-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_1/scaffold_1_1-219866

-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_23-T1
Valid prediction for GlimmerHMM_glimmerT_1-T1
Valid prediction for GeneMark_model.30_t
Valid prediction for GlimmerHMM_glimmerT_20-T1
Valid prediction for CodingQuarry_transcript_2499-T1
Valid prediction for GeneMark_model.15_t
Valid prediction for GeneMark_model.16_t
Valid prediction for snap_scaffold_1-snap.12-T1
Valid prediction for snap_scaffold_1-snap.37-T1
Valid prediction for snap_scaffold_1-snap.41-T1
Valid prediction for Augustus_model.g18.t1
Valid prediction for GlimmerHMM_glimmerT_21-T1
Valid prediction for pasa_asmbl_1396.p1
Valid prediction for GlimmerHMM_glimmerT_12-T1
Valid prediction for Augustus_model.g13.t1
Valid prediction for snap_scaffold_1-snap.16-T1
Valid prediction for GlimmerHMM_glimmerT_24-T1
Valid prediction for GeneMark_model.18_t
Valid prediction for snap_scaffold_1-snap.26-T1
Couldn't classify 188880, 188946
Couldn't classify 190260, 190398
Sorry, prediction pasa_asmbl_2770.p1 fails validation.
(GAA)	 CT	188880-188946	GT	AGG
(AGG)	 AG	189327-189519	GT	AAG
(ACC)	 AG	190260-190398	AG	AGA
add_exon() Sorry, pasa_asmbl_2770.p1 189327-189519-terminal-3 is invalid.
-recovered pasa_asmbl_2770.p1, terminal, 189327, 189519
-recovered pasa_asmbl_2770.p1, internal, 189327, 189519
Valid prediction for GeneMark_model.27_t
Valid prediction for snap_scaffold_1-snap.18-T1
Valid prediction for GeneMark_model.24_t
Valid prediction for GlimmerHMM_glimmerT_2-T1
Valid prediction for snap_scaffold_1-snap.25-T1
Valid prediction for GeneMark_model.22_t
Valid prediction for HiQ_model.g15.t1
Valid prediction for snap_scaffold_1-snap.35-T1
Valid prediction for Augustus_model.g9.t1
Valid prediction for Augustus_model.g8.t1
Valid prediction for HiQ_model.g2.t1
Valid prediction for snap_scaffold_1-snap.4-T1
Valid prediction for GeneMark_model.26_t
Valid prediction for pasa_asmbl_1384.p1
Valid prediction for HiQ_model.g10.t1
Couldn't classify 430, 532
Sorry, prediction GeneMark_model.1_t fails validation.
(ATA)	 AG	430-532	GT	AGG
(AAC)	 AG	803-893	GT	GGG
(CCG)	 AG	944-1192	TG	AGT
-recovered GeneMark_model.1_t, terminal, 944, 1192
-recovered GeneMark_model.1_t, internal, 430, 532
-recovered GeneMark_model.1_t, internal, 803, 893
Couldn't classify 94419, 94571
Sorry, prediction pasa_asmbl_2727.p1 fails validation.
(GAT)	 CA	94419-94571	GT	AGG
(GGG)	 AG	94815-94953	GT	CGG
(CTA)	 AG	95447-95670	GT	ATG
(CCC)	 AG	96310-96516	GT	AGG
(GTG)	 AG	96888-97131	GT	AGG
(ACC)	 AG	97397-97644	CT	GAC
-recovered pasa_asmbl_2727.p1, terminal, 97397, 97644
-recovered pasa_asmbl_2727.p1, internal, 94815, 94953
-recovered pasa_asmbl_2727.p1, internal, 95447, 95670
-recovered pasa_asmbl_2727.p1, internal, 96310, 96516
-recovered pasa_asmbl_2727.p1, internal, 96888, 97131
Valid prediction for GlimmerHMM_glimmerT_19-T1
Valid prediction for GlimmerHMM_glimmerT_14-T1
Valid prediction for GeneMark_model.25_t
Valid prediction for GlimmerHMM_glimmerT_13-T1
Valid prediction for Augustus_model.g21.t1
Valid prediction for snap_scaffold_1-snap.36-T1
Valid prediction for snap_scaffold_1-snap.43-T1
Valid prediction for GlimmerHMM_glimmerT_10-T1
Valid prediction for snap_scaffold_1-snap.22-T1
Valid prediction for GeneMark_model.28_t
Valid prediction for snap_scaffold_1-snap.34-T1
Valid prediction for GeneMark_model.4_t
Couldn't classify 195117, 195275
Couldn't classify 196243, 196416
Sorry, prediction pasa_asmbl_2706.p1 fails validation.
(ATC)	 AG	195117-195275	GT	AGG
(GTA)	 AG	196243-196416	GT	ACG
-recovered pasa_asmbl_2706.p1, internal, 195117, 195275
-recovered pasa_asmbl_2706.p1, internal, 196243, 196416
Valid prediction for GeneMark_model.17_t
Valid prediction for snap_scaffold_1-snap.24-T1
Valid prediction for Augustus_model.g20.t1
Valid prediction for snap_scaffold_1-snap.3-T1
Couldn't classify 200095, 200176
Sorry, prediction pasa_asmbl_1402.p2 fails validation.
(AAA)	 AG	200095-200176	GT	GGG
(GTT)	 AG	200360-200508	GT	GGG
(AAG)	 AG	200962-201228	GT	AAG
-recovered pasa_asmbl_1402.p2, terminal, 200962, 201228
-recovered pasa_asmbl_1402.p2, internal, 200095, 200176
-recovered pasa_asmbl_1402.p2, internal, 200360, 200508
-recovered pasa_asmbl_1402.p2, internal, 200962, 201228
Valid prediction for GlimmerHMM_glimmerT_15-T1
Valid prediction for snap_scaffold_1-snap.2-T1
Valid prediction for GlimmerHMM_glimmerT_25-T1
Valid prediction for Augustus_model.g7.t1
Valid prediction for Augustus_model.g12.t1
Valid prediction for snap_scaffold_1-snap.40-T1
Valid prediction for GeneMark_model.14_t
Valid prediction for GeneMark_model.21_t
Valid prediction for GlimmerHMM_glimmerT_11-T1
Valid prediction for GeneMark_model.2_t
Valid prediction for pasa_asmbl_1391.p1
Valid prediction for snap_scaffold_1-snap.29-T1
Valid prediction for Augustus_model.g22.t1
Valid prediction for snap_scaffold_1-snap.46-T1
Valid prediction for snap_scaffold_1-snap.23-T1
Valid prediction for Augustus_model.g1.t1
add_exon() Sorry, Augustus_model.g1.t1 1-220-initial-1 is invalid.
add_exon() Sorry, Augustus_model.g1.t1 365-532-internal-2 is invalid.
add_exon() Sorry, Augustus_model.g1.t1 883-1150-internal-2 is invalid.
add_exon() Sorry, Augustus_model.g1.t1 1397-1512-internal-3 is invalid.
add_exon() Sorry, Augustus_model.g1.t1 2256-2372-internal-2 is invalid.
add_exon() Sorry, Augustus_model.g1.t1 3988-4204-internal-3 is invalid.
add_exon() Sorry, Augustus_model.g1.t1 4333-6109-internal-1 is invalid.
add_exon() Sorry, Augustus_model.g1.t1 6268-6435-internal-2 is invalid.
add_exon() Sorry, Augustus_model.g1.t1 6818-6985-internal-2 is invalid.
add_exon() Sorry, Augustus_model.g1.t1 8399-8532-internal-2 is invalid.
add_exon() Sorry, Augustus_model.g1.t1 8817-8961-internal-1 is invalid.
add_exon() Sorry, Augustus_model.g1.t1 9816-9986-internal-2 is invalid.
add_exon() Sorry, Augustus_model.g1.t1 11363-11533-internal-2 is invalid.
add_exon() Sorry, Augustus_model.g1.t1 12790-12948-internal-2 is invalid.
add_exon() Sorry, Augustus_model.g1.t1 16078-16613-terminal-1 is invalid.
Valid prediction for CodingQuarry_transcript_2500-T1
Valid prediction for GlimmerHMM_glimmerT_26-T1
Valid prediction for GeneMark_model.10_t
Valid prediction for snap_scaffold_1-snap.20-T1
Valid prediction for Augustus_model.g14.t1
Valid prediction for snap_scaffold_1-snap.27-T1
Valid prediction for GlimmerHMM_glimmerT_16-T1
Valid prediction for snap_scaffold_1-snap.1-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_1-snap.45-T1
Valid prediction for Augustus_model.g17.t1
Valid prediction for snap_scaffold_1-snap.44-T1
Valid prediction for GeneMark_model.12_t
Valid prediction for snap_scaffold_1-snap.39-T1
Valid prediction for GlimmerHMM_glimmerT_7-T1
Valid prediction for GlimmerHMM_glimmerT_17-T1
Valid prediction for GeneMark_model.20_t
Valid prediction for snap_scaffold_1-snap.47-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_1-snap.30-T1
Valid prediction for GeneMark_model.6_t
Valid prediction for snap_scaffold_1-snap.11-T1
Valid prediction for snap_scaffold_1-snap.33-T1
Valid prediction for GlimmerHMM_glimmerT_9-T1
Valid prediction for HiQ_model.g5.t1
Valid prediction for snap_scaffold_1-snap.17-T1
Valid prediction for snap_scaffold_1-snap.7-T1
Valid prediction for Augustus_model.g4.t1
Valid prediction for pasa_asmbl_2.p1
Valid prediction for GeneMark_model.13_t
Valid prediction for snap_scaffold_1-snap.14-T1
Valid prediction for snap_scaffold_1-snap.21-T1
Valid prediction for pasa_asmbl_1.p1
Valid prediction for snap_scaffold_1-snap.13-T1
Valid prediction for snap_scaffold_1-snap.5-T1
Valid prediction for GlimmerHMM_glimmerT_4-T1
Valid prediction for snap_scaffold_1-snap.31-T1
Valid prediction for GeneMark_model.9_t
Valid prediction for GeneMark_model.3_t
Valid prediction for snap_scaffold_1-snap.19-T1
Valid prediction for GlimmerHMM_glimmerT_3-T1
Valid prediction for GlimmerHMM_glimmerT_8-T1
Valid prediction for snap_scaffold_1-snap.15-T1
Valid prediction for snap_scaffold_1-snap.38-T1
Valid prediction for Augustus_model.g6.t1
Valid prediction for GeneMark_model.23_t
Valid prediction for snap_scaffold_1-snap.32-T1
Valid prediction for Augustus_model.g3.t1
Valid prediction for Augustus_model.g19.t1
Valid prediction for Augustus_model.g11.t1
Valid prediction for GeneMark_model.5_t
Valid prediction for GlimmerHMM_glimmerT_18-T1
Valid prediction for GeneMark_model.11_t
Valid prediction for GeneMark_model.19_t
Valid prediction for snap_scaffold_1-snap.28-T1
Valid prediction for GeneMark_model.29_t
Valid prediction for snap_scaffold_1-snap.42-T1
Valid prediction for snap_scaffold_1-snap.8-T1
Couldn't classify 130986, 131393
Sorry, prediction pasa_asmbl_1390.p3 fails validation.
(GTG)	 CT	130986-131393	CC	AAC
Valid prediction for snap_scaffold_1-snap.10-T1
Valid prediction for GeneMark_model.7_t
Valid prediction for pasa_asmbl_14.p1
Valid prediction for snap_scaffold_1-snap.6-T1
Valid prediction for GlimmerHMM_glimmerT_6-T1
Valid prediction for snap_scaffold_1-snap.9-T1
Valid prediction for GlimmerHMM_glimmerT_5-T1
Valid prediction for GlimmerHMM_glimmerT_22-T1
Valid prediction for HiQ_model.g16.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 55618, rend_intergenic: 55166  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59180, rend_intergenic: 55771  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76004, rend_intergenic: 73075  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78265, rend_intergenic: 76156  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88803, rend_intergenic: 86092  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153936, rend_intergenic: 140087  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 219866
-exon list size: 561


building trellis

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-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 55618, rend_intergenic: 55166  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59180, rend_intergenic: 55771  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76004, rend_intergenic: 73075  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 78265, rend_intergenic: 76156  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 88803, rend_intergenic: 86092  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153936, rend_intergenic: 140087  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 25 predictions persist after filtering for low support