-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_17/scaffold_17_11522156-11701822

-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_42054-T1
Valid prediction for snap_scaffold_17-snap.2357-T1
Valid prediction for snap_scaffold_17-snap.2354-T1
Valid prediction for GeneMark_model.72565_t
Valid prediction for Augustus_model.g28188.t1
Valid prediction for GeneMark_model.72573_t
Valid prediction for GeneMark_model.72593_t
Valid prediction for snap_scaffold_17-snap.2366-T1
Valid prediction for GlimmerHMM_glimmerT_42050-T1
Valid prediction for GeneMark_model.72555_t
Valid prediction for snap_scaffold_17-snap.2349-T1
Valid prediction for snap_scaffold_17-snap.2374-T1
Valid prediction for snap_scaffold_17-snap.2347-T1
Valid prediction for GlimmerHMM_glimmerT_42069-T1
Valid prediction for GlimmerHMM_glimmerT_42057-T1
Valid prediction for snap_scaffold_17-snap.2372-T1
Valid prediction for Augustus_model.g28189.t1
Valid prediction for GlimmerHMM_glimmerT_42070-T1
Valid prediction for GeneMark_model.72582_t
Valid prediction for GlimmerHMM_glimmerT_42068-T1
Couldn't classify 54829, 55692
Sorry, prediction pasa_asmbl_18364.p1 fails validation.
(GTG)	 AC	54829-55692	AA	GAA
Valid prediction for snap_scaffold_17-snap.2350-T1
Valid prediction for Augustus_model.g28201.t1
Valid prediction for Augustus_model.g28192.t1
Valid prediction for CodingQuarry_transcript_22136-T1
Valid prediction for GlimmerHMM_glimmerT_42049-T1
Valid prediction for Augustus_model.g28197.t1
Valid prediction for GeneMark_model.72577_t
Couldn't classify 53761, 54072
Sorry, prediction pasa_asmbl_18661.p1 fails validation.
(TGT)	 TC	53761-54072	AT	CCA
Valid prediction for snap_scaffold_17-snap.2379-T1
Valid prediction for Augustus_model.g28186.t1
Valid prediction for CodingQuarry_transcript_22135-T1
Valid prediction for Augustus_model.g28200.t1
Valid prediction for GlimmerHMM_glimmerT_42060-T1
Valid prediction for CodingQuarry_transcript_22134-T1
Valid prediction for snap_scaffold_17-snap.2373-T1
Valid prediction for GeneMark_model.72580_t
Valid prediction for Augustus_model.g28184.t1
Valid prediction for GeneMark_model.72557_t
Valid prediction for GlimmerHMM_glimmerT_42048-T1
Valid prediction for snap_scaffold_17-snap.2367-T1
Valid prediction for pasa_asmbl_18362.p1
Valid prediction for snap_scaffold_17-snap.2356-T1
Valid prediction for GeneMark_model.72586_t
Valid prediction for GlimmerHMM_glimmerT_42065-T1
Valid prediction for Augustus_model.g28198.t1
Valid prediction for GeneMark_model.72561_t
Valid prediction for GeneMark_model.72590_t
Valid prediction for GeneMark_model.72559_t
Valid prediction for GlimmerHMM_glimmerT_42067-T1
Valid prediction for CodingQuarry_transcript_22137-T1
Valid prediction for GeneMark_model.72563_t
Valid prediction for snap_scaffold_17-snap.2360-T1
Valid prediction for snap_scaffold_17-snap.2377-T1
Valid prediction for GlimmerHMM_glimmerT_42052-T1
Valid prediction for snap_scaffold_17-snap.2344-T1
Couldn't classify 8939, 9216
Couldn't classify 9608, 9644
Sorry, prediction pasa_asmbl_18603.p1 fails validation.
(CCC)	 GC	8939-9216	GT	AGG
(ATC)	 AG	9608-9644	GA	AGG
Valid prediction for GeneMark_model.72569_t
Valid prediction for GeneMark_model.72579_t
Valid prediction for snap_scaffold_17-snap.2368-T1
Valid prediction for GeneMark_model.72567_t
Valid prediction for GeneMark_model.72588_t

-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 pasa_asmbl_19337.p1
Valid prediction for snap_scaffold_17-snap.2376-T1
Valid prediction for CodingQuarry_transcript_22139-T1
Valid prediction for snap_scaffold_17-snap.2355-T1
Valid prediction for GeneMark_model.72585_t
Valid prediction for snap_scaffold_17-snap.2378-T1
Valid prediction for snap_scaffold_17-snap.2346-T1
Valid prediction for snap_scaffold_17-snap.2348-T1
Valid prediction for GeneMark_model.72562_t
Valid prediction for Augustus_model.g28196.t1
Valid prediction for Augustus_model.g28191.t1
Valid prediction for GlimmerHMM_glimmerT_42058-T1
Valid prediction for GlimmerHMM_glimmerT_42055-T1
Valid prediction for GeneMark_model.72592_t
Valid prediction for Augustus_model.g28199.t1
Valid prediction for GlimmerHMM_glimmerT_42059-T1
Valid prediction for GeneMark_model.72574_t
Couldn't classify 97170, 97307
Sorry, prediction pasa_asmbl_19339.p1 fails validation.
(GAA)	 CA	97170-97307	GT	TGG
(GCA)	 AG	97668-97982	GG	AGG
-recovered pasa_asmbl_19339.p1, terminal, 97668, 97982
Valid prediction for GeneMark_model.72584_t
Valid prediction for snap_scaffold_17-snap.2351-T1
Valid prediction for CodingQuarry_transcript_22143-T1
Valid prediction for GeneMark_model.72571_t
Valid prediction for GlimmerHMM_glimmerT_42053-T1
Valid prediction for GeneMark_model.72589_t
Valid prediction for snap_scaffold_17-snap.2358-T1
Valid prediction for GeneMark_model.72583_t
Valid prediction for snap_scaffold_17-snap.2352-T1
Valid prediction for HiQ_model.g28193.t1
Valid prediction for snap_scaffold_17-snap.2365-T1
Valid prediction for snap_scaffold_17-snap.2362-T1
Valid prediction for GeneMark_model.72575_t
Valid prediction for GlimmerHMM_glimmerT_42064-T1
Valid prediction for snap_scaffold_17-snap.2343-T1
Valid prediction for snap_scaffold_17-snap.2369-T1
Valid prediction for GeneMark_model.72560_t
Valid prediction for snap_scaffold_17-snap.2364-T1
Valid prediction for Augustus_model.g28195.t1
Valid prediction for GlimmerHMM_glimmerT_42056-T1
Valid prediction for snap_scaffold_17-snap.2363-T1
Valid prediction for Augustus_model.g28187.t1
Valid prediction for GlimmerHMM_glimmerT_42063-T1
Valid prediction for CodingQuarry_transcript_22142-T1
Valid prediction for snap_scaffold_17-snap.2353-T1
Valid prediction for snap_scaffold_17-snap.2371-T1
Couldn't classify 89277, 89429
Sorry, prediction pasa_asmbl_19343.p1 fails validation.
(GAA)	 AG	89277-89429	GT	AGG
(GAG)	 AG	89783-89897	GT	GAG
(CTC)	 AG	90232-90408	GT	CGG
(AGA)	 AG	90895-91039	GT	GGG
(GTT)	 AG	91267-91666	AG	GAA
-recovered pasa_asmbl_19343.p1, terminal, 91267, 91666
-recovered pasa_asmbl_19343.p1, internal, 89277, 89429
-recovered pasa_asmbl_19343.p1, internal, 89783, 89897
-recovered pasa_asmbl_19343.p1, internal, 90232, 90408
-recovered pasa_asmbl_19343.p1, internal, 90895, 91039
Valid prediction for GlimmerHMM_glimmerT_42051-T1
Valid prediction for pasa_asmbl_19347.p1
Valid prediction for GlimmerHMM_glimmerT_42062-T1
Valid prediction for GeneMark_model.72581_t
Valid prediction for GeneMark_model.72568_t
Valid prediction for snap_scaffold_17-snap.2361-T1
Couldn't classify 158478, 158522
Sorry, prediction pasa_asmbl_19332.p1 fails validation.
(CGG)	 GA	158478-158522	GT	AGG
(ATG)	 AG	158778-158848	GT	AAG
(GTC)	 AG	159207-159307	GT	AGG
(CGT)	 AG	159483-159666	GT	GGG
(AGG)	 AG	159925-159979	GT	AGG
(GTT)	 AG	160100-160126	GT	AAG
-recovered pasa_asmbl_19332.p1, initial, 158778, 158848
add_exon() Sorry, pasa_asmbl_19332.p1 159207-159307-terminal-2 is invalid.
-recovered pasa_asmbl_19332.p1, terminal, 159207, 159307
-recovered pasa_asmbl_19332.p1, terminal, 160100, 160126
-recovered pasa_asmbl_19332.p1, internal, 158778, 158848
-recovered pasa_asmbl_19332.p1, internal, 159207, 159307
-recovered pasa_asmbl_19332.p1, internal, 159483, 159666
-recovered pasa_asmbl_19332.p1, internal, 159925, 159979
-recovered pasa_asmbl_19332.p1, internal, 160100, 160126
Valid prediction for GeneMark_model.72558_t
Valid prediction for snap_scaffold_17-snap.2375-T1
Valid prediction for CodingQuarry_transcript_22141-T1
Valid prediction for GeneMark_model.72564_t
Valid prediction for pasa_asmbl_19333.p1
Valid prediction for GeneMark_model.72566_t
Valid prediction for snap_scaffold_17-snap.2370-T1
Valid prediction for GeneMark_model.72594_t
Valid prediction for GlimmerHMM_glimmerT_42066-T1
Valid prediction for GeneMark_model.72591_t
Valid prediction for Augustus_model.g28185.t1
Valid prediction for GeneMark_model.72578_t
Valid prediction for GeneMark_model.72587_t
Valid prediction for GeneMark_model.72556_t
Valid prediction for snap_scaffold_17-snap.2345-T1
Valid prediction for CodingQuarry_transcript_22140-T1
Valid prediction for GeneMark_model.72572_t
Valid prediction for GeneMark_model.72576_t
Valid prediction for Augustus_model.g28190.t1
Couldn't classify 94902, 94959
Couldn't classify 96916, 97073
Sorry, prediction pasa_asmbl_19340.p1 fails validation.
(GTA)	 CT	94902-94959	GT	AGG
(GTA)	 AG	95111-95256	GT	CGG
(GGT)	 AG	95369-95554	GT	AGG
(GAC)	 AG	95682-95834	GT	AGG
(AAC)	 AG	96066-96210	GT	GGG
(GCT)	 AG	96534-96761	GT	AGG
(GAA)	 AG	96916-97073	CC	CCC
-recovered pasa_asmbl_19340.p1, internal, 95111, 95256
-recovered pasa_asmbl_19340.p1, internal, 95369, 95554
-recovered pasa_asmbl_19340.p1, internal, 95682, 95834
-recovered pasa_asmbl_19340.p1, internal, 96066, 96210
-recovered pasa_asmbl_19340.p1, internal, 96534, 96761
Valid prediction for HiQ_model.g28194.t1
Valid prediction for GlimmerHMM_glimmerT_42061-T1
Valid prediction for snap_scaffold_17-snap.2359-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 7551, rend_intergenic: 1725  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13288, rend_intergenic: 9016  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23269, rend_intergenic: 21433  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33735, rend_intergenic: 25263  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41642, rend_intergenic: 39218  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131482, rend_intergenic: 118800  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159007, rend_intergenic: 152294  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176452, rend_intergenic: 172673  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 179667
-exon list size: 559


building trellis

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-found 35 predictions from path traversal
Error with prediction: snap lend_intergenic: 7551, rend_intergenic: 1725  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 13288, rend_intergenic: 9016  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23269, rend_intergenic: 21433  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33735, rend_intergenic: 25263  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41642, rend_intergenic: 39218  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131482, rend_intergenic: 118800  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159007, rend_intergenic: 152294  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 176452, rend_intergenic: 172673  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 26 predictions persist after filtering for low support