-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_5/scaffold_5_11426891-11606653

-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.21902_t
Valid prediction for snap_scaffold_5-snap.2134-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_12951-T1
Valid prediction for snap_scaffold_5-snap.2135-T1
Valid prediction for GlimmerHMM_glimmerT_12947-T1
Valid prediction for CodingQuarry_transcript_52123-T1
Valid prediction for Augustus_model.g8631.t1
Valid prediction for snap_scaffold_5-snap.2148-T1
Couldn't classify 6349, 6383
Sorry, prediction pasa_asmbl_44409.p1 fails validation.
(ATG)	 GG	5194-5263	GT	TGG
(GTC)	 AG	5365-5556	GT	GGG
(GTG)	 AG	5744-5827	GT	AGG
(GAG)	 AG	5983-6141	GT	AGG
(ATG)	 AG	6349-6383	AC	ACA
-recovered pasa_asmbl_44409.p1, initial, 5194, 5263
-recovered pasa_asmbl_44409.p1, internal, 5365, 5556
-recovered pasa_asmbl_44409.p1, internal, 5744, 5827
-recovered pasa_asmbl_44409.p1, internal, 5983, 6141
Valid prediction for CodingQuarry_transcript_52128-T1
Valid prediction for snap_scaffold_5-snap.2151-T1
Valid prediction for GeneMark_model.21885_t
Valid prediction for GlimmerHMM_glimmerT_12942-T1
Valid prediction for GeneMark_model.21900_t
Valid prediction for snap_scaffold_5-snap.2160-T1
Valid prediction for GeneMark_model.21913_t
Valid prediction for snap_scaffold_5-snap.2139-T1
Valid prediction for snap_scaffold_5-snap.2128-T1
Valid prediction for GlimmerHMM_glimmerT_12941-T1
Couldn't classify 21584, 21673
Sorry, prediction pasa_asmbl_44412.p1 fails validation.
(GGC)	 CA	21584-21673	GC	AGG
(AGT)	 AG	21901-22024	GT	AGG
(GTG)	 AG	22126-22278	GT	AGG
(CCA)	 AG	22491-22673	GT	AGG
(GTG)	 AG	22846-22964	CC	AAC
add_exon() Sorry, pasa_asmbl_44412.p1 22491-22673-terminal-1 is invalid.
-recovered pasa_asmbl_44412.p1, terminal, 22491, 22673
-recovered pasa_asmbl_44412.p1, terminal, 22846, 22964
-recovered pasa_asmbl_44412.p1, internal, 21901, 22024
-recovered pasa_asmbl_44412.p1, internal, 22126, 22278
-recovered pasa_asmbl_44412.p1, internal, 22491, 22673
Valid prediction for GeneMark_model.21895_t
Valid prediction for GeneMark_model.21898_t
Valid prediction for GeneMark_model.21907_t
Valid prediction for GeneMark_model.21904_t
Valid prediction for GlimmerHMM_glimmerT_12965-T1
Valid prediction for CodingQuarry_transcript_52125-T1
Valid prediction for snap_scaffold_5-snap.2155-T1
Valid prediction for GeneMark_model.21883_t
Valid prediction for snap_scaffold_5-snap.2161-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for Augustus_model.g8619.t1
Valid prediction for snap_scaffold_5-snap.2131-T1
Valid prediction for GeneMark_model.21915_t
Valid prediction for GlimmerHMM_glimmerT_12958-T1
Valid prediction for GlimmerHMM_glimmerT_12964-T1
Couldn't classify 127462, 127803
Sorry, prediction pasa_asmbl_44420.p1 fails validation.
(AAC)	 GT	127462-127803	TG	GAT
Valid prediction for GlimmerHMM_glimmerT_12963-T1
Valid prediction for GeneMark_model.21893_t
Valid prediction for Augustus_model.g8632.t1
Valid prediction for Augustus_model.g8636.t1
Valid prediction for GlimmerHMM_glimmerT_12967-T1
Valid prediction for GeneMark_model.21889_t
Valid prediction for GeneMark_model.21910_t
Valid prediction for HiQ_model.g8633.t1
Valid prediction for CodingQuarry_transcript_52122-T1
Valid prediction for Augustus_model.g8635.t1
Valid prediction for snap_scaffold_5-snap.2132-T1
Valid prediction for snap_scaffold_5-snap.2154-T1
Valid prediction for GlimmerHMM_glimmerT_12937-T1
Valid prediction for Augustus_model.g8621.t1
Valid prediction for Augustus_model.g8627.t1
Valid prediction for snap_scaffold_5-snap.2141-T1
Valid prediction for GeneMark_model.21908_t
Valid prediction for GlimmerHMM_glimmerT_12938-T1
Valid prediction for snap_scaffold_5-snap.2130-T1
Valid prediction for snap_scaffold_5-snap.2143-T1
Valid prediction for CodingQuarry_transcript_52124-T1
Valid prediction for GlimmerHMM_glimmerT_12940-T1
Valid prediction for GlimmerHMM_glimmerT_12960-T1
Valid prediction for GeneMark_model.21881_t
Valid prediction for pasa_asmbl_44417.p1
Valid prediction for pasa_asmbl_44411.p1
Valid prediction for Augustus_model.g8622.t1
Valid prediction for snap_scaffold_5-snap.2156-T1
Valid prediction for CodingQuarry_transcript_52127-T1
Valid prediction for GlimmerHMM_glimmerT_12957-T1
Valid prediction for snap_scaffold_5-snap.2145-T1
Valid prediction for GlimmerHMM_glimmerT_12966-T1
Valid prediction for GlimmerHMM_glimmerT_12945-T1
Valid prediction for GlimmerHMM_glimmerT_12955-T1
Valid prediction for snap_scaffold_5-snap.2157-T1
Valid prediction for GeneMark_model.21882_t
Couldn't classify 77776, 78324
Sorry, prediction pasa_asmbl_44414.p1 fails validation.
(AGA)	 CA	77776-78324	GA	GAG
Valid prediction for GlimmerHMM_glimmerT_12950-T1
Valid prediction for snap_scaffold_5-snap.2158-T1
Valid prediction for snap_scaffold_5-snap.2149-T1
Valid prediction for GeneMark_model.21905_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_5-snap.2142-T1
Valid prediction for GeneMark_model.21914_t
Valid prediction for snap_scaffold_5-snap.2127-T1
Valid prediction for Augustus_model.g8629.t1
Valid prediction for GeneMark_model.21899_t
Couldn't classify 132577, 132706
Sorry, prediction pasa_asmbl_45794.p1 fails validation.
(AGG)	 AG	132577-132706	GT	ACG
(CCC)	 AG	132902-133045	GT	AGG
(AGG)	 AG	133686-133975	AA	AAA
-recovered pasa_asmbl_45794.p1, terminal, 133686, 133975
-recovered pasa_asmbl_45794.p1, internal, 132577, 132706
-recovered pasa_asmbl_45794.p1, internal, 132902, 133045
Valid prediction for GlimmerHMM_glimmerT_12956-T1
Valid prediction for pasa_asmbl_45798.p1
Valid prediction for GeneMark_model.21906_t
Valid prediction for Augustus_model.g8623.t1
Valid prediction for GeneMark_model.21894_t
Valid prediction for snap_scaffold_5-snap.2147-T1
Valid prediction for GlimmerHMM_glimmerT_12943-T1
Valid prediction for GlimmerHMM_glimmerT_12952-T1
Valid prediction for Augustus_model.g8624.t1
Valid prediction for CodingQuarry_transcript_52129-T1
Valid prediction for snap_scaffold_5-snap.2163-T1
Valid prediction for GeneMark_model.21897_t
Valid prediction for snap_scaffold_5-snap.2162-T1
Valid prediction for HiQ_model.g8637.t1
Valid prediction for GeneMark_model.21912_t
Valid prediction for GlimmerHMM_glimmerT_12959-T1
Couldn't classify 172344, 172421
Sorry, prediction pasa_asmbl_45791.p1 fails validation.
(ATG)	 TC	171066-171161	GT	CTG
(GTT)	 AG	171285-171411	GT	CGG
(GGT)	 AG	171566-171690	GT	AGG
(CGG)	 AG	171807-171929	GT	AGG
(GCA)	 AG	172010-172129	GT	AGG
(GTT)	 AG	172209-172271	GT	AGG
(ATT)	 AG	172344-172421	AC	GAA
-recovered pasa_asmbl_45791.p1, initial, 171066, 171161
-recovered pasa_asmbl_45791.p1, internal, 171285, 171411
-recovered pasa_asmbl_45791.p1, internal, 171566, 171690
-recovered pasa_asmbl_45791.p1, internal, 171807, 171929
-recovered pasa_asmbl_45791.p1, internal, 172010, 172129
-recovered pasa_asmbl_45791.p1, internal, 172209, 172271
Valid prediction for snap_scaffold_5-snap.2137-T1
Valid prediction for GlimmerHMM_glimmerT_12953-T1
Valid prediction for snap_scaffold_5-snap.2159-T1
Couldn't classify 146316, 146381
Sorry, prediction pasa_asmbl_45793.p1 fails validation.
(TCA)	 AA	146316-146381	GT	CTG
(TTC)	 AG	146559-146588	GT	AGG
(AAC)	 AG	146895-146966	GT	GGG
(AGG)	 AG	147170-147388	AT	AGA
-recovered pasa_asmbl_45793.p1, terminal, 147170, 147388
-recovered pasa_asmbl_45793.p1, internal, 146559, 146588
-recovered pasa_asmbl_45793.p1, internal, 146895, 146966
Valid prediction for HiQ_model.g8620.t1
Valid prediction for GeneMark_model.21890_t
Valid prediction for GlimmerHMM_glimmerT_12961-T1
Valid prediction for GeneMark_model.21892_t
Valid prediction for GlimmerHMM_glimmerT_12939-T1
Valid prediction for GlimmerHMM_glimmerT_12962-T1
Valid prediction for snap_scaffold_5-snap.2129-T1
Valid prediction for GeneMark_model.21888_t
Valid prediction for GlimmerHMM_glimmerT_12968-T1
Valid prediction for snap_scaffold_5-snap.2138-T1
Valid prediction for GeneMark_model.21909_t
Valid prediction for GeneMark_model.21886_t
Valid prediction for Augustus_model.g8626.t1
Valid prediction for GeneMark_model.21901_t
Valid prediction for snap_scaffold_5-snap.2136-T1
Valid prediction for snap_scaffold_5-snap.2146-T1
Valid prediction for pasa_asmbl_46358.p1
Valid prediction for Augustus_model.g8630.t1
Valid prediction for GlimmerHMM_glimmerT_12949-T1
Valid prediction for GeneMark_model.21887_t
Couldn't classify 176140, 176377
Couldn't classify 176535, 176659
Sorry, prediction pasa_asmbl_45790.p1 fails validation.
(GCA)	 GG	176140-176377	GT	AGG
(GAA)	 AG	176535-176659	AC	GGA
Valid prediction for snap_scaffold_5-snap.2144-T1
Valid prediction for GlimmerHMM_glimmerT_12948-T1
Valid prediction for GeneMark_model.21916_t
Valid prediction for Augustus_model.g8634.t1
Valid prediction for GlimmerHMM_glimmerT_12944-T1
Valid prediction for GeneMark_model.21891_t
Valid prediction for GeneMark_model.21884_t
Valid prediction for snap_scaffold_5-snap.2152-T1
Valid prediction for snap_scaffold_5-snap.2150-T1
Couldn't classify 98159, 98312
Sorry, prediction pasa_asmbl_46366.p1 fails validation.
(CTG)	 TT	98159-98312	GT	TGG
(AAC)	 AG	98452-98570	GT	AGG
(GTG)	 AG	98731-98850	AG	AAA
-recovered pasa_asmbl_46366.p1, terminal, 98731, 98850
-recovered pasa_asmbl_46366.p1, internal, 98452, 98570
Valid prediction for Augustus_model.g8628.t1
Valid prediction for snap_scaffold_5-snap.2153-T1
Valid prediction for snap_scaffold_5-snap.2133-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for CodingQuarry_transcript_52126-T1
Valid prediction for GeneMark_model.21896_t
Valid prediction for GlimmerHMM_glimmerT_12946-T1
Valid prediction for Augustus_model.g8625.t1
Valid prediction for GlimmerHMM_glimmerT_12954-T1
Valid prediction for snap_scaffold_5-snap.2140-T1
Valid prediction for GeneMark_model.21903_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 48911, rend_intergenic: 45741  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68835, rend_intergenic: 57423  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70867, rend_intergenic: 69217  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78629, rend_intergenic: 75224  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96258, rend_intergenic: 84114  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101702, rend_intergenic: 99562  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104960, rend_intergenic: 102429  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111729, rend_intergenic: 108390  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143164, rend_intergenic: 141544  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 179763
-exon list size: 519


building trellis

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-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 48911, rend_intergenic: 45741  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 68835, rend_intergenic: 57423  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 70867, rend_intergenic: 69217  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78629, rend_intergenic: 75224  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96258, rend_intergenic: 84114  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101702, rend_intergenic: 99562  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104960, rend_intergenic: 102429  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111729, rend_intergenic: 108390  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 143164, rend_intergenic: 141544  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support