-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_14/scaffold_14_4640666-4817299

-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_34508-T1
Valid prediction for snap_scaffold_14-snap.933-T1
Valid prediction for snap_scaffold_14-snap.915-T1
Valid prediction for snap_scaffold_14-snap.912-T1
Valid prediction for snap_scaffold_14-snap.936-T1
Valid prediction for snap_scaffold_14-snap.921-T1
Valid prediction for GeneMark_model.59083_t
Valid prediction for snap_scaffold_14-snap.916-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_14-snap.931-T1
Valid prediction for snap_scaffold_14-snap.905-T1
Valid prediction for GeneMark_model.59070_t
Valid prediction for GlimmerHMM_glimmerT_34488-T1
Valid prediction for Augustus_model.g23192.t1
Valid prediction for GeneMark_model.59076_t
Valid prediction for GlimmerHMM_glimmerT_34492-T1
Valid prediction for GeneMark_model.59064_t
Valid prediction for snap_scaffold_14-snap.940-T1
Valid prediction for GeneMark_model.59097_t
Valid prediction for GlimmerHMM_glimmerT_34507-T1
Valid prediction for GeneMark_model.59094_t
Valid prediction for snap_scaffold_14-snap.904-T1
Valid prediction for GeneMark_model.59072_t
Valid prediction for snap_scaffold_14-snap.907-T1
Valid prediction for snap_scaffold_14-snap.937-T1
Valid prediction for GeneMark_model.59062_t
Valid prediction for snap_scaffold_14-snap.939-T1
Valid prediction for GeneMark_model.59080_t
Valid prediction for Augustus_model.g23194.t1
Valid prediction for GeneMark_model.59087_t
Valid prediction for snap_scaffold_14-snap.910-T1
Valid prediction for snap_scaffold_14-snap.925-T1
Valid prediction for GeneMark_model.59085_t
Valid prediction for GeneMark_model.59092_t
Valid prediction for GlimmerHMM_glimmerT_34501-T1
Valid prediction for GeneMark_model.59089_t
Valid prediction for snap_scaffold_14-snap.908-T1
Valid prediction for GeneMark_model.59054_t
Valid prediction for snap_scaffold_14-snap.913-T1
Valid prediction for GeneMark_model.59057_t
Valid prediction for Augustus_model.g23196.t1
Valid prediction for GeneMark_model.59060_t
Valid prediction for GeneMark_model.59090_t
Valid prediction for snap_scaffold_14-snap.935-T1
Valid prediction for GlimmerHMM_glimmerT_34498-T1
Valid prediction for snap_scaffold_14-snap.909-T1
Valid prediction for snap_scaffold_14-snap.928-T1
Valid prediction for GeneMark_model.59058_t
Valid prediction for Augustus_model.g23198.t1
Valid prediction for snap_scaffold_14-snap.927-T1
Valid prediction for GeneMark_model.59066_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 snap_scaffold_14-snap.923-T1
Valid prediction for GeneMark_model.59065_t
Valid prediction for GeneMark_model.59088_t
Couldn't classify 112149, 112177
Sorry, prediction pasa_asmbl_13048.p2 fails validation.
(ATG)	 CC	111094-111258	GT	TGG
(GCT)	 AG	111449-111638	GT	AGG
(CTC)	 AG	111920-112039	GT	AGG
(ACG)	 AG	112149-112177	GC	TGG
-recovered pasa_asmbl_13048.p2, initial, 111094, 111258
-recovered pasa_asmbl_13048.p2, internal, 111449, 111638
-recovered pasa_asmbl_13048.p2, internal, 111920, 112039
-recovered pasa_asmbl_13048.p2, internal, 112149, 112177
Valid prediction for Augustus_model.g23186.t1
Valid prediction for snap_scaffold_14-snap.938-T1
Valid prediction for GlimmerHMM_glimmerT_34490-T1
Valid prediction for GlimmerHMM_glimmerT_34481-T1
Valid prediction for Augustus_model.g23193.t1
Valid prediction for HiQ_model.g23195.t1
Valid prediction for snap_scaffold_14-snap.919-T1
Valid prediction for GeneMark_model.59061_t
Valid prediction for Augustus_model.g23190.t1
Valid prediction for GlimmerHMM_glimmerT_34494-T1
Valid prediction for GlimmerHMM_glimmerT_34495-T1
Valid prediction for snap_scaffold_14-snap.903-T1
Valid prediction for GlimmerHMM_glimmerT_34493-T1
Valid prediction for snap_scaffold_14-snap.932-T1
Valid prediction for snap_scaffold_14-snap.934-T1
Valid prediction for snap_scaffold_14-snap.918-T1
Valid prediction for GlimmerHMM_glimmerT_34482-T1
Valid prediction for GlimmerHMM_glimmerT_34487-T1
Valid prediction for Augustus_model.g23191.t1
Valid prediction for GlimmerHMM_glimmerT_34496-T1
Valid prediction for GeneMark_model.59077_t
Valid prediction for GeneMark_model.59067_t
Valid prediction for GlimmerHMM_glimmerT_34486-T1
Valid prediction for GeneMark_model.59056_t
Valid prediction for snap_scaffold_14-snap.911-T1
Valid prediction for snap_scaffold_14-snap.922-T1
Valid prediction for GlimmerHMM_glimmerT_34500-T1
Valid prediction for Augustus_model.g23182.t1
Valid prediction for GeneMark_model.59096_t
Valid prediction for CodingQuarry_transcript_15590-T1
Valid prediction for GlimmerHMM_glimmerT_34502-T1
Valid prediction for GeneMark_model.59082_t
Valid prediction for GlimmerHMM_glimmerT_34483-T1
Valid prediction for snap_scaffold_14-snap.920-T1
Couldn't classify 130679, 130744
Couldn't classify 131664, 131799
Sorry, prediction pasa_asmbl_13043.p1 fails validation.
(GGC)	 TG	130679-130744	GT	AGG
(ATC)	 AG	131145-131240	GT	AGG
(GGG)	 AG	131349-131545	GT	AGG
(GTG)	 AG	131664-131799	CA	ACC
-recovered pasa_asmbl_13043.p1, internal, 131145, 131240
-recovered pasa_asmbl_13043.p1, internal, 131349, 131545
Valid prediction for GeneMark_model.59078_t
Valid prediction for snap_scaffold_14-snap.906-T1
Valid prediction for GeneMark_model.59081_t
Valid prediction for Augustus_model.g23185.t1
Valid prediction for GeneMark_model.59073_t
Valid prediction for Augustus_model.g23189.t1
Valid prediction for GlimmerHMM_glimmerT_34489-T1
Valid prediction for GlimmerHMM_glimmerT_34499-T1
Couldn't classify 112691, 112871
Sorry, prediction pasa_asmbl_13046.p1 fails validation.
(TCT)	 GG	112691-112871	GT	GGG
(ACG)	 AG	113243-113393	GT	AGG
(GGA)	 AG	114643-114832	AC	AGA
-recovered pasa_asmbl_13046.p1, terminal, 114643, 114832
-recovered pasa_asmbl_13046.p1, internal, 113243, 113393
Valid prediction for snap_scaffold_14-snap.926-T1
Valid prediction for GlimmerHMM_glimmerT_34480-T1
Valid prediction for GlimmerHMM_glimmerT_34503-T1
Valid prediction for snap_scaffold_14-snap.914-T1
Valid prediction for GlimmerHMM_glimmerT_34485-T1
Valid prediction for snap_scaffold_14-snap.901-T1
Valid prediction for GlimmerHMM_glimmerT_34491-T1
Valid prediction for GeneMark_model.59075_t
Valid prediction for GeneMark_model.59071_t
Valid prediction for GlimmerHMM_glimmerT_34505-T1
Valid prediction for GeneMark_model.59093_t
Valid prediction for snap_scaffold_14-snap.902-T1
Valid prediction for Augustus_model.g23187.t1
Valid prediction for GeneMark_model.59068_t
Valid prediction for snap_scaffold_14-snap.930-T1
Valid prediction for GeneMark_model.59059_t
Valid prediction for GeneMark_model.59086_t
Valid prediction for Augustus_model.g23188.t1
Valid prediction for Augustus_model.g23183.t1
Valid prediction for GeneMark_model.59091_t
Valid prediction for GeneMark_model.59069_t
Valid prediction for GeneMark_model.59095_t
Valid prediction for snap_scaffold_14-snap.924-T1
Valid prediction for GeneMark_model.59084_t
Valid prediction for GlimmerHMM_glimmerT_34497-T1
Valid prediction for GeneMark_model.59055_t
Valid prediction for snap_scaffold_14-snap.929-T1
Valid prediction for snap_scaffold_14-snap.917-T1
Valid prediction for GeneMark_model.59079_t
Valid prediction for GlimmerHMM_glimmerT_34506-T1
Valid prediction for GlimmerHMM_glimmerT_34484-T1
Valid prediction for GlimmerHMM_glimmerT_34504-T1
Valid prediction for GeneMark_model.59074_t
Valid prediction for GeneMark_model.59063_t
Valid prediction for Augustus_model.g23197.t1
Valid prediction for Augustus_model.g23181.t1
Valid prediction for Augustus_model.g23184.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 16362, rend_intergenic: 12031  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20955, rend_intergenic: 16471  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37536, rend_intergenic: 21537  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50953, rend_intergenic: 39857  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64719, rend_intergenic: 60959  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92321, rend_intergenic: 88886  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115907, rend_intergenic: 104884  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121271, rend_intergenic: 116825  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137885, rend_intergenic: 135131  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 176634
-exon list size: 728


building trellis

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-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 16362, rend_intergenic: 12031  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 20955, rend_intergenic: 16471  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37536, rend_intergenic: 21537  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50953, rend_intergenic: 39857  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64719, rend_intergenic: 60959  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92321, rend_intergenic: 88886  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115907, rend_intergenic: 104884  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121271, rend_intergenic: 116825  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137885, rend_intergenic: 135131  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 22 predictions persist after filtering for low support