-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_27/scaffold_27_5928278-6199778

-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_27-snap.1429-T1
Couldn't classify 146749, 146750
Couldn't classify 149067, 149068
Sorry, prediction CodingQuarry_transcript_41912-T1 fails validation.
(ATG)	 AG	146749-146750	GT	ATG
(GTC)	 AG	146853-146909	GT	GTG
(ACT)	 AG	147267-147324	GT	AAG
(TTC)	 AG	148176-148215	GT	CGG
(ATG)	 AG	148507-148680	GT	TTG
(GAA)	 AG	149067-149068	AA	GAA
add_exon() Sorry, CodingQuarry_transcript_41912-T1 148507-148680-initial-1 is invalid.
-recovered CodingQuarry_transcript_41912-T1, initial, 148507, 148680
-recovered CodingQuarry_transcript_41912-T1, internal, 146749, 146750
-recovered CodingQuarry_transcript_41912-T1, internal, 146853, 146909
-recovered CodingQuarry_transcript_41912-T1, internal, 147267, 147324
-recovered CodingQuarry_transcript_41912-T1, internal, 148176, 148215
-recovered CodingQuarry_transcript_41912-T1, internal, 148507, 148680
Valid prediction for snap_scaffold_27-snap.1403-T1
Valid prediction for Augustus_model.g38042.t1
Valid prediction for GlimmerHMM_glimmerT_57412-T1
Valid prediction for Augustus_model.g38044.t1
Valid prediction for Augustus_model.g38047.t1
Valid prediction for snap_scaffold_27-snap.1395-T1
Valid prediction for snap_scaffold_27-snap.1435-T1
Valid prediction for snap_scaffold_27-snap.1416-T1
Valid prediction for snap_scaffold_27-snap.1437-T1
Valid prediction for snap_scaffold_27-snap.1419-T1
Valid prediction for GlimmerHMM_glimmerT_57430-T1
Valid prediction for GlimmerHMM_glimmerT_57418-T1
Valid prediction for pasa_asmbl_36367.p1
Valid prediction for snap_scaffold_27-snap.1405-T1
Sorry, intron length (5) is less than minimum required (10)
Sorry, intron length (7) is less than minimum required (10)
Valid prediction for GlimmerHMM_glimmerT_57434-T1
Valid prediction for snap_scaffold_27-snap.1410-T1
Valid prediction for Augustus_model.g38033.t1
Valid prediction for snap_scaffold_27-snap.1433-T1
Valid prediction for CodingQuarry_transcript_41909-T1
Valid prediction for snap_scaffold_27-snap.1420-T1
Valid prediction for snap_scaffold_27-snap.1434-T1
Sorry, intron length (3) is less than minimum required (10)
Valid prediction for snap_scaffold_27-snap.1421-T1
Valid prediction for GlimmerHMM_glimmerT_57431-T1
Valid prediction for snap_scaffold_27-snap.1425-T1
Valid prediction for GlimmerHMM_glimmerT_57425-T1
Valid prediction for GlimmerHMM_glimmerT_57423-T1
Valid prediction for snap_scaffold_27-snap.1414-T1
Valid prediction for snap_scaffold_27-snap.1415-T1
Valid prediction for pasa_asmbl_36380.p1
Valid prediction for snap_scaffold_27-snap.1450-T1
Valid prediction for GlimmerHMM_glimmerT_57408-T1
Valid prediction for Augustus_model.g38043.t1
Valid prediction for Augustus_model.g38032.t1
Couldn't classify 14741, 14950
Sorry, prediction pasa_asmbl_36577.p1 fails validation.
(GCT)	 AG	14741-14950	GT	AGG
(GTG)	 AG	15226-15399	GT	AGG
(ATC)	 AG	15613-15702	GT	AGG
(GGC)	 AG	15853-16014	GT	AGG
(GGA)	 AG	16323-16441	GT	TTG
(CCT)	 AG	16695-16767	AC	AAA
-recovered pasa_asmbl_36577.p1, terminal, 16695, 16767
-recovered pasa_asmbl_36577.p1, internal, 14741, 14950
-recovered pasa_asmbl_36577.p1, internal, 15226, 15399
-recovered pasa_asmbl_36577.p1, internal, 15613, 15702
-recovered pasa_asmbl_36577.p1, internal, 15853, 16014
-recovered pasa_asmbl_36577.p1, internal, 16323, 16441
Valid prediction for GlimmerHMM_glimmerT_57429-T1
Valid prediction for GlimmerHMM_glimmerT_57415-T1
Valid prediction for GlimmerHMM_glimmerT_57410-T1
Valid prediction for snap_scaffold_27-snap.1409-T1
Valid prediction for GlimmerHMM_glimmerT_57427-T1
Valid prediction for GlimmerHMM_glimmerT_57420-T1
Valid prediction for snap_scaffold_27-snap.1402-T1
Sorry, intron length (5) is less than minimum required (10)
Valid prediction for Augustus_model.g38041.t1
Valid prediction for Augustus_model.g38046.t1
Valid prediction for snap_scaffold_27-snap.1447-T1
Valid prediction for GlimmerHMM_glimmerT_57414-T1
Valid prediction for snap_scaffold_27-snap.1398-T1
Valid prediction for snap_scaffold_27-snap.1401-T1
Valid prediction for Augustus_model.g38034.t1
Valid prediction for GlimmerHMM_glimmerT_57407-T1
Valid prediction for GlimmerHMM_glimmerT_57432-T1
Valid prediction for HiQ_model.g38050.t1
Valid prediction for snap_scaffold_27-snap.1397-T1
Sorry, intron length (9) is less than minimum required (10)
Valid prediction for Augustus_model.g38048.t1
Valid prediction for snap_scaffold_27-snap.1439-T1
Valid prediction for snap_scaffold_27-snap.1449-T1
Valid prediction for GlimmerHMM_glimmerT_57433-T1
Valid prediction for snap_scaffold_27-snap.1445-T1
Valid prediction for snap_scaffold_27-snap.1399-T1
Valid prediction for GlimmerHMM_glimmerT_57422-T1
Valid prediction for snap_scaffold_27-snap.1394-T1
Valid prediction for snap_scaffold_27-snap.1396-T1
Valid prediction for snap_scaffold_27-snap.1442-T1
Valid prediction for snap_scaffold_27-snap.1426-T1
Valid prediction for snap_scaffold_27-snap.1408-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.g38037.t1
Valid prediction for snap_scaffold_27-snap.1422-T1
Valid prediction for snap_scaffold_27-snap.1443-T1
Valid prediction for snap_scaffold_27-snap.1444-T1
Valid prediction for snap_scaffold_27-snap.1436-T1
Valid prediction for pasa_asmbl_37047.p3
Valid prediction for GlimmerHMM_glimmerT_57426-T1
Valid prediction for snap_scaffold_27-snap.1423-T1
Valid prediction for Augustus_model.g38039.t1
Valid prediction for snap_scaffold_27-snap.1400-T1
Valid prediction for snap_scaffold_27-snap.1418-T1
Valid prediction for snap_scaffold_27-snap.1440-T1
Valid prediction for snap_scaffold_27-snap.1407-T1
Valid prediction for snap_scaffold_27-snap.1441-T1
Valid prediction for GlimmerHMM_glimmerT_57416-T1
Valid prediction for Augustus_model.g38038.t1
Valid prediction for snap_scaffold_27-snap.1413-T1
Valid prediction for snap_scaffold_27-snap.1411-T1
Valid prediction for GlimmerHMM_glimmerT_57409-T1
Valid prediction for snap_scaffold_27-snap.1430-T1
Valid prediction for Augustus_model.g38049.t1
Valid prediction for snap_scaffold_27-snap.1446-T1
Valid prediction for snap_scaffold_27-snap.1427-T1
Valid prediction for GlimmerHMM_glimmerT_57428-T1
Valid prediction for Augustus_model.g38040.t1
Valid prediction for GlimmerHMM_glimmerT_57417-T1
Valid prediction for snap_scaffold_27-snap.1412-T1
Valid prediction for snap_scaffold_27-snap.1432-T1
Valid prediction for snap_scaffold_27-snap.1424-T1
Valid prediction for snap_scaffold_27-snap.1431-T1
Valid prediction for snap_scaffold_27-snap.1406-T1
Valid prediction for GlimmerHMM_glimmerT_57419-T1
Valid prediction for snap_scaffold_27-snap.1448-T1
Valid prediction for GlimmerHMM_glimmerT_57411-T1
Valid prediction for snap_scaffold_27-snap.1404-T1
Valid prediction for Augustus_model.g38035.t1
Valid prediction for snap_scaffold_27-snap.1417-T1
Valid prediction for snap_scaffold_27-snap.1438-T1
Valid prediction for Augustus_model.g38036.t1
Valid prediction for GlimmerHMM_glimmerT_57421-T1
Valid prediction for Augustus_model.g38045.t1
Valid prediction for GlimmerHMM_glimmerT_57424-T1
Valid prediction for snap_scaffold_27-snap.1428-T1
Valid prediction for GlimmerHMM_glimmerT_57413-T1

-loading the search evidence (protein and EST search results, strand: -)
-scoring exons (strand: -)Error with prediction: snap lend_intergenic: 30457, rend_intergenic: 24340  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47990, rend_intergenic: 30585  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49622, rend_intergenic: 48838  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61013, rend_intergenic: 50005  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71038, rend_intergenic: 67291  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75143, rend_intergenic: 73541  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96196, rend_intergenic: 88434  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113149, rend_intergenic: 96960  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126409, rend_intergenic: 114306  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156273, rend_intergenic: 152706  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 198920, rend_intergenic: 173938  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 211656, rend_intergenic: 206718  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 226401, rend_intergenic: 223508  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 232339, rend_intergenic: 228257  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 237161, rend_intergenic: 232454  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 246752, rend_intergenic: 237952  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 250562, rend_intergenic: 247396  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 260545, rend_intergenic: 252381  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 263733, rend_intergenic: 261151  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-building DP trellis

-building trellis in range 1 - 271501
-exon list size: 525


building trellis

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-found 35 predictions from path traversal
Error with prediction: snap lend_intergenic: 30457, rend_intergenic: 24340  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 47990, rend_intergenic: 30585  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 49622, rend_intergenic: 48838  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 61013, rend_intergenic: 50005  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 71038, rend_intergenic: 67291  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 75143, rend_intergenic: 73541  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 96196, rend_intergenic: 88434  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 113149, rend_intergenic: 96960  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 126409, rend_intergenic: 114306  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 156273, rend_intergenic: 152706  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 198920, rend_intergenic: 173938  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 211656, rend_intergenic: 206718  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 226401, rend_intergenic: 223508  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 232339, rend_intergenic: 228257  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 237161, rend_intergenic: 232454  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 246752, rend_intergenic: 237952  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 250562, rend_intergenic: 247396  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 260545, rend_intergenic: 252381  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.
Error with prediction: snap lend_intergenic: 263733, rend_intergenic: 261151  at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218.

-reporting highest scoring path thru the trellis.
-found 21 predictions persist after filtering for low support