-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_5/scaffold_5_7777879-8007213

-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_12487-T1
Valid prediction for snap_scaffold_5-snap.1532-T1
Valid prediction for GeneMark_model.21242_t
Valid prediction for GlimmerHMM_glimmerT_12495-T1
Valid prediction for GeneMark_model.21257_t
Valid prediction for GeneMark_model.21268_t
Valid prediction for GlimmerHMM_glimmerT_12485-T1
Valid prediction for GlimmerHMM_glimmerT_12493-T1
Valid prediction for GlimmerHMM_glimmerT_12480-T1
Valid prediction for GeneMark_model.21252_t
Valid prediction for GeneMark_model.21270_t
Couldn't classify 112403, 112519
Sorry, prediction pasa_asmbl_44181.p1 fails validation.
(GCA)	 AG	112403-112519	GT	AGG
(GGC)	 AG	112970-113085	GT	AGG
(TTT)	 AG	113518-113816	GT	ATG
(TCA)	 AG	113935-114248	GT	AGG
(GAG)	 AG	115339-115569	GT	AGG
(ATC)	 AG	116471-116665	AC	AAA
-recovered pasa_asmbl_44181.p1, terminal, 116471, 116665
-recovered pasa_asmbl_44181.p1, internal, 112403, 112519
-recovered pasa_asmbl_44181.p1, internal, 112970, 113085
-recovered pasa_asmbl_44181.p1, internal, 113518, 113816
-recovered pasa_asmbl_44181.p1, internal, 113935, 114248
-recovered pasa_asmbl_44181.p1, internal, 115339, 115569
Valid prediction for snap_scaffold_5-snap.1562-T1
Valid prediction for GeneMark_model.21244_t
Valid prediction for GeneMark_model.21239_t
Valid prediction for GeneMark_model.21248_t
Valid prediction for snap_scaffold_5-snap.1542-T1
Valid prediction for snap_scaffold_5-snap.1543-T1
Valid prediction for snap_scaffold_5-snap.1548-T1
Valid prediction for snap_scaffold_5-snap.1556-T1
Valid prediction for snap_scaffold_5-snap.1559-T1
Valid prediction for GlimmerHMM_glimmerT_12498-T1
Valid prediction for GeneMark_model.21272_t
Valid prediction for snap_scaffold_5-snap.1537-T1
Valid prediction for GlimmerHMM_glimmerT_12501-T1
Valid prediction for GeneMark_model.21266_t
Valid prediction for Augustus_model.g8275.t1
Valid prediction for snap_scaffold_5-snap.1553-T1
Valid prediction for snap_scaffold_5-snap.1534-T1
Valid prediction for snap_scaffold_5-snap.1530-T1
Valid prediction for snap_scaffold_5-snap.1531-T1
Valid prediction for GeneMark_model.21264_t
Valid prediction for GeneMark_model.21259_t
Valid prediction for Augustus_model.g8280.t1
Valid prediction for GeneMark_model.21255_t
Valid prediction for GeneMark_model.21265_t
Valid prediction for snap_scaffold_5-snap.1539-T1
Valid prediction for GlimmerHMM_glimmerT_12482-T1
Valid prediction for GlimmerHMM_glimmerT_12491-T1
Valid prediction for snap_scaffold_5-snap.1528-T1
Valid prediction for GeneMark_model.21237_t
Valid prediction for GeneMark_model.21236_t
Couldn't classify 62877, 63767
Sorry, prediction pasa_asmbl_44180.p1 fails validation.
(ATG)	 AC	62877-63767	AG	AGA
Valid prediction for CodingQuarry_transcript_52003-T1
Valid prediction for snap_scaffold_5-snap.1544-T1
Valid prediction for snap_scaffold_5-snap.1550-T1
Valid prediction for GeneMark_model.21276_t
Valid prediction for snap_scaffold_5-snap.1536-T1
Valid prediction for GeneMark_model.21262_t
Valid prediction for Augustus_model.g8272.t1
Valid prediction for Augustus_model.g8276.t1
Valid prediction for Augustus_model.g8279.t1
Valid prediction for snap_scaffold_5-snap.1526-T1
Valid prediction for Augustus_model.g8274.t1
Valid prediction for Augustus_model.g8277.t1
Valid prediction for GlimmerHMM_glimmerT_12496-T1
Valid prediction for Augustus_model.g8278.t1
Couldn't classify 36186, 36248
Couldn't classify 43144, 43279
Sorry, prediction pasa_asmbl_44177.p1 fails validation.
(TGC)	 AC	36186-36248	GT	TGG
(GAT)	 AG	37147-37237	GT	AAG
(TAC)	 AG	38010-38062	GT	AGG
(GAC)	 AG	38263-38451	GT	AGG
(GAT)	 AG	41067-41164	GT	CGG
(GTT)	 AG	41734-41820	GT	CGG
(ATT)	 AG	43144-43279	GT	AGG
-recovered pasa_asmbl_44177.p1, internal, 37147, 37237
-recovered pasa_asmbl_44177.p1, internal, 38010, 38062
-recovered pasa_asmbl_44177.p1, internal, 38263, 38451
-recovered pasa_asmbl_44177.p1, internal, 41067, 41164
-recovered pasa_asmbl_44177.p1, internal, 41734, 41820
-recovered pasa_asmbl_44177.p1, internal, 43144, 43279
Valid prediction for GeneMark_model.21254_t
Couldn't classify 43543, 43585
Couldn't classify 46538, 46627
Sorry, prediction pasa_asmbl_45075.p1 fails validation.
(CCT)	 CC	43543-43585	GT	TGG
(GCT)	 AG	43960-44079	GT	AGG
(TTA)	 AG	45870-45949	GT	AGG
(GAC)	 AG	46538-46627	GT	AGG
-recovered pasa_asmbl_45075.p1, internal, 43960, 44079
-recovered pasa_asmbl_45075.p1, internal, 45870, 45949
-recovered pasa_asmbl_45075.p1, internal, 46538, 46627
Valid prediction for snap_scaffold_5-snap.1547-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_5-snap.1552-T1
Valid prediction for snap_scaffold_5-snap.1541-T1
Valid prediction for CodingQuarry_transcript_52004-T1
Valid prediction for GeneMark_model.21274_t
Valid prediction for GlimmerHMM_glimmerT_12492-T1
Valid prediction for GeneMark_model.21261_t
Valid prediction for GlimmerHMM_glimmerT_12483-T1
Valid prediction for GeneMark_model.21263_t
Valid prediction for GeneMark_model.21273_t
Valid prediction for snap_scaffold_5-snap.1563-T1
Valid prediction for Augustus_model.g8282.t1
Valid prediction for GeneMark_model.21253_t
Valid prediction for GeneMark_model.21271_t
Valid prediction for snap_scaffold_5-snap.1540-T1
Valid prediction for Augustus_model.g8285.t1
Valid prediction for snap_scaffold_5-snap.1557-T1
Valid prediction for snap_scaffold_5-snap.1560-T1
Valid prediction for snap_scaffold_5-snap.1555-T1
Valid prediction for snap_scaffold_5-snap.1535-T1
Valid prediction for GlimmerHMM_glimmerT_12494-T1
Valid prediction for snap_scaffold_5-snap.1558-T1
Valid prediction for GeneMark_model.21241_t
Valid prediction for snap_scaffold_5-snap.1551-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_12486-T1
Valid prediction for GlimmerHMM_glimmerT_12502-T1
Valid prediction for pasa_asmbl_45577.p1
Valid prediction for GeneMark_model.21258_t
Valid prediction for Augustus_model.g8273.t1
Valid prediction for GeneMark_model.21245_t
Valid prediction for Augustus_model.g8283.t1
Valid prediction for GlimmerHMM_glimmerT_12503-T1
Valid prediction for GeneMark_model.21247_t
Valid prediction for GlimmerHMM_glimmerT_12504-T1
Valid prediction for GeneMark_model.21249_t
Valid prediction for snap_scaffold_5-snap.1545-T1
Valid prediction for snap_scaffold_5-snap.1538-T1
Valid prediction for GeneMark_model.21277_t
Valid prediction for snap_scaffold_5-snap.1554-T1
Valid prediction for GeneMark_model.21251_t
Valid prediction for GlimmerHMM_glimmerT_12500-T1
Valid prediction for GlimmerHMM_glimmerT_12481-T1
Valid prediction for Augustus_model.g8281.t1
Valid prediction for GlimmerHMM_glimmerT_12488-T1
Valid prediction for GeneMark_model.21250_t
Valid prediction for GlimmerHMM_glimmerT_12484-T1
Valid prediction for GeneMark_model.21275_t
Valid prediction for snap_scaffold_5-snap.1533-T1
Valid prediction for GlimmerHMM_glimmerT_12489-T1
Valid prediction for GeneMark_model.21240_t
Valid prediction for GeneMark_model.21238_t
Valid prediction for snap_scaffold_5-snap.1549-T1
Valid prediction for snap_scaffold_5-snap.1527-T1
Valid prediction for GlimmerHMM_glimmerT_12490-T1
Valid prediction for GeneMark_model.21256_t
Valid prediction for Augustus_model.g8284.t1
Valid prediction for GeneMark_model.21269_t
Valid prediction for snap_scaffold_5-snap.1564-T1
Valid prediction for GeneMark_model.21260_t
Valid prediction for GeneMark_model.21243_t
Valid prediction for snap_scaffold_5-snap.1546-T1
Valid prediction for snap_scaffold_5-snap.1529-T1
Valid prediction for GeneMark_model.21267_t
Valid prediction for GlimmerHMM_glimmerT_12499-T1
Valid prediction for snap_scaffold_5-snap.1561-T1
Valid prediction for GlimmerHMM_glimmerT_12497-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 15614, rend_intergenic: 10305  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46713, rend_intergenic: 43471  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83592, rend_intergenic: 78683  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97593, rend_intergenic: 89832  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116665, rend_intergenic: 112960  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151300, rend_intergenic: 148739  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155260, rend_intergenic: 151635  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162451, rend_intergenic: 156427  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 194043, rend_intergenic: 187299  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 220421, rend_intergenic: 213157  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 229335
-exon list size: 533


building trellis

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98.1    
98.3    
98.5    
98.7    
98.9    
99.1    
99.3    
99.4    
99.6    
99.8    
-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 15614, rend_intergenic: 10305  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46713, rend_intergenic: 43471  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83592, rend_intergenic: 78683  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97593, rend_intergenic: 89832  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 116665, rend_intergenic: 112960  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 151300, rend_intergenic: 148739  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155260, rend_intergenic: 151635  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 162451, rend_intergenic: 156427  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 194043, rend_intergenic: 187299  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 220421, rend_intergenic: 213157  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support