-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_11/scaffold_11_5545129-5722233

-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 GlimmerHMM_glimmerT_27149-T1
Valid prediction for snap_scaffold_11-snap.1366-T1
Valid prediction for pasa_asmbl_5572.p1
Valid prediction for snap_scaffold_11-snap.1368-T1
Valid prediction for snap_scaffold_11-snap.1328-T1
Valid prediction for CodingQuarry_transcript_8077-T1
Valid prediction for GlimmerHMM_glimmerT_27163-T1
Valid prediction for snap_scaffold_11-snap.1353-T1
Valid prediction for GlimmerHMM_glimmerT_27151-T1
Couldn't classify 124669, 125049
Sorry, prediction pasa_asmbl_5580.p1 fails validation.
(TCT)	 CG	124669-125049	GT	GAG
Valid prediction for snap_scaffold_11-snap.1363-T1
Valid prediction for snap_scaffold_11-snap.1356-T1
Valid prediction for GlimmerHMM_glimmerT_27162-T1
Valid prediction for Augustus_model.g17956.t1
Valid prediction for snap_scaffold_11-snap.1372-T1
Valid prediction for HiQ_model.g17964.t1
Valid prediction for GlimmerHMM_glimmerT_27148-T1
Couldn't classify 114617, 114624
Couldn't classify 117293, 117370
Sorry, prediction pasa_asmbl_5577.p1 fails validation.
(TCC)	 AC	114617-114624	GT	TTG
(TGT)	 AG	114805-114881	GT	AGG
(GGC)	 AG	115267-115490	GT	AGG
(CCC)	 AG	117293-117370	GA	GTG
-recovered pasa_asmbl_5577.p1, internal, 114805, 114881
-recovered pasa_asmbl_5577.p1, internal, 115267, 115490
Valid prediction for GlimmerHMM_glimmerT_27160-T1
Valid prediction for GlimmerHMM_glimmerT_27145-T1
Couldn't classify 114268, 114346
Sorry, prediction pasa_asmbl_5575.p2 fails validation.
(ATG)	 AG	109849-109854	GT	AGG
(GCA)	 AG	110211-110321	GT	AGG
(GTG)	 AG	111671-111736	GT	GGG
(GTG)	 AG	112155-112245	GT	GGG
(TGT)	 AG	112512-112591	GT	AGG
(ACG)	 AG	112728-112825	GT	GTG
(AGC)	 AG	114268-114346	AA	GGA
-recovered pasa_asmbl_5575.p2, initial, 109849, 109854
-recovered pasa_asmbl_5575.p2, internal, 109849, 109854
-recovered pasa_asmbl_5575.p2, internal, 110211, 110321
-recovered pasa_asmbl_5575.p2, internal, 111671, 111736
-recovered pasa_asmbl_5575.p2, internal, 112155, 112245
-recovered pasa_asmbl_5575.p2, internal, 112512, 112591
-recovered pasa_asmbl_5575.p2, internal, 112728, 112825
Valid prediction for Augustus_model.g17969.t1
Valid prediction for GlimmerHMM_glimmerT_27153-T1
Valid prediction for snap_scaffold_11-snap.1354-T1
Couldn't classify 138743, 139576
Sorry, prediction pasa_asmbl_5581.p1 fails validation.
(CCA)	 TC	138743-139576	CA	AGC
Valid prediction for GlimmerHMM_glimmerT_27144-T1
Valid prediction for snap_scaffold_11-snap.1345-T1
Valid prediction for snap_scaffold_11-snap.1327-T1
Valid prediction for snap_scaffold_11-snap.1334-T1
Valid prediction for snap_scaffold_11-snap.1333-T1
Valid prediction for GlimmerHMM_glimmerT_27158-T1
Valid prediction for GlimmerHMM_glimmerT_27159-T1
Valid prediction for snap_scaffold_11-snap.1336-T1
Valid prediction for snap_scaffold_11-snap.1348-T1
Valid prediction for Augustus_model.g17965.t1
Valid prediction for snap_scaffold_11-snap.1338-T1
Couldn't classify 169852, 169870
Couldn't classify 173154, 173317
Sorry, prediction pasa_asmbl_5583.p1 fails validation.
(AAG)	 AC	169852-169870	GT	GGG
(CCT)	 AG	169988-170061	GT	TGG
(GAT)	 AG	170194-170328	GT	AGG
(GGT)	 AG	170959-171226	GT	AGG
(ATG)	 AG	173154-173317	AG	TGA
-recovered pasa_asmbl_5583.p1, internal, 169988, 170061
-recovered pasa_asmbl_5583.p1, internal, 170194, 170328
-recovered pasa_asmbl_5583.p1, internal, 170959, 171226
Valid prediction for snap_scaffold_11-snap.1349-T1
Valid prediction for snap_scaffold_11-snap.1357-T1
Valid prediction for snap_scaffold_11-snap.1332-T1
Valid prediction for snap_scaffold_11-snap.1362-T1
Valid prediction for snap_scaffold_11-snap.1330-T1
Valid prediction for snap_scaffold_11-snap.1341-T1
Valid prediction for Augustus_model.g17959.t1
Valid prediction for snap_scaffold_11-snap.1351-T1
Valid prediction for snap_scaffold_11-snap.1355-T1
Valid prediction for snap_scaffold_11-snap.1370-T1
Valid prediction for Augustus_model.g17970.t1
Valid prediction for snap_scaffold_11-snap.1326-T1
Valid prediction for snap_scaffold_11-snap.1346-T1
Couldn't classify 118098, 118195
Couldn't classify 121658, 121953
Sorry, prediction pasa_asmbl_5578.p1 fails validation.
(ATT)	 AG	118098-118195	GT	AAG
(ATA)	 AG	118429-118672	GT	GGG
(GGG)	 AG	119338-119612	GT	AGG
(GGG)	 AG	119836-119997	GT	AGG
(GTA)	 AG	120487-120571	GT	AGG
(AAC)	 AG	120818-121010	GT	AGG
(GGA)	 AG	121431-121493	GT	CGG
(AAG)	 AG	121658-121953	GC	AGG
-recovered pasa_asmbl_5578.p1, internal, 118098, 118195
-recovered pasa_asmbl_5578.p1, internal, 118429, 118672
-recovered pasa_asmbl_5578.p1, internal, 119338, 119612
-recovered pasa_asmbl_5578.p1, internal, 119836, 119997
-recovered pasa_asmbl_5578.p1, internal, 120487, 120571
-recovered pasa_asmbl_5578.p1, internal, 120818, 121010
-recovered pasa_asmbl_5578.p1, internal, 121431, 121493
-recovered pasa_asmbl_5578.p1, internal, 121658, 121953
Valid prediction for Augustus_model.g17967.t1
Valid prediction for snap_scaffold_11-snap.1360-T1
Valid prediction for snap_scaffold_11-snap.1344-T1
Valid prediction for snap_scaffold_11-snap.1340-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.g17957.t1
Valid prediction for GlimmerHMM_glimmerT_27156-T1
Couldn't classify 100372, 100542
Sorry, prediction pasa_asmbl_6675.p1 fails validation.
(ATG)	 GC	94636-94704	GT	AGG
(TTG)	 AG	95584-95689	GT	AGG
(TGC)	 AG	97156-97285	GT	GAG
(GAT)	 AG	99793-99826	GT	TGG
(GAC)	 AG	100372-100542	GT	AGG
-recovered pasa_asmbl_6675.p1, initial, 94636, 94704
-recovered pasa_asmbl_6675.p1, internal, 95584, 95689
-recovered pasa_asmbl_6675.p1, internal, 97156, 97285
-recovered pasa_asmbl_6675.p1, internal, 99793, 99826
-recovered pasa_asmbl_6675.p1, internal, 100372, 100542
Valid prediction for Augustus_model.g17962.t1
Valid prediction for snap_scaffold_11-snap.1347-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for Augustus_model.g17958.t1
Valid prediction for snap_scaffold_11-snap.1369-T1
Valid prediction for GlimmerHMM_glimmerT_27152-T1
Valid prediction for GlimmerHMM_glimmerT_27161-T1
Valid prediction for GlimmerHMM_glimmerT_27147-T1
Valid prediction for GlimmerHMM_glimmerT_27150-T1
Valid prediction for Augustus_model.g17968.t1
Valid prediction for snap_scaffold_11-snap.1367-T1
Valid prediction for Augustus_model.g17960.t1
Valid prediction for snap_scaffold_11-snap.1335-T1
Valid prediction for snap_scaffold_11-snap.1339-T1
Valid prediction for CodingQuarry_transcript_8078-T1
Valid prediction for GlimmerHMM_glimmerT_27143-T1
Valid prediction for GlimmerHMM_glimmerT_27146-T1
Valid prediction for snap_scaffold_11-snap.1361-T1
Valid prediction for snap_scaffold_11-snap.1350-T1
Valid prediction for Augustus_model.g17963.t1
Valid prediction for snap_scaffold_11-snap.1329-T1
Valid prediction for snap_scaffold_11-snap.1371-T1
Valid prediction for snap_scaffold_11-snap.1342-T1
Valid prediction for snap_scaffold_11-snap.1331-T1
Valid prediction for HiQ_model.g17966.t1
Valid prediction for GlimmerHMM_glimmerT_27155-T1
Valid prediction for snap_scaffold_11-snap.1359-T1
Valid prediction for GlimmerHMM_glimmerT_27154-T1
Valid prediction for Augustus_model.g17955.t1
Valid prediction for snap_scaffold_11-snap.1337-T1
Valid prediction for Augustus_model.g17961.t1
Valid prediction for GlimmerHMM_glimmerT_27164-T1
Valid prediction for snap_scaffold_11-snap.1365-T1
Valid prediction for snap_scaffold_11-snap.1325-T1
Valid prediction for snap_scaffold_11-snap.1364-T1
Valid prediction for snap_scaffold_11-snap.1352-T1
Valid prediction for snap_scaffold_11-snap.1343-T1
Valid prediction for GlimmerHMM_glimmerT_27157-T1
Valid prediction for snap_scaffold_11-snap.1358-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 9721, rend_intergenic: 4066  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23715, rend_intergenic: 20245  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41116, rend_intergenic: 26372  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56636, rend_intergenic: 55855  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59835, rend_intergenic: 56722  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66401, rend_intergenic: 60077  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67067, rend_intergenic: 66431  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74496, rend_intergenic: 70249  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79191, rend_intergenic: 75123  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86433, rend_intergenic: 79601  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90839, rend_intergenic: 86987  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98486, rend_intergenic: 91375  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124978, rend_intergenic: 121560  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137363, rend_intergenic: 133504  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148275, rend_intergenic: 141244  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152290, rend_intergenic: 149119  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156792, rend_intergenic: 154103  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157235, rend_intergenic: 156941  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163898, rend_intergenic: 160490  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167205, rend_intergenic: 165133  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174447, rend_intergenic: 172715  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 177105
-exon list size: 433


building trellis

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98.9    
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99.8    
-found 24 predictions from path traversal
Error with prediction: snap lend_intergenic: 9721, rend_intergenic: 4066  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 23715, rend_intergenic: 20245  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 41116, rend_intergenic: 26372  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 56636, rend_intergenic: 55855  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59835, rend_intergenic: 56722  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66401, rend_intergenic: 60077  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 67067, rend_intergenic: 66431  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 74496, rend_intergenic: 70249  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 79191, rend_intergenic: 75123  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86433, rend_intergenic: 79601  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 90839, rend_intergenic: 86987  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 98486, rend_intergenic: 91375  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 124978, rend_intergenic: 121560  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 137363, rend_intergenic: 133504  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 148275, rend_intergenic: 141244  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 152290, rend_intergenic: 149119  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156792, rend_intergenic: 154103  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 157235, rend_intergenic: 156941  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163898, rend_intergenic: 160490  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 167205, rend_intergenic: 165133  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 174447, rend_intergenic: 172715  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 18 predictions persist after filtering for low support