-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_18/scaffold_18_7255861-7464196

-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_18-snap.1553-T1
Valid prediction for snap_scaffold_18-snap.1567-T1
Valid prediction for GeneMark_model.75372_t
Valid prediction for Augustus_model.g29229.t1
Valid prediction for GeneMark_model.75346_t
Valid prediction for Augustus_model.g29220.t1
Valid prediction for Augustus_model.g29228.t1
Valid prediction for GlimmerHMM_glimmerT_43641-T1
Valid prediction for snap_scaffold_18-snap.1560-T1
Valid prediction for Augustus_model.g29234.t1
Valid prediction for Augustus_model.g29232.t1
Couldn't classify 24441, 24516
Sorry, prediction pasa_asmbl_20767.p1 fails validation.
(CCT)	 TA	24441-24516	GT	AGG
(GCG)	 AG	26244-26509	GT	AGG
(GAT)	 AG	26627-26735	GT	AGG
(TGG)	 AG	26841-27001	GT	AGG
(CTG)	 AG	27092-27220	GT	AGG
-recovered pasa_asmbl_20767.p1, terminal, 27092, 27220
-recovered pasa_asmbl_20767.p1, internal, 26244, 26509
-recovered pasa_asmbl_20767.p1, internal, 26627, 26735
-recovered pasa_asmbl_20767.p1, internal, 26841, 27001
-recovered pasa_asmbl_20767.p1, internal, 27092, 27220
Valid prediction for snap_scaffold_18-snap.1546-T1
Valid prediction for GeneMark_model.75343_t
Valid prediction for GeneMark_model.75354_t
Valid prediction for GeneMark_model.75349_t
Valid prediction for GeneMark_model.75352_t
Valid prediction for Augustus_model.g29214.t1
Valid prediction for snap_scaffold_18-snap.1540-T1
Valid prediction for Augustus_model.g29237.t1
Valid prediction for GlimmerHMM_glimmerT_43634-T1
Valid prediction for snap_scaffold_18-snap.1565-T1
Valid prediction for Augustus_model.g29219.t1
Valid prediction for GeneMark_model.75371_t
Valid prediction for GlimmerHMM_glimmerT_43649-T1
Valid prediction for GeneMark_model.75347_t
Valid prediction for snap_scaffold_18-snap.1536-T1
Valid prediction for Augustus_model.g29221.t1
Valid prediction for Augustus_model.g29236.t1
Valid prediction for GlimmerHMM_glimmerT_43645-T1
Valid prediction for GeneMark_model.75367_t
Valid prediction for GlimmerHMM_glimmerT_43640-T1
Valid prediction for snap_scaffold_18-snap.1555-T1
Valid prediction for GeneMark_model.75361_t
Valid prediction for GlimmerHMM_glimmerT_43632-T1
Valid prediction for GeneMark_model.75336_t
Valid prediction for Augustus_model.g29218.t1
Couldn't classify 19861, 20331
Couldn't classify 21263, 21334
Sorry, prediction pasa_asmbl_20765.p1 fails validation.
(GAG)	 AC	19861-20331	GT	AGG
(GTG)	 AG	21263-21334	CA	AGC
Valid prediction for Augustus_model.g29222.t1
Valid prediction for snap_scaffold_18-snap.1543-T1
Valid prediction for GeneMark_model.75365_t
Valid prediction for snap_scaffold_18-snap.1558-T1
Valid prediction for GeneMark_model.75373_t
Valid prediction for Augustus_model.g29227.t1
Valid prediction for CodingQuarry_transcript_23762-T1
Valid prediction for GlimmerHMM_glimmerT_43637-T1
Valid prediction for Augustus_model.g29230.t1
Couldn't classify 201863, 201988
Sorry, prediction pasa_asmbl_20771.p1 fails validation.
(CAA)	 AG	201863-201988	GT	ACG
(TAT)	 AG	204585-204656	GT	GGG
(AAA)	 AG	206155-206241	GT	AGG
(AAC)	 AG	206461-206598	GT	TGG
(AAC)	 AG	206714-206911	CC	AAC
-recovered pasa_asmbl_20771.p1, terminal, 206714, 206911
-recovered pasa_asmbl_20771.p1, internal, 201863, 201988
-recovered pasa_asmbl_20771.p1, internal, 204585, 204656
-recovered pasa_asmbl_20771.p1, internal, 206155, 206241
-recovered pasa_asmbl_20771.p1, internal, 206461, 206598
Valid prediction for GeneMark_model.75370_t
Valid prediction for Augustus_model.g29224.t1
Valid prediction for GeneMark_model.75363_t
Valid prediction for snap_scaffold_18-snap.1548-T1
Valid prediction for snap_scaffold_18-snap.1522-T1
Valid prediction for GlimmerHMM_glimmerT_43646-T1
Couldn't classify 14147, 14320
Couldn't classify 19618, 19701
Sorry, prediction pasa_asmbl_20763.p1 fails validation.
(GAG)	 CA	14147-14320	GT	AGG
(ATC)	 AG	14647-14787	GT	GGG
(ATG)	 AG	15850-16017	GT	AGG
(GAC)	 AG	16744-16924	GT	AGG
(TGG)	 AG	17097-17180	GT	AGG
(GTG)	 AG	17529-17684	GT	CGG
(GTA)	 AG	18734-18843	GT	AGG
(GTG)	 AG	18935-19076	GT	CAG
(TCC)	 AG	19288-19481	GT	AGG
(CTA)	 AG	19618-19701	AG	CCA
-recovered pasa_asmbl_20763.p1, initial, 15850, 16017
-recovered pasa_asmbl_20763.p1, internal, 14647, 14787
-recovered pasa_asmbl_20763.p1, internal, 15850, 16017
-recovered pasa_asmbl_20763.p1, internal, 16744, 16924
-recovered pasa_asmbl_20763.p1, internal, 17097, 17180
-recovered pasa_asmbl_20763.p1, internal, 17529, 17684
-recovered pasa_asmbl_20763.p1, internal, 18734, 18843
-recovered pasa_asmbl_20763.p1, internal, 18935, 19076
-recovered pasa_asmbl_20763.p1, internal, 19288, 19481
Valid prediction for GeneMark_model.75357_t
Valid prediction for GeneMark_model.75345_t
Valid prediction for snap_scaffold_18-snap.1525-T1
Valid prediction for GeneMark_model.75338_t
Valid prediction for snap_scaffold_18-snap.1542-T1
Valid prediction for snap_scaffold_18-snap.1535-T1
Valid prediction for CodingQuarry_transcript_23761-T1
Valid prediction for snap_scaffold_18-snap.1539-T1
Valid prediction for Augustus_model.g29216.t1
Couldn't classify 21497, 21957
Couldn't classify 24151, 24192
Sorry, prediction pasa_asmbl_20766.p1 fails validation.
(CCG)	 AG	21497-21957	GT	AGG
(TGG)	 AG	23144-23292	GT	AGG
(ATG)	 AG	23767-23924	GT	TGG
(GTG)	 AG	24151-24192	GT	GGG
add_exon() Sorry, pasa_asmbl_20766.p1 23767-23924-initial-1 is invalid.
-recovered pasa_asmbl_20766.p1, initial, 23767, 23924
-recovered pasa_asmbl_20766.p1, internal, 21497, 21957
-recovered pasa_asmbl_20766.p1, internal, 23144, 23292
-recovered pasa_asmbl_20766.p1, internal, 23767, 23924
-recovered pasa_asmbl_20766.p1, internal, 24151, 24192
Valid prediction for snap_scaffold_18-snap.1530-T1
Valid prediction for GlimmerHMM_glimmerT_43644-T1
Valid prediction for Augustus_model.g29226.t1
Valid prediction for GlimmerHMM_glimmerT_43639-T1
Valid prediction for GeneMark_model.75359_t
Couldn't classify 156734, 157033
Sorry, prediction pasa_asmbl_20769.p1 fails validation.
(CCA)	 CG	156734-157033	AG	GGA
Valid prediction for GlimmerHMM_glimmerT_43642-T1
Valid prediction for Augustus_model.g29223.t1
Valid prediction for snap_scaffold_18-snap.1561-T1
Valid prediction for Augustus_model.g29235.t1
Valid prediction for snap_scaffold_18-snap.1551-T1
Valid prediction for Augustus_model.g29231.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 snap_scaffold_18-snap.1537-T1
Valid prediction for snap_scaffold_18-snap.1544-T1
Valid prediction for snap_scaffold_18-snap.1562-T1
Valid prediction for GeneMark_model.75334_t
Valid prediction for snap_scaffold_18-snap.1552-T1
Valid prediction for GeneMark_model.75356_t
Valid prediction for GeneMark_model.75350_t
Valid prediction for snap_scaffold_18-snap.1529-T1
Valid prediction for GlimmerHMM_glimmerT_43633-T1
Valid prediction for snap_scaffold_18-snap.1531-T1
Valid prediction for GeneMark_model.75351_t
Valid prediction for GeneMark_model.75360_t
Valid prediction for GlimmerHMM_glimmerT_43638-T1
Valid prediction for GeneMark_model.75335_t
Valid prediction for GlimmerHMM_glimmerT_43643-T1
Valid prediction for Augustus_model.g29225.t1
Valid prediction for snap_scaffold_18-snap.1532-T1
Valid prediction for snap_scaffold_18-snap.1547-T1
Valid prediction for GeneMark_model.75355_t
Valid prediction for snap_scaffold_18-snap.1568-T1
Valid prediction for snap_scaffold_18-snap.1533-T1
Valid prediction for snap_scaffold_18-snap.1554-T1
Valid prediction for GlimmerHMM_glimmerT_43650-T1
Valid prediction for snap_scaffold_18-snap.1563-T1
Valid prediction for snap_scaffold_18-snap.1528-T1
Valid prediction for GeneMark_model.75353_t
Valid prediction for GlimmerHMM_glimmerT_43635-T1
Valid prediction for GeneMark_model.75362_t
Valid prediction for snap_scaffold_18-snap.1550-T1
Valid prediction for snap_scaffold_18-snap.1541-T1
Valid prediction for snap_scaffold_18-snap.1557-T1
Valid prediction for snap_scaffold_18-snap.1527-T1
Valid prediction for GeneMark_model.75369_t
Valid prediction for Augustus_model.g29233.t1
Valid prediction for snap_scaffold_18-snap.1549-T1
Valid prediction for snap_scaffold_18-snap.1526-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for snap_scaffold_18-snap.1523-T1
Valid prediction for GeneMark_model.75348_t
Valid prediction for snap_scaffold_18-snap.1559-T1
Valid prediction for GlimmerHMM_glimmerT_43636-T1
Valid prediction for GlimmerHMM_glimmerT_43631-T1
Valid prediction for GeneMark_model.75341_t
Valid prediction for GlimmerHMM_glimmerT_43647-T1
Valid prediction for GeneMark_model.75358_t
Valid prediction for snap_scaffold_18-snap.1534-T1
Valid prediction for Augustus_model.g29215.t1
Valid prediction for GeneMark_model.75340_t
Valid prediction for snap_scaffold_18-snap.1564-T1
Valid prediction for GeneMark_model.75339_t
Valid prediction for snap_scaffold_18-snap.1556-T1
Valid prediction for snap_scaffold_18-snap.1566-T1
Valid prediction for snap_scaffold_18-snap.1545-T1
Valid prediction for snap_scaffold_18-snap.1538-T1
Valid prediction for GeneMark_model.75344_t
Valid prediction for snap_scaffold_18-snap.1524-T1
Valid prediction for Augustus_model.g29217.t1
Valid prediction for GlimmerHMM_glimmerT_43651-T1
Valid prediction for GeneMark_model.75366_t
Valid prediction for GlimmerHMM_glimmerT_43648-T1
Valid prediction for GeneMark_model.75337_t
Valid prediction for GeneMark_model.75364_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 17362, rend_intergenic: 13584  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30713, rend_intergenic: 17554  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41300, rend_intergenic: 38224  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47512, rend_intergenic: 41453  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85126, rend_intergenic: 81603  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99992, rend_intergenic: 96028  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104074, rend_intergenic: 101048  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104901, rend_intergenic: 104650  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116614, rend_intergenic: 106694  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126089, rend_intergenic: 124030  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148933, rend_intergenic: 146694  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158470, rend_intergenic: 150762  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164123, rend_intergenic: 159307  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186718, rend_intergenic: 182584  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 208336
-exon list size: 569


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 32 predictions from path traversal
Error with prediction: snap lend_intergenic: 17362, rend_intergenic: 13584  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30713, rend_intergenic: 17554  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41300, rend_intergenic: 38224  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47512, rend_intergenic: 41453  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85126, rend_intergenic: 81603  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 99992, rend_intergenic: 96028  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104074, rend_intergenic: 101048  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 104901, rend_intergenic: 104650  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116614, rend_intergenic: 106694  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126089, rend_intergenic: 124030  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148933, rend_intergenic: 146694  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158470, rend_intergenic: 150762  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 164123, rend_intergenic: 159307  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186718, rend_intergenic: 182584  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 22 predictions persist after filtering for low support