-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_6/scaffold_6_16405242-16531197

-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_6-snap.3486-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_16669-T1
Valid prediction for snap_scaffold_6-snap.3493-T1
Valid prediction for GeneMark_model.27886_t
Valid prediction for GeneMark_model.27899_t
Valid prediction for snap_scaffold_6-snap.3481-T1
Valid prediction for snap_scaffold_6-snap.3477-T1
Valid prediction for GeneMark_model.27893_t
Valid prediction for snap_scaffold_6-snap.3473-T1
Valid prediction for snap_scaffold_6-snap.3492-T1
Valid prediction for snap_scaffold_6-snap.3479-T1
Valid prediction for GeneMark_model.27880_t
Valid prediction for GlimmerHMM_glimmerT_16672-T1
Valid prediction for GeneMark_model.27892_t
Couldn't classify 78215, 78913
Sorry, prediction pasa_asmbl_49072.p1 fails validation.
(AGA)	 CA	78215-78913	CA	AAC
Valid prediction for GeneMark_model.27902_t
Valid prediction for GeneMark_model.27864_t
Valid prediction for snap_scaffold_6-snap.3468-T1
Valid prediction for snap_scaffold_6-snap.3478-T1
Valid prediction for GlimmerHMM_glimmerT_16678-T1
Valid prediction for GeneMark_model.27903_t
Valid prediction for Augustus_model.g11222.t1
Valid prediction for GeneMark_model.27890_t
Valid prediction for Augustus_model.g11216.t1
Couldn't classify 48621, 48827
Sorry, prediction CodingQuarry_transcript_55230-T1 fails validation.
(ATG)	 AC	46180-46243	GT	GCG
(AGA)	 AG	46784-46888	GT	AGG
(GTG)	 AG	47082-47304	GT	TGG
(GTG)	 AG	47788-47895	GT	AGG
(AAT)	 GA	48621-48827	GT	GAG
(GGT)	 AG	49128-49203	GT	CGG
(GGC)	 AG	49895-50085	GT	ACG
(TCA)	 AG	50307-50397	GT	AGG
(CAT)	 AG	51065-51070	GT	AAG
-recovered CodingQuarry_transcript_55230-T1, initial, 46180, 46243
-recovered CodingQuarry_transcript_55230-T1, terminal, 51065, 51070
-recovered CodingQuarry_transcript_55230-T1, internal, 46784, 46888
-recovered CodingQuarry_transcript_55230-T1, internal, 47082, 47304
-recovered CodingQuarry_transcript_55230-T1, internal, 47788, 47895
-recovered CodingQuarry_transcript_55230-T1, internal, 49128, 49203
-recovered CodingQuarry_transcript_55230-T1, internal, 49895, 50085
-recovered CodingQuarry_transcript_55230-T1, internal, 50307, 50397
-recovered CodingQuarry_transcript_55230-T1, internal, 51065, 51070
Valid prediction for snap_scaffold_6-snap.3476-T1
Valid prediction for GlimmerHMM_glimmerT_16664-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GeneMark_model.27894_t
Valid prediction for GeneMark_model.27885_t
Valid prediction for GeneMark_model.27866_t
Valid prediction for GeneMark_model.27868_t
Valid prediction for GlimmerHMM_glimmerT_16670-T1
Couldn't classify 61664, 61770
Sorry, prediction pasa_asmbl_47636.p1 fails validation.
(ATC)	 GT	61664-61770	GT	AGG
(ACT)	 AG	61953-62083	GT	AGG
(GGT)	 AG	62247-62347	GT	CTG
(ATA)	 AG	63864-63914	GA	GAG
-recovered pasa_asmbl_47636.p1, terminal, 63864, 63914
-recovered pasa_asmbl_47636.p1, internal, 61953, 62083
-recovered pasa_asmbl_47636.p1, internal, 62247, 62347
Valid prediction for GlimmerHMM_glimmerT_16671-T1
Valid prediction for GeneMark_model.27896_t
Valid prediction for GeneMark_model.27874_t
Valid prediction for Augustus_model.g11220.t1
Valid prediction for snap_scaffold_6-snap.3482-T1
Valid prediction for GlimmerHMM_glimmerT_16660-T1
Valid prediction for snap_scaffold_6-snap.3465-T1
Valid prediction for Augustus_model.g11211.t1
Valid prediction for Augustus_model.g11218.t1
Valid prediction for Augustus_model.g11217.t1
Valid prediction for GlimmerHMM_glimmerT_16667-T1
Valid prediction for Augustus_model.g11215.t1
Couldn't classify 71165, 71804
Sorry, prediction pasa_asmbl_47641.p1 fails validation.
(GCA)	 GG	71165-71804	GT	AGG
(GCG)	 AG	72240-72523	AA	AGA
-recovered pasa_asmbl_47641.p1, terminal, 72240, 72523
Valid prediction for Augustus_model.g11213.t1
Valid prediction for GlimmerHMM_glimmerT_16659-T1
Valid prediction for GeneMark_model.27898_t
Valid prediction for GeneMark_model.27882_t
Valid prediction for snap_scaffold_6-snap.3470-T1
Valid prediction for GeneMark_model.27878_t
Valid prediction for Augustus_model.g11209.t1
Valid prediction for GeneMark_model.27888_t
Valid prediction for GeneMark_model.27872_t
Valid prediction for GlimmerHMM_glimmerT_16662-T1
Valid prediction for snap_scaffold_6-snap.3488-T1
Valid prediction for GlimmerHMM_glimmerT_16676-T1
Valid prediction for GeneMark_model.27870_t
Valid prediction for snap_scaffold_6-snap.3484-T1
Valid prediction for GeneMark_model.27875_t
Valid prediction for Augustus_model.g11208.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 GeneMark_model.27904_t
Valid prediction for snap_scaffold_6-snap.3471-T1
Valid prediction for GeneMark_model.27905_t
Valid prediction for Augustus_model.g11221.t1
Valid prediction for GlimmerHMM_glimmerT_16665-T1
Valid prediction for GeneMark_model.27887_t
Valid prediction for Augustus_model.g11219.t1
Valid prediction for GeneMark_model.27873_t
Valid prediction for GlimmerHMM_glimmerT_16680-T1
Valid prediction for Augustus_model.g11224.t1
Valid prediction for GlimmerHMM_glimmerT_16674-T1
Valid prediction for snap_scaffold_6-snap.3469-T1
Valid prediction for GlimmerHMM_glimmerT_16666-T1
Valid prediction for GeneMark_model.27867_t
Valid prediction for GeneMark_model.27884_t
Valid prediction for GlimmerHMM_glimmerT_16668-T1
Valid prediction for HiQ_model.g11210.t1
Valid prediction for GeneMark_model.27876_t
Couldn't classify 43949, 44149
Sorry, prediction pasa_asmbl_49073.p1 fails validation.
(GAC)	 AG	43949-44149	GT	AGG
(GTG)	 AG	44251-44622	AT	GAA
-recovered pasa_asmbl_49073.p1, terminal, 44251, 44622
-recovered pasa_asmbl_49073.p1, internal, 43949, 44149
Valid prediction for snap_scaffold_6-snap.3475-T1
Valid prediction for GeneMark_model.27865_t
Valid prediction for snap_scaffold_6-snap.3483-T1
Valid prediction for snap_scaffold_6-snap.3466-T1
Valid prediction for snap_scaffold_6-snap.3472-T1
Valid prediction for GeneMark_model.27877_t
Valid prediction for snap_scaffold_6-snap.3467-T1
Valid prediction for GlimmerHMM_glimmerT_16679-T1
Valid prediction for GeneMark_model.27891_t
Valid prediction for GeneMark_model.27871_t
Valid prediction for GeneMark_model.27883_t
Couldn't classify 89438, 89514
Sorry, prediction pasa_asmbl_49065.p1 fails validation.
(GAC)	 TA	89438-89514	GT	GGG
(AGC)	 AG	91094-91165	GT	GTG
(GTT)	 AG	91440-91557	GT	CGG
(GAT)	 AG	92452-92514	GT	AGG
(TGG)	 AG	92854-93013	GT	AGG
(GGT)	 AG	93301-93431	GA	GAG
add_exon() Sorry, pasa_asmbl_49065.p1 92854-93013-terminal-3 is invalid.
-recovered pasa_asmbl_49065.p1, terminal, 92854, 93013
-recovered pasa_asmbl_49065.p1, terminal, 93301, 93431
-recovered pasa_asmbl_49065.p1, internal, 91094, 91165
-recovered pasa_asmbl_49065.p1, internal, 91440, 91557
-recovered pasa_asmbl_49065.p1, internal, 92452, 92514
-recovered pasa_asmbl_49065.p1, internal, 92854, 93013
Valid prediction for GlimmerHMM_glimmerT_16661-T1
Valid prediction for GeneMark_model.27901_t
Valid prediction for snap_scaffold_6-snap.3490-T1
Valid prediction for Augustus_model.g11214.t1
Valid prediction for snap_scaffold_6-snap.3487-T1
Valid prediction for GlimmerHMM_glimmerT_16673-T1
Valid prediction for GeneMark_model.27869_t
Valid prediction for CodingQuarry_transcript_55227-T1
Valid prediction for GeneMark_model.27900_t
Couldn't classify 4468, 4851
Couldn't classify 10389, 10454
Sorry, prediction pasa_asmbl_49076.p1 fails validation.
(GGA)	 CA	4468-4851	GT	AGG
(AGC)	 AG	5177-5421	GT	AGG
(AGC)	 AG	6011-6192	GT	CGG
(GCT)	 AG	7039-7215	GT	AGG
(GGA)	 AG	7652-7808	GT	ATG
(GTG)	 AG	8056-8266	GT	AGG
(GCC)	 AG	8801-9164	GT	AGG
(GTG)	 AG	9348-9814	GT	AGG
(GAG)	 AG	10389-10454	AC	CCA
-recovered pasa_asmbl_49076.p1, internal, 5177, 5421
-recovered pasa_asmbl_49076.p1, internal, 6011, 6192
-recovered pasa_asmbl_49076.p1, internal, 7039, 7215
-recovered pasa_asmbl_49076.p1, internal, 7652, 7808
-recovered pasa_asmbl_49076.p1, internal, 8056, 8266
-recovered pasa_asmbl_49076.p1, internal, 8801, 9164
-recovered pasa_asmbl_49076.p1, internal, 9348, 9814
Valid prediction for snap_scaffold_6-snap.3474-T1
Valid prediction for GeneMark_model.27889_t
Valid prediction for snap_scaffold_6-snap.3485-T1
Valid prediction for GeneMark_model.27895_t
Valid prediction for CodingQuarry_transcript_55228-T1
Valid prediction for snap_scaffold_6-snap.3480-T1
Valid prediction for CodingQuarry_transcript_55229-T1
Valid prediction for pasa_asmbl_49071.p1
Valid prediction for CodingQuarry_transcript_55231-T1
Valid prediction for GlimmerHMM_glimmerT_16677-T1
Valid prediction for snap_scaffold_6-snap.3491-T1
Valid prediction for snap_scaffold_6-snap.3464-T1
Valid prediction for HiQ_model.g11212.t1
Valid prediction for snap_scaffold_6-snap.3489-T1
Valid prediction for Augustus_model.g11223.t1
Valid prediction for GeneMark_model.27897_t
Valid prediction for GlimmerHMM_glimmerT_16663-T1
Valid prediction for GeneMark_model.27881_t
Valid prediction for GeneMark_model.27879_t
Valid prediction for GlimmerHMM_glimmerT_16675-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 13865, rend_intergenic: 7479  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21404, rend_intergenic: 17888  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24157, rend_intergenic: 22392  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84442, rend_intergenic: 78479  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86817, rend_intergenic: 85475  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90039, rend_intergenic: 87570  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108940, rend_intergenic: 103300  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121414, rend_intergenic: 112228  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 96179, rend_intergenic: 96176  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 125956
-exon list size: 492


building trellis

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-found 20 predictions from path traversal
Error with prediction: snap lend_intergenic: 13865, rend_intergenic: 7479  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 21404, rend_intergenic: 17888  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 24157, rend_intergenic: 22392  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 84442, rend_intergenic: 78479  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86817, rend_intergenic: 85475  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90039, rend_intergenic: 87570  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 108940, rend_intergenic: 103300  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121414, rend_intergenic: 112228  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 96179, rend_intergenic: 96176  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support