-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_27/scaffold_27_4689029-4918205

-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 pasa_asmbl_36319.p1
Valid prediction for snap_scaffold_27-snap.1114-T1
Valid prediction for snap_scaffold_27-snap.1115-T1
Valid prediction for snap_scaffold_27-snap.1138-T1
Couldn't classify 199487, 199600
Couldn't classify 206043, 206075
Sorry, prediction pasa_asmbl_36322.p1 fails validation.
(GCG)	 CC	199487-199600	GT	AGG
(CTG)	 AG	199913-200036	GT	AGG
(AGA)	 AG	200948-201138	GT	AGG
(ACA)	 AG	201338-201476	GT	GGG
(AGG)	 AG	201582-201775	GT	AGG
(TAC)	 AG	201892-202037	GT	AAG
(TCT)	 AG	202302-202423	GT	AGG
(ACG)	 AG	202527-202637	GT	CGG
(GCC)	 AG	203650-203840	GT	GAG
(TGC)	 AG	205490-205612	GT	ACG
(GGC)	 AG	206043-206075	GC	AAG
add_exon() Sorry, pasa_asmbl_36322.p1 199913-200036-terminal-3 is invalid.
-recovered pasa_asmbl_36322.p1, terminal, 199913, 200036
-recovered pasa_asmbl_36322.p1, internal, 199913, 200036
-recovered pasa_asmbl_36322.p1, internal, 200948, 201138
-recovered pasa_asmbl_36322.p1, internal, 201338, 201476
-recovered pasa_asmbl_36322.p1, internal, 201582, 201775
-recovered pasa_asmbl_36322.p1, internal, 201892, 202037
-recovered pasa_asmbl_36322.p1, internal, 202302, 202423
-recovered pasa_asmbl_36322.p1, internal, 202527, 202637
-recovered pasa_asmbl_36322.p1, internal, 203650, 203840
-recovered pasa_asmbl_36322.p1, internal, 205490, 205612
-recovered pasa_asmbl_36322.p1, internal, 206043, 206075
Valid prediction for snap_scaffold_27-snap.1105-T1
Valid prediction for snap_scaffold_27-snap.1135-T1
Valid prediction for CodingQuarry_transcript_41885-T1
Valid prediction for GlimmerHMM_glimmerT_57235-T1
Valid prediction for GlimmerHMM_glimmerT_57242-T1
Valid prediction for GlimmerHMM_glimmerT_57237-T1
Valid prediction for snap_scaffold_27-snap.1101-T1
Valid prediction for Augustus_model.g37958.t1
Valid prediction for snap_scaffold_27-snap.1131-T1
Valid prediction for GlimmerHMM_glimmerT_57256-T1
Valid prediction for GlimmerHMM_glimmerT_57250-T1
Valid prediction for Augustus_model.g37946.t1
Valid prediction for Augustus_model.g37945.t1
Valid prediction for GlimmerHMM_glimmerT_57259-T1
Valid prediction for HiQ_model.g37952.t1
Valid prediction for Augustus_model.g37947.t1
Valid prediction for snap_scaffold_27-snap.1122-T1
Valid prediction for snap_scaffold_27-snap.1119-T1
Valid prediction for snap_scaffold_27-snap.1129-T1
Valid prediction for snap_scaffold_27-snap.1113-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for CodingQuarry_transcript_41881-T1
Valid prediction for GlimmerHMM_glimmerT_57246-T1
Valid prediction for snap_scaffold_27-snap.1106-T1
Valid prediction for GlimmerHMM_glimmerT_57253-T1
Valid prediction for Augustus_model.g37954.t1
Valid prediction for GlimmerHMM_glimmerT_57255-T1
Valid prediction for GlimmerHMM_glimmerT_57238-T1
Valid prediction for snap_scaffold_27-snap.1100-T1
Valid prediction for GlimmerHMM_glimmerT_57260-T1
Valid prediction for snap_scaffold_27-snap.1134-T1
Valid prediction for snap_scaffold_27-snap.1111-T1
Valid prediction for snap_scaffold_27-snap.1127-T1
Valid prediction for snap_scaffold_27-snap.1102-T1
Valid prediction for GlimmerHMM_glimmerT_57254-T1
Valid prediction for snap_scaffold_27-snap.1108-T1
Valid prediction for snap_scaffold_27-snap.1142-T1
Valid prediction for snap_scaffold_27-snap.1128-T1
Valid prediction for snap_scaffold_27-snap.1139-T1
Valid prediction for CodingQuarry_transcript_41882-T1
Valid prediction for GlimmerHMM_glimmerT_57244-T1
Valid prediction for snap_scaffold_27-snap.1120-T1
Couldn't classify 46962, 47273
Sorry, prediction pasa_asmbl_36311.p1 fails validation.
(GGA)	 AC	46962-47273	AT	GAA
Valid prediction for Augustus_model.g37955.t1
Valid prediction for snap_scaffold_27-snap.1109-T1
Valid prediction for snap_scaffold_27-snap.1099-T1
Valid prediction for pasa_asmbl_36316.p1
Valid prediction for Augustus_model.g37943.t1
Valid prediction for snap_scaffold_27-snap.1136-T1
Valid prediction for Augustus_model.g37956.t1
Valid prediction for GlimmerHMM_glimmerT_57241-T1
Valid prediction for snap_scaffold_27-snap.1097-T1
Valid prediction for GlimmerHMM_glimmerT_57239-T1
Valid prediction for snap_scaffold_27-snap.1125-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_27-snap.1132-T1
Valid prediction for GlimmerHMM_glimmerT_57251-T1
Couldn't classify 100962, 101110
Couldn't classify 101739, 101925
Sorry, prediction pasa_asmbl_37172.p1 fails validation.
(CTA)	 GC	100962-101110	GT	AGG
(GTG)	 AG	101739-101925	GA	TCG
Valid prediction for Augustus_model.g37957.t1
Valid prediction for pasa_asmbl_36968.p1
Valid prediction for snap_scaffold_27-snap.1118-T1
Valid prediction for GlimmerHMM_glimmerT_57249-T1
Valid prediction for GlimmerHMM_glimmerT_57233-T1
Couldn't classify 145236, 145291
Sorry, prediction pasa_asmbl_36964.p1 fails validation.
(AGC)	 AC	145236-145291	GT	AGG
(GTC)	 AG	146340-146952	GT	AGG
(CTG)	 AG	147227-147371	GT	AGG
(AGC)	 AG	148689-148781	GT	GAG
(ACA)	 AG	149423-149568	GT	AGG
(CTG)	 AG	151557-151706	GT	AGG
(CGG)	 AG	152299-152498	GT	AGG
(GGA)	 AG	152731-152856	GT	AGG
(GAT)	 AG	153087-153319	GT	GGG
(GCC)	 AG	153888-154142	GT	AGG
(ATG)	 AG	154600-154715	CA	GAC
-recovered pasa_asmbl_36964.p1, terminal, 154600, 154715
-recovered pasa_asmbl_36964.p1, internal, 146340, 146952
-recovered pasa_asmbl_36964.p1, internal, 147227, 147371
-recovered pasa_asmbl_36964.p1, internal, 148689, 148781
-recovered pasa_asmbl_36964.p1, internal, 149423, 149568
-recovered pasa_asmbl_36964.p1, internal, 151557, 151706
-recovered pasa_asmbl_36964.p1, internal, 152299, 152498
-recovered pasa_asmbl_36964.p1, internal, 152731, 152856
-recovered pasa_asmbl_36964.p1, internal, 153087, 153319
-recovered pasa_asmbl_36964.p1, internal, 153888, 154142
Valid prediction for snap_scaffold_27-snap.1112-T1
Valid prediction for GlimmerHMM_glimmerT_57252-T1
Valid prediction for CodingQuarry_transcript_41886-T1
Valid prediction for GlimmerHMM_glimmerT_57236-T1
Valid prediction for snap_scaffold_27-snap.1103-T1
Valid prediction for snap_scaffold_27-snap.1121-T1
Valid prediction for GlimmerHMM_glimmerT_57261-T1
Valid prediction for HiQ_model.g37951.t1
Valid prediction for snap_scaffold_27-snap.1130-T1
Valid prediction for GlimmerHMM_glimmerT_57245-T1
Valid prediction for snap_scaffold_27-snap.1140-T1
Valid prediction for GlimmerHMM_glimmerT_57248-T1
Valid prediction for snap_scaffold_27-snap.1124-T1
Valid prediction for snap_scaffold_27-snap.1116-T1
Valid prediction for snap_scaffold_27-snap.1137-T1
Couldn't classify 143960, 144256
Sorry, prediction pasa_asmbl_36967.p1 fails validation.
(GGG)	 GC	143960-144256	GG	GTG
Valid prediction for Augustus_model.g37941.t1
Valid prediction for snap_scaffold_27-snap.1107-T1
Valid prediction for Augustus_model.g37942.t1
Valid prediction for HiQ_model.g37949.t1
Valid prediction for snap_scaffold_27-snap.1123-T1
Valid prediction for CodingQuarry_transcript_41883-T1
Valid prediction for Augustus_model.g37944.t1
Valid prediction for GlimmerHMM_glimmerT_57243-T1
Valid prediction for snap_scaffold_27-snap.1104-T1
Valid prediction for snap_scaffold_27-snap.1117-T1
Valid prediction for snap_scaffold_27-snap.1098-T1
Valid prediction for Augustus_model.g37953.t1
Valid prediction for HiQ_model.g37950.t1
Valid prediction for GlimmerHMM_glimmerT_57234-T1
Valid prediction for snap_scaffold_27-snap.1096-T1
Couldn't classify 207832, 207883
Sorry, prediction pasa_asmbl_36961.p1 fails validation.
(GCA)	 CG	207832-207883	GT	AGG
(TGC)	 AG	209103-209214	GT	GGG
(GTC)	 AG	211084-211226	GT	AGG
(GTG)	 AG	212180-212361	AC	GAA
-recovered pasa_asmbl_36961.p1, terminal, 212180, 212361
-recovered pasa_asmbl_36961.p1, internal, 209103, 209214
-recovered pasa_asmbl_36961.p1, internal, 211084, 211226
Valid prediction for GlimmerHMM_glimmerT_57257-T1
Valid prediction for snap_scaffold_27-snap.1110-T1
Valid prediction for snap_scaffold_27-snap.1133-T1
Valid prediction for Augustus_model.g37948.t1
Valid prediction for snap_scaffold_27-snap.1126-T1
Valid prediction for snap_scaffold_27-snap.1143-T1
Valid prediction for GlimmerHMM_glimmerT_57240-T1
Valid prediction for pasa_asmbl_36973.p1
Couldn't classify 103275, 103416
Couldn't classify 104607, 104657
Sorry, prediction pasa_asmbl_37186.p1 fails validation.
(GAC)	 AG	103275-103416	GT	AGG
(GGA)	 AG	104143-104249	GT	AGG
(AAC)	 AG	104607-104657	GT	AGG
-recovered pasa_asmbl_37186.p1, internal, 103275, 103416
-recovered pasa_asmbl_37186.p1, internal, 104143, 104249
-recovered pasa_asmbl_37186.p1, internal, 104607, 104657
Valid prediction for CodingQuarry_transcript_41884-T1
Valid prediction for snap_scaffold_27-snap.1141-T1
Valid prediction for GlimmerHMM_glimmerT_57258-T1
Valid prediction for GlimmerHMM_glimmerT_57247-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 23671, rend_intergenic: 16635  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42449, rend_intergenic: 23839  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49172, rend_intergenic: 43862  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52631, rend_intergenic: 49215  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56478, rend_intergenic: 55128  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71721, rend_intergenic: 67597  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98234, rend_intergenic: 74482  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126116, rend_intergenic: 123409  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137939, rend_intergenic: 130882  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155119, rend_intergenic: 143060  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162142, rend_intergenic: 155127  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163449, rend_intergenic: 163267  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172403, rend_intergenic: 163471  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 190851, rend_intergenic: 172786  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 201243, rend_intergenic: 193980  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 207652, rend_intergenic: 203592  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 221424, rend_intergenic: 208850  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 227449, rend_intergenic: 222101  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 229177
-exon list size: 475


building trellis

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-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 23671, rend_intergenic: 16635  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 42449, rend_intergenic: 23839  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49172, rend_intergenic: 43862  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 52631, rend_intergenic: 49215  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56478, rend_intergenic: 55128  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71721, rend_intergenic: 67597  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98234, rend_intergenic: 74482  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126116, rend_intergenic: 123409  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137939, rend_intergenic: 130882  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155119, rend_intergenic: 143060  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162142, rend_intergenic: 155127  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163449, rend_intergenic: 163267  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 172403, rend_intergenic: 163471  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 190851, rend_intergenic: 172786  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 201243, rend_intergenic: 193980  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 207652, rend_intergenic: 203592  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 221424, rend_intergenic: 208850  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 227449, rend_intergenic: 222101  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support