-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_6/scaffold_6_1-154260

-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 pasa_asmbl_46583.p1
Valid prediction for CodingQuarry_transcript_54745-T1
Valid prediction for snap_scaffold_6-snap.11-T1
Valid prediction for HiQ_model.g9483.t1
Valid prediction for GeneMark_model.23684_t
Valid prediction for GeneMark_model.23675_t
Valid prediction for GlimmerHMM_glimmerT_14207-T1
Valid prediction for GeneMark_model.23667_t
Valid prediction for GlimmerHMM_glimmerT_14210-T1
Valid prediction for GeneMark_model.23692_t
Valid prediction for snap_scaffold_6-snap.26-T1
Valid prediction for GlimmerHMM_glimmerT_14195-T1
Valid prediction for GlimmerHMM_glimmerT_14205-T1
Valid prediction for HiQ_model.g9486.t1
Valid prediction for GeneMark_model.23682_t
Valid prediction for snap_scaffold_6-snap.9-T1
Valid prediction for GeneMark_model.23672_t
Valid prediction for snap_scaffold_6-snap.31-T1
Valid prediction for GeneMark_model.23669_t
Valid prediction for GlimmerHMM_glimmerT_14185-T1
Valid prediction for GeneMark_model.23698_t
Valid prediction for snap_scaffold_6-snap.17-T1
Valid prediction for Augustus_model.g9488.t1
Valid prediction for snap_scaffold_6-snap.4-T1
Valid prediction for pasa_asmbl_46581.p1
Valid prediction for GeneMark_model.23688_t
Valid prediction for snap_scaffold_6-snap.20-T1
Valid prediction for Augustus_model.g9474.t1
add_exon() Sorry, Augustus_model.g9474.t1 711-848-initial-1 is invalid.
add_exon() Sorry, Augustus_model.g9474.t1 1010-1091-internal-1 is invalid.
add_exon() Sorry, Augustus_model.g9474.t1 2552-3128-terminal-1 is invalid.
Valid prediction for Augustus_model.g9485.t1
Valid prediction for GlimmerHMM_glimmerT_14188-T1
Valid prediction for snap_scaffold_6-snap.2-T1
add_exon() Sorry, snap_scaffold_6-snap.2-T1 711-848-initial-1 is invalid.
add_exon() Sorry, snap_scaffold_6-snap.2-T1 1010-1091-internal-1 is invalid.
add_exon() Sorry, snap_scaffold_6-snap.2-T1 2538-3096-internal-2 is invalid.
add_exon() Sorry, snap_scaffold_6-snap.2-T1 5300-5436-internal-3 is invalid.
add_exon() Sorry, snap_scaffold_6-snap.2-T1 7161-7268-terminal-2 is invalid.
Valid prediction for GlimmerHMM_glimmerT_14194-T1
Valid prediction for Augustus_model.g9475.t1
Valid prediction for snap_scaffold_6-snap.23-T1
Valid prediction for Augustus_model.g9487.t1
Valid prediction for GlimmerHMM_glimmerT_14213-T1
Valid prediction for GlimmerHMM_glimmerT_14186-T1
Valid prediction for GeneMark_model.23677_t
Valid prediction for GlimmerHMM_glimmerT_14206-T1
Valid prediction for snap_scaffold_6-snap.19-T1
Valid prediction for snap_scaffold_6-snap.21-T1
Valid prediction for snap_scaffold_6-snap.40-T1
Valid prediction for snap_scaffold_6-snap.41-T1
Valid prediction for GeneMark_model.23679_t
Valid prediction for snap_scaffold_6-snap.14-T1
Valid prediction for CodingQuarry_transcript_54742-T1
Valid prediction for GeneMark_model.23690_t
Valid prediction for GlimmerHMM_glimmerT_14189-T1
Valid prediction for GlimmerHMM_glimmerT_14198-T1
Valid prediction for GeneMark_model.23691_t
Valid prediction for Augustus_model.g9477.t1
Couldn't classify 51565, 52141
Sorry, prediction pasa_asmbl_47886.p1 fails validation.
(GTT)	 GA	51565-52141	GT	TAG
(TGA)	 AG	52271-52341	CC	GAC
-recovered pasa_asmbl_47886.p1, terminal, 52271, 52341
Valid prediction for snap_scaffold_6-snap.7-T1
Valid prediction for snap_scaffold_6-snap.37-T1
Couldn't classify 10665, 10985
Sorry, prediction pasa_asmbl_47954.p1 fails validation.
(ATG)	 CA	10665-10985	CT	TCC
Valid prediction for Augustus_model.g9491.t1
Valid prediction for GlimmerHMM_glimmerT_14200-T1
Valid prediction for GeneMark_model.23670_t
Valid prediction for snap_scaffold_6-snap.38-T1
Valid prediction for Augustus_model.g9480.t1
Valid prediction for GlimmerHMM_glimmerT_14209-T1
Valid prediction for GeneMark_model.23703_t
Valid prediction for GlimmerHMM_glimmerT_14208-T1
Couldn't classify 50365, 51152
Sorry, prediction pasa_asmbl_46579.p1 fails validation.
(ATG)	 AG	50121-50151	GT	GGG
(CAG)	 AG	50365-51152	GG	GAG
-recovered pasa_asmbl_46579.p1, initial, 50121, 50151
-recovered pasa_asmbl_46579.p1, internal, 50121, 50151
Valid prediction for GeneMark_model.23693_t
Valid prediction for GeneMark_model.23699_t
Valid prediction for GeneMark_model.23696_t
Valid prediction for CodingQuarry_transcript_54741-T1
Valid prediction for pasa_asmbl_46584.p1
Valid prediction for snap_scaffold_6-snap.32-T1
Valid prediction for snap_scaffold_6-snap.30-T1
Valid prediction for snap_scaffold_6-snap.15-T1
Valid prediction for snap_scaffold_6-snap.34-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.23695_t
Couldn't classify 17557, 17584
Sorry, prediction pasa_asmbl_47969.p1 fails validation.
(CCT)	 GA	17557-17584	GT	AGG
(GCC)	 AG	17956-18138	GT	AGG
(ACA)	 AG	19822-19946	GT	AGG
(GGT)	 AG	20072-20187	GT	CGG
(GAA)	 AG	20643-20847	CG	AGC
-recovered pasa_asmbl_47969.p1, terminal, 20643, 20847
-recovered pasa_asmbl_47969.p1, internal, 17956, 18138
-recovered pasa_asmbl_47969.p1, internal, 19822, 19946
-recovered pasa_asmbl_47969.p1, internal, 20072, 20187
Valid prediction for snap_scaffold_6-snap.6-T1
Valid prediction for CodingQuarry_transcript_54739-T1
Valid prediction for snap_scaffold_6-snap.5-T1
Valid prediction for snap_scaffold_6-snap.27-T1
Valid prediction for snap_scaffold_6-snap.10-T1
Valid prediction for GeneMark_model.23674_t
Valid prediction for GeneMark_model.23697_t
Valid prediction for GlimmerHMM_glimmerT_14196-T1
Valid prediction for GlimmerHMM_glimmerT_14201-T1
Valid prediction for GlimmerHMM_glimmerT_14199-T1
Valid prediction for snap_scaffold_6-snap.3-T1
Valid prediction for GlimmerHMM_glimmerT_14212-T1
Valid prediction for GeneMark_model.23687_t
Valid prediction for snap_scaffold_6-snap.29-T1
Valid prediction for pasa_asmbl_47962.p1
Couldn't classify 153447, 153567
Sorry, prediction snap_scaffold_6-snap.1-T1 fails validation.
(ATG)	 GC	151650-151696	GT	AGG
(GTC)	 AG	152786-153045	GT	AGG
(CCA)	 AG	153447-153567	GT	AAG
-recovered snap_scaffold_6-snap.1-T1, initial, 151650, 151696
-recovered snap_scaffold_6-snap.1-T1, internal, 152786, 153045
-recovered snap_scaffold_6-snap.1-T1, internal, 153447, 153567
Valid prediction for GlimmerHMM_glimmerT_14191-T1
Valid prediction for snap_scaffold_6-snap.24-T1
Valid prediction for snap_scaffold_6-snap.33-T1
Valid prediction for GlimmerHMM_glimmerT_14192-T1
Valid prediction for GeneMark_model.23671_t
Valid prediction for Augustus_model.g9490.t1
Valid prediction for snap_scaffold_6-snap.25-T1
Valid prediction for snap_scaffold_6-snap.22-T1
Valid prediction for CodingQuarry_transcript_54738-T1
Valid prediction for GeneMark_model.23668_t
Valid prediction for GlimmerHMM_glimmerT_14203-T1
Valid prediction for pasa_asmbl_47959.p1
Valid prediction for HiQ_model.g9489.t1
Valid prediction for GeneMark_model.23694_t
Valid prediction for snap_scaffold_6-snap.8-T1
Valid prediction for GeneMark_model.23680_t
Valid prediction for GlimmerHMM_glimmerT_14193-T1
Valid prediction for GlimmerHMM_glimmerT_14184-T1
Valid prediction for pasa_asmbl_47961.p1
Valid prediction for GeneMark_model.23681_t
Couldn't classify 140602, 141141
Sorry, prediction pasa_asmbl_47957.p1 fails validation.
(CTT)	 CA	140602-141141	TT	GGT
Valid prediction for GlimmerHMM_glimmerT_14202-T1
Valid prediction for snap_scaffold_6-snap.42-T1
Valid prediction for snap_scaffold_6-snap.36-T1
Valid prediction for CodingQuarry_transcript_54743-T1
Valid prediction for snap_scaffold_6-snap.28-T1
Valid prediction for Augustus_model.g9482.t1
Valid prediction for GlimmerHMM_glimmerT_14204-T1
Valid prediction for GeneMark_model.23678_t
Valid prediction for GeneMark_model.23704_t
Valid prediction for GlimmerHMM_glimmerT_14190-T1
Couldn't classify 25879, 26502
Sorry, prediction pasa_asmbl_47967.p1 fails validation.
(TGG)	 CA	25879-26502	TA	GAT
Valid prediction for Augustus_model.g9481.t1
Valid prediction for GeneMark_model.23689_t
Couldn't classify 153447, 153519
Sorry, prediction GeneMark_model.23666_t fails validation.
(ATG)	 CC	153189-153258	GT	GAG
(CCA)	 AG	153447-153519	GT	GAG
-recovered GeneMark_model.23666_t, initial, 153189, 153258
-recovered GeneMark_model.23666_t, internal, 153447, 153519
Valid prediction for GeneMark_model.23686_t
Valid prediction for CodingQuarry_transcript_54740-T1
Valid prediction for HiQ_model.g9479.t1
Valid prediction for GlimmerHMM_glimmerT_14197-T1
Valid prediction for snap_scaffold_6-snap.16-T1
Valid prediction for snap_scaffold_6-snap.13-T1
Valid prediction for GeneMark_model.23702_t
Valid prediction for GlimmerHMM_glimmerT_14211-T1
Valid prediction for snap_scaffold_6-snap.18-T1
Valid prediction for GeneMark_model.23673_t
Valid prediction for Augustus_model.g9484.t1
Valid prediction for GeneMark_model.23683_t
Valid prediction for Augustus_model.g9478.t1
Valid prediction for GeneMark_model.23676_t
Valid prediction for snap_scaffold_6-snap.35-T1
Valid prediction for GeneMark_model.23685_t
Valid prediction for GeneMark_model.23705_t
Valid prediction for snap_scaffold_6-snap.39-T1
Couldn't classify 139710, 139904
Couldn't classify 140173, 140286
Sorry, prediction pasa_asmbl_49302.p1 fails validation.
(GAT)	 CA	139710-139904	GT	AGG
(GTG)	 AG	140173-140286	AA	CCA
Valid prediction for GeneMark_model.23701_t
Valid prediction for Augustus_model.g9476.t1
Valid prediction for GlimmerHMM_glimmerT_14187-T1
Valid prediction for snap_scaffold_6-snap.12-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 2611, rend_intergenic: 711  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 7268, rend_intergenic: 3865  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 9093, rend_intergenic: 7355  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 10607, rend_intergenic: 9551  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14573, rend_intergenic: 10665  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18729, rend_intergenic: 15636  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26596, rend_intergenic: 23872  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29327, rend_intergenic: 27337  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34958, rend_intergenic: 34777  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42699, rend_intergenic: 39645  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43659, rend_intergenic: 42892  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63287, rend_intergenic: 60537  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72006, rend_intergenic: 67650  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103638, rend_intergenic: 101210  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111291, rend_intergenic: 108281  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130022, rend_intergenic: 128805  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151491, rend_intergenic: 133414  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 154260
-exon list size: 547


building trellis

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-found 37 predictions from path traversal
Error with prediction: snap lend_intergenic: 2611, rend_intergenic: 711  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 7268, rend_intergenic: 3865  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 9093, rend_intergenic: 7355  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 10607, rend_intergenic: 9551  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14573, rend_intergenic: 10665  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18729, rend_intergenic: 15636  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26596, rend_intergenic: 23872  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 29327, rend_intergenic: 27337  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 34958, rend_intergenic: 34777  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42699, rend_intergenic: 39645  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43659, rend_intergenic: 42892  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63287, rend_intergenic: 60537  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72006, rend_intergenic: 67650  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103638, rend_intergenic: 101210  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 111291, rend_intergenic: 108281  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130022, rend_intergenic: 128805  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151491, rend_intergenic: 133414  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 25 predictions persist after filtering for low support