-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_28/scaffold_28_949039-1137312

-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_28-snap.212-T1
Valid prediction for GlimmerHMM_glimmerT_58093-T1
Valid prediction for snap_scaffold_28-snap.226-T1
Valid prediction for snap_scaffold_28-snap.234-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for Augustus_model.g38461.t1
Valid prediction for Augustus_model.g38453.t1
Valid prediction for snap_scaffold_28-snap.245-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_28-snap.228-T1
Valid prediction for snap_scaffold_28-snap.240-T1
Valid prediction for snap_scaffold_28-snap.232-T1
Valid prediction for snap_scaffold_28-snap.223-T1
Valid prediction for GlimmerHMM_glimmerT_58081-T1
Valid prediction for snap_scaffold_28-snap.224-T1
Valid prediction for snap_scaffold_28-snap.236-T1
Valid prediction for snap_scaffold_28-snap.247-T1
Valid prediction for snap_scaffold_28-snap.246-T1
Valid prediction for snap_scaffold_28-snap.217-T1
Valid prediction for snap_scaffold_28-snap.243-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for Augustus_model.g38462.t1
Valid prediction for CodingQuarry_transcript_43529-T1
Valid prediction for snap_scaffold_28-snap.248-T1
Valid prediction for snap_scaffold_28-snap.218-T1
Valid prediction for snap_scaffold_28-snap.249-T1
Valid prediction for GlimmerHMM_glimmerT_58087-T1
Valid prediction for GlimmerHMM_glimmerT_58079-T1
Valid prediction for snap_scaffold_28-snap.210-T1
Valid prediction for snap_scaffold_28-snap.235-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_28-snap.238-T1
Valid prediction for Augustus_model.g38454.t1
Valid prediction for snap_scaffold_28-snap.250-T1
Valid prediction for GlimmerHMM_glimmerT_58086-T1
Valid prediction for snap_scaffold_28-snap.214-T1
Valid prediction for GlimmerHMM_glimmerT_58077-T1
Valid prediction for pasa_asmbl_37300.p1
Valid prediction for HiQ_model.g38448.t1
Valid prediction for GlimmerHMM_glimmerT_58085-T1
Valid prediction for snap_scaffold_28-snap.230-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.g38452.t1
Valid prediction for snap_scaffold_28-snap.225-T1
Valid prediction for Augustus_model.g38451.t1
Valid prediction for GlimmerHMM_glimmerT_58073-T1
Couldn't classify 155505, 155810
Sorry, prediction pasa_asmbl_37951.p2 fails validation.
(CCG)	 GG	155505-155810	AC	AAA
Valid prediction for snap_scaffold_28-snap.229-T1
Valid prediction for snap_scaffold_28-snap.237-T1
Couldn't classify 21361, 21520
Couldn't classify 23119, 23218
Sorry, prediction pasa_asmbl_37970.p1 fails validation.
(CGC)	 GG	21361-21520	GT	AGG
(ACA)	 AG	21827-21939	GT	AGG
(AAA)	 AG	22732-22847	GT	AGG
(GCT)	 AG	23119-23218	GC	CAG
-recovered pasa_asmbl_37970.p1, internal, 21827, 21939
-recovered pasa_asmbl_37970.p1, internal, 22732, 22847
-recovered pasa_asmbl_37970.p1, internal, 23119, 23218
Valid prediction for GlimmerHMM_glimmerT_58089-T1
Valid prediction for GlimmerHMM_glimmerT_58088-T1
Valid prediction for Augustus_model.g38444.t1
Valid prediction for snap_scaffold_28-snap.233-T1
Valid prediction for HiQ_model.g38445.t1
Valid prediction for GlimmerHMM_glimmerT_58069-T1
Valid prediction for snap_scaffold_28-snap.239-T1
Valid prediction for GlimmerHMM_glimmerT_58071-T1
Valid prediction for snap_scaffold_28-snap.209-T1
Valid prediction for GlimmerHMM_glimmerT_58070-T1
Valid prediction for CodingQuarry_transcript_43528-T1
Valid prediction for GlimmerHMM_glimmerT_58091-T1
Valid prediction for snap_scaffold_28-snap.220-T1
Valid prediction for Augustus_model.g38441.t1
Valid prediction for Augustus_model.g38457.t1
Valid prediction for snap_scaffold_28-snap.219-T1
Valid prediction for pasa_asmbl_37952.p1
Valid prediction for GlimmerHMM_glimmerT_58074-T1
Valid prediction for GlimmerHMM_glimmerT_58092-T1
Valid prediction for snap_scaffold_28-snap.215-T1
Valid prediction for CodingQuarry_transcript_43527-T1
Valid prediction for GlimmerHMM_glimmerT_58083-T1
Valid prediction for snap_scaffold_28-snap.227-T1
Valid prediction for snap_scaffold_28-snap.241-T1
Couldn't classify 31007, 31369
Sorry, prediction pasa_asmbl_37965.p1 fails validation.
(CGC)	 GC	31007-31369	GC	GAG
Valid prediction for HiQ_model.g38456.t1
Valid prediction for snap_scaffold_28-snap.231-T1
Valid prediction for pasa_asmbl_37954.p1
Valid prediction for Augustus_model.g38455.t1
Valid prediction for GlimmerHMM_glimmerT_58080-T1
Valid prediction for Augustus_model.g38458.t1
Valid prediction for HiQ_model.g38447.t1
Valid prediction for Augustus_model.g38460.t1
Valid prediction for snap_scaffold_28-snap.216-T1
Couldn't classify 24906, 25055
Couldn't classify 26191, 26357
Sorry, prediction pasa_asmbl_38549.p1 fails validation.
(ATC)	 AC	24906-25055	GT	AGG
(GAG)	 AG	25407-25500	GT	CAG
(GCT)	 AG	26191-26357	AT	GCA
-recovered pasa_asmbl_38549.p1, internal, 25407, 25500
Valid prediction for snap_scaffold_28-snap.244-T1
Valid prediction for GlimmerHMM_glimmerT_58082-T1
Valid prediction for Augustus_model.g38450.t1
Valid prediction for snap_scaffold_28-snap.242-T1
Valid prediction for Augustus_model.g38442.t1
Valid prediction for GlimmerHMM_glimmerT_58076-T1
Valid prediction for Augustus_model.g38449.t1
Valid prediction for GlimmerHMM_glimmerT_58084-T1
Valid prediction for Augustus_model.g38459.t1
Valid prediction for Augustus_model.g38443.t1
Valid prediction for snap_scaffold_28-snap.213-T1
Valid prediction for Augustus_model.g38440.t1
Valid prediction for GlimmerHMM_glimmerT_58078-T1
Valid prediction for GlimmerHMM_glimmerT_58075-T1
Valid prediction for snap_scaffold_28-snap.211-T1
Valid prediction for snap_scaffold_28-snap.222-T1
Valid prediction for Augustus_model.g38446.t1
Couldn't classify 27872, 27941
Couldn't classify 28083, 28654
Sorry, prediction pasa_asmbl_37969.p1 fails validation.
(GCC)	 CC	27872-27941	GT	CGG
(AAA)	 AG	28083-28654	AG	AGA
Valid prediction for snap_scaffold_28-snap.221-T1
Valid prediction for GlimmerHMM_glimmerT_58090-T1
Valid prediction for GlimmerHMM_glimmerT_58072-T1
Couldn't classify 128367, 128477
Sorry, prediction pasa_asmbl_37959.p1 fails validation.
(TGC)	 AC	128367-128477	GT	GAG
(AAT)	 AG	129218-129307	GT	AGG
(ATA)	 AG	129664-129900	AT	AAA
-recovered pasa_asmbl_37959.p1, terminal, 129664, 129900
-recovered pasa_asmbl_37959.p1, internal, 129218, 129307

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 12834, rend_intergenic: 5590  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21900, rend_intergenic: 20391  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31623, rend_intergenic: 26489  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36469, rend_intergenic: 33634  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54432, rend_intergenic: 47033  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72008, rend_intergenic: 68225  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109566, rend_intergenic: 107066  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126361, rend_intergenic: 110017  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127675, rend_intergenic: 127668  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132182, rend_intergenic: 127770  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133090, rend_intergenic: 132432  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138942, rend_intergenic: 133607  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145664, rend_intergenic: 142081  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158612, rend_intergenic: 156906  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181131, rend_intergenic: 158666  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 188274
-exon list size: 420


building trellis

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97.9    
98.1    
98.3    
98.6    
98.8    
99.1    
99.3    
99.5    
99.8    
-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 12834, rend_intergenic: 5590  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21900, rend_intergenic: 20391  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31623, rend_intergenic: 26489  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 36469, rend_intergenic: 33634  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 54432, rend_intergenic: 47033  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72008, rend_intergenic: 68225  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109566, rend_intergenic: 107066  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126361, rend_intergenic: 110017  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 127675, rend_intergenic: 127668  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 132182, rend_intergenic: 127770  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 133090, rend_intergenic: 132432  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 138942, rend_intergenic: 133607  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145664, rend_intergenic: 142081  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 158612, rend_intergenic: 156906  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181131, rend_intergenic: 158666  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