-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_16/scaffold_16_7480577-7701919

-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 pasa_asmbl_16339.p1
Couldn't classify 79346, 79417
Couldn't classify 80713, 80742
Sorry, prediction pasa_asmbl_16352.p1 fails validation.
(GGA)	 AC	79346-79417	GT	AGG
(GTG)	 AG	79895-80100	GT	AAG
(CTA)	 AG	80479-80611	GT	AGG
(GCC)	 AG	80713-80742	GA	CAG
-recovered pasa_asmbl_16352.p1, internal, 79895, 80100
-recovered pasa_asmbl_16352.p1, internal, 80479, 80611
Valid prediction for GlimmerHMM_glimmerT_38569-T1
Valid prediction for snap_scaffold_16-snap.1372-T1
Valid prediction for CodingQuarry_transcript_20009-T1
Valid prediction for snap_scaffold_16-snap.1402-T1
Valid prediction for HiQ_model.g25736.t1
Valid prediction for CodingQuarry_transcript_20004-T1
Valid prediction for CodingQuarry_transcript_20006-T1
Valid prediction for GlimmerHMM_glimmerT_38564-T1
Couldn't classify 37383, 37553
Sorry, prediction pasa_asmbl_16341.p1 fails validation.
(GTA)	 GT	37383-37553	GT	CAG
(AAT)	 AG	38590-38722	GT	AGG
(AGG)	 AG	39049-39175	GT	GGG
(ACA)	 AG	39326-39418	GT	AGG
(CAC)	 AG	39531-39643	GT	AGG
(CTG)	 AG	39777-39820	CC	AAC
add_exon() Sorry, pasa_asmbl_16341.p1 38590-38722-terminal-3 is invalid.
-recovered pasa_asmbl_16341.p1, terminal, 38590, 38722
-recovered pasa_asmbl_16341.p1, terminal, 39777, 39820
-recovered pasa_asmbl_16341.p1, internal, 38590, 38722
-recovered pasa_asmbl_16341.p1, internal, 39049, 39175
-recovered pasa_asmbl_16341.p1, internal, 39326, 39418
-recovered pasa_asmbl_16341.p1, internal, 39531, 39643
Valid prediction for GlimmerHMM_glimmerT_38580-T1
Valid prediction for Augustus_model.g25738.t1
Valid prediction for snap_scaffold_16-snap.1389-T1
Valid prediction for GlimmerHMM_glimmerT_38573-T1
Valid prediction for snap_scaffold_16-snap.1398-T1
Valid prediction for GlimmerHMM_glimmerT_38568-T1
Valid prediction for Augustus_model.g25750.t1
Valid prediction for Augustus_model.g25739.t1
Valid prediction for snap_scaffold_16-snap.1368-T1
Sorry, intron length (7) is less than minimum required (10)
Couldn't classify 121671, 121742
Sorry, prediction pasa_asmbl_16354.p1 fails validation.
(TAC)	 AG	121671-121742	GT	AGG
(AAC)	 AG	121868-121956	GT	AGG
(CTG)	 AG	122116-122221	GT	AGG
(ATG)	 AG	122294-122353	GT	TGG
(GGT)	 AG	122491-122582	GT	AGG
(ATG)	 AG	122716-122750	GT	CGG
(TGC)	 AG	122912-122991	GT	AGG
(CAA)	 AG	123089-123188	GT	AGG
(GAG)	 AG	123331-123455	GT	AGG
(GAT)	 AG	125270-125374	GT	CGG
(GAT)	 AG	125464-125590	GT	CCG
(GTA)	 AG	125763-125944	GT	TGG
(GCC)	 AG	126110-126253	AA	AGA
-recovered pasa_asmbl_16354.p1, initial, 122294, 122353
add_exon() Sorry, pasa_asmbl_16354.p1 122716-122750-initial-1 is invalid.
-recovered pasa_asmbl_16354.p1, initial, 122716, 122750
-recovered pasa_asmbl_16354.p1, terminal, 123089, 123188
-recovered pasa_asmbl_16354.p1, terminal, 126110, 126253
-recovered pasa_asmbl_16354.p1, internal, 121671, 121742
-recovered pasa_asmbl_16354.p1, internal, 121868, 121956
-recovered pasa_asmbl_16354.p1, internal, 122116, 122221
-recovered pasa_asmbl_16354.p1, internal, 122294, 122353
-recovered pasa_asmbl_16354.p1, internal, 122491, 122582
-recovered pasa_asmbl_16354.p1, internal, 122716, 122750
-recovered pasa_asmbl_16354.p1, internal, 122912, 122991
-recovered pasa_asmbl_16354.p1, internal, 123089, 123188
-recovered pasa_asmbl_16354.p1, internal, 123331, 123455
-recovered pasa_asmbl_16354.p1, internal, 125270, 125374
-recovered pasa_asmbl_16354.p1, internal, 125464, 125590
-recovered pasa_asmbl_16354.p1, internal, 125763, 125944
Valid prediction for GlimmerHMM_glimmerT_38578-T1
Valid prediction for Augustus_model.g25753.t1
Valid prediction for Augustus_model.g25751.t1
Valid prediction for snap_scaffold_16-snap.1393-T1
Valid prediction for snap_scaffold_16-snap.1366-T1
Valid prediction for snap_scaffold_16-snap.1375-T1
Valid prediction for GlimmerHMM_glimmerT_38558-T1
Valid prediction for CodingQuarry_transcript_20001-T1
Valid prediction for snap_scaffold_16-snap.1380-T1
Valid prediction for CodingQuarry_transcript_20003-T1
Valid prediction for Augustus_model.g25752.t1
Valid prediction for pasa_asmbl_16347.p1
Couldn't classify 34990, 35095
Couldn't classify 37433, 37601
Sorry, prediction pasa_asmbl_16343.p1 fails validation.
(CAT)	 CC	34990-35095	GT	TTG
(TCA)	 AG	35758-35784	GT	CAG
(TAA)	 AG	36587-36681	GT	AGG
(TTC)	 AG	36783-36903	GT	AGG
(CTG)	 AG	37032-37101	GT	ATG
(GTG)	 AG	37194-37226	GT	TGG
(GGT)	 AG	37433-37601	CT	CCC
-recovered pasa_asmbl_16343.p1, internal, 35758, 35784
-recovered pasa_asmbl_16343.p1, internal, 36587, 36681
-recovered pasa_asmbl_16343.p1, internal, 36783, 36903
-recovered pasa_asmbl_16343.p1, internal, 37032, 37101
-recovered pasa_asmbl_16343.p1, internal, 37194, 37226
Valid prediction for Augustus_model.g25749.t1
Valid prediction for GlimmerHMM_glimmerT_38587-T1
Valid prediction for GlimmerHMM_glimmerT_38583-T1
Valid prediction for snap_scaffold_16-snap.1363-T1
Valid prediction for GlimmerHMM_glimmerT_38565-T1
Valid prediction for GlimmerHMM_glimmerT_38560-T1
Valid prediction for snap_scaffold_16-snap.1387-T1
Valid prediction for snap_scaffold_16-snap.1373-T1
Valid prediction for HiQ_model.g25734.t1
Valid prediction for snap_scaffold_16-snap.1376-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for Augustus_model.g25747.t1
Couldn't classify 67022, 67089
Sorry, prediction pasa_asmbl_16349.p1 fails validation.
(ATG)	 TC	66132-66180	GT	TGG
(CAG)	 AG	66422-66546	GT	AGG
(GTG)	 AG	66639-66735	GT	TGG
(ATG)	 AG	66830-66910	GT	AGG
(GTA)	 AG	67022-67089	AG	ACA
-recovered pasa_asmbl_16349.p1, initial, 66132, 66180
-recovered pasa_asmbl_16349.p1, initial, 66830, 66910
-recovered pasa_asmbl_16349.p1, internal, 66422, 66546
-recovered pasa_asmbl_16349.p1, internal, 66639, 66735
-recovered pasa_asmbl_16349.p1, internal, 66830, 66910
Valid prediction for GlimmerHMM_glimmerT_38563-T1
Valid prediction for Augustus_model.g25742.t1
Valid prediction for GlimmerHMM_glimmerT_38575-T1
Valid prediction for GlimmerHMM_glimmerT_38586-T1
Valid prediction for GlimmerHMM_glimmerT_38561-T1
Valid prediction for Augustus_model.g25743.t1
Valid prediction for HiQ_model.g25745.t1
Valid prediction for HiQ_model.g25740.t1
Valid prediction for pasa_asmbl_16340.p1
Valid prediction for snap_scaffold_16-snap.1370-T1
Valid prediction for GlimmerHMM_glimmerT_38588-T1
Couldn't classify 49596, 49640
Sorry, prediction pasa_asmbl_16345.p1 fails validation.
(ACC)	 CC	49596-49640	GT	AGG
(TTG)	 AG	49753-49858	GT	CTG
(TGA)	 AG	50221-50378	GC	GAG
-recovered pasa_asmbl_16345.p1, terminal, 50221, 50378
-recovered pasa_asmbl_16345.p1, internal, 49753, 49858
-recovered pasa_asmbl_16345.p1, internal, 50221, 50378
Valid prediction for CodingQuarry_transcript_20005-T1
Valid prediction for GlimmerHMM_glimmerT_38566-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_16-snap.1392-T1
Valid prediction for GlimmerHMM_glimmerT_38557-T1
Valid prediction for snap_scaffold_16-snap.1365-T1
Valid prediction for pasa_asmbl_17181.p1
Valid prediction for GlimmerHMM_glimmerT_38574-T1
Couldn't classify 187211, 187660
Sorry, prediction pasa_asmbl_17180.p1 fails validation.
(ATT)	 CC	187211-187660	AT	GAA
Valid prediction for CodingQuarry_transcript_20008-T1
Valid prediction for CodingQuarry_transcript_20010-T1
Valid prediction for snap_scaffold_16-snap.1386-T1
Valid prediction for GlimmerHMM_glimmerT_38576-T1
Valid prediction for snap_scaffold_16-snap.1377-T1
Valid prediction for GlimmerHMM_glimmerT_38585-T1
Valid prediction for GlimmerHMM_glimmerT_38577-T1
Valid prediction for snap_scaffold_16-snap.1400-T1
Valid prediction for GlimmerHMM_glimmerT_38567-T1
Valid prediction for GlimmerHMM_glimmerT_38570-T1
Valid prediction for GlimmerHMM_glimmerT_38571-T1
Valid prediction for CodingQuarry_transcript_20002-T1
Valid prediction for CodingQuarry_transcript_20011-T1
Valid prediction for snap_scaffold_16-snap.1396-T1
Valid prediction for GlimmerHMM_glimmerT_38556-T1
Valid prediction for snap_scaffold_16-snap.1403-T1
Valid prediction for Augustus_model.g25733.t1
Valid prediction for GlimmerHMM_glimmerT_38579-T1
Valid prediction for snap_scaffold_16-snap.1404-T1
Valid prediction for snap_scaffold_16-snap.1390-T1
Valid prediction for snap_scaffold_16-snap.1371-T1
Valid prediction for pasa_asmbl_17185.p1
Valid prediction for Augustus_model.g25737.t1
Valid prediction for snap_scaffold_16-snap.1383-T1
Valid prediction for snap_scaffold_16-snap.1381-T1
Valid prediction for snap_scaffold_16-snap.1399-T1
Valid prediction for snap_scaffold_16-snap.1394-T1
Valid prediction for pasa_asmbl_17183.p1
Valid prediction for GlimmerHMM_glimmerT_38582-T1
Valid prediction for HiQ_model.g25746.t1
Valid prediction for snap_scaffold_16-snap.1388-T1
Valid prediction for Augustus_model.g25735.t1
Valid prediction for snap_scaffold_16-snap.1395-T1
Valid prediction for snap_scaffold_16-snap.1397-T1
Valid prediction for pasa_asmbl_17187.p1
Valid prediction for snap_scaffold_16-snap.1374-T1
Valid prediction for GlimmerHMM_glimmerT_38581-T1
Valid prediction for snap_scaffold_16-snap.1379-T1
Valid prediction for snap_scaffold_16-snap.1364-T1
Valid prediction for CodingQuarry_transcript_20007-T1
Valid prediction for snap_scaffold_16-snap.1385-T1
Valid prediction for HiQ_model.g25744.t1
Valid prediction for snap_scaffold_16-snap.1401-T1
Valid prediction for snap_scaffold_16-snap.1384-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for Augustus_model.g25748.t1
Valid prediction for pasa_asmbl_17179.p1
Valid prediction for Augustus_model.g25754.t1
Valid prediction for snap_scaffold_16-snap.1367-T1
Valid prediction for GlimmerHMM_glimmerT_38562-T1
Valid prediction for snap_scaffold_16-snap.1378-T1
Valid prediction for GlimmerHMM_glimmerT_38572-T1
Valid prediction for snap_scaffold_16-snap.1369-T1
Valid prediction for snap_scaffold_16-snap.1382-T1
Valid prediction for HiQ_model.g25741.t1
Valid prediction for GlimmerHMM_glimmerT_38589-T1
Valid prediction for snap_scaffold_16-snap.1391-T1
Valid prediction for GlimmerHMM_glimmerT_38584-T1
Valid prediction for GlimmerHMM_glimmerT_38559-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: GlimmerHMM lend_intergenic: 167060, rend_intergenic: 167057  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50371, rend_intergenic: 47164  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63927, rend_intergenic: 62054  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91551, rend_intergenic: 70372  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101340, rend_intergenic: 92874  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135885, rend_intergenic: 131381  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173220, rend_intergenic: 157129  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179552, rend_intergenic: 173557  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 191572, rend_intergenic: 180353  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 202777, rend_intergenic: 197393  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 215024, rend_intergenic: 202808  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 221343
-exon list size: 485


building trellis

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-found 30 predictions from path traversal
Error with prediction: GlimmerHMM lend_intergenic: 167060, rend_intergenic: 167057  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 50371, rend_intergenic: 47164  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 63927, rend_intergenic: 62054  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 91551, rend_intergenic: 70372  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 101340, rend_intergenic: 92874  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135885, rend_intergenic: 131381  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 173220, rend_intergenic: 157129  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 179552, rend_intergenic: 173557  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 191572, rend_intergenic: 180353  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 202777, rend_intergenic: 197393  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 215024, rend_intergenic: 202808  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 22 predictions persist after filtering for low support