-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_14/scaffold_14_3332939-3504354

-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 GeneMark_model.58610_t
Valid prediction for snap_scaffold_14-snap.598-T1
Valid prediction for snap_scaffold_14-snap.578-T1
Valid prediction for GeneMark_model.58630_t
Valid prediction for GeneMark_model.58597_t
Valid prediction for GeneMark_model.58632_t
Valid prediction for snap_scaffold_14-snap.568-T1
Valid prediction for GeneMark_model.58622_t
Valid prediction for GlimmerHMM_glimmerT_34275-T1
Valid prediction for snap_scaffold_14-snap.600-T1
Valid prediction for GlimmerHMM_glimmerT_34285-T1
Valid prediction for snap_scaffold_14-snap.595-T1
Valid prediction for GeneMark_model.58590_t
Valid prediction for GeneMark_model.58603_t
Valid prediction for GeneMark_model.58595_t
Valid prediction for GeneMark_model.58604_t
Valid prediction for GeneMark_model.58615_t
Valid prediction for GeneMark_model.58587_t
Valid prediction for GeneMark_model.58641_t
Valid prediction for GeneMark_model.58626_t
Valid prediction for GeneMark_model.58639_t
Valid prediction for Augustus_model.g23056.t1
Valid prediction for snap_scaffold_14-snap.570-T1
Valid prediction for Augustus_model.g23054.t1
Valid prediction for GeneMark_model.58594_t
Valid prediction for GeneMark_model.58600_t
Valid prediction for Augustus_model.g23055.t1
Valid prediction for GeneMark_model.58624_t
Valid prediction for GeneMark_model.58628_t
Valid prediction for snap_scaffold_14-snap.585-T1
Valid prediction for GlimmerHMM_glimmerT_34287-T1
Valid prediction for Augustus_model.g23059.t1
Valid prediction for snap_scaffold_14-snap.599-T1
Valid prediction for GeneMark_model.58606_t
Valid prediction for GeneMark_model.58634_t
Valid prediction for GeneMark_model.58592_t
Valid prediction for snap_scaffold_14-snap.564-T1
Valid prediction for GeneMark_model.58616_t
Valid prediction for GeneMark_model.58642_t
Valid prediction for snap_scaffold_14-snap.575-T1
Valid prediction for GlimmerHMM_glimmerT_34284-T1
Valid prediction for GeneMark_model.58608_t
Valid prediction for snap_scaffold_14-snap.588-T1
Valid prediction for snap_scaffold_14-snap.573-T1
Valid prediction for GeneMark_model.58620_t
Valid prediction for snap_scaffold_14-snap.587-T1
Valid prediction for snap_scaffold_14-snap.580-T1
Valid prediction for GlimmerHMM_glimmerT_34270-T1
Valid prediction for snap_scaffold_14-snap.572-T1
Valid prediction for Augustus_model.g23058.t1
Valid prediction for snap_scaffold_14-snap.591-T1
Valid prediction for GeneMark_model.58585_t
Valid prediction for GlimmerHMM_glimmerT_34273-T1
Valid prediction for GeneMark_model.58588_t
Valid prediction for Augustus_model.g23063.t1
Valid prediction for GlimmerHMM_glimmerT_34276-T1
Couldn't classify 57013, 57518
Couldn't classify 57564, 58032
Sorry, prediction CodingQuarry_transcript_15570-T1 fails validation.
(ATG)	 CT	57013-57518	CT	TCC
(CTT)	 AC	57564-58032	AT	AAA
Valid prediction for snap_scaffold_14-snap.594-T1
Valid prediction for GlimmerHMM_glimmerT_34269-T1
Valid prediction for GeneMark_model.58636_t
Valid prediction for snap_scaffold_14-snap.589-T1
Valid prediction for GlimmerHMM_glimmerT_34279-T1
Valid prediction for GlimmerHMM_glimmerT_34272-T1
Valid prediction for GeneMark_model.58613_t
Valid prediction for Augustus_model.g23064.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: -)Couldn't classify 58751, 58858
Couldn't classify 59584, 59661
Sorry, prediction pasa_asmbl_13794.p1 fails validation.
(TTC)	 TG	58751-58858	GT	AGG
(TCT)	 AG	59080-59241	GT	AGG
(AAC)	 AG	59584-59661	AC	AGA
-recovered pasa_asmbl_13794.p1, internal, 59080, 59241
Valid prediction for GeneMark_model.58640_t
Valid prediction for snap_scaffold_14-snap.567-T1
Valid prediction for GlimmerHMM_glimmerT_34286-T1
Valid prediction for snap_scaffold_14-snap.592-T1
Valid prediction for GeneMark_model.58586_t
Valid prediction for GeneMark_model.58627_t
Valid prediction for GeneMark_model.58635_t
Valid prediction for GlimmerHMM_glimmerT_34268-T1
Valid prediction for GeneMark_model.58593_t
Valid prediction for GeneMark_model.58633_t
Valid prediction for GeneMark_model.58605_t
Valid prediction for snap_scaffold_14-snap.574-T1
Valid prediction for GeneMark_model.58619_t
Valid prediction for GeneMark_model.58607_t
Couldn't classify 72498, 72664
Sorry, prediction pasa_asmbl_12993.p1 fails validation.
(CGC)	 AG	72498-72664	GT	AGG
(ATG)	 AG	72909-73035	GT	AGG
(GTG)	 AG	73302-73403	GT	AGG
(GCA)	 AG	73978-74124	GT	AGG
(ATT)	 AG	74338-74496	GT	AGG
(GAG)	 AG	74597-74763	GT	AGG
(TGT)	 AG	74928-75122	GT	AGG
(AGT)	 AG	75883-75994	CT	AGC
-recovered pasa_asmbl_12993.p1, initial, 72909, 73035
add_exon() Sorry, pasa_asmbl_12993.p1 74928-75122-terminal-1 is invalid.
-recovered pasa_asmbl_12993.p1, terminal, 74928, 75122
-recovered pasa_asmbl_12993.p1, terminal, 75883, 75994
-recovered pasa_asmbl_12993.p1, internal, 72498, 72664
-recovered pasa_asmbl_12993.p1, internal, 72909, 73035
-recovered pasa_asmbl_12993.p1, internal, 73302, 73403
-recovered pasa_asmbl_12993.p1, internal, 73978, 74124
-recovered pasa_asmbl_12993.p1, internal, 74338, 74496
-recovered pasa_asmbl_12993.p1, internal, 74597, 74763
-recovered pasa_asmbl_12993.p1, internal, 74928, 75122
Valid prediction for GlimmerHMM_glimmerT_34277-T1
Valid prediction for GeneMark_model.58629_t
Valid prediction for snap_scaffold_14-snap.566-T1
Valid prediction for Augustus_model.g23053.t1
Valid prediction for GeneMark_model.58611_t
Valid prediction for snap_scaffold_14-snap.579-T1
Couldn't classify 50884, 51057
Couldn't classify 52225, 52281
Sorry, prediction pasa_asmbl_13773.p2 fails validation.
(GCC)	 AA	50884-51057	GT	CGG
(GTT)	 AG	51538-51663	GT	TGG
(CTG)	 AG	52225-52281	GT	GGG
-recovered pasa_asmbl_13773.p2, internal, 51538, 51663
-recovered pasa_asmbl_13773.p2, internal, 52225, 52281
Valid prediction for snap_scaffold_14-snap.586-T1
Valid prediction for GeneMark_model.58602_t
Valid prediction for snap_scaffold_14-snap.565-T1
Valid prediction for GeneMark_model.58612_t
Valid prediction for snap_scaffold_14-snap.597-T1
Valid prediction for snap_scaffold_14-snap.577-T1
Valid prediction for snap_scaffold_14-snap.571-T1
Valid prediction for GeneMark_model.58637_t
Valid prediction for snap_scaffold_14-snap.581-T1
Valid prediction for GeneMark_model.58614_t
Couldn't classify 125593, 126009
Sorry, prediction pasa_asmbl_12991.p1 fails validation.
(GAC)	 GA	125593-126009	TT	AAT
Valid prediction for snap_scaffold_14-snap.593-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for Augustus_model.g23061.t1
Valid prediction for Augustus_model.g23062.t1
Valid prediction for GeneMark_model.58621_t
Valid prediction for GeneMark_model.58617_t
Valid prediction for snap_scaffold_14-snap.576-T1
Valid prediction for GeneMark_model.58625_t
Valid prediction for snap_scaffold_14-snap.583-T1
Valid prediction for GeneMark_model.58618_t
Valid prediction for GeneMark_model.58631_t
Valid prediction for GlimmerHMM_glimmerT_34281-T1
Valid prediction for Augustus_model.g23057.t1
Valid prediction for GeneMark_model.58589_t
Valid prediction for GlimmerHMM_glimmerT_34271-T1
Valid prediction for GlimmerHMM_glimmerT_34274-T1
Valid prediction for GeneMark_model.58601_t
Valid prediction for GeneMark_model.58623_t
Valid prediction for GeneMark_model.58643_t
Valid prediction for CodingQuarry_transcript_15568-T1
Valid prediction for GlimmerHMM_glimmerT_34283-T1
Valid prediction for GeneMark_model.58599_t
Valid prediction for snap_scaffold_14-snap.569-T1
Valid prediction for snap_scaffold_14-snap.596-T1
Valid prediction for snap_scaffold_14-snap.584-T1
Valid prediction for GeneMark_model.58596_t
Valid prediction for Augustus_model.g23060.t1
Couldn't classify 65287, 65310
Couldn't classify 68251, 68403
Sorry, prediction pasa_asmbl_12995.p1 fails validation.
(CCC)	 GC	65287-65310	GT	AGG
(ACG)	 AG	65880-66063	GT	CGG
(AGG)	 AG	67670-67775	GT	AGG
(GCA)	 AG	67947-68103	GT	GGG
(GTG)	 AG	68251-68403	CA	CGC
-recovered pasa_asmbl_12995.p1, internal, 65880, 66063
-recovered pasa_asmbl_12995.p1, internal, 67670, 67775
-recovered pasa_asmbl_12995.p1, internal, 67947, 68103
Valid prediction for GeneMark_model.58609_t
Valid prediction for GlimmerHMM_glimmerT_34282-T1
Valid prediction for GlimmerHMM_glimmerT_34280-T1
Valid prediction for CodingQuarry_transcript_15572-T1
Valid prediction for GeneMark_model.58638_t
Valid prediction for snap_scaffold_14-snap.590-T1
Valid prediction for pasa_asmbl_12985.p1
Valid prediction for GeneMark_model.58591_t
Valid prediction for GlimmerHMM_glimmerT_34278-T1
Valid prediction for snap_scaffold_14-snap.582-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 40359, rend_intergenic: 33524  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54253, rend_intergenic: 43053  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63184, rend_intergenic: 60031  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65636, rend_intergenic: 63300  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69454, rend_intergenic: 68304  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70845, rend_intergenic: 69706  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85651, rend_intergenic: 71281  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99108, rend_intergenic: 95463  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109323, rend_intergenic: 100738  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114330, rend_intergenic: 109696  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125043, rend_intergenic: 116646  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130250, rend_intergenic: 126842  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146872, rend_intergenic: 139119  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150272, rend_intergenic: 147023  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 171416
-exon list size: 629


building trellis

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-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 40359, rend_intergenic: 33524  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54253, rend_intergenic: 43053  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63184, rend_intergenic: 60031  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65636, rend_intergenic: 63300  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69454, rend_intergenic: 68304  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70845, rend_intergenic: 69706  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85651, rend_intergenic: 71281  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99108, rend_intergenic: 95463  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109323, rend_intergenic: 100738  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 114330, rend_intergenic: 109696  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125043, rend_intergenic: 116646  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130250, rend_intergenic: 126842  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 146872, rend_intergenic: 139119  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150272, rend_intergenic: 147023  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 12 predictions persist after filtering for low support