-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_21/scaffold_21_11102797-11323516

-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 Augustus_model.g32471.t1
Couldn't classify 213847, 214005
Sorry, prediction pasa_asmbl_28958.p1 fails validation.
(GCA)	 CA	213847-214005	GT	GGG
(GTG)	 AG	214134-214264	GT	AGG
(TAT)	 AG	214348-214438	GT	AGG
(GTG)	 AG	215309-215393	GT	AGG
(GTG)	 AG	215506-215582	GT	AGG
(GTG)	 AG	215776-215884	GT	ATG
(CTA)	 AG	216079-216186	GT	TGG
(AGG)	 AG	216668-216756	GT	TGG
(GTT)	 AG	217144-217284	GT	TAG
(GCG)	 AG	217444-217586	GT	TGG
(GAG)	 AG	217980-218104	GT	AGG
(GAA)	 AG	218243-218433	GT	AGG
(ATC)	 AG	218639-218710	GC	GAG
-recovered pasa_asmbl_28958.p1, terminal, 218639, 218710
-recovered pasa_asmbl_28958.p1, internal, 214134, 214264
-recovered pasa_asmbl_28958.p1, internal, 214348, 214438
-recovered pasa_asmbl_28958.p1, internal, 215309, 215393
-recovered pasa_asmbl_28958.p1, internal, 215506, 215582
-recovered pasa_asmbl_28958.p1, internal, 215776, 215884
-recovered pasa_asmbl_28958.p1, internal, 216079, 216186
-recovered pasa_asmbl_28958.p1, internal, 216668, 216756
-recovered pasa_asmbl_28958.p1, internal, 217144, 217284
-recovered pasa_asmbl_28958.p1, internal, 217444, 217586
-recovered pasa_asmbl_28958.p1, internal, 217980, 218104
-recovered pasa_asmbl_28958.p1, internal, 218243, 218433
-recovered pasa_asmbl_28958.p1, internal, 218639, 218710
Valid prediction for GlimmerHMM_glimmerT_48597-T1
Valid prediction for GlimmerHMM_glimmerT_48602-T1
Valid prediction for snap_scaffold_21-snap.2391-T1
Valid prediction for GlimmerHMM_glimmerT_48617-T1
Valid prediction for snap_scaffold_21-snap.2421-T1
Valid prediction for Augustus_model.g32469.t1
Valid prediction for snap_scaffold_21-snap.2398-T1
Valid prediction for CodingQuarry_transcript_32748-T1
Valid prediction for pasa_asmbl_28915.p1
Valid prediction for snap_scaffold_21-snap.2389-T1
Valid prediction for snap_scaffold_21-snap.2411-T1
Valid prediction for GlimmerHMM_glimmerT_48605-T1
Valid prediction for pasa_asmbl_28920.p1
Valid prediction for pasa_asmbl_28916.p1
Valid prediction for snap_scaffold_21-snap.2400-T1
Valid prediction for pasa_asmbl_28921.p1
Valid prediction for GlimmerHMM_glimmerT_48595-T1
Valid prediction for GlimmerHMM_glimmerT_48593-T1
Valid prediction for snap_scaffold_21-snap.2406-T1
Valid prediction for GlimmerHMM_glimmerT_48591-T1
Valid prediction for GlimmerHMM_glimmerT_48606-T1
Valid prediction for snap_scaffold_21-snap.2395-T1
Valid prediction for snap_scaffold_21-snap.2417-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_48615-T1
Valid prediction for snap_scaffold_21-snap.2403-T1
Valid prediction for snap_scaffold_21-snap.2393-T1
Valid prediction for GlimmerHMM_glimmerT_48592-T1
Valid prediction for snap_scaffold_21-snap.2396-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for snap_scaffold_21-snap.2408-T1
Valid prediction for snap_scaffold_21-snap.2420-T1
Valid prediction for snap_scaffold_21-snap.2422-T1
Valid prediction for HiQ_model.g32476.t1
Valid prediction for CodingQuarry_transcript_32747-T1
Valid prediction for GlimmerHMM_glimmerT_48603-T1
Valid prediction for snap_scaffold_21-snap.2407-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for snap_scaffold_21-snap.2401-T1
Valid prediction for snap_scaffold_21-snap.2392-T1
Valid prediction for GlimmerHMM_glimmerT_48614-T1
Valid prediction for Augustus_model.g32473.t1
Valid prediction for HiQ_model.g32485.t1
Valid prediction for snap_scaffold_21-snap.2423-T1
Valid prediction for snap_scaffold_21-snap.2424-T1
Valid prediction for GlimmerHMM_glimmerT_48590-T1
Valid prediction for GlimmerHMM_glimmerT_48604-T1
Valid prediction for CodingQuarry_transcript_32739-T1
Valid prediction for snap_scaffold_21-snap.2404-T1
Valid prediction for Augustus_model.g32486.t1
Valid prediction for snap_scaffold_21-snap.2405-T1
Valid prediction for CodingQuarry_transcript_32746-T1
Valid prediction for HiQ_model.g32475.t1
Valid prediction for GlimmerHMM_glimmerT_48616-T1
Valid prediction for Augustus_model.g32474.t1
Valid prediction for Augustus_model.g32477.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: -)Couldn't classify 77931, 78104
Couldn't classify 79674, 79763
Sorry, prediction pasa_asmbl_28102.p1 fails validation.
(AGG)	 TC	77931-78104	GC	AGG
(GTG)	 AG	78208-78375	GT	AGG
(GTC)	 AG	79085-79246	GT	TGG
(CTG)	 AG	79674-79763	GA	GCG
-recovered pasa_asmbl_28102.p1, internal, 78208, 78375
-recovered pasa_asmbl_28102.p1, internal, 79085, 79246
Valid prediction for Augustus_model.g32470.t1
Couldn't classify 99392, 99422
Sorry, prediction pasa_asmbl_28095.p2 fails validation.
(TCT)	 GT	99392-99422	GT	GGG
(AGT)	 AG	99685-99799	GT	TGG
(TCC)	 AG	100045-100231	CC	GAC
-recovered pasa_asmbl_28095.p2, terminal, 100045, 100231
-recovered pasa_asmbl_28095.p2, internal, 99685, 99799
Valid prediction for snap_scaffold_21-snap.2409-T1
Valid prediction for snap_scaffold_21-snap.2388-T1
Valid prediction for GlimmerHMM_glimmerT_48607-T1
Couldn't classify 81503, 81619
Couldn't classify 82438, 82518
Sorry, prediction pasa_asmbl_28101.p2 fails validation.
(GTG)	 GC	81503-81619	GT	AGG
(AAA)	 AG	81721-81819	GT	TTG
(CTT)	 AG	81911-81979	GT	AGG
(AGG)	 AG	82438-82518	CA	AGC
-recovered pasa_asmbl_28101.p2, internal, 81721, 81819
-recovered pasa_asmbl_28101.p2, internal, 81911, 81979
Valid prediction for snap_scaffold_21-snap.2419-T1
Valid prediction for snap_scaffold_21-snap.2416-T1
Valid prediction for snap_scaffold_21-snap.2390-T1
Valid prediction for CodingQuarry_transcript_32742-T1
Valid prediction for GlimmerHMM_glimmerT_48610-T1
Valid prediction for GlimmerHMM_glimmerT_48612-T1
Valid prediction for snap_scaffold_21-snap.2418-T1
Valid prediction for Augustus_model.g32468.t1
Valid prediction for GlimmerHMM_glimmerT_48599-T1
Valid prediction for CodingQuarry_transcript_32743-T1
Valid prediction for Augustus_model.g32480.t1
Valid prediction for HiQ_model.g32482.t1
Valid prediction for pasa_asmbl_28113.p1
Valid prediction for snap_scaffold_21-snap.2402-T1
Valid prediction for snap_scaffold_21-snap.2425-T1
Valid prediction for snap_scaffold_21-snap.2394-T1
Valid prediction for GlimmerHMM_glimmerT_48598-T1
Couldn't classify 58798, 58831
Couldn't classify 60255, 60274
Sorry, prediction pasa_asmbl_28111.p1 fails validation.
(CCA)	 TC	58798-58831	GT	CGG
(TTT)	 AG	58918-59060	GT	AGG
(GCC)	 AG	59170-59362	GT	AGG
(AAA)	 AG	59454-59562	GT	AGG
(ATC)	 AG	59970-60070	GT	AGG
(GAG)	 AG	60255-60274	AC	GGA
-recovered pasa_asmbl_28111.p1, internal, 58918, 59060
-recovered pasa_asmbl_28111.p1, internal, 59170, 59362
-recovered pasa_asmbl_28111.p1, internal, 59454, 59562
-recovered pasa_asmbl_28111.p1, internal, 59970, 60070
Valid prediction for HiQ_model.g32484.t1
Valid prediction for snap_scaffold_21-snap.2399-T1
Valid prediction for Augustus_model.g32483.t1
Valid prediction for CodingQuarry_transcript_32745-T1
Valid prediction for GlimmerHMM_glimmerT_48594-T1
Valid prediction for snap_scaffold_21-snap.2410-T1
Valid prediction for snap_scaffold_21-snap.2397-T1
Valid prediction for GlimmerHMM_glimmerT_48600-T1
Valid prediction for snap_scaffold_21-snap.2414-T1
Valid prediction for HiQ_model.g32481.t1
Valid prediction for pasa_asmbl_28116.p1
Valid prediction for GlimmerHMM_glimmerT_48608-T1
Valid prediction for Augustus_model.g32479.t1
Valid prediction for snap_scaffold_21-snap.2412-T1
Couldn't classify 63772, 64243
Couldn't classify 66179, 66252
Sorry, prediction pasa_asmbl_28105.p1 fails validation.
(ACT)	 GT	63772-64243	GT	TGG
(GTA)	 AG	66179-66252	AC	GTA
Valid prediction for Augustus_model.g32478.t1
Valid prediction for CodingQuarry_transcript_32741-T1
Couldn't classify 69648, 69722
Sorry, prediction pasa_asmbl_28103.p1 fails validation.
(CAG)	 AA	69648-69722	GT	AGG
(GAG)	 AG	70109-70191	GT	AAG
(TCA)	 AG	70301-70397	GT	CGG
(CAT)	 AG	70717-70885	GT	AGG
(TAA)	 AG	71795-71904	AC	GAA
-recovered pasa_asmbl_28103.p1, terminal, 71795, 71904
-recovered pasa_asmbl_28103.p1, internal, 70109, 70191
-recovered pasa_asmbl_28103.p1, internal, 70301, 70397
-recovered pasa_asmbl_28103.p1, internal, 70717, 70885
Valid prediction for GlimmerHMM_glimmerT_48601-T1
Valid prediction for GlimmerHMM_glimmerT_48611-T1
Couldn't classify 89676, 89689
Couldn't classify 92321, 92443
Sorry, prediction pasa_asmbl_28098.p1 fails validation.
(GCT)	 GT	89676-89689	GT	AGG
(CGA)	 AG	89840-90008	GT	AGG
(ATC)	 AG	90750-90962	GT	TGG
(AAG)	 AG	91125-91275	GT	AGG
(TTC)	 AG	91396-91511	GT	AGG
(AGC)	 AG	92101-92187	GT	AGG
(AAC)	 AG	92321-92443	GG	CAG
-recovered pasa_asmbl_28098.p1, internal, 89840, 90008
-recovered pasa_asmbl_28098.p1, internal, 90750, 90962
-recovered pasa_asmbl_28098.p1, internal, 91125, 91275
-recovered pasa_asmbl_28098.p1, internal, 91396, 91511
-recovered pasa_asmbl_28098.p1, internal, 92101, 92187
Valid prediction for GlimmerHMM_glimmerT_48609-T1
Valid prediction for snap_scaffold_21-snap.2413-T1
Couldn't classify 60595, 60637
Sorry, prediction pasa_asmbl_28107.p1 fails validation.
(CCT)	 TT	60595-60637	GT	AGG
(GGT)	 AG	60752-60919	GT	TGG
(CTG)	 AG	61133-61281	GT	AGG
(ACA)	 AG	61367-61524	GC	AGG
(AGA)	 AG	61612-61659	GT	AGG
(TGA)	 AG	61802-61920	GT	CGG
(ACA)	 AG	62015-62248	GT	AGG
(GTA)	 AG	62458-62640	GT	AGG
(AGG)	 AG	63072-63208	GA	AGG
add_exon() Sorry, pasa_asmbl_28107.p1 62015-62248-terminal-1 is invalid.
-recovered pasa_asmbl_28107.p1, terminal, 62015, 62248
-recovered pasa_asmbl_28107.p1, terminal, 63072, 63208
-recovered pasa_asmbl_28107.p1, internal, 60752, 60919
-recovered pasa_asmbl_28107.p1, internal, 61133, 61281
-recovered pasa_asmbl_28107.p1, internal, 61367, 61524
-recovered pasa_asmbl_28107.p1, internal, 61612, 61659
-recovered pasa_asmbl_28107.p1, internal, 61802, 61920
-recovered pasa_asmbl_28107.p1, internal, 62015, 62248
-recovered pasa_asmbl_28107.p1, internal, 62458, 62640
Valid prediction for GlimmerHMM_glimmerT_48613-T1
Valid prediction for CodingQuarry_transcript_32744-T1
Couldn't classify 87977, 88435
Sorry, prediction pasa_asmbl_28099.p1 fails validation.
(CCA)	 AC	87977-88435	GT	TCG
Valid prediction for Augustus_model.g32472.t1
Couldn't classify 97560, 97741
Sorry, prediction pasa_asmbl_28096.p1 fails validation.
(ATG)	 TC	94582-94987	GT	CAG
(GTG)	 AG	95096-95365	GC	AGG
(GTC)	 AG	95810-95907	GT	AGG
(GGC)	 AG	96366-96513	GT	AGG
(AGA)	 AG	96723-96871	GT	AGG
(TTC)	 AG	97146-97260	GT	CGG
(GTG)	 AG	97560-97741	CT	GAC
-recovered pasa_asmbl_28096.p1, initial, 94582, 94987
-recovered pasa_asmbl_28096.p1, internal, 95096, 95365
-recovered pasa_asmbl_28096.p1, internal, 95810, 95907
-recovered pasa_asmbl_28096.p1, internal, 96366, 96513
-recovered pasa_asmbl_28096.p1, internal, 96723, 96871
-recovered pasa_asmbl_28096.p1, internal, 97146, 97260
Valid prediction for snap_scaffold_21-snap.2415-T1
Valid prediction for GlimmerHMM_glimmerT_48596-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 11027, rend_intergenic: 6974  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18090, rend_intergenic: 16910  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63083, rend_intergenic: 53833  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64635, rend_intergenic: 63324  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90895, rend_intergenic: 88406  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126953, rend_intergenic: 120150  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145128, rend_intergenic: 141884  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168746, rend_intergenic: 167173  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169022, rend_intergenic: 168815  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 218710, rend_intergenic: 215772  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 220720
-exon list size: 392


building trellis

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42.9    
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98.2    
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-found 26 predictions from path traversal
Error with prediction: snap lend_intergenic: 11027, rend_intergenic: 6974  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18090, rend_intergenic: 16910  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63083, rend_intergenic: 53833  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64635, rend_intergenic: 63324  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90895, rend_intergenic: 88406  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126953, rend_intergenic: 120150  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 145128, rend_intergenic: 141884  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 168746, rend_intergenic: 167173  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 169022, rend_intergenic: 168815  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 218710, rend_intergenic: 215772  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

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