-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_17/scaffold_17_8910326-9136232

-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 GeneMark_model.71795_t
Valid prediction for snap_scaffold_17-snap.1811-T1
Valid prediction for snap_scaffold_17-snap.1783-T1
Valid prediction for CodingQuarry_transcript_22052-T1
Valid prediction for snap_scaffold_17-snap.1782-T1
Valid prediction for GlimmerHMM_glimmerT_41711-T1
Valid prediction for pasa_asmbl_18186.p1
Valid prediction for snap_scaffold_17-snap.1810-T1
Valid prediction for snap_scaffold_17-snap.1779-T1
Valid prediction for Augustus_model.g27952.t1
Valid prediction for GeneMark_model.71785_t
Valid prediction for snap_scaffold_17-snap.1790-T1
Valid prediction for GlimmerHMM_glimmerT_41714-T1
Valid prediction for GeneMark_model.71821_t
Valid prediction for snap_scaffold_17-snap.1788-T1
Valid prediction for Augustus_model.g27957.t1
Valid prediction for snap_scaffold_17-snap.1791-T1
Valid prediction for GlimmerHMM_glimmerT_41716-T1
Valid prediction for snap_scaffold_17-snap.1781-T1
Valid prediction for GlimmerHMM_glimmerT_41715-T1
Valid prediction for Augustus_model.g27967.t1
Valid prediction for snap_scaffold_17-snap.1813-T1
Valid prediction for Augustus_model.g27958.t1
Valid prediction for GeneMark_model.71790_t
Valid prediction for GeneMark_model.71793_t
Valid prediction for snap_scaffold_17-snap.1787-T1
Valid prediction for GlimmerHMM_glimmerT_41709-T1
Valid prediction for CodingQuarry_transcript_22051-T1
Valid prediction for GlimmerHMM_glimmerT_41719-T1
Valid prediction for snap_scaffold_17-snap.1812-T1
Valid prediction for Augustus_model.g27960.t1
Valid prediction for snap_scaffold_17-snap.1777-T1
Valid prediction for GlimmerHMM_glimmerT_41706-T1
Valid prediction for HiQ_model.g27959.t1
Valid prediction for HiQ_model.g27965.t1
Valid prediction for Augustus_model.g27962.t1
Valid prediction for GeneMark_model.71776_t
Valid prediction for pasa_asmbl_18181.p1
Valid prediction for GeneMark_model.71791_t
Valid prediction for Augustus_model.g27951.t1
Valid prediction for GlimmerHMM_glimmerT_41712-T1
Couldn't classify 51551, 51646
Sorry, prediction pasa_asmbl_18176.p2 fails validation.
(ATG)	 CC	50376-50437	GT	TGG
(TGG)	 AG	50546-50767	GT	CTG
(GAT)	 AG	51054-51192	GT	AGG
(CCG)	 AG	51551-51646	TA	AGT
-recovered pasa_asmbl_18176.p2, initial, 50376, 50437
-recovered pasa_asmbl_18176.p2, internal, 50546, 50767
-recovered pasa_asmbl_18176.p2, internal, 51054, 51192
Valid prediction for GeneMark_model.71817_t
Valid prediction for snap_scaffold_17-snap.1800-T1
Valid prediction for snap_scaffold_17-snap.1793-T1
Valid prediction for CodingQuarry_transcript_22054-T1
Valid prediction for GeneMark_model.71818_t
Valid prediction for CodingQuarry_transcript_22055-T1
Valid prediction for snap_scaffold_17-snap.1795-T1
Valid prediction for snap_scaffold_17-snap.1774-T1
Valid prediction for GlimmerHMM_glimmerT_41704-T1
Valid prediction for GeneMark_model.71805_t
Valid prediction for Augustus_model.g27954.t1
Valid prediction for pasa_asmbl_18175.p1
Couldn't classify 53418, 53563
Sorry, prediction pasa_asmbl_18177.p1 fails validation.
(GGG)	 GT	53418-53563	GT	ACG
(AGA)	 AG	54290-54335	GT	AGG
(CCA)	 AG	54729-54818	GT	AAG
(ATG)	 AG	55474-55560	GT	TGG
(AGA)	 AG	55635-55715	AT	AGA
-recovered pasa_asmbl_18177.p1, initial, 55474, 55560
-recovered pasa_asmbl_18177.p1, terminal, 55635, 55715
-recovered pasa_asmbl_18177.p1, internal, 54290, 54335
-recovered pasa_asmbl_18177.p1, internal, 54729, 54818
-recovered pasa_asmbl_18177.p1, internal, 55474, 55560
Valid prediction for GlimmerHMM_glimmerT_41730-T1
Valid prediction for snap_scaffold_17-snap.1776-T1
Valid prediction for GeneMark_model.71813_t
Valid prediction for GlimmerHMM_glimmerT_41717-T1
Valid prediction for snap_scaffold_17-snap.1775-T1
Valid prediction for GlimmerHMM_glimmerT_41705-T1
Valid prediction for snap_scaffold_17-snap.1798-T1
Valid prediction for GlimmerHMM_glimmerT_41722-T1
Valid prediction for Augustus_model.g27950.t1
Valid prediction for GlimmerHMM_glimmerT_41707-T1
Valid prediction for snap_scaffold_17-snap.1808-T1
Valid prediction for GeneMark_model.71801_t
Valid prediction for GlimmerHMM_glimmerT_41713-T1
Valid prediction for GeneMark_model.71797_t
Valid prediction for Augustus_model.g27956.t1
Valid prediction for GeneMark_model.71814_t
Valid prediction for GeneMark_model.71811_t
Valid prediction for CodingQuarry_transcript_22053-T1
Valid prediction for GeneMark_model.71788_t
Valid prediction for GeneMark_model.71783_t
Valid prediction for GeneMark_model.71779_t
Valid prediction for GeneMark_model.71815_t
Valid prediction for GeneMark_model.71778_t
Valid prediction for GeneMark_model.71787_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 Augustus_model.g27961.t1
Valid prediction for snap_scaffold_17-snap.1786-T1
Valid prediction for GeneMark_model.71810_t
Valid prediction for GlimmerHMM_glimmerT_41726-T1
Valid prediction for CodingQuarry_transcript_22057-T1
Couldn't classify 59163, 59720
Sorry, prediction pasa_asmbl_19195.p1 fails validation.
(GAT)	 CT	59163-59720	GA	CAG
Couldn't classify 59820, 59955
Sorry, prediction pasa_asmbl_19194.p1 fails validation.
(CCC)	 AC	59820-59955	GT	AGG
(ATG)	 AG	61818-61925	GT	AGG
(ACG)	 AG	62143-62301	GT	CAG
(CCA)	 AG	62385-62467	GT	TAG
(CTT)	 AG	62595-62739	GT	ATG
(CCT)	 AG	62866-63048	GT	AGG
(GGG)	 AG	63236-63351	AT	AAA
-recovered pasa_asmbl_19194.p1, initial, 61818, 61925
-recovered pasa_asmbl_19194.p1, terminal, 63236, 63351
-recovered pasa_asmbl_19194.p1, internal, 61818, 61925
-recovered pasa_asmbl_19194.p1, internal, 62143, 62301
-recovered pasa_asmbl_19194.p1, internal, 62385, 62467
-recovered pasa_asmbl_19194.p1, internal, 62595, 62739
-recovered pasa_asmbl_19194.p1, internal, 62866, 63048
Valid prediction for GlimmerHMM_glimmerT_41718-T1
Valid prediction for snap_scaffold_17-snap.1801-T1
Valid prediction for GeneMark_model.71809_t
Valid prediction for GeneMark_model.71777_t
Valid prediction for CodingQuarry_transcript_22060-T1
Valid prediction for CodingQuarry_transcript_22056-T1
Valid prediction for GeneMark_model.71796_t
Valid prediction for GlimmerHMM_glimmerT_41727-T1
Valid prediction for CodingQuarry_transcript_22059-T1
Valid prediction for pasa_asmbl_19196.p1
Valid prediction for snap_scaffold_17-snap.1784-T1
Valid prediction for GlimmerHMM_glimmerT_41729-T1
Valid prediction for GeneMark_model.71806_t
Valid prediction for GeneMark_model.71800_t
Valid prediction for snap_scaffold_17-snap.1802-T1
Valid prediction for snap_scaffold_17-snap.1806-T1
Valid prediction for CodingQuarry_transcript_22061-T1
Valid prediction for HiQ_model.g27970.t1
Valid prediction for CodingQuarry_transcript_22058-T1
Valid prediction for Augustus_model.g27953.t1
Valid prediction for GlimmerHMM_glimmerT_41725-T1
Valid prediction for snap_scaffold_17-snap.1797-T1
Couldn't classify 23044, 23112
Couldn't classify 26451, 26490
Sorry, prediction pasa_asmbl_19205.p1 fails validation.
(GAA)	 CA	23044-23112	GT	AGG
(GAT)	 AG	23654-23759	GT	GGG
(CTC)	 AG	24580-24674	GT	AGG
(TTT)	 AG	24891-25002	GT	AGG
(GCA)	 AG	25114-25208	GT	AGG
(ACC)	 AG	25338-25481	GT	AGG
(GCG)	 AG	25631-25869	GT	AGG
(TCT)	 AG	26451-26490	GT	CTG
-recovered pasa_asmbl_19205.p1, internal, 23654, 23759
-recovered pasa_asmbl_19205.p1, internal, 24580, 24674
-recovered pasa_asmbl_19205.p1, internal, 24891, 25002
-recovered pasa_asmbl_19205.p1, internal, 25114, 25208
-recovered pasa_asmbl_19205.p1, internal, 25338, 25481
-recovered pasa_asmbl_19205.p1, internal, 25631, 25869
-recovered pasa_asmbl_19205.p1, internal, 26451, 26490
Valid prediction for GlimmerHMM_glimmerT_41721-T1
Valid prediction for GlimmerHMM_glimmerT_41723-T1
Valid prediction for GeneMark_model.71784_t
Valid prediction for GeneMark_model.71782_t
Valid prediction for snap_scaffold_17-snap.1809-T1
Valid prediction for HiQ_model.g27966.t1
Valid prediction for GeneMark_model.71807_t
Valid prediction for snap_scaffold_17-snap.1803-T1
Valid prediction for GlimmerHMM_glimmerT_41728-T1
Valid prediction for snap_scaffold_17-snap.1804-T1
Valid prediction for Augustus_model.g27968.t1
Valid prediction for GeneMark_model.71780_t
Valid prediction for pasa_asmbl_19200.p1
Valid prediction for snap_scaffold_17-snap.1789-T1
Valid prediction for GeneMark_model.71808_t
Valid prediction for Augustus_model.g27971.t1
Valid prediction for GeneMark_model.71803_t
Valid prediction for GeneMark_model.71781_t
Valid prediction for Augustus_model.g27972.t1
Valid prediction for GeneMark_model.71819_t
Valid prediction for GlimmerHMM_glimmerT_41724-T1
Valid prediction for GeneMark_model.71816_t
Valid prediction for snap_scaffold_17-snap.1792-T1
Valid prediction for GlimmerHMM_glimmerT_41710-T1
Valid prediction for snap_scaffold_17-snap.1778-T1
Valid prediction for snap_scaffold_17-snap.1807-T1
Valid prediction for GlimmerHMM_glimmerT_41708-T1
Valid prediction for pasa_asmbl_19189.p1
Valid prediction for GlimmerHMM_glimmerT_41720-T1
Valid prediction for HiQ_model.g27969.t1
Valid prediction for GeneMark_model.71812_t
Valid prediction for GeneMark_model.71794_t
Valid prediction for Augustus_model.g27964.t1
Valid prediction for Augustus_model.g27963.t1
Valid prediction for snap_scaffold_17-snap.1794-T1
Valid prediction for GeneMark_model.71786_t
Valid prediction for GeneMark_model.71792_t
Valid prediction for snap_scaffold_17-snap.1796-T1
Valid prediction for GeneMark_model.71789_t
Valid prediction for snap_scaffold_17-snap.1785-T1
Valid prediction for snap_scaffold_17-snap.1799-T1
Valid prediction for GeneMark_model.71820_t
Valid prediction for pasa_asmbl_19201.p1
Couldn't classify 116808, 116869
Sorry, prediction pasa_asmbl_19182.p1 fails validation.
(GAC)	 GC	116808-116869	GT	AGG
(TTC)	 AG	117054-117158	GT	CTG
(AGC)	 AG	117456-117568	GT	CGG
(CGG)	 AG	118166-118416	CC	AAC
-recovered pasa_asmbl_19182.p1, terminal, 118166, 118416
-recovered pasa_asmbl_19182.p1, internal, 117054, 117158
-recovered pasa_asmbl_19182.p1, internal, 117456, 117568
Valid prediction for CodingQuarry_transcript_22062-T1
Valid prediction for GlimmerHMM_glimmerT_41731-T1
Valid prediction for CodingQuarry_transcript_22063-T1
Valid prediction for snap_scaffold_17-snap.1780-T1
Valid prediction for Augustus_model.g27955.t1
Valid prediction for snap_scaffold_17-snap.1805-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 66145, rend_intergenic: 61228  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72804, rend_intergenic: 68392  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80050, rend_intergenic: 73979  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89035, rend_intergenic: 85064  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135986, rend_intergenic: 133541  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 197198, rend_intergenic: 185789  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 220961, rend_intergenic: 197494  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 225907
-exon list size: 587


building trellis

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99.8    
-found 31 predictions from path traversal
Error with prediction: snap lend_intergenic: 66145, rend_intergenic: 61228  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 72804, rend_intergenic: 68392  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 80050, rend_intergenic: 73979  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 89035, rend_intergenic: 85064  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 135986, rend_intergenic: 133541  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 197198, rend_intergenic: 185789  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 220961, rend_intergenic: 197494  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