-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_12/scaffold_12_12631453-12838539

-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_12-snap.2377-T1
Valid prediction for GeneMark_model.53272_t
Valid prediction for GeneMark_model.53254_t
Valid prediction for GeneMark_model.53274_t
Valid prediction for snap_scaffold_12-snap.2365-T1
Valid prediction for HiQ_model.g20614.t1
Couldn't classify 191188, 191313
Couldn't classify 195277, 195421
Sorry, prediction pasa_asmbl_8993.p1 fails validation.
(TGT)	 CC	191188-191313	GT	AGG
(GTG)	 AG	192245-192422	GT	CAG
(ACA)	 AG	193258-193422	GT	GTG
(TGT)	 AG	193542-193711	GT	AGG
(GTG)	 AG	194906-194997	GT	AGG
(TGT)	 AG	195277-195421	AG	GGA
-recovered pasa_asmbl_8993.p1, internal, 192245, 192422
-recovered pasa_asmbl_8993.p1, internal, 193258, 193422
-recovered pasa_asmbl_8993.p1, internal, 193542, 193711
-recovered pasa_asmbl_8993.p1, internal, 194906, 194997
Valid prediction for Augustus_model.g20608.t1
Valid prediction for snap_scaffold_12-snap.2367-T1
Valid prediction for GeneMark_model.53262_t
Valid prediction for snap_scaffold_12-snap.2359-T1
Valid prediction for GeneMark_model.53267_t
Valid prediction for GlimmerHMM_glimmerT_30899-T1
Valid prediction for snap_scaffold_12-snap.2374-T1
Valid prediction for snap_scaffold_12-snap.2361-T1
Valid prediction for Augustus_model.g20602.t1
Valid prediction for Augustus_model.g20607.t1
Valid prediction for snap_scaffold_12-snap.2364-T1
Valid prediction for GlimmerHMM_glimmerT_30892-T1
Couldn't classify 3346, 3483
Sorry, prediction pasa_asmbl_8983.p1 fails validation.
(CAG)	 CT	3346-3483	GT	GGG
(GTG)	 AG	4744-5034	AG	AGA
-recovered pasa_asmbl_8983.p1, terminal, 4744, 5034
Valid prediction for GeneMark_model.53252_t
Valid prediction for GeneMark_model.53257_t
Valid prediction for Augustus_model.g20603.t1
Valid prediction for GlimmerHMM_glimmerT_30878-T1
Valid prediction for Augustus_model.g20616.t1
Valid prediction for GlimmerHMM_glimmerT_30891-T1
Valid prediction for Augustus_model.g20613.t1
Valid prediction for GeneMark_model.53269_t
Valid prediction for CodingQuarry_transcript_10403-T1
Valid prediction for GlimmerHMM_glimmerT_30890-T1
Valid prediction for snap_scaffold_12-snap.2382-T1
Valid prediction for snap_scaffold_12-snap.2371-T1
Valid prediction for GeneMark_model.53265_t
Couldn't classify 174840, 175556
Sorry, prediction pasa_asmbl_8992.p1 fails validation.
(ACC)	 GT	174840-175556	CG	AGC
Valid prediction for GlimmerHMM_glimmerT_30888-T1
Valid prediction for snap_scaffold_12-snap.2375-T1
Valid prediction for GeneMark_model.53247_t
Valid prediction for snap_scaffold_12-snap.2370-T1
Valid prediction for GlimmerHMM_glimmerT_30872-T1
Valid prediction for GeneMark_model.53253_t
Valid prediction for GeneMark_model.53278_t
Couldn't classify 156731, 156768
Couldn't classify 157653, 157706
Sorry, prediction pasa_asmbl_8984.p1 fails validation.
(CCT)	 CC	156731-156768	GT	CTG
(GTC)	 AG	156975-157062	GT	AGG
(GCG)	 AG	157215-157336	GT	CTG
(GTG)	 AG	157440-157539	GT	AGG
(ACC)	 AG	157653-157706	CT	AGC
-recovered pasa_asmbl_8984.p1, internal, 156975, 157062
-recovered pasa_asmbl_8984.p1, internal, 157215, 157336
-recovered pasa_asmbl_8984.p1, internal, 157440, 157539
Valid prediction for Augustus_model.g20611.t1
Valid prediction for snap_scaffold_12-snap.2347-T1
Valid prediction for GlimmerHMM_glimmerT_30883-T1
Valid prediction for GlimmerHMM_glimmerT_30879-T1
Valid prediction for GeneMark_model.53280_t
Valid prediction for GeneMark_model.53245_t
Valid prediction for CodingQuarry_transcript_10404-T1
Valid prediction for Augustus_model.g20609.t1
Valid prediction for pasa_asmbl_8988.p1
Valid prediction for Augustus_model.g20606.t1
Valid prediction for GlimmerHMM_glimmerT_30877-T1
Valid prediction for snap_scaffold_12-snap.2357-T1
Valid prediction for GeneMark_model.53249_t
Valid prediction for GeneMark_model.53260_t
Valid prediction for Augustus_model.g20615.t1
Valid prediction for GlimmerHMM_glimmerT_30880-T1
Valid prediction for Augustus_model.g20604.t1
Couldn't classify 173887, 174037
Couldn't classify 174425, 174541
Sorry, prediction pasa_asmbl_8991.p1 fails validation.
(GAG)	 AG	173887-174037	GT	TGG
(CAG)	 AG	174131-174249	GT	AGG
(TTT)	 AG	174425-174541	GT	CAG
-recovered pasa_asmbl_8991.p1, internal, 173887, 174037
-recovered pasa_asmbl_8991.p1, internal, 174131, 174249
-recovered pasa_asmbl_8991.p1, internal, 174425, 174541
Valid prediction for snap_scaffold_12-snap.2373-T1
Valid prediction for GlimmerHMM_glimmerT_30874-T1
Valid prediction for GeneMark_model.53264_t
Valid prediction for Augustus_model.g20617.t1
Valid prediction for snap_scaffold_12-snap.2346-T1
Valid prediction for GlimmerHMM_glimmerT_30897-T1
Valid prediction for GlimmerHMM_glimmerT_30884-T1
Valid prediction for GeneMark_model.53244_t
Valid prediction for GlimmerHMM_glimmerT_30885-T1
Valid prediction for snap_scaffold_12-snap.2354-T1
Valid prediction for snap_scaffold_12-snap.2353-T1
Valid prediction for GeneMark_model.53270_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.53268_t
Valid prediction for GlimmerHMM_glimmerT_30887-T1
Valid prediction for Augustus_model.g20605.t1
Valid prediction for snap_scaffold_12-snap.2351-T1
Valid prediction for snap_scaffold_12-snap.2358-T1
Valid prediction for snap_scaffold_12-snap.2368-T1
Valid prediction for snap_scaffold_12-snap.2380-T1
Valid prediction for snap_scaffold_12-snap.2356-T1
Valid prediction for snap_scaffold_12-snap.2363-T1
Valid prediction for snap_scaffold_12-snap.2348-T1
Valid prediction for GlimmerHMM_glimmerT_30886-T1
Valid prediction for snap_scaffold_12-snap.2369-T1
Valid prediction for GeneMark_model.53271_t
Valid prediction for GeneMark_model.53261_t
Valid prediction for GeneMark_model.53258_t
Valid prediction for GlimmerHMM_glimmerT_30882-T1
Valid prediction for GlimmerHMM_glimmerT_30881-T1
Valid prediction for GeneMark_model.53246_t
Valid prediction for snap_scaffold_12-snap.2379-T1
Valid prediction for snap_scaffold_12-snap.2378-T1
Valid prediction for pasa_asmbl_8023.p1
Couldn't classify 9055, 9360
Sorry, prediction pasa_asmbl_8022.p1 fails validation.
(ATG)	 TT	9055-9360	CT	GTC
Valid prediction for GeneMark_model.53251_t
Valid prediction for snap_scaffold_12-snap.2350-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for CodingQuarry_transcript_10405-T1
Valid prediction for GeneMark_model.53279_t
Valid prediction for GeneMark_model.53256_t
Valid prediction for snap_scaffold_12-snap.2352-T1
Valid prediction for HiQ_model.g20612.t1
Valid prediction for GeneMark_model.53275_t
Valid prediction for Augustus_model.g20619.t1
Valid prediction for GlimmerHMM_glimmerT_30900-T1
Valid prediction for snap_scaffold_12-snap.2360-T1
Valid prediction for snap_scaffold_12-snap.2362-T1
Valid prediction for GeneMark_model.53277_t
Valid prediction for snap_scaffold_12-snap.2372-T1
Valid prediction for snap_scaffold_12-snap.2355-T1
Valid prediction for snap_scaffold_12-snap.2376-T1
Valid prediction for GlimmerHMM_glimmerT_30876-T1
Valid prediction for GeneMark_model.53273_t
Valid prediction for GlimmerHMM_glimmerT_30894-T1
Valid prediction for snap_scaffold_12-snap.2349-T1
Valid prediction for GeneMark_model.53248_t
Valid prediction for GeneMark_model.53266_t
Valid prediction for GlimmerHMM_glimmerT_30875-T1
Valid prediction for GlimmerHMM_glimmerT_30873-T1
Couldn't classify 40132, 40206
Sorry, prediction pasa_asmbl_8021.p1 fails validation.
(TGG)	 AT	40132-40206	GT	AGG
(GAC)	 AG	40817-40885	GT	AGG
(GCA)	 AG	41095-41229	GT	GAG
(GGA)	 AG	41422-41498	GT	AGG
(GTT)	 AG	41621-41759	GT	AGG
(GCG)	 AG	41984-42069	GT	CGG
(TTC)	 AG	42190-42281	GT	AGG
(TCT)	 AG	42495-42672	GT	CGG
(GGA)	 AG	43052-43223	GT	GGG
(AAC)	 AG	43320-43463	GT	CGG
(GTA)	 AG	43564-43746	CA	AAC
-recovered pasa_asmbl_8021.p1, terminal, 43564, 43746
-recovered pasa_asmbl_8021.p1, internal, 40817, 40885
-recovered pasa_asmbl_8021.p1, internal, 41095, 41229
-recovered pasa_asmbl_8021.p1, internal, 41422, 41498
-recovered pasa_asmbl_8021.p1, internal, 41621, 41759
-recovered pasa_asmbl_8021.p1, internal, 41984, 42069
-recovered pasa_asmbl_8021.p1, internal, 42190, 42281
-recovered pasa_asmbl_8021.p1, internal, 42495, 42672
-recovered pasa_asmbl_8021.p1, internal, 43052, 43223
-recovered pasa_asmbl_8021.p1, internal, 43320, 43463
Valid prediction for GeneMark_model.53259_t
Valid prediction for snap_scaffold_12-snap.2366-T1
Valid prediction for GlimmerHMM_glimmerT_30898-T1
Valid prediction for GlimmerHMM_glimmerT_30895-T1
Valid prediction for GeneMark_model.53250_t
Valid prediction for GeneMark_model.53263_t
Valid prediction for HiQ_model.g20618.t1
Valid prediction for GlimmerHMM_glimmerT_30889-T1
Valid prediction for GlimmerHMM_glimmerT_30893-T1
Couldn't classify 5001, 5149
Sorry, prediction pasa_asmbl_8024.p1 fails validation.
(ATG)	 AC	1418-1886	GT	AGG
(AGG)	 AG	3787-3863	GT	GGG
(ATG)	 AG	3943-4087	GT	AGG
(GCA)	 AG	4512-4685	GT	AGG
(ACG)	 AG	4784-4864	GT	CTG
(CCA)	 AG	5001-5149	CT	CGC
-recovered pasa_asmbl_8024.p1, initial, 1418, 1886
-recovered pasa_asmbl_8024.p1, initial, 3943, 4087
-recovered pasa_asmbl_8024.p1, internal, 3787, 3863
-recovered pasa_asmbl_8024.p1, internal, 3943, 4087
-recovered pasa_asmbl_8024.p1, internal, 4512, 4685
-recovered pasa_asmbl_8024.p1, internal, 4784, 4864
Valid prediction for GeneMark_model.53255_t
Valid prediction for GeneMark_model.53281_t
Valid prediction for GlimmerHMM_glimmerT_30896-T1
Valid prediction for snap_scaffold_12-snap.2381-T1
Valid prediction for Augustus_model.g20610.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 68536, rend_intergenic: 66438  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97916, rend_intergenic: 97016  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128025, rend_intergenic: 122725  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136767, rend_intergenic: 133324  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175556, rend_intergenic: 175505  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179811, rend_intergenic: 177379  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195568, rend_intergenic: 180103  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 206284, rend_intergenic: 202171  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 207087
-exon list size: 542


building trellis

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-found 29 predictions from path traversal
Error with prediction: snap lend_intergenic: 68536, rend_intergenic: 66438  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 97916, rend_intergenic: 97016  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 128025, rend_intergenic: 122725  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 136767, rend_intergenic: 133324  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 175556, rend_intergenic: 175505  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179811, rend_intergenic: 177379  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 195568, rend_intergenic: 180103  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 206284, rend_intergenic: 202171  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