-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_13/scaffold_13_9756447-9932295

-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_32903-T1
Valid prediction for GlimmerHMM_glimmerT_32913-T1
Valid prediction for GlimmerHMM_glimmerT_32908-T1
Valid prediction for Augustus_model.g22105.t1
Valid prediction for Augustus_model.g22100.t1
Valid prediction for snap_scaffold_13-snap.1799-T1
Valid prediction for GlimmerHMM_glimmerT_32907-T1
Valid prediction for GeneMark_model.56136_t
Valid prediction for GlimmerHMM_glimmerT_32899-T1
Valid prediction for GeneMark_model.56127_t
Valid prediction for GeneMark_model.56114_t
Valid prediction for Augustus_model.g22093.t1
Valid prediction for Augustus_model.g22088.t1
Valid prediction for GlimmerHMM_glimmerT_32916-T1
Valid prediction for GeneMark_model.56118_t
Valid prediction for GeneMark_model.56128_t
Valid prediction for GeneMark_model.56119_t
Valid prediction for GlimmerHMM_glimmerT_32898-T1
Valid prediction for snap_scaffold_13-snap.1783-T1
Valid prediction for Augustus_model.g22095.t1
Valid prediction for snap_scaffold_13-snap.1803-T1
Valid prediction for GeneMark_model.56124_t
Valid prediction for Augustus_model.g22096.t1
Valid prediction for Augustus_model.g22091.t1
Valid prediction for GeneMark_model.56123_t
Valid prediction for GeneMark_model.56125_t
Valid prediction for snap_scaffold_13-snap.1802-T1
Valid prediction for snap_scaffold_13-snap.1784-T1
Valid prediction for snap_scaffold_13-snap.1797-T1
Valid prediction for snap_scaffold_13-snap.1781-T1
Valid prediction for Augustus_model.g22101.t1
Valid prediction for GeneMark_model.56145_t
Valid prediction for GeneMark_model.56129_t
Valid prediction for Augustus_model.g22092.t1
Valid prediction for snap_scaffold_13-snap.1800-T1
Valid prediction for snap_scaffold_13-snap.1787-T1
Valid prediction for GeneMark_model.56116_t
Valid prediction for GeneMark_model.56137_t
Valid prediction for GlimmerHMM_glimmerT_32912-T1
Valid prediction for Augustus_model.g22103.t1
Valid prediction for GlimmerHMM_glimmerT_32902-T1
Valid prediction for GeneMark_model.56144_t
Valid prediction for snap_scaffold_13-snap.1780-T1
Valid prediction for GeneMark_model.56122_t
Valid prediction for GeneMark_model.56111_t
Valid prediction for GlimmerHMM_glimmerT_32904-T1
Valid prediction for snap_scaffold_13-snap.1778-T1
Valid prediction for snap_scaffold_13-snap.1798-T1
Valid prediction for snap_scaffold_13-snap.1788-T1
Valid prediction for Augustus_model.g22094.t1
Valid prediction for GeneMark_model.56120_t
Valid prediction for GeneMark_model.56138_t
Valid prediction for GlimmerHMM_glimmerT_32911-T1
Valid prediction for snap_scaffold_13-snap.1789-T1
Valid prediction for snap_scaffold_13-snap.1796-T1
Valid prediction for GeneMark_model.56112_t
Valid prediction for GeneMark_model.56133_t
Valid prediction for GlimmerHMM_glimmerT_32906-T1
Valid prediction for GeneMark_model.56134_t
Valid prediction for GlimmerHMM_glimmerT_32910-T1
Valid prediction for snap_scaffold_13-snap.1785-T1
Valid prediction for snap_scaffold_13-snap.1793-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 GlimmerHMM_glimmerT_32900-T1
Valid prediction for GlimmerHMM_glimmerT_32914-T1
Valid prediction for snap_scaffold_13-snap.1790-T1
Valid prediction for GeneMark_model.56126_t
Valid prediction for GeneMark_model.56143_t
Valid prediction for snap_scaffold_13-snap.1791-T1
Valid prediction for GlimmerHMM_glimmerT_32897-T1
Valid prediction for GeneMark_model.56113_t
Valid prediction for Augustus_model.g22102.t1
Valid prediction for HiQ_model.g22089.t1
Valid prediction for Augustus_model.g22097.t1
Valid prediction for GeneMark_model.56140_t
Valid prediction for snap_scaffold_13-snap.1805-T1
Valid prediction for snap_scaffold_13-snap.1801-T1
Valid prediction for snap_scaffold_13-snap.1804-T1
Valid prediction for GeneMark_model.56115_t
Valid prediction for CodingQuarry_transcript_13183-T1
Valid prediction for GeneMark_model.56139_t
Valid prediction for snap_scaffold_13-snap.1776-T1
Valid prediction for GeneMark_model.56132_t
Valid prediction for snap_scaffold_13-snap.1782-T1
Valid prediction for GlimmerHMM_glimmerT_32896-T1
Couldn't classify 8958, 9167
Sorry, prediction pasa_asmbl_10007.p1 fails validation.
(GTT)	 AG	8958-9167	GT	CTG
(TGT)	 AG	9975-10071	GT	AGG
(ATC)	 AG	10885-10925	TG	AGT
-recovered pasa_asmbl_10007.p1, terminal, 10885, 10925
-recovered pasa_asmbl_10007.p1, internal, 8958, 9167
-recovered pasa_asmbl_10007.p1, internal, 9975, 10071
Valid prediction for snap_scaffold_13-snap.1775-T1
Valid prediction for Augustus_model.g22098.t1
Valid prediction for snap_scaffold_13-snap.1792-T1
Valid prediction for HiQ_model.g22106.t1
Valid prediction for snap_scaffold_13-snap.1795-T1
Valid prediction for snap_scaffold_13-snap.1777-T1
Valid prediction for GeneMark_model.56121_t
Valid prediction for GeneMark_model.56117_t
Valid prediction for GlimmerHMM_glimmerT_32909-T1
Valid prediction for GeneMark_model.56142_t
Valid prediction for GlimmerHMM_glimmerT_32901-T1
Valid prediction for GlimmerHMM_glimmerT_32905-T1
Valid prediction for snap_scaffold_13-snap.1794-T1
Valid prediction for Augustus_model.g22099.t1
Valid prediction for GlimmerHMM_glimmerT_32915-T1
Couldn't classify 32977, 33074
Couldn't classify 35668, 35728
Couldn't classify 35814, 35829
Sorry, prediction pasa_asmbl_10004.p1 fails validation.
(GAC)	 TG	32977-33074	GT	GAG
(GCC)	 AG	33256-33440	GT	CGG
(GTG)	 AG	33687-33798	GT	AGG
(GCT)	 AG	34244-34346	GT	AGG
(CGG)	 AG	34585-34753	GT	GGG
(ATG)	 AG	34913-35013	GT	AGG
(GGG)	 AG	35168-35302	GT	AGG
(AAC)	 AG	35460-35535	GT	TGG
(ATG)	 AG	35668-35728	AT	TCA
(GTA)	 AC	35814-35829	TG	GAT
add_exon() Sorry, pasa_asmbl_10004.p1 34913-35013-initial-1 is invalid.
-recovered pasa_asmbl_10004.p1, initial, 34913, 35013
-recovered pasa_asmbl_10004.p1, terminal, 33687, 33798
-recovered pasa_asmbl_10004.p1, internal, 33256, 33440
-recovered pasa_asmbl_10004.p1, internal, 33687, 33798
-recovered pasa_asmbl_10004.p1, internal, 34244, 34346
-recovered pasa_asmbl_10004.p1, internal, 34585, 34753
-recovered pasa_asmbl_10004.p1, internal, 34913, 35013
-recovered pasa_asmbl_10004.p1, internal, 35168, 35302
-recovered pasa_asmbl_10004.p1, internal, 35460, 35535
Valid prediction for Augustus_model.g22090.t1
Valid prediction for GeneMark_model.56131_t
Valid prediction for snap_scaffold_13-snap.1779-T1
Valid prediction for CodingQuarry_transcript_13184-T1
Valid prediction for pasa_asmbl_10002.p1
Valid prediction for Augustus_model.g22104.t1
Valid prediction for GeneMark_model.56135_t
Valid prediction for GeneMark_model.56130_t
Valid prediction for snap_scaffold_13-snap.1786-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 46953, rend_intergenic: 43555  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67747, rend_intergenic: 65836  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94868, rend_intergenic: 91413  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100440, rend_intergenic: 99327  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102388, rend_intergenic: 101208  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112038, rend_intergenic: 110219  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147892, rend_intergenic: 141732  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 175849
-exon list size: 446


building trellis

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-found 23 predictions from path traversal
Error with prediction: snap lend_intergenic: 46953, rend_intergenic: 43555  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67747, rend_intergenic: 65836  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94868, rend_intergenic: 91413  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100440, rend_intergenic: 99327  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102388, rend_intergenic: 101208  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 112038, rend_intergenic: 110219  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147892, rend_intergenic: 141732  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

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