-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_10/scaffold_10_5997918-6243744

-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_25331-T1
Valid prediction for snap_scaffold_10-snap.1250-T1
Valid prediction for HiQ_model.g16990.t1
Valid prediction for pasa_asmbl_4495.p1
Valid prediction for snap_scaffold_10-snap.1257-T1
Valid prediction for snap_scaffold_10-snap.1277-T1
Valid prediction for GeneMark_model.43282_t
Valid prediction for GlimmerHMM_glimmerT_25349-T1
Valid prediction for snap_scaffold_10-snap.1276-T1
Valid prediction for HiQ_model.g16989.t1
Valid prediction for GeneMark_model.43278_t
Valid prediction for GlimmerHMM_glimmerT_25354-T1
Valid prediction for GlimmerHMM_glimmerT_25338-T1
Valid prediction for GeneMark_model.43307_t
Valid prediction for GlimmerHMM_glimmerT_25345-T1
Valid prediction for GeneMark_model.43294_t
Valid prediction for snap_scaffold_10-snap.1280-T1
Valid prediction for Augustus_model.g16993.t1
Valid prediction for snap_scaffold_10-snap.1253-T1
Valid prediction for GlimmerHMM_glimmerT_25337-T1
Valid prediction for Augustus_model.g17007.t1
Valid prediction for GeneMark_model.43276_t
Valid prediction for GlimmerHMM_glimmerT_25329-T1
Valid prediction for GeneMark_model.43283_t
Valid prediction for GeneMark_model.43305_t
Valid prediction for GlimmerHMM_glimmerT_25330-T1
Valid prediction for GeneMark_model.43269_t
Valid prediction for GlimmerHMM_glimmerT_25348-T1
Valid prediction for GeneMark_model.43301_t
Valid prediction for snap_scaffold_10-snap.1252-T1
Valid prediction for HiQ_model.g16995.t1
Valid prediction for GeneMark_model.43299_t
Valid prediction for snap_scaffold_10-snap.1283-T1
Valid prediction for snap_scaffold_10-snap.1281-T1
Valid prediction for pasa_asmbl_4503.p1
Couldn't classify 4269, 4442
Sorry, prediction pasa_asmbl_4494.p1 fails validation.
(GCT)	 AC	4269-4442	GT	TGG
(GGC)	 AG	4592-4703	GT	AGG
(ATA)	 AG	4840-4954	GT	TGG
(GAT)	 AG	5039-5088	GT	TAG
(TTC)	 AG	5213-5286	GT	CTG
(CAA)	 AG	5382-5432	GT	AGG
(ACA)	 AG	5525-5626	GT	AGG
(ATC)	 AG	5741-5869	GT	CGG
(CAT)	 AG	6012-6248	TC	AGT
-recovered pasa_asmbl_4494.p1, terminal, 6012, 6248
-recovered pasa_asmbl_4494.p1, internal, 4592, 4703
-recovered pasa_asmbl_4494.p1, internal, 4840, 4954
-recovered pasa_asmbl_4494.p1, internal, 5039, 5088
-recovered pasa_asmbl_4494.p1, internal, 5213, 5286
-recovered pasa_asmbl_4494.p1, internal, 5382, 5432
-recovered pasa_asmbl_4494.p1, internal, 5525, 5626
-recovered pasa_asmbl_4494.p1, internal, 5741, 5869
Valid prediction for HiQ_model.g16996.t1
Valid prediction for GeneMark_model.43306_t
Valid prediction for Augustus_model.g17011.t1
Valid prediction for GeneMark_model.43308_t
Valid prediction for GeneMark_model.43284_t
Valid prediction for GeneMark_model.43300_t
Valid prediction for snap_scaffold_10-snap.1251-T1
Valid prediction for CodingQuarry_transcript_5419-T1
Valid prediction for GeneMark_model.43270_t
Valid prediction for Augustus_model.g17013.t1
Valid prediction for Augustus_model.g17009.t1
Valid prediction for GeneMark_model.43271_t
Valid prediction for GeneMark_model.43304_t
Valid prediction for Augustus_model.g17010.t1
Valid prediction for GeneMark_model.43297_t
Valid prediction for CodingQuarry_transcript_5420-T1
Valid prediction for GlimmerHMM_glimmerT_25332-T1
Valid prediction for GeneMark_model.43274_t
Valid prediction for pasa_asmbl_4493.p1
Valid prediction for snap_scaffold_10-snap.1282-T1
Valid prediction for GeneMark_model.43303_t
Valid prediction for snap_scaffold_10-snap.1278-T1
Valid prediction for Augustus_model.g17001.t1
Valid prediction for GlimmerHMM_glimmerT_25350-T1
Valid prediction for snap_scaffold_10-snap.1261-T1
Valid prediction for snap_scaffold_10-snap.1267-T1
Valid prediction for snap_scaffold_10-snap.1287-T1
Valid prediction for HiQ_model.g16988.t1
Valid prediction for GlimmerHMM_glimmerT_25352-T1
Valid prediction for snap_scaffold_10-snap.1256-T1
Valid prediction for GlimmerHMM_glimmerT_25335-T1
Valid prediction for snap_scaffold_10-snap.1284-T1
Valid prediction for snap_scaffold_10-snap.1279-T1
Valid prediction for GeneMark_model.43275_t
Valid prediction for GeneMark_model.43280_t

-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 GeneMark_model.43277_t
Valid prediction for GeneMark_model.43286_t
Valid prediction for GeneMark_model.43292_t
Valid prediction for pasa_asmbl_3354.p1
Valid prediction for HiQ_model.g16991.t1
Valid prediction for snap_scaffold_10-snap.1269-T1
Valid prediction for snap_scaffold_10-snap.1268-T1
Valid prediction for Augustus_model.g17012.t1
Valid prediction for Augustus_model.g16998.t1
Valid prediction for Augustus_model.g17005.t1
Valid prediction for GeneMark_model.43273_t
Valid prediction for CodingQuarry_transcript_5422-T1
Valid prediction for Augustus_model.g17003.t1
Valid prediction for snap_scaffold_10-snap.1275-T1
Valid prediction for GlimmerHMM_glimmerT_25347-T1
Valid prediction for GlimmerHMM_glimmerT_25353-T1
Valid prediction for GeneMark_model.43293_t
Valid prediction for GlimmerHMM_glimmerT_25341-T1
Valid prediction for Augustus_model.g16992.t1
Valid prediction for snap_scaffold_10-snap.1254-T1
Couldn't classify 151089, 151517
Sorry, prediction pasa_asmbl_3351.p1 fails validation.
(ATT)	 AG	151089-151517	AT	ACA
Valid prediction for GeneMark_model.43296_t
Valid prediction for GeneMark_model.43281_t
Valid prediction for GeneMark_model.43295_t
Valid prediction for GlimmerHMM_glimmerT_25333-T1
Valid prediction for pasa_asmbl_3335.p1
Valid prediction for GlimmerHMM_glimmerT_25342-T1
Valid prediction for pasa_asmbl_3348.p1
Valid prediction for CodingQuarry_transcript_5426-T1
Valid prediction for GeneMark_model.43289_t
Valid prediction for snap_scaffold_10-snap.1255-T1
Valid prediction for snap_scaffold_10-snap.1258-T1
Valid prediction for HiQ_model.g17004.t1
Valid prediction for snap_scaffold_10-snap.1286-T1
Valid prediction for GeneMark_model.43285_t
Valid prediction for Augustus_model.g16999.t1
Valid prediction for snap_scaffold_10-snap.1273-T1
Valid prediction for snap_scaffold_10-snap.1260-T1
Valid prediction for Augustus_model.g17000.t1
Valid prediction for GlimmerHMM_glimmerT_25344-T1
Valid prediction for snap_scaffold_10-snap.1259-T1
Valid prediction for snap_scaffold_10-snap.1266-T1
Valid prediction for CodingQuarry_transcript_5421-T1
Couldn't classify 149949, 150758
Sorry, prediction pasa_asmbl_3353.p1 fails validation.
(ATG)	 AG	149949-150758	CC	TAC
Valid prediction for GeneMark_model.43302_t
Valid prediction for snap_scaffold_10-snap.1263-T1
Couldn't classify 220552, 220878
Sorry, prediction pasa_asmbl_4009.p1 fails validation.
(ATG)	 GC	220552-220878	AC	CGA
Valid prediction for GlimmerHMM_glimmerT_25339-T1
Valid prediction for snap_scaffold_10-snap.1285-T1
Couldn't classify 108968, 108995
Couldn't classify 112767, 112853
Sorry, prediction pasa_asmbl_3355.p1 fails validation.
(GGG)	 CA	108968-108995	GT	AGG
(GTC)	 AG	109487-109617	GT	TGG
(GGT)	 AG	111022-111057	GT	AGG
(GGA)	 AG	111943-111978	GT	CAG
(GGC)	 AG	112767-112853	AG	GCA
-recovered pasa_asmbl_3355.p1, internal, 109487, 109617
-recovered pasa_asmbl_3355.p1, internal, 111022, 111057
-recovered pasa_asmbl_3355.p1, internal, 111943, 111978
Valid prediction for GlimmerHMM_glimmerT_25346-T1
Valid prediction for snap_scaffold_10-snap.1272-T1
Valid prediction for GeneMark_model.43288_t
Valid prediction for snap_scaffold_10-snap.1274-T1
Valid prediction for GlimmerHMM_glimmerT_25351-T1
Valid prediction for Augustus_model.g16994.t1
Valid prediction for GlimmerHMM_glimmerT_25340-T1
Valid prediction for Augustus_model.g17006.t1
Valid prediction for snap_scaffold_10-snap.1264-T1
Valid prediction for GeneMark_model.43290_t
Valid prediction for CodingQuarry_transcript_5427-T1
Valid prediction for GeneMark_model.43272_t
Valid prediction for GeneMark_model.43279_t
Valid prediction for Augustus_model.g17008.t1
Valid prediction for GlimmerHMM_glimmerT_25336-T1
Valid prediction for CodingQuarry_transcript_5424-T1
Valid prediction for CodingQuarry_transcript_5428-T1
Valid prediction for HiQ_model.g16997.t1
Couldn't classify 154093, 154212
Sorry, prediction pasa_asmbl_4012.p1 fails validation.
(AGT)	 TA	154093-154212	GT	AGG
(GAC)	 AG	154322-154822	GA	AGG
-recovered pasa_asmbl_4012.p1, terminal, 154322, 154822
Valid prediction for GlimmerHMM_glimmerT_25343-T1
Valid prediction for snap_scaffold_10-snap.1262-T1
Valid prediction for GeneMark_model.43291_t
Valid prediction for GlimmerHMM_glimmerT_25334-T1
Valid prediction for CodingQuarry_transcript_5429-T1
Valid prediction for GeneMark_model.43287_t
Valid prediction for snap_scaffold_10-snap.1288-T1
Valid prediction for snap_scaffold_10-snap.1270-T1
Valid prediction for snap_scaffold_10-snap.1271-T1
Valid prediction for Augustus_model.g17002.t1
Valid prediction for snap_scaffold_10-snap.1265-T1
Valid prediction for GeneMark_model.43298_t
Couldn't classify 104943, 104997
Couldn't classify 105946, 106082
Sorry, prediction pasa_asmbl_4078.p1 fails validation.
(AGG)	 GC	104943-104997	GT	AGG
(ACT)	 AG	105445-105579	GT	GGG
(ACA)	 AG	105946-106082	GG	GAG
-recovered pasa_asmbl_4078.p1, internal, 105445, 105579

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 66824, rend_intergenic: 54663  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82840, rend_intergenic: 81791  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 232157, rend_intergenic: 231491  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 245827
-exon list size: 512


building trellis

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-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 66824, rend_intergenic: 54663  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 82840, rend_intergenic: 81791  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 232157, rend_intergenic: 231491  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 23 predictions persist after filtering for low support