p1, internal, 188056, 188115
Valid prediction for snap_scaffold_7-snap.285-T1
Valid prediction for snap_scaffold_7-snap.270-T1
Valid prediction for snap_scaffold_7-snap.267-T1
Valid prediction for GlimmerHMM_glimmerT_16866-T1
Valid prediction for GlimmerHMM_glimmerT_16856-T1
Valid prediction for Augustus_model.g11264.t1
Valid prediction for snap_scaffold_7-snap.265-T1
Valid prediction for GlimmerHMM_glimmerT_16860-T1
Valid prediction for GlimmerHMM_glimmerT_16877-T1
Valid prediction for snap_scaffold_7-snap.298-T1
Valid prediction for pasa_asmbl_50708.p1
Valid prediction for snap_scaffold_7-snap.272-T1
Valid prediction for GlimmerHMM_glimmerT_16850-T1
Valid prediction for GlimmerHMM_glimmerT_16875-T1
Valid prediction for CodingQuarry_transcript_57437-T1
Valid prediction for Augustus_model.g11261.t1
Valid prediction for GlimmerHMM_glimmerT_16853-T1
Couldn't classify 28562, 28636
Sorry, prediction pasa_asmbl_50712.p2 fails validation.
(CTT)	 AG	28562-28636	GT	AGG
(GAC)	 AG	28877-28987	GT	TGG
(GTT)	 AG	29112-29261	CG	GAC
-recovered pasa_asmbl_50712.p2, terminal, 29112, 29261
-recovered pasa_asmbl_50712.p2, internal, 28562, 28636
-recovered pasa_asmbl_50712.p2, internal, 28877, 28987
Valid prediction for GlimmerHMM_glimmerT_16876-T1
Valid prediction for snap_scaffold_7-snap.307-T1
Valid prediction for GlimmerHMM_glimmerT_16861-T1
Valid prediction for snap_scaffold_7-snap.303-T1
Valid prediction for GlimmerHMM_glimmerT_16852-T1
Valid prediction for Augustus_model.g11263.t1
Couldn't classify 16243, 16317
Couldn't classify 16833, 16984
Sorry, prediction CodingQuarry_transcript_57438-T1 fails validation.
(ATG)	 GA	11899-11922	GT	AGG
(GGG)	 AG	12677-12712	GT	AGG
(GGA)	 AG	13474-13518	GT	CAG
(GGA)	 AG	13915-13947	GT	AGG
(AAA)	 AG	15170-15316	GT	CTG
(GGG)	 AG	15470-15524	GT	ATG
(CGG)	 AG	15735-15923	GT	AGG
(GAG)	 AG	16243-16317	CA	CCC
(AGG)	 CC	16833-16984	TG	GAT
-recovered CodingQuarry_transcript_57438-T1, initial, 11899, 11922
-recovered CodingQuarry_transcript_57438-T1, internal, 12677, 12712
-recovered CodingQuarry_transcript_57438-T1, internal, 13474, 13518
-recovered CodingQuarry_transcript_57438-T1, internal, 13915, 13947
-recovered CodingQuarry_transcript_57438-T1, internal, 15170, 15316
-recovered CodingQuarry_transcript_57438-T1, internal, 15470, 15524
-recovered CodingQuarry_transcript_57438-T1, internal, 15735, 15923
Valid prediction for Augustus_model.g11245.t1
Valid prediction for Augustus_model.g11256.t1
Valid prediction for GlimmerHMM_glimmerT_16854-T1
Valid prediction for GlimmerHMM_glimmerT_16849-T1
Valid prediction for snap_scaffold_7-snap.290-T1
Valid prediction for snap_scaffold_7-snap.276-T1
Valid prediction for GlimmerHMM_glimmerT_16869-T1
Valid prediction for snap_scaffold_7-snap.310-T1
Valid prediction for HiQ_model.g11265.t1
Valid prediction for snap_scaffold_7-snap.278-T1
Valid prediction for snap_scaffold_7-snap.286-T1
Valid prediction for snap_scaffold_7-snap.312-T1
Valid prediction for snap_scaffold_7-snap.283-T1
Valid prediction for Augustus_model.g11250.t1
Couldn't classify 10306, 10350
Sorry, prediction pasa_asmbl_50714.p1 fails validation.
(GGC)	 AG	10306-10350	GT	AGG
(GGT)	 AG	10616-10669	GT	CTG
(GGC)	 AG	10747-10800	GT	AAG
(GGT)	 AG	11546-11599	GT	AGG
(GGT)	 AG	11851-11922	GT	AGG
(GGG)	 AG	12677-12712	GT	AGG
(GGA)	 AG	13474-13518	GT	CAG
(GGA)	 AG	13915-13947	GT	AGG
(AAA)	 AG	15170-15316	GT	CTG
(GGG)	 AG	15470-15524	GT	ATG
(CGG)	 AG	15735-15923	GT	AGG
(GAG)	 AG	16243-16320	GT	AGG
(GGC)	 AG	16835-17028	AG	GAA
-recovered pasa_asmbl_50714.p1, terminal, 16835, 17028
-recovered pasa_asmbl_50714.p1, internal, 10306, 10350
-recovered pasa_asmbl_50714.p1, internal, 10616, 10669
-recovered pasa_asmbl_50714.p1, internal, 10747, 10800
-recovered pasa_asmbl_50714.p1, internal, 11546, 11599
-recovered pasa_asmbl_50714.p1, internal, 11851, 11922
-recovered pasa_asmbl_50714.p1, internal, 12677, 12712
-recovered pasa_asmbl_50714.p1, internal, 13474, 13518
-recovered pasa_asmbl_50714.p1, internal, 13915, 13947
-recovered pasa_asmbl_50714.p1, internal, 15170, 15316
-recovered pasa_asmbl_50714.p1, internal, 15470, 15524
-recovered pasa_asmbl_50714.p1, internal, 15735, 15923
-recovered pasa_asmbl_50714.p1, internal, 16243, 16320
Valid prediction for snap_scaffold_7-snap.295-T1
Valid prediction for Augustus_model.g11247.t1
Valid prediction for Augustus_model.g11259.t1
Valid prediction for snap_scaffold_7-snap.309-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 6265, rend_intergenic: 4066  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13429, rend_intergenic: 9315  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20199, rend_intergenic: 17593  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32694, rend_intergenic: 25310  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59292, rend_intergenic: 42979  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75231, rend_intergenic: 68073  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92692, rend_intergenic: 83437  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96606, rend_intergenic: 94634  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122960, rend_intergenic: 116248  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145649, rend_intergenic: 144809  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151586, rend_intergenic: 151295  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171210, rend_intergenic: 168668  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 193152, rend_intergenic: 189692  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 206650
-exon list size: 440


building trellis

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-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 6265, rend_intergenic: 4066  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13429, rend_intergenic: 9315  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20199, rend_intergenic: 17593  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32694, rend_intergenic: 25310  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59292, rend_intergenic: 42979  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75231, rend_intergenic: 68073  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92692, rend_intergenic: 83437  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96606, rend_intergenic: 94634  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122960, rend_intergenic: 116248  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145649, rend_intergenic: 144809  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151586, rend_intergenic: 151295  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171210, rend_intergenic: 168668  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 193152, rend_intergenic: 189692  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 27 predictions persist after filtering for low support