-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_18/scaffold_18_6347912-6536798

-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 GeneMark_model.75070_t
Valid prediction for snap_scaffold_18-snap.1354-T1
Valid prediction for GeneMark_model.75098_t
Valid prediction for GeneMark_model.75110_t
Valid prediction for GlimmerHMM_glimmerT_43516-T1
Valid prediction for GeneMark_model.75080_t
Valid prediction for snap_scaffold_18-snap.1336-T1
Valid prediction for GlimmerHMM_glimmerT_43515-T1
Valid prediction for snap_scaffold_18-snap.1351-T1
Valid prediction for snap_scaffold_18-snap.1330-T1
Valid prediction for GeneMark_model.75085_t
Valid prediction for GeneMark_model.75102_t
Valid prediction for GlimmerHMM_glimmerT_43501-T1
Valid prediction for snap_scaffold_18-snap.1356-T1
Valid prediction for Augustus_model.g29124.t1
Valid prediction for GlimmerHMM_glimmerT_43523-T1
Valid prediction for GeneMark_model.75069_t
Valid prediction for GlimmerHMM_glimmerT_43510-T1
Valid prediction for snap_scaffold_18-snap.1337-T1
Valid prediction for snap_scaffold_18-snap.1346-T1
Valid prediction for GlimmerHMM_glimmerT_43507-T1
Valid prediction for Augustus_model.g29120.t1
Valid prediction for Augustus_model.g29128.t1
Valid prediction for snap_scaffold_18-snap.1358-T1
Valid prediction for GeneMark_model.75104_t
Valid prediction for GeneMark_model.75119_t
Valid prediction for GlimmerHMM_glimmerT_43519-T1
Valid prediction for snap_scaffold_18-snap.1341-T1
Valid prediction for GlimmerHMM_glimmerT_43522-T1
Valid prediction for snap_scaffold_18-snap.1333-T1
Valid prediction for GeneMark_model.75076_t
Valid prediction for GlimmerHMM_glimmerT_43502-T1
Valid prediction for GlimmerHMM_glimmerT_43509-T1
Valid prediction for GeneMark_model.75117_t
Valid prediction for GeneMark_model.75087_t
Valid prediction for GlimmerHMM_glimmerT_43521-T1
Valid prediction for Augustus_model.g29113.t1
Valid prediction for GeneMark_model.75113_t
Valid prediction for GeneMark_model.75094_t
Valid prediction for Augustus_model.g29129.t1
Valid prediction for GlimmerHMM_glimmerT_43498-T1
Valid prediction for pasa_asmbl_20707.p1
Valid prediction for GeneMark_model.75121_t
Valid prediction for GeneMark_model.75081_t
Valid prediction for snap_scaffold_18-snap.1360-T1
Valid prediction for GlimmerHMM_glimmerT_43506-T1
Valid prediction for GeneMark_model.75083_t
Valid prediction for GlimmerHMM_glimmerT_43513-T1
Valid prediction for GeneMark_model.75077_t
Valid prediction for GeneMark_model.75100_t
Valid prediction for CodingQuarry_transcript_23734-T1
Valid prediction for Augustus_model.g29119.t1
Valid prediction for snap_scaffold_18-snap.1345-T1
Valid prediction for snap_scaffold_18-snap.1357-T1
Valid prediction for GlimmerHMM_glimmerT_43524-T1
Valid prediction for snap_scaffold_18-snap.1362-T1
Valid prediction for GeneMark_model.75090_t
Valid prediction for GeneMark_model.75089_t
Valid prediction for snap_scaffold_18-snap.1339-T1
Valid prediction for GeneMark_model.75123_t
Valid prediction for snap_scaffold_18-snap.1349-T1
Valid prediction for GeneMark_model.75074_t
Valid prediction for GeneMark_model.75092_t
Valid prediction for Augustus_model.g29112.t1
Valid prediction for HiQ_model.g29121.t1
Valid prediction for GeneMark_model.75072_t
Valid prediction for GeneMark_model.75107_t
Valid prediction for snap_scaffold_18-snap.1340-T1
Valid prediction for GeneMark_model.75126_t
Valid prediction for GeneMark_model.75096_t
Valid prediction for GeneMark_model.75118_t
Valid prediction for GlimmerHMM_glimmerT_43504-T1
Valid prediction for GlimmerHMM_glimmerT_43500-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 GeneMark_model.75088_t
Valid prediction for GlimmerHMM_glimmerT_43511-T1
Valid prediction for Augustus_model.g29125.t1
Valid prediction for snap_scaffold_18-snap.1348-T1
Valid prediction for GlimmerHMM_glimmerT_43505-T1
Valid prediction for GeneMark_model.75108_t
Valid prediction for GeneMark_model.75093_t
Valid prediction for snap_scaffold_18-snap.1359-T1
Valid prediction for Augustus_model.g29115.t1
Valid prediction for GeneMark_model.75124_t
Valid prediction for snap_scaffold_18-snap.1361-T1
Valid prediction for GeneMark_model.75095_t
Valid prediction for snap_scaffold_18-snap.1353-T1
Valid prediction for GlimmerHMM_glimmerT_43514-T1
Valid prediction for Augustus_model.g29123.t1
Valid prediction for GeneMark_model.75071_t
Valid prediction for GeneMark_model.75114_t
Valid prediction for GeneMark_model.75122_t
Valid prediction for Augustus_model.g29111.t1
Valid prediction for GlimmerHMM_glimmerT_43503-T1
Valid prediction for GeneMark_model.75116_t
Couldn't classify 97710, 97734
Sorry, prediction pasa_asmbl_19938.p2 fails validation.
(CAA)	 CC	97710-97734	GT	TGG
(ACA)	 AG	98373-98396	GT	TGG
(GTC)	 AG	101358-101541	GT	CAG
(GCA)	 AG	101843-101885	GT	ATG
(TTG)	 AG	102768-102935	TG	AGT
-recovered pasa_asmbl_19938.p2, terminal, 102768, 102935
-recovered pasa_asmbl_19938.p2, internal, 98373, 98396
-recovered pasa_asmbl_19938.p2, internal, 101358, 101541
-recovered pasa_asmbl_19938.p2, internal, 101843, 101885
Valid prediction for GlimmerHMM_glimmerT_43499-T1
Valid prediction for GeneMark_model.75115_t
Valid prediction for Augustus_model.g29118.t1
Valid prediction for GlimmerHMM_glimmerT_43508-T1
Valid prediction for GlimmerHMM_glimmerT_43517-T1
Valid prediction for GeneMark_model.75075_t
Couldn't classify 96780, 96914
Couldn't classify 97408, 97563
Sorry, prediction pasa_asmbl_19937.p1 fails validation.
(TCG)	 AG	96780-96914	GT	AGG
(GAC)	 AG	97024-97110	GT	ACG
(ACA)	 AG	97408-97563	CT	TCC
-recovered pasa_asmbl_19937.p1, internal, 96780, 96914
-recovered pasa_asmbl_19937.p1, internal, 97024, 97110
Valid prediction for GlimmerHMM_glimmerT_43512-T1
Valid prediction for GeneMark_model.75109_t
Couldn't classify 104504, 104710
Sorry, prediction pasa_asmbl_19933.p1 fails validation.
(CCT)	 CA	104504-104710	GT	ATG
(GTG)	 AG	104933-105041	GT	AGG
(ATG)	 AG	105141-105202	GT	AGG
-recovered pasa_asmbl_19933.p1, initial, 105141, 105202
-recovered pasa_asmbl_19933.p1, terminal, 105141, 105202
-recovered pasa_asmbl_19933.p1, internal, 104933, 105041
-recovered pasa_asmbl_19933.p1, internal, 105141, 105202
Valid prediction for snap_scaffold_18-snap.1347-T1
Valid prediction for GeneMark_model.75097_t
Valid prediction for snap_scaffold_18-snap.1343-T1
Valid prediction for snap_scaffold_18-snap.1350-T1
Valid prediction for snap_scaffold_18-snap.1331-T1
Valid prediction for Augustus_model.g29117.t1
Valid prediction for GlimmerHMM_glimmerT_43497-T1
Valid prediction for GeneMark_model.75106_t
Valid prediction for GlimmerHMM_glimmerT_43520-T1
Valid prediction for GeneMark_model.75078_t
Valid prediction for snap_scaffold_18-snap.1335-T1
Valid prediction for snap_scaffold_18-snap.1352-T1
Valid prediction for snap_scaffold_18-snap.1355-T1
Valid prediction for Augustus_model.g29122.t1
Couldn't classify 39519, 40397
Sorry, prediction pasa_asmbl_19941.p1 fails validation.
(AAC)	 CC	39519-40397	GA	ACG
Valid prediction for GeneMark_model.75073_t
Valid prediction for CodingQuarry_transcript_23735-T1
Valid prediction for Augustus_model.g29126.t1
Valid prediction for GeneMark_model.75099_t
Valid prediction for snap_scaffold_18-snap.1332-T1
Valid prediction for GeneMark_model.75082_t
Valid prediction for snap_scaffold_18-snap.1342-T1
Valid prediction for GeneMark_model.75120_t
Valid prediction for GeneMark_model.75103_t
Valid prediction for snap_scaffold_18-snap.1334-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_18-snap.1363-T1
Valid prediction for snap_scaffold_18-snap.1344-T1
Valid prediction for snap_scaffold_18-snap.1338-T1
Valid prediction for GeneMark_model.75091_t
Valid prediction for GeneMark_model.75084_t
Valid prediction for Augustus_model.g29110.t1
Valid prediction for Augustus_model.g29116.t1
Valid prediction for GeneMark_model.75125_t
Valid prediction for Augustus_model.g29127.t1
Valid prediction for GeneMark_model.75111_t
Valid prediction for GeneMark_model.75112_t
Valid prediction for Augustus_model.g29114.t1
Valid prediction for GlimmerHMM_glimmerT_43518-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 28215, rend_intergenic: 8541  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43758, rend_intergenic: 31799  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50433, rend_intergenic: 46033  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57383, rend_intergenic: 55374  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122710, rend_intergenic: 121955  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134242, rend_intergenic: 130929  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173065, rend_intergenic: 164792  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180038, rend_intergenic: 175912  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186719, rend_intergenic: 181436  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 188887
-exon list size: 637


building trellis

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99.8    
-found 40 predictions from path traversal
Error with prediction: snap lend_intergenic: 28215, rend_intergenic: 8541  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43758, rend_intergenic: 31799  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50433, rend_intergenic: 46033  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 57383, rend_intergenic: 55374  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122710, rend_intergenic: 121955  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 134242, rend_intergenic: 130929  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173065, rend_intergenic: 164792  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180038, rend_intergenic: 175912  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186719, rend_intergenic: 181436  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 14 predictions persist after filtering for low support