-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_14/scaffold_14_6384635-6530206

-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_14-snap.1348-T1
Valid prediction for snap_scaffold_14-snap.1327-T1
Couldn't classify 33814, 33991
Couldn't classify 34668, 34834
Sorry, prediction pasa_asmbl_12057.p1 fails validation.
(CTT)	 AA	33814-33991	GT	ACG
(AGT)	 AG	34091-34249	GT	AGG
(AGT)	 AG	34424-34561	GT	ATG
(CAA)	 AG	34668-34834	AG	TAA
-recovered pasa_asmbl_12057.p1, internal, 34091, 34249
-recovered pasa_asmbl_12057.p1, internal, 34424, 34561
Valid prediction for GlimmerHMM_glimmerT_34768-T1
Valid prediction for GeneMark_model.59589_t
Couldn't classify 120358, 120416
Couldn't classify 121667, 121759
Sorry, prediction pasa_asmbl_12058.p1 fails validation.
(GTC)	 CT	120358-120416	GT	GGG
(AAC)	 AG	120993-121117	GT	AGG
(GGA)	 AG	121213-121328	GT	CCG
(TCT)	 AG	121667-121759	CC	TCC
-recovered pasa_asmbl_12058.p1, internal, 120993, 121117
-recovered pasa_asmbl_12058.p1, internal, 121213, 121328
Valid prediction for GlimmerHMM_glimmerT_34772-T1
Valid prediction for GlimmerHMM_glimmerT_34778-T1
Valid prediction for snap_scaffold_14-snap.1326-T1
Valid prediction for Augustus_model.g23385.t1
Valid prediction for Augustus_model.g23375.t1
Valid prediction for GeneMark_model.59572_t
Valid prediction for Augustus_model.g23386.t1
Valid prediction for snap_scaffold_14-snap.1321-T1
Valid prediction for CodingQuarry_transcript_15619-T1
Valid prediction for snap_scaffold_14-snap.1339-T1
Valid prediction for snap_scaffold_14-snap.1345-T1
Valid prediction for GeneMark_model.59591_t
Valid prediction for GeneMark_model.59590_t
Valid prediction for GeneMark_model.59578_t
Valid prediction for GeneMark_model.59581_t
Valid prediction for snap_scaffold_14-snap.1351-T1
Valid prediction for snap_scaffold_14-snap.1332-T1
Valid prediction for snap_scaffold_14-snap.1325-T1
Couldn't classify 124336, 125436
Sorry, prediction pasa_asmbl_12060.p1 fails validation.
(GCC)	 AG	124336-125436	AC	GCA
Valid prediction for GlimmerHMM_glimmerT_34776-T1
Valid prediction for GlimmerHMM_glimmerT_34794-T1
Valid prediction for GlimmerHMM_glimmerT_34795-T1
Valid prediction for GeneMark_model.59575_t
Valid prediction for snap_scaffold_14-snap.1329-T1
Valid prediction for HiQ_model.g23381.t1
Valid prediction for snap_scaffold_14-snap.1357-T1
Valid prediction for GeneMark_model.59594_t
Valid prediction for snap_scaffold_14-snap.1341-T1
Valid prediction for Augustus_model.g23370.t1
Valid prediction for pasa_asmbl_12055.p1
Valid prediction for Augustus_model.g23387.t1
Valid prediction for Augustus_model.g23376.t1
Valid prediction for snap_scaffold_14-snap.1346-T1
Valid prediction for snap_scaffold_14-snap.1350-T1
Valid prediction for GlimmerHMM_glimmerT_34789-T1
Valid prediction for GlimmerHMM_glimmerT_34773-T1
Valid prediction for GeneMark_model.59583_t
Valid prediction for snap_scaffold_14-snap.1353-T1
Valid prediction for GeneMark_model.59598_t
Valid prediction for GeneMark_model.59592_t
Couldn't classify 123385, 123846
Sorry, prediction pasa_asmbl_12059.p1 fails validation.
(GCC)	 AT	123385-123846	CC	CCC
Valid prediction for GeneMark_model.59579_t
Valid prediction for snap_scaffold_14-snap.1337-T1
Valid prediction for GeneMark_model.59596_t
Valid prediction for GlimmerHMM_glimmerT_34790-T1
Couldn't classify 41104, 41184
Sorry, prediction pasa_asmbl_12669.p1 fails validation.
(ATG)	 AC	38953-39025	GT	AGG
(CGG)	 AG	39336-39465	GT	GAG
(GGA)	 AG	39719-39915	GT	CAG
(TAA)	 AG	40097-40251	GT	ATG
(GTT)	 AG	40341-40509	GT	TGG
(CGT)	 AG	40652-40754	GT	AAG
(AAT)	 AG	40863-40941	GT	AGG
(AGC)	 AG	41104-41184	AC	TCA
-recovered pasa_asmbl_12669.p1, initial, 38953, 39025
-recovered pasa_asmbl_12669.p1, internal, 39336, 39465
-recovered pasa_asmbl_12669.p1, internal, 39719, 39915
-recovered pasa_asmbl_12669.p1, internal, 40097, 40251
-recovered pasa_asmbl_12669.p1, internal, 40341, 40509
-recovered pasa_asmbl_12669.p1, internal, 40652, 40754
-recovered pasa_asmbl_12669.p1, internal, 40863, 40941
Valid prediction for GeneMark_model.59577_t
Valid prediction for HiQ_model.g23373.t1
Valid prediction for snap_scaffold_14-snap.1354-T1
Valid prediction for CodingQuarry_transcript_15625-T1
Valid prediction for GlimmerHMM_glimmerT_34783-T1
Valid prediction for GlimmerHMM_glimmerT_34775-T1
Valid prediction for GlimmerHMM_glimmerT_34792-T1
Valid prediction for GlimmerHMM_glimmerT_34787-T1
Valid prediction for snap_scaffold_14-snap.1338-T1
Valid prediction for GlimmerHMM_glimmerT_34791-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.g23384.t1
Valid prediction for GlimmerHMM_glimmerT_34785-T1
Valid prediction for GlimmerHMM_glimmerT_34786-T1
Valid prediction for snap_scaffold_14-snap.1347-T1
Valid prediction for GlimmerHMM_glimmerT_34774-T1
Valid prediction for HiQ_model.g23371.t1
Valid prediction for snap_scaffold_14-snap.1344-T1
Valid prediction for GeneMark_model.59588_t
Valid prediction for GeneMark_model.59595_t
Valid prediction for GeneMark_model.59584_t
Valid prediction for GlimmerHMM_glimmerT_34796-T1
Valid prediction for GlimmerHMM_glimmerT_34769-T1
Valid prediction for Augustus_model.g23382.t1
Valid prediction for GlimmerHMM_glimmerT_34782-T1
Valid prediction for snap_scaffold_14-snap.1331-T1
Valid prediction for snap_scaffold_14-snap.1328-T1
Valid prediction for CodingQuarry_transcript_15620-T1
Valid prediction for Augustus_model.g23388.t1
Valid prediction for pasa_asmbl_13110.p1
Valid prediction for CodingQuarry_transcript_15618-T1
Valid prediction for snap_scaffold_14-snap.1349-T1
Valid prediction for snap_scaffold_14-snap.1336-T1
Valid prediction for snap_scaffold_14-snap.1324-T1
Valid prediction for GeneMark_model.59597_t
Valid prediction for GeneMark_model.59599_t
Valid prediction for CodingQuarry_transcript_15626-T1
Valid prediction for snap_scaffold_14-snap.1340-T1
Valid prediction for snap_scaffold_14-snap.1356-T1
Valid prediction for Augustus_model.g23389.t1
Valid prediction for GeneMark_model.59573_t
Valid prediction for GeneMark_model.59582_t
Valid prediction for snap_scaffold_14-snap.1322-T1
Valid prediction for GlimmerHMM_glimmerT_34797-T1
Valid prediction for snap_scaffold_14-snap.1330-T1
Valid prediction for GlimmerHMM_glimmerT_34779-T1
Valid prediction for GlimmerHMM_glimmerT_34793-T1
Valid prediction for GeneMark_model.59585_t
Valid prediction for GlimmerHMM_glimmerT_34780-T1
Couldn't classify 61086, 61169
Sorry, prediction pasa_asmbl_13120.p1 fails validation.
(ATC)	 AG	61086-61169	GT	AGG
(TGG)	 AG	61266-61332	GT	AGG
(CTG)	 AG	62635-62754	GT	AGG
(AAT)	 AG	62912-63075	CA	GAC
-recovered pasa_asmbl_13120.p1, terminal, 62912, 63075
-recovered pasa_asmbl_13120.p1, internal, 61086, 61169
-recovered pasa_asmbl_13120.p1, internal, 61266, 61332
-recovered pasa_asmbl_13120.p1, internal, 62635, 62754
Valid prediction for snap_scaffold_14-snap.1323-T1
Valid prediction for snap_scaffold_14-snap.1343-T1
Valid prediction for GeneMark_model.59576_t
Valid prediction for CodingQuarry_transcript_15624-T1
Valid prediction for GeneMark_model.59587_t
Valid prediction for snap_scaffold_14-snap.1335-T1
Valid prediction for snap_scaffold_14-snap.1355-T1
Valid prediction for GlimmerHMM_glimmerT_34777-T1
Valid prediction for CodingQuarry_transcript_15623-T1
Couldn't classify 91836, 91944
Sorry, prediction pasa_asmbl_13114.p1 fails validation.
(GAT)	 AG	91836-91944	GT	AGG
(GTG)	 AG	92272-92363	GT	AGG
(GCT)	 AG	92587-92682	GT	AGG
(CTC)	 AG	95170-95295	GT	AGG
(ATT)	 AG	97452-97481	AG	GAA
-recovered pasa_asmbl_13114.p1, terminal, 97452, 97481
-recovered pasa_asmbl_13114.p1, internal, 91836, 91944
-recovered pasa_asmbl_13114.p1, internal, 92272, 92363
-recovered pasa_asmbl_13114.p1, internal, 92587, 92682
-recovered pasa_asmbl_13114.p1, internal, 95170, 95295
Valid prediction for HiQ_model.g23372.t1
Valid prediction for GlimmerHMM_glimmerT_34771-T1
Valid prediction for Augustus_model.g23378.t1
Valid prediction for GlimmerHMM_glimmerT_34770-T1
Valid prediction for GeneMark_model.59574_t
Valid prediction for GeneMark_model.59593_t
Valid prediction for GeneMark_model.59580_t
Valid prediction for GlimmerHMM_glimmerT_34784-T1
Valid prediction for CodingQuarry_transcript_15617-T1
Valid prediction for GeneMark_model.59586_t
Valid prediction for CodingQuarry_transcript_15621-T1
Valid prediction for GlimmerHMM_glimmerT_34788-T1
Valid prediction for HiQ_model.g23380.t1
Valid prediction for GlimmerHMM_glimmerT_34781-T1
Valid prediction for snap_scaffold_14-snap.1342-T1
Valid prediction for pasa_asmbl_13805.p1
Valid prediction for pasa_asmbl_13107.p2
Valid prediction for snap_scaffold_14-snap.1333-T1
Valid prediction for HiQ_model.g23379.t1
Valid prediction for pasa_asmbl_13116.p1
Valid prediction for Augustus_model.g23374.t1
Valid prediction for Augustus_model.g23383.t1
Valid prediction for HiQ_model.g23377.t1
Valid prediction for CodingQuarry_transcript_15622-T1
Valid prediction for snap_scaffold_14-snap.1334-T1
Valid prediction for snap_scaffold_14-snap.1352-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 25327, rend_intergenic: 20443  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54686, rend_intergenic: 48229  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79043, rend_intergenic: 78773  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86012, rend_intergenic: 82498  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107958, rend_intergenic: 105403  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110389, rend_intergenic: 108737  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118404, rend_intergenic: 111404  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125514, rend_intergenic: 119924  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 145572
-exon list size: 500


building trellis

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-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 25327, rend_intergenic: 20443  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54686, rend_intergenic: 48229  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79043, rend_intergenic: 78773  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86012, rend_intergenic: 82498  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 107958, rend_intergenic: 105403  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110389, rend_intergenic: 108737  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 118404, rend_intergenic: 111404  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125514, rend_intergenic: 119924  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 27 predictions persist after filtering for low support