-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_19/scaffold_19_2726129-2946527

-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_19-snap.618-T1
Valid prediction for Augustus_model.g29060.t1
Valid prediction for pasa_asmbl_21292.p1
Valid prediction for HiQ_model.g29065.t1
Valid prediction for GlimmerHMM_glimmerT_43790-T1
Couldn't classify 79287, 79341
Couldn't classify 80702, 80756
Sorry, prediction pasa_asmbl_21284.p1 fails validation.
(TTG)	 AG	79287-79341	GT	AGG
(TCA)	 AG	79491-79573	GT	AGG
(GTG)	 AG	79903-79976	GT	AGG
(AGG)	 AG	80273-80347	GT	TTG
(CAC)	 AG	80702-80756	GT	CGG
-recovered pasa_asmbl_21284.p1, internal, 79287, 79341
-recovered pasa_asmbl_21284.p1, internal, 79491, 79573
-recovered pasa_asmbl_21284.p1, internal, 79903, 79976
-recovered pasa_asmbl_21284.p1, internal, 80273, 80347
-recovered pasa_asmbl_21284.p1, internal, 80702, 80756
Valid prediction for GlimmerHMM_glimmerT_43802-T1
Valid prediction for snap_scaffold_19-snap.607-T1
Valid prediction for GlimmerHMM_glimmerT_43797-T1
Valid prediction for Augustus_model.g29063.t1
Valid prediction for GlimmerHMM_glimmerT_43775-T1
Valid prediction for Augustus_model.g29057.t1
Valid prediction for snap_scaffold_19-snap.596-T1
Couldn't classify 139956, 139995
Sorry, prediction pasa_asmbl_21287.p1 fails validation.
(GGT)	 AA	139956-139995	GT	TGG
(GGC)	 AG	140100-140357	GT	GGG
(AGA)	 AG	141100-141327	GT	TGG
(AAC)	 AG	141907-142134	GT	AGG
(TCC)	 AG	143314-143544	GT	GTG
(GTA)	 AG	143722-143897	GT	ACG
(GGA)	 AG	144103-144232	GT	AGG
(GAT)	 AG	144370-144541	GT	GGG
(GAC)	 AG	146893-147050	GT	AGG
(GTA)	 AG	147304-147427	GT	AGG
(GGA)	 AG	147618-147729	GG	GAG
-recovered pasa_asmbl_21287.p1, terminal, 147618, 147729
-recovered pasa_asmbl_21287.p1, internal, 140100, 140357
-recovered pasa_asmbl_21287.p1, internal, 141100, 141327
-recovered pasa_asmbl_21287.p1, internal, 141907, 142134
-recovered pasa_asmbl_21287.p1, internal, 143314, 143544
-recovered pasa_asmbl_21287.p1, internal, 143722, 143897
-recovered pasa_asmbl_21287.p1, internal, 144103, 144232
-recovered pasa_asmbl_21287.p1, internal, 144370, 144541
-recovered pasa_asmbl_21287.p1, internal, 146893, 147050
-recovered pasa_asmbl_21287.p1, internal, 147304, 147427
Valid prediction for snap_scaffold_19-snap.626-T1
Valid prediction for snap_scaffold_19-snap.592-T1
Valid prediction for snap_scaffold_19-snap.608-T1
Valid prediction for GlimmerHMM_glimmerT_43793-T1
Couldn't classify 54168, 54415
Sorry, prediction pasa_asmbl_21277.p1 fails validation.
(GAT)	 AA	54168-54415	GT	AAG
(GTC)	 AG	54621-54792	GA	AGG
-recovered pasa_asmbl_21277.p1, terminal, 54621, 54792
Valid prediction for Augustus_model.g29055.t1
Valid prediction for snap_scaffold_19-snap.624-T1
Valid prediction for GlimmerHMM_glimmerT_43798-T1
Valid prediction for GlimmerHMM_glimmerT_43786-T1
Couldn't classify 164257, 164343
Couldn't classify 165031, 165338
Sorry, prediction pasa_asmbl_21290.p1 fails validation.
(GAT)	 AG	164257-164343	GT	AGG
(GTG)	 AG	164641-164821	GT	AGG
(GTG)	 AG	165031-165338	GG	AGG
-recovered pasa_asmbl_21290.p1, internal, 164257, 164343
-recovered pasa_asmbl_21290.p1, internal, 164641, 164821
Valid prediction for Augustus_model.g29069.t1
Valid prediction for GlimmerHMM_glimmerT_43792-T1
Valid prediction for CodingQuarry_transcript_25609-T1
Valid prediction for snap_scaffold_19-snap.599-T1
Valid prediction for snap_scaffold_19-snap.615-T1
Valid prediction for Augustus_model.g29070.t1
Valid prediction for pasa_asmbl_21295.p1
Valid prediction for GlimmerHMM_glimmerT_43791-T1
Valid prediction for GlimmerHMM_glimmerT_43782-T1
Couldn't classify 212284, 212506
Sorry, prediction pasa_asmbl_21294.p1 fails validation.
(CGT)	 AG	212284-212506	GT	TGG
(ATG)	 AG	212768-212916	GT	TGG
(GCT)	 AG	213167-214141	AG	AGA
-recovered pasa_asmbl_21294.p1, initial, 212768, 212916
-recovered pasa_asmbl_21294.p1, terminal, 213167, 214141
-recovered pasa_asmbl_21294.p1, internal, 212284, 212506
-recovered pasa_asmbl_21294.p1, internal, 212768, 212916
Valid prediction for GlimmerHMM_glimmerT_43779-T1
Valid prediction for CodingQuarry_transcript_25610-T1
Valid prediction for snap_scaffold_19-snap.613-T1
Valid prediction for pasa_asmbl_21286.p1
Valid prediction for CodingQuarry_transcript_25612-T1
Valid prediction for snap_scaffold_19-snap.602-T1
Couldn't classify 165402, 165609
Couldn't classify 165727, 165815
Sorry, prediction pasa_asmbl_21958.p1 fails validation.
(GAG)	 CG	165402-165609	GT	AGG
(GTT)	 AG	165727-165815	CA	CCC
Valid prediction for snap_scaffold_19-snap.620-T1
Valid prediction for GlimmerHMM_glimmerT_43776-T1
Valid prediction for snap_scaffold_19-snap.595-T1
Valid prediction for snap_scaffold_19-snap.604-T1
Valid prediction for CodingQuarry_transcript_25607-T1
Valid prediction for CodingQuarry_transcript_25614-T1
Valid prediction for snap_scaffold_19-snap.621-T1
Valid prediction for GlimmerHMM_glimmerT_43778-T1
Valid prediction for snap_scaffold_19-snap.610-T1
Valid prediction for GlimmerHMM_glimmerT_43795-T1
Valid prediction for Augustus_model.g29061.t1
Valid prediction for Augustus_model.g29059.t1
Valid prediction for GlimmerHMM_glimmerT_43787-T1
Valid prediction for GlimmerHMM_glimmerT_43781-T1
Valid prediction for snap_scaffold_19-snap.600-T1
Valid prediction for snap_scaffold_19-snap.631-T1
Couldn't classify 82236, 82256
Couldn't classify 83371, 83408
Sorry, prediction pasa_asmbl_21285.p1 fails validation.
(CTC)	 AG	82236-82256	GT	TGG
(ACG)	 AG	82523-82689	GT	AGG
(GGA)	 AG	82821-82881	GT	AGG
(GGG)	 AG	83023-83149	GT	AGG
(ACC)	 AG	83371-83408	AA	GGA
add_exon() Sorry, pasa_asmbl_21285.p1 83023-83149-terminal-3 is invalid.
-recovered pasa_asmbl_21285.p1, terminal, 83023, 83149
-recovered pasa_asmbl_21285.p1, internal, 82236, 82256
-recovered pasa_asmbl_21285.p1, internal, 82523, 82689
-recovered pasa_asmbl_21285.p1, internal, 82821, 82881
-recovered pasa_asmbl_21285.p1, internal, 83023, 83149
Valid prediction for snap_scaffold_19-snap.630-T1
Valid prediction for snap_scaffold_19-snap.598-T1
Valid prediction for GlimmerHMM_glimmerT_43801-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_19-snap.593-T1
Valid prediction for GlimmerHMM_glimmerT_43785-T1
Valid prediction for snap_scaffold_19-snap.619-T1
Valid prediction for Augustus_model.g29054.t1
Valid prediction for HiQ_model.g29062.t1
Valid prediction for pasa_asmbl_22072.p1
Valid prediction for snap_scaffold_19-snap.614-T1
Valid prediction for Augustus_model.g29066.t1
Valid prediction for snap_scaffold_19-snap.628-T1
Valid prediction for Augustus_model.g29068.t1
Couldn't classify 26204, 26223
Couldn't classify 26269, 26365
Sorry, prediction CodingQuarry_transcript_25613-T1 fails validation.
(ATG)	 GG	24135-24257	GT	AGG
(GCA)	 AG	24358-24443	GT	ATG
(GGT)	 AG	24733-24847	GT	GGG
(GCG)	 AG	25267-25382	GT	GGG
(GTG)	 AG	25460-25545	GT	GGG
(GAT)	 AG	25771-25917	GT	CGG
(GTA)	 AG	26204-26223	TT	TGT
(CCC)	 TT	26269-26365	GT	TGG
(GAG)	 AG	26532-26660	GT	TGG
(GTT)	 AG	26792-26865	AC	AGA
-recovered CodingQuarry_transcript_25613-T1, initial, 24135, 24257
-recovered CodingQuarry_transcript_25613-T1, terminal, 26792, 26865
-recovered CodingQuarry_transcript_25613-T1, internal, 24358, 24443
-recovered CodingQuarry_transcript_25613-T1, internal, 24733, 24847
-recovered CodingQuarry_transcript_25613-T1, internal, 25267, 25382
-recovered CodingQuarry_transcript_25613-T1, internal, 25460, 25545
-recovered CodingQuarry_transcript_25613-T1, internal, 25771, 25917
-recovered CodingQuarry_transcript_25613-T1, internal, 26532, 26660
Valid prediction for CodingQuarry_transcript_25611-T1
Valid prediction for snap_scaffold_19-snap.603-T1
Valid prediction for snap_scaffold_19-snap.629-T1
Valid prediction for snap_scaffold_19-snap.601-T1
Valid prediction for snap_scaffold_19-snap.611-T1
Valid prediction for snap_scaffold_19-snap.617-T1
Valid prediction for snap_scaffold_19-snap.622-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for snap_scaffold_19-snap.625-T1
Valid prediction for GlimmerHMM_glimmerT_43780-T1
Valid prediction for GlimmerHMM_glimmerT_43800-T1
Valid prediction for GlimmerHMM_glimmerT_43799-T1
Valid prediction for snap_scaffold_19-snap.605-T1
Valid prediction for snap_scaffold_19-snap.597-T1
Valid prediction for GlimmerHMM_glimmerT_43783-T1
Valid prediction for snap_scaffold_19-snap.609-T1
Valid prediction for GlimmerHMM_glimmerT_43789-T1
Valid prediction for snap_scaffold_19-snap.606-T1
Valid prediction for GlimmerHMM_glimmerT_43796-T1
Valid prediction for GlimmerHMM_glimmerT_43777-T1
Valid prediction for Augustus_model.g29067.t1
Valid prediction for Augustus_model.g29056.t1
Valid prediction for GlimmerHMM_glimmerT_43794-T1
Valid prediction for snap_scaffold_19-snap.616-T1
Valid prediction for GlimmerHMM_glimmerT_43788-T1
Valid prediction for snap_scaffold_19-snap.594-T1
Valid prediction for snap_scaffold_19-snap.623-T1
Valid prediction for snap_scaffold_19-snap.612-T1
Valid prediction for Augustus_model.g29058.t1
Valid prediction for snap_scaffold_19-snap.632-T1
Valid prediction for snap_scaffold_19-snap.627-T1
Valid prediction for GlimmerHMM_glimmerT_43784-T1
Valid prediction for Augustus_model.g29064.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 27205, rend_intergenic: 21334  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38244, rend_intergenic: 33598  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38908, rend_intergenic: 38273  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46257, rend_intergenic: 39670  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55401, rend_intergenic: 51519  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61701, rend_intergenic: 59084  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67243, rend_intergenic: 61864  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77081, rend_intergenic: 74001  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89872, rend_intergenic: 84880  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100211, rend_intergenic: 98497  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145956, rend_intergenic: 117124  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153542, rend_intergenic: 149258  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168865, rend_intergenic: 156353  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180114, rend_intergenic: 177877  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188501, rend_intergenic: 180817  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 220344, rend_intergenic: 215931  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 220399
-exon list size: 462


building trellis

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-found 28 predictions from path traversal
Error with prediction: snap lend_intergenic: 27205, rend_intergenic: 21334  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38244, rend_intergenic: 33598  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 38908, rend_intergenic: 38273  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46257, rend_intergenic: 39670  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 55401, rend_intergenic: 51519  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61701, rend_intergenic: 59084  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67243, rend_intergenic: 61864  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77081, rend_intergenic: 74001  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89872, rend_intergenic: 84880  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100211, rend_intergenic: 98497  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145956, rend_intergenic: 117124  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 153542, rend_intergenic: 149258  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168865, rend_intergenic: 156353  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 180114, rend_intergenic: 177877  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188501, rend_intergenic: 180817  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 220344, rend_intergenic: 215931  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 24 predictions persist after filtering for low support