-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_11/scaffold_11_14931454-15175673

-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.3088-T1
Valid prediction for snap_scaffold_11-snap.3063-T1
Valid prediction for GlimmerHMM_glimmerT_28318-T1
Valid prediction for GlimmerHMM_glimmerT_28320-T1
Valid prediction for snap_scaffold_11-snap.3103-T1
Valid prediction for Augustus_model.g18766.t1
Valid prediction for GlimmerHMM_glimmerT_28316-T1
Valid prediction for GlimmerHMM_glimmerT_28332-T1
Valid prediction for Augustus_model.g18757.t1
Valid prediction for snap_scaffold_11-snap.3070-T1
Valid prediction for GlimmerHMM_glimmerT_28337-T1
Valid prediction for snap_scaffold_11-snap.3095-T1
Valid prediction for GlimmerHMM_glimmerT_28339-T1
Valid prediction for GlimmerHMM_glimmerT_28327-T1
Valid prediction for snap_scaffold_11-snap.3073-T1
Valid prediction for snap_scaffold_11-snap.3105-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_11-snap.3076-T1
Couldn't classify 146127, 146254
Sorry, prediction pasa_asmbl_6108.p1 fails validation.
(GTG)	 AG	146127-146254	GT	GAG
(AAT)	 AG	146888-147158	CA	GAC
-recovered pasa_asmbl_6108.p1, terminal, 146888, 147158
-recovered pasa_asmbl_6108.p1, internal, 146127, 146254
Valid prediction for snap_scaffold_11-snap.3091-T1
Valid prediction for Augustus_model.g18754.t1
Valid prediction for Augustus_model.g18763.t1
Valid prediction for snap_scaffold_11-snap.3060-T1
Valid prediction for snap_scaffold_11-snap.3100-T1
Valid prediction for snap_scaffold_11-snap.3067-T1
Valid prediction for snap_scaffold_11-snap.3066-T1
Valid prediction for snap_scaffold_11-snap.3094-T1
Valid prediction for Augustus_model.g18756.t1
Valid prediction for snap_scaffold_11-snap.3083-T1
Valid prediction for GlimmerHMM_glimmerT_28338-T1
Valid prediction for GlimmerHMM_glimmerT_28329-T1
Valid prediction for snap_scaffold_11-snap.3072-T1
Valid prediction for Augustus_model.g18771.t1
Valid prediction for GlimmerHMM_glimmerT_28324-T1
Valid prediction for snap_scaffold_11-snap.3065-T1
Valid prediction for GlimmerHMM_glimmerT_28326-T1
Valid prediction for GlimmerHMM_glimmerT_28340-T1
Valid prediction for Augustus_model.g18769.t1
Couldn't classify 126840, 126881
Sorry, prediction pasa_asmbl_6107.p1 fails validation.
(ATG)	 GG	125067-125199	GT	AGG
(ATA)	 AG	125837-125988	GT	AGG
(CTG)	 AG	126216-126324	GT	TGG
(TTC)	 AG	126483-126634	GT	AGG
(AGA)	 AG	126840-126881	TC	TGT
-recovered pasa_asmbl_6107.p1, initial, 125067, 125199
-recovered pasa_asmbl_6107.p1, internal, 125837, 125988
-recovered pasa_asmbl_6107.p1, internal, 126216, 126324
-recovered pasa_asmbl_6107.p1, internal, 126483, 126634
Valid prediction for GlimmerHMM_glimmerT_28315-T1
Valid prediction for Augustus_model.g18753.t1
Valid prediction for snap_scaffold_11-snap.3059-T1
Valid prediction for GlimmerHMM_glimmerT_28341-T1
Valid prediction for snap_scaffold_11-snap.3090-T1
Valid prediction for GlimmerHMM_glimmerT_28313-T1
Valid prediction for snap_scaffold_11-snap.3096-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_28314-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 GlimmerHMM_glimmerT_28342-T1
Valid prediction for pasa_asmbl_7185.p1
Valid prediction for GlimmerHMM_glimmerT_28334-T1
Valid prediction for GlimmerHMM_glimmerT_28331-T1
Valid prediction for snap_scaffold_11-snap.3099-T1
Valid prediction for snap_scaffold_11-snap.3071-T1
Valid prediction for snap_scaffold_11-snap.3082-T1
Valid prediction for GlimmerHMM_glimmerT_28323-T1
Valid prediction for snap_scaffold_11-snap.3069-T1
Valid prediction for snap_scaffold_11-snap.3078-T1
Valid prediction for Augustus_model.g18774.t1
Valid prediction for Augustus_model.g18768.t1
Couldn't classify 17812, 19476
Sorry, prediction pasa_asmbl_7186.p1 fails validation.
(GGG)	 GA	17812-19476	TC	AAT
Couldn't classify 14258, 14344
Couldn't classify 16478, 16573
Sorry, prediction pasa_asmbl_7187.p1 fails validation.
(CTT)	 CT	14258-14344	GT	ATG
(ATG)	 AG	14709-14822	GT	AGG
(ATT)	 AG	15051-15207	GT	CGG
(AGT)	 AG	15674-15804	GT	AGG
(CTC)	 AG	16478-16573	CC	CGC
-recovered pasa_asmbl_7187.p1, initial, 14709, 14822
-recovered pasa_asmbl_7187.p1, internal, 14709, 14822
-recovered pasa_asmbl_7187.p1, internal, 15051, 15207
-recovered pasa_asmbl_7187.p1, internal, 15674, 15804
Valid prediction for Augustus_model.g18764.t1
Valid prediction for Augustus_model.g18775.t1
Valid prediction for GlimmerHMM_glimmerT_28336-T1
Valid prediction for GlimmerHMM_glimmerT_28328-T1
Valid prediction for GlimmerHMM_glimmerT_28317-T1
Valid prediction for snap_scaffold_11-snap.3093-T1
Valid prediction for GlimmerHMM_glimmerT_28312-T1
Valid prediction for GlimmerHMM_glimmerT_28330-T1
Valid prediction for snap_scaffold_11-snap.3061-T1
Valid prediction for snap_scaffold_11-snap.3068-T1
Couldn't classify 59386, 59881
Couldn't classify 68214, 68267
Sorry, prediction pasa_asmbl_7184.p1 fails validation.
(GAG)	 AG	59386-59881	GT	AGG
(GAT)	 AG	60514-60686	GT	AGG
(GCC)	 AG	61910-62134	GT	AGG
(ATT)	 AG	65111-65296	GT	TGG
(ATC)	 AG	65498-65644	GT	AGG
(ATC)	 AG	68214-68267	GT	AGG
-recovered pasa_asmbl_7184.p1, internal, 59386, 59881
-recovered pasa_asmbl_7184.p1, internal, 60514, 60686
-recovered pasa_asmbl_7184.p1, internal, 61910, 62134
-recovered pasa_asmbl_7184.p1, internal, 65111, 65296
-recovered pasa_asmbl_7184.p1, internal, 65498, 65644
-recovered pasa_asmbl_7184.p1, internal, 68214, 68267
Valid prediction for snap_scaffold_11-snap.3080-T1
Valid prediction for snap_scaffold_11-snap.3097-T1
Valid prediction for snap_scaffold_11-snap.3102-T1
Valid prediction for snap_scaffold_11-snap.3079-T1
Valid prediction for Augustus_model.g18767.t1
Valid prediction for Augustus_model.g18765.t1
Couldn't classify 10243, 10266
Couldn't classify 11791, 11943
Sorry, prediction pasa_asmbl_7188.p1 fails validation.
(AGT)	 AG	10243-10266	GT	AAG
(TGC)	 AG	10706-10867	GT	AGG
(AGT)	 AG	11000-11156	GT	TGG
(GGA)	 AG	11495-11622	GT	AGG
(CTC)	 AG	11791-11943	CA	AGC
-recovered pasa_asmbl_7188.p1, internal, 10243, 10266
-recovered pasa_asmbl_7188.p1, internal, 10706, 10867
-recovered pasa_asmbl_7188.p1, internal, 11000, 11156
-recovered pasa_asmbl_7188.p1, internal, 11495, 11622
Valid prediction for snap_scaffold_11-snap.3062-T1
Valid prediction for GlimmerHMM_glimmerT_28343-T1
Valid prediction for snap_scaffold_11-snap.3104-T1
Valid prediction for snap_scaffold_11-snap.3087-T1
Valid prediction for Augustus_model.g18759.t1
Valid prediction for snap_scaffold_11-snap.3077-T1
Valid prediction for Augustus_model.g18762.t1
Valid prediction for GlimmerHMM_glimmerT_28325-T1
Valid prediction for CodingQuarry_transcript_8317-T1
Valid prediction for GlimmerHMM_glimmerT_28321-T1
Valid prediction for Augustus_model.g18772.t1
Valid prediction for snap_scaffold_11-snap.3064-T1
Couldn't classify 87009, 87077
Sorry, prediction pasa_asmbl_7180.p1 fails validation.
(GAC)	 AG	87009-87077	GT	AGG
(ATG)	 AG	88092-88217	GT	AGG
(AAG)	 AG	88977-89085	GT	AGG
(CCA)	 AG	91226-91405	GT	TGG
(AGG)	 AG	91552-91670	GT	AGG
(GTA)	 AG	92101-92209	GT	CGG
(TGT)	 AG	92639-92697	GT	TGG
(ACT)	 AG	92842-92944	GT	AGG
(GAA)	 AG	93079-93166	GT	AGG
(TGT)	 AG	93443-93597	GT	AGG
(GTT)	 AG	93853-94568	GG	AGG
-recovered pasa_asmbl_7180.p1, initial, 88092, 88217
add_exon() Sorry, pasa_asmbl_7180.p1 93443-93597-terminal-2 is invalid.
-recovered pasa_asmbl_7180.p1, terminal, 93443, 93597
-recovered pasa_asmbl_7180.p1, terminal, 93853, 94568
-recovered pasa_asmbl_7180.p1, internal, 87009, 87077
-recovered pasa_asmbl_7180.p1, internal, 88092, 88217
-recovered pasa_asmbl_7180.p1, internal, 88977, 89085
-recovered pasa_asmbl_7180.p1, internal, 91226, 91405
-recovered pasa_asmbl_7180.p1, internal, 91552, 91670
-recovered pasa_asmbl_7180.p1, internal, 92101, 92209
-recovered pasa_asmbl_7180.p1, internal, 92639, 92697
-recovered pasa_asmbl_7180.p1, internal, 92842, 92944
-recovered pasa_asmbl_7180.p1, internal, 93079, 93166
-recovered pasa_asmbl_7180.p1, internal, 93443, 93597
Valid prediction for snap_scaffold_11-snap.3092-T1
Valid prediction for snap_scaffold_11-snap.3101-T1
Valid prediction for Augustus_model.g18773.t1
Valid prediction for Augustus_model.g18761.t1
Valid prediction for snap_scaffold_11-snap.3074-T1
Valid prediction for GlimmerHMM_glimmerT_28322-T1
Valid prediction for snap_scaffold_11-snap.3081-T1
Valid prediction for GlimmerHMM_glimmerT_28333-T1
Valid prediction for GlimmerHMM_glimmerT_28319-T1
Valid prediction for snap_scaffold_11-snap.3086-T1
Valid prediction for Augustus_model.g18758.t1
Valid prediction for Augustus_model.g18755.t1
Valid prediction for snap_scaffold_11-snap.3075-T1
Couldn't classify 71669, 71839
Couldn't classify 75145, 75230
Sorry, prediction pasa_asmbl_7182.p1 fails validation.
(CAG)	 CC	71669-71839	GT	AGG
(GTG)	 AG	72468-72572	GT	AGG
(TTG)	 AG	72700-72778	GT	TGG
(GTT)	 AG	72939-73028	GT	AGG
(GAC)	 AG	73202-73429	GT	AGG
(ATG)	 AG	75145-75230	CC	GGC
-recovered pasa_asmbl_7182.p1, internal, 72468, 72572
-recovered pasa_asmbl_7182.p1, internal, 72700, 72778
-recovered pasa_asmbl_7182.p1, internal, 72939, 73028
-recovered pasa_asmbl_7182.p1, internal, 73202, 73429
Valid prediction for Augustus_model.g18760.t1
Valid prediction for GlimmerHMM_glimmerT_28335-T1
Valid prediction for snap_scaffold_11-snap.3089-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_11-snap.3084-T1
Valid prediction for snap_scaffold_11-snap.3098-T1
Valid prediction for snap_scaffold_11-snap.3058-T1
Valid prediction for Augustus_model.g18770.t1
Valid prediction for snap_scaffold_11-snap.3085-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 7568, rend_intergenic: 1931  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 12363, rend_intergenic: 9452  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18300, rend_intergenic: 16461  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33750, rend_intergenic: 19654  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44759, rend_intergenic: 33871  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46975, rend_intergenic: 45007  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53575, rend_intergenic: 47126  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59835, rend_intergenic: 53657  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62708, rend_intergenic: 59859  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131054, rend_intergenic: 126479  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161728, rend_intergenic: 155281  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163713, rend_intergenic: 161930  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186649, rend_intergenic: 168560  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199705, rend_intergenic: 196420  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 218125, rend_intergenic: 216841  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 237432, rend_intergenic: 227698  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 244220
-exon list size: 395


building trellis

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-found 35 predictions from path traversal
Error with prediction: snap lend_intergenic: 7568, rend_intergenic: 1931  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 12363, rend_intergenic: 9452  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 18300, rend_intergenic: 16461  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 33750, rend_intergenic: 19654  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 44759, rend_intergenic: 33871  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 46975, rend_intergenic: 45007  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 53575, rend_intergenic: 47126  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59835, rend_intergenic: 53657  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 62708, rend_intergenic: 59859  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 131054, rend_intergenic: 126479  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 161728, rend_intergenic: 155281  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 163713, rend_intergenic: 161930  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 186649, rend_intergenic: 168560  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 199705, rend_intergenic: 196420  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 218125, rend_intergenic: 216841  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 237432, rend_intergenic: 227698  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.
GOT 5prime partial gene.

-reporting highest scoring path thru the trellis.
-found 18 predictions persist after filtering for low support

-building DP trellis

-building trellis in range 233979 - 244220
-exon list size: 5


building trellis

14.3    
28.6    
42.9    
57.1    
71.4    
85.7    
-found 1 predictions from path traversal

-reporting highest scoring path thru the trellis.
-found 0 predictions persist after filtering for low support