-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_22/scaffold_22_3781935-3967917

-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_22-snap.697-T1
Valid prediction for snap_scaffold_22-snap.711-T1
Valid prediction for Augustus_model.g32861.t1
Valid prediction for Augustus_model.g32862.t1
Valid prediction for snap_scaffold_22-snap.702-T1
Valid prediction for Augustus_model.g32852.t1
Valid prediction for pasa_asmbl_29958.p1
Valid prediction for Augustus_model.g32857.t1
Valid prediction for snap_scaffold_22-snap.693-T1
Valid prediction for CodingQuarry_transcript_34125-T1
Valid prediction for GlimmerHMM_glimmerT_49257-T1
Valid prediction for snap_scaffold_22-snap.699-T1
Valid prediction for GlimmerHMM_glimmerT_49239-T1
Valid prediction for GlimmerHMM_glimmerT_49246-T1
Couldn't classify 51336, 51413
Sorry, prediction pasa_asmbl_29959.p1 fails validation.
(TTC)	 GT	51336-51413	GT	AGG
(GGG)	 AG	52041-52200	GT	AGG
(GGG)	 AG	52368-52468	GT	AGG
(GTA)	 AG	52624-52745	GT	AGG
(GTT)	 AG	52927-53002	GT	AGG
(GAC)	 AG	53087-53138	GT	ATG
(CGT)	 AG	53315-53471	GT	AAG
(TAA)	 AG	53727-53832	CC	GAC
-recovered pasa_asmbl_29959.p1, terminal, 53727, 53832
-recovered pasa_asmbl_29959.p1, internal, 52041, 52200
-recovered pasa_asmbl_29959.p1, internal, 52368, 52468
-recovered pasa_asmbl_29959.p1, internal, 52624, 52745
-recovered pasa_asmbl_29959.p1, internal, 52927, 53002
-recovered pasa_asmbl_29959.p1, internal, 53087, 53138
-recovered pasa_asmbl_29959.p1, internal, 53315, 53471
Valid prediction for GlimmerHMM_glimmerT_49231-T1
Valid prediction for snap_scaffold_22-snap.704-T1
Valid prediction for snap_scaffold_22-snap.729-T1
Valid prediction for Augustus_model.g32849.t1
Valid prediction for GlimmerHMM_glimmerT_49237-T1
Valid prediction for GlimmerHMM_glimmerT_49249-T1
Couldn't classify 88847, 88957
Couldn't classify 93916, 93957
Sorry, prediction pasa_asmbl_29960.p1 fails validation.
(AGG)	 CT	88847-88957	GT	CGG
(AGC)	 AG	89075-89159	GT	AGG
(GTG)	 AG	90468-90643	GT	AGG
(GTT)	 AG	91846-91896	GT	AGG
(GCA)	 AG	93916-93957	TT	ACT
-recovered pasa_asmbl_29960.p1, terminal, 89075, 89159
-recovered pasa_asmbl_29960.p1, internal, 89075, 89159
-recovered pasa_asmbl_29960.p1, internal, 90468, 90643
-recovered pasa_asmbl_29960.p1, internal, 91846, 91896
Valid prediction for snap_scaffold_22-snap.700-T1
Valid prediction for GlimmerHMM_glimmerT_49256-T1
Valid prediction for snap_scaffold_22-snap.707-T1
Valid prediction for GlimmerHMM_glimmerT_49250-T1
Valid prediction for GlimmerHMM_glimmerT_49235-T1
Valid prediction for snap_scaffold_22-snap.715-T1
Valid prediction for snap_scaffold_22-snap.723-T1
Valid prediction for Augustus_model.g32859.t1
Valid prediction for snap_scaffold_22-snap.696-T1
Couldn't classify 168642, 168732
Couldn't classify 171010, 171042
Sorry, prediction pasa_asmbl_29964.p1 fails validation.
(CTC)	 TG	168642-168732	GT	TGG
(GCT)	 AG	169395-169478	GT	TGG
(GAG)	 AG	170568-170662	GT	ACG
(TTT)	 AG	170803-170925	GT	GTG
(CAA)	 AG	171010-171042	CA	GGC
-recovered pasa_asmbl_29964.p1, internal, 169395, 169478
-recovered pasa_asmbl_29964.p1, internal, 170568, 170662
-recovered pasa_asmbl_29964.p1, internal, 170803, 170925
Valid prediction for snap_scaffold_22-snap.728-T1
Valid prediction for Augustus_model.g32858.t1
Valid prediction for HiQ_model.g32855.t1
Valid prediction for CodingQuarry_transcript_34124-T1
Valid prediction for snap_scaffold_22-snap.714-T1
Valid prediction for snap_scaffold_22-snap.712-T1
Couldn't classify 95193, 95303
Sorry, prediction pasa_asmbl_29961.p1 fails validation.
(ATC)	 GG	95193-95303	GT	AGG
(AGT)	 AG	96077-96171	GT	AGG
(GAG)	 AG	96310-96397	GT	CTG
(GGG)	 AG	97258-97358	GT	AAG
(GAG)	 AG	97877-97954	GT	AGG
(GTC)	 AG	98195-98258	GT	GGG
(ATC)	 AG	99859-99933	GT	TAG
(GAT)	 AG	100223-100306	GT	AGG
(ACT)	 AG	100436-100555	AA	GAA
-recovered pasa_asmbl_29961.p1, terminal, 100436, 100555
-recovered pasa_asmbl_29961.p1, internal, 96077, 96171
-recovered pasa_asmbl_29961.p1, internal, 96310, 96397
-recovered pasa_asmbl_29961.p1, internal, 97258, 97358
-recovered pasa_asmbl_29961.p1, internal, 97877, 97954
-recovered pasa_asmbl_29961.p1, internal, 98195, 98258
-recovered pasa_asmbl_29961.p1, internal, 99859, 99933
-recovered pasa_asmbl_29961.p1, internal, 100223, 100306
Valid prediction for snap_scaffold_22-snap.716-T1
Valid prediction for Augustus_model.g32854.t1
Valid prediction for snap_scaffold_22-snap.717-T1
Valid prediction for GlimmerHMM_glimmerT_49244-T1
Valid prediction for snap_scaffold_22-snap.732-T1
Couldn't classify 183244, 183320
Sorry, prediction pasa_asmbl_29965.p1 fails validation.
(GCT)	 CA	183244-183320	GT	ACG
(GAA)	 AG	183419-183513	GT	CTG
(CTC)	 AG	183609-183844	AG	AGA
-recovered pasa_asmbl_29965.p1, terminal, 183609, 183844
-recovered pasa_asmbl_29965.p1, internal, 183419, 183513
Valid prediction for GlimmerHMM_glimmerT_49255-T1
Valid prediction for snap_scaffold_22-snap.685-T1
Valid prediction for GlimmerHMM_glimmerT_49241-T1
Valid prediction for GlimmerHMM_glimmerT_49251-T1
Valid prediction for GlimmerHMM_glimmerT_49245-T1
Valid prediction for GlimmerHMM_glimmerT_49229-T1
Valid prediction for snap_scaffold_22-snap.690-T1
Valid prediction for Augustus_model.g32860.t1
Valid prediction for HiQ_model.g32850.t1
Valid prediction for snap_scaffold_22-snap.720-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_22-snap.695-T1
Valid prediction for snap_scaffold_22-snap.705-T1
Valid prediction for snap_scaffold_22-snap.708-T1
Valid prediction for snap_scaffold_22-snap.686-T1
Valid prediction for snap_scaffold_22-snap.713-T1
Valid prediction for snap_scaffold_22-snap.724-T1
Valid prediction for snap_scaffold_22-snap.730-T1
Valid prediction for Augustus_model.g32853.t1
Valid prediction for Augustus_model.g32856.t1
Valid prediction for GlimmerHMM_glimmerT_49252-T1
Valid prediction for snap_scaffold_22-snap.722-T1
Valid prediction for Augustus_model.g32851.t1
Valid prediction for snap_scaffold_22-snap.706-T1
Valid prediction for snap_scaffold_22-snap.701-T1
Valid prediction for GlimmerHMM_glimmerT_49226-T1
Valid prediction for snap_scaffold_22-snap.691-T1
Valid prediction for GlimmerHMM_glimmerT_49224-T1
Valid prediction for GlimmerHMM_glimmerT_49254-T1
Couldn't classify 174052, 174139
Couldn't classify 179379, 179464
Sorry, prediction pasa_asmbl_29187.p1 fails validation.
(GCT)	 AG	174052-174139	GT	AGG
(GTA)	 AG	174850-174908	GT	AGG
(AAG)	 AG	175307-175357	GT	ATG
(GTG)	 AG	176307-176384	GT	ATG
(GCC)	 AG	176775-176918	GT	AGG
(GGT)	 AG	177818-177935	GT	AGG
(GGC)	 AG	178354-178758	GT	AGG
(GCC)	 AG	179379-179464	AA	GTA
-recovered pasa_asmbl_29187.p1, internal, 174052, 174139
-recovered pasa_asmbl_29187.p1, internal, 174850, 174908
-recovered pasa_asmbl_29187.p1, internal, 175307, 175357
-recovered pasa_asmbl_29187.p1, internal, 176307, 176384
-recovered pasa_asmbl_29187.p1, internal, 176775, 176918
-recovered pasa_asmbl_29187.p1, internal, 177818, 177935
-recovered pasa_asmbl_29187.p1, internal, 178354, 178758
Valid prediction for Augustus_model.g32847.t1
Valid prediction for GlimmerHMM_glimmerT_49236-T1
Valid prediction for GlimmerHMM_glimmerT_49232-T1
Valid prediction for snap_scaffold_22-snap.687-T1
Couldn't classify 134956, 135069
Couldn't classify 136777, 136995
Sorry, prediction pasa_asmbl_29194.p1 fails validation.
(GGA)	 AC	134956-135069	GT	CAG
(ATG)	 AG	135515-135718	GT	AGG
(AAG)	 AG	136495-136590	GT	CTG
(AGG)	 AG	136777-136995	GA	GGG
-recovered pasa_asmbl_29194.p1, initial, 135515, 135718
-recovered pasa_asmbl_29194.p1, internal, 135515, 135718
-recovered pasa_asmbl_29194.p1, internal, 136495, 136590
Valid prediction for snap_scaffold_22-snap.709-T1
Valid prediction for snap_scaffold_22-snap.718-T1
Valid prediction for snap_scaffold_22-snap.688-T1
Valid prediction for snap_scaffold_22-snap.725-T1
Valid prediction for GlimmerHMM_glimmerT_49227-T1
Valid prediction for snap_scaffold_22-snap.731-T1
Valid prediction for GlimmerHMM_glimmerT_49230-T1
Valid prediction for GlimmerHMM_glimmerT_49238-T1
Valid prediction for GlimmerHMM_glimmerT_49228-T1
Valid prediction for snap_scaffold_22-snap.710-T1
Valid prediction for GlimmerHMM_glimmerT_49240-T1
Valid prediction for GlimmerHMM_glimmerT_49234-T1
Valid prediction for GlimmerHMM_glimmerT_49242-T1
Valid prediction for snap_scaffold_22-snap.727-T1
Valid prediction for GlimmerHMM_glimmerT_49225-T1
Valid prediction for GlimmerHMM_glimmerT_49253-T1
Valid prediction for snap_scaffold_22-snap.703-T1
Valid prediction for GlimmerHMM_glimmerT_49233-T1
Valid prediction for snap_scaffold_22-snap.694-T1
Valid prediction for snap_scaffold_22-snap.721-T1
Valid prediction for GlimmerHMM_glimmerT_49248-T1
Valid prediction for Augustus_model.g32848.t1
Valid prediction for snap_scaffold_22-snap.692-T1
Valid prediction for snap_scaffold_22-snap.719-T1
Valid prediction for snap_scaffold_22-snap.698-T1
Valid prediction for GlimmerHMM_glimmerT_49247-T1
Valid prediction for snap_scaffold_22-snap.689-T1
Couldn't classify 167069, 167253
Couldn't classify 169779, 169872
Sorry, prediction pasa_asmbl_29191.p1 fails validation.
(GTG)	 CA	167069-167253	GT	AAG
(ACA)	 AG	169056-169168	GT	CAG
(ACT)	 AG	169546-169672	GT	AAG
(GGA)	 AG	169779-169872	GT	AGG
-recovered pasa_asmbl_29191.p1, internal, 169056, 169168
-recovered pasa_asmbl_29191.p1, internal, 169546, 169672
-recovered pasa_asmbl_29191.p1, internal, 169779, 169872
Valid prediction for GlimmerHMM_glimmerT_49243-T1
Valid prediction for snap_scaffold_22-snap.726-T1
Valid prediction for snap_scaffold_22-snap.684-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 15237, rend_intergenic: 9604  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23313, rend_intergenic: 15461  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31844, rend_intergenic: 29235  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42115, rend_intergenic: 40592  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50469, rend_intergenic: 48918  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60477, rend_intergenic: 54940  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72458, rend_intergenic: 70928  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75509, rend_intergenic: 73610  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79402, rend_intergenic: 75692  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88580, rend_intergenic: 80698  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100555, rend_intergenic: 88885  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144025, rend_intergenic: 137683  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144498, rend_intergenic: 144113  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161515, rend_intergenic: 145244  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162805, rend_intergenic: 161747  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173111, rend_intergenic: 169414  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 185983
-exon list size: 415


building trellis

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-found 36 predictions from path traversal
Error with prediction: snap lend_intergenic: 15237, rend_intergenic: 9604  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23313, rend_intergenic: 15461  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31844, rend_intergenic: 29235  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42115, rend_intergenic: 40592  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50469, rend_intergenic: 48918  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 60477, rend_intergenic: 54940  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72458, rend_intergenic: 70928  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75509, rend_intergenic: 73610  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79402, rend_intergenic: 75692  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88580, rend_intergenic: 80698  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100555, rend_intergenic: 88885  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144025, rend_intergenic: 137683  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 144498, rend_intergenic: 144113  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161515, rend_intergenic: 145244  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162805, rend_intergenic: 161747  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173111, rend_intergenic: 169414  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