-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_4/scaffold_4_19204306-19332879

-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 49214, 49243
Sorry, prediction pasa_asmbl_43477.p1 fails validation.
(AGG)	 AG	49214-49243	GT	TGG
(ATG)	 AG	49974-50180	GT	AGG
(AAG)	 AG	50414-50560	GT	GGG
(GTG)	 AG	51744-51992	TG	AGT
-recovered pasa_asmbl_43477.p1, initial, 49974, 50180
-recovered pasa_asmbl_43477.p1, terminal, 51744, 51992
-recovered pasa_asmbl_43477.p1, internal, 49214, 49243
-recovered pasa_asmbl_43477.p1, internal, 49974, 50180
-recovered pasa_asmbl_43477.p1, internal, 50414, 50560
Valid prediction for GeneMark_model.19038_t
Valid prediction for GlimmerHMM_glimmerT_11493-T1
Valid prediction for GlimmerHMM_glimmerT_11477-T1
Valid prediction for CodingQuarry_transcript_49288-T1
Valid prediction for Augustus_model.g7585.t1
Valid prediction for GeneMark_model.19058_t
Valid prediction for Augustus_model.g7586.t1
Couldn't classify 73313, 73990
Sorry, prediction pasa_asmbl_43478.p1 fails validation.
(ATG)	 AA	73313-73990	AG	GGA
Valid prediction for GlimmerHMM_glimmerT_11475-T1
Valid prediction for GeneMark_model.19034_t
Valid prediction for GlimmerHMM_glimmerT_11491-T1
Valid prediction for GeneMark_model.19055_t
Valid prediction for GlimmerHMM_glimmerT_11487-T1
Valid prediction for GeneMark_model.19031_t
Valid prediction for snap_scaffold_4-snap.3954-T1
Valid prediction for snap_scaffold_4-snap.3964-T1
Valid prediction for GlimmerHMM_glimmerT_11476-T1
Valid prediction for HiQ_model.g7576.t1
Valid prediction for snap_scaffold_4-snap.3967-T1
Valid prediction for Augustus_model.g7581.t1
Valid prediction for GeneMark_model.19053_t
Valid prediction for GeneMark_model.19033_t
Valid prediction for GlimmerHMM_glimmerT_11494-T1
Valid prediction for GeneMark_model.19049_t
Valid prediction for snap_scaffold_4-snap.3960-T1
Valid prediction for Augustus_model.g7584.t1
Valid prediction for GeneMark_model.19036_t
Couldn't classify 47078, 47202
Couldn't classify 49046, 49063
Sorry, prediction pasa_asmbl_43555.p1 fails validation.
(GCC)	 AG	47078-47202	GT	CTG
(GGT)	 AG	48367-48523	GT	CAG
(GAG)	 AG	49046-49063	GT	ACG
-recovered pasa_asmbl_43555.p1, internal, 47078, 47202
-recovered pasa_asmbl_43555.p1, internal, 48367, 48523
-recovered pasa_asmbl_43555.p1, internal, 49046, 49063
Valid prediction for GeneMark_model.19059_t
Valid prediction for GeneMark_model.19051_t
Valid prediction for snap_scaffold_4-snap.3948-T1
Valid prediction for snap_scaffold_4-snap.3963-T1
Valid prediction for snap_scaffold_4-snap.3969-T1
Valid prediction for snap_scaffold_4-snap.3952-T1
Valid prediction for pasa_asmbl_43474.p1
Valid prediction for GlimmerHMM_glimmerT_11481-T1
Valid prediction for Augustus_model.g7578.t1
Valid prediction for GlimmerHMM_glimmerT_11483-T1
Valid prediction for GeneMark_model.19028_t
Valid prediction for GeneMark_model.19042_t
Valid prediction for GlimmerHMM_glimmerT_11495-T1
Valid prediction for snap_scaffold_4-snap.3951-T1
Valid prediction for GeneMark_model.19062_t
Valid prediction for snap_scaffold_4-snap.3968-T1
Sorry, intron length (8) is less than minimum required (10)
Valid prediction for GeneMark_model.19044_t
Valid prediction for GeneMark_model.19060_t
Valid prediction for GeneMark_model.19029_t
Valid prediction for snap_scaffold_4-snap.3965-T1
Valid prediction for snap_scaffold_4-snap.3955-T1
Valid prediction for snap_scaffold_4-snap.3959-T1
Valid prediction for snap_scaffold_4-snap.3971-T1
Couldn't classify 37780, 37869
Couldn't classify 40372, 40380
Sorry, prediction pasa_asmbl_43476.p1 fails validation.
(TCA)	 AC	37780-37869	GT	AGG
(GTT)	 AG	38672-38797	GT	CGG
(GTG)	 AG	39231-39434	GT	ACG
(AAG)	 AG	39807-39977	GT	AGG
(GTC)	 AG	40372-40380	GG	AAG
-recovered pasa_asmbl_43476.p1, internal, 38672, 38797
-recovered pasa_asmbl_43476.p1, internal, 39231, 39434
-recovered pasa_asmbl_43476.p1, internal, 39807, 39977
Valid prediction for GeneMark_model.19026_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 snap_scaffold_4-snap.3957-T1
Valid prediction for Augustus_model.g7579.t1
Valid prediction for snap_scaffold_4-snap.3970-T1
Valid prediction for snap_scaffold_4-snap.3953-T1
Valid prediction for GeneMark_model.19037_t
Valid prediction for GeneMark_model.19043_t
Valid prediction for Augustus_model.g7580.t1
Couldn't classify 56535, 56636
Sorry, prediction pasa_asmbl_42172.p1 fails validation.
(GAT)	 GT	56535-56636	GT	AGG
(GCT)	 AG	57636-57753	GT	TGG
(ATA)	 AG	57984-58046	GT	AGG
(GGA)	 AG	58225-58298	GA	GAG
-recovered pasa_asmbl_42172.p1, terminal, 58225, 58298
-recovered pasa_asmbl_42172.p1, internal, 57636, 57753
-recovered pasa_asmbl_42172.p1, internal, 57984, 58046
Couldn't classify 124412, 124741
Sorry, prediction pasa_asmbl_42167.p1 fails validation.
(GTG)	 AG	124412-124741	GT	TGG
-recovered pasa_asmbl_42167.p1, internal, 124412, 124741
Valid prediction for GeneMark_model.19040_t
Valid prediction for GlimmerHMM_glimmerT_11488-T1
Valid prediction for GeneMark_model.19047_t
Valid prediction for Augustus_model.g7583.t1
Valid prediction for Augustus_model.g7575.t1
Valid prediction for GeneMark_model.19027_t
Valid prediction for GeneMark_model.19056_t
Valid prediction for Augustus_model.g7587.t1
Valid prediction for GlimmerHMM_glimmerT_11474-T1
Valid prediction for GlimmerHMM_glimmerT_11478-T1
Valid prediction for GeneMark_model.19054_t
Valid prediction for snap_scaffold_4-snap.3961-T1
Valid prediction for GeneMark_model.19039_t
Valid prediction for CodingQuarry_transcript_49290-T1
Valid prediction for Augustus_model.g7582.t1
Valid prediction for snap_scaffold_4-snap.3966-T1
Valid prediction for Augustus_model.g7577.t1
Valid prediction for GlimmerHMM_glimmerT_11496-T1
Couldn't classify 68606, 68678
Sorry, prediction pasa_asmbl_42310.p1 fails validation.
(ATG)	 AA	66713-66827	GT	AGG
(TTC)	 AG	66920-67044	GT	GGG
(TTG)	 AG	67263-67444	GT	ACG
(AGA)	 AG	67727-67851	GT	AGG
(AGA)	 AG	67985-68093	GT	CGG
(TCA)	 AG	68606-68678	GA	ACG
-recovered pasa_asmbl_42310.p1, initial, 66713, 66827
-recovered pasa_asmbl_42310.p1, internal, 66920, 67044
-recovered pasa_asmbl_42310.p1, internal, 67263, 67444
-recovered pasa_asmbl_42310.p1, internal, 67727, 67851
-recovered pasa_asmbl_42310.p1, internal, 67985, 68093
Valid prediction for GeneMark_model.19048_t
Valid prediction for snap_scaffold_4-snap.3949-T1
Couldn't classify 124994, 125293
Sorry, prediction pasa_asmbl_42166.p2 fails validation.
(GAG)	 GT	124994-125293	GG	GAG
Valid prediction for GeneMark_model.19030_t
Valid prediction for GeneMark_model.19045_t
Valid prediction for snap_scaffold_4-snap.3956-T1
Valid prediction for GeneMark_model.19061_t
Valid prediction for GeneMark_model.19052_t
Valid prediction for GlimmerHMM_glimmerT_11490-T1
Valid prediction for GlimmerHMM_glimmerT_11479-T1
Valid prediction for snap_scaffold_4-snap.3950-T1
Valid prediction for GlimmerHMM_glimmerT_11486-T1
Couldn't classify 61310, 61428
Couldn't classify 62919, 63252
Sorry, prediction pasa_asmbl_42169.p1 fails validation.
(GAT)	 GA	61310-61428	GT	AGG
(GTA)	 AG	62919-63252	GA	AGG
Valid prediction for GeneMark_model.19050_t
Valid prediction for snap_scaffold_4-snap.3962-T1
Valid prediction for GeneMark_model.19032_t
Valid prediction for GlimmerHMM_glimmerT_11480-T1
Valid prediction for snap_scaffold_4-snap.3958-T1
Valid prediction for GeneMark_model.19041_t
Valid prediction for GlimmerHMM_glimmerT_11492-T1
Valid prediction for GlimmerHMM_glimmerT_11484-T1
Valid prediction for GlimmerHMM_glimmerT_11485-T1
Valid prediction for GlimmerHMM_glimmerT_11482-T1
Valid prediction for GeneMark_model.19035_t
Valid prediction for CodingQuarry_transcript_49289-T1
Valid prediction for GeneMark_model.19046_t
Valid prediction for GeneMark_model.19063_t
Valid prediction for GlimmerHMM_glimmerT_11489-T1
Valid prediction for GeneMark_model.19057_t

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 13218, rend_intergenic: 10001  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27206, rend_intergenic: 16661  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30396, rend_intergenic: 29129  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51992, rend_intergenic: 32524  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61862, rend_intergenic: 55129  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65576, rend_intergenic: 63078  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83923, rend_intergenic: 75902  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87533, rend_intergenic: 86460  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102506, rend_intergenic: 88150  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126223, rend_intergenic: 107853  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 128574
-exon list size: 508


building trellis

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-found 17 predictions from path traversal
Error with prediction: snap lend_intergenic: 13218, rend_intergenic: 10001  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 27206, rend_intergenic: 16661  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 30396, rend_intergenic: 29129  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 51992, rend_intergenic: 32524  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61862, rend_intergenic: 55129  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 65576, rend_intergenic: 63078  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83923, rend_intergenic: 75902  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 87533, rend_intergenic: 86460  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 102506, rend_intergenic: 88150  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126223, rend_intergenic: 107853  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 14 predictions persist after filtering for low support