-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_28/scaffold_28_1583781-1714816

-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_59593-T1
Valid prediction for HiQ_model.g39654.t1
Valid prediction for Augustus_model.g39660.t1
Valid prediction for GlimmerHMM_glimmerT_59570-T1
Valid prediction for snap_scaffold_28-snap.388-T1
Valid prediction for pasa_asmbl_38010.p1
Valid prediction for GlimmerHMM_glimmerT_59579-T1
Valid prediction for snap_scaffold_28-snap.375-T1
Valid prediction for GeneMark_model.104038_t
Valid prediction for Augustus_model.g39658.t1
Valid prediction for GeneMark_model.104029_t
Valid prediction for snap_scaffold_28-snap.387-T1
Valid prediction for snap_scaffold_28-snap.381-T1
Valid prediction for GeneMark_model.104032_t
Valid prediction for snap_scaffold_28-snap.378-T1
Valid prediction for GlimmerHMM_glimmerT_59581-T1
Valid prediction for GeneMark_model.104024_t
Valid prediction for Augustus_model.g39650.t1
Valid prediction for GeneMark_model.104020_t
Valid prediction for GeneMark_model.104034_t
Valid prediction for snap_scaffold_28-snap.369-T1
Valid prediction for snap_scaffold_28-snap.393-T1
Valid prediction for snap_scaffold_28-snap.389-T1
Valid prediction for Augustus_model.g39651.t1
Valid prediction for GlimmerHMM_glimmerT_59575-T1
Valid prediction for Augustus_model.g39653.t1
Valid prediction for GlimmerHMM_glimmerT_59580-T1
Valid prediction for GlimmerHMM_glimmerT_59587-T1
Valid prediction for snap_scaffold_28-snap.376-T1
Valid prediction for Augustus_model.g39652.t1
Valid prediction for GeneMark_model.104042_t
Valid prediction for GlimmerHMM_glimmerT_59591-T1
Valid prediction for GeneMark_model.104017_t
Valid prediction for GeneMark_model.104043_t
Valid prediction for CodingQuarry_transcript_43444-T1
Valid prediction for GlimmerHMM_glimmerT_59576-T1
Valid prediction for CodingQuarry_transcript_43447-T1
Valid prediction for snap_scaffold_28-snap.382-T1
Valid prediction for snap_scaffold_28-snap.392-T1
Valid prediction for GeneMark_model.104036_t
Valid prediction for CodingQuarry_transcript_43446-T1
Valid prediction for snap_scaffold_28-snap.377-T1
Valid prediction for pasa_asmbl_38009.p1
Valid prediction for HiQ_model.g39647.t1
Valid prediction for snap_scaffold_28-snap.372-T1
Valid prediction for Augustus_model.g39657.t1
Valid prediction for GlimmerHMM_glimmerT_59577-T1
Valid prediction for GeneMark_model.104023_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: -)Couldn't classify 27247, 27544
Couldn't classify 29042, 29114
Sorry, prediction pasa_asmbl_37331.p1 fails validation.
(GGT)	 TA	27247-27544	GT	TGG
(ATG)	 AG	28148-28322	GT	AGG
(CCT)	 AG	28526-28680	GT	AGG
(AGA)	 AG	28794-28956	GT	AGG
(CGG)	 AG	29042-29114	GG	CTG
add_exon() Sorry, pasa_asmbl_37331.p1 28148-28322-initial-1 is invalid.
-recovered pasa_asmbl_37331.p1, initial, 28148, 28322
-recovered pasa_asmbl_37331.p1, internal, 28148, 28322
-recovered pasa_asmbl_37331.p1, internal, 28526, 28680
-recovered pasa_asmbl_37331.p1, internal, 28794, 28956
Valid prediction for GlimmerHMM_glimmerT_59578-T1
Couldn't classify 56302, 56494
Sorry, prediction pasa_asmbl_37325.p1 fails validation.
(GAG)	 CG	56302-56494	GT	CGG
(TCC)	 AG	56644-56846	GT	AGG
(GTG)	 AG	57166-57303	GT	AGG
(GCA)	 AG	57563-57724	GT	AGG
(GTG)	 AG	57836-58204	GT	AGG
(ATT)	 AG	58316-58393	GT	AGG
(GTG)	 AG	58520-58783	GT	AGG
(TCT)	 AG	59185-59279	GT	AAG
(GGC)	 AG	59434-59650	GT	AGG
(GAC)	 AG	59749-59892	GT	AGG
(CTT)	 AG	59996-60310	GT	AGG
(GTG)	 AG	60421-60560	GT	CAG
(GTC)	 AG	60756-60888	GT	AGG
(GTG)	 AG	61044-61166	GT	AGG
(AGC)	 AG	61260-61424	GT	AGG
(CAA)	 AG	61784-61950	GT	AAG
(GCA)	 AG	62138-62336	TG	AAT
-recovered pasa_asmbl_37325.p1, terminal, 62138, 62336
-recovered pasa_asmbl_37325.p1, internal, 56644, 56846
-recovered pasa_asmbl_37325.p1, internal, 57166, 57303
-recovered pasa_asmbl_37325.p1, internal, 57563, 57724
-recovered pasa_asmbl_37325.p1, internal, 57836, 58204
-recovered pasa_asmbl_37325.p1, internal, 58316, 58393
-recovered pasa_asmbl_37325.p1, internal, 58520, 58783
-recovered pasa_asmbl_37325.p1, internal, 59185, 59279
-recovered pasa_asmbl_37325.p1, internal, 59434, 59650
-recovered pasa_asmbl_37325.p1, internal, 59749, 59892
-recovered pasa_asmbl_37325.p1, internal, 59996, 60310
-recovered pasa_asmbl_37325.p1, internal, 60421, 60560
-recovered pasa_asmbl_37325.p1, internal, 60756, 60888
-recovered pasa_asmbl_37325.p1, internal, 61044, 61166
-recovered pasa_asmbl_37325.p1, internal, 61260, 61424
-recovered pasa_asmbl_37325.p1, internal, 61784, 61950
Valid prediction for GeneMark_model.104027_t
Valid prediction for snap_scaffold_28-snap.385-T1
Valid prediction for snap_scaffold_28-snap.368-T1
Valid prediction for GlimmerHMM_glimmerT_59586-T1
Valid prediction for snap_scaffold_28-snap.396-T1
Valid prediction for pasa_asmbl_37317.p1
Valid prediction for GeneMark_model.104016_t
Couldn't classify 53718, 53832
Couldn't classify 55119, 55409
Sorry, prediction pasa_asmbl_37326.p1 fails validation.
(GAT)	 CA	53718-53832	GT	GTG
(CTG)	 AG	54827-54939	GT	GGG
(TCC)	 AG	55119-55409	AC	GGA
-recovered pasa_asmbl_37326.p1, internal, 54827, 54939
Valid prediction for GeneMark_model.104028_t
Valid prediction for GeneMark_model.104025_t
Valid prediction for GeneMark_model.104026_t
Valid prediction for GlimmerHMM_glimmerT_59584-T1
Valid prediction for snap_scaffold_28-snap.373-T1
Valid prediction for GeneMark_model.104018_t
Valid prediction for GeneMark_model.104019_t
Valid prediction for GlimmerHMM_glimmerT_59582-T1
Couldn't classify 10512, 10539
Sorry, prediction pasa_asmbl_37333.p1 fails validation.
(TTC)	 CC	10512-10539	GT	CGG
(GCT)	 AG	11506-11764	GT	AGG
(AGA)	 AG	11917-13225	CT	AGC
-recovered pasa_asmbl_37333.p1, terminal, 11917, 13225
-recovered pasa_asmbl_37333.p1, internal, 11506, 11764
Valid prediction for snap_scaffold_28-snap.386-T1
Valid prediction for Augustus_model.g39648.t1
Valid prediction for GeneMark_model.104035_t
Valid prediction for GlimmerHMM_glimmerT_59572-T1
Couldn't classify 24457, 24522
Couldn't classify 27091, 27143
Sorry, prediction pasa_asmbl_37864.p1 fails validation.
(GTG)	 GG	24457-24522	GT	AGG
(GTT)	 AG	25042-25162	GT	AGG
(GGT)	 AG	25858-25957	GT	AGG
(CAC)	 AG	26816-26925	GT	GAG
(ATA)	 AG	27091-27143	AC	GAA
-recovered pasa_asmbl_37864.p1, internal, 25042, 25162
-recovered pasa_asmbl_37864.p1, internal, 25858, 25957
-recovered pasa_asmbl_37864.p1, internal, 26816, 26925
Valid prediction for GeneMark_model.104041_t
Valid prediction for GeneMark_model.104039_t
Valid prediction for CodingQuarry_transcript_43448-T1
Valid prediction for GeneMark_model.104021_t
Valid prediction for Augustus_model.g39659.t1
Valid prediction for Augustus_model.g39656.t1
Valid prediction for GlimmerHMM_glimmerT_59585-T1
Valid prediction for snap_scaffold_28-snap.391-T1
Valid prediction for GlimmerHMM_glimmerT_59569-T1
Valid prediction for GeneMark_model.104030_t
Valid prediction for GeneMark_model.104022_t
Couldn't classify 30025, 30069
Sorry, prediction pasa_asmbl_37329.p2 fails validation.
(GAC)	 TG	30025-30069	GT	AGG
(AAC)	 AG	30258-30345	GT	TGG
(ATT)	 AG	30473-30580	GT	AGG
(TTG)	 AG	30873-30945	GT	ATG
(GAA)	 AG	31200-31242	AA	GAA
-recovered pasa_asmbl_37329.p2, terminal, 31200, 31242
-recovered pasa_asmbl_37329.p2, internal, 30258, 30345
-recovered pasa_asmbl_37329.p2, internal, 30473, 30580
-recovered pasa_asmbl_37329.p2, internal, 30873, 30945
Couldn't classify 65698, 65962
Couldn't classify 68424, 68483
Sorry, prediction pasa_asmbl_37321.p1 fails validation.
(GAC)	 CA	65698-65962	GT	CGG
(AGA)	 AG	66516-66710	GT	GGG
(CAG)	 AG	66765-66961	GT	AGG
(GAG)	 AG	67419-67607	GT	CGG
(GGA)	 AG	67749-67871	GT	ATG
(GTG)	 AG	67969-68035	GT	AGG
(ACC)	 AG	68127-68308	GC	AGG
(GCT)	 AG	68424-68483	AA	AAA
-recovered pasa_asmbl_37321.p1, internal, 66516, 66710
-recovered pasa_asmbl_37321.p1, internal, 66765, 66961
-recovered pasa_asmbl_37321.p1, internal, 67419, 67607
-recovered pasa_asmbl_37321.p1, internal, 67749, 67871
-recovered pasa_asmbl_37321.p1, internal, 67969, 68035
-recovered pasa_asmbl_37321.p1, internal, 68127, 68308
Valid prediction for HiQ_model.g39655.t1
Valid prediction for GeneMark_model.104037_t
Valid prediction for CodingQuarry_transcript_43451-T1
Valid prediction for snap_scaffold_28-snap.383-T1
Valid prediction for snap_scaffold_28-snap.370-T1
Valid prediction for GlimmerHMM_glimmerT_59568-T1
Valid prediction for snap_scaffold_28-snap.395-T1
Valid prediction for snap_scaffold_28-snap.380-T1
Valid prediction for snap_scaffold_28-snap.384-T1
Valid prediction for GlimmerHMM_glimmerT_59574-T1
Valid prediction for GlimmerHMM_glimmerT_59589-T1
Valid prediction for snap_scaffold_28-snap.390-T1
Valid prediction for GeneMark_model.104033_t
Valid prediction for snap_scaffold_28-snap.379-T1
Valid prediction for GlimmerHMM_glimmerT_59573-T1
Valid prediction for GeneMark_model.104031_t
Valid prediction for GlimmerHMM_glimmerT_59583-T1
Valid prediction for snap_scaffold_28-snap.374-T1
Valid prediction for GlimmerHMM_glimmerT_59588-T1
Valid prediction for HiQ_model.g39646.t1
Valid prediction for Augustus_model.g39649.t1
Valid prediction for GlimmerHMM_glimmerT_59571-T1
Valid prediction for CodingQuarry_transcript_43449-T1
Valid prediction for snap_scaffold_28-snap.371-T1
Valid prediction for GlimmerHMM_glimmerT_59590-T1
Valid prediction for GlimmerHMM_glimmerT_59592-T1
Valid prediction for snap_scaffold_28-snap.394-T1
Valid prediction for CodingQuarry_transcript_43450-T1
Couldn't classify 68665, 68857
Sorry, prediction pasa_asmbl_37320.p1 fails validation.
(AGA)	 AC	68665-68857	GT	AGG
(GCA)	 AG	68976-69879	GT	GGG
(GGA)	 AG	70029-70160	GT	AGG
(CTG)	 AG	70445-70694	AG	AAA
-recovered pasa_asmbl_37320.p1, terminal, 70445, 70694
-recovered pasa_asmbl_37320.p1, internal, 68976, 69879
-recovered pasa_asmbl_37320.p1, internal, 70029, 70160

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 26502, rend_intergenic: 25228  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37986, rend_intergenic: 35962  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93769, rend_intergenic: 90178  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 131036
-exon list size: 466


building trellis

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-found 20 predictions from path traversal
Error with prediction: snap lend_intergenic: 26502, rend_intergenic: 25228  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37986, rend_intergenic: 35962  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 93769, rend_intergenic: 90178  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 16 predictions persist after filtering for low support