-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_25/scaffold_25_6313250-6478003

-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: +)Couldn't classify 152756, 152825
Couldn't classify 153202, 153482
Sorry, prediction pasa_asmbl_33853.p1 fails validation.
(TCT)	 AC	152756-152825	GT	TGG
(AGA)	 AG	153202-153482	CT	CCC
Valid prediction for GlimmerHMM_glimmerT_55602-T1
Valid prediction for snap_scaffold_25-snap.1354-T1
Couldn't classify 123835, 123973
Sorry, prediction pasa_asmbl_33627.p1 fails validation.
(AAG)	 AC	123835-123973	GT	AGG
(GTT)	 AG	124820-124932	GT	AGG
(GTG)	 AG	125420-125509	GT	ATG
(GCA)	 AG	127920-128012	TC	GAT
-recovered pasa_asmbl_33627.p1, terminal, 127920, 128012
-recovered pasa_asmbl_33627.p1, internal, 124820, 124932
-recovered pasa_asmbl_33627.p1, internal, 125420, 125509
Valid prediction for Augustus_model.g37110.t1
Valid prediction for GeneMark_model.97033_t
Valid prediction for snap_scaffold_25-snap.1343-T1
Valid prediction for GlimmerHMM_glimmerT_55629-T1
Valid prediction for GeneMark_model.97031_t
Valid prediction for snap_scaffold_25-snap.1349-T1
Couldn't classify 157481, 157600
Couldn't classify 159025, 159167
Sorry, prediction pasa_asmbl_33630.p2 fails validation.
(CGG)	 CG	157481-157600	GT	AGG
(CGC)	 AG	157846-157966	GT	GGG
(ACT)	 AG	159025-159167	GT	GGG
-recovered pasa_asmbl_33630.p2, internal, 157846, 157966
-recovered pasa_asmbl_33630.p2, internal, 159025, 159167
Valid prediction for GlimmerHMM_glimmerT_55611-T1
Valid prediction for GeneMark_model.97026_t
Valid prediction for GeneMark_model.97012_t
Valid prediction for snap_scaffold_25-snap.1366-T1
Valid prediction for GlimmerHMM_glimmerT_55616-T1
Valid prediction for GeneMark_model.97028_t
Valid prediction for GeneMark_model.97047_t
Valid prediction for GeneMark_model.97045_t
Valid prediction for snap_scaffold_25-snap.1336-T1
Couldn't classify 18795, 18814
Couldn't classify 19961, 20012
Sorry, prediction pasa_asmbl_33623.p1 fails validation.
(CTG)	 AC	18795-18814	GT	AAG
(GTT)	 AG	19008-19141	GT	AGG
(AGG)	 AG	19440-19517	GT	AGG
(GCC)	 AG	19645-19717	GT	ATG
(CTC)	 AG	19822-19845	GT	AGG
(TAC)	 AG	19961-20012	GT	TCG
-recovered pasa_asmbl_33623.p1, internal, 19008, 19141
-recovered pasa_asmbl_33623.p1, internal, 19440, 19517
-recovered pasa_asmbl_33623.p1, internal, 19645, 19717
-recovered pasa_asmbl_33623.p1, internal, 19822, 19845
-recovered pasa_asmbl_33623.p1, internal, 19961, 20012
Valid prediction for GlimmerHMM_glimmerT_55614-T1
Valid prediction for GlimmerHMM_glimmerT_55613-T1
Valid prediction for snap_scaffold_25-snap.1335-T1
Valid prediction for GeneMark_model.97037_t
Valid prediction for snap_scaffold_25-snap.1360-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_55624-T1
Valid prediction for GeneMark_model.97024_t
Valid prediction for snap_scaffold_25-snap.1344-T1
Valid prediction for snap_scaffold_25-snap.1345-T1
Valid prediction for snap_scaffold_25-snap.1365-T1
Valid prediction for snap_scaffold_25-snap.1348-T1
Valid prediction for GeneMark_model.97010_t
Valid prediction for snap_scaffold_25-snap.1359-T1
Valid prediction for GeneMark_model.97035_t
Valid prediction for GlimmerHMM_glimmerT_55617-T1
Valid prediction for Augustus_model.g37107.t1
Valid prediction for GeneMark_model.97019_t
Valid prediction for GeneMark_model.97005_t
Valid prediction for GeneMark_model.97016_t
Valid prediction for GlimmerHMM_glimmerT_55628-T1
Valid prediction for snap_scaffold_25-snap.1355-T1
Valid prediction for GeneMark_model.97011_t
Valid prediction for GeneMark_model.97049_t
Valid prediction for GlimmerHMM_glimmerT_55606-T1
Valid prediction for snap_scaffold_25-snap.1357-T1
Valid prediction for Augustus_model.g37111.t1
Valid prediction for GeneMark_model.97007_t
Valid prediction for snap_scaffold_25-snap.1334-T1
Valid prediction for GeneMark_model.97043_t
Valid prediction for snap_scaffold_25-snap.1340-T1
Valid prediction for Augustus_model.g37108.t1
Valid prediction for Augustus_model.g37103.t1
Valid prediction for GeneMark_model.97014_t
Valid prediction for snap_scaffold_25-snap.1353-T1
Valid prediction for Augustus_model.g37116.t1
Valid prediction for snap_scaffold_25-snap.1331-T1
Valid prediction for snap_scaffold_25-snap.1350-T1
Valid prediction for GlimmerHMM_glimmerT_55620-T1
Valid prediction for Augustus_model.g37113.t1
Valid prediction for GlimmerHMM_glimmerT_55626-T1
Valid prediction for GeneMark_model.97039_t
Valid prediction for snap_scaffold_25-snap.1362-T1
Valid prediction for GeneMark_model.97008_t
Valid prediction for Augustus_model.g37105.t1
Valid prediction for GlimmerHMM_glimmerT_55622-T1
Valid prediction for snap_scaffold_25-snap.1333-T1
Valid prediction for GlimmerHMM_glimmerT_55607-T1
Valid prediction for Augustus_model.g37112.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 CodingQuarry_transcript_38678-T1
Valid prediction for GeneMark_model.97044_t
Valid prediction for GeneMark_model.97050_t
Valid prediction for pasa_asmbl_34336.p1
Valid prediction for GlimmerHMM_glimmerT_55625-T1
Valid prediction for snap_scaffold_25-snap.1332-T1
Valid prediction for snap_scaffold_25-snap.1363-T1
Valid prediction for GlimmerHMM_glimmerT_55618-T1
Valid prediction for GeneMark_model.97048_t
Valid prediction for GeneMark_model.97038_t
Valid prediction for HiQ_model.g37102.t1
Couldn't classify 86358, 86432
Sorry, prediction GeneMark_model.97023_t fails validation.
(ATG)	 GC	84784-84863	GT	CGG
(AGA)	 AG	85111-85125	GT	GAG
(GAG)	 AG	85150-85197	GT	GGG
(TTT)	 AG	85219-85228	GT	TAG
(GGG)	 AG	85544-85660	GT	AGG
(CGG)	 AG	85694-85916	GT	AAG
(GGG)	 AG	86314-86326	GT	GAG
(TGG)	 AG	86358-86432	GC	ACG
-recovered GeneMark_model.97023_t, initial, 84784, 84863
-recovered GeneMark_model.97023_t, internal, 85111, 85125
-recovered GeneMark_model.97023_t, internal, 85150, 85197
-recovered GeneMark_model.97023_t, internal, 85219, 85228
-recovered GeneMark_model.97023_t, internal, 85544, 85660
-recovered GeneMark_model.97023_t, internal, 85694, 85916
-recovered GeneMark_model.97023_t, internal, 86314, 86326
-recovered GeneMark_model.97023_t, internal, 86358, 86432
Valid prediction for GlimmerHMM_glimmerT_55605-T1
Valid prediction for GeneMark_model.97017_t
Valid prediction for Augustus_model.g37106.t1
Valid prediction for GeneMark_model.97009_t
Valid prediction for snap_scaffold_25-snap.1330-T1
Valid prediction for Augustus_model.g37114.t1
Valid prediction for GeneMark_model.97042_t
Valid prediction for snap_scaffold_25-snap.1352-T1
Couldn't classify 155623, 155925
Sorry, prediction pasa_asmbl_33621.p3 fails validation.
(TGC)	 CA	155623-155925	CG	AAC
Valid prediction for GlimmerHMM_glimmerT_55609-T1
Valid prediction for pasa_asmbl_34329.p1
Valid prediction for snap_scaffold_25-snap.1338-T1
Valid prediction for GlimmerHMM_glimmerT_55604-T1
Valid prediction for GlimmerHMM_glimmerT_55627-T1
Valid prediction for snap_scaffold_25-snap.1370-T1
Valid prediction for snap_scaffold_25-snap.1341-T1
Valid prediction for snap_scaffold_25-snap.1358-T1
Valid prediction for GlimmerHMM_glimmerT_55603-T1
Valid prediction for GeneMark_model.97030_t
Valid prediction for GeneMark_model.97032_t
Valid prediction for GeneMark_model.97018_t
Valid prediction for Augustus_model.g37109.t1
Valid prediction for CodingQuarry_transcript_38677-T1
Valid prediction for snap_scaffold_25-snap.1364-T1
Valid prediction for snap_scaffold_25-snap.1347-T1
Valid prediction for GeneMark_model.97020_t
Valid prediction for GeneMark_model.97004_t
Valid prediction for GeneMark_model.97015_t
Valid prediction for snap_scaffold_25-snap.1356-T1
Valid prediction for GlimmerHMM_glimmerT_55621-T1
Valid prediction for snap_scaffold_25-snap.1346-T1
Valid prediction for snap_scaffold_25-snap.1342-T1
Valid prediction for snap_scaffold_25-snap.1337-T1
Valid prediction for HiQ_model.g37115.t1
Valid prediction for GlimmerHMM_glimmerT_55608-T1
Valid prediction for GeneMark_model.97040_t
Valid prediction for snap_scaffold_25-snap.1369-T1
Valid prediction for GeneMark_model.97041_t
Valid prediction for GeneMark_model.97025_t
Valid prediction for GeneMark_model.97013_t
Valid prediction for GeneMark_model.97027_t
Valid prediction for GeneMark_model.97034_t
Valid prediction for GeneMark_model.97006_t
Valid prediction for GeneMark_model.97029_t
Valid prediction for snap_scaffold_25-snap.1361-T1
Valid prediction for CodingQuarry_transcript_38676-T1
Valid prediction for GeneMark_model.97021_t
Valid prediction for GlimmerHMM_glimmerT_55619-T1
Valid prediction for snap_scaffold_25-snap.1339-T1
Valid prediction for Augustus_model.g37104.t1
Valid prediction for GeneMark_model.97046_t
Couldn't classify 104920, 105006
Sorry, prediction GeneMark_model.97022_t fails validation.
(CGT)	 AG	104920-105006	GT	AAG
(ACA)	 AG	105208-105309	CA	GAC
-recovered GeneMark_model.97022_t, terminal, 105208, 105309
-recovered GeneMark_model.97022_t, internal, 104920, 105006
Valid prediction for snap_scaffold_25-snap.1368-T1
Valid prediction for GlimmerHMM_glimmerT_55612-T1
Valid prediction for GlimmerHMM_glimmerT_55610-T1
Valid prediction for GlimmerHMM_glimmerT_55623-T1
Valid prediction for snap_scaffold_25-snap.1351-T1
Valid prediction for GlimmerHMM_glimmerT_55615-T1
Valid prediction for GeneMark_model.97036_t
Valid prediction for GeneMark_model.97003_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 97743, rend_intergenic: 90638  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115477, rend_intergenic: 113221  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123255, rend_intergenic: 119944  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 164754
-exon list size: 591


building trellis

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-found 33 predictions from path traversal
Error with prediction: snap lend_intergenic: 97743, rend_intergenic: 90638  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 115477, rend_intergenic: 113221  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 123255, rend_intergenic: 119944  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 27 predictions persist after filtering for low support