-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_25/scaffold_25_6475594-6612905

-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: +)Couldn't classify 32706, 32976
Couldn't classify 33515, 33585
Sorry, prediction pasa_asmbl_33633.p1 fails validation.
(CAG)	 CT	32706-32976	GT	AGG
(AAA)	 AG	33515-33585	CC	TGC
Valid prediction for GlimmerHMM_glimmerT_55646-T1
Valid prediction for snap_scaffold_25-snap.1380-T1
Valid prediction for GeneMark_model.97069_t
Valid prediction for Augustus_model.g37120.t1
Valid prediction for snap_scaffold_25-snap.1376-T1
Couldn't classify 12267, 12281
Sorry, prediction GeneMark_model.97053_t fails validation.
(ATG)	 AA	5679-5776	GT	GCG
(GGG)	 AG	5816-5918	GT	CGG
(TCG)	 AG	5955-6012	GT	TGG
(GCA)	 AG	6385-6558	GT	AGG
(CAG)	 AG	7191-7233	GT	AGG
(GTG)	 AG	7263-7504	GT	CGG
(GCG)	 AG	7621-7811	GT	TGG
(AGC)	 AG	7921-8087	GT	AGG
(GAG)	 AG	8208-8258	GT	CTG
(GCC)	 AG	8892-8960	GT	GGG
(GAG)	 AG	8986-9006	GT	GGG
(GTG)	 AG	9030-9035	GT	AGG
(GAG)	 AG	9058-9129	GT	GGG
(GAT)	 AG	9215-9274	GT	AGG
(AGG)	 AG	9534-9542	GT	GGG
(ACC)	 AG	10442-10504	GT	GGG
(GGA)	 AG	10576-10680	GT	GCG
(AGA)	 AG	11616-11747	GT	GGG
(GGG)	 AG	11794-11856	GT	GAG
(AGA)	 AG	11900-12026	GT	AGG
(TAC)	 AG	12060-12103	GT	GAG
(AGA)	 AG	12148-12153	GT	AGG
(AAA)	 AG	12178-12207	GT	GAG
(AGA)	 AG	12235-12246	GT	AGG
(AAA)	 AG	12267-12281	GT	AAG
-recovered GeneMark_model.97053_t, initial, 5679, 5776
-recovered GeneMark_model.97053_t, internal, 5816, 5918
-recovered GeneMark_model.97053_t, internal, 5955, 6012
-recovered GeneMark_model.97053_t, internal, 6385, 6558
-recovered GeneMark_model.97053_t, internal, 7191, 7233
-recovered GeneMark_model.97053_t, internal, 7263, 7504
-recovered GeneMark_model.97053_t, internal, 7621, 7811
-recovered GeneMark_model.97053_t, internal, 7921, 8087
-recovered GeneMark_model.97053_t, internal, 8208, 8258
-recovered GeneMark_model.97053_t, internal, 8892, 8960
-recovered GeneMark_model.97053_t, internal, 8986, 9006
-recovered GeneMark_model.97053_t, internal, 9030, 9035
-recovered GeneMark_model.97053_t, internal, 9058, 9129
-recovered GeneMark_model.97053_t, internal, 9215, 9274
-recovered GeneMark_model.97053_t, internal, 9534, 9542
-recovered GeneMark_model.97053_t, internal, 10442, 10504
-recovered GeneMark_model.97053_t, internal, 10576, 10680
-recovered GeneMark_model.97053_t, internal, 11616, 11747
-recovered GeneMark_model.97053_t, internal, 11794, 11856
-recovered GeneMark_model.97053_t, internal, 11900, 12026
-recovered GeneMark_model.97053_t, internal, 12060, 12103
-recovered GeneMark_model.97053_t, internal, 12148, 12153
-recovered GeneMark_model.97053_t, internal, 12178, 12207
-recovered GeneMark_model.97053_t, internal, 12235, 12246
-recovered GeneMark_model.97053_t, internal, 12267, 12281
Valid prediction for GeneMark_model.97079_t
Valid prediction for snap_scaffold_25-snap.1378-T1
Valid prediction for snap_scaffold_25-snap.1406-T1
Valid prediction for GlimmerHMM_glimmerT_55635-T1
Valid prediction for GeneMark_model.97073_t
Valid prediction for GeneMark_model.97076_t
Valid prediction for snap_scaffold_25-snap.1382-T1
Valid prediction for snap_scaffold_25-snap.1384-T1
Valid prediction for GlimmerHMM_glimmerT_55631-T1
Valid prediction for snap_scaffold_25-snap.1392-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_55641-T1
Valid prediction for Augustus_model.g37121.t1
Valid prediction for GeneMark_model.97057_t
Valid prediction for GlimmerHMM_glimmerT_55634-T1
Valid prediction for GeneMark_model.97059_t
Valid prediction for snap_scaffold_25-snap.1391-T1
Valid prediction for GlimmerHMM_glimmerT_55639-T1
Valid prediction for GeneMark_model.97067_t
Valid prediction for snap_scaffold_25-snap.1381-T1
Valid prediction for GlimmerHMM_glimmerT_55638-T1
Couldn't classify 21102, 21194
Sorry, prediction GeneMark_model.97054_t fails validation.
(GGC)	 AG	21102-21194	GT	GAG
(AGA)	 AG	21220-21228	GT	GAG
(CAA)	 AG	21324-21374	GC	GAG
(AGA)	 AG	21408-21422	GC	GAG
(ACA)	 AG	21446-21454	GT	GAG
(AGA)	 AG	23545-23550	GT	AGG
(AAA)	 AG	23574-23662	GT	TGG
(GAC)	 AG	23740-24080	CG	AAC
add_exon() Sorry, GeneMark_model.97054_t 21102-21194-terminal-1 is invalid.
-recovered GeneMark_model.97054_t, terminal, 21102, 21194
-recovered GeneMark_model.97054_t, terminal, 23740, 24080
-recovered GeneMark_model.97054_t, internal, 21102, 21194
-recovered GeneMark_model.97054_t, internal, 21220, 21228
-recovered GeneMark_model.97054_t, internal, 21324, 21374
-recovered GeneMark_model.97054_t, internal, 21408, 21422
-recovered GeneMark_model.97054_t, internal, 21446, 21454
-recovered GeneMark_model.97054_t, internal, 23545, 23550
-recovered GeneMark_model.97054_t, internal, 23574, 23662
Valid prediction for GeneMark_model.97082_t
Valid prediction for Augustus_model.g37119.t1
Valid prediction for GeneMark_model.97061_t
Valid prediction for snap_scaffold_25-snap.1372-T1
Valid prediction for GeneMark_model.97052_t
Valid prediction for Augustus_model.g37122.t1
Valid prediction for Augustus_model.g37128.t1
Valid prediction for snap_scaffold_25-snap.1387-T1
Valid prediction for GlimmerHMM_glimmerT_55644-T1
Valid prediction for GlimmerHMM_glimmerT_55654-T1
Valid prediction for GeneMark_model.97084_t
Couldn't classify 6432, 6558
Couldn't classify 8208, 8304
Sorry, prediction pasa_asmbl_33632.p1 fails validation.
(CTT)	 CC	6432-6558	GT	AGG
(GGC)	 AG	7313-7504	GT	CGG
(GCG)	 AG	7621-7811	GT	TGG
(AGC)	 AG	7921-8087	GT	AGG
(GAG)	 AG	8208-8304	GG	TTG
-recovered pasa_asmbl_33632.p1, internal, 7313, 7504
-recovered pasa_asmbl_33632.p1, internal, 7621, 7811
-recovered pasa_asmbl_33632.p1, internal, 7921, 8087
Valid prediction for snap_scaffold_25-snap.1403-T1
Valid prediction for GeneMark_model.97070_t
Couldn't classify 43608, 43847
Sorry, prediction pasa_asmbl_33634.p1 fails validation.
(TAC)	 TC	43608-43847	GT	TGG
(GAC)	 AG	45557-45667	GT	TGG
(GCT)	 AG	46621-46689	GT	CTG
(AGC)	 AG	46980-47123	GG	AAG
-recovered pasa_asmbl_33634.p1, terminal, 46980, 47123
-recovered pasa_asmbl_33634.p1, internal, 45557, 45667
-recovered pasa_asmbl_33634.p1, internal, 46621, 46689
Valid prediction for snap_scaffold_25-snap.1375-T1
Valid prediction for Augustus_model.g37118.t1
Valid prediction for GlimmerHMM_glimmerT_55649-T1
Valid prediction for snap_scaffold_25-snap.1371-T1
Valid prediction for GlimmerHMM_glimmerT_55636-T1
Valid prediction for GeneMark_model.97065_t
Valid prediction for GlimmerHMM_glimmerT_55652-T1
Valid prediction for GeneMark_model.97086_t
Valid prediction for snap_scaffold_25-snap.1407-T1
Valid prediction for GeneMark_model.97075_t
Valid prediction for GeneMark_model.97077_t
Valid prediction for GlimmerHMM_glimmerT_55637-T1
Valid prediction for GeneMark_model.97064_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 CodingQuarry_transcript_38679-T1
Valid prediction for snap_scaffold_25-snap.1402-T1
Valid prediction for Augustus_model.g37125.t1
Valid prediction for snap_scaffold_25-snap.1377-T1
Valid prediction for snap_scaffold_25-snap.1396-T1
Valid prediction for GeneMark_model.97068_t
Valid prediction for snap_scaffold_25-snap.1408-T1
Valid prediction for GeneMark_model.97085_t
Valid prediction for GeneMark_model.97063_t
Valid prediction for GeneMark_model.97055_t
Valid prediction for GlimmerHMM_glimmerT_55648-T1
Valid prediction for Augustus_model.g37130.t1
Valid prediction for GeneMark_model.97066_t
Valid prediction for GlimmerHMM_glimmerT_55647-T1
Valid prediction for GeneMark_model.97062_t
Valid prediction for snap_scaffold_25-snap.1398-T1
Valid prediction for GeneMark_model.97058_t
Valid prediction for Augustus_model.g37127.t1
Valid prediction for GlimmerHMM_glimmerT_55642-T1
Valid prediction for GeneMark_model.97051_t
Valid prediction for HiQ_model.g37123.t1
Valid prediction for snap_scaffold_25-snap.1385-T1
Valid prediction for pasa_asmbl_34339.p1
Valid prediction for snap_scaffold_25-snap.1394-T1
Valid prediction for snap_scaffold_25-snap.1395-T1
Valid prediction for GeneMark_model.97072_t
Valid prediction for GeneMark_model.97081_t
Valid prediction for snap_scaffold_25-snap.1383-T1
Valid prediction for Augustus_model.g37126.t1
Valid prediction for GlimmerHMM_glimmerT_55640-T1
Valid prediction for snap_scaffold_25-snap.1386-T1
Valid prediction for snap_scaffold_25-snap.1400-T1
Valid prediction for GeneMark_model.97074_t
Valid prediction for snap_scaffold_25-snap.1373-T1
Valid prediction for Augustus_model.g37129.t1
Valid prediction for GeneMark_model.97071_t
Valid prediction for snap_scaffold_25-snap.1390-T1
Valid prediction for snap_scaffold_25-snap.1388-T1
Valid prediction for GlimmerHMM_glimmerT_55653-T1
Valid prediction for snap_scaffold_25-snap.1374-T1
Valid prediction for GlimmerHMM_glimmerT_55633-T1
Valid prediction for GeneMark_model.97080_t
Valid prediction for snap_scaffold_25-snap.1404-T1
Valid prediction for GeneMark_model.97078_t
Valid prediction for snap_scaffold_25-snap.1399-T1
Valid prediction for snap_scaffold_25-snap.1405-T1
Valid prediction for snap_scaffold_25-snap.1393-T1
Valid prediction for GeneMark_model.97056_t
Valid prediction for GeneMark_model.97083_t
Valid prediction for GlimmerHMM_glimmerT_55643-T1
Valid prediction for Augustus_model.g37124.t1
Valid prediction for GeneMark_model.97060_t
Valid prediction for snap_scaffold_25-snap.1401-T1
Valid prediction for snap_scaffold_25-snap.1389-T1
Valid prediction for GlimmerHMM_glimmerT_55650-T1
Valid prediction for GlimmerHMM_glimmerT_55645-T1
Valid prediction for GlimmerHMM_glimmerT_55651-T1
Valid prediction for Augustus_model.g37131.t1
Valid prediction for Augustus_model.g37132.t1
Valid prediction for GlimmerHMM_glimmerT_55632-T1
Valid prediction for snap_scaffold_25-snap.1397-T1
Valid prediction for snap_scaffold_25-snap.1379-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 9328, rend_intergenic: 6381  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23791, rend_intergenic: 10559  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33029, rend_intergenic: 28774  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37496, rend_intergenic: 35363  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39700, rend_intergenic: 37743  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76404, rend_intergenic: 74826  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84453, rend_intergenic: 80627  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122799, rend_intergenic: 118520  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126894, rend_intergenic: 122805  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 137312
-exon list size: 554


building trellis

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-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 9328, rend_intergenic: 6381  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23791, rend_intergenic: 10559  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33029, rend_intergenic: 28774  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37496, rend_intergenic: 35363  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 39700, rend_intergenic: 37743  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 76404, rend_intergenic: 74826  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84453, rend_intergenic: 80627  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 122799, rend_intergenic: 118520  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126894, rend_intergenic: 122805  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 19 predictions persist after filtering for low support