-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_14/scaffold_14_1981073-2184474

-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_14-snap.349-T1
Valid prediction for GeneMark_model.58339_t
Valid prediction for GeneMark_model.58369_t
Valid prediction for GeneMark_model.58358_t
Valid prediction for GlimmerHMM_glimmerT_34106-T1
Valid prediction for GeneMark_model.58340_t
Valid prediction for GeneMark_model.58356_t
Valid prediction for snap_scaffold_14-snap.343-T1
Valid prediction for snap_scaffold_14-snap.328-T1
Valid prediction for GlimmerHMM_glimmerT_34097-T1
Valid prediction for GlimmerHMM_glimmerT_34100-T1
Valid prediction for GlimmerHMM_glimmerT_34116-T1
Valid prediction for GeneMark_model.58365_t
Valid prediction for CodingQuarry_transcript_15527-T1
Valid prediction for Augustus_model.g22950.t1
Valid prediction for snap_scaffold_14-snap.338-T1
Valid prediction for GlimmerHMM_glimmerT_34124-T1
Valid prediction for snap_scaffold_14-snap.337-T1
Valid prediction for snap_scaffold_14-snap.340-T1
Valid prediction for GlimmerHMM_glimmerT_34121-T1
Valid prediction for GeneMark_model.58354_t
Couldn't classify 83319, 83397
Sorry, prediction pasa_asmbl_11818.p1 fails validation.
(GTC)	 CA	83319-83397	GT	CGG
(AGA)	 AG	83924-84017	GT	AGG
(GTT)	 AG	84542-84615	GT	AGG
(AAC)	 AG	85859-85995	GT	ACG
(TGC)	 AG	86548-86638	GT	ATG
(ATG)	 AG	86953-87029	GT	ATG
(GGC)	 AG	87186-87222	GT	AGG
(GAC)	 AG	87812-87909	GT	AGG
(GAT)	 AG	88625-88744	GT	ATG
(CAG)	 AG	89867-90030	GT	AGG
(TGC)	 AG	90147-90282	GT	ACG
(ATG)	 AG	90424-90573	GT	AGG
(AAA)	 AG	90782-90875	GT	ATG
(ATG)	 AG	91349-91425	GT	ACG
(GGC)	 AG	91556-91690	GT	AGG
(GAA)	 AG	91896-92021	GT	CGG
(GAG)	 AG	92323-92474	GT	AGG
(TGC)	 AG	92773-92908	GT	TGG
(GAA)	 AG	93188-93262	CC	GAC
add_exon() Sorry, pasa_asmbl_11818.p1 86953-87029-initial-1 is invalid.
-recovered pasa_asmbl_11818.p1, initial, 86953, 87029
-recovered pasa_asmbl_11818.p1, initial, 90424, 90573
add_exon() Sorry, pasa_asmbl_11818.p1 91349-91425-initial-1 is invalid.
-recovered pasa_asmbl_11818.p1, initial, 91349, 91425
-recovered pasa_asmbl_11818.p1, terminal, 93188, 93262
-recovered pasa_asmbl_11818.p1, internal, 83924, 84017
-recovered pasa_asmbl_11818.p1, internal, 84542, 84615
-recovered pasa_asmbl_11818.p1, internal, 85859, 85995
-recovered pasa_asmbl_11818.p1, internal, 86548, 86638
-recovered pasa_asmbl_11818.p1, internal, 86953, 87029
-recovered pasa_asmbl_11818.p1, internal, 87186, 87222
-recovered pasa_asmbl_11818.p1, internal, 87812, 87909
-recovered pasa_asmbl_11818.p1, internal, 88625, 88744
-recovered pasa_asmbl_11818.p1, internal, 89867, 90030
-recovered pasa_asmbl_11818.p1, internal, 90147, 90282
-recovered pasa_asmbl_11818.p1, internal, 90424, 90573
-recovered pasa_asmbl_11818.p1, internal, 90782, 90875
-recovered pasa_asmbl_11818.p1, internal, 91349, 91425
-recovered pasa_asmbl_11818.p1, internal, 91556, 91690
-recovered pasa_asmbl_11818.p1, internal, 91896, 92021
-recovered pasa_asmbl_11818.p1, internal, 92323, 92474
-recovered pasa_asmbl_11818.p1, internal, 92773, 92908
Valid prediction for snap_scaffold_14-snap.347-T1
Valid prediction for GeneMark_model.58361_t
Valid prediction for GeneMark_model.58351_t
Valid prediction for Augustus_model.g22948.t1
Valid prediction for snap_scaffold_14-snap.334-T1
Valid prediction for snap_scaffold_14-snap.336-T1
Valid prediction for GlimmerHMM_glimmerT_34122-T1
Valid prediction for Augustus_model.g22939.t1
Valid prediction for GeneMark_model.58352_t
Valid prediction for Augustus_model.g22952.t1
Couldn't classify 105630, 105758
Sorry, prediction pasa_asmbl_11819.p1 fails validation.
(GAG)	 CA	105630-105758	GT	AGG
(TAT)	 AG	105972-106089	GT	GGG
(GCC)	 AG	107046-107196	GT	AGG
(GAA)	 AG	107353-107512	GT	AGG
(GGC)	 AG	107630-107827	GT	AGG
(TCA)	 AG	107944-108195	GT	GGG
(GCC)	 AG	108451-108558	GT	AGG
(GTA)	 AG	108657-108794	GT	AGG
(ATA)	 AG	108898-109107	AC	AAA
-recovered pasa_asmbl_11819.p1, terminal, 108898, 109107
-recovered pasa_asmbl_11819.p1, internal, 105972, 106089
-recovered pasa_asmbl_11819.p1, internal, 107046, 107196
-recovered pasa_asmbl_11819.p1, internal, 107353, 107512
-recovered pasa_asmbl_11819.p1, internal, 107630, 107827
-recovered pasa_asmbl_11819.p1, internal, 107944, 108195
-recovered pasa_asmbl_11819.p1, internal, 108451, 108558
-recovered pasa_asmbl_11819.p1, internal, 108657, 108794
Valid prediction for GlimmerHMM_glimmerT_34102-T1
Valid prediction for Augustus_model.g22947.t1
Valid prediction for GlimmerHMM_glimmerT_34118-T1
Valid prediction for snap_scaffold_14-snap.346-T1
Valid prediction for GlimmerHMM_glimmerT_34101-T1
Valid prediction for GeneMark_model.58374_t
Valid prediction for GeneMark_model.58347_t
Valid prediction for Augustus_model.g22941.t1
Valid prediction for GlimmerHMM_glimmerT_34123-T1
Valid prediction for snap_scaffold_14-snap.355-T1
Valid prediction for GeneMark_model.58359_t
Valid prediction for snap_scaffold_14-snap.329-T1
Valid prediction for GlimmerHMM_glimmerT_34114-T1
Valid prediction for GlimmerHMM_glimmerT_34110-T1
Valid prediction for GlimmerHMM_glimmerT_34109-T1
Valid prediction for snap_scaffold_14-snap.330-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_34119-T1
Couldn't classify 19120, 19479
Sorry, prediction pasa_asmbl_11817.p2 fails validation.
(CTC)	 AC	19120-19479	GG	GAG
Valid prediction for GeneMark_model.58371_t
Valid prediction for Augustus_model.g22944.t1
Valid prediction for GeneMark_model.58367_t
Valid prediction for Augustus_model.g22940.t1
Valid prediction for GlimmerHMM_glimmerT_34126-T1
Valid prediction for GlimmerHMM_glimmerT_34105-T1
Valid prediction for GeneMark_model.58349_t
Valid prediction for GlimmerHMM_glimmerT_34099-T1
Valid prediction for Augustus_model.g22953.t1
Valid prediction for Augustus_model.g22943.t1
Valid prediction for HiQ_model.g22945.t1
Valid prediction for snap_scaffold_14-snap.353-T1
Valid prediction for snap_scaffold_14-snap.331-T1
Valid prediction for GlimmerHMM_glimmerT_34112-T1
Valid prediction for GlimmerHMM_glimmerT_34103-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_14-snap.348-T1
Valid prediction for GeneMark_model.58357_t
Valid prediction for snap_scaffold_14-snap.332-T1
Valid prediction for GlimmerHMM_glimmerT_34108-T1
Valid prediction for snap_scaffold_14-snap.350-T1
Valid prediction for Augustus_model.g22942.t1
Valid prediction for GeneMark_model.58343_t
Valid prediction for CodingQuarry_transcript_15528-T1
Valid prediction for HiQ_model.g22949.t1
Valid prediction for GeneMark_model.58345_t
Valid prediction for GlimmerHMM_glimmerT_34111-T1
Valid prediction for snap_scaffold_14-snap.345-T1
Valid prediction for GeneMark_model.58350_t
Couldn't classify 54470, 54590
Sorry, prediction pasa_asmbl_12896.p1 fails validation.
(CAC)	 CA	54470-54590	GT	AGG
(GCA)	 AG	55102-55167	GT	AGG
(AGG)	 AG	55256-55392	GT	CAG
(ACG)	 AG	55600-55758	GT	AAG
(GAG)	 AG	56067-56160	GT	AGG
(CAC)	 AG	56441-56611	GT	AGG
(TGC)	 AG	56728-56904	GT	CAG
(TTG)	 AG	57041-57214	GT	CGG
(ACA)	 AG	57304-57431	GT	AGG
(TGT)	 AG	57539-57673	GT	AGG
(GTG)	 AG	57785-58003	GT	AGG
(GAT)	 AG	58112-58219	GT	GGG
(GAC)	 AG	58594-58753	GT	TGG
(AGA)	 AG	59235-59353	GT	AGG
(ATC)	 AG	59458-59692	GT	TGG
(GGG)	 AG	60283-60510	GT	CAG
(GCT)	 AG	60704-60834	GT	AGG
(GTG)	 AG	60918-61058	GT	AGG
(GTC)	 AG	61231-61328	GT	CGG
(TGT)	 AG	61522-61661	GT	AGG
(ATA)	 AG	61751-61758	GC	GAG
-recovered pasa_asmbl_12896.p1, terminal, 61751, 61758
-recovered pasa_asmbl_12896.p1, internal, 55102, 55167
-recovered pasa_asmbl_12896.p1, internal, 55256, 55392
-recovered pasa_asmbl_12896.p1, internal, 55600, 55758
-recovered pasa_asmbl_12896.p1, internal, 56067, 56160
-recovered pasa_asmbl_12896.p1, internal, 56441, 56611
-recovered pasa_asmbl_12896.p1, internal, 56728, 56904
-recovered pasa_asmbl_12896.p1, internal, 57041, 57214
-recovered pasa_asmbl_12896.p1, internal, 57304, 57431
-recovered pasa_asmbl_12896.p1, internal, 57539, 57673
-recovered pasa_asmbl_12896.p1, internal, 57785, 58003
-recovered pasa_asmbl_12896.p1, internal, 58112, 58219
-recovered pasa_asmbl_12896.p1, internal, 58594, 58753
-recovered pasa_asmbl_12896.p1, internal, 59235, 59353
-recovered pasa_asmbl_12896.p1, internal, 59458, 59692
-recovered pasa_asmbl_12896.p1, internal, 60283, 60510
-recovered pasa_asmbl_12896.p1, internal, 60704, 60834
-recovered pasa_asmbl_12896.p1, internal, 60918, 61058
-recovered pasa_asmbl_12896.p1, internal, 61231, 61328
-recovered pasa_asmbl_12896.p1, internal, 61522, 61661
-recovered pasa_asmbl_12896.p1, internal, 61751, 61758
Valid prediction for GeneMark_model.58346_t
Valid prediction for GeneMark_model.58373_t
Valid prediction for GeneMark_model.58360_t
Valid prediction for snap_scaffold_14-snap.352-T1
Valid prediction for snap_scaffold_14-snap.351-T1
Valid prediction for GlimmerHMM_glimmerT_34115-T1
Valid prediction for GeneMark_model.58370_t
Valid prediction for GeneMark_model.58335_t
Valid prediction for GeneMark_model.58366_t
Valid prediction for HiQ_model.g22951.t1
Valid prediction for snap_scaffold_14-snap.341-T1
Valid prediction for GeneMark_model.58341_t
Valid prediction for GeneMark_model.58336_t
Valid prediction for GeneMark_model.58355_t
Valid prediction for Augustus_model.g22938.t1
Valid prediction for snap_scaffold_14-snap.335-T1
Valid prediction for pasa_asmbl_12902.p1
Valid prediction for GlimmerHMM_glimmerT_34113-T1
Valid prediction for GlimmerHMM_glimmerT_34104-T1
Valid prediction for GlimmerHMM_glimmerT_34117-T1
Valid prediction for snap_scaffold_14-snap.339-T1
Valid prediction for GeneMark_model.58344_t
Valid prediction for GeneMark_model.58342_t
Valid prediction for GeneMark_model.58362_t
Valid prediction for snap_scaffold_14-snap.356-T1
Valid prediction for GlimmerHMM_glimmerT_34098-T1
Valid prediction for GeneMark_model.58348_t
Valid prediction for snap_scaffold_14-snap.333-T1
Valid prediction for Augustus_model.g22946.t1
Valid prediction for GeneMark_model.58376_t
Valid prediction for snap_scaffold_14-snap.354-T1
Valid prediction for GlimmerHMM_glimmerT_34125-T1
Valid prediction for GlimmerHMM_glimmerT_34107-T1
Valid prediction for GlimmerHMM_glimmerT_34127-T1
Valid prediction for GeneMark_model.58364_t
Valid prediction for GeneMark_model.58353_t
Valid prediction for GeneMark_model.58375_t
Valid prediction for GeneMark_model.58338_t
Valid prediction for snap_scaffold_14-snap.344-T1
Valid prediction for snap_scaffold_14-snap.342-T1
Valid prediction for GlimmerHMM_glimmerT_34120-T1
Valid prediction for GeneMark_model.58368_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 77020, rend_intergenic: 70614  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109107, rend_intergenic: 106783  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150451, rend_intergenic: 143033  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155084, rend_intergenic: 152258  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165894, rend_intergenic: 155149  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170360, rend_intergenic: 166644  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180074, rend_intergenic: 176204  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 139981, rend_intergenic: 139978  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 203402
-exon list size: 549


building trellis

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92.0    
92.2    
92.4    
92.6    
92.7    
92.9    
93.1    
93.3    
93.5    
93.6    
93.8    
94.0    
94.2    
94.4    
94.6    
94.7    
94.9    
95.1    
95.3    
95.5    
95.6    
95.8    
96.0    
96.2    
96.4    
96.6    
96.7    
96.9    
97.1    
97.3    
97.5    
97.6    
97.8    
98.0    
98.2    
98.4    
98.5    
98.7    
98.9    
99.1    
99.3    
99.5    
99.6    
99.8    
-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 77020, rend_intergenic: 70614  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109107, rend_intergenic: 106783  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 150451, rend_intergenic: 143033  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 155084, rend_intergenic: 152258  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165894, rend_intergenic: 155149  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 170360, rend_intergenic: 166644  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180074, rend_intergenic: 176204  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 139981, rend_intergenic: 139978  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 20 predictions persist after filtering for low support