-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_9/scaffold_9_5732300-5878236

-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 HiQ_model.g15180.t1
Valid prediction for snap_scaffold_9-snap.1242-T1
Valid prediction for GeneMark_model.38999_t
Valid prediction for snap_scaffold_9-snap.1249-T1
Valid prediction for snap_scaffold_9-snap.1247-T1
Valid prediction for GeneMark_model.38986_t
Couldn't classify 61947, 62308
Sorry, prediction pasa_asmbl_54055.p1 fails validation.
(AGA)	 TG	61947-62308	GT	GCG
(GAG)	 AG	62486-62730	GT	AGG
(CCA)	 AG	62821-62988	GT	GGG
(GCT)	 AG	63634-64229	TT	GAT
add_exon() Sorry, pasa_asmbl_54055.p1 62486-62730-terminal-2 is invalid.
-recovered pasa_asmbl_54055.p1, terminal, 62486, 62730
-recovered pasa_asmbl_54055.p1, terminal, 63634, 64229
-recovered pasa_asmbl_54055.p1, internal, 62486, 62730
-recovered pasa_asmbl_54055.p1, internal, 62821, 62988
Valid prediction for GlimmerHMM_glimmerT_22704-T1
Valid prediction for GlimmerHMM_glimmerT_22709-T1
Valid prediction for GlimmerHMM_glimmerT_22692-T1
Valid prediction for Augustus_model.g15183.t1
Valid prediction for GlimmerHMM_glimmerT_22697-T1
Valid prediction for Augustus_model.g15182.t1
Valid prediction for snap_scaffold_9-snap.1250-T1
Valid prediction for snap_scaffold_9-snap.1227-T1
Valid prediction for snap_scaffold_9-snap.1229-T1
Couldn't classify 129045, 129262
Sorry, prediction pasa_asmbl_54056.p1 fails validation.
(ACC)	 AC	129045-129262	GT	AGG
(CCT)	 AG	130763-130916	GA	AGG
-recovered pasa_asmbl_54056.p1, terminal, 130763, 130916
Valid prediction for GlimmerHMM_glimmerT_22707-T1
Valid prediction for GlimmerHMM_glimmerT_22686-T1
Valid prediction for snap_scaffold_9-snap.1248-T1
Valid prediction for snap_scaffold_9-snap.1219-T1
Valid prediction for GlimmerHMM_glimmerT_22687-T1
Valid prediction for GeneMark_model.38995_t
Valid prediction for GeneMark_model.39016_t
Valid prediction for GeneMark_model.39005_t
Valid prediction for GlimmerHMM_glimmerT_22695-T1
Valid prediction for GlimmerHMM_glimmerT_22698-T1
Valid prediction for GlimmerHMM_glimmerT_22720-T1
Valid prediction for GlimmerHMM_glimmerT_22711-T1
Valid prediction for GlimmerHMM_glimmerT_22710-T1
Valid prediction for snap_scaffold_9-snap.1230-T1
Valid prediction for snap_scaffold_9-snap.1251-T1
Valid prediction for Augustus_model.g15185.t1
Valid prediction for GeneMark_model.39001_t
Valid prediction for GlimmerHMM_glimmerT_22719-T1
Valid prediction for GeneMark_model.39011_t
Valid prediction for GlimmerHMM_glimmerT_22713-T1
Valid prediction for GeneMark_model.39013_t
Valid prediction for snap_scaffold_9-snap.1240-T1
Valid prediction for Augustus_model.g15184.t1
Valid prediction for GeneMark_model.39004_t
Valid prediction for snap_scaffold_9-snap.1237-T1
Valid prediction for snap_scaffold_9-snap.1238-T1
Valid prediction for GeneMark_model.39008_t
Valid prediction for GlimmerHMM_glimmerT_22717-T1
Valid prediction for GlimmerHMM_glimmerT_22706-T1
Valid prediction for GeneMark_model.38997_t
Valid prediction for GlimmerHMM_glimmerT_22718-T1
Valid prediction for snap_scaffold_9-snap.1235-T1
Valid prediction for Augustus_model.g15188.t1
Valid prediction for snap_scaffold_9-snap.1231-T1
Valid prediction for snap_scaffold_9-snap.1226-T1
Valid prediction for snap_scaffold_9-snap.1234-T1
Valid prediction for snap_scaffold_9-snap.1232-T1
Valid prediction for GeneMark_model.38993_t
Valid prediction for snap_scaffold_9-snap.1217-T1
Valid prediction for Augustus_model.g15189.t1
Valid prediction for GeneMark_model.39012_t
Valid prediction for GeneMark_model.38991_t
Valid prediction for GlimmerHMM_glimmerT_22688-T1
Valid prediction for GlimmerHMM_glimmerT_22705-T1
Valid prediction for GeneMark_model.39002_t
Valid prediction for GeneMark_model.38988_t
Valid prediction for GeneMark_model.39007_t
Valid prediction for GlimmerHMM_glimmerT_22716-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 CodingQuarry_transcript_62031-T1
Couldn't classify 95352, 95546
Couldn't classify 95951, 96125
Sorry, prediction pasa_asmbl_54997.p1 fails validation.
(TCT)	 TA	95352-95546	GT	AGG
(GAC)	 AG	95706-95824	GT	AAG
(GTA)	 AG	95951-96125	AA	AGA
-recovered pasa_asmbl_54997.p1, internal, 95706, 95824
Valid prediction for GeneMark_model.39015_t
Valid prediction for GeneMark_model.38987_t
Valid prediction for GlimmerHMM_glimmerT_22702-T1
Valid prediction for GlimmerHMM_glimmerT_22691-T1
Valid prediction for GlimmerHMM_glimmerT_22712-T1
Valid prediction for snap_scaffold_9-snap.1225-T1
Valid prediction for GlimmerHMM_glimmerT_22715-T1
Valid prediction for Augustus_model.g15176.t1
Valid prediction for GeneMark_model.38985_t
Valid prediction for snap_scaffold_9-snap.1241-T1
Valid prediction for GlimmerHMM_glimmerT_22701-T1
Valid prediction for snap_scaffold_9-snap.1239-T1
Valid prediction for GeneMark_model.38990_t
Valid prediction for GlimmerHMM_glimmerT_22685-T1
Valid prediction for GeneMark_model.38998_t
Couldn't classify 69452, 69515
Couldn't classify 75278, 75360
Sorry, prediction pasa_asmbl_55001.p1 fails validation.
(GAC)	 TG	69452-69515	GT	AGG
(GTC)	 AG	70797-70930	GT	GGG
(TGC)	 AG	72623-72723	GT	AGG
(GTC)	 AG	72872-72978	GT	AGG
(GGA)	 AG	74169-74348	GT	GGG
(ACG)	 AG	75278-75360	AA	CCA
-recovered pasa_asmbl_55001.p1, internal, 70797, 70930
-recovered pasa_asmbl_55001.p1, internal, 72623, 72723
-recovered pasa_asmbl_55001.p1, internal, 72872, 72978
-recovered pasa_asmbl_55001.p1, internal, 74169, 74348
Couldn't classify 99045, 99123
Sorry, prediction pasa_asmbl_54995.p1 fails validation.
(CCT)	 AC	99045-99123	GT	TGG
(GAG)	 AG	99442-99563	GT	AGG
(GAG)	 AG	99702-99857	GT	GGG
(GCC)	 AG	100252-100373	GT	AGG
(GTG)	 AG	100497-100677	GT	AGG
(CTG)	 AG	101154-101240	GT	AGG
(GTG)	 AG	101868-101978	GT	AGG
(GTC)	 AG	102081-102216	GT	TGG
(GTA)	 AG	102590-102717	GT	AGG
(CAT)	 AG	102871-102972	GT	AGG
(GGA)	 AG	103485-103619	GT	AGG
(ATG)	 AG	103968-104153	CG	GAC
-recovered pasa_asmbl_54995.p1, terminal, 103968, 104153
-recovered pasa_asmbl_54995.p1, internal, 99442, 99563
-recovered pasa_asmbl_54995.p1, internal, 99702, 99857
-recovered pasa_asmbl_54995.p1, internal, 100252, 100373
-recovered pasa_asmbl_54995.p1, internal, 100497, 100677
-recovered pasa_asmbl_54995.p1, internal, 101154, 101240
-recovered pasa_asmbl_54995.p1, internal, 101868, 101978
-recovered pasa_asmbl_54995.p1, internal, 102081, 102216
-recovered pasa_asmbl_54995.p1, internal, 102590, 102717
-recovered pasa_asmbl_54995.p1, internal, 102871, 102972
-recovered pasa_asmbl_54995.p1, internal, 103485, 103619
Valid prediction for snap_scaffold_9-snap.1218-T1
Valid prediction for GlimmerHMM_glimmerT_22690-T1
Valid prediction for Augustus_model.g15177.t1
Valid prediction for snap_scaffold_9-snap.1220-T1
Valid prediction for GeneMark_model.39009_t
Valid prediction for GlimmerHMM_glimmerT_22703-T1
Valid prediction for HiQ_model.g15174.t1
Valid prediction for Augustus_model.g15186.t1
Valid prediction for GeneMark_model.38992_t
Valid prediction for snap_scaffold_9-snap.1223-T1
Valid prediction for CodingQuarry_transcript_62029-T1
Valid prediction for snap_scaffold_9-snap.1228-T1
Valid prediction for CodingQuarry_transcript_62028-T1
Valid prediction for GlimmerHMM_glimmerT_22696-T1
Valid prediction for snap_scaffold_9-snap.1243-T1
Valid prediction for GeneMark_model.39010_t
Valid prediction for HiQ_model.g15187.t1
Valid prediction for HiQ_model.g15175.t1
Valid prediction for GlimmerHMM_glimmerT_22699-T1
Valid prediction for snap_scaffold_9-snap.1215-T1
Valid prediction for GlimmerHMM_glimmerT_22694-T1
Couldn't classify 97432, 97726
Couldn't classify 98941, 98975
Sorry, prediction pasa_asmbl_54996.p1 fails validation.
(GTG)	 AA	97432-97726	GT	AGG
(GGA)	 AG	97832-97989	GT	AGG
(ATG)	 AG	98173-98379	GT	AGG
(GTG)	 AG	98623-98722	GT	AGG
(ACT)	 AG	98941-98975	CA	AGC
-recovered pasa_asmbl_54996.p1, initial, 98173, 98379
-recovered pasa_asmbl_54996.p1, internal, 97832, 97989
-recovered pasa_asmbl_54996.p1, internal, 98173, 98379
-recovered pasa_asmbl_54996.p1, internal, 98623, 98722
Valid prediction for GlimmerHMM_glimmerT_22714-T1
Valid prediction for pasa_asmbl_54991.p1
Valid prediction for pasa_asmbl_54998.p1
Valid prediction for GeneMark_model.39006_t
Valid prediction for GlimmerHMM_glimmerT_22708-T1
Valid prediction for Augustus_model.g15178.t1
Valid prediction for snap_scaffold_9-snap.1244-T1
Valid prediction for GeneMark_model.38996_t
Valid prediction for pasa_asmbl_55003.p1
Valid prediction for snap_scaffold_9-snap.1252-T1
Valid prediction for GlimmerHMM_glimmerT_22693-T1
Valid prediction for GlimmerHMM_glimmerT_22689-T1
Valid prediction for HiQ_model.g15179.t1
Valid prediction for GeneMark_model.39014_t
Valid prediction for snap_scaffold_9-snap.1224-T1
Valid prediction for CodingQuarry_transcript_62032-T1
Valid prediction for snap_scaffold_9-snap.1216-T1
Valid prediction for snap_scaffold_9-snap.1246-T1
Valid prediction for snap_scaffold_9-snap.1221-T1
Valid prediction for snap_scaffold_9-snap.1222-T1
Valid prediction for GeneMark_model.38989_t
Valid prediction for GlimmerHMM_glimmerT_22700-T1
Valid prediction for Augustus_model.g15181.t1
Valid prediction for GeneMark_model.39000_t
Valid prediction for GeneMark_model.39003_t
Valid prediction for snap_scaffold_9-snap.1236-T1
Valid prediction for snap_scaffold_9-snap.1233-T1
Valid prediction for Augustus_model.g15173.t1
Valid prediction for GeneMark_model.38994_t
Valid prediction for snap_scaffold_9-snap.1245-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 58514, rend_intergenic: 46393  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70861, rend_intergenic: 68768  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72871, rend_intergenic: 71618  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76544, rend_intergenic: 74171  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86895, rend_intergenic: 85536  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91864, rend_intergenic: 89210  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99142, rend_intergenic: 97516  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 145937
-exon list size: 570


building trellis

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-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 58514, rend_intergenic: 46393  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70861, rend_intergenic: 68768  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72871, rend_intergenic: 71618  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76544, rend_intergenic: 74171  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86895, rend_intergenic: 85536  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91864, rend_intergenic: 89210  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99142, rend_intergenic: 97516  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 24 predictions persist after filtering for low support