-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_5/scaffold_5_6447135-6677573

-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.g7928.t1
Valid prediction for snap_scaffold_5-snap.1290-T1
Valid prediction for GlimmerHMM_glimmerT_12088-T1
Valid prediction for snap_scaffold_5-snap.1269-T1
Valid prediction for snap_scaffold_5-snap.1295-T1
Valid prediction for snap_scaffold_5-snap.1283-T1
Valid prediction for Augustus_model.g7930.t1
Valid prediction for pasa_asmbl_45441.p1
Valid prediction for GlimmerHMM_glimmerT_12087-T1
Valid prediction for snap_scaffold_5-snap.1272-T1
Valid prediction for CodingQuarry_transcript_52100-T1
Couldn't classify 117228, 117500
Sorry, prediction pasa_asmbl_45438.p1 fails validation.
(ATG)	 TG	117228-117500	GG	AGG
Valid prediction for snap_scaffold_5-snap.1298-T1
Valid prediction for snap_scaffold_5-snap.1277-T1
Valid prediction for GlimmerHMM_glimmerT_12102-T1
Valid prediction for snap_scaffold_5-snap.1274-T1
Valid prediction for snap_scaffold_5-snap.1305-T1
Valid prediction for GlimmerHMM_glimmerT_12081-T1
Couldn't classify 113352, 113497
Sorry, prediction pasa_asmbl_45430.p2 fails validation.
(ATG)	 GG	112116-112207	GT	AGG
(ATG)	 AG	112941-113041	GT	TGG
(ATG)	 AG	113352-113497	TA	TGT
-recovered pasa_asmbl_45430.p2, initial, 112116, 112207
add_exon() Sorry, pasa_asmbl_45430.p2 112941-113041-initial-1 is invalid.
-recovered pasa_asmbl_45430.p2, initial, 112941, 113041
-recovered pasa_asmbl_45430.p2, internal, 112941, 113041
Valid prediction for Augustus_model.g7929.t1
Valid prediction for snap_scaffold_5-snap.1297-T1
Valid prediction for GlimmerHMM_glimmerT_12097-T1
Valid prediction for GlimmerHMM_glimmerT_12105-T1
Valid prediction for GlimmerHMM_glimmerT_12091-T1
Valid prediction for snap_scaffold_5-snap.1285-T1
Valid prediction for GlimmerHMM_glimmerT_12096-T1
Valid prediction for snap_scaffold_5-snap.1287-T1
Valid prediction for GlimmerHMM_glimmerT_12094-T1
Valid prediction for GlimmerHMM_glimmerT_12090-T1
Valid prediction for Augustus_model.g7931.t1
Valid prediction for GlimmerHMM_glimmerT_12086-T1
Valid prediction for HiQ_model.g7947.t1
Valid prediction for snap_scaffold_5-snap.1294-T1
Valid prediction for snap_scaffold_5-snap.1289-T1
Valid prediction for snap_scaffold_5-snap.1271-T1
Valid prediction for Augustus_model.g7925.t1
Valid prediction for snap_scaffold_5-snap.1313-T1
Valid prediction for snap_scaffold_5-snap.1312-T1
Valid prediction for Augustus_model.g7927.t1
Valid prediction for snap_scaffold_5-snap.1309-T1
Valid prediction for GlimmerHMM_glimmerT_12089-T1
Valid prediction for snap_scaffold_5-snap.1307-T1
Valid prediction for GlimmerHMM_glimmerT_12082-T1
Valid prediction for Augustus_model.g7932.t1
Valid prediction for Augustus_model.g7926.t1
Valid prediction for GlimmerHMM_glimmerT_12085-T1
Valid prediction for snap_scaffold_5-snap.1280-T1
Valid prediction for Augustus_model.g7936.t1
Valid prediction for Augustus_model.g7924.t1
Valid prediction for snap_scaffold_5-snap.1278-T1
Valid prediction for CodingQuarry_transcript_52094-T1
Valid prediction for snap_scaffold_5-snap.1301-T1
Valid prediction for Augustus_model.g7922.t1
Valid prediction for snap_scaffold_5-snap.1292-T1
Valid prediction for HiQ_model.g7935.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 Augustus_model.g7939.t1
Valid prediction for snap_scaffold_5-snap.1314-T1
Valid prediction for Augustus_model.g7937.t1
Valid prediction for pasa_asmbl_44116.p1
Valid prediction for Augustus_model.g7945.t1
Valid prediction for Augustus_model.g7948.t1
Valid prediction for HiQ_model.g7940.t1
Valid prediction for CodingQuarry_transcript_52095-T1
Valid prediction for snap_scaffold_5-snap.1270-T1
Valid prediction for snap_scaffold_5-snap.1310-T1
Valid prediction for pasa_asmbl_44922.p1
Valid prediction for snap_scaffold_5-snap.1284-T1
Valid prediction for snap_scaffold_5-snap.1276-T1
Couldn't classify 81762, 82064
Sorry, prediction pasa_asmbl_44109.p1 fails validation.
(ATG)	 GG	81762-82064	GA	GTG
Valid prediction for HiQ_model.g7941.t1
Valid prediction for snap_scaffold_5-snap.1275-T1
Valid prediction for pasa_asmbl_44127.p1
Valid prediction for Augustus_model.g7933.t1
Valid prediction for GlimmerHMM_glimmerT_12083-T1
Valid prediction for snap_scaffold_5-snap.1296-T1
Valid prediction for CodingQuarry_transcript_52096-T1
Valid prediction for snap_scaffold_5-snap.1293-T1
Couldn't classify 25767, 26027
Couldn't classify 26666, 26745
Sorry, prediction pasa_asmbl_45043.p1 fails validation.
(GTC)	 AG	25767-26027	GT	ATG
(GTT)	 AG	26226-26361	GT	AGG
(AGA)	 AG	26666-26745	GT	AGG
-recovered pasa_asmbl_45043.p1, internal, 25767, 26027
-recovered pasa_asmbl_45043.p1, internal, 26226, 26361
-recovered pasa_asmbl_45043.p1, internal, 26666, 26745
Couldn't classify 69697, 70284
Sorry, prediction pasa_asmbl_44113.p1 fails validation.
(GGA)	 CG	69697-70284	AC	GAA
Valid prediction for snap_scaffold_5-snap.1282-T1
Valid prediction for Augustus_model.g7934.t1
Valid prediction for GlimmerHMM_glimmerT_12101-T1
Valid prediction for snap_scaffold_5-snap.1299-T1
Valid prediction for snap_scaffold_5-snap.1311-T1
Valid prediction for snap_scaffold_5-snap.1300-T1
Valid prediction for GlimmerHMM_glimmerT_12103-T1
Valid prediction for GlimmerHMM_glimmerT_12084-T1
Valid prediction for snap_scaffold_5-snap.1303-T1
Valid prediction for snap_scaffold_5-snap.1306-T1
Valid prediction for snap_scaffold_5-snap.1281-T1
Couldn't classify 50036, 50128
Sorry, prediction pasa_asmbl_44121.p1 fails validation.
(ATG)	 CC	47729-48286	GT	AGG
(CAG)	 AG	50036-50128	GG	TCG
-recovered pasa_asmbl_44121.p1, initial, 47729, 48286
Valid prediction for GlimmerHMM_glimmerT_12093-T1
Couldn't classify 69360, 69545
Sorry, prediction pasa_asmbl_44115.p1 fails validation.
(ATG)	 AC	67505-67565	GT	AGG
(TGA)	 AG	68272-68454	GT	AGG
(TGA)	 AG	69078-69229	GT	AGG
(GTG)	 AG	69360-69545	GA	CTG
-recovered pasa_asmbl_44115.p1, initial, 67505, 67565
-recovered pasa_asmbl_44115.p1, internal, 68272, 68454
-recovered pasa_asmbl_44115.p1, internal, 69078, 69229
Valid prediction for snap_scaffold_5-snap.1273-T1
Valid prediction for CodingQuarry_transcript_52099-T1
Valid prediction for pasa_asmbl_44097.p1
Valid prediction for GlimmerHMM_glimmerT_12099-T1
Couldn't classify 59873, 60121
Sorry, prediction pasa_asmbl_44120.p1 fails validation.
(ATG)	 AT	57262-57300	GT	TGG
(ATG)	 AG	57440-57596	GT	AGG
(AAC)	 AG	57712-57860	GT	GGG
(TAT)	 AG	59550-59735	GT	AGG
(CCT)	 AG	59873-60121	CA	TCC
-recovered pasa_asmbl_44120.p1, initial, 57262, 57300
-recovered pasa_asmbl_44120.p1, initial, 57440, 57596
-recovered pasa_asmbl_44120.p1, internal, 57440, 57596
-recovered pasa_asmbl_44120.p1, internal, 57712, 57860
-recovered pasa_asmbl_44120.p1, internal, 59550, 59735
Valid prediction for snap_scaffold_5-snap.1286-T1
Valid prediction for snap_scaffold_5-snap.1291-T1
Valid prediction for snap_scaffold_5-snap.1302-T1
Valid prediction for snap_scaffold_5-snap.1304-T1
Valid prediction for snap_scaffold_5-snap.1308-T1
Valid prediction for Augustus_model.g7944.t1
Valid prediction for GlimmerHMM_glimmerT_12104-T1
Valid prediction for Augustus_model.g7938.t1
Valid prediction for GlimmerHMM_glimmerT_12098-T1
Valid prediction for Augustus_model.g7942.t1
Valid prediction for GlimmerHMM_glimmerT_12092-T1
Valid prediction for snap_scaffold_5-snap.1279-T1
Valid prediction for GlimmerHMM_glimmerT_12106-T1
Couldn't classify 89428, 89677
Sorry, prediction pasa_asmbl_44105.p1 fails validation.
(NTC)	 AT	89428-89677	GT	AGG
(GCC)	 AG	89829-90087	GT	GAG
(AAA)	 AG	91345-91477	GT	AGG
(ATC)	 AG	93224-93358	GT	AGG
(GTG)	 AG	93499-93602	GT	AAG
(GGA)	 AG	93758-93995	AA	AAA
-recovered pasa_asmbl_44105.p1, terminal, 93758, 93995
-recovered pasa_asmbl_44105.p1, internal, 89829, 90087
-recovered pasa_asmbl_44105.p1, internal, 91345, 91477
-recovered pasa_asmbl_44105.p1, internal, 93224, 93358
-recovered pasa_asmbl_44105.p1, internal, 93499, 93602
Valid prediction for GlimmerHMM_glimmerT_12100-T1
Valid prediction for HiQ_model.g7946.t1
Valid prediction for CodingQuarry_transcript_52097-T1
Valid prediction for Augustus_model.g7943.t1
Valid prediction for snap_scaffold_5-snap.1288-T1
Valid prediction for GlimmerHMM_glimmerT_12095-T1
Valid prediction for Augustus_model.g7923.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 5264, rend_intergenic: 5239  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18013, rend_intergenic: 5945  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35906, rend_intergenic: 18032  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41586, rend_intergenic: 38519  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53218, rend_intergenic: 41829  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62634, rend_intergenic: 53823  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66962, rend_intergenic: 63439  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72439, rend_intergenic: 67032  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77788, rend_intergenic: 72529  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81116, rend_intergenic: 77874  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83555, rend_intergenic: 81563  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85437, rend_intergenic: 83585  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86273, rend_intergenic: 85835  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89321, rend_intergenic: 86493  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101136, rend_intergenic: 93009  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109114, rend_intergenic: 105838  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121811, rend_intergenic: 117106  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139421, rend_intergenic: 128847  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140535, rend_intergenic: 140349  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171490, rend_intergenic: 168931  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173242, rend_intergenic: 172042  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182711, rend_intergenic: 176910  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188128, rend_intergenic: 185982  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192916, rend_intergenic: 189135  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 222166, rend_intergenic: 217810  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 230439
-exon list size: 499


building trellis

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-found 32 predictions from path traversal
Error with prediction: snap lend_intergenic: 5264, rend_intergenic: 5239  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18013, rend_intergenic: 5945  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35906, rend_intergenic: 18032  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41586, rend_intergenic: 38519  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53218, rend_intergenic: 41829  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62634, rend_intergenic: 53823  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66962, rend_intergenic: 63439  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72439, rend_intergenic: 67032  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 77788, rend_intergenic: 72529  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 81116, rend_intergenic: 77874  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83555, rend_intergenic: 81563  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 85437, rend_intergenic: 83585  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86273, rend_intergenic: 85835  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89321, rend_intergenic: 86493  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101136, rend_intergenic: 93009  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 109114, rend_intergenic: 105838  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 121811, rend_intergenic: 117106  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 139421, rend_intergenic: 128847  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 140535, rend_intergenic: 140349  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 171490, rend_intergenic: 168931  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173242, rend_intergenic: 172042  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 182711, rend_intergenic: 176910  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 188128, rend_intergenic: 185982  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 192916, rend_intergenic: 189135  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 222166, rend_intergenic: 217810  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 23 predictions persist after filtering for low support