-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_14/scaffold_14_5392622-5601170

-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 CodingQuarry_transcript_15600-T1
Valid prediction for HiQ_model.g23295.t1
Valid prediction for GeneMark_model.59308_t
Valid prediction for snap_scaffold_14-snap.1117-T1
Couldn't classify 167423, 167712
Sorry, prediction pasa_asmbl_12000.p1 fails validation.
(GAG)	 AG	167423-167712	GT	AAG
(ACA)	 AG	167913-168118	GT	AGG
(GTA)	 AG	168515-168606	GT	TGG
(TAA)	 AG	168718-168720	TA	AAT
-recovered pasa_asmbl_12000.p1, terminal, 168718, 168720
-recovered pasa_asmbl_12000.p1, internal, 167423, 167712
-recovered pasa_asmbl_12000.p1, internal, 167913, 168118
-recovered pasa_asmbl_12000.p1, internal, 168515, 168606
Valid prediction for GeneMark_model.59297_t
Valid prediction for HiQ_model.g23276.t1
Valid prediction for GeneMark_model.59282_t
Couldn't classify 174173, 174195
Sorry, prediction pasa_asmbl_12003.p1 fails validation.
(AAT)	 AC	174173-174195	GT	AGG
(CAT)	 AG	174378-174550	GT	AGG
(GGA)	 AG	174744-174994	GA	GAG
-recovered pasa_asmbl_12003.p1, terminal, 174744, 174994
-recovered pasa_asmbl_12003.p1, internal, 174378, 174550
Valid prediction for GeneMark_model.59278_t
Valid prediction for pasa_asmbl_12005.p1
Valid prediction for pasa_asmbl_12006.p1
Valid prediction for GlimmerHMM_glimmerT_34621-T1
Valid prediction for GlimmerHMM_glimmerT_34639-T1
Valid prediction for HiQ_model.g23291.t1
Valid prediction for GlimmerHMM_glimmerT_34633-T1
Valid prediction for Augustus_model.g23271.t1
Valid prediction for snap_scaffold_14-snap.1119-T1
Valid prediction for snap_scaffold_14-snap.1110-T1
Valid prediction for GeneMark_model.59298_t
Valid prediction for Augustus_model.g23285.t1
Couldn't classify 56763, 56805
Sorry, prediction pasa_asmbl_11990.p1 fails validation.
(AAC)	 AT	56763-56805	GC	AGG
(TAT)	 AG	57080-57208	GT	TGG
(GCA)	 AG	57343-57491	GT	AGG
(ATT)	 AG	57714-57783	GT	GGG
(CGA)	 AG	57941-58139	GT	GGG
(TGT)	 AG	58299-58467	GT	TGG
(ATT)	 AG	58583-58791	GT	GTG
(GGA)	 AG	58894-58920	GT	GAG
(GAT)	 AG	59504-59683	GT	CAG
(CAA)	 AG	60013-60039	GT	AGG
(GAA)	 AG	60132-60138	CA	GAC
-recovered pasa_asmbl_11990.p1, terminal, 58894, 58920
-recovered pasa_asmbl_11990.p1, terminal, 60132, 60138
-recovered pasa_asmbl_11990.p1, internal, 57080, 57208
-recovered pasa_asmbl_11990.p1, internal, 57343, 57491
-recovered pasa_asmbl_11990.p1, internal, 57714, 57783
-recovered pasa_asmbl_11990.p1, internal, 57941, 58139
-recovered pasa_asmbl_11990.p1, internal, 58299, 58467
-recovered pasa_asmbl_11990.p1, internal, 58583, 58791
-recovered pasa_asmbl_11990.p1, internal, 58894, 58920
-recovered pasa_asmbl_11990.p1, internal, 59504, 59683
-recovered pasa_asmbl_11990.p1, internal, 60013, 60039
Couldn't classify 39442, 41271
Sorry, prediction pasa_asmbl_11989.p1 fails validation.
(CCT)	 CT	39442-41271	GT	AGG
Valid prediction for CodingQuarry_transcript_15602-T1
Valid prediction for GlimmerHMM_glimmerT_34613-T1
Couldn't classify 140567, 140637
Sorry, prediction pasa_asmbl_11997.p1 fails validation.
(CCG)	 AA	140567-140637	GT	ACG
(GTT)	 AG	140884-141029	GT	AAG
(GAA)	 AG	141271-141324	GT	AGG
(GCA)	 AG	141452-141540	GT	GGG
(GTC)	 AG	141988-142063	GT	AGG
(AGT)	 AG	142204-142316	GA	GAG
-recovered pasa_asmbl_11997.p1, terminal, 142204, 142316
-recovered pasa_asmbl_11997.p1, internal, 140884, 141029
-recovered pasa_asmbl_11997.p1, internal, 141271, 141324
-recovered pasa_asmbl_11997.p1, internal, 141452, 141540
-recovered pasa_asmbl_11997.p1, internal, 141988, 142063
Valid prediction for HiQ_model.g23286.t1
Valid prediction for GlimmerHMM_glimmerT_34615-T1
Valid prediction for GlimmerHMM_glimmerT_34642-T1
Valid prediction for GlimmerHMM_glimmerT_34641-T1
Valid prediction for pasa_asmbl_12004.p1
Valid prediction for pasa_asmbl_12008.p1
Valid prediction for HiQ_model.g23292.t1
Valid prediction for Augustus_model.g23272.t1
Valid prediction for GeneMark_model.59302_t
Valid prediction for snap_scaffold_14-snap.1120-T1
Valid prediction for HiQ_model.g23282.t1
Valid prediction for Augustus_model.g23274.t1
Valid prediction for snap_scaffold_14-snap.1122-T1
Valid prediction for GlimmerHMM_glimmerT_34630-T1
Valid prediction for Augustus_model.g23289.t1
Valid prediction for GlimmerHMM_glimmerT_34626-T1
Valid prediction for snap_scaffold_14-snap.1126-T1
Valid prediction for snap_scaffold_14-snap.1123-T1
Valid prediction for snap_scaffold_14-snap.1100-T1
Valid prediction for GeneMark_model.59280_t
Valid prediction for snap_scaffold_14-snap.1098-T1
Valid prediction for GlimmerHMM_glimmerT_34634-T1
Valid prediction for snap_scaffold_14-snap.1129-T1
Valid prediction for snap_scaffold_14-snap.1115-T1
Valid prediction for GeneMark_model.59299_t
Valid prediction for GeneMark_model.59288_t
Valid prediction for GeneMark_model.59306_t
Valid prediction for snap_scaffold_14-snap.1114-T1
Valid prediction for snap_scaffold_14-snap.1127-T1
Valid prediction for GeneMark_model.59285_t
Valid prediction for snap_scaffold_14-snap.1124-T1
Valid prediction for GlimmerHMM_glimmerT_34628-T1
Valid prediction for snap_scaffold_14-snap.1118-T1
Valid prediction for GeneMark_model.59304_t
Couldn't classify 157487, 157663
Couldn't classify 158454, 158693
Sorry, prediction pasa_asmbl_11999.p1 fails validation.
(AAC)	 AG	157487-157663	GT	TGG
(GTT)	 AG	158454-158693	CC	CCC
-recovered pasa_asmbl_11999.p1, internal, 157487, 157663
Valid prediction for Augustus_model.g23287.t1
Valid prediction for GeneMark_model.59293_t
Valid prediction for snap_scaffold_14-snap.1109-T1
Valid prediction for Augustus_model.g23294.t1
Valid prediction for snap_scaffold_14-snap.1131-T1
Couldn't classify 173199, 173467
Couldn't classify 174086, 174118
Sorry, prediction pasa_asmbl_12002.p1 fails validation.
(ATA)	 CC	173199-173467	GT	CGG
(CTA)	 AG	173610-173793	GT	AGG
(GTG)	 AG	174086-174118	GG	TTG
-recovered pasa_asmbl_12002.p1, internal, 173610, 173793
Valid prediction for snap_scaffold_14-snap.1116-T1
Valid prediction for snap_scaffold_14-snap.1121-T1
Valid prediction for snap_scaffold_14-snap.1108-T1
Valid prediction for GlimmerHMM_glimmerT_34627-T1
Valid prediction for CodingQuarry_transcript_15598-T1
Valid prediction for GlimmerHMM_glimmerT_34635-T1
Valid prediction for GlimmerHMM_glimmerT_34622-T1
Valid prediction for pasa_asmbl_11995.p1
Valid prediction for GlimmerHMM_glimmerT_34632-T1
Valid prediction for GlimmerHMM_glimmerT_34619-T1
Valid prediction for GeneMark_model.59310_t
Valid prediction for GlimmerHMM_glimmerT_34638-T1
Valid prediction for GeneMark_model.59301_t
Valid prediction for GlimmerHMM_glimmerT_34625-T1
Valid prediction for snap_scaffold_14-snap.1104-T1
Valid prediction for CodingQuarry_transcript_15601-T1
Valid prediction for snap_scaffold_14-snap.1105-T1
Valid prediction for GeneMark_model.59290_t
Valid prediction for snap_scaffold_14-snap.1102-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.g23279.t1
Valid prediction for GeneMark_model.59279_t
Valid prediction for GeneMark_model.59309_t
Valid prediction for GlimmerHMM_glimmerT_34637-T1
Valid prediction for GlimmerHMM_glimmerT_34612-T1
Valid prediction for GlimmerHMM_glimmerT_34620-T1
Valid prediction for CodingQuarry_transcript_15599-T1
Valid prediction for snap_scaffold_14-snap.1097-T1
Valid prediction for GeneMark_model.59300_t
Valid prediction for GlimmerHMM_glimmerT_34629-T1
Valid prediction for Augustus_model.g23280.t1
Valid prediction for snap_scaffold_14-snap.1112-T1
Valid prediction for HiQ_model.g23278.t1
Valid prediction for GeneMark_model.59303_t
Valid prediction for GlimmerHMM_glimmerT_34624-T1
Valid prediction for GeneMark_model.59295_t
Valid prediction for GlimmerHMM_glimmerT_34616-T1
Valid prediction for Augustus_model.g23283.t1
Valid prediction for snap_scaffold_14-snap.1096-T1
Valid prediction for GlimmerHMM_glimmerT_34618-T1
Valid prediction for CodingQuarry_transcript_15595-T1
Valid prediction for Augustus_model.g23281.t1
Valid prediction for GeneMark_model.59281_t
Valid prediction for Augustus_model.g23275.t1
Couldn't classify 85877, 86030
Sorry, prediction pasa_asmbl_13061.p1 fails validation.
(TGG)	 GC	85877-86030	GT	GAG
(AAT)	 AG	87453-87586	GT	AGG
(CTG)	 AG	88027-88136	GT	ACG
(CAT)	 AG	88350-88476	GT	TAG
(GTT)	 AG	88715-88807	GT	GAG
-recovered pasa_asmbl_13061.p1, terminal, 88715, 88807
-recovered pasa_asmbl_13061.p1, internal, 87453, 87586
-recovered pasa_asmbl_13061.p1, internal, 88027, 88136
-recovered pasa_asmbl_13061.p1, internal, 88350, 88476
-recovered pasa_asmbl_13061.p1, internal, 88715, 88807
Valid prediction for HiQ_model.g23293.t1
Valid prediction for GeneMark_model.59292_t
Valid prediction for GeneMark_model.59294_t
Couldn't classify 12880, 13131
Sorry, prediction pasa_asmbl_13064.p1 fails validation.
(TTT)	 CC	12880-13131	GT	AGG
(CTG)	 AG	13857-14477	AA	GAA
-recovered pasa_asmbl_13064.p1, terminal, 13857, 14477
Valid prediction for GeneMark_model.59283_t
Valid prediction for snap_scaffold_14-snap.1103-T1
Valid prediction for GeneMark_model.59307_t
Valid prediction for GlimmerHMM_glimmerT_34640-T1
Valid prediction for Augustus_model.g23290.t1
Valid prediction for Augustus_model.g23273.t1
Valid prediction for snap_scaffold_14-snap.1125-T1
Valid prediction for CodingQuarry_transcript_15593-T1
Valid prediction for GeneMark_model.59284_t
Valid prediction for GlimmerHMM_glimmerT_34617-T1
Valid prediction for HiQ_model.g23288.t1
Valid prediction for GeneMark_model.59291_t
Valid prediction for snap_scaffold_14-snap.1099-T1
Valid prediction for snap_scaffold_14-snap.1107-T1
Valid prediction for snap_scaffold_14-snap.1101-T1
Valid prediction for GeneMark_model.59296_t
Valid prediction for GeneMark_model.59287_t
Valid prediction for HiQ_model.g23284.t1
Valid prediction for GlimmerHMM_glimmerT_34636-T1
Valid prediction for pasa_asmbl_13060.p1
Valid prediction for GeneMark_model.59286_t
Valid prediction for snap_scaffold_14-snap.1095-T1
Valid prediction for GlimmerHMM_glimmerT_34623-T1
Valid prediction for snap_scaffold_14-snap.1128-T1
Valid prediction for CodingQuarry_transcript_15597-T1
Valid prediction for GlimmerHMM_glimmerT_34614-T1
Valid prediction for snap_scaffold_14-snap.1111-T1
Valid prediction for Augustus_model.g23277.t1
Valid prediction for CodingQuarry_transcript_15594-T1
Valid prediction for CodingQuarry_transcript_15596-T1
Valid prediction for snap_scaffold_14-snap.1106-T1
Valid prediction for snap_scaffold_14-snap.1130-T1
Valid prediction for Augustus_model.g23270.t1
Valid prediction for snap_scaffold_14-snap.1113-T1
Valid prediction for GlimmerHMM_glimmerT_34631-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 32029, rend_intergenic: 29987  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55396, rend_intergenic: 47744  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88580, rend_intergenic: 86489  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 17179, rend_intergenic: 17176  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 208549
-exon list size: 564


building trellis

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98.2    
98.4    
98.6    
98.8    
98.9    
99.1    
99.3    
99.5    
99.6    
99.8    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 32029, rend_intergenic: 29987  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55396, rend_intergenic: 47744  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88580, rend_intergenic: 86489  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 17179, rend_intergenic: 17176  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 26 predictions persist after filtering for low support