-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_5/scaffold_5_5571680-5788925

-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 156924, 157008
Sorry, prediction pasa_asmbl_45357.p1 fails validation.
(CTT)	 AG	156924-157008	GT	AGG
(ACG)	 AG	157235-157549	GT	AGG
(AGG)	 AG	157690-157792	GT	AGG
(TGT)	 AG	157920-158038	GT	AAG
(ACA)	 AG	158136-158176	GT	AGG
(GAA)	 AG	158374-158556	CG	AGC
add_exon() Sorry, pasa_asmbl_45357.p1 156924-157008-terminal-3 is invalid.
-recovered pasa_asmbl_45357.p1, terminal, 156924, 157008
-recovered pasa_asmbl_45357.p1, terminal, 158374, 158556
-recovered pasa_asmbl_45357.p1, internal, 156924, 157008
-recovered pasa_asmbl_45357.p1, internal, 157235, 157549
-recovered pasa_asmbl_45357.p1, internal, 157690, 157792
-recovered pasa_asmbl_45357.p1, internal, 157920, 158038
-recovered pasa_asmbl_45357.p1, internal, 158136, 158176
Valid prediction for GlimmerHMM_glimmerT_11965-T1
Valid prediction for snap_scaffold_5-snap.1127-T1
Valid prediction for CodingQuarry_transcript_52063-T1
Valid prediction for pasa_asmbl_45350.p1
Valid prediction for CodingQuarry_transcript_52061-T1
Valid prediction for GlimmerHMM_glimmerT_11982-T1
Couldn't classify 176137, 176271
Couldn't classify 177658, 178319
Sorry, prediction pasa_asmbl_45369.p1 fails validation.
(AGT)	 AC	176137-176271	GT	TGG
(GTC)	 AG	176429-176561	GT	AGG
(CTC)	 AG	176762-176905	GT	GGG
(GTC)	 AG	177203-177364	GT	AGG
(GAG)	 AG	177658-178319	AA	GTA
-recovered pasa_asmbl_45369.p1, internal, 176429, 176561
-recovered pasa_asmbl_45369.p1, internal, 176762, 176905
-recovered pasa_asmbl_45369.p1, internal, 177203, 177364
Valid prediction for pasa_asmbl_45348.p1
Valid prediction for GlimmerHMM_glimmerT_11964-T1
Valid prediction for snap_scaffold_5-snap.1112-T1
Valid prediction for snap_scaffold_5-snap.1132-T1
Valid prediction for HiQ_model.g7832.t1
Valid prediction for GlimmerHMM_glimmerT_11979-T1
Valid prediction for snap_scaffold_5-snap.1124-T1
Valid prediction for snap_scaffold_5-snap.1099-T1
Valid prediction for snap_scaffold_5-snap.1126-T1
Valid prediction for GlimmerHMM_glimmerT_11961-T1
Valid prediction for GlimmerHMM_glimmerT_11954-T1
Valid prediction for Augustus_model.g7828.t1
Valid prediction for snap_scaffold_5-snap.1116-T1
Valid prediction for CodingQuarry_transcript_52065-T1
Valid prediction for Augustus_model.g7843.t1
Valid prediction for GlimmerHMM_glimmerT_11953-T1
Valid prediction for snap_scaffold_5-snap.1121-T1
Valid prediction for snap_scaffold_5-snap.1101-T1
Valid prediction for Augustus_model.g7845.t1
Valid prediction for CodingQuarry_transcript_52066-T1
Valid prediction for snap_scaffold_5-snap.1125-T1
Valid prediction for HiQ_model.g7841.t1
Valid prediction for snap_scaffold_5-snap.1111-T1
Valid prediction for GlimmerHMM_glimmerT_11950-T1
Valid prediction for snap_scaffold_5-snap.1114-T1
Couldn't classify 181632, 181844
Sorry, prediction pasa_asmbl_45370.p1 fails validation.
(GGT)	 TA	181632-181844	GT	TGG
(GTG)	 AG	182653-182746	GT	AGG
(GCT)	 AG	184402-184619	CA	AAC
-recovered pasa_asmbl_45370.p1, terminal, 184402, 184619
-recovered pasa_asmbl_45370.p1, internal, 182653, 182746
Valid prediction for HiQ_model.g7830.t1
Valid prediction for CodingQuarry_transcript_52062-T1
Valid prediction for Augustus_model.g7836.t1
Valid prediction for snap_scaffold_5-snap.1109-T1
Valid prediction for GlimmerHMM_glimmerT_11977-T1
Valid prediction for GlimmerHMM_glimmerT_11975-T1
Valid prediction for pasa_asmbl_45366.p1
Valid prediction for snap_scaffold_5-snap.1120-T1
Valid prediction for GlimmerHMM_glimmerT_11969-T1
Valid prediction for Augustus_model.g7846.t1
Valid prediction for snap_scaffold_5-snap.1094-T1
Valid prediction for CodingQuarry_transcript_52060-T1
Valid prediction for Augustus_model.g7839.t1
Valid prediction for GlimmerHMM_glimmerT_11970-T1
Valid prediction for GlimmerHMM_glimmerT_11972-T1
Valid prediction for GlimmerHMM_glimmerT_11948-T1
Valid prediction for pasa_asmbl_45351.p1
Valid prediction for snap_scaffold_5-snap.1096-T1
Valid prediction for GlimmerHMM_glimmerT_11952-T1
Valid prediction for snap_scaffold_5-snap.1117-T1
Valid prediction for snap_scaffold_5-snap.1098-T1
Valid prediction for snap_scaffold_5-snap.1104-T1
Valid prediction for Augustus_model.g7831.t1
Valid prediction for snap_scaffold_5-snap.1093-T1
Valid prediction for Augustus_model.g7844.t1
Valid prediction for CodingQuarry_transcript_52064-T1
Valid prediction for snap_scaffold_5-snap.1110-T1
Valid prediction for GlimmerHMM_glimmerT_11967-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_5-snap.1131-T1
Couldn't classify 141398, 141424
Sorry, prediction pasa_asmbl_44055.p1 fails validation.
(CTG)	 AA	141398-141424	GT	AGG
(TCA)	 AG	141558-141756	GT	AGG
(ACC)	 AG	141846-141943	GT	AGG
(GAG)	 AG	142237-142332	GT	GGG
(GAC)	 AG	142532-142703	GT	AGG
(GCT)	 AG	142894-143159	GT	AGG
(GAG)	 AG	143271-143422	GT	TGG
(TCC)	 AG	143546-143617	GT	AGG
(GAT)	 AG	143741-143967	GT	AGG
(GCC)	 AG	144132-144250	GT	AGG
(GTG)	 AG	144539-144730	GT	TGG
(ATG)	 AG	144904-144999	GC	GAG
add_exon() Sorry, pasa_asmbl_44055.p1 144904-144999-initial-1 is invalid.
-recovered pasa_asmbl_44055.p1, initial, 144904, 144999
add_exon() Sorry, pasa_asmbl_44055.p1 143546-143617-terminal-1 is invalid.
-recovered pasa_asmbl_44055.p1, terminal, 143546, 143617
add_exon() Sorry, pasa_asmbl_44055.p1 143741-143967-terminal-2 is invalid.
-recovered pasa_asmbl_44055.p1, terminal, 143741, 143967
-recovered pasa_asmbl_44055.p1, terminal, 144904, 144999
-recovered pasa_asmbl_44055.p1, internal, 141558, 141756
-recovered pasa_asmbl_44055.p1, internal, 141846, 141943
-recovered pasa_asmbl_44055.p1, internal, 142237, 142332
-recovered pasa_asmbl_44055.p1, internal, 142532, 142703
-recovered pasa_asmbl_44055.p1, internal, 142894, 143159
-recovered pasa_asmbl_44055.p1, internal, 143271, 143422
-recovered pasa_asmbl_44055.p1, internal, 143546, 143617
-recovered pasa_asmbl_44055.p1, internal, 143741, 143967
-recovered pasa_asmbl_44055.p1, internal, 144132, 144250
-recovered pasa_asmbl_44055.p1, internal, 144539, 144730
-recovered pasa_asmbl_44055.p1, internal, 144904, 144999
Valid prediction for snap_scaffold_5-snap.1130-T1
Valid prediction for GlimmerHMM_glimmerT_11976-T1
Valid prediction for snap_scaffold_5-snap.1105-T1
Valid prediction for Augustus_model.g7847.t1
Valid prediction for snap_scaffold_5-snap.1106-T1
Valid prediction for snap_scaffold_5-snap.1122-T1
Valid prediction for GlimmerHMM_glimmerT_11947-T1
Valid prediction for snap_scaffold_5-snap.1123-T1
Valid prediction for snap_scaffold_5-snap.1108-T1
Valid prediction for GlimmerHMM_glimmerT_11983-T1
Valid prediction for snap_scaffold_5-snap.1115-T1
Valid prediction for snap_scaffold_5-snap.1092-T1
Valid prediction for Augustus_model.g7838.t1
Valid prediction for GlimmerHMM_glimmerT_11968-T1
Valid prediction for Augustus_model.g7834.t1
Valid prediction for Augustus_model.g7837.t1
Valid prediction for GlimmerHMM_glimmerT_11959-T1
Valid prediction for GlimmerHMM_glimmerT_11956-T1
Valid prediction for Augustus_model.g7840.t1
Valid prediction for Augustus_model.g7849.t1
Valid prediction for snap_scaffold_5-snap.1118-T1
Valid prediction for GlimmerHMM_glimmerT_11971-T1
Valid prediction for Augustus_model.g7833.t1
Valid prediction for snap_scaffold_5-snap.1102-T1
Valid prediction for GlimmerHMM_glimmerT_11963-T1
Valid prediction for GlimmerHMM_glimmerT_11966-T1
Valid prediction for snap_scaffold_5-snap.1128-T1
Valid prediction for GlimmerHMM_glimmerT_11980-T1
Valid prediction for GlimmerHMM_glimmerT_11955-T1
Couldn't classify 152569, 152623
Couldn't classify 154589, 154755
Sorry, prediction pasa_asmbl_44945.p1 fails validation.
(GCT)	 CA	152569-152623	GT	AGG
(CTG)	 AG	153406-153471	GT	AGG
(TCC)	 AG	153832-153966	GT	AGG
(CCG)	 AG	154589-154755	GG	TCG
-recovered pasa_asmbl_44945.p1, internal, 153406, 153471
-recovered pasa_asmbl_44945.p1, internal, 153832, 153966
Valid prediction for GlimmerHMM_glimmerT_11978-T1
Valid prediction for GlimmerHMM_glimmerT_11981-T1
Valid prediction for snap_scaffold_5-snap.1095-T1
Valid prediction for GlimmerHMM_glimmerT_11973-T1
Valid prediction for GlimmerHMM_glimmerT_11951-T1
Valid prediction for Augustus_model.g7842.t1
Valid prediction for GlimmerHMM_glimmerT_11960-T1
Valid prediction for GlimmerHMM_glimmerT_11962-T1
Valid prediction for Augustus_model.g7848.t1
Valid prediction for Augustus_model.g7827.t1
Valid prediction for GlimmerHMM_glimmerT_11946-T1
Valid prediction for GlimmerHMM_glimmerT_11957-T1
Valid prediction for Augustus_model.g7835.t1
Valid prediction for snap_scaffold_5-snap.1119-T1
Valid prediction for snap_scaffold_5-snap.1113-T1
Couldn't classify 171118, 171489
Sorry, prediction pasa_asmbl_46350.p1 fails validation.
(CCC)	 CT	171118-171489	GT	GTG
Valid prediction for snap_scaffold_5-snap.1097-T1
Valid prediction for snap_scaffold_5-snap.1129-T1
Valid prediction for GlimmerHMM_glimmerT_11974-T1
Valid prediction for snap_scaffold_5-snap.1107-T1
Valid prediction for snap_scaffold_5-snap.1103-T1
Valid prediction for GlimmerHMM_glimmerT_11949-T1
Valid prediction for Augustus_model.g7829.t1
Couldn't classify 157985, 158074
Sorry, prediction pasa_asmbl_44052.p1 fails validation.
(GAT)	 CA	157985-158074	GT	ATG
(GGC)	 AG	158372-158567	GT	GGG
(AGC)	 AG	158703-158842	GT	GGG
(GAC)	 AG	160538-160697	GT	AGG
(GTA)	 AG	161374-161510	GT	AGG
(CCC)	 AG	164509-164695	GT	ACG
(AGG)	 AG	164935-164978	AT	AAA
add_exon() Sorry, pasa_asmbl_44052.p1 160538-160697-terminal-3 is invalid.
-recovered pasa_asmbl_44052.p1, terminal, 160538, 160697
-recovered pasa_asmbl_44052.p1, terminal, 164935, 164978
-recovered pasa_asmbl_44052.p1, internal, 158372, 158567
-recovered pasa_asmbl_44052.p1, internal, 158703, 158842
-recovered pasa_asmbl_44052.p1, internal, 160538, 160697
-recovered pasa_asmbl_44052.p1, internal, 161374, 161510
-recovered pasa_asmbl_44052.p1, internal, 164509, 164695
Valid prediction for GlimmerHMM_glimmerT_11958-T1
Valid prediction for snap_scaffold_5-snap.1100-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 9632, rend_intergenic: 3931  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16661, rend_intergenic: 10721  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37922, rend_intergenic: 35561  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41717, rend_intergenic: 38833  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59361, rend_intergenic: 50115  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104640, rend_intergenic: 73065  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117324, rend_intergenic: 107574  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131101, rend_intergenic: 117464  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133985, rend_intergenic: 131493  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144859, rend_intergenic: 134216  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148665, rend_intergenic: 145132  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156500, rend_intergenic: 150446  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 213771, rend_intergenic: 210854  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 217246
-exon list size: 461


building trellis

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-found 34 predictions from path traversal
Error with prediction: snap lend_intergenic: 9632, rend_intergenic: 3931  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 16661, rend_intergenic: 10721  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37922, rend_intergenic: 35561  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41717, rend_intergenic: 38833  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59361, rend_intergenic: 50115  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104640, rend_intergenic: 73065  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 117324, rend_intergenic: 107574  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131101, rend_intergenic: 117464  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133985, rend_intergenic: 131493  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144859, rend_intergenic: 134216  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148665, rend_intergenic: 145132  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156500, rend_intergenic: 150446  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 213771, rend_intergenic: 210854  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 25 predictions persist after filtering for low support