-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_6/scaffold_6_7150327-7396421 -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_55089-T1 Valid prediction for Augustus_model.g9875.t1 Valid prediction for Augustus_model.g9887.t1 Valid prediction for snap_scaffold_6-snap.1639-T1 Valid prediction for Augustus_model.g9889.t1 Valid prediction for snap_scaffold_6-snap.1611-T1 Valid prediction for snap_scaffold_6-snap.1632-T1 Valid prediction for Augustus_model.g9888.t1 Couldn't classify 4251, 4330 Sorry, prediction pasa_asmbl_47047.p1 fails validation. (CAA) AG 4251-4330 GT AGG (GTG) AG 4565-4670 GT AGG (TAC) AG 4877-4993 GT AGG (GTG) AG 5771-5935 GT GGG (GAC) AG 6131-6259 GT AGG (GCT) AG 6586-6741 GT AGG (GTG) AG 6887-7000 GT CTG (GTG) AG 7195-7287 GT CAG (GAC) AG 7402-7518 CG AAC -recovered pasa_asmbl_47047.p1, terminal, 4251, 4330 -recovered pasa_asmbl_47047.p1, terminal, 7402, 7518 -recovered pasa_asmbl_47047.p1, internal, 4251, 4330 -recovered pasa_asmbl_47047.p1, internal, 4565, 4670 -recovered pasa_asmbl_47047.p1, internal, 4877, 4993 -recovered pasa_asmbl_47047.p1, internal, 5771, 5935 -recovered pasa_asmbl_47047.p1, internal, 6131, 6259 -recovered pasa_asmbl_47047.p1, internal, 6586, 6741 -recovered pasa_asmbl_47047.p1, internal, 6887, 7000 -recovered pasa_asmbl_47047.p1, internal, 7195, 7287 Valid prediction for snap_scaffold_6-snap.1642-T1 Valid prediction for pasa_asmbl_47048.p1 Couldn't classify 195877, 195963 Sorry, prediction pasa_asmbl_47072.p1 fails validation. (TCA) CC 195877-195963 GT AGG (CGG) AG 198233-198297 GT AGG (GAA) AG 199298-199364 GT AGG (GGG) AG 199446-199564 GT AGG (AGA) AG 200394-200474 GT AGG (ACA) AG 200848-200960 GT AGG (ACA) AG 201774-201922 GT GGG (AAC) AG 202346-202507 GA AGG -recovered pasa_asmbl_47072.p1, terminal, 202346, 202507 -recovered pasa_asmbl_47072.p1, internal, 198233, 198297 -recovered pasa_asmbl_47072.p1, internal, 199298, 199364 -recovered pasa_asmbl_47072.p1, internal, 199446, 199564 -recovered pasa_asmbl_47072.p1, internal, 200394, 200474 -recovered pasa_asmbl_47072.p1, internal, 200848, 200960 -recovered pasa_asmbl_47072.p1, internal, 201774, 201922 Valid prediction for CodingQuarry_transcript_55088-T1 Valid prediction for Augustus_model.g9884.t1 Valid prediction for snap_scaffold_6-snap.1608-T1 Couldn't classify 139826, 139950 Sorry, prediction pasa_asmbl_47063.p1 fails validation. (ATG) CC 139081-139711 GT AGG (GGT) AG 139826-139950 CC GGC -recovered pasa_asmbl_47063.p1, initial, 139081, 139711 Valid prediction for HiQ_model.g9882.t1 Valid prediction for GlimmerHMM_glimmerT_14913-T1 Valid prediction for Augustus_model.g9868.t1 Valid prediction for GlimmerHMM_glimmerT_14937-T1 Valid prediction for GlimmerHMM_glimmerT_14918-T1 Valid prediction for Augustus_model.g9883.t1 Valid prediction for GlimmerHMM_glimmerT_14928-T1 Valid prediction for snap_scaffold_6-snap.1622-T1 Valid prediction for GlimmerHMM_glimmerT_14922-T1 Valid prediction for Augustus_model.g9885.t1 Valid prediction for pasa_asmbl_47062.p1 Valid prediction for HiQ_model.g9873.t1 Valid prediction for snap_scaffold_6-snap.1636-T1 Valid prediction for snap_scaffold_6-snap.1615-T1 Valid prediction for snap_scaffold_6-snap.1641-T1 Couldn't classify 140011, 140029 Sorry, prediction pasa_asmbl_47065.p3 fails validation. (GCC) CC 140011-140029 GT AGG (GCT) AG 140227-140597 GT AGG -recovered pasa_asmbl_47065.p3, terminal, 140227, 140597 -recovered pasa_asmbl_47065.p3, internal, 140227, 140597 Valid prediction for CodingQuarry_transcript_55099-T1 Valid prediction for GlimmerHMM_glimmerT_14916-T1 Valid prediction for snap_scaffold_6-snap.1633-T1 Valid prediction for snap_scaffold_6-snap.1643-T1 Valid prediction for CodingQuarry_transcript_55097-T1 Valid prediction for CodingQuarry_transcript_55093-T1 Valid prediction for snap_scaffold_6-snap.1630-T1 Valid prediction for snap_scaffold_6-snap.1618-T1 Valid prediction for snap_scaffold_6-snap.1634-T1 Sorry, intron length (4) is less than minimum required (10) Sorry, intron length (4) is less than minimum required (10) Valid prediction for GlimmerHMM_glimmerT_14931-T1 Valid prediction for GlimmerHMM_glimmerT_14920-T1 Valid prediction for pasa_asmbl_47068.p1 Valid prediction for GlimmerHMM_glimmerT_14932-T1 Valid prediction for Augustus_model.g9886.t1 Valid prediction for snap_scaffold_6-snap.1609-T1 Valid prediction for snap_scaffold_6-snap.1637-T1 Valid prediction for GlimmerHMM_glimmerT_14929-T1 Couldn't classify 167497, 167999 Sorry, prediction pasa_asmbl_47070.p1 fails validation. (TCC) CC 167497-167999 GT AGG (CAT) AG 168135-168400 GT AGG (CTG) AG 168656-168841 GT AGG (TCC) AG 168996-169111 GT AGG (GTG) AG 169293-169424 CG GAC -recovered pasa_asmbl_47070.p1, terminal, 169293, 169424 -recovered pasa_asmbl_47070.p1, internal, 168135, 168400 -recovered pasa_asmbl_47070.p1, internal, 168656, 168841 -recovered pasa_asmbl_47070.p1, internal, 168996, 169111 Valid prediction for HiQ_model.g9867.t1 Valid prediction for GlimmerHMM_glimmerT_14938-T1 Valid prediction for snap_scaffold_6-snap.1617-T1 Valid prediction for snap_scaffold_6-snap.1631-T1 Valid prediction for GlimmerHMM_glimmerT_14927-T1 Valid prediction for GlimmerHMM_glimmerT_14930-T1 Valid prediction for snap_scaffold_6-snap.1644-T1 Valid prediction for snap_scaffold_6-snap.1607-T1 Valid prediction for pasa_asmbl_47052.p1 Valid prediction for GlimmerHMM_glimmerT_14935-T1 Valid prediction for snap_scaffold_6-snap.1620-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: -)Couldn't classify 202077, 202090 Sorry, prediction pasa_asmbl_48484.p1 fails validation. (TCT) CA 202077-202090 GT AGG (TGT) AG 202210-202377 GT GGG (CTG) AG 202817-203021 GT TGG (CTC) AG 203245-203430 GT AGG (GTT) AG 203514-203639 GT AGG (GGT) AG 203756-203914 GA AAG -recovered pasa_asmbl_48484.p1, terminal, 203756, 203914 -recovered pasa_asmbl_48484.p1, internal, 202210, 202377 -recovered pasa_asmbl_48484.p1, internal, 202817, 203021 -recovered pasa_asmbl_48484.p1, internal, 203245, 203430 -recovered pasa_asmbl_48484.p1, internal, 203514, 203639 Valid prediction for Augustus_model.g9879.t1 Valid prediction for snap_scaffold_6-snap.1606-T1 Valid prediction for snap_scaffold_6-snap.1616-T1 Valid prediction for Augustus_model.g9877.t1 Valid prediction for HiQ_model.g9881.t1 Valid prediction for snap_scaffold_6-snap.1638-T1 Valid prediction for pasa_asmbl_48483.p1 Valid prediction for HiQ_model.g9871.t1 Valid prediction for snap_scaffold_6-snap.1624-T1 Valid prediction for snap_scaffold_6-snap.1640-T1 Valid prediction for pasa_asmbl_48490.p1 Valid prediction for GlimmerHMM_glimmerT_14926-T1 Valid prediction for Augustus_model.g9876.t1 Valid prediction for GlimmerHMM_glimmerT_14921-T1 Valid prediction for GlimmerHMM_glimmerT_14924-T1 Valid prediction for GlimmerHMM_glimmerT_14915-T1 Valid prediction for CodingQuarry_transcript_55091-T1 Valid prediction for snap_scaffold_6-snap.1629-T1 Valid prediction for snap_scaffold_6-snap.1623-T1 Valid prediction for snap_scaffold_6-snap.1645-T1 Valid prediction for GlimmerHMM_glimmerT_14914-T1 Valid prediction for snap_scaffold_6-snap.1621-T1 Valid prediction for GlimmerHMM_glimmerT_14912-T1 Valid prediction for GlimmerHMM_glimmerT_14919-T1 Valid prediction for GlimmerHMM_glimmerT_14925-T1 Valid prediction for snap_scaffold_6-snap.1625-T1 Valid prediction for GlimmerHMM_glimmerT_14934-T1 Couldn't classify 129759, 129878 Sorry, prediction pasa_asmbl_48486.p1 fails validation. (GAG) AC 129759-129878 GT TGG (GCC) AG 130011-130100 GT AGG (ATC) AG 130374-130514 GC AGG (GAG) AG 130619-130712 GT CAG (GCT) AG 130934-131080 GT AGG (AGA) AG 132805-132911 GT AGG (GAC) AG 133022-133120 AA AGA -recovered pasa_asmbl_48486.p1, terminal, 133022, 133120 -recovered pasa_asmbl_48486.p1, internal, 130011, 130100 -recovered pasa_asmbl_48486.p1, internal, 130374, 130514 -recovered pasa_asmbl_48486.p1, internal, 130619, 130712 -recovered pasa_asmbl_48486.p1, internal, 130934, 131080 -recovered pasa_asmbl_48486.p1, internal, 132805, 132911 Valid prediction for CodingQuarry_transcript_55095-T1 Valid prediction for pasa_asmbl_48480.p1 Couldn't classify 128975, 129079 Sorry, prediction pasa_asmbl_48487.p1 fails validation. (ATG) AC 125547-125561 GT AGG (AGG) AG 126781-126928 GT AGG (ATT) AG 127628-127810 GT GGG (ACC) AG 127939-128178 GT GGG (GCC) AG 128274-128356 GT AGG (GTG) AG 128454-128558 GT ATG (ACT) AG 128737-128835 GT TGG (GAC) AG 128975-129079 GA AGG -recovered pasa_asmbl_48487.p1, initial, 125547, 125561 -recovered pasa_asmbl_48487.p1, internal, 126781, 126928 -recovered pasa_asmbl_48487.p1, internal, 127628, 127810 -recovered pasa_asmbl_48487.p1, internal, 127939, 128178 -recovered pasa_asmbl_48487.p1, internal, 128274, 128356 -recovered pasa_asmbl_48487.p1, internal, 128454, 128558 -recovered pasa_asmbl_48487.p1, internal, 128737, 128835 Couldn't classify 114774, 116373 Sorry, prediction pasa_asmbl_48489.p1 fails validation. (CGT) AT 114774-116373 GT AGG (GTG) AG 116658-116943 GT AGG (GTA) AG 117231-117363 GT AGG (GAC) AG 117472-117756 CA GAC add_exon() Sorry, pasa_asmbl_48489.p1 116658-116943-terminal-3 is invalid. -recovered pasa_asmbl_48489.p1, terminal, 116658, 116943 -recovered pasa_asmbl_48489.p1, terminal, 117472, 117756 -recovered pasa_asmbl_48489.p1, internal, 116658, 116943 -recovered pasa_asmbl_48489.p1, internal, 117231, 117363 Valid prediction for snap_scaffold_6-snap.1613-T1 Valid prediction for HiQ_model.g9878.t1 Valid prediction for snap_scaffold_6-snap.1619-T1 Valid prediction for Augustus_model.g9872.t1 Valid prediction for GlimmerHMM_glimmerT_14936-T1 Valid prediction for snap_scaffold_6-snap.1635-T1 Valid prediction for CodingQuarry_transcript_55096-T1 Valid prediction for CodingQuarry_transcript_55092-T1 Valid prediction for GlimmerHMM_glimmerT_14917-T1 Couldn't classify 200482, 200616 Couldn't classify 201746, 201851 Sorry, prediction pasa_asmbl_48485.p1 fails validation. (ACA) CC 200482-200616 GT ATG (TGC) AG 200705-200863 GT CAG (CTG) AG 201183-201339 GT GGG (GGA) AG 201560-201635 GT AGG (CCT) AG 201746-201851 GT AGG -recovered pasa_asmbl_48485.p1, internal, 200705, 200863 -recovered pasa_asmbl_48485.p1, internal, 201183, 201339 -recovered pasa_asmbl_48485.p1, internal, 201560, 201635 -recovered pasa_asmbl_48485.p1, internal, 201746, 201851 Valid prediction for snap_scaffold_6-snap.1626-T1 Valid prediction for HiQ_model.g9870.t1 Valid prediction for snap_scaffold_6-snap.1627-T1 Valid prediction for GlimmerHMM_glimmerT_14923-T1 Couldn't classify 199275, 199312 Couldn't classify 200102, 200160 Sorry, prediction pasa_asmbl_49324.p1 fails validation. (GGA) GT 199275-199312 GT AGG (TCT) AG 199599-199756 GT GGG (GTG) AG 199848-199925 GT GGG (GCA) AG 200102-200160 CA CCC -recovered pasa_asmbl_49324.p1, internal, 199599, 199756 -recovered pasa_asmbl_49324.p1, internal, 199848, 199925 Valid prediction for snap_scaffold_6-snap.1628-T1 Valid prediction for CodingQuarry_transcript_55094-T1 Valid prediction for snap_scaffold_6-snap.1612-T1 Valid prediction for snap_scaffold_6-snap.1610-T1 Valid prediction for Augustus_model.g9869.t1 Valid prediction for CodingQuarry_transcript_55090-T1 Valid prediction for Augustus_model.g9874.t1 Valid prediction for GlimmerHMM_glimmerT_14933-T1 Valid prediction for Augustus_model.g9880.t1 Valid prediction for snap_scaffold_6-snap.1614-T1 -loading the search evidence (protein and EST search results, strand: -) -scoring exons (strand: -)Error with prediction: snap lend_intergenic: 28567, rend_intergenic: 27211 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 81659, rend_intergenic: 67803 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 90797, rend_intergenic: 84088 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 99913, rend_intergenic: 98504 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 105332, rend_intergenic: 103748 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 177584, rend_intergenic: 175272 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 180841, rend_intergenic: 178346 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 198898, rend_intergenic: 186405 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 203781, rend_intergenic: 200341 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: GlimmerHMM lend_intergenic: 26188, rend_intergenic: 26185 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -building DP trellis -building trellis in range 1 - 246095 -exon list size: 401 building trellis 0.2 0.5 0.7 1.0 1.2 1.5 1.7 2.0 2.2 2.5 2.7 3.0 3.2 3.5 3.7 4.0 4.2 4.5 4.7 5.0 5.2 5.5 5.7 6.0 6.2 6.5 6.7 6.9 7.2 7.4 7.7 7.9 8.2 8.4 8.7 8.9 9.2 9.4 9.7 9.9 10.2 10.4 10.7 10.9 11.2 11.4 11.7 11.9 12.2 12.4 12.7 12.9 13.2 13.4 13.6 13.9 14.1 14.4 14.6 14.9 15.1 15.4 15.6 15.9 16.1 16.4 16.6 16.9 17.1 17.4 17.6 17.9 18.1 18.4 18.6 18.9 19.1 19.4 19.6 19.9 20.1 20.3 20.6 20.8 21.1 21.3 21.6 21.8 22.1 22.3 22.6 22.8 23.1 23.3 23.6 23.8 24.1 24.3 24.6 24.8 25.1 25.3 25.6 25.8 26.1 26.3 26.6 26.8 27.0 27.3 27.5 27.8 28.0 28.3 28.5 28.8 29.0 29.3 29.5 29.8 30.0 30.3 30.5 30.8 31.0 31.3 31.5 31.8 32.0 32.3 32.5 32.8 33.0 33.3 33.5 33.7 34.0 34.2 34.5 34.7 35.0 35.2 35.5 35.7 36.0 36.2 36.5 36.7 37.0 37.2 37.5 37.7 38.0 38.2 38.5 38.7 39.0 39.2 39.5 39.7 40.0 40.2 40.4 40.7 40.9 41.2 41.4 41.7 41.9 42.2 42.4 42.7 42.9 43.2 43.4 43.7 43.9 44.2 44.4 44.7 44.9 45.2 45.4 45.7 45.9 46.2 46.4 46.7 46.9 47.1 47.4 47.6 47.9 48.1 48.4 48.6 48.9 49.1 49.4 49.6 49.9 50.1 50.4 50.6 50.9 51.1 51.4 51.6 51.9 52.1 52.4 52.6 52.9 53.1 53.3 53.6 53.8 54.1 54.3 54.6 54.8 55.1 55.3 55.6 55.8 56.1 56.3 56.6 56.8 57.1 57.3 57.6 57.8 58.1 58.3 58.6 58.8 59.1 59.3 59.6 59.8 60.0 60.3 60.5 60.8 61.0 61.3 61.5 61.8 62.0 62.3 62.5 62.8 63.0 63.3 63.5 63.8 64.0 64.3 64.5 64.8 65.0 65.3 65.5 65.8 66.0 66.3 66.5 66.7 67.0 67.2 67.5 67.7 68.0 68.2 68.5 68.7 69.0 69.2 69.5 69.7 70.0 70.2 70.5 70.7 71.0 71.2 71.5 71.7 72.0 72.2 72.5 72.7 73.0 73.2 73.4 73.7 73.9 74.2 74.4 74.7 74.9 75.2 75.4 75.7 75.9 76.2 76.4 76.7 76.9 77.2 77.4 77.7 77.9 78.2 78.4 78.7 78.9 79.2 79.4 79.7 79.9 80.1 80.4 80.6 80.9 81.1 81.4 81.6 81.9 82.1 82.4 82.6 82.9 83.1 83.4 83.6 83.9 84.1 84.4 84.6 84.9 85.1 85.4 85.6 85.9 86.1 86.4 86.6 86.8 87.1 87.3 87.6 87.8 88.1 88.3 88.6 88.8 89.1 89.3 89.6 89.8 90.1 90.3 90.6 90.8 91.1 91.3 91.6 91.8 92.1 92.3 92.6 92.8 93.1 93.3 93.5 93.8 94.0 94.3 94.5 94.8 95.0 95.3 95.5 95.8 96.0 96.3 96.5 96.8 97.0 97.3 97.5 97.8 98.0 98.3 98.5 98.8 99.0 99.3 99.5 99.8 -found 34 predictions from path traversal Error with prediction: snap lend_intergenic: 28567, rend_intergenic: 27211 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 81659, rend_intergenic: 67803 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 90797, rend_intergenic: 84088 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 99913, rend_intergenic: 98504 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 105332, rend_intergenic: 103748 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 177584, rend_intergenic: 175272 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 180841, rend_intergenic: 178346 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 198898, rend_intergenic: 186405 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 203781, rend_intergenic: 200341 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: GlimmerHMM lend_intergenic: 26188, rend_intergenic: 26185 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. GOT 5prime partial gene. -reporting highest scoring path thru the trellis. -found 28 predictions persist after filtering for low support -building DP trellis -building trellis in range 223055 - 246095 -exon list size: 7 building trellis 11.1 22.2 33.3 44.4 55.6 66.7 77.8 88.9 -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 223055 - 239540 -exon list size: 3 building trellis 20.0 40.0 60.0 80.0 -found 1 predictions from path traversal -reporting highest scoring path thru the trellis. -found 0 predictions persist after filtering for low support -building DP trellis -building trellis in range 223055 - 237983 -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 226862 - 237983 -exon list size: 1 building trellis 33.3 66.7 -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