-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_28/scaffold_28_8196312-8334256

-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.105728_t
Valid prediction for GeneMark_model.105692_t
Valid prediction for Augustus_model.g40397.t1
Valid prediction for snap_scaffold_28-snap.1881-T1
Valid prediction for GlimmerHMM_glimmerT_60696-T1
Couldn't classify 122604, 123146
Sorry, prediction pasa_asmbl_38434.p1 fails validation.
(CAG)	 GA	122604-123146	TG	AGT
Valid prediction for GeneMark_model.105715_t
Valid prediction for snap_scaffold_28-snap.1891-T1
Valid prediction for GeneMark_model.105702_t
Valid prediction for GlimmerHMM_glimmerT_60689-T1
Valid prediction for GeneMark_model.105714_t
Valid prediction for GeneMark_model.105696_t
Valid prediction for snap_scaffold_28-snap.1868-T1
Valid prediction for CodingQuarry_transcript_43635-T1
Valid prediction for GeneMark_model.105725_t
Valid prediction for Augustus_model.g40404.t1
Valid prediction for GeneMark_model.105732_t
Couldn't classify 67212, 67301
Sorry, prediction pasa_asmbl_38425.p1 fails validation.
(GGT)	 CA	67212-67301	GT	AGG
(AGT)	 AG	67401-67460	GT	GGG
(GGA)	 AG	67612-67698	GT	AGG
(CTT)	 AG	68066-68146	GT	AGG
(CTC)	 AG	68299-68524	GT	TGG
(GTG)	 AG	68697-68808	GT	AGG
(CAC)	 AG	68970-69240	GC	AGG
-recovered pasa_asmbl_38425.p1, terminal, 68970, 69240
-recovered pasa_asmbl_38425.p1, internal, 67401, 67460
-recovered pasa_asmbl_38425.p1, internal, 67612, 67698
-recovered pasa_asmbl_38425.p1, internal, 68066, 68146
-recovered pasa_asmbl_38425.p1, internal, 68299, 68524
-recovered pasa_asmbl_38425.p1, internal, 68697, 68808
-recovered pasa_asmbl_38425.p1, internal, 68970, 69240
Valid prediction for Augustus_model.g40415.t1
Valid prediction for GeneMark_model.105705_t
Valid prediction for snap_scaffold_28-snap.1876-T1
Valid prediction for snap_scaffold_28-snap.1878-T1
Valid prediction for GlimmerHMM_glimmerT_60686-T1
Valid prediction for GeneMark_model.105712_t
Valid prediction for GeneMark_model.105718_t
Couldn't classify 121709, 121747
Couldn't classify 122430, 122615
Sorry, prediction pasa_asmbl_38433.p1 fails validation.
(CTA)	 AG	121709-121747	GT	AGG
(GTT)	 AG	121863-122048	GC	AGG
(GTG)	 AG	122430-122615	GG	GCG
-recovered pasa_asmbl_38433.p1, internal, 121709, 121747
-recovered pasa_asmbl_38433.p1, internal, 121863, 122048
Valid prediction for snap_scaffold_28-snap.1882-T1
Valid prediction for Augustus_model.g40407.t1
Valid prediction for Augustus_model.g40406.t1
Valid prediction for snap_scaffold_28-snap.1874-T1
Valid prediction for snap_scaffold_28-snap.1887-T1
Valid prediction for snap_scaffold_28-snap.1859-T1
Valid prediction for Augustus_model.g40414.t1
Valid prediction for GlimmerHMM_glimmerT_60692-T1
Couldn't classify 79696, 79746
Sorry, prediction pasa_asmbl_38430.p1 fails validation.
(ATG)	 CA	77675-77784	GT	AGG
(TGG)	 AG	78199-78312	GT	GGG
(GCT)	 AG	78624-78786	GT	AGG
(GGA)	 AG	79696-79746	GC	CTG
-recovered pasa_asmbl_38430.p1, initial, 77675, 77784
-recovered pasa_asmbl_38430.p1, internal, 78199, 78312
-recovered pasa_asmbl_38430.p1, internal, 78624, 78786
-recovered pasa_asmbl_38430.p1, internal, 79696, 79746
Valid prediction for GeneMark_model.105710_t
Valid prediction for Augustus_model.g40402.t1
Valid prediction for GeneMark_model.105698_t
Valid prediction for GeneMark_model.105730_t
Valid prediction for GeneMark_model.105722_t
Valid prediction for GeneMark_model.105691_t
Valid prediction for GeneMark_model.105708_t
Valid prediction for snap_scaffold_28-snap.1871-T1
Valid prediction for snap_scaffold_28-snap.1872-T1
Valid prediction for GeneMark_model.105695_t
Valid prediction for GeneMark_model.105693_t
Valid prediction for Augustus_model.g40401.t1
Valid prediction for snap_scaffold_28-snap.1893-T1
Valid prediction for snap_scaffold_28-snap.1879-T1
Valid prediction for GeneMark_model.105733_t
Valid prediction for snap_scaffold_28-snap.1864-T1
Valid prediction for GlimmerHMM_glimmerT_60707-T1
Valid prediction for snap_scaffold_28-snap.1861-T1
Valid prediction for snap_scaffold_28-snap.1892-T1
Valid prediction for snap_scaffold_28-snap.1873-T1
Valid prediction for snap_scaffold_28-snap.1895-T1
Valid prediction for GeneMark_model.105700_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 GeneMark_model.105716_t
Valid prediction for GlimmerHMM_glimmerT_60697-T1
Valid prediction for GlimmerHMM_glimmerT_60704-T1
Valid prediction for GlimmerHMM_glimmerT_60688-T1
Valid prediction for GeneMark_model.105711_t
Valid prediction for GlimmerHMM_glimmerT_60702-T1
Valid prediction for snap_scaffold_28-snap.1884-T1
Valid prediction for snap_scaffold_28-snap.1886-T1
Valid prediction for GeneMark_model.105713_t
Valid prediction for GeneMark_model.105731_t
Valid prediction for CodingQuarry_transcript_43637-T1
Valid prediction for pasa_asmbl_37781.p1
Valid prediction for GlimmerHMM_glimmerT_60691-T1
Valid prediction for GeneMark_model.105719_t
Valid prediction for Augustus_model.g40408.t1
Valid prediction for snap_scaffold_28-snap.1894-T1
Valid prediction for GlimmerHMM_glimmerT_60695-T1
Valid prediction for GeneMark_model.105707_t
Valid prediction for snap_scaffold_28-snap.1877-T1
Valid prediction for GlimmerHMM_glimmerT_60698-T1
Valid prediction for GeneMark_model.105703_t
Couldn't classify 33731, 33835
Sorry, prediction pasa_asmbl_37780.p2 fails validation.
(AGA)	 GG	33731-33835	GT	TGG
(ACT)	 AG	34351-34404	GT	GTG
(ATC)	 AG	35110-35215	GT	TGG
(GCG)	 AG	35352-35500	AC	AAA
-recovered pasa_asmbl_37780.p2, terminal, 35352, 35500
-recovered pasa_asmbl_37780.p2, internal, 34351, 34404
-recovered pasa_asmbl_37780.p2, internal, 35110, 35215
Valid prediction for snap_scaffold_28-snap.1890-T1
Valid prediction for GlimmerHMM_glimmerT_60706-T1
Valid prediction for GeneMark_model.105709_t
Valid prediction for HiQ_model.g40412.t1
Valid prediction for Augustus_model.g40411.t1
Valid prediction for snap_scaffold_28-snap.1875-T1
Valid prediction for GeneMark_model.105724_t
Valid prediction for GlimmerHMM_glimmerT_60708-T1
Valid prediction for Augustus_model.g40405.t1
Valid prediction for snap_scaffold_28-snap.1860-T1
Valid prediction for HiQ_model.g40413.t1
Valid prediction for GlimmerHMM_glimmerT_60700-T1
Couldn't classify 65359, 65635
Couldn't classify 65806, 65864
Sorry, prediction pasa_asmbl_37882.p1 fails validation.
(TCC)	 CA	65359-65635	GT	AGG
(GGG)	 AG	65806-65864	AC	CCA
Couldn't classify 51407, 51472
Couldn't classify 53258, 53277
Sorry, prediction pasa_asmbl_37894.p1 fails validation.
(TTC)	 CC	51407-51472	GT	AGG
(TCA)	 AG	52708-52872	GT	TGG
(TCC)	 AG	52985-53063	GT	AGG
(GCC)	 AG	53258-53277	GA	CAG
add_exon() Sorry, pasa_asmbl_37894.p1 52985-53063-terminal-3 is invalid.
-recovered pasa_asmbl_37894.p1, terminal, 52985, 53063
-recovered pasa_asmbl_37894.p1, internal, 52708, 52872
-recovered pasa_asmbl_37894.p1, internal, 52985, 53063
Valid prediction for GeneMark_model.105717_t
Valid prediction for GlimmerHMM_glimmerT_60693-T1
Valid prediction for snap_scaffold_28-snap.1863-T1
Valid prediction for snap_scaffold_28-snap.1885-T1
Valid prediction for GlimmerHMM_glimmerT_60703-T1
Valid prediction for GeneMark_model.105721_t
Valid prediction for GeneMark_model.105699_t
Valid prediction for GeneMark_model.105726_t
Valid prediction for snap_scaffold_28-snap.1865-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for CodingQuarry_transcript_43638-T1
Valid prediction for snap_scaffold_28-snap.1862-T1
Valid prediction for GlimmerHMM_glimmerT_60687-T1
Valid prediction for GeneMark_model.105704_t
Valid prediction for snap_scaffold_28-snap.1869-T1
Valid prediction for GeneMark_model.105694_t
Valid prediction for GlimmerHMM_glimmerT_60701-T1
Valid prediction for snap_scaffold_28-snap.1867-T1
Valid prediction for GlimmerHMM_glimmerT_60694-T1
Valid prediction for snap_scaffold_28-snap.1889-T1
Valid prediction for Augustus_model.g40398.t1
Valid prediction for GlimmerHMM_glimmerT_60699-T1
Valid prediction for GeneMark_model.105701_t
Valid prediction for HiQ_model.g40416.t1
Valid prediction for snap_scaffold_28-snap.1866-T1
Valid prediction for GeneMark_model.105727_t
Valid prediction for GeneMark_model.105697_t
Valid prediction for Augustus_model.g40403.t1
Valid prediction for GlimmerHMM_glimmerT_60690-T1
Valid prediction for CodingQuarry_transcript_43641-T1
Valid prediction for Augustus_model.g40409.t1
Valid prediction for Augustus_model.g40400.t1
Valid prediction for GeneMark_model.105720_t
Valid prediction for snap_scaffold_28-snap.1880-T1
Valid prediction for CodingQuarry_transcript_43640-T1
Valid prediction for GeneMark_model.105723_t
Valid prediction for snap_scaffold_28-snap.1883-T1
Valid prediction for snap_scaffold_28-snap.1858-T1
Valid prediction for GeneMark_model.105706_t
Valid prediction for Augustus_model.g40399.t1
Valid prediction for snap_scaffold_28-snap.1870-T1
Valid prediction for GeneMark_model.105729_t
Valid prediction for Augustus_model.g40410.t1
Valid prediction for GeneMark_model.105690_t
Valid prediction for GlimmerHMM_glimmerT_60705-T1
Valid prediction for snap_scaffold_28-snap.1888-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 12341, rend_intergenic: 9454  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26105, rend_intergenic: 20960  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31889, rend_intergenic: 28208  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33630, rend_intergenic: 32473  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45075, rend_intergenic: 36666  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55335, rend_intergenic: 54287  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59537, rend_intergenic: 55956  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62189, rend_intergenic: 59706  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69240, rend_intergenic: 68218  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97094, rend_intergenic: 95366  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119689, rend_intergenic: 105645  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 137945
-exon list size: 620


building trellis

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99.7    
99.8    
-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 12341, rend_intergenic: 9454  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 26105, rend_intergenic: 20960  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31889, rend_intergenic: 28208  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33630, rend_intergenic: 32473  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 45075, rend_intergenic: 36666  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55335, rend_intergenic: 54287  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59537, rend_intergenic: 55956  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62189, rend_intergenic: 59706  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 69240, rend_intergenic: 68218  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97094, rend_intergenic: 95366  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 119689, rend_intergenic: 105645  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 23 predictions persist after filtering for low support