-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_3/scaffold_3_9592227-9828680

-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_7104-T1
Valid prediction for snap_scaffold_3-snap.1905-T1
Valid prediction for snap_scaffold_3-snap.1914-T1
Valid prediction for Augustus_model.g4636.t1
Valid prediction for snap_scaffold_3-snap.1934-T1
Valid prediction for Augustus_model.g4624.t1
Valid prediction for GlimmerHMM_glimmerT_7094-T1
Valid prediction for GlimmerHMM_glimmerT_7092-T1
Valid prediction for CodingQuarry_transcript_46239-T1
Valid prediction for snap_scaffold_3-snap.1913-T1
Valid prediction for Augustus_model.g4629.t1
Valid prediction for GlimmerHMM_glimmerT_7113-T1
Valid prediction for snap_scaffold_3-snap.1912-T1
Valid prediction for snap_scaffold_3-snap.1904-T1
Couldn't classify 82197, 82280
Sorry, prediction pasa_asmbl_40233.p1 fails validation.
(GTC)	 TG	82197-82280	GT	ACG
(GGC)	 AG	82413-82509	GT	AGG
(TGG)	 AG	82665-82833	GT	AGG
(TCT)	 AG	83067-83199	GT	AGG
(CTC)	 AG	83390-83568	GT	AAG
(CTC)	 AG	83670-83685	GC	GAG
-recovered pasa_asmbl_40233.p1, terminal, 83670, 83685
-recovered pasa_asmbl_40233.p1, internal, 82413, 82509
-recovered pasa_asmbl_40233.p1, internal, 82665, 82833
-recovered pasa_asmbl_40233.p1, internal, 83067, 83199
-recovered pasa_asmbl_40233.p1, internal, 83390, 83568
-recovered pasa_asmbl_40233.p1, internal, 83670, 83685
Valid prediction for snap_scaffold_3-snap.1906-T1
Valid prediction for snap_scaffold_3-snap.1923-T1
Valid prediction for GlimmerHMM_glimmerT_7101-T1
Valid prediction for GlimmerHMM_glimmerT_7105-T1
Valid prediction for snap_scaffold_3-snap.1929-T1
Valid prediction for pasa_asmbl_40234.p1
Valid prediction for snap_scaffold_3-snap.1937-T1
Valid prediction for snap_scaffold_3-snap.1894-T1
Valid prediction for GlimmerHMM_glimmerT_7116-T1
Couldn't classify 80466, 80655
Sorry, prediction pasa_asmbl_40232.p1 fails validation.
(ATG)	 TT	78889-78918	GT	TGG
(GAC)	 AG	79787-79901	GT	TGG
(GTG)	 AG	80101-80296	GT	AGG
(TTA)	 AG	80466-80655	CC	TGC
-recovered pasa_asmbl_40232.p1, initial, 78889, 78918
-recovered pasa_asmbl_40232.p1, internal, 79787, 79901
-recovered pasa_asmbl_40232.p1, internal, 80101, 80296
Valid prediction for HiQ_model.g4638.t1
Valid prediction for GlimmerHMM_glimmerT_7091-T1
Valid prediction for GlimmerHMM_glimmerT_7107-T1
Valid prediction for snap_scaffold_3-snap.1921-T1
Valid prediction for snap_scaffold_3-snap.1925-T1
Valid prediction for Augustus_model.g4634.t1
Valid prediction for Augustus_model.g4623.t1
Valid prediction for snap_scaffold_3-snap.1902-T1
Valid prediction for GlimmerHMM_glimmerT_7111-T1
Valid prediction for GlimmerHMM_glimmerT_7095-T1
Valid prediction for snap_scaffold_3-snap.1927-T1
Valid prediction for snap_scaffold_3-snap.1909-T1
Valid prediction for GlimmerHMM_glimmerT_7099-T1
Valid prediction for snap_scaffold_3-snap.1919-T1
Valid prediction for GlimmerHMM_glimmerT_7108-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_7106-T1
Couldn't classify 233683, 234084
Sorry, prediction pasa_asmbl_39059.p1 fails validation.
(GAG)	 GC	233683-234084	AC	CCA
Valid prediction for GlimmerHMM_glimmerT_7112-T1
Valid prediction for CodingQuarry_transcript_46237-T1
Valid prediction for Augustus_model.g4630.t1
Couldn't classify 229606, 229678
Sorry, prediction pasa_asmbl_39060.p1 fails validation.
(TGT)	 TG	229606-229678	GT	CGG
(ATG)	 AG	229810-229932	GT	GGG
(CCA)	 AG	230133-230236	GT	TGG
(CTT)	 AG	230358-230413	GT	AGG
(AGA)	 AG	230542-230702	GT	CGG
(AGG)	 AG	230935-231069	GT	AGG
(AAT)	 AG	231193-231273	GT	CTG
(TTT)	 AG	231414-231501	GT	AAG
(GAA)	 AG	231585-231765	GT	CAG
(CCT)	 AG	231976-232119	CC	AAC
add_exon() Sorry, pasa_asmbl_39060.p1 229810-229932-initial-1 is invalid.
-recovered pasa_asmbl_39060.p1, initial, 229810, 229932
-recovered pasa_asmbl_39060.p1, terminal, 230935, 231069
-recovered pasa_asmbl_39060.p1, terminal, 231976, 232119
-recovered pasa_asmbl_39060.p1, internal, 229810, 229932
-recovered pasa_asmbl_39060.p1, internal, 230133, 230236
-recovered pasa_asmbl_39060.p1, internal, 230358, 230413
-recovered pasa_asmbl_39060.p1, internal, 230542, 230702
-recovered pasa_asmbl_39060.p1, internal, 230935, 231069
-recovered pasa_asmbl_39060.p1, internal, 231193, 231273
-recovered pasa_asmbl_39060.p1, internal, 231414, 231501
-recovered pasa_asmbl_39060.p1, internal, 231585, 231765
Valid prediction for snap_scaffold_3-snap.1915-T1
Valid prediction for Augustus_model.g4631.t1
Valid prediction for GlimmerHMM_glimmerT_7115-T1
Valid prediction for GlimmerHMM_glimmerT_7096-T1
Valid prediction for GlimmerHMM_glimmerT_7114-T1
Valid prediction for snap_scaffold_3-snap.1908-T1
Valid prediction for GlimmerHMM_glimmerT_7088-T1
Valid prediction for snap_scaffold_3-snap.1896-T1
Valid prediction for GlimmerHMM_glimmerT_7100-T1
Valid prediction for GlimmerHMM_glimmerT_7093-T1
Valid prediction for Augustus_model.g4635.t1
Valid prediction for snap_scaffold_3-snap.1916-T1
Valid prediction for Augustus_model.g4625.t1
Valid prediction for Augustus_model.g4627.t1
Couldn't classify 203866, 204042
Couldn't classify 204684, 204707
Sorry, prediction pasa_asmbl_39714.p1 fails validation.
(GCC)	 TG	203866-204042	GT	CGG
(TTG)	 AG	204333-204458	GT	AGG
(ATT)	 AG	204684-204707	TC	GGT
-recovered pasa_asmbl_39714.p1, internal, 204333, 204458
Valid prediction for snap_scaffold_3-snap.1933-T1
Couldn't classify 164145, 164567
Couldn't classify 166282, 166701
Sorry, prediction pasa_asmbl_39066.p1 fails validation.
(GCC)	 GG	164145-164567	GT	AAG
(GTG)	 AG	165434-165582	GT	AGG
(GAA)	 AG	165917-166157	GT	AGG
(GCC)	 AG	166282-166701	CA	AGC
-recovered pasa_asmbl_39066.p1, internal, 165434, 165582
-recovered pasa_asmbl_39066.p1, internal, 165917, 166157
Valid prediction for Augustus_model.g4626.t1
Valid prediction for GlimmerHMM_glimmerT_7109-T1
Valid prediction for snap_scaffold_3-snap.1907-T1
Valid prediction for snap_scaffold_3-snap.1936-T1
Couldn't classify 225859, 225971
Sorry, prediction pasa_asmbl_39062.p1 fails validation.
(ATG)	 TC	221568-221829	GT	AGG
(GCA)	 AG	223536-225608	GT	AGG
(GCA)	 AG	225859-225971	GG	ACG
-recovered pasa_asmbl_39062.p1, initial, 221568, 221829
-recovered pasa_asmbl_39062.p1, internal, 223536, 225608
Valid prediction for GlimmerHMM_glimmerT_7102-T1
Valid prediction for snap_scaffold_3-snap.1920-T1
Valid prediction for GlimmerHMM_glimmerT_7089-T1
Couldn't classify 205673, 206962
Sorry, prediction pasa_asmbl_39063.p1 fails validation.
(GAT)	 CC	205673-206962	GG	GAG
Couldn't classify 46292, 46638
Sorry, prediction pasa_asmbl_39069.p1 fails validation.
(ATG)	 CT	45059-45193	GT	AGG
(AAG)	 AG	45759-46086	GT	AGG
(ATG)	 AG	46292-46638	TC	ACT
-recovered pasa_asmbl_39069.p1, initial, 45059, 45193
-recovered pasa_asmbl_39069.p1, internal, 45759, 46086
Valid prediction for snap_scaffold_3-snap.1903-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for HiQ_model.g4637.t1
Valid prediction for snap_scaffold_3-snap.1932-T1
Valid prediction for GlimmerHMM_glimmerT_7110-T1
Valid prediction for snap_scaffold_3-snap.1892-T1
Valid prediction for snap_scaffold_3-snap.1931-T1
Valid prediction for snap_scaffold_3-snap.1922-T1
Valid prediction for snap_scaffold_3-snap.1926-T1
Valid prediction for GlimmerHMM_glimmerT_7097-T1
Valid prediction for snap_scaffold_3-snap.1935-T1
Valid prediction for snap_scaffold_3-snap.1897-T1
Valid prediction for snap_scaffold_3-snap.1899-T1
Valid prediction for GlimmerHMM_glimmerT_7103-T1
Valid prediction for snap_scaffold_3-snap.1895-T1
Valid prediction for snap_scaffold_3-snap.1901-T1
Valid prediction for Augustus_model.g4622.t1
Valid prediction for snap_scaffold_3-snap.1924-T1
Sorry, intron length (7) is less than minimum required (10)
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g4621.t1
Valid prediction for snap_scaffold_3-snap.1911-T1
Valid prediction for Augustus_model.g4620.t1
Valid prediction for snap_scaffold_3-snap.1917-T1
Couldn't classify 135237, 135512
Couldn't classify 140281, 140298
Sorry, prediction pasa_asmbl_39716.p1 fails validation.
(AAC)	 AG	135237-135512	GT	AGG
(GAC)	 AG	137484-137579	GT	AGG
(CTG)	 AG	140281-140298	CA	AGC
-recovered pasa_asmbl_39716.p1, internal, 135237, 135512
-recovered pasa_asmbl_39716.p1, internal, 137484, 137579
Valid prediction for snap_scaffold_3-snap.1928-T1
Valid prediction for snap_scaffold_3-snap.1930-T1
Valid prediction for Augustus_model.g4632.t1
Valid prediction for snap_scaffold_3-snap.1898-T1
Valid prediction for Augustus_model.g4639.t1
Valid prediction for Augustus_model.g4633.t1
Valid prediction for snap_scaffold_3-snap.1918-T1
Valid prediction for GlimmerHMM_glimmerT_7090-T1
Valid prediction for GlimmerHMM_glimmerT_7098-T1
Valid prediction for snap_scaffold_3-snap.1910-T1
Valid prediction for snap_scaffold_3-snap.1893-T1
Valid prediction for snap_scaffold_3-snap.1900-T1
Valid prediction for Augustus_model.g4628.t1
Couldn't classify 226182, 226224
Couldn't classify 227706, 227794
Sorry, prediction pasa_asmbl_39683.p1 fails validation.
(CCC)	 GT	226182-226224	GT	GGG
(CCA)	 AG	226425-226528	GT	TGG
(CTT)	 AG	226650-226705	GT	AGG
(AGA)	 AG	226834-226994	GT	CGG
(AGG)	 AG	227227-227361	GT	AGG
(AAT)	 AG	227485-227565	GT	CTG
(TTT)	 AG	227706-227794	TA	AGT
-recovered pasa_asmbl_39683.p1, terminal, 227227, 227361
-recovered pasa_asmbl_39683.p1, internal, 226425, 226528
-recovered pasa_asmbl_39683.p1, internal, 226650, 226705
-recovered pasa_asmbl_39683.p1, internal, 226834, 226994
-recovered pasa_asmbl_39683.p1, internal, 227227, 227361
-recovered pasa_asmbl_39683.p1, internal, 227485, 227565

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 13588, rend_intergenic: 9586  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45186, rend_intergenic: 40603  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66466, rend_intergenic: 54067  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90111, rend_intergenic: 80121  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115471, rend_intergenic: 90687  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132881, rend_intergenic: 115567  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136516, rend_intergenic: 133304  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149975, rend_intergenic: 138462  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151234, rend_intergenic: 150920  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157440, rend_intergenic: 152778  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158811, rend_intergenic: 157743  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171314, rend_intergenic: 169016  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180014, rend_intergenic: 178365  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181268, rend_intergenic: 180766  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185726, rend_intergenic: 182160  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 236454
-exon list size: 483


building trellis

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-found 38 predictions from path traversal
Error with prediction: snap lend_intergenic: 13588, rend_intergenic: 9586  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45186, rend_intergenic: 40603  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66466, rend_intergenic: 54067  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90111, rend_intergenic: 80121  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115471, rend_intergenic: 90687  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132881, rend_intergenic: 115567  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136516, rend_intergenic: 133304  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 149975, rend_intergenic: 138462  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151234, rend_intergenic: 150920  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157440, rend_intergenic: 152778  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158811, rend_intergenic: 157743  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171314, rend_intergenic: 169016  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180014, rend_intergenic: 178365  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181268, rend_intergenic: 180766  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185726, rend_intergenic: 182160  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 28 predictions persist after filtering for low support