-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_18/scaffold_18_1376299-1538133

-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_41769-T1
Valid prediction for snap_scaffold_18-snap.305-T1
Valid prediction for snap_scaffold_18-snap.309-T1
Valid prediction for snap_scaffold_18-snap.287-T1
Couldn't classify 55240, 55336
Sorry, prediction pasa_asmbl_20351.p1 fails validation.
(ATG)	 TT	54038-54052	GT	AGG
(CTT)	 AG	54172-54248	GT	CGG
(ACA)	 AG	54387-54447	GT	AGG
(ATT)	 AG	54532-54672	GT	AGG
(ATG)	 AG	54787-54903	GT	AGG
(GCT)	 AG	55022-55116	GT	AGG
(GTT)	 AG	55240-55336	GC	ACG
-recovered pasa_asmbl_20351.p1, initial, 54038, 54052
-recovered pasa_asmbl_20351.p1, initial, 54787, 54903
-recovered pasa_asmbl_20351.p1, internal, 54172, 54248
-recovered pasa_asmbl_20351.p1, internal, 54387, 54447
-recovered pasa_asmbl_20351.p1, internal, 54532, 54672
-recovered pasa_asmbl_20351.p1, internal, 54787, 54903
-recovered pasa_asmbl_20351.p1, internal, 55022, 55116
-recovered pasa_asmbl_20351.p1, internal, 55240, 55336
Valid prediction for snap_scaffold_18-snap.307-T1
Valid prediction for GlimmerHMM_glimmerT_41791-T1
Valid prediction for CodingQuarry_transcript_23657-T1
Valid prediction for GlimmerHMM_glimmerT_41789-T1
Valid prediction for GlimmerHMM_glimmerT_41784-T1
Valid prediction for snap_scaffold_18-snap.283-T1
Valid prediction for HiQ_model.g27805.t1
Valid prediction for pasa_asmbl_20359.p1
Valid prediction for snap_scaffold_18-snap.298-T1
Couldn't classify 1731, 2145
Couldn't classify 2167, 2180
Sorry, prediction pasa_asmbl_20345.p1 fails validation.
(CTC)	 GC	1731-2145	GT	AGG
(GCA)	 AG	2167-2180	GG	AGG
Valid prediction for HiQ_model.g27794.t1
Couldn't classify 55874, 55888
Couldn't classify 56963, 57078
Sorry, prediction CodingQuarry_transcript_23655-T1 fails validation.
(ATG)	 TC	55874-55888	AA	GGA
(CAG)	 CA	56963-57078	GT	AGG
(TGC)	 AG	57680-57740	CC	AGC
-recovered CodingQuarry_transcript_23655-T1, terminal, 57680, 57740
Valid prediction for HiQ_model.g27809.t1
Couldn't classify 52883, 52888
Couldn't classify 53624, 53643
Sorry, prediction pasa_asmbl_20350.p1 fails validation.
(GAC)	 CT	52883-52888	GT	ATG
(GAG)	 AG	52973-53080	GT	AGG
(CTG)	 AG	53195-53286	GT	CCG
(GGA)	 AG	53383-53522	GT	AGG
(ATC)	 AG	53624-53643	AT	TGA
add_exon() Sorry, pasa_asmbl_20350.p1 53383-53522-terminal-2 is invalid.
-recovered pasa_asmbl_20350.p1, terminal, 53383, 53522
-recovered pasa_asmbl_20350.p1, internal, 52973, 53080
-recovered pasa_asmbl_20350.p1, internal, 53195, 53286
-recovered pasa_asmbl_20350.p1, internal, 53383, 53522
Valid prediction for Augustus_model.g27798.t1
Valid prediction for snap_scaffold_18-snap.294-T1
Valid prediction for snap_scaffold_18-snap.280-T1
Valid prediction for GlimmerHMM_glimmerT_41792-T1
Valid prediction for Augustus_model.g27800.t1
Valid prediction for snap_scaffold_18-snap.311-T1
Couldn't classify 50269, 50463
Sorry, prediction pasa_asmbl_20349.p1 fails validation.
(ATG)	 CT	48269-48388	GT	CGG
(ATG)	 AG	50269-50463	AC	TCA
-recovered pasa_asmbl_20349.p1, initial, 48269, 48388
Valid prediction for GlimmerHMM_glimmerT_41774-T1
Valid prediction for GlimmerHMM_glimmerT_41768-T1
Valid prediction for GlimmerHMM_glimmerT_41770-T1
Valid prediction for snap_scaffold_18-snap.293-T1
Valid prediction for Augustus_model.g27792.t1
Valid prediction for CodingQuarry_transcript_23660-T1
Valid prediction for GlimmerHMM_glimmerT_41780-T1
Valid prediction for snap_scaffold_18-snap.291-T1
Valid prediction for snap_scaffold_18-snap.276-T1
Valid prediction for snap_scaffold_18-snap.302-T1
Valid prediction for snap_scaffold_18-snap.314-T1
Valid prediction for CodingQuarry_transcript_23662-T1
Valid prediction for snap_scaffold_18-snap.300-T1
Valid prediction for snap_scaffold_18-snap.313-T1
Valid prediction for CodingQuarry_transcript_23654-T1
Couldn't classify 1272, 1721
Sorry, prediction pasa_asmbl_20344.p1 fails validation.
(ATC)	 AG	1272-1721	CC	CCC
Valid prediction for snap_scaffold_18-snap.278-T1
Valid prediction for pasa_asmbl_20357.p1
Valid prediction for GlimmerHMM_glimmerT_41778-T1
Couldn't classify 122981, 123046
Sorry, prediction pasa_asmbl_20354.p1 fails validation.
(GGG)	 AC	122981-123046	GT	TGG
(ACT)	 AG	123438-123518	GT	CGG
(TCG)	 AG	123644-123752	GT	AGG
(TCA)	 AG	123848-123945	TT	AGT
-recovered pasa_asmbl_20354.p1, terminal, 123848, 123945
-recovered pasa_asmbl_20354.p1, internal, 123438, 123518
-recovered pasa_asmbl_20354.p1, internal, 123644, 123752
Valid prediction for snap_scaffold_18-snap.296-T1
Valid prediction for snap_scaffold_18-snap.281-T1
Valid prediction for pasa_asmbl_20348.p1
Valid prediction for HiQ_model.g27807.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_18-snap.282-T1
Valid prediction for snap_scaffold_18-snap.289-T1
Valid prediction for snap_scaffold_18-snap.295-T1
Valid prediction for GlimmerHMM_glimmerT_41790-T1
Valid prediction for HiQ_model.g27806.t1
Valid prediction for HiQ_model.g27804.t1
Valid prediction for snap_scaffold_18-snap.288-T1
Valid prediction for GlimmerHMM_glimmerT_41776-T1
Valid prediction for pasa_asmbl_19618.p1
Couldn't classify 35938, 36010
Sorry, prediction CodingQuarry_transcript_23658-T1 fails validation.
(ATG)	 TT	34387-34390	GT	GGG
(TTG)	 AG	34913-34993	GT	CGG
(GCT)	 AG	35687-35796	GT	AGG
(GGC)	 AG	35938-36010	TA	GGT
(CTG)	 AG	36334-36347	GC	GAG
-recovered CodingQuarry_transcript_23658-T1, initial, 34387, 34390
-recovered CodingQuarry_transcript_23658-T1, terminal, 36334, 36347
-recovered CodingQuarry_transcript_23658-T1, internal, 34913, 34993
-recovered CodingQuarry_transcript_23658-T1, internal, 35687, 35796
-recovered CodingQuarry_transcript_23658-T1, internal, 36334, 36347
Couldn't classify 27833, 27901
Sorry, prediction pasa_asmbl_19626.p1 fails validation.
(TCA)	 CA	27833-27901	GT	TGG
(GAG)	 AG	27988-28041	GT	AGG
(ACA)	 AG	28137-28246	GT	AGG
(GAG)	 AG	28377-28479	GT	CTG
(GAC)	 AG	28605-28679	GT	TGG
(TTG)	 AG	29053-29175	CA	GAC
-recovered pasa_asmbl_19626.p1, terminal, 29053, 29175
-recovered pasa_asmbl_19626.p1, internal, 27988, 28041
-recovered pasa_asmbl_19626.p1, internal, 28137, 28246
-recovered pasa_asmbl_19626.p1, internal, 28377, 28479
-recovered pasa_asmbl_19626.p1, internal, 28605, 28679
Valid prediction for GlimmerHMM_glimmerT_41788-T1
Valid prediction for snap_scaffold_18-snap.304-T1
Valid prediction for GlimmerHMM_glimmerT_41794-T1
Valid prediction for pasa_asmbl_19613.p1
Valid prediction for HiQ_model.g27793.t1
Valid prediction for snap_scaffold_18-snap.306-T1
Valid prediction for snap_scaffold_18-snap.312-T1
Valid prediction for GlimmerHMM_glimmerT_41781-T1
Valid prediction for Augustus_model.g27791.t1
Valid prediction for snap_scaffold_18-snap.297-T1
Valid prediction for GlimmerHMM_glimmerT_41775-T1
Valid prediction for GlimmerHMM_glimmerT_41772-T1
Valid prediction for CodingQuarry_transcript_23659-T1
Valid prediction for snap_scaffold_18-snap.285-T1
Valid prediction for snap_scaffold_18-snap.310-T1
Valid prediction for pasa_asmbl_19625.p1
Valid prediction for GlimmerHMM_glimmerT_41787-T1
Valid prediction for GlimmerHMM_glimmerT_41785-T1
Valid prediction for Augustus_model.g27801.t1
Valid prediction for CodingQuarry_transcript_23653-T1
Valid prediction for Augustus_model.g27797.t1
Valid prediction for snap_scaffold_18-snap.275-T1
Valid prediction for snap_scaffold_18-snap.284-T1
Valid prediction for Augustus_model.g27795.t1
Valid prediction for snap_scaffold_18-snap.292-T1
Valid prediction for GlimmerHMM_glimmerT_41779-T1
Valid prediction for GlimmerHMM_glimmerT_41782-T1
Valid prediction for GlimmerHMM_glimmerT_41783-T1
Valid prediction for Augustus_model.g27808.t1
Valid prediction for snap_scaffold_18-snap.303-T1
Valid prediction for GlimmerHMM_glimmerT_41771-T1
Valid prediction for snap_scaffold_18-snap.279-T1
Valid prediction for GlimmerHMM_glimmerT_41773-T1
Valid prediction for snap_scaffold_18-snap.301-T1
Valid prediction for Augustus_model.g27803.t1
Valid prediction for GlimmerHMM_glimmerT_41767-T1
Valid prediction for GlimmerHMM_glimmerT_41793-T1
Valid prediction for Augustus_model.g27796.t1
Valid prediction for Augustus_model.g27810.t1
Valid prediction for snap_scaffold_18-snap.308-T1
Valid prediction for Augustus_model.g27799.t1
Valid prediction for CodingQuarry_transcript_23661-T1
Valid prediction for pasa_asmbl_19624.p1
Valid prediction for GlimmerHMM_glimmerT_41795-T1
Valid prediction for snap_scaffold_18-snap.277-T1
Valid prediction for GlimmerHMM_glimmerT_41786-T1
Valid prediction for GlimmerHMM_glimmerT_41777-T1
Valid prediction for snap_scaffold_18-snap.286-T1
Valid prediction for Augustus_model.g27802.t1
Valid prediction for snap_scaffold_18-snap.299-T1
Couldn't classify 100468, 100852
Sorry, prediction pasa_asmbl_19623.p1 fails validation.
(GAT)	 CG	100468-100852	GT	AGG
(GAC)	 AG	101070-101188	GT	AGG
(GTG)	 AG	101635-101823	GT	AAG
-recovered pasa_asmbl_19623.p1, terminal, 101635, 101823
-recovered pasa_asmbl_19623.p1, internal, 101070, 101188
-recovered pasa_asmbl_19623.p1, internal, 101635, 101823
Valid prediction for snap_scaffold_18-snap.290-T1
Valid prediction for CodingQuarry_transcript_23656-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 11233, rend_intergenic: 10202  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15362, rend_intergenic: 11353  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18242, rend_intergenic: 15979  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22951, rend_intergenic: 18418  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25696, rend_intergenic: 22961  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58040, rend_intergenic: 53294  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91618, rend_intergenic: 91141  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94618, rend_intergenic: 92206  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105491, rend_intergenic: 102464  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109679, rend_intergenic: 106542  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141157, rend_intergenic: 139073  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151970, rend_intergenic: 143158  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160935, rend_intergenic: 152584  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 161835
-exon list size: 426


building trellis

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99.5    
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-found 24 predictions from path traversal
Error with prediction: snap lend_intergenic: 11233, rend_intergenic: 10202  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 15362, rend_intergenic: 11353  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18242, rend_intergenic: 15979  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22951, rend_intergenic: 18418  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 25696, rend_intergenic: 22961  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58040, rend_intergenic: 53294  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91618, rend_intergenic: 91141  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94618, rend_intergenic: 92206  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 105491, rend_intergenic: 102464  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109679, rend_intergenic: 106542  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141157, rend_intergenic: 139073  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151970, rend_intergenic: 143158  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160935, rend_intergenic: 152584  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support