-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_16/scaffold_16_7198142-7483487

-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.67430_t
Valid prediction for GeneMark_model.67406_t
Valid prediction for GlimmerHMM_glimmerT_39377-T1
Valid prediction for GlimmerHMM_glimmerT_39388-T1
Valid prediction for snap_scaffold_16-snap.1351-T1
Valid prediction for snap_scaffold_16-snap.1372-T1
Valid prediction for GeneMark_model.67394_t
Valid prediction for GeneMark_model.67429_t
Valid prediction for GeneMark_model.67438_t
Valid prediction for GeneMark_model.67392_t
Valid prediction for snap_scaffold_16-snap.1359-T1
Valid prediction for GeneMark_model.67411_t
Valid prediction for GeneMark_model.67404_t
Valid prediction for GeneMark_model.67397_t
Valid prediction for Augustus_model.g26462.t1
Valid prediction for GlimmerHMM_glimmerT_39381-T1
Valid prediction for GeneMark_model.67433_t
Valid prediction for snap_scaffold_16-snap.1362-T1
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for snap_scaffold_16-snap.1350-T1
Valid prediction for GeneMark_model.67414_t
Valid prediction for Augustus_model.g26464.t1
Valid prediction for Augustus_model.g26454.t1
Valid prediction for GlimmerHMM_glimmerT_39390-T1
Valid prediction for snap_scaffold_16-snap.1377-T1
Valid prediction for snap_scaffold_16-snap.1349-T1
Valid prediction for GlimmerHMM_glimmerT_39379-T1
Valid prediction for snap_scaffold_16-snap.1374-T1
Valid prediction for CodingQuarry_transcript_19959-T1
Valid prediction for snap_scaffold_16-snap.1366-T1
Valid prediction for GeneMark_model.67422_t
Valid prediction for GeneMark_model.67444_t
Valid prediction for snap_scaffold_16-snap.1335-T1
Valid prediction for CodingQuarry_transcript_19961-T1
Valid prediction for Augustus_model.g26460.t1
Valid prediction for GeneMark_model.67432_t
Valid prediction for HiQ_model.g26456.t1
Valid prediction for snap_scaffold_16-snap.1330-T1
Valid prediction for GeneMark_model.67441_t
Valid prediction for GlimmerHMM_glimmerT_39382-T1
Valid prediction for GlimmerHMM_glimmerT_39376-T1
Valid prediction for GlimmerHMM_glimmerT_39389-T1
Valid prediction for snap_scaffold_16-snap.1367-T1
Valid prediction for pasa_asmbl_17130.p1
Valid prediction for GeneMark_model.67410_t
Valid prediction for pasa_asmbl_17133.p1
Valid prediction for GlimmerHMM_glimmerT_39386-T1
Valid prediction for snap_scaffold_16-snap.1343-T1
Valid prediction for Augustus_model.g26455.t1
Valid prediction for GeneMark_model.67424_t
Valid prediction for snap_scaffold_16-snap.1347-T1
Valid prediction for GeneMark_model.67420_t
Valid prediction for HiQ_model.g26450.t1
Valid prediction for snap_scaffold_16-snap.1342-T1
Valid prediction for GeneMark_model.67431_t
Valid prediction for Augustus_model.g26463.t1
Valid prediction for snap_scaffold_16-snap.1338-T1
Valid prediction for snap_scaffold_16-snap.1345-T1
Valid prediction for GlimmerHMM_glimmerT_39370-T1
Valid prediction for Augustus_model.g26459.t1
Valid prediction for snap_scaffold_16-snap.1363-T1
Valid prediction for GeneMark_model.67399_t
Valid prediction for snap_scaffold_16-snap.1357-T1
Sorry, intron length (4) is less than minimum required (10)
Valid prediction for GeneMark_model.67409_t
Valid prediction for snap_scaffold_16-snap.1341-T1
Valid prediction for CodingQuarry_transcript_19960-T1
Valid prediction for snap_scaffold_16-snap.1336-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for GeneMark_model.67436_t
Couldn't classify 76383, 76501
Sorry, prediction pasa_asmbl_17128.p1 fails validation.
(AGT)	 AC	76383-76501	GT	AGG
(ACT)	 AG	76762-76866	GT	AAG
(CTC)	 AG	76983-77222	GT	AGG
(GAA)	 AG	78257-78460	GT	AAG
(ACC)	 AG	78579-78708	GT	AGG
(GAC)	 AG	78896-78978	GT	AGG
(CCC)	 AG	79552-79682	GT	AGG
(ATC)	 AG	79836-79960	GT	AGG
(AAC)	 AG	80234-80509	CA	GAC
add_exon() Sorry, pasa_asmbl_17128.p1 76762-76866-terminal-1 is invalid.
-recovered pasa_asmbl_17128.p1, terminal, 76762, 76866
-recovered pasa_asmbl_17128.p1, terminal, 80234, 80509
-recovered pasa_asmbl_17128.p1, internal, 76762, 76866
-recovered pasa_asmbl_17128.p1, internal, 76983, 77222
-recovered pasa_asmbl_17128.p1, internal, 78257, 78460
-recovered pasa_asmbl_17128.p1, internal, 78579, 78708
-recovered pasa_asmbl_17128.p1, internal, 78896, 78978
-recovered pasa_asmbl_17128.p1, internal, 79552, 79682
-recovered pasa_asmbl_17128.p1, internal, 79836, 79960
Valid prediction for snap_scaffold_16-snap.1334-T1
Valid prediction for snap_scaffold_16-snap.1340-T1
Valid prediction for GeneMark_model.67402_t
Valid prediction for GeneMark_model.67440_t
Valid prediction for snap_scaffold_16-snap.1361-T1
Valid prediction for GeneMark_model.67412_t
Valid prediction for GlimmerHMM_glimmerT_39387-T1
Valid prediction for snap_scaffold_16-snap.1329-T1
Valid prediction for GeneMark_model.67443_t
Valid prediction for HiQ_model.g26457.t1
Valid prediction for snap_scaffold_16-snap.1364-T1
Valid prediction for snap_scaffold_16-snap.1346-T1
Valid prediction for snap_scaffold_16-snap.1369-T1
Valid prediction for snap_scaffold_16-snap.1337-T1
Valid prediction for snap_scaffold_16-snap.1356-T1
Valid prediction for snap_scaffold_16-snap.1355-T1
Valid prediction for Augustus_model.g26461.t1
Valid prediction for GeneMark_model.67421_t
Valid prediction for GeneMark_model.67416_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.g26449.t1
Valid prediction for GlimmerHMM_glimmerT_39383-T1
Valid prediction for GlimmerHMM_glimmerT_39374-T1
Valid prediction for GeneMark_model.67425_t
Valid prediction for GeneMark_model.67445_t
Valid prediction for snap_scaffold_16-snap.1353-T1
Valid prediction for snap_scaffold_16-snap.1348-T1
Valid prediction for snap_scaffold_16-snap.1376-T1
Valid prediction for GeneMark_model.67419_t
Valid prediction for Augustus_model.g26452.t1
Valid prediction for snap_scaffold_16-snap.1371-T1
Valid prediction for snap_scaffold_16-snap.1370-T1
Valid prediction for CodingQuarry_transcript_19958-T1
Valid prediction for GeneMark_model.67391_t
Valid prediction for snap_scaffold_16-snap.1354-T1
Valid prediction for pasa_asmbl_16345.p1
Valid prediction for snap_scaffold_16-snap.1333-T1
Valid prediction for CodingQuarry_transcript_19957-T1
Valid prediction for GlimmerHMM_glimmerT_39373-T1
Valid prediction for GlimmerHMM_glimmerT_39372-T1
Valid prediction for Augustus_model.g26451.t1
Valid prediction for GeneMark_model.67427_t
Valid prediction for snap_scaffold_16-snap.1368-T1
Valid prediction for snap_scaffold_16-snap.1339-T1
Valid prediction for GeneMark_model.67428_t
Valid prediction for pasa_asmbl_16344.p1
Valid prediction for GlimmerHMM_glimmerT_39375-T1
Valid prediction for GlimmerHMM_glimmerT_39384-T1
Valid prediction for GeneMark_model.67434_t
Valid prediction for GeneMark_model.67408_t
Valid prediction for GlimmerHMM_glimmerT_39380-T1
Valid prediction for snap_scaffold_16-snap.1352-T1
Valid prediction for GlimmerHMM_glimmerT_39378-T1
Valid prediction for snap_scaffold_16-snap.1331-T1
Valid prediction for GeneMark_model.67435_t
Valid prediction for GlimmerHMM_glimmerT_39391-T1
Valid prediction for GeneMark_model.67442_t
Valid prediction for GeneMark_model.67426_t
Valid prediction for GeneMark_model.67415_t
Valid prediction for snap_scaffold_16-snap.1344-T1
Valid prediction for GeneMark_model.67393_t
Valid prediction for GeneMark_model.67418_t
Valid prediction for Augustus_model.g26458.t1
Valid prediction for snap_scaffold_16-snap.1360-T1
Valid prediction for GeneMark_model.67439_t
Valid prediction for CodingQuarry_transcript_19956-T1
Valid prediction for GeneMark_model.67395_t
Valid prediction for GeneMark_model.67401_t
Valid prediction for pasa_asmbl_16356.p1
Valid prediction for GeneMark_model.67396_t
Valid prediction for GeneMark_model.67403_t
Valid prediction for GlimmerHMM_glimmerT_39385-T1
Valid prediction for GlimmerHMM_glimmerT_39371-T1
Valid prediction for snap_scaffold_16-snap.1375-T1
Valid prediction for GeneMark_model.67400_t
Valid prediction for Augustus_model.g26453.t1
Valid prediction for GeneMark_model.67413_t
Valid prediction for HiQ_model.g26448.t1
Valid prediction for GeneMark_model.67417_t
Valid prediction for snap_scaffold_16-snap.1373-T1
Valid prediction for GeneMark_model.67437_t
Valid prediction for GeneMark_model.67423_t
Valid prediction for snap_scaffold_16-snap.1332-T1
Valid prediction for snap_scaffold_16-snap.1358-T1
Valid prediction for GeneMark_model.67405_t
Valid prediction for snap_scaffold_16-snap.1365-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 12869, rend_intergenic: 9639  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64255, rend_intergenic: 20381  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156708, rend_intergenic: 145500  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 197552, rend_intergenic: 192297  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 209835, rend_intergenic: 204502  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 211407, rend_intergenic: 210486  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 237691, rend_intergenic: 231520  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 251346, rend_intergenic: 246510  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 261465, rend_intergenic: 255185  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 264722, rend_intergenic: 263013  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 285346
-exon list size: 679


building trellis

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-found 32 predictions from path traversal
Error with prediction: snap lend_intergenic: 12869, rend_intergenic: 9639  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 64255, rend_intergenic: 20381  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156708, rend_intergenic: 145500  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 197552, rend_intergenic: 192297  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 209835, rend_intergenic: 204502  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 211407, rend_intergenic: 210486  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 237691, rend_intergenic: 231520  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 251346, rend_intergenic: 246510  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 261465, rend_intergenic: 255185  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 264722, rend_intergenic: 263013  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
GOT 5prime partial gene.

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