-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_2/scaffold_2_1766039-1892581

-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_3340-T1
Valid prediction for snap_scaffold_2-snap.437-T1
Valid prediction for GeneMark_model.5386_t
Valid prediction for snap_scaffold_2-snap.434-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GeneMark_model.5390_t
Valid prediction for GeneMark_model.5369_t
Valid prediction for snap_scaffold_2-snap.430-T1
Valid prediction for snap_scaffold_2-snap.412-T1
Valid prediction for snap_scaffold_2-snap.408-T1
Valid prediction for GeneMark_model.5364_t
Valid prediction for GlimmerHMM_glimmerT_3343-T1
Valid prediction for Augustus_model.g2239.t1
Valid prediction for snap_scaffold_2-snap.424-T1
Valid prediction for Augustus_model.g2235.t1
Valid prediction for GeneMark_model.5387_t
Valid prediction for GlimmerHMM_glimmerT_3346-T1
Valid prediction for GlimmerHMM_glimmerT_3335-T1
Valid prediction for snap_scaffold_2-snap.422-T1
Couldn't classify 83147, 83270
Couldn't classify 84555, 84676
Sorry, prediction pasa_asmbl_24248.p1 fails validation.
(ATC)	 AC	83147-83270	GT	AGG
(ATA)	 AG	83492-83617	GT	CGG
(ACG)	 AG	83845-83964	GT	AGG
(ATA)	 AG	84062-84193	GT	GGG
(ACG)	 AG	84555-84676	AC	AGA
-recovered pasa_asmbl_24248.p1, internal, 83492, 83617
-recovered pasa_asmbl_24248.p1, internal, 83845, 83964
-recovered pasa_asmbl_24248.p1, internal, 84062, 84193
Valid prediction for GeneMark_model.5361_t
Valid prediction for GeneMark_model.5374_t
Valid prediction for snap_scaffold_2-snap.409-T1
Valid prediction for GlimmerHMM_glimmerT_3342-T1
Valid prediction for Augustus_model.g2243.t1
Valid prediction for snap_scaffold_2-snap.407-T1
Couldn't classify 74844, 74962
Couldn't classify 82150, 82217
Sorry, prediction pasa_asmbl_24247.p1 fails validation.
(GCA)	 CA	74844-74962	GT	AGG
(GAT)	 AG	77480-77612	GT	AGG
(ATG)	 AG	79331-79475	GT	TGG
(CTT)	 AG	80779-80844	GT	AGG
(GTA)	 AG	81308-81397	GT	AGG
(ACA)	 AG	81782-81919	GT	AGG
(ATA)	 AG	82150-82217	TC	GCT
-recovered pasa_asmbl_24247.p1, initial, 79331, 79475
-recovered pasa_asmbl_24247.p1, internal, 77480, 77612
-recovered pasa_asmbl_24247.p1, internal, 79331, 79475
-recovered pasa_asmbl_24247.p1, internal, 80779, 80844
-recovered pasa_asmbl_24247.p1, internal, 81308, 81397
-recovered pasa_asmbl_24247.p1, internal, 81782, 81919
Valid prediction for GlimmerHMM_glimmerT_3341-T1
Valid prediction for Augustus_model.g2242.t1
Valid prediction for snap_scaffold_2-snap.436-T1
Valid prediction for GeneMark_model.5388_t
Valid prediction for GeneMark_model.5367_t
Valid prediction for Augustus_model.g2245.t1
Valid prediction for GeneMark_model.5380_t
Valid prediction for snap_scaffold_2-snap.415-T1
Valid prediction for GlimmerHMM_glimmerT_3345-T1
Valid prediction for snap_scaffold_2-snap.413-T1
Valid prediction for GlimmerHMM_glimmerT_3337-T1
Valid prediction for snap_scaffold_2-snap.416-T1
Valid prediction for GeneMark_model.5378_t
Valid prediction for snap_scaffold_2-snap.428-T1
Valid prediction for GlimmerHMM_glimmerT_3330-T1
Valid prediction for Augustus_model.g2240.t1
Valid prediction for GeneMark_model.5362_t
Valid prediction for snap_scaffold_2-snap.410-T1
Valid prediction for GlimmerHMM_glimmerT_3339-T1
Valid prediction for GeneMark_model.5382_t
Valid prediction for GeneMark_model.5372_t
Valid prediction for Augustus_model.g2244.t1
Valid prediction for GeneMark_model.5384_t
Valid prediction for snap_scaffold_2-snap.419-T1
Valid prediction for GeneMark_model.5376_t

-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 GlimmerHMM_glimmerT_3333-T1
Valid prediction for snap_scaffold_2-snap.427-T1
Valid prediction for GeneMark_model.5383_t
Valid prediction for snap_scaffold_2-snap.421-T1
Valid prediction for Augustus_model.g2236.t1
Couldn't classify 69296, 69367
Couldn't classify 70109, 70183
Sorry, prediction pasa_asmbl_24062.p1 fails validation.
(GTA)	 AA	69296-69367	GT	AGG
(CTG)	 AG	69452-69568	GT	AGG
(CCT)	 AG	69684-69761	GT	AGG
(GCA)	 AG	70109-70183	CT	AGC
-recovered pasa_asmbl_24062.p1, internal, 69452, 69568
-recovered pasa_asmbl_24062.p1, internal, 69684, 69761
Valid prediction for GeneMark_model.5360_t
Valid prediction for snap_scaffold_2-snap.438-T1
Valid prediction for snap_scaffold_2-snap.435-T1
Valid prediction for GlimmerHMM_glimmerT_3332-T1
Valid prediction for GeneMark_model.5371_t
Valid prediction for CodingQuarry_transcript_28405-T1
Valid prediction for GeneMark_model.5370_t
Valid prediction for GeneMark_model.5381_t
Couldn't classify 108757, 108840
Couldn't classify 109522, 109633
Sorry, prediction pasa_asmbl_22896.p1 fails validation.
(CCA)	 CC	108757-108840	GT	TGG
(GTG)	 AG	109196-109320	GT	CGG
(GTC)	 AG	109522-109633	AA	GCA
-recovered pasa_asmbl_22896.p1, internal, 109196, 109320
Valid prediction for Augustus_model.g2237.t1
Valid prediction for Augustus_model.g2238.t1
Valid prediction for snap_scaffold_2-snap.433-T1
Valid prediction for Augustus_model.g2233.t1
Valid prediction for snap_scaffold_2-snap.431-T1
Valid prediction for snap_scaffold_2-snap.425-T1
Valid prediction for GeneMark_model.5385_t
Valid prediction for snap_scaffold_2-snap.411-T1
Valid prediction for GeneMark_model.5365_t
Valid prediction for GlimmerHMM_glimmerT_3334-T1
Valid prediction for GeneMark_model.5389_t
Valid prediction for snap_scaffold_2-snap.414-T1
Valid prediction for snap_scaffold_2-snap.420-T1
Valid prediction for Augustus_model.g2234.t1
Valid prediction for GlimmerHMM_glimmerT_3338-T1
Valid prediction for snap_scaffold_2-snap.423-T1
Valid prediction for GeneMark_model.5379_t
Valid prediction for snap_scaffold_2-snap.441-T1
Valid prediction for snap_scaffold_2-snap.417-T1
Valid prediction for GlimmerHMM_glimmerT_3344-T1
Valid prediction for snap_scaffold_2-snap.439-T1
Valid prediction for GlimmerHMM_glimmerT_3331-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GeneMark_model.5366_t
Valid prediction for Augustus_model.g2241.t1
Valid prediction for GlimmerHMM_glimmerT_3329-T1
Valid prediction for GeneMark_model.5377_t
Valid prediction for GeneMark_model.5373_t
Valid prediction for snap_scaffold_2-snap.432-T1
Valid prediction for snap_scaffold_2-snap.426-T1
Couldn't classify 121582, 121743
Couldn't classify 123321, 123556
Sorry, prediction pasa_asmbl_22894.p1 fails validation.
(GAG)	 GA	121582-121743	GT	TGG
(TGG)	 AG	121922-122215	GT	AGG
(GTG)	 AG	122681-122879	GT	AGG
(GAG)	 AG	123321-123556	CT	CCC
add_exon() Sorry, pasa_asmbl_22894.p1 122681-122879-terminal-3 is invalid.
-recovered pasa_asmbl_22894.p1, terminal, 122681, 122879
-recovered pasa_asmbl_22894.p1, internal, 121922, 122215
-recovered pasa_asmbl_22894.p1, internal, 122681, 122879
Valid prediction for GeneMark_model.5375_t
Valid prediction for snap_scaffold_2-snap.418-T1
Valid prediction for GlimmerHMM_glimmerT_3336-T1
Valid prediction for GeneMark_model.5368_t
Valid prediction for snap_scaffold_2-snap.429-T1
Valid prediction for GeneMark_model.5363_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 37714, rend_intergenic: 33776  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47693, rend_intergenic: 43515  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75352, rend_intergenic: 74443  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86916, rend_intergenic: 77249  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87656, rend_intergenic: 86923  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89684, rend_intergenic: 88356  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94200, rend_intergenic: 91178  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100179, rend_intergenic: 99810  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103473, rend_intergenic: 100359  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 126543
-exon list size: 623


building trellis

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-found 27 predictions from path traversal
Error with prediction: snap lend_intergenic: 37714, rend_intergenic: 33776  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47693, rend_intergenic: 43515  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75352, rend_intergenic: 74443  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 86916, rend_intergenic: 77249  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87656, rend_intergenic: 86923  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89684, rend_intergenic: 88356  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 94200, rend_intergenic: 91178  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 100179, rend_intergenic: 99810  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 103473, rend_intergenic: 100359  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support