-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_11/scaffold_11_17109469-17306235

-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 snap_scaffold_11-snap.3549-T1
Valid prediction for GlimmerHMM_glimmerT_29201-T1
Valid prediction for GlimmerHMM_glimmerT_29208-T1
Valid prediction for HiQ_model.g19495.t1
Valid prediction for GeneMark_model.50428_t
Valid prediction for GeneMark_model.50413_t
Valid prediction for snap_scaffold_11-snap.3515-T1
Valid prediction for GlimmerHMM_glimmerT_29213-T1
Valid prediction for HiQ_model.g19492.t1
Valid prediction for snap_scaffold_11-snap.3543-T1
Valid prediction for GeneMark_model.50417_t
Valid prediction for GlimmerHMM_glimmerT_29215-T1
Valid prediction for GlimmerHMM_glimmerT_29204-T1
Valid prediction for snap_scaffold_11-snap.3522-T1
Valid prediction for snap_scaffold_11-snap.3528-T1
Valid prediction for GeneMark_model.50439_t
Valid prediction for snap_scaffold_11-snap.3537-T1
Valid prediction for GeneMark_model.50437_t
Valid prediction for Augustus_model.g19488.t1
Valid prediction for Augustus_model.g19490.t1
Valid prediction for GlimmerHMM_glimmerT_29206-T1
Couldn't classify 93775, 93831
Sorry, prediction pasa_asmbl_6184.p1 fails validation.
(ACT)	 AC	93775-93831	GT	AGG
(GTG)	 AG	93922-94183	GT	AGG
(AGT)	 AG	94301-94578	GC	AGG
-recovered pasa_asmbl_6184.p1, terminal, 94301, 94578
-recovered pasa_asmbl_6184.p1, internal, 93922, 94183
-recovered pasa_asmbl_6184.p1, internal, 94301, 94578
Valid prediction for GlimmerHMM_glimmerT_29225-T1
Valid prediction for GeneMark_model.50435_t
Valid prediction for snap_scaffold_11-snap.3514-T1
Valid prediction for Augustus_model.g19502.t1
Valid prediction for GeneMark_model.50421_t
Valid prediction for GeneMark_model.50412_t
Valid prediction for Augustus_model.g19493.t1
Valid prediction for GlimmerHMM_glimmerT_29219-T1
Valid prediction for GeneMark_model.50405_t
Couldn't classify 108328, 108459
Couldn't classify 109908, 110027
Sorry, prediction pasa_asmbl_6185.p1 fails validation.
(GGT)	 CA	108328-108459	GT	AGG
(GTG)	 AG	108711-108881	GT	ATG
(GAG)	 AG	109145-109285	GT	AGG
(GTG)	 AG	109908-110027	CA	TCC
-recovered pasa_asmbl_6185.p1, internal, 108711, 108881
-recovered pasa_asmbl_6185.p1, internal, 109145, 109285
Valid prediction for snap_scaffold_11-snap.3525-T1
Valid prediction for GeneMark_model.50448_t
Valid prediction for GeneMark_model.50423_t
Valid prediction for Augustus_model.g19489.t1
Valid prediction for snap_scaffold_11-snap.3548-T1
Valid prediction for snap_scaffold_11-snap.3542-T1
Valid prediction for GlimmerHMM_glimmerT_29224-T1
Valid prediction for snap_scaffold_11-snap.3535-T1
Valid prediction for Augustus_model.g19497.t1
Valid prediction for snap_scaffold_11-snap.3531-T1
Valid prediction for GeneMark_model.50442_t
Valid prediction for Augustus_model.g19487.t1
Valid prediction for snap_scaffold_11-snap.3510-T1
Valid prediction for snap_scaffold_11-snap.3546-T1
Valid prediction for snap_scaffold_11-snap.3539-T1
Valid prediction for snap_scaffold_11-snap.3524-T1
Valid prediction for GeneMark_model.50411_t
Valid prediction for GeneMark_model.50403_t
Valid prediction for GeneMark_model.50426_t
Valid prediction for snap_scaffold_11-snap.3544-T1
Valid prediction for GeneMark_model.50444_t
Couldn't classify 101524, 101558
Couldn't classify 104775, 104927
Sorry, prediction pasa_asmbl_6314.p2 fails validation.
(CTG)	 AT	101524-101558	GT	AGG
(GAG)	 AG	101788-101902	GT	AGG
(GTC)	 AG	104775-104927	CT	AGC
-recovered pasa_asmbl_6314.p2, internal, 101788, 101902
Valid prediction for Augustus_model.g19501.t1
Valid prediction for GeneMark_model.50409_t
Valid prediction for GlimmerHMM_glimmerT_29222-T1
Valid prediction for snap_scaffold_11-snap.3523-T1
Valid prediction for snap_scaffold_11-snap.3530-T1
Valid prediction for GeneMark_model.50446_t
Valid prediction for GeneMark_model.50425_t
Valid prediction for snap_scaffold_11-snap.3519-T1
Valid prediction for GeneMark_model.50429_t
Valid prediction for GeneMark_model.50419_t
Valid prediction for GeneMark_model.50432_t
Valid prediction for snap_scaffold_11-snap.3513-T1
Valid prediction for GlimmerHMM_glimmerT_29212-T1
Valid prediction for GlimmerHMM_glimmerT_29211-T1
Valid prediction for GlimmerHMM_glimmerT_29203-T1
Valid prediction for GeneMark_model.50422_t
Valid prediction for GlimmerHMM_glimmerT_29214-T1
Valid prediction for GeneMark_model.50415_t
Valid prediction for CodingQuarry_transcript_8331-T1
Valid prediction for GlimmerHMM_glimmerT_29217-T1
Valid prediction for snap_scaffold_11-snap.3521-T1
Valid prediction for snap_scaffold_11-snap.3540-T1
Valid prediction for GlimmerHMM_glimmerT_29210-T1
Valid prediction for GeneMark_model.50407_t
Valid prediction for snap_scaffold_11-snap.3534-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.g19491.t1
Valid prediction for GlimmerHMM_glimmerT_29223-T1
Valid prediction for GeneMark_model.50420_t
Valid prediction for snap_scaffold_11-snap.3536-T1
Valid prediction for snap_scaffold_11-snap.3517-T1
Valid prediction for GeneMark_model.50430_t
Valid prediction for GeneMark_model.50447_t
Valid prediction for Augustus_model.g19503.t1
Valid prediction for Augustus_model.g19498.t1
Valid prediction for GeneMark_model.50443_t
Valid prediction for pasa_asmbl_7235.p1
Valid prediction for snap_scaffold_11-snap.3527-T1
Valid prediction for GeneMark_model.50445_t
Valid prediction for snap_scaffold_11-snap.3538-T1
Valid prediction for GlimmerHMM_glimmerT_29209-T1
Valid prediction for GlimmerHMM_glimmerT_29221-T1
Valid prediction for snap_scaffold_11-snap.3529-T1
Valid prediction for GlimmerHMM_glimmerT_29207-T1
Valid prediction for GeneMark_model.50402_t
Valid prediction for snap_scaffold_11-snap.3511-T1
Valid prediction for GeneMark_model.50434_t
Valid prediction for Augustus_model.g19499.t1
Valid prediction for GlimmerHMM_glimmerT_29226-T1
Valid prediction for snap_scaffold_11-snap.3509-T1
Valid prediction for GeneMark_model.50414_t
Valid prediction for Augustus_model.g19500.t1
Valid prediction for snap_scaffold_11-snap.3508-T1
Valid prediction for GeneMark_model.50449_t
Valid prediction for GeneMark_model.50418_t
Valid prediction for GeneMark_model.50441_t
Valid prediction for Augustus_model.g19494.t1
Valid prediction for snap_scaffold_11-snap.3533-T1
Couldn't classify 6972, 7163
Sorry, prediction pasa_asmbl_7240.p1 fails validation.
(CCT)	 CC	6972-7163	GT	TGG
(TTT)	 AG	8128-8238	GT	AGG
(CTC)	 AG	8444-8536	GT	AGG
(CTT)	 AG	8725-8855	GT	AGG
(GTT)	 AG	9038-9097	GT	AGG
(TAT)	 AG	9723-9831	GT	AGG
(CTG)	 AG	10015-10068	GT	CGG
(GTG)	 AG	10216-10386	GT	AGG
(GTG)	 AG	10562-10689	GT	AAG
(GAC)	 AG	11572-11673	GT	AAG
(AGA)	 AG	11845-11917	GT	AGG
(CTC)	 AG	12674-12808	AC	AGA
add_exon() Sorry, pasa_asmbl_7240.p1 11572-11673-terminal-1 is invalid.
-recovered pasa_asmbl_7240.p1, terminal, 11572, 11673
-recovered pasa_asmbl_7240.p1, terminal, 12674, 12808
-recovered pasa_asmbl_7240.p1, internal, 8128, 8238
-recovered pasa_asmbl_7240.p1, internal, 8444, 8536
-recovered pasa_asmbl_7240.p1, internal, 8725, 8855
-recovered pasa_asmbl_7240.p1, internal, 9038, 9097
-recovered pasa_asmbl_7240.p1, internal, 9723, 9831
-recovered pasa_asmbl_7240.p1, internal, 10015, 10068
-recovered pasa_asmbl_7240.p1, internal, 10216, 10386
-recovered pasa_asmbl_7240.p1, internal, 10562, 10689
-recovered pasa_asmbl_7240.p1, internal, 11572, 11673
-recovered pasa_asmbl_7240.p1, internal, 11845, 11917
Valid prediction for snap_scaffold_11-snap.3518-T1
Valid prediction for snap_scaffold_11-snap.3547-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_11-snap.3512-T1
Valid prediction for GeneMark_model.50406_t
Valid prediction for snap_scaffold_11-snap.3541-T1
Valid prediction for GlimmerHMM_glimmerT_29202-T1
Valid prediction for GeneMark_model.50440_t
Valid prediction for GeneMark_model.50433_t
Valid prediction for snap_scaffold_11-snap.3545-T1
Valid prediction for GeneMark_model.50410_t
Valid prediction for GeneMark_model.50408_t
Valid prediction for GlimmerHMM_glimmerT_29220-T1
Couldn't classify 109139, 109543
Sorry, prediction pasa_asmbl_7232.p1 fails validation.
(GGC)	 TG	109139-109543	TC	TGT
Valid prediction for GeneMark_model.50416_t
Valid prediction for GeneMark_model.50427_t
Valid prediction for snap_scaffold_11-snap.3516-T1
Valid prediction for GlimmerHMM_glimmerT_29218-T1
Valid prediction for CodingQuarry_transcript_8332-T1
Valid prediction for snap_scaffold_11-snap.3532-T1
Valid prediction for HiQ_model.g19496.t1
Valid prediction for GeneMark_model.50438_t
Valid prediction for snap_scaffold_11-snap.3526-T1
Valid prediction for GlimmerHMM_glimmerT_29205-T1
Valid prediction for snap_scaffold_11-snap.3520-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GeneMark_model.50404_t
Valid prediction for GlimmerHMM_glimmerT_29216-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 9880, rend_intergenic: 7987  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22487, rend_intergenic: 13334  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31769, rend_intergenic: 22907  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40512, rend_intergenic: 34640  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43228, rend_intergenic: 40765  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66341, rend_intergenic: 49074  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83126, rend_intergenic: 78248  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110129, rend_intergenic: 105168  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120962, rend_intergenic: 112885  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125156, rend_intergenic: 123834  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135535, rend_intergenic: 130050  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181235, rend_intergenic: 177477  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 194204, rend_intergenic: 185187  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 94578, rend_intergenic: 94575  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 196767
-exon list size: 602


building trellis

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-found 32 predictions from path traversal
Error with prediction: snap lend_intergenic: 9880, rend_intergenic: 7987  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 22487, rend_intergenic: 13334  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 31769, rend_intergenic: 22907  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 40512, rend_intergenic: 34640  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 43228, rend_intergenic: 40765  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 66341, rend_intergenic: 49074  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 83126, rend_intergenic: 78248  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 110129, rend_intergenic: 105168  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 120962, rend_intergenic: 112885  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 125156, rend_intergenic: 123834  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135535, rend_intergenic: 130050  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 181235, rend_intergenic: 177477  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 194204, rend_intergenic: 185187  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: GlimmerHMM lend_intergenic: 94578, rend_intergenic: 94575  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 17 predictions persist after filtering for low support