-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_6/scaffold_6_4136317-4326500

-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: +)Couldn't classify 173081, 173097
Sorry, prediction pasa_asmbl_46875.p1 fails validation.
(GAA)	 TT	173081-173097	GT	AGG
(CAT)	 AG	173574-173680	GT	CCG
(GCC)	 AG	173867-173989	GT	TGG
(GTA)	 AG	174218-174338	GT	ATG
(GTA)	 AG	174685-174795	GT	TCG
(CGA)	 AG	175175-175301	GG	GAG
-recovered pasa_asmbl_46875.p1, terminal, 175175, 175301
-recovered pasa_asmbl_46875.p1, internal, 173574, 173680
-recovered pasa_asmbl_46875.p1, internal, 173867, 173989
-recovered pasa_asmbl_46875.p1, internal, 174218, 174338
-recovered pasa_asmbl_46875.p1, internal, 174685, 174795
Valid prediction for GlimmerHMM_glimmerT_14469-T1
Valid prediction for snap_scaffold_6-snap.1015-T1
Valid prediction for snap_scaffold_6-snap.989-T1
Valid prediction for snap_scaffold_6-snap.1014-T1
Valid prediction for GlimmerHMM_glimmerT_14464-T1
Valid prediction for snap_scaffold_6-snap.1018-T1
Valid prediction for HiQ_model.g9584.t1
Valid prediction for snap_scaffold_6-snap.990-T1
Valid prediction for GlimmerHMM_glimmerT_14467-T1
Valid prediction for snap_scaffold_6-snap.1004-T1
Valid prediction for HiQ_model.g9583.t1
Valid prediction for GlimmerHMM_glimmerT_14481-T1
Valid prediction for snap_scaffold_6-snap.992-T1
Valid prediction for snap_scaffold_6-snap.996-T1
Valid prediction for GlimmerHMM_glimmerT_14460-T1
Valid prediction for GlimmerHMM_glimmerT_14474-T1
Valid prediction for GlimmerHMM_glimmerT_14461-T1
Valid prediction for Augustus_model.g9569.t1
Valid prediction for snap_scaffold_6-snap.1016-T1
Valid prediction for snap_scaffold_6-snap.991-T1
Valid prediction for snap_scaffold_6-snap.981-T1
Valid prediction for GlimmerHMM_glimmerT_14479-T1
Valid prediction for Augustus_model.g9577.t1
Valid prediction for snap_scaffold_6-snap.1002-T1
Valid prediction for snap_scaffold_6-snap.1012-T1
Valid prediction for snap_scaffold_6-snap.1000-T1
Valid prediction for GlimmerHMM_glimmerT_14463-T1
Valid prediction for snap_scaffold_6-snap.1009-T1
Couldn't classify 181540, 181745
Sorry, prediction pasa_asmbl_46882.p1 fails validation.
(CTG)	 GT	181540-181745	GT	AGG
(ATC)	 AG	181993-182137	GT	AGG
(GAA)	 AG	182223-182338	GT	AGG
(GTG)	 AG	182461-182553	GT	AAG
(GTA)	 AG	182679-183156	GC	AGG
-recovered pasa_asmbl_46882.p1, terminal, 182679, 183156
-recovered pasa_asmbl_46882.p1, internal, 181993, 182137
-recovered pasa_asmbl_46882.p1, internal, 182223, 182338
-recovered pasa_asmbl_46882.p1, internal, 182461, 182553
-recovered pasa_asmbl_46882.p1, internal, 182679, 183156
Valid prediction for GlimmerHMM_glimmerT_14456-T1
Valid prediction for CodingQuarry_transcript_55012-T1
Valid prediction for snap_scaffold_6-snap.984-T1
Valid prediction for snap_scaffold_6-snap.999-T1
Valid prediction for snap_scaffold_6-snap.986-T1
Valid prediction for GlimmerHMM_glimmerT_14472-T1
Valid prediction for GlimmerHMM_glimmerT_14480-T1
Valid prediction for snap_scaffold_6-snap.987-T1
Valid prediction for CodingQuarry_transcript_55011-T1
Valid prediction for GlimmerHMM_glimmerT_14452-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_6-snap.1011-T1
Valid prediction for Augustus_model.g9575.t1
Valid prediction for snap_scaffold_6-snap.1013-T1
Valid prediction for snap_scaffold_6-snap.980-T1
Valid prediction for GlimmerHMM_glimmerT_14476-T1
Valid prediction for snap_scaffold_6-snap.1001-T1
Valid prediction for GlimmerHMM_glimmerT_14449-T1
Valid prediction for GlimmerHMM_glimmerT_14455-T1
Couldn't classify 145834, 146283
Sorry, prediction pasa_asmbl_48294.p1 fails validation.
(CCA)	 AC	145834-146283	CA	AGC
Valid prediction for GlimmerHMM_glimmerT_14451-T1
Valid prediction for GlimmerHMM_glimmerT_14450-T1
Valid prediction for GlimmerHMM_glimmerT_14475-T1
Valid prediction for GlimmerHMM_glimmerT_14468-T1
Valid prediction for CodingQuarry_transcript_55006-T1
Couldn't classify 36689, 36804
Couldn't classify 39153, 39307
Sorry, prediction CodingQuarry_transcript_55009-T1 fails validation.
(ATG)	 AG	29661-29720	GT	GGG
(GGC)	 AG	31113-31232	GT	AGG
(ACC)	 AG	31448-31570	GT	AGG
(AAG)	 AG	31852-31988	GT	AGG
(TAA)	 AG	32730-32797	GT	AGG
(CCC)	 AG	34068-34228	GT	AGG
(ATG)	 AG	36339-36419	GT	AGG
(GTG)	 AG	36516-36574	GT	AGG
(GAT)	 AG	36689-36804	CA	GAC
(TAG)	 TA	39153-39307	GT	AGG
(GTT)	 AG	39466-39561	GT	CTG
(GAG)	 AG	39664-39948	AG	AAA
-recovered CodingQuarry_transcript_55009-T1, initial, 29661, 29720
-recovered CodingQuarry_transcript_55009-T1, initial, 36339, 36419
-recovered CodingQuarry_transcript_55009-T1, terminal, 39664, 39948
-recovered CodingQuarry_transcript_55009-T1, internal, 29661, 29720
-recovered CodingQuarry_transcript_55009-T1, internal, 31113, 31232
-recovered CodingQuarry_transcript_55009-T1, internal, 31448, 31570
-recovered CodingQuarry_transcript_55009-T1, internal, 31852, 31988
-recovered CodingQuarry_transcript_55009-T1, internal, 32730, 32797
-recovered CodingQuarry_transcript_55009-T1, internal, 34068, 34228
-recovered CodingQuarry_transcript_55009-T1, internal, 36339, 36419
-recovered CodingQuarry_transcript_55009-T1, internal, 36516, 36574
-recovered CodingQuarry_transcript_55009-T1, internal, 39466, 39561
Valid prediction for GlimmerHMM_glimmerT_14477-T1
Valid prediction for snap_scaffold_6-snap.998-T1
Valid prediction for snap_scaffold_6-snap.1003-T1
Valid prediction for GlimmerHMM_glimmerT_14462-T1
Valid prediction for snap_scaffold_6-snap.994-T1
Valid prediction for Augustus_model.g9570.t1
Valid prediction for GlimmerHMM_glimmerT_14470-T1
Valid prediction for Augustus_model.g9564.t1
Valid prediction for snap_scaffold_6-snap.983-T1
Valid prediction for GlimmerHMM_glimmerT_14473-T1
Couldn't classify 171794, 171906
Sorry, prediction pasa_asmbl_48290.p1 fails validation.
(AAG)	 TG	171794-171906	GT	GGG
(AGA)	 AG	173560-173668	GT	AGG
(GTG)	 AG	174016-174160	GT	AGG
(GGG)	 AG	174258-174376	GT	TGG
(TTG)	 AG	174511-174602	GT	TGG
(GGC)	 AG	174838-174954	GT	ATG
(GGA)	 AG	175257-175427	GT	AGG
(GTA)	 AG	175675-175783	GT	AGG
(GCT)	 AG	175893-176063	GT	AGG
(AAC)	 AG	176185-176352	GT	CGG
(AAA)	 AG	176520-176657	GT	AGG
(GTT)	 AG	176769-176789	CC	GAC
add_exon() Sorry, pasa_asmbl_48290.p1 174016-174160-terminal-3 is invalid.
-recovered pasa_asmbl_48290.p1, terminal, 174016, 174160
-recovered pasa_asmbl_48290.p1, terminal, 176769, 176789
-recovered pasa_asmbl_48290.p1, internal, 173560, 173668
-recovered pasa_asmbl_48290.p1, internal, 174016, 174160
-recovered pasa_asmbl_48290.p1, internal, 174258, 174376
-recovered pasa_asmbl_48290.p1, internal, 174511, 174602
-recovered pasa_asmbl_48290.p1, internal, 174838, 174954
-recovered pasa_asmbl_48290.p1, internal, 175257, 175427
-recovered pasa_asmbl_48290.p1, internal, 175675, 175783
-recovered pasa_asmbl_48290.p1, internal, 175893, 176063
-recovered pasa_asmbl_48290.p1, internal, 176185, 176352
-recovered pasa_asmbl_48290.p1, internal, 176520, 176657
Valid prediction for snap_scaffold_6-snap.975-T1
Valid prediction for CodingQuarry_transcript_55008-T1
Valid prediction for GlimmerHMM_glimmerT_14457-T1
Valid prediction for snap_scaffold_6-snap.993-T1
Valid prediction for snap_scaffold_6-snap.1006-T1
Valid prediction for HiQ_model.g9579.t1
Valid prediction for GlimmerHMM_glimmerT_14453-T1
Valid prediction for CodingQuarry_transcript_55004-T1
Valid prediction for Augustus_model.g9573.t1
Valid prediction for HiQ_model.g9566.t1
Valid prediction for HiQ_model.g9581.t1
Valid prediction for pasa_asmbl_49339.p1
Valid prediction for snap_scaffold_6-snap.978-T1
Valid prediction for CodingQuarry_transcript_55007-T1
Valid prediction for snap_scaffold_6-snap.997-T1
Couldn't classify 143201, 143254
Couldn't classify 144829, 145464
Sorry, prediction pasa_asmbl_48295.p1 fails validation.
(TCG)	 CA	143201-143254	GT	AGG
(CTG)	 AG	143566-143590	GT	CGG
(ACT)	 AG	144694-144725	GT	AGG
(GGG)	 AG	144829-145464	TT	GCT
-recovered pasa_asmbl_48295.p1, internal, 143566, 143590
-recovered pasa_asmbl_48295.p1, internal, 144694, 144725
Valid prediction for GlimmerHMM_glimmerT_14458-T1
Valid prediction for Augustus_model.g9580.t1
Valid prediction for pasa_asmbl_48301.p1
Valid prediction for Augustus_model.g9572.t1
Couldn't classify 77168, 77350
Sorry, prediction pasa_asmbl_48298.p2 fails validation.
(TCG)	 AG	77168-77350	GT	ACG
(ATT)	 AG	79824-79902	GT	AGG
(CAG)	 AG	80770-80870	GT	GGG
(AAG)	 AG	81126-81299	GC	GAG
-recovered pasa_asmbl_48298.p2, terminal, 81126, 81299
-recovered pasa_asmbl_48298.p2, internal, 77168, 77350
-recovered pasa_asmbl_48298.p2, internal, 79824, 79902
-recovered pasa_asmbl_48298.p2, internal, 80770, 80870
-recovered pasa_asmbl_48298.p2, internal, 81126, 81299
Valid prediction for snap_scaffold_6-snap.1005-T1
Valid prediction for snap_scaffold_6-snap.977-T1
Valid prediction for GlimmerHMM_glimmerT_14466-T1
Valid prediction for HiQ_model.g9565.t1
Valid prediction for snap_scaffold_6-snap.1010-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_6-snap.979-T1
Valid prediction for snap_scaffold_6-snap.982-T1
Valid prediction for Augustus_model.g9582.t1
Valid prediction for GlimmerHMM_glimmerT_14478-T1
Valid prediction for snap_scaffold_6-snap.995-T1
Valid prediction for Augustus_model.g9574.t1
Valid prediction for snap_scaffold_6-snap.985-T1
Valid prediction for snap_scaffold_6-snap.1017-T1
Valid prediction for GlimmerHMM_glimmerT_14447-T1
Couldn't classify 41761, 42144
Sorry, prediction pasa_asmbl_48305.p3 fails validation.
(GGT)	 GG	41761-42144	AC	AAA
Valid prediction for Augustus_model.g9576.t1
Valid prediction for snap_scaffold_6-snap.1008-T1
Valid prediction for GlimmerHMM_glimmerT_14482-T1
Valid prediction for GlimmerHMM_glimmerT_14454-T1
Valid prediction for Augustus_model.g9578.t1
Valid prediction for snap_scaffold_6-snap.976-T1
Valid prediction for GlimmerHMM_glimmerT_14471-T1
Valid prediction for Augustus_model.g9568.t1
Valid prediction for pasa_asmbl_48289.p1
Valid prediction for GlimmerHMM_glimmerT_14448-T1
Valid prediction for Augustus_model.g9567.t1
Valid prediction for GlimmerHMM_glimmerT_14459-T1
Valid prediction for snap_scaffold_6-snap.1007-T1
Valid prediction for GlimmerHMM_glimmerT_14465-T1
Valid prediction for snap_scaffold_6-snap.988-T1
Valid prediction for Augustus_model.g9571.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 23801, rend_intergenic: 23320  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28881, rend_intergenic: 24676  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61757, rend_intergenic: 49254  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62477, rend_intergenic: 62107  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73131, rend_intergenic: 63060  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82849, rend_intergenic: 73751  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93524, rend_intergenic: 87920  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95237, rend_intergenic: 93794  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100621, rend_intergenic: 95473  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113716, rend_intergenic: 108886  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126060, rend_intergenic: 113970  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127757, rend_intergenic: 126070  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159522, rend_intergenic: 156290  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170926, rend_intergenic: 164538  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180838, rend_intergenic: 180250  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 190184
-exon list size: 446


building trellis

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-found 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 23801, rend_intergenic: 23320  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 28881, rend_intergenic: 24676  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61757, rend_intergenic: 49254  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62477, rend_intergenic: 62107  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 73131, rend_intergenic: 63060  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82849, rend_intergenic: 73751  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93524, rend_intergenic: 87920  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 95237, rend_intergenic: 93794  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100621, rend_intergenic: 95473  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113716, rend_intergenic: 108886  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126060, rend_intergenic: 113970  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127757, rend_intergenic: 126070  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 159522, rend_intergenic: 156290  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170926, rend_intergenic: 164538  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180838, rend_intergenic: 180250  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 22 predictions persist after filtering for low support