-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_1/scaffold_1_6560610-6708241

-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_931-T1
Valid prediction for GeneMark_model.1146_t
Valid prediction for GlimmerHMM_glimmerT_908-T1
Valid prediction for snap_scaffold_1-snap.1132-T1
Valid prediction for snap_scaffold_1-snap.1121-T1
Valid prediction for GeneMark_model.1144_t
Valid prediction for GlimmerHMM_glimmerT_914-T1
Valid prediction for GeneMark_model.1122_t
Valid prediction for CodingQuarry_transcript_2657-T1
Valid prediction for Augustus_model.g677.t1
Valid prediction for GlimmerHMM_glimmerT_920-T1
Valid prediction for snap_scaffold_1-snap.1124-T1
Valid prediction for GlimmerHMM_glimmerT_902-T1
Valid prediction for Augustus_model.g676.t1
Valid prediction for GeneMark_model.1114_t
Valid prediction for snap_scaffold_1-snap.1142-T1
Valid prediction for snap_scaffold_1-snap.1129-T1
Valid prediction for GlimmerHMM_glimmerT_923-T1
Valid prediction for GlimmerHMM_glimmerT_910-T1
Valid prediction for GeneMark_model.1135_t
Valid prediction for GeneMark_model.1133_t
Valid prediction for Augustus_model.g683.t1
Valid prediction for Augustus_model.g682.t1
Valid prediction for snap_scaffold_1-snap.1112-T1
Valid prediction for GeneMark_model.1124_t
Valid prediction for GlimmerHMM_glimmerT_918-T1
Valid prediction for GlimmerHMM_glimmerT_899-T1
Valid prediction for snap_scaffold_1-snap.1109-T1
Valid prediction for GlimmerHMM_glimmerT_905-T1
Valid prediction for GlimmerHMM_glimmerT_926-T1
Valid prediction for GlimmerHMM_glimmerT_903-T1
Valid prediction for Augustus_model.g679.t1
Valid prediction for GlimmerHMM_glimmerT_912-T1
Valid prediction for GeneMark_model.1140_t
Couldn't classify 99173, 99494
Sorry, prediction pasa_asmbl_1833.p1 fails validation.
(GGT)	 AC	99173-99494	GT	AGG
(GTC)	 AG	100018-100122	GT	AGG
(GTC)	 AG	100910-101101	GT	AGG
(GTA)	 AG	101238-101336	GT	AGG
(GTC)	 AG	101590-101702	CT	AGC
-recovered pasa_asmbl_1833.p1, terminal, 101590, 101702
-recovered pasa_asmbl_1833.p1, internal, 100018, 100122
-recovered pasa_asmbl_1833.p1, internal, 100910, 101101
-recovered pasa_asmbl_1833.p1, internal, 101238, 101336
Valid prediction for GeneMark_model.1150_t
Valid prediction for GlimmerHMM_glimmerT_922-T1
Valid prediction for CodingQuarry_transcript_2656-T1
Valid prediction for GeneMark_model.1142_t
Valid prediction for GeneMark_model.1113_t
Valid prediction for snap_scaffold_1-snap.1110-T1
Couldn't classify 93417, 93545
Couldn't classify 95346, 95513
Sorry, prediction pasa_asmbl_2824.p1 fails validation.
(GTG)	 AG	93417-93545	GT	CGG
(AGG)	 AG	95346-95513	CA	GCC
-recovered pasa_asmbl_2824.p1, internal, 93417, 93545
Valid prediction for GeneMark_model.1149_t
Valid prediction for Augustus_model.g670.t1
Valid prediction for snap_scaffold_1-snap.1143-T1
Valid prediction for snap_scaffold_1-snap.1114-T1
Valid prediction for GeneMark_model.1138_t
Valid prediction for Augustus_model.g681.t1
Valid prediction for GlimmerHMM_glimmerT_904-T1
Valid prediction for snap_scaffold_1-snap.1119-T1
Valid prediction for snap_scaffold_1-snap.1123-T1
Valid prediction for GeneMark_model.1109_t
Valid prediction for GlimmerHMM_glimmerT_911-T1
Valid prediction for snap_scaffold_1-snap.1117-T1
Valid prediction for snap_scaffold_1-snap.1130-T1
Valid prediction for snap_scaffold_1-snap.1134-T1
Valid prediction for Augustus_model.g667.t1
Valid prediction for GeneMark_model.1129_t
Valid prediction for snap_scaffold_1-snap.1133-T1
Valid prediction for snap_scaffold_1-snap.1138-T1
Valid prediction for GeneMark_model.1128_t
Valid prediction for pasa_asmbl_1832.p1
Valid prediction for GlimmerHMM_glimmerT_924-T1
Valid prediction for Augustus_model.g687.t1
Valid prediction for Augustus_model.g674.t1
Valid prediction for GeneMark_model.1117_t
Valid prediction for snap_scaffold_1-snap.1115-T1
Valid prediction for snap_scaffold_1-snap.1140-T1
Valid prediction for Augustus_model.g688.t1
Valid prediction for snap_scaffold_1-snap.1125-T1
Valid prediction for GeneMark_model.1130_t
Valid prediction for Augustus_model.g669.t1
Valid prediction for Augustus_model.g680.t1
Valid prediction for snap_scaffold_1-snap.1116-T1
Valid prediction for GeneMark_model.1111_t
Valid prediction for GlimmerHMM_glimmerT_928-T1
Valid prediction for HiQ_model.g671.t1
Couldn't classify 119895, 121181
Sorry, prediction pasa_asmbl_1838.p1 fails validation.
(GAC)	 GC	119895-121181	GT	AGG
(GAG)	 AG	121317-121334	GC	AAG
-recovered pasa_asmbl_1838.p1, terminal, 121317, 121334
-recovered pasa_asmbl_1838.p1, internal, 121317, 121334
Valid prediction for GeneMark_model.1143_t
Valid prediction for GeneMark_model.1115_t
Valid prediction for Augustus_model.g685.t1
Valid prediction for GeneMark_model.1120_t
Valid prediction for snap_scaffold_1-snap.1136-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 Augustus_model.g668.t1
Valid prediction for Augustus_model.g678.t1
Valid prediction for GeneMark_model.1118_t
Valid prediction for GlimmerHMM_glimmerT_901-T1
Valid prediction for Augustus_model.g684.t1
Valid prediction for GlimmerHMM_glimmerT_917-T1
Valid prediction for GeneMark_model.1141_t
Valid prediction for snap_scaffold_1-snap.1113-T1
Valid prediction for GlimmerHMM_glimmerT_900-T1
Valid prediction for snap_scaffold_1-snap.1137-T1
Valid prediction for GlimmerHMM_glimmerT_909-T1
Valid prediction for GlimmerHMM_glimmerT_916-T1
Valid prediction for GlimmerHMM_glimmerT_927-T1
Valid prediction for snap_scaffold_1-snap.1126-T1
Valid prediction for snap_scaffold_1-snap.1139-T1
Valid prediction for GlimmerHMM_glimmerT_929-T1
Valid prediction for GeneMark_model.1134_t
Valid prediction for GlimmerHMM_glimmerT_915-T1
Valid prediction for GeneMark_model.1125_t
Valid prediction for snap_scaffold_1-snap.1118-T1
Valid prediction for snap_scaffold_1-snap.1111-T1
Valid prediction for GeneMark_model.1112_t
Valid prediction for GeneMark_model.1110_t
Valid prediction for Augustus_model.g672.t1
Valid prediction for GeneMark_model.1123_t
Valid prediction for snap_scaffold_1-snap.1141-T1
Valid prediction for GeneMark_model.1139_t
Valid prediction for GlimmerHMM_glimmerT_921-T1
Valid prediction for GeneMark_model.1145_t
Valid prediction for Augustus_model.g686.t1
Valid prediction for snap_scaffold_1-snap.1120-T1
Valid prediction for GlimmerHMM_glimmerT_919-T1
Valid prediction for GeneMark_model.1137_t
Valid prediction for GeneMark_model.1131_t
Valid prediction for GeneMark_model.1121_t
Valid prediction for GeneMark_model.1147_t
Valid prediction for pasa_asmbl_385.p1
Valid prediction for GlimmerHMM_glimmerT_907-T1
Valid prediction for GlimmerHMM_glimmerT_930-T1
Couldn't classify 131789, 131828
Couldn't classify 134296, 134437
Sorry, prediction pasa_asmbl_381.p1 fails validation.
(GAT)	 CC	131789-131828	GT	TGG
(AGC)	 AG	131956-132027	GT	CGG
(ATG)	 AG	132160-132275	GT	CGG
(GGT)	 AG	132782-132843	GT	AGG
(GTG)	 AG	132980-133292	GT	CGG
(TTG)	 AG	133951-134051	GT	AGG
(CAA)	 AG	134296-134437	GT	GGG
add_exon() Sorry, pasa_asmbl_381.p1 132160-132275-initial-1 is invalid.
-recovered pasa_asmbl_381.p1, initial, 132160, 132275
-recovered pasa_asmbl_381.p1, internal, 131956, 132027
-recovered pasa_asmbl_381.p1, internal, 132160, 132275
-recovered pasa_asmbl_381.p1, internal, 132782, 132843
-recovered pasa_asmbl_381.p1, internal, 132980, 133292
-recovered pasa_asmbl_381.p1, internal, 133951, 134051
-recovered pasa_asmbl_381.p1, internal, 134296, 134437
Valid prediction for GeneMark_model.1116_t
Valid prediction for snap_scaffold_1-snap.1131-T1
Valid prediction for snap_scaffold_1-snap.1122-T1
Valid prediction for snap_scaffold_1-snap.1135-T1
Valid prediction for GeneMark_model.1119_t
Valid prediction for Augustus_model.g673.t1
Valid prediction for Augustus_model.g675.t1
Valid prediction for GeneMark_model.1136_t
Valid prediction for GlimmerHMM_glimmerT_925-T1
Valid prediction for snap_scaffold_1-snap.1127-T1
Valid prediction for GeneMark_model.1132_t
Valid prediction for snap_scaffold_1-snap.1128-T1
Valid prediction for GlimmerHMM_glimmerT_913-T1
Valid prediction for GlimmerHMM_glimmerT_906-T1
Valid prediction for GeneMark_model.1127_t
Valid prediction for GeneMark_model.1126_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 11200, rend_intergenic: 8178  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44321, rend_intergenic: 41329  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51308, rend_intergenic: 47705  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58591, rend_intergenic: 53783  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75322, rend_intergenic: 65418  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80676, rend_intergenic: 75896  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89612, rend_intergenic: 87589  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97534, rend_intergenic: 90359  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101813, rend_intergenic: 100136  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108856, rend_intergenic: 107362  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130298, rend_intergenic: 126996  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136999, rend_intergenic: 130770  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 6580, rend_intergenic: 6577  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 147632
-exon list size: 604


building trellis

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-found 35 predictions from path traversal
Error with prediction: snap lend_intergenic: 11200, rend_intergenic: 8178  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44321, rend_intergenic: 41329  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51308, rend_intergenic: 47705  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 58591, rend_intergenic: 53783  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75322, rend_intergenic: 65418  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80676, rend_intergenic: 75896  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89612, rend_intergenic: 87589  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97534, rend_intergenic: 90359  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101813, rend_intergenic: 100136  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108856, rend_intergenic: 107362  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 130298, rend_intergenic: 126996  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136999, rend_intergenic: 130770  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 6580, rend_intergenic: 6577  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support