-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_4/scaffold_4_4668511-4915607

-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_9308-T1
Valid prediction for Augustus_model.g5981.t1
Valid prediction for snap_scaffold_4-snap.1071-T1
Valid prediction for GlimmerHMM_glimmerT_9319-T1
Couldn't classify 10918, 11063
Sorry, prediction pasa_asmbl_41294.p1 fails validation.
(CTC)	 CC	10918-11063	GT	AGG
(GTA)	 AG	11789-11996	CT	GAC
-recovered pasa_asmbl_41294.p1, terminal, 11789, 11996
Valid prediction for Augustus_model.g5994.t1
Valid prediction for snap_scaffold_4-snap.1073-T1
Valid prediction for GlimmerHMM_glimmerT_9302-T1
Valid prediction for GlimmerHMM_glimmerT_9292-T1
Valid prediction for snap_scaffold_4-snap.1099-T1
Valid prediction for GlimmerHMM_glimmerT_9290-T1
Valid prediction for GlimmerHMM_glimmerT_9289-T1
Valid prediction for snap_scaffold_4-snap.1117-T1
Valid prediction for GlimmerHMM_glimmerT_9301-T1
Valid prediction for Augustus_model.g5992.t1
Valid prediction for snap_scaffold_4-snap.1089-T1
Valid prediction for snap_scaffold_4-snap.1116-T1
Valid prediction for GlimmerHMM_glimmerT_9317-T1
Valid prediction for snap_scaffold_4-snap.1082-T1
Couldn't classify 237396, 237569
Sorry, prediction pasa_asmbl_41313.p1 fails validation.
(GTG)	 AC	237396-237569	GT	AAG
(AGT)	 AG	237733-237811	GT	CGG
(GTG)	 AG	238237-238351	GT	AAG
(GCG)	 AG	238511-238593	GT	AGG
(GCT)	 AG	238905-238968	GT	GGG
(GAA)	 AG	239116-239184	GT	AGG
(GAC)	 AG	239283-239423	GT	AAG
(GTG)	 AG	239544-239655	GT	TGG
(ATC)	 AG	239804-239830	GT	TGG
(CTA)	 AG	239991-240065	GT	CTG
(GCA)	 AG	240260-240461	GT	AGG
(CCA)	 AG	240728-240815	GT	CAG
(GAC)	 AG	240910-241027	GT	GGG
(GCG)	 AG	241320-241539	GT	CGG
(GCC)	 AG	241902-241989	GT	GTG
(GAT)	 AG	242130-242213	GT	AGG
(GAC)	 AG	242391-242536	GT	CGG
(AGG)	 AG	242654-242736	GT	AGG
(GGG)	 AG	242951-243033	GT	ACG
(GCC)	 AG	243192-243283	GT	TGG
(GTT)	 AG	243486-243769	CA	GAC
-recovered pasa_asmbl_41313.p1, terminal, 243486, 243769
-recovered pasa_asmbl_41313.p1, internal, 237733, 237811
-recovered pasa_asmbl_41313.p1, internal, 238237, 238351
-recovered pasa_asmbl_41313.p1, internal, 238511, 238593
-recovered pasa_asmbl_41313.p1, internal, 238905, 238968
-recovered pasa_asmbl_41313.p1, internal, 239116, 239184
-recovered pasa_asmbl_41313.p1, internal, 239283, 239423
-recovered pasa_asmbl_41313.p1, internal, 239544, 239655
-recovered pasa_asmbl_41313.p1, internal, 239804, 239830
-recovered pasa_asmbl_41313.p1, internal, 239991, 240065
-recovered pasa_asmbl_41313.p1, internal, 240260, 240461
-recovered pasa_asmbl_41313.p1, internal, 240728, 240815
-recovered pasa_asmbl_41313.p1, internal, 240910, 241027
-recovered pasa_asmbl_41313.p1, internal, 241320, 241539
-recovered pasa_asmbl_41313.p1, internal, 241902, 241989
-recovered pasa_asmbl_41313.p1, internal, 242130, 242213
-recovered pasa_asmbl_41313.p1, internal, 242391, 242536
-recovered pasa_asmbl_41313.p1, internal, 242654, 242736
-recovered pasa_asmbl_41313.p1, internal, 242951, 243033
-recovered pasa_asmbl_41313.p1, internal, 243192, 243283
Valid prediction for Augustus_model.g5993.t1
Valid prediction for Augustus_model.g5999.t1
Valid prediction for snap_scaffold_4-snap.1104-T1
Valid prediction for GlimmerHMM_glimmerT_9316-T1
Valid prediction for snap_scaffold_4-snap.1111-T1
Valid prediction for GlimmerHMM_glimmerT_9309-T1
Valid prediction for GlimmerHMM_glimmerT_9293-T1
Valid prediction for Augustus_model.g5978.t1
Valid prediction for HiQ_model.g6002.t1
Valid prediction for snap_scaffold_4-snap.1075-T1
Valid prediction for Augustus_model.g5985.t1
Valid prediction for snap_scaffold_4-snap.1103-T1
Valid prediction for GlimmerHMM_glimmerT_9318-T1
Valid prediction for snap_scaffold_4-snap.1076-T1
Valid prediction for GlimmerHMM_glimmerT_9299-T1
Valid prediction for snap_scaffold_4-snap.1113-T1
Valid prediction for GlimmerHMM_glimmerT_9288-T1
Valid prediction for GlimmerHMM_glimmerT_9312-T1
Valid prediction for snap_scaffold_4-snap.1088-T1
Valid prediction for snap_scaffold_4-snap.1098-T1
Valid prediction for snap_scaffold_4-snap.1097-T1
Valid prediction for GlimmerHMM_glimmerT_9310-T1
Valid prediction for Augustus_model.g5989.t1
Valid prediction for Augustus_model.g5980.t1
Valid prediction for snap_scaffold_4-snap.1090-T1
Valid prediction for snap_scaffold_4-snap.1101-T1
Valid prediction for GlimmerHMM_glimmerT_9287-T1
Valid prediction for pasa_asmbl_41303.p1
Valid prediction for GlimmerHMM_glimmerT_9307-T1
Valid prediction for Augustus_model.g5984.t1
Valid prediction for Augustus_model.g5990.t1
Valid prediction for snap_scaffold_4-snap.1072-T1
Valid prediction for CodingQuarry_transcript_48968-T1
Valid prediction for Augustus_model.g5979.t1
Valid prediction for snap_scaffold_4-snap.1094-T1
Valid prediction for GlimmerHMM_glimmerT_9321-T1
Valid prediction for GlimmerHMM_glimmerT_9306-T1
Valid prediction for snap_scaffold_4-snap.1087-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_4-snap.1112-T1
Valid prediction for snap_scaffold_4-snap.1092-T1
Valid prediction for GlimmerHMM_glimmerT_9303-T1
Valid prediction for GlimmerHMM_glimmerT_9295-T1
Valid prediction for snap_scaffold_4-snap.1083-T1
Valid prediction for GlimmerHMM_glimmerT_9311-T1
Valid prediction for GlimmerHMM_glimmerT_9298-T1
Valid prediction for GlimmerHMM_glimmerT_9304-T1
Valid prediction for snap_scaffold_4-snap.1086-T1
Valid prediction for GlimmerHMM_glimmerT_9296-T1
Valid prediction for snap_scaffold_4-snap.1084-T1
Valid prediction for Augustus_model.g5991.t1
Valid prediction for Augustus_model.g5986.t1
Valid prediction for snap_scaffold_4-snap.1106-T1
Couldn't classify 24248, 25225
Sorry, prediction pasa_asmbl_42539.p1 fails validation.
(AGC)	 AC	24248-25225	GT	AGG
(AAT)	 AG	25401-25496	CG	AAC
-recovered pasa_asmbl_42539.p1, terminal, 25401, 25496
Valid prediction for GlimmerHMM_glimmerT_9313-T1
Valid prediction for pasa_asmbl_42534.p1
Valid prediction for GlimmerHMM_glimmerT_9314-T1
Couldn't classify 20209, 20298
Sorry, prediction pasa_asmbl_42542.p1 fails validation.
(ATG)	 AA	17293-17348	GT	AGG
(TGT)	 AG	17686-17870	GT	TGG
(CAA)	 AG	19284-19366	GT	AGG
(GTG)	 AG	19731-19820	GT	AGG
(TCT)	 AG	20209-20298	AC	CCA
-recovered pasa_asmbl_42542.p1, initial, 17293, 17348
-recovered pasa_asmbl_42542.p1, internal, 17686, 17870
-recovered pasa_asmbl_42542.p1, internal, 19284, 19366
-recovered pasa_asmbl_42542.p1, internal, 19731, 19820
Valid prediction for Augustus_model.g6000.t1
Valid prediction for snap_scaffold_4-snap.1105-T1
Valid prediction for Augustus_model.g5982.t1
Valid prediction for Augustus_model.g5983.t1
Valid prediction for snap_scaffold_4-snap.1091-T1
Valid prediction for CodingQuarry_transcript_48969-T1
Valid prediction for snap_scaffold_4-snap.1100-T1
Valid prediction for GlimmerHMM_glimmerT_9297-T1
Valid prediction for snap_scaffold_4-snap.1074-T1
Valid prediction for snap_scaffold_4-snap.1085-T1
Valid prediction for snap_scaffold_4-snap.1078-T1
Valid prediction for snap_scaffold_4-snap.1079-T1
Couldn't classify 241667, 241966
Sorry, prediction pasa_asmbl_41292.p2 fails validation.
(CTG)	 AC	241667-241966	GT	GAG
Couldn't classify 55311, 55419
Sorry, prediction pasa_asmbl_43663.p1 fails validation.
(ATG)	 GG	53674-53844	GT	AGG
(CTC)	 AG	54277-54448	GT	GAG
(GTG)	 AG	54954-55077	GT	ACG
(GTC)	 AG	55311-55419	GG	CAG
-recovered pasa_asmbl_43663.p1, initial, 53674, 53844
-recovered pasa_asmbl_43663.p1, internal, 54277, 54448
-recovered pasa_asmbl_43663.p1, internal, 54954, 55077
Valid prediction for GlimmerHMM_glimmerT_9320-T1
Couldn't classify 21601, 21702
Couldn't classify 23848, 24061
Sorry, prediction pasa_asmbl_42540.p1 fails validation.
(TAC)	 CG	21601-21702	GT	TTG
(GCC)	 AG	22801-23003	GT	AGG
(AGG)	 AG	23190-23299	GT	AAG
(TGA)	 AG	23564-23705	GT	ACG
(GGA)	 AG	23848-24061	TA	TCT
-recovered pasa_asmbl_42540.p1, internal, 22801, 23003
-recovered pasa_asmbl_42540.p1, internal, 23190, 23299
-recovered pasa_asmbl_42540.p1, internal, 23564, 23705
Valid prediction for GlimmerHMM_glimmerT_9305-T1
Valid prediction for snap_scaffold_4-snap.1095-T1
Valid prediction for Augustus_model.g6001.t1
Valid prediction for GlimmerHMM_glimmerT_9291-T1
Valid prediction for GlimmerHMM_glimmerT_9300-T1
Couldn't classify 212830, 212917
Couldn't classify 214331, 214468
Sorry, prediction pasa_asmbl_43636.p1 fails validation.
(AAG)	 AT	212830-212917	GT	AGG
(GAT)	 AG	213082-213209	GT	AGG
(AAC)	 AG	213805-214032	GT	AGG
(GAC)	 AG	214331-214468	GA	GAG
-recovered pasa_asmbl_43636.p1, internal, 213082, 213209
-recovered pasa_asmbl_43636.p1, internal, 213805, 214032
Valid prediction for CodingQuarry_transcript_48965-T1
Valid prediction for HiQ_model.g5996.t1
Valid prediction for snap_scaffold_4-snap.1093-T1
Valid prediction for Augustus_model.g5995.t1
Valid prediction for snap_scaffold_4-snap.1107-T1
Valid prediction for snap_scaffold_4-snap.1102-T1
Valid prediction for snap_scaffold_4-snap.1115-T1
Valid prediction for Augustus_model.g5987.t1
Valid prediction for snap_scaffold_4-snap.1096-T1
Valid prediction for GlimmerHMM_glimmerT_9294-T1
Valid prediction for snap_scaffold_4-snap.1077-T1
Valid prediction for snap_scaffold_4-snap.1109-T1
Valid prediction for snap_scaffold_4-snap.1114-T1
Valid prediction for snap_scaffold_4-snap.1110-T1
Valid prediction for Augustus_model.g5997.t1
Valid prediction for snap_scaffold_4-snap.1080-T1
Valid prediction for GlimmerHMM_glimmerT_9315-T1
Couldn't classify 60108, 60240
Sorry, prediction pasa_asmbl_42535.p1 fails validation.
(GCA)	 CA	60108-60240	GT	GGG
(ATT)	 AG	60562-60677	GT	AGG
(CGC)	 AG	62483-62605	GT	GCG
(GCT)	 AG	63201-63387	GT	AGG
(GGC)	 AG	63602-63819	GT	AGG
(CTG)	 AG	65538-65846	GC	GAG
-recovered pasa_asmbl_42535.p1, terminal, 65538, 65846
-recovered pasa_asmbl_42535.p1, internal, 60562, 60677
-recovered pasa_asmbl_42535.p1, internal, 62483, 62605
-recovered pasa_asmbl_42535.p1, internal, 63201, 63387
-recovered pasa_asmbl_42535.p1, internal, 63602, 63819
-recovered pasa_asmbl_42535.p1, internal, 65538, 65846
Valid prediction for Augustus_model.g5998.t1
Valid prediction for snap_scaffold_4-snap.1108-T1
Valid prediction for snap_scaffold_4-snap.1081-T1
Valid prediction for Augustus_model.g5988.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 176385, rend_intergenic: 176382  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 11484, rend_intergenic: 7963  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14223, rend_intergenic: 11487  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24561, rend_intergenic: 19559  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49628, rend_intergenic: 46855  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51361, rend_intergenic: 49922  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154659, rend_intergenic: 152121  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 194294, rend_intergenic: 191457  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 209419, rend_intergenic: 207768  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 247097
-exon list size: 499


building trellis

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-found 36 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 176385, rend_intergenic: 176382  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 11484, rend_intergenic: 7963  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 14223, rend_intergenic: 11487  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24561, rend_intergenic: 19559  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49628, rend_intergenic: 46855  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51361, rend_intergenic: 49922  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 154659, rend_intergenic: 152121  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 194294, rend_intergenic: 191457  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 209419, rend_intergenic: 207768  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 32 predictions persist after filtering for low support