-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_17/scaffold_17_8734467-8912795

-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 CodingQuarry_transcript_22047-T1
Valid prediction for snap_scaffold_17-snap.1749-T1
Valid prediction for GeneMark_model.71760_t
Valid prediction for GeneMark_model.71748_t
Valid prediction for Augustus_model.g27948.t1
Valid prediction for GlimmerHMM_glimmerT_41689-T1
Valid prediction for GeneMark_model.71770_t
Valid prediction for GeneMark_model.71765_t
Valid prediction for GlimmerHMM_glimmerT_41698-T1
Valid prediction for snap_scaffold_17-snap.1752-T1
Valid prediction for GlimmerHMM_glimmerT_41700-T1
Valid prediction for Augustus_model.g27943.t1
Valid prediction for GeneMark_model.71773_t
Valid prediction for GeneMark_model.71764_t
Valid prediction for Augustus_model.g27949.t1
Valid prediction for GlimmerHMM_glimmerT_41696-T1
Valid prediction for GeneMark_model.71750_t
Couldn't classify 148282, 148377
Sorry, prediction pasa_asmbl_18169.p1 fails validation.
(ATG)	 AA	147369-147638	GT	AGG
(GAA)	 AG	147886-147948	GT	ATG
(GAG)	 AG	148282-148377	CC	GAC
-recovered pasa_asmbl_18169.p1, initial, 147369, 147638
-recovered pasa_asmbl_18169.p1, internal, 147886, 147948
Valid prediction for GeneMark_model.71744_t
Valid prediction for snap_scaffold_17-snap.1744-T1
Valid prediction for GlimmerHMM_glimmerT_41699-T1
Valid prediction for HiQ_model.g27946.t1
Valid prediction for HiQ_model.g27947.t1
Valid prediction for GeneMark_model.71756_t
Valid prediction for snap_scaffold_17-snap.1764-T1
Valid prediction for snap_scaffold_17-snap.1745-T1
Valid prediction for snap_scaffold_17-snap.1763-T1
Valid prediction for GlimmerHMM_glimmerT_41701-T1
Couldn't classify 126013, 126018
Sorry, prediction pasa_asmbl_18160.p1 fails validation.
(TAT)	 TC	126013-126018	GT	TGG
(GAG)	 AG	126268-126516	GT	TGG
(GCT)	 AG	126650-126761	GT	CCG
(TGT)	 AG	126903-127111	GT	AGG
(GGA)	 AG	127299-127448	GT	AGG
(ATC)	 AG	127612-127677	CT	AAC
-recovered pasa_asmbl_18160.p1, terminal, 127612, 127677
-recovered pasa_asmbl_18160.p1, internal, 126268, 126516
-recovered pasa_asmbl_18160.p1, internal, 126650, 126761
-recovered pasa_asmbl_18160.p1, internal, 126903, 127111
-recovered pasa_asmbl_18160.p1, internal, 127299, 127448
Valid prediction for CodingQuarry_transcript_22050-T1
Couldn't classify 121593, 121701
Couldn't classify 122890, 122962
Sorry, prediction pasa_asmbl_18158.p1 fails validation.
(GTT)	 AG	121593-121701	GT	AGG
(CCG)	 AG	121909-121997	GC	AGG
(GAG)	 AG	122122-122212	GT	AGG
(GGG)	 AG	122326-122453	GT	AGG
(GGA)	 AG	122564-122667	GT	AGG
(TCG)	 AG	122890-122962	GC	GAG
-recovered pasa_asmbl_18158.p1, internal, 121593, 121701
-recovered pasa_asmbl_18158.p1, internal, 121909, 121997
-recovered pasa_asmbl_18158.p1, internal, 122122, 122212
-recovered pasa_asmbl_18158.p1, internal, 122326, 122453
-recovered pasa_asmbl_18158.p1, internal, 122564, 122667
-recovered pasa_asmbl_18158.p1, internal, 122890, 122962
Valid prediction for CodingQuarry_transcript_22046-T1
Valid prediction for Augustus_model.g27941.t1
Valid prediction for snap_scaffold_17-snap.1747-T1
Valid prediction for Augustus_model.g27931.t1
Couldn't classify 149650, 149802
Sorry, prediction pasa_asmbl_18170.p1 fails validation.
(GAG)	 AG	149650-149802	GT	AGG
(GTG)	 AG	151236-151409	GT	AGG
(GAG)	 AG	151542-152216	GA	GAG
-recovered pasa_asmbl_18170.p1, terminal, 151542, 152216
-recovered pasa_asmbl_18170.p1, internal, 149650, 149802
-recovered pasa_asmbl_18170.p1, internal, 151236, 151409
Valid prediction for snap_scaffold_17-snap.1743-T1
Valid prediction for pasa_asmbl_18161.p1
Valid prediction for snap_scaffold_17-snap.1751-T1
Couldn't classify 123135, 123154
Couldn't classify 125116, 125145
Sorry, prediction pasa_asmbl_18159.p1 fails validation.
(AAC)	 AC	123135-123154	GT	AGG
(TGA)	 AG	123391-123478	GT	AGG
(GAG)	 AG	123603-123696	GT	GGG
(ACC)	 AG	124060-124130	GT	AGG
(ACT)	 AG	124279-124404	GT	AGG
(GTG)	 AG	124503-124607	GT	AGG
(CAA)	 AG	124921-124989	GT	AGG
(AGT)	 AG	125116-125145	TG	AGT
-recovered pasa_asmbl_18159.p1, internal, 123391, 123478
-recovered pasa_asmbl_18159.p1, internal, 123603, 123696
-recovered pasa_asmbl_18159.p1, internal, 124060, 124130
-recovered pasa_asmbl_18159.p1, internal, 124279, 124404
-recovered pasa_asmbl_18159.p1, internal, 124503, 124607
-recovered pasa_asmbl_18159.p1, internal, 124921, 124989
Valid prediction for pasa_asmbl_18166.p1
Valid prediction for snap_scaffold_17-snap.1769-T1
Valid prediction for GeneMark_model.71745_t
Valid prediction for snap_scaffold_17-snap.1768-T1
Valid prediction for HiQ_model.g27944.t1
Valid prediction for GlimmerHMM_glimmerT_41687-T1
Valid prediction for Augustus_model.g27930.t1
Valid prediction for GeneMark_model.71767_t
Valid prediction for GlimmerHMM_glimmerT_41702-T1
Valid prediction for GeneMark_model.71762_t
Valid prediction for GeneMark_model.71741_t
Valid prediction for GeneMark_model.71747_t
Valid prediction for GlimmerHMM_glimmerT_41690-T1
Valid prediction for GeneMark_model.71775_t
Valid prediction for snap_scaffold_17-snap.1772-T1
Valid prediction for snap_scaffold_17-snap.1770-T1
Valid prediction for GlimmerHMM_glimmerT_41695-T1
Valid prediction for GeneMark_model.71768_t
Valid prediction for GeneMark_model.71774_t
Valid prediction for snap_scaffold_17-snap.1767-T1
Valid prediction for snap_scaffold_17-snap.1762-T1
Valid prediction for GlimmerHMM_glimmerT_41681-T1
Valid prediction for GlimmerHMM_glimmerT_41703-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 CodingQuarry_transcript_22040-T1
Valid prediction for snap_scaffold_17-snap.1759-T1
Valid prediction for GeneMark_model.71755_t
Valid prediction for snap_scaffold_17-snap.1755-T1
Valid prediction for snap_scaffold_17-snap.1766-T1
Valid prediction for GlimmerHMM_glimmerT_41684-T1
Couldn't classify 38732, 38765
Sorry, prediction pasa_asmbl_19179.p1 fails validation.
(CTG)	 TC	38732-38765	GT	AGG
(ACA)	 AG	38976-39094	GT	ATG
(CCG)	 AG	40863-40994	GT	AGG
(GTG)	 AG	41125-41234	GT	CGG
(ACT)	 AG	41907-42051	GT	GGG
(GTG)	 AG	42152-42299	GT	TAG
(TCG)	 AG	42446-42462	AA	AGA
-recovered pasa_asmbl_19179.p1, terminal, 42446, 42462
-recovered pasa_asmbl_19179.p1, internal, 38976, 39094
-recovered pasa_asmbl_19179.p1, internal, 40863, 40994
-recovered pasa_asmbl_19179.p1, internal, 41125, 41234
-recovered pasa_asmbl_19179.p1, internal, 41907, 42051
-recovered pasa_asmbl_19179.p1, internal, 42152, 42299
Valid prediction for GeneMark_model.71763_t
Valid prediction for GeneMark_model.71749_t
Valid prediction for CodingQuarry_transcript_22045-T1
Valid prediction for snap_scaffold_17-snap.1750-T1
Valid prediction for GeneMark_model.71766_t
Valid prediction for snap_scaffold_17-snap.1771-T1
Valid prediction for GeneMark_model.71743_t
Valid prediction for CodingQuarry_transcript_22048-T1
Valid prediction for GeneMark_model.71771_t
Valid prediction for GlimmerHMM_glimmerT_41682-T1
Valid prediction for CodingQuarry_transcript_22043-T1
Valid prediction for GeneMark_model.71758_t
Valid prediction for snap_scaffold_17-snap.1746-T1
Valid prediction for snap_scaffold_17-snap.1773-T1
Couldn't classify 37345, 37375
Couldn't classify 38582, 38638
Sorry, prediction pasa_asmbl_19181.p1 fails validation.
(AAA)	 CA	37345-37375	GT	AGG
(GCA)	 AG	37750-37980	GT	GGG
(TTC)	 AG	38099-38226	GT	AGG
(GTT)	 AG	38370-38462	GT	AGG
(GTG)	 AG	38582-38638	GA	GAG
-recovered pasa_asmbl_19181.p1, internal, 37750, 37980
-recovered pasa_asmbl_19181.p1, internal, 38099, 38226
-recovered pasa_asmbl_19181.p1, internal, 38370, 38462
Valid prediction for HiQ_model.g27939.t1
Valid prediction for Augustus_model.g27932.t1
Valid prediction for CodingQuarry_transcript_22044-T1
Valid prediction for GeneMark_model.71759_t
Valid prediction for CodingQuarry_transcript_22049-T1
Valid prediction for snap_scaffold_17-snap.1765-T1
Valid prediction for GlimmerHMM_glimmerT_41693-T1
Valid prediction for GeneMark_model.71742_t
Valid prediction for GeneMark_model.71746_t
Valid prediction for snap_scaffold_17-snap.1758-T1
Valid prediction for Augustus_model.g27935.t1
Couldn't classify 140869, 140940
Sorry, prediction pasa_asmbl_19160.p1 fails validation.
(GGC)	 GA	140869-140940	GT	AGG
(CCT)	 AG	141362-141463	GT	AGG
(ACA)	 AG	142644-142724	GT	AGG
(GCT)	 AG	143177-143275	AC	AGA
-recovered pasa_asmbl_19160.p1, terminal, 143177, 143275
-recovered pasa_asmbl_19160.p1, internal, 141362, 141463
-recovered pasa_asmbl_19160.p1, internal, 142644, 142724
Valid prediction for GlimmerHMM_glimmerT_41694-T1
Valid prediction for HiQ_model.g27945.t1
Valid prediction for GlimmerHMM_glimmerT_41686-T1
Valid prediction for HiQ_model.g27938.t1
Valid prediction for GeneMark_model.71761_t
Valid prediction for Augustus_model.g27933.t1
Valid prediction for Augustus_model.g27937.t1
Valid prediction for GlimmerHMM_glimmerT_41683-T1
Valid prediction for CodingQuarry_transcript_22042-T1
Valid prediction for GlimmerHMM_glimmerT_41685-T1
Valid prediction for HiQ_model.g27942.t1
Valid prediction for snap_scaffold_17-snap.1757-T1
Valid prediction for pasa_asmbl_19167.p1
Couldn't classify 74106, 74167
Sorry, prediction pasa_asmbl_19172.p1 fails validation.
(GAG)	 CT	74106-74167	GT	GAG
(GTA)	 AG	74257-74355	GT	AGG
(CTA)	 AG	74455-74593	GT	AGG
(AGG)	 AG	74737-74806	GT	TGG
(CAT)	 AG	74928-75000	GT	AGG
(AAC)	 AG	75540-75633	GT	AGG
(GAC)	 AG	75766-75858	GT	CGG
(CTG)	 AG	75992-76049	GT	TGG
(GTG)	 AG	76173-76309	AT	GAA
-recovered pasa_asmbl_19172.p1, terminal, 76173, 76309
-recovered pasa_asmbl_19172.p1, internal, 74257, 74355
-recovered pasa_asmbl_19172.p1, internal, 74455, 74593
-recovered pasa_asmbl_19172.p1, internal, 74737, 74806
-recovered pasa_asmbl_19172.p1, internal, 74928, 75000
-recovered pasa_asmbl_19172.p1, internal, 75540, 75633
-recovered pasa_asmbl_19172.p1, internal, 75766, 75858
-recovered pasa_asmbl_19172.p1, internal, 75992, 76049
Valid prediction for pasa_asmbl_19168.p1
Valid prediction for snap_scaffold_17-snap.1756-T1
Valid prediction for snap_scaffold_17-snap.1754-T1
Valid prediction for CodingQuarry_transcript_22041-T1
Valid prediction for GlimmerHMM_glimmerT_41688-T1
Valid prediction for snap_scaffold_17-snap.1753-T1
Valid prediction for GlimmerHMM_glimmerT_41691-T1
Valid prediction for snap_scaffold_17-snap.1748-T1
Valid prediction for Augustus_model.g27934.t1
Valid prediction for GlimmerHMM_glimmerT_41692-T1
Valid prediction for GeneMark_model.71751_t
Valid prediction for GeneMark_model.71754_t
Valid prediction for GeneMark_model.71769_t
Valid prediction for snap_scaffold_17-snap.1761-T1
Valid prediction for GeneMark_model.71753_t
Valid prediction for Augustus_model.g27936.t1
Valid prediction for pasa_asmbl_19176.p1
Valid prediction for GlimmerHMM_glimmerT_41697-T1
Valid prediction for GeneMark_model.71752_t
Valid prediction for pasa_asmbl_19165.p1
Valid prediction for GeneMark_model.71772_t
Valid prediction for snap_scaffold_17-snap.1760-T1
Valid prediction for Augustus_model.g27940.t1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 34711, rend_intergenic: 32759  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35668, rend_intergenic: 34728  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37595, rend_intergenic: 35817  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59357, rend_intergenic: 41161  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165368, rend_intergenic: 163727  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 178329
-exon list size: 484


building trellis

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98.4    
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98.8    
99.0    
99.2    
99.4    
99.6    
99.8    
-found 22 predictions from path traversal
Error with prediction: snap lend_intergenic: 34711, rend_intergenic: 32759  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 35668, rend_intergenic: 34728  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 37595, rend_intergenic: 35817  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 59357, rend_intergenic: 41161  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 165368, rend_intergenic: 163727  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