-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_11/scaffold_11_192962-316573

-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_26850-T1
Valid prediction for snap_scaffold_11-snap.42-T1
Couldn't classify 29015, 29225
Sorry, prediction pasa_asmbl_5237.p1 fails validation.
(AGT)	 GC	29015-29225	GT	AGG
(GTG)	 AG	29444-29607	CC	GAC
-recovered pasa_asmbl_5237.p1, terminal, 29444, 29607
Valid prediction for snap_scaffold_11-snap.49-T1
Valid prediction for GeneMark_model.46365_t
Valid prediction for GlimmerHMM_glimmerT_26841-T1
Valid prediction for GeneMark_model.46371_t
Valid prediction for snap_scaffold_11-snap.50-T1
Valid prediction for GeneMark_model.46350_t
Valid prediction for snap_scaffold_11-snap.38-T1
Valid prediction for GlimmerHMM_glimmerT_26837-T1
Couldn't classify 25270, 25287
Couldn't classify 26561, 26587
Sorry, prediction pasa_asmbl_5236.p1 fails validation.
(ATC)	 AC	25270-25287	GT	AGG
(ATG)	 AG	26143-26403	GT	AGG
(GCC)	 AG	26561-26587	AC	GGA
-recovered pasa_asmbl_5236.p1, initial, 26143, 26403
-recovered pasa_asmbl_5236.p1, internal, 26143, 26403
Valid prediction for GeneMark_model.46346_t
Valid prediction for snap_scaffold_11-snap.46-T1
Valid prediction for snap_scaffold_11-snap.43-T1
Valid prediction for GlimmerHMM_glimmerT_26844-T1
Valid prediction for GeneMark_model.46347_t
Valid prediction for snap_scaffold_11-snap.65-T1
Valid prediction for Augustus_model.g17967.t1
Valid prediction for Augustus_model.g17962.t1
Valid prediction for Augustus_model.g17964.t1
Valid prediction for GlimmerHMM_glimmerT_26845-T1
Valid prediction for GlimmerHMM_glimmerT_26843-T1
Valid prediction for GeneMark_model.46357_t
Valid prediction for GeneMark_model.46354_t
Valid prediction for Augustus_model.g17966.t1
Valid prediction for snap_scaffold_11-snap.53-T1
Valid prediction for snap_scaffold_11-snap.48-T1
Valid prediction for GeneMark_model.46352_t
Valid prediction for snap_scaffold_11-snap.56-T1
Valid prediction for GeneMark_model.46364_t
Valid prediction for snap_scaffold_11-snap.54-T1
Valid prediction for GeneMark_model.46367_t
Valid prediction for snap_scaffold_11-snap.67-T1
Valid prediction for snap_scaffold_11-snap.44-T1
Valid prediction for GeneMark_model.46361_t
Valid prediction for GeneMark_model.46359_t
Valid prediction for Augustus_model.g17969.t1
Valid prediction for GlimmerHMM_glimmerT_26839-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 GeneMark_model.46351_t
Valid prediction for snap_scaffold_11-snap.62-T1
Valid prediction for snap_scaffold_11-snap.45-T1
Valid prediction for GeneMark_model.46353_t
Valid prediction for GeneMark_model.46363_t
Valid prediction for snap_scaffold_11-snap.66-T1
Couldn't classify 112035, 112095
Sorry, prediction pasa_asmbl_6352.p1 fails validation.
(AGG)	 CC	112035-112095	GT	GGG
(ACT)	 AG	112209-112295	GT	TGG
(ACC)	 AG	112399-112652	CT	GAC
-recovered pasa_asmbl_6352.p1, terminal, 112399, 112652
-recovered pasa_asmbl_6352.p1, internal, 112209, 112295
Valid prediction for snap_scaffold_11-snap.55-T1
Valid prediction for snap_scaffold_11-snap.57-T1
Valid prediction for snap_scaffold_11-snap.60-T1
Valid prediction for GeneMark_model.46368_t
Valid prediction for pasa_asmbl_6363.p1
Valid prediction for GlimmerHMM_glimmerT_26842-T1
Valid prediction for GlimmerHMM_glimmerT_26840-T1
Valid prediction for snap_scaffold_11-snap.58-T1
Valid prediction for GeneMark_model.46358_t
Valid prediction for snap_scaffold_11-snap.59-T1
Valid prediction for GlimmerHMM_glimmerT_26846-T1
Valid prediction for snap_scaffold_11-snap.41-T1
Valid prediction for Augustus_model.g17963.t1
Valid prediction for snap_scaffold_11-snap.47-T1
Valid prediction for GlimmerHMM_glimmerT_26848-T1
Valid prediction for GeneMark_model.46348_t
Valid prediction for snap_scaffold_11-snap.61-T1
Valid prediction for GeneMark_model.46370_t
Valid prediction for GlimmerHMM_glimmerT_26835-T1
Valid prediction for GlimmerHMM_glimmerT_26851-T1
Valid prediction for CodingQuarry_transcript_7912-T1
Valid prediction for snap_scaffold_11-snap.51-T1
Valid prediction for snap_scaffold_11-snap.64-T1
Valid prediction for GeneMark_model.46349_t
Valid prediction for HiQ_model.g17968.t1
Valid prediction for GeneMark_model.46372_t
Valid prediction for GeneMark_model.46355_t
Valid prediction for Augustus_model.g17970.t1
Valid prediction for snap_scaffold_11-snap.63-T1
Valid prediction for GlimmerHMM_glimmerT_26849-T1
Couldn't classify 101581, 101667
Couldn't classify 105112, 105224
Sorry, prediction pasa_asmbl_6357.p1 fails validation.
(AAG)	 GG	101581-101667	GT	AGG
(GTC)	 AG	103354-103420	GT	TGG
(GTT)	 AG	104857-104976	GT	AGG
(TGG)	 AG	105112-105224	TA	CGT
-recovered pasa_asmbl_6357.p1, internal, 103354, 103420
-recovered pasa_asmbl_6357.p1, internal, 104857, 104976
Couldn't classify 106300, 106491
Couldn't classify 106864, 107079
Sorry, prediction pasa_asmbl_6356.p1 fails validation.
(CCA)	 CT	106300-106491	GT	AGG
(ATG)	 AG	106864-107079	AG	GCA
Valid prediction for GeneMark_model.46369_t
Valid prediction for GlimmerHMM_glimmerT_26836-T1
Couldn't classify 110656, 110831
Sorry, prediction pasa_asmbl_6354.p1 fails validation.
(GAT)	 CA	110656-110831	GT	AGG
(GTA)	 AG	110982-111153	TG	GAT
-recovered pasa_asmbl_6354.p1, terminal, 110982, 111153
Valid prediction for GeneMark_model.46356_t
Valid prediction for snap_scaffold_11-snap.52-T1
Valid prediction for Augustus_model.g17965.t1
Valid prediction for GeneMark_model.46360_t
Valid prediction for snap_scaffold_11-snap.40-T1
Valid prediction for GeneMark_model.46366_t
Valid prediction for snap_scaffold_11-snap.39-T1
Couldn't classify 100786, 101373
Sorry, prediction pasa_asmbl_6358.p1 fails validation.
(TTC)	 AG	100786-101373	CT	GCC
Valid prediction for GlimmerHMM_glimmerT_26838-T1
Valid prediction for GlimmerHMM_glimmerT_26847-T1
Valid prediction for GlimmerHMM_glimmerT_26834-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 22974, rend_intergenic: 13931  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29607, rend_intergenic: 28348  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32127, rend_intergenic: 29790  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45251, rend_intergenic: 40735  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48354, rend_intergenic: 45274  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62373, rend_intergenic: 58858  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117258, rend_intergenic: 114229  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 123612
-exon list size: 436


building trellis

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-found 22 predictions from path traversal
Error with prediction: snap lend_intergenic: 22974, rend_intergenic: 13931  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29607, rend_intergenic: 28348  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 32127, rend_intergenic: 29790  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45251, rend_intergenic: 40735  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 48354, rend_intergenic: 45274  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62373, rend_intergenic: 58858  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117258, rend_intergenic: 114229  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 18 predictions persist after filtering for low support