-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_13/scaffold_13_3867295-3993903

-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 CodingQuarry_transcript_12939-T1
Valid prediction for GlimmerHMM_glimmerT_32160-T1
Valid prediction for GlimmerHMM_glimmerT_32157-T1
Couldn't classify 10738, 10889
Sorry, prediction pasa_asmbl_10726.p1 fails validation.
(GCA)	 GA	10738-10889	GT	AGG
(GGC)	 AG	11017-11106	GT	AGG
(GTT)	 AG	11250-11311	GT	ATG
(ACG)	 AG	11408-11571	GT	AGG
(GTA)	 AG	11702-11878	AG	AAA
-recovered pasa_asmbl_10726.p1, terminal, 11702, 11878
-recovered pasa_asmbl_10726.p1, internal, 11017, 11106
-recovered pasa_asmbl_10726.p1, internal, 11250, 11311
-recovered pasa_asmbl_10726.p1, internal, 11408, 11571
Valid prediction for HiQ_model.g21511.t1
Valid prediction for GeneMark_model.55051_t
Valid prediction for Augustus_model.g21516.t1
Valid prediction for GeneMark_model.55050_t
Valid prediction for pasa_asmbl_10729.p1
Couldn't classify 36524, 36651
Sorry, prediction pasa_asmbl_10728.p1 fails validation.
(GTT)	 AG	36524-36651	GT	AGG
(GAA)	 AG	36882-37112	GT	AGG
(CTA)	 AG	37367-37601	GT	TGG
(GGT)	 AG	37794-37943	GT	AGG
(GTG)	 AG	38514-38648	CT	AGC
-recovered pasa_asmbl_10728.p1, terminal, 38514, 38648
-recovered pasa_asmbl_10728.p1, internal, 36524, 36651
-recovered pasa_asmbl_10728.p1, internal, 36882, 37112
-recovered pasa_asmbl_10728.p1, internal, 37367, 37601
-recovered pasa_asmbl_10728.p1, internal, 37794, 37943
Couldn't classify 34325, 34399
Couldn't classify 35097, 35146
Sorry, prediction pasa_asmbl_11671.p1 fails validation.
(AAT)	 CC	34325-34399	GT	AGG
(GTG)	 AG	34611-34851	GT	TGG
(GCA)	 AG	35097-35146	AC	CCA
-recovered pasa_asmbl_11671.p1, internal, 34611, 34851
Valid prediction for GeneMark_model.55070_t
Valid prediction for Augustus_model.g21518.t1
Valid prediction for GeneMark_model.55060_t
Valid prediction for GlimmerHMM_glimmerT_32163-T1
Valid prediction for snap_scaffold_13-snap.715-T1
Valid prediction for GlimmerHMM_glimmerT_32156-T1
Valid prediction for GlimmerHMM_glimmerT_32161-T1
Valid prediction for snap_scaffold_13-snap.714-T1
Valid prediction for GlimmerHMM_glimmerT_32172-T1
Couldn't classify 33392, 33403
Sorry, prediction pasa_asmbl_10727.p1 fails validation.
(ATG)	 AG	31234-31318	GT	AGG
(GAG)	 AG	32391-32493	GT	AGG
(GCT)	 AG	32789-33026	GT	AGG
(GTG)	 AG	33392-33403	AA	GGA
-recovered pasa_asmbl_10727.p1, initial, 31234, 31318
-recovered pasa_asmbl_10727.p1, internal, 31234, 31318
-recovered pasa_asmbl_10727.p1, internal, 32391, 32493
-recovered pasa_asmbl_10727.p1, internal, 32789, 33026
Valid prediction for snap_scaffold_13-snap.724-T1
Valid prediction for GeneMark_model.55052_t
Valid prediction for snap_scaffold_13-snap.730-T1
Valid prediction for GlimmerHMM_glimmerT_32158-T1
Valid prediction for snap_scaffold_13-snap.732-T1
Valid prediction for snap_scaffold_13-snap.710-T1
Valid prediction for CodingQuarry_transcript_12942-T1
Valid prediction for GeneMark_model.55053_t
Valid prediction for GeneMark_model.55055_t
Valid prediction for HiQ_model.g21515.t1
Valid prediction for snap_scaffold_13-snap.709-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for snap_scaffold_13-snap.723-T1
Valid prediction for GeneMark_model.55043_t
Valid prediction for Augustus_model.g21512.t1
Valid prediction for GeneMark_model.55045_t
Valid prediction for GlimmerHMM_glimmerT_32162-T1
Valid prediction for GeneMark_model.55047_t
Valid prediction for CodingQuarry_transcript_12941-T1
Valid prediction for CodingQuarry_transcript_12940-T1
Valid prediction for snap_scaffold_13-snap.713-T1
Valid prediction for Augustus_model.g21523.t1
Valid prediction for GlimmerHMM_glimmerT_32173-T1
Valid prediction for GeneMark_model.55058_t
Valid prediction for GlimmerHMM_glimmerT_32165-T1
Valid prediction for Augustus_model.g21513.t1
Valid prediction for snap_scaffold_13-snap.718-T1
Valid prediction for snap_scaffold_13-snap.712-T1
Valid prediction for pasa_asmbl_11592.p1
Valid prediction for Augustus_model.g21514.t1
Valid prediction for GeneMark_model.55064_t
Valid prediction for GeneMark_model.55072_t

-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_13-snap.735-T1
Valid prediction for GlimmerHMM_glimmerT_32164-T1
Valid prediction for GeneMark_model.55071_t
Valid prediction for GeneMark_model.55066_t
Valid prediction for GeneMark_model.55059_t
Valid prediction for GeneMark_model.55062_t
Valid prediction for Augustus_model.g21524.t1
Valid prediction for HiQ_model.g21517.t1
Valid prediction for GlimmerHMM_glimmerT_32166-T1
Valid prediction for GeneMark_model.55046_t
Couldn't classify 67672, 67696
Sorry, prediction pasa_asmbl_9555.p1 fails validation.
(CCC)	 AG	67672-67696	GT	AGG
(GAG)	 AG	67799-67947	GT	GGG
(GAA)	 AG	68428-68634	GT	AGG
(ACA)	 AG	68749-68878	GT	AAG
(ATG)	 AG	68994-69055	GT	AGG
(GAG)	 AG	69147-69219	GT	AGG
(TGT)	 AG	69417-69568	GT	AGG
(GCG)	 AG	70410-70491	GT	AGG
(AAG)	 AG	70618-70712	GT	AGG
(CAA)	 AG	71195-71241	GT	ACG
(GGA)	 AG	71446-71573	GT	CGG
(GTT)	 AG	71678-71973	CC	GAC
-recovered pasa_asmbl_9555.p1, initial, 68994, 69055
-recovered pasa_asmbl_9555.p1, terminal, 71678, 71973
-recovered pasa_asmbl_9555.p1, internal, 67672, 67696
-recovered pasa_asmbl_9555.p1, internal, 67799, 67947
-recovered pasa_asmbl_9555.p1, internal, 68428, 68634
-recovered pasa_asmbl_9555.p1, internal, 68749, 68878
-recovered pasa_asmbl_9555.p1, internal, 68994, 69055
-recovered pasa_asmbl_9555.p1, internal, 69147, 69219
-recovered pasa_asmbl_9555.p1, internal, 69417, 69568
-recovered pasa_asmbl_9555.p1, internal, 70410, 70491
-recovered pasa_asmbl_9555.p1, internal, 70618, 70712
-recovered pasa_asmbl_9555.p1, internal, 71195, 71241
-recovered pasa_asmbl_9555.p1, internal, 71446, 71573
Valid prediction for GlimmerHMM_glimmerT_32179-T1
Valid prediction for snap_scaffold_13-snap.720-T1
Valid prediction for snap_scaffold_13-snap.738-T1
Valid prediction for GlimmerHMM_glimmerT_32170-T1
Valid prediction for GlimmerHMM_glimmerT_32159-T1
Valid prediction for GlimmerHMM_glimmerT_32171-T1
Couldn't classify 36412, 36505
Couldn't classify 40428, 40598
Sorry, prediction pasa_asmbl_9558.p1 fails validation.
(TTC)	 AG	36412-36505	GT	AGG
(ACA)	 AG	37975-38162	GT	AGG
(GAC)	 AG	38284-38382	GT	AGG
(GAG)	 AG	38806-38970	GT	ATG
(GCC)	 AG	39231-39330	GT	AAG
(ACT)	 AG	39478-39632	GT	TGG
(GTT)	 AG	39830-39952	GT	AGG
(GTT)	 AG	40119-40301	GT	AGG
(GTG)	 AG	40428-40598	GG	ACG
add_exon() Sorry, pasa_asmbl_9558.p1 36412-36505-terminal-3 is invalid.
-recovered pasa_asmbl_9558.p1, terminal, 36412, 36505
-recovered pasa_asmbl_9558.p1, internal, 36412, 36505
-recovered pasa_asmbl_9558.p1, internal, 37975, 38162
-recovered pasa_asmbl_9558.p1, internal, 38284, 38382
-recovered pasa_asmbl_9558.p1, internal, 38806, 38970
-recovered pasa_asmbl_9558.p1, internal, 39231, 39330
-recovered pasa_asmbl_9558.p1, internal, 39478, 39632
-recovered pasa_asmbl_9558.p1, internal, 39830, 39952
-recovered pasa_asmbl_9558.p1, internal, 40119, 40301
Valid prediction for snap_scaffold_13-snap.727-T1
Valid prediction for GlimmerHMM_glimmerT_32178-T1
Valid prediction for snap_scaffold_13-snap.725-T1
Valid prediction for snap_scaffold_13-snap.716-T1
Valid prediction for Augustus_model.g21520.t1
Valid prediction for GeneMark_model.55069_t
Valid prediction for Augustus_model.g21528.t1
Valid prediction for GlimmerHMM_glimmerT_32177-T1
Valid prediction for Augustus_model.g21521.t1
Valid prediction for snap_scaffold_13-snap.736-T1
Valid prediction for GeneMark_model.55061_t
Valid prediction for Augustus_model.g21522.t1
Valid prediction for GeneMark_model.55057_t
Valid prediction for snap_scaffold_13-snap.726-T1
Valid prediction for snap_scaffold_13-snap.731-T1
Valid prediction for GlimmerHMM_glimmerT_32174-T1
Valid prediction for snap_scaffold_13-snap.711-T1
Valid prediction for GeneMark_model.55063_t
Valid prediction for Augustus_model.g21527.t1
Valid prediction for GeneMark_model.55044_t
Valid prediction for GlimmerHMM_glimmerT_32169-T1
Valid prediction for GlimmerHMM_glimmerT_32168-T1
Valid prediction for GeneMark_model.55056_t
Valid prediction for snap_scaffold_13-snap.721-T1
Valid prediction for GlimmerHMM_glimmerT_32176-T1
Valid prediction for pasa_asmbl_9561.p1
Valid prediction for Augustus_model.g21530.t1
Valid prediction for GeneMark_model.55054_t
Valid prediction for snap_scaffold_13-snap.729-T1
Valid prediction for snap_scaffold_13-snap.728-T1
Valid prediction for GeneMark_model.55073_t
Valid prediction for snap_scaffold_13-snap.722-T1
Valid prediction for snap_scaffold_13-snap.719-T1
Valid prediction for Augustus_model.g21526.t1
Valid prediction for Augustus_model.g21525.t1
Valid prediction for snap_scaffold_13-snap.733-T1
Valid prediction for CodingQuarry_transcript_12943-T1
Valid prediction for GeneMark_model.55067_t
Valid prediction for snap_scaffold_13-snap.734-T1
Valid prediction for GlimmerHMM_glimmerT_32175-T1
Valid prediction for GeneMark_model.55065_t
Valid prediction for snap_scaffold_13-snap.737-T1
Valid prediction for GeneMark_model.55048_t
Valid prediction for Augustus_model.g21519.t1
Valid prediction for GlimmerHMM_glimmerT_32167-T1
Valid prediction for HiQ_model.g21529.t1
Valid prediction for snap_scaffold_13-snap.717-T1
Couldn't classify 29982, 30359
Sorry, prediction pasa_asmbl_9560.p1 fails validation.
(CCA)	 AG	29982-30359	GT	AGG
-recovered pasa_asmbl_9560.p1, internal, 29982, 30359

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 31882, rend_intergenic: 28197  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83166, rend_intergenic: 79851  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92578, rend_intergenic: 85817  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103610, rend_intergenic: 98983  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 126609
-exon list size: 455


building trellis

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-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 31882, rend_intergenic: 28197  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83166, rend_intergenic: 79851  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 92578, rend_intergenic: 85817  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103610, rend_intergenic: 98983  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 24 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 1 - 10845
-exon list size: 2


building trellis

25.0    
50.0    
75.0    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support