-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_23/scaffold_23_7130677-7334280

-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 snap_scaffold_23-snap.1329-T1
Valid prediction for HiQ_model.g34293.t1
Valid prediction for snap_scaffold_23-snap.1297-T1
Valid prediction for GlimmerHMM_glimmerT_51261-T1
Valid prediction for pasa_asmbl_31683.p1
Valid prediction for GlimmerHMM_glimmerT_51262-T1
Couldn't classify 16035, 16127
Couldn't classify 18968, 19022
Sorry, prediction pasa_asmbl_31676.p1 fails validation.
(CTG)	 AC	16035-16127	GT	AGG
(GAC)	 AG	16234-16392	GT	CTG
(GTG)	 AG	18563-18660	GT	AGG
(AGA)	 AG	18968-19022	GT	AGG
-recovered pasa_asmbl_31676.p1, internal, 16234, 16392
-recovered pasa_asmbl_31676.p1, internal, 18563, 18660
-recovered pasa_asmbl_31676.p1, internal, 18968, 19022
Valid prediction for Augustus_model.g34288.t1
Valid prediction for snap_scaffold_23-snap.1320-T1
Valid prediction for snap_scaffold_23-snap.1312-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for snap_scaffold_23-snap.1307-T1
Valid prediction for Augustus_model.g34289.t1
Valid prediction for snap_scaffold_23-snap.1344-T1
Valid prediction for snap_scaffold_23-snap.1332-T1
Valid prediction for GlimmerHMM_glimmerT_51257-T1
Valid prediction for Augustus_model.g34287.t1
Valid prediction for snap_scaffold_23-snap.1338-T1
Valid prediction for GlimmerHMM_glimmerT_51272-T1
Valid prediction for snap_scaffold_23-snap.1314-T1
Valid prediction for GlimmerHMM_glimmerT_51271-T1
Couldn't classify 201281, 201775
Sorry, prediction pasa_asmbl_31687.p2 fails validation.
(GTG)	 TT	201281-201775	TG	GAT
Valid prediction for pasa_asmbl_31685.p1
Valid prediction for snap_scaffold_23-snap.1324-T1
Valid prediction for Augustus_model.g34303.t1
Couldn't classify 33276, 33504
Couldn't classify 41218, 41428
Sorry, prediction pasa_asmbl_31678.p1 fails validation.
(CAG)	 TG	33276-33504	GT	AGG
(AAC)	 AG	36414-36498	GT	TGG
(CAC)	 AG	38381-38478	GT	GGG
(GTA)	 AG	38851-38989	GT	CGG
(GAT)	 AG	41218-41428	GA	GGG
-recovered pasa_asmbl_31678.p1, internal, 36414, 36498
-recovered pasa_asmbl_31678.p1, internal, 38381, 38478
-recovered pasa_asmbl_31678.p1, internal, 38851, 38989
Valid prediction for GlimmerHMM_glimmerT_51253-T1
Valid prediction for HiQ_model.g34297.t1
Valid prediction for Augustus_model.g34292.t1
Valid prediction for GlimmerHMM_glimmerT_51255-T1
Valid prediction for snap_scaffold_23-snap.1313-T1
Valid prediction for snap_scaffold_23-snap.1331-T1
Valid prediction for Augustus_model.g34290.t1
Couldn't classify 6697, 6771
Couldn't classify 10504, 10549
Sorry, prediction pasa_asmbl_31675.p1 fails validation.
(AAT)	 GG	6697-6771	GT	GGG
(TTG)	 AG	7080-7154	GT	AGG
(CTG)	 AG	9423-9518	GT	AGG
(GAC)	 AG	10057-10217	GT	AGG
(CCT)	 AG	10504-10549	CT	AGC
-recovered pasa_asmbl_31675.p1, internal, 7080, 7154
-recovered pasa_asmbl_31675.p1, internal, 9423, 9518
-recovered pasa_asmbl_31675.p1, internal, 10057, 10217
Valid prediction for GlimmerHMM_glimmerT_51263-T1
Valid prediction for GlimmerHMM_glimmerT_51256-T1
Valid prediction for snap_scaffold_23-snap.1309-T1
Valid prediction for CodingQuarry_transcript_35712-T1
Valid prediction for snap_scaffold_23-snap.1343-T1
Valid prediction for snap_scaffold_23-snap.1319-T1
Valid prediction for snap_scaffold_23-snap.1295-T1
Valid prediction for snap_scaffold_23-snap.1330-T1
Valid prediction for GlimmerHMM_glimmerT_51265-T1
Valid prediction for GlimmerHMM_glimmerT_51280-T1
Valid prediction for CodingQuarry_transcript_35711-T1
Valid prediction for Augustus_model.g34291.t1
Valid prediction for GlimmerHMM_glimmerT_51274-T1
Valid prediction for GlimmerHMM_glimmerT_51254-T1
Couldn't classify 19744, 19854
Couldn't classify 26933, 27036
Sorry, prediction pasa_asmbl_31677.p1 fails validation.
(GAG)	 CA	19744-19854	GT	CTG
(GTG)	 AG	19987-20163	GT	AGG
(ACT)	 AG	20442-20628	GT	AGG
(ACC)	 AG	21611-21741	GT	CGG
(GTG)	 AG	21834-22008	GT	AGG
(AGT)	 AG	22250-22424	GT	AGG
(TGA)	 AG	24116-24257	GT	AGG
(GTG)	 AG	26485-26533	GT	CTG
(TCT)	 AG	26933-27036	GT	AGG
-recovered pasa_asmbl_31677.p1, internal, 19987, 20163
-recovered pasa_asmbl_31677.p1, internal, 20442, 20628
-recovered pasa_asmbl_31677.p1, internal, 21611, 21741
-recovered pasa_asmbl_31677.p1, internal, 21834, 22008
-recovered pasa_asmbl_31677.p1, internal, 22250, 22424
-recovered pasa_asmbl_31677.p1, internal, 24116, 24257
-recovered pasa_asmbl_31677.p1, internal, 26485, 26533
-recovered pasa_asmbl_31677.p1, internal, 26933, 27036
Valid prediction for snap_scaffold_23-snap.1333-T1
Valid prediction for snap_scaffold_23-snap.1315-T1
Valid prediction for snap_scaffold_23-snap.1323-T1
Valid prediction for Augustus_model.g34299.t1
Valid prediction for snap_scaffold_23-snap.1302-T1
Valid prediction for GlimmerHMM_glimmerT_51267-T1
Valid prediction for GlimmerHMM_glimmerT_51276-T1
Valid prediction for snap_scaffold_23-snap.1310-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 snap_scaffold_23-snap.1337-T1
Valid prediction for GlimmerHMM_glimmerT_51269-T1
Valid prediction for GlimmerHMM_glimmerT_51258-T1
Valid prediction for GlimmerHMM_glimmerT_51275-T1
Valid prediction for Augustus_model.g34301.t1
Valid prediction for snap_scaffold_23-snap.1321-T1
Valid prediction for GlimmerHMM_glimmerT_51260-T1
Valid prediction for snap_scaffold_23-snap.1340-T1
Valid prediction for CodingQuarry_transcript_35714-T1
Valid prediction for snap_scaffold_23-snap.1311-T1
Valid prediction for snap_scaffold_23-snap.1303-T1
Valid prediction for GlimmerHMM_glimmerT_51264-T1
Valid prediction for HiQ_model.g34298.t1
Valid prediction for snap_scaffold_23-snap.1299-T1
Valid prediction for snap_scaffold_23-snap.1298-T1
Valid prediction for snap_scaffold_23-snap.1296-T1
Valid prediction for snap_scaffold_23-snap.1335-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_23-snap.1304-T1
Couldn't classify 87819, 87842
Couldn't classify 89153, 89278
Sorry, prediction pasa_asmbl_31228.p1 fails validation.
(GCC)	 CT	87819-87842	GT	ATG
(AGT)	 AG	88130-88297	GT	AGG
(ACG)	 AG	89153-89278	GA	GGG
-recovered pasa_asmbl_31228.p1, internal, 88130, 88297
Valid prediction for GlimmerHMM_glimmerT_51279-T1
Valid prediction for snap_scaffold_23-snap.1308-T1
Valid prediction for snap_scaffold_23-snap.1336-T1
Valid prediction for HiQ_model.g34302.t1
Valid prediction for snap_scaffold_23-snap.1317-T1
Valid prediction for snap_scaffold_23-snap.1328-T1
Valid prediction for snap_scaffold_23-snap.1326-T1
Valid prediction for snap_scaffold_23-snap.1305-T1
Valid prediction for snap_scaffold_23-snap.1327-T1
Valid prediction for snap_scaffold_23-snap.1322-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_51273-T1
Valid prediction for CodingQuarry_transcript_35716-T1
Valid prediction for snap_scaffold_23-snap.1325-T1
Valid prediction for pasa_asmbl_31026.p1
Valid prediction for snap_scaffold_23-snap.1301-T1
Valid prediction for GlimmerHMM_glimmerT_51277-T1
Valid prediction for snap_scaffold_23-snap.1339-T1
Valid prediction for Augustus_model.g34296.t1
Couldn't classify 13108, 13671
Sorry, prediction pasa_asmbl_31028.p1 fails validation.
(TTC)	 AC	13108-13671	TG	GAT
Valid prediction for GlimmerHMM_glimmerT_51259-T1
Valid prediction for pasa_asmbl_31029.p1
Valid prediction for snap_scaffold_23-snap.1306-T1
Valid prediction for Augustus_model.g34295.t1
Valid prediction for GlimmerHMM_glimmerT_51266-T1
Valid prediction for snap_scaffold_23-snap.1294-T1
Valid prediction for GlimmerHMM_glimmerT_51268-T1
Couldn't classify 74419, 74577
Couldn't classify 78059, 78109
Sorry, prediction pasa_asmbl_31020.p1 fails validation.
(TCT)	 TC	74419-74577	GT	AGG
(GAA)	 AG	75068-75156	GT	GGG
(GAA)	 AG	75274-75328	GT	AGG
(GCG)	 AG	78059-78109	GG	CAG
-recovered pasa_asmbl_31020.p1, internal, 75068, 75156
-recovered pasa_asmbl_31020.p1, internal, 75274, 75328
Valid prediction for snap_scaffold_23-snap.1316-T1
Valid prediction for snap_scaffold_23-snap.1341-T1
Valid prediction for snap_scaffold_23-snap.1342-T1
Valid prediction for Augustus_model.g34294.t1
Valid prediction for GlimmerHMM_glimmerT_51270-T1
Valid prediction for CodingQuarry_transcript_35713-T1
Valid prediction for snap_scaffold_23-snap.1300-T1
Valid prediction for CodingQuarry_transcript_35717-T1
Valid prediction for snap_scaffold_23-snap.1318-T1
Valid prediction for snap_scaffold_23-snap.1334-T1
Valid prediction for Augustus_model.g34300.t1
Valid prediction for GlimmerHMM_glimmerT_51278-T1
Valid prediction for CodingQuarry_transcript_35715-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 10145, rend_intergenic: 5739  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 10770, rend_intergenic: 10173  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14641, rend_intergenic: 14248  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33509, rend_intergenic: 15114  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36973, rend_intergenic: 35342  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46474, rend_intergenic: 36999  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67125, rend_intergenic: 64251  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85201, rend_intergenic: 82022  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107379, rend_intergenic: 100975  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118161, rend_intergenic: 112885  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126954, rend_intergenic: 118193  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134620, rend_intergenic: 128222  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141518, rend_intergenic: 134950  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160281, rend_intergenic: 157687  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173573, rend_intergenic: 169413  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185716, rend_intergenic: 182021  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199211, rend_intergenic: 197630  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 135897, rend_intergenic: 135894  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 203604
-exon list size: 402


building trellis

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-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 10145, rend_intergenic: 5739  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 10770, rend_intergenic: 10173  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14641, rend_intergenic: 14248  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33509, rend_intergenic: 15114  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36973, rend_intergenic: 35342  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46474, rend_intergenic: 36999  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67125, rend_intergenic: 64251  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85201, rend_intergenic: 82022  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107379, rend_intergenic: 100975  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118161, rend_intergenic: 112885  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126954, rend_intergenic: 118193  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134620, rend_intergenic: 128222  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 141518, rend_intergenic: 134950  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 160281, rend_intergenic: 157687  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173573, rend_intergenic: 169413  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 185716, rend_intergenic: 182021  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199211, rend_intergenic: 197630  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 135897, rend_intergenic: 135894  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