-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_17/scaffold_17_9386522-9614161

-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_40848-T1
Couldn't classify 102103, 102307
Sorry, prediction pasa_asmbl_19094.p1 fails validation.
(CTC)	 GT	102103-102307	GT	TGG
(CAT)	 AG	102493-102563	GT	TGG
(GTG)	 AG	102860-103084	TG	AGT
-recovered pasa_asmbl_19094.p1, terminal, 102860, 103084
-recovered pasa_asmbl_19094.p1, internal, 102493, 102563
Valid prediction for snap_scaffold_17-snap.1854-T1
Valid prediction for snap_scaffold_17-snap.1877-T1
Valid prediction for pasa_asmbl_19119.p1
Valid prediction for GlimmerHMM_glimmerT_40834-T1
Valid prediction for CodingQuarry_transcript_22118-T1
Valid prediction for snap_scaffold_17-snap.1880-T1
Valid prediction for snap_scaffold_17-snap.1882-T1
Valid prediction for snap_scaffold_17-snap.1871-T1
Valid prediction for GlimmerHMM_glimmerT_40837-T1
Valid prediction for Augustus_model.g27246.t1
Valid prediction for CodingQuarry_transcript_22120-T1
Valid prediction for GlimmerHMM_glimmerT_40846-T1
Valid prediction for Augustus_model.g27263.t1
Valid prediction for snap_scaffold_17-snap.1873-T1
Couldn't classify 107437, 107507
Sorry, prediction pasa_asmbl_19098.p1 fails validation.
(ATG)	 TA	105208-105424	GT	AGG
(GGC)	 AG	105632-105827	GT	AGG
(AAG)	 AG	106038-106203	GT	GAG
(GGT)	 AG	106313-106391	GT	GGG
(AGC)	 AG	106493-106594	GT	AGG
(ACT)	 AG	106742-106872	GT	GGG
(GGT)	 AG	107145-107250	GT	TGG
(CAT)	 AG	107437-107507	GT	TGG
-recovered pasa_asmbl_19098.p1, initial, 105208, 105424
-recovered pasa_asmbl_19098.p1, internal, 105632, 105827
-recovered pasa_asmbl_19098.p1, internal, 106038, 106203
-recovered pasa_asmbl_19098.p1, internal, 106313, 106391
-recovered pasa_asmbl_19098.p1, internal, 106493, 106594
-recovered pasa_asmbl_19098.p1, internal, 106742, 106872
-recovered pasa_asmbl_19098.p1, internal, 107145, 107250
-recovered pasa_asmbl_19098.p1, internal, 107437, 107507
Valid prediction for Augustus_model.g27250.t1
Valid prediction for GlimmerHMM_glimmerT_40839-T1
Valid prediction for snap_scaffold_17-snap.1862-T1
Valid prediction for snap_scaffold_17-snap.1851-T1
Valid prediction for snap_scaffold_17-snap.1860-T1
Valid prediction for GlimmerHMM_glimmerT_40849-T1
Valid prediction for GlimmerHMM_glimmerT_40841-T1
Valid prediction for GlimmerHMM_glimmerT_40853-T1
Valid prediction for snap_scaffold_17-snap.1887-T1
Valid prediction for CodingQuarry_transcript_22123-T1
Valid prediction for CodingQuarry_transcript_22124-T1
Couldn't classify 177155, 177449
Sorry, prediction pasa_asmbl_19112.p1 fails validation.
(TCG)	 TT	177155-177449	GT	AGG
(GTT)	 AG	179374-179578	GT	AGG
(GAC)	 AG	179893-180072	GT	CGG
(GAG)	 AG	180188-180305	GT	GGG
(GTG)	 AG	180658-180852	GT	AGG
(TCT)	 AG	180996-181127	GT	AGG
(CTG)	 AG	181260-181361	GT	AGG
(CAC)	 AG	181511-181651	GT	AGG
(CTG)	 AG	182098-182268	GT	GAG
-recovered pasa_asmbl_19112.p1, terminal, 182098, 182268
-recovered pasa_asmbl_19112.p1, internal, 179374, 179578
-recovered pasa_asmbl_19112.p1, internal, 179893, 180072
-recovered pasa_asmbl_19112.p1, internal, 180188, 180305
-recovered pasa_asmbl_19112.p1, internal, 180658, 180852
-recovered pasa_asmbl_19112.p1, internal, 180996, 181127
-recovered pasa_asmbl_19112.p1, internal, 181260, 181361
-recovered pasa_asmbl_19112.p1, internal, 181511, 181651
-recovered pasa_asmbl_19112.p1, internal, 182098, 182268
Valid prediction for GlimmerHMM_glimmerT_40852-T1
Valid prediction for pasa_asmbl_19083.p1
Valid prediction for HiQ_model.g27254.t1
Valid prediction for Augustus_model.g27253.t1
Valid prediction for snap_scaffold_17-snap.1868-T1
Valid prediction for Augustus_model.g27241.t1
Valid prediction for GlimmerHMM_glimmerT_40847-T1
Valid prediction for snap_scaffold_17-snap.1864-T1
Valid prediction for Augustus_model.g27262.t1
Valid prediction for CodingQuarry_transcript_22121-T1
Valid prediction for CodingQuarry_transcript_22122-T1
Valid prediction for snap_scaffold_17-snap.1883-T1
Valid prediction for GlimmerHMM_glimmerT_40851-T1
Valid prediction for Augustus_model.g27248.t1
Valid prediction for pasa_asmbl_19104.p2
Couldn't classify 89775, 89822
Sorry, prediction pasa_asmbl_19090.p1 fails validation.
(AAG)	 TC	89775-89822	GT	AGG
(GCA)	 AG	90399-90543	GT	AAG
(ACC)	 AG	90680-90806	GT	AGG
(GTT)	 AG	91140-91262	GT	AAG
(GAA)	 AG	91615-91711	CC	GAC
-recovered pasa_asmbl_19090.p1, terminal, 91615, 91711
-recovered pasa_asmbl_19090.p1, internal, 90399, 90543
-recovered pasa_asmbl_19090.p1, internal, 90680, 90806
-recovered pasa_asmbl_19090.p1, internal, 91140, 91262
Couldn't classify 36604, 36744
Couldn't classify 37395, 37588
Sorry, prediction pasa_asmbl_19079.p1 fails validation.
(CGC)	 CC	36604-36744	GT	TGG
(GGT)	 AG	36900-37070	GT	GGG
(GAG)	 AG	37242-37314	GT	AGG
(GGA)	 AG	37395-37588	GG	AGG
-recovered pasa_asmbl_19079.p1, internal, 36900, 37070
-recovered pasa_asmbl_19079.p1, internal, 37242, 37314
Valid prediction for snap_scaffold_17-snap.1865-T1
Valid prediction for Augustus_model.g27258.t1
Valid prediction for CodingQuarry_transcript_22128-T1
Valid prediction for snap_scaffold_17-snap.1878-T1
Valid prediction for Augustus_model.g27256.t1
Valid prediction for GlimmerHMM_glimmerT_40831-T1
Valid prediction for pasa_asmbl_19101.p1
Valid prediction for snap_scaffold_17-snap.1857-T1
Valid prediction for Augustus_model.g27244.t1
Valid prediction for snap_scaffold_17-snap.1870-T1
Valid prediction for GlimmerHMM_glimmerT_40843-T1
Couldn't classify 88557, 88711
Sorry, prediction pasa_asmbl_19089.p1 fails validation.
(ATG)	 TT	87840-87866	GT	CAG
(GAC)	 AG	87977-88108	GT	AGG
(GTA)	 AG	88271-88364	GT	AGG
(GTT)	 AG	88557-88711	CC	AGC
-recovered pasa_asmbl_19089.p1, initial, 87840, 87866
-recovered pasa_asmbl_19089.p1, internal, 87977, 88108
-recovered pasa_asmbl_19089.p1, internal, 88271, 88364
Valid prediction for HiQ_model.g27255.t1
Valid prediction for GlimmerHMM_glimmerT_40856-T1
Valid prediction for CodingQuarry_transcript_22125-T1
Valid prediction for HiQ_model.g27259.t1
Valid prediction for snap_scaffold_17-snap.1853-T1
Valid prediction for CodingQuarry_transcript_22127-T1
Valid prediction for Augustus_model.g27247.t1
Valid prediction for GlimmerHMM_glimmerT_40840-T1
Valid prediction for snap_scaffold_17-snap.1855-T1
Valid prediction for pasa_asmbl_19093.p1
Valid prediction for pasa_asmbl_19102.p1
Valid prediction for snap_scaffold_17-snap.1885-T1
Valid prediction for CodingQuarry_transcript_22129-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 Augustus_model.g27260.t1
Valid prediction for GlimmerHMM_glimmerT_40832-T1
Valid prediction for HiQ_model.g27261.t1
Valid prediction for snap_scaffold_17-snap.1872-T1
Valid prediction for Augustus_model.g27242.t1
Valid prediction for snap_scaffold_17-snap.1884-T1
Valid prediction for Augustus_model.g27251.t1
Valid prediction for GlimmerHMM_glimmerT_40838-T1
Valid prediction for snap_scaffold_17-snap.1888-T1
Valid prediction for GlimmerHMM_glimmerT_40844-T1
Valid prediction for Augustus_model.g27243.t1
Valid prediction for snap_scaffold_17-snap.1889-T1
Valid prediction for snap_scaffold_17-snap.1879-T1
Valid prediction for snap_scaffold_17-snap.1886-T1
Valid prediction for snap_scaffold_17-snap.1875-T1
Valid prediction for snap_scaffold_17-snap.1881-T1
Valid prediction for Augustus_model.g27239.t1
Valid prediction for snap_scaffold_17-snap.1876-T1
Valid prediction for GlimmerHMM_glimmerT_40833-T1
Valid prediction for GlimmerHMM_glimmerT_40850-T1
Couldn't classify 200641, 200728
Couldn't classify 202468, 202561
Sorry, prediction pasa_asmbl_18175.p1 fails validation.
(GGT)	 GA	200641-200728	GT	CGG
(TGG)	 AG	201656-201816	GT	AGG
(ATC)	 AG	201978-202087	GT	AAG
(GAA)	 AG	202468-202561	GT	CCG
-recovered pasa_asmbl_18175.p1, internal, 201656, 201816
-recovered pasa_asmbl_18175.p1, internal, 201978, 202087
-recovered pasa_asmbl_18175.p1, internal, 202468, 202561
Valid prediction for Augustus_model.g27249.t1
Couldn't classify 154428, 156764
Sorry, prediction pasa_asmbl_18178.p1 fails validation.
(GTG)	 CG	154428-156764	AA	AGA
Valid prediction for snap_scaffold_17-snap.1861-T1
Valid prediction for snap_scaffold_17-snap.1856-T1
Valid prediction for snap_scaffold_17-snap.1866-T1
Valid prediction for snap_scaffold_17-snap.1859-T1
Couldn't classify 216446, 216604
Sorry, prediction pasa_asmbl_18174.p1 fails validation.
(AGG)	 CC	216446-216604	GT	AGG
(GAC)	 AG	216877-217035	GG	AGG
-recovered pasa_asmbl_18174.p1, terminal, 216877, 217035
Valid prediction for CodingQuarry_transcript_22131-T1
Valid prediction for Augustus_model.g27252.t1
Valid prediction for Augustus_model.g27245.t1
Valid prediction for snap_scaffold_17-snap.1863-T1
Valid prediction for GlimmerHMM_glimmerT_40842-T1
Valid prediction for CodingQuarry_transcript_22126-T1
Valid prediction for Augustus_model.g27240.t1
Valid prediction for GlimmerHMM_glimmerT_40855-T1
Valid prediction for HiQ_model.g27238.t1
Valid prediction for GlimmerHMM_glimmerT_40835-T1
Valid prediction for GlimmerHMM_glimmerT_40854-T1
Valid prediction for pasa_asmbl_18180.p2
Valid prediction for pasa_asmbl_18179.p1
Valid prediction for HiQ_model.g27257.t1
Valid prediction for snap_scaffold_17-snap.1869-T1
Valid prediction for GlimmerHMM_glimmerT_40836-T1
Couldn't classify 180653, 180725
Sorry, prediction pasa_asmbl_18177.p1 fails validation.
(AGC)	 GC	180653-180725	GT	AGG
(GCA)	 AG	181562-181731	GT	AGG
(AAT)	 AG	181970-182146	GG	AGG
-recovered pasa_asmbl_18177.p1, terminal, 181970, 182146
-recovered pasa_asmbl_18177.p1, internal, 181562, 181731
Valid prediction for snap_scaffold_17-snap.1874-T1
Valid prediction for GlimmerHMM_glimmerT_40845-T1
Valid prediction for snap_scaffold_17-snap.1852-T1
Valid prediction for pasa_asmbl_18181.p1
Valid prediction for snap_scaffold_17-snap.1867-T1
Valid prediction for snap_scaffold_17-snap.1858-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 25971, rend_intergenic: 11152  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41400, rend_intergenic: 28725  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53663, rend_intergenic: 45495  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66798, rend_intergenic: 58513  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69441, rend_intergenic: 67342  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79002, rend_intergenic: 74620  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91830, rend_intergenic: 82061  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97538, rend_intergenic: 95073  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118844, rend_intergenic: 115422  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147538, rend_intergenic: 144869  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188899, rend_intergenic: 188269  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 202377, rend_intergenic: 190958  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 226630, rend_intergenic: 212993  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 227640
-exon list size: 509


building trellis

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-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 25971, rend_intergenic: 11152  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41400, rend_intergenic: 28725  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53663, rend_intergenic: 45495  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66798, rend_intergenic: 58513  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69441, rend_intergenic: 67342  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79002, rend_intergenic: 74620  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91830, rend_intergenic: 82061  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97538, rend_intergenic: 95073  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118844, rend_intergenic: 115422  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 147538, rend_intergenic: 144869  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188899, rend_intergenic: 188269  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 202377, rend_intergenic: 190958  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 226630, rend_intergenic: 212993  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 26 predictions persist after filtering for low support