-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_2/scaffold_2_8141607-8525968 -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.6842_t Valid prediction for snap_scaffold_2-snap.1704-T1 Valid prediction for GlimmerHMM_glimmerT_4260-T1 Valid prediction for Augustus_model.g2871.t1 Couldn't classify 144436, 144530 Couldn't classify 144624, 144831 Sorry, prediction pasa_asmbl_25379.p1 fails validation. (GAT) AG 144436-144530 GT AGG (GAA) AG 144624-144831 CT TGC -recovered pasa_asmbl_25379.p1, internal, 144436, 144530 Couldn't classify 116225, 116620 Sorry, prediction pasa_asmbl_24655.p1 fails validation. (GTG) AG 116225-116620 GG TCG Valid prediction for GeneMark_model.6836_t Valid prediction for GeneMark_model.6835_t Couldn't classify 168008, 168037 Couldn't classify 172364, 172482 Sorry, prediction pasa_asmbl_24669.p1 fails validation. (AAG) GA 168008-168037 GT AGG (ATG) AG 168300-168386 GT GGG (GGC) AG 169735-169796 GT GAG (AAA) AG 170385-170495 GT AGG (ACC) AG 170868-171050 GT AGG (TTA) AG 171281-171420 GT AGG (TGA) AG 171630-171855 GT TGG (GTT) AG 171944-172044 GT TGG (CAA) AG 172207-172248 GT ATG (CTC) AG 172364-172482 CA AGC -recovered pasa_asmbl_24669.p1, initial, 168300, 168386 -recovered pasa_asmbl_24669.p1, internal, 168300, 168386 -recovered pasa_asmbl_24669.p1, internal, 169735, 169796 -recovered pasa_asmbl_24669.p1, internal, 170385, 170495 -recovered pasa_asmbl_24669.p1, internal, 170868, 171050 -recovered pasa_asmbl_24669.p1, internal, 171281, 171420 -recovered pasa_asmbl_24669.p1, internal, 171630, 171855 -recovered pasa_asmbl_24669.p1, internal, 171944, 172044 -recovered pasa_asmbl_24669.p1, internal, 172207, 172248 Valid prediction for snap_scaffold_2-snap.1705-T1 Valid prediction for GeneMark_model.6855_t Valid prediction for Augustus_model.g2876.t1 Valid prediction for snap_scaffold_2-snap.1700-T1 Valid prediction for Augustus_model.g2868.t1 Valid prediction for Augustus_model.g2869.t1 Valid prediction for GeneMark_model.6841_t Valid prediction for pasa_asmbl_24672.p1 Valid prediction for GeneMark_model.6848_t Valid prediction for GlimmerHMM_glimmerT_4268-T1 Sorry, intron length (3) is less than minimum required (10) Couldn't classify 172741, 172802 Couldn't classify 174118, 174187 Sorry, prediction pasa_asmbl_24670.p1 fails validation. (AAC) AG 172741-172802 GT AGG (GTG) AG 172978-173194 GT CGG (ATC) AG 173292-173381 GT AGG (GGG) AG 173496-173686 GT AAG (GTT) AG 173795-173983 GT AAG (GTG) AG 174118-174187 AT ACA -recovered pasa_asmbl_24670.p1, internal, 172741, 172802 -recovered pasa_asmbl_24670.p1, internal, 172978, 173194 -recovered pasa_asmbl_24670.p1, internal, 173292, 173381 -recovered pasa_asmbl_24670.p1, internal, 173496, 173686 -recovered pasa_asmbl_24670.p1, internal, 173795, 173983 Valid prediction for GlimmerHMM_glimmerT_4246-T1 Valid prediction for GlimmerHMM_glimmerT_4274-T1 Valid prediction for GeneMark_model.6843_t Valid prediction for GeneMark_model.6849_t Valid prediction for snap_scaffold_2-snap.1714-T1 Sorry, intron length (3) is less than minimum required (10) Valid prediction for GlimmerHMM_glimmerT_4263-T1 Valid prediction for Augustus_model.g2880.t1 Valid prediction for CodingQuarry_transcript_28572-T1 Valid prediction for snap_scaffold_2-snap.1703-T1 Valid prediction for GlimmerHMM_glimmerT_4270-T1 Valid prediction for GlimmerHMM_glimmerT_4257-T1 Valid prediction for snap_scaffold_2-snap.1706-T1 Valid prediction for snap_scaffold_2-snap.1698-T1 Valid prediction for GlimmerHMM_glimmerT_4258-T1 Valid prediction for Augustus_model.g2878.t1 Valid prediction for GlimmerHMM_glimmerT_4262-T1 Valid prediction for GeneMark_model.6844_t Valid prediction for snap_scaffold_2-snap.1712-T1 Sorry, intron length (4) is less than minimum required (10) Valid prediction for snap_scaffold_2-snap.1702-T1 Valid prediction for GlimmerHMM_glimmerT_4249-T1 Valid prediction for snap_scaffold_2-snap.1723-T1 Valid prediction for snap_scaffold_2-snap.1697-T1 Valid prediction for snap_scaffold_2-snap.1709-T1 Valid prediction for GlimmerHMM_glimmerT_4266-T1 Valid prediction for snap_scaffold_2-snap.1694-T1 Valid prediction for Augustus_model.g2860.t1 Couldn't classify 134357, 134456 Sorry, prediction pasa_asmbl_24656.p1 fails validation. (GGA) CA 134357-134456 GT CAG (GTC) AG 134554-134823 GT AGG (TGA) AG 135423-135587 GT AGG (GTA) AG 135811-136009 GT GAG (GAC) AG 136805-136940 GT CAG (AAT) AG 137573-137745 GT CGG (TAC) AG 137853-137917 GT AGG (GAT) AG 138222-138598 AT AGA add_exon() Sorry, pasa_asmbl_24656.p1 135423-135587-terminal-1 is invalid. -recovered pasa_asmbl_24656.p1, terminal, 135423, 135587 add_exon() Sorry, pasa_asmbl_24656.p1 137853-137917-terminal-2 is invalid. -recovered pasa_asmbl_24656.p1, terminal, 137853, 137917 -recovered pasa_asmbl_24656.p1, terminal, 138222, 138598 -recovered pasa_asmbl_24656.p1, internal, 134554, 134823 -recovered pasa_asmbl_24656.p1, internal, 135423, 135587 -recovered pasa_asmbl_24656.p1, internal, 135811, 136009 -recovered pasa_asmbl_24656.p1, internal, 136805, 136940 -recovered pasa_asmbl_24656.p1, internal, 137573, 137745 -recovered pasa_asmbl_24656.p1, internal, 137853, 137917 Valid prediction for snap_scaffold_2-snap.1696-T1 Valid prediction for snap_scaffold_2-snap.1692-T1 Valid prediction for HiQ_model.g2864.t1 Valid prediction for snap_scaffold_2-snap.1707-T1 Valid prediction for GlimmerHMM_glimmerT_4273-T1 Valid prediction for Augustus_model.g2861.t1 Valid prediction for GlimmerHMM_glimmerT_4253-T1 Valid prediction for GeneMark_model.6839_t Couldn't classify 174245, 174280 Sorry, prediction pasa_asmbl_24671.p1 fails validation. (GAG) AG 174245-174280 GT AGG (AAC) AG 174487-174639 GT AGG (CGC) AG 175140-175211 GT AGG (GAC) AG 175619-175768 GT AGG (GTG) AG 175871-176019 GT AAG (TTC) AG 176117-176213 GT AGG (GAA) AG 176308-176400 GT AGG (GTG) AG 176508-176681 GT GGG (GCG) AG 177195-177406 GT AGG (ACT) AG 177507-177646 GT AGG (CCA) AG 177720-177858 GT AAG (GTT) AG 177942-178092 GT AAG (ATC) AG 178196-178318 GC AGG (ACC) AG 178451-178573 GT AGG (GAT) AG 178704-178844 GT AGG (GTT) AG 179095-179208 GT TAG (TGC) AG 179421-179599 GT CGG (GAA) AG 179696-179795 GT ACG (AAG) AG 179917-180118 GT TGG (ATA) AG 180223-180472 GC AGG (GCA) AG 180821-181112 AG GAA -recovered pasa_asmbl_24671.p1, terminal, 180821, 181112 -recovered pasa_asmbl_24671.p1, internal, 174245, 174280 -recovered pasa_asmbl_24671.p1, internal, 174487, 174639 -recovered pasa_asmbl_24671.p1, internal, 175140, 175211 -recovered pasa_asmbl_24671.p1, internal, 175619, 175768 -recovered pasa_asmbl_24671.p1, internal, 175871, 176019 -recovered pasa_asmbl_24671.p1, internal, 176117, 176213 -recovered pasa_asmbl_24671.p1, internal, 176308, 176400 -recovered pasa_asmbl_24671.p1, internal, 176508, 176681 -recovered pasa_asmbl_24671.p1, internal, 177195, 177406 -recovered pasa_asmbl_24671.p1, internal, 177507, 177646 -recovered pasa_asmbl_24671.p1, internal, 177720, 177858 -recovered pasa_asmbl_24671.p1, internal, 177942, 178092 -recovered pasa_asmbl_24671.p1, internal, 178196, 178318 -recovered pasa_asmbl_24671.p1, internal, 178451, 178573 -recovered pasa_asmbl_24671.p1, internal, 178704, 178844 -recovered pasa_asmbl_24671.p1, internal, 179095, 179208 -recovered pasa_asmbl_24671.p1, internal, 179421, 179599 -recovered pasa_asmbl_24671.p1, internal, 179696, 179795 -recovered pasa_asmbl_24671.p1, internal, 179917, 180118 -recovered pasa_asmbl_24671.p1, internal, 180223, 180472 Valid prediction for Augustus_model.g2870.t1 Valid prediction for GeneMark_model.6831_t Valid prediction for HiQ_model.g2874.t1 Valid prediction for Augustus_model.g2872.t1 Valid prediction for snap_scaffold_2-snap.1691-T1 Couldn't classify 45171, 45277 Sorry, prediction pasa_asmbl_24652.p1 fails validation. (TCC) CG 45171-45277 GT GGG (GGA) AG 45955-46118 GT TAG (GTA) AG 48425-48666 GT ATG (ATT) AG 49488-49612 GT AGG (GAA) AG 51147-51261 GT TGG (AAA) AG 51586-52042 GT TGG (ACC) AG 52404-52467 GT ATG (AAA) AG 52882-53053 GT AGG (CTT) AG 53179-53223 GT AGG (AAG) AG 53346-53456 CT AGC -recovered pasa_asmbl_24652.p1, terminal, 53346, 53456 -recovered pasa_asmbl_24652.p1, internal, 45955, 46118 -recovered pasa_asmbl_24652.p1, internal, 48425, 48666 -recovered pasa_asmbl_24652.p1, internal, 49488, 49612 -recovered pasa_asmbl_24652.p1, internal, 51147, 51261 -recovered pasa_asmbl_24652.p1, internal, 51586, 52042 -recovered pasa_asmbl_24652.p1, internal, 52404, 52467 -recovered pasa_asmbl_24652.p1, internal, 52882, 53053 -recovered pasa_asmbl_24652.p1, internal, 53179, 53223 Valid prediction for snap_scaffold_2-snap.1708-T1 Valid prediction for snap_scaffold_2-snap.1722-T1 Valid prediction for GeneMark_model.6847_t Valid prediction for snap_scaffold_2-snap.1720-T1 Valid prediction for snap_scaffold_2-snap.1716-T1 Valid prediction for CodingQuarry_transcript_28573-T1 Valid prediction for GeneMark_model.6837_t Valid prediction for GlimmerHMM_glimmerT_4254-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_4255-T1 Valid prediction for HiQ_model.g2879.t1 Valid prediction for GeneMark_model.6851_t Valid prediction for Augustus_model.g2877.t1 Valid prediction for GlimmerHMM_glimmerT_4250-T1 Valid prediction for GeneMark_model.6850_t Valid prediction for GlimmerHMM_glimmerT_4275-T1 Valid prediction for GeneMark_model.6838_t Valid prediction for CodingQuarry_transcript_28571-T1 Valid prediction for GeneMark_model.6856_t Valid prediction for GlimmerHMM_glimmerT_4272-T1 Valid prediction for Augustus_model.g2866.t1 Valid prediction for snap_scaffold_2-snap.1693-T1 Valid prediction for GeneMark_model.6832_t Valid prediction for GeneMark_model.6833_t Valid prediction for GlimmerHMM_glimmerT_4248-T1 Valid prediction for Augustus_model.g2875.t1 Valid prediction for GlimmerHMM_glimmerT_4261-T1 Valid prediction for GeneMark_model.6852_t Valid prediction for GlimmerHMM_glimmerT_4256-T1 Valid prediction for Augustus_model.g2867.t1 Valid prediction for GeneMark_model.6846_t Valid prediction for snap_scaffold_2-snap.1699-T1 Valid prediction for GeneMark_model.6857_t Valid prediction for GlimmerHMM_glimmerT_4271-T1 Valid prediction for snap_scaffold_2-snap.1718-T1 Valid prediction for GlimmerHMM_glimmerT_4267-T1 Valid prediction for snap_scaffold_2-snap.1719-T1 Valid prediction for Augustus_model.g2862.t1 Valid prediction for pasa_asmbl_23349.p1 Valid prediction for snap_scaffold_2-snap.1710-T1 Valid prediction for GlimmerHMM_glimmerT_4247-T1 Valid prediction for GlimmerHMM_glimmerT_4264-T1 Couldn't classify 373011, 373090 Sorry, prediction pasa_asmbl_23337.p1 fails validation. (GAA) AG 373011-373090 GT AAG (GGC) AG 374637-374683 GT CGG (GGG) AG 377468-377573 GC AGG (GGA) AG 377757-377826 CA AAC -recovered pasa_asmbl_23337.p1, terminal, 377757, 377826 -recovered pasa_asmbl_23337.p1, internal, 373011, 373090 -recovered pasa_asmbl_23337.p1, internal, 374637, 374683 -recovered pasa_asmbl_23337.p1, internal, 377468, 377573 Valid prediction for GlimmerHMM_glimmerT_4251-T1 Valid prediction for GlimmerHMM_glimmerT_4265-T1 Valid prediction for snap_scaffold_2-snap.1717-T1 Valid prediction for snap_scaffold_2-snap.1695-T1 Valid prediction for snap_scaffold_2-snap.1715-T1 Valid prediction for snap_scaffold_2-snap.1701-T1 Valid prediction for Augustus_model.g2865.t1 Valid prediction for GeneMark_model.6834_t Valid prediction for GeneMark_model.6853_t Valid prediction for CodingQuarry_transcript_28574-T1 Valid prediction for GlimmerHMM_glimmerT_4252-T1 Valid prediction for GeneMark_model.6854_t Valid prediction for snap_scaffold_2-snap.1721-T1 Valid prediction for GlimmerHMM_glimmerT_4259-T1 Valid prediction for snap_scaffold_2-snap.1711-T1 Valid prediction for GlimmerHMM_glimmerT_4269-T1 Valid prediction for snap_scaffold_2-snap.1713-T1 Couldn't classify 368691, 368883 Sorry, prediction pasa_asmbl_23339.p1 fails validation. (CCT) CA 368691-368883 GT AGG (ACG) AG 369954-370135 GT AGG (CTT) AG 370322-370399 GT AGG (GCC) AG 371320-371457 GT CTG (GGA) AG 371567-371653 CG GAC -recovered pasa_asmbl_23339.p1, terminal, 371567, 371653 -recovered pasa_asmbl_23339.p1, internal, 369954, 370135 -recovered pasa_asmbl_23339.p1, internal, 370322, 370399 -recovered pasa_asmbl_23339.p1, internal, 371320, 371457 Valid prediction for HiQ_model.g2873.t1 Valid prediction for GeneMark_model.6840_t Valid prediction for Augustus_model.g2863.t1 -loading the search evidence (protein and EST search results, strand: -) -scoring exons (strand: -)Error with prediction: snap lend_intergenic: 107514, rend_intergenic: 105560 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -building DP trellis -building trellis in range 1 - 384362 -exon list size: 425 building trellis 0.2 0.5 0.7 0.9 1.2 1.4 1.6 1.9 2.1 2.3 2.6 2.8 3.0 3.3 3.5 3.7 4.0 4.2 4.4 4.7 4.9 5.2 5.4 5.6 5.9 6.1 6.3 6.6 6.8 7.0 7.3 7.5 7.7 8.0 8.2 8.4 8.7 8.9 9.1 9.4 9.6 9.8 10.1 10.3 10.5 10.8 11.0 11.2 11.5 11.7 11.9 12.2 12.4 12.6 12.9 13.1 13.3 13.6 13.8 14.1 14.3 14.5 14.8 15.0 15.2 15.5 15.7 15.9 16.2 16.4 16.6 16.9 17.1 17.3 17.6 17.8 18.0 18.3 18.5 18.7 19.0 19.2 19.4 19.7 19.9 20.1 20.4 20.6 20.8 21.1 21.3 21.5 21.8 22.0 22.2 22.5 22.7 23.0 23.2 23.4 23.7 23.9 24.1 24.4 24.6 24.8 25.1 25.3 25.5 25.8 26.0 26.2 26.5 26.7 26.9 27.2 27.4 27.6 27.9 28.1 28.3 28.6 28.8 29.0 29.3 29.5 29.7 30.0 30.2 30.4 30.7 30.9 31.1 31.4 31.6 31.9 32.1 32.3 32.6 32.8 33.0 33.3 33.5 33.7 34.0 34.2 34.4 34.7 34.9 35.1 35.4 35.6 35.8 36.1 36.3 36.5 36.8 37.0 37.2 37.5 37.7 37.9 38.2 38.4 38.6 38.9 39.1 39.3 39.6 39.8 40.0 40.3 40.5 40.7 41.0 41.2 41.5 41.7 41.9 42.2 42.4 42.6 42.9 43.1 43.3 43.6 43.8 44.0 44.3 44.5 44.7 45.0 45.2 45.4 45.7 45.9 46.1 46.4 46.6 46.8 47.1 47.3 47.5 47.8 48.0 48.2 48.5 48.7 48.9 49.2 49.4 49.6 49.9 50.1 50.4 50.6 50.8 51.1 51.3 51.5 51.8 52.0 52.2 52.5 52.7 52.9 53.2 53.4 53.6 53.9 54.1 54.3 54.6 54.8 55.0 55.3 55.5 55.7 56.0 56.2 56.4 56.7 56.9 57.1 57.4 57.6 57.8 58.1 58.3 58.5 58.8 59.0 59.3 59.5 59.7 60.0 60.2 60.4 60.7 60.9 61.1 61.4 61.6 61.8 62.1 62.3 62.5 62.8 63.0 63.2 63.5 63.7 63.9 64.2 64.4 64.6 64.9 65.1 65.3 65.6 65.8 66.0 66.3 66.5 66.7 67.0 67.2 67.4 67.7 67.9 68.1 68.4 68.6 68.9 69.1 69.3 69.6 69.8 70.0 70.3 70.5 70.7 71.0 71.2 71.4 71.7 71.9 72.1 72.4 72.6 72.8 73.1 73.3 73.5 73.8 74.0 74.2 74.5 74.7 74.9 75.2 75.4 75.6 75.9 76.1 76.3 76.6 76.8 77.0 77.3 77.5 77.8 78.0 78.2 78.5 78.7 78.9 79.2 79.4 79.6 79.9 80.1 80.3 80.6 80.8 81.0 81.3 81.5 81.7 82.0 82.2 82.4 82.7 82.9 83.1 83.4 83.6 83.8 84.1 84.3 84.5 84.8 85.0 85.2 85.5 85.7 85.9 86.2 86.4 86.7 86.9 87.1 87.4 87.6 87.8 88.1 88.3 88.5 88.8 89.0 89.2 89.5 89.7 89.9 90.2 90.4 90.6 90.9 91.1 91.3 91.6 91.8 92.0 92.3 92.5 92.7 93.0 93.2 93.4 93.7 93.9 94.1 94.4 94.6 94.8 95.1 95.3 95.6 95.8 96.0 96.3 96.5 96.7 97.0 97.2 97.4 97.7 97.9 98.1 98.4 98.6 98.8 99.1 99.3 99.5 99.8 -found 22 predictions from path traversal Error with prediction: snap lend_intergenic: 107514, rend_intergenic: 105560 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -reporting highest scoring path thru the trellis. -found 19 predictions persist after filtering for low support -building DP trellis -building trellis in range 370550 - 384362 -exon list size: 2 building trellis 25.0 50.0 75.0 -found 1 predictions from path traversal GOT 5prime partial gene. -reporting highest scoring path thru the trellis. -found 0 predictions persist after filtering for low support -building DP trellis -building trellis in range 371251 - 384362 -exon list size: 1 building trellis 33.3 66.7 -found 1 predictions from path traversal -reporting highest scoring path thru the trellis. -found 0 predictions persist after filtering for low support