-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~Funannotate/fun/predict_misc/EVM/scaffold_137 -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: +)Couldn't classify 12948, 13010 Sorry, prediction GlimmerHMM_glimmerT_61365-T1 fails validation. (ATG) AC 8796-8823 GT ACG (CGG) AG 9355-9515 GT AGG (CAC) AG 11770-11875 GT AGG (GTA) AG 12454-12785 GT AGG (GTC) AG 12948-13010 GT CTG -recovered GlimmerHMM_glimmerT_61365-T1, initial, 8796, 8823 -recovered GlimmerHMM_glimmerT_61365-T1, internal, 9355, 9515 -recovered GlimmerHMM_glimmerT_61365-T1, internal, 11770, 11875 -recovered GlimmerHMM_glimmerT_61365-T1, internal, 12454, 12785 -recovered GlimmerHMM_glimmerT_61365-T1, internal, 12948, 13010 Couldn't classify 12948, 13029 Sorry, prediction Augustus_model.g40817.t1 fails validation. (ATG) CA 9012-9060 GT AGG (CGG) AG 9355-9515 GT AGG (CAC) AG 11770-11875 GT AGG (GTA) AG 12454-12785 GT AGG (GTC) AG 12948-13029 GT GGG -recovered Augustus_model.g40817.t1, initial, 9012, 9060 -recovered Augustus_model.g40817.t1, internal, 9355, 9515 -recovered Augustus_model.g40817.t1, internal, 11770, 11875 -recovered Augustus_model.g40817.t1, internal, 12454, 12785 -recovered Augustus_model.g40817.t1, internal, 12948, 13029 Couldn't classify 960, 1107 Sorry, prediction GeneMark_model.106699_t fails validation. (AGA) AG 960-1107 GT GAG (GGG) AG 1131-1211 GT GGG (AGG) AG 1246-1278 GT AGG (GGA) AG 1305-1313 GT AGG (GAG) AG 1336-1359 GT GAG (GAA) AG 1384-1416 GT CGG (GGA) AG 1441-1491 GT GAG (CGA) AG 1619-1645 GT GAG (AGA) AG 1669-1805 GC GAG (AGA) AG 1838-2135 GT GAG (ACA) AG 2187-2319 GA GAG -recovered GeneMark_model.106699_t, terminal, 1441, 1491 -recovered GeneMark_model.106699_t, terminal, 2187, 2319 -recovered GeneMark_model.106699_t, internal, 960, 1107 -recovered GeneMark_model.106699_t, internal, 1131, 1211 -recovered GeneMark_model.106699_t, internal, 1246, 1278 -recovered GeneMark_model.106699_t, internal, 1305, 1313 -recovered GeneMark_model.106699_t, internal, 1336, 1359 -recovered GeneMark_model.106699_t, internal, 1384, 1416 -recovered GeneMark_model.106699_t, internal, 1441, 1491 -recovered GeneMark_model.106699_t, internal, 1619, 1645 -recovered GeneMark_model.106699_t, internal, 1669, 1805 -recovered GeneMark_model.106699_t, internal, 1838, 2135 Couldn't classify 12948, 13029 Sorry, prediction snap_scaffold_137-snap.3-T1 fails validation. (ATG) CA 9012-9060 GT AGG (CGG) AG 9355-9515 GT AGG (CAC) AG 11770-11875 GT AGG (GTA) AG 12454-12785 GT AGG (GTC) AG 12948-13029 GT GGG -recovered snap_scaffold_137-snap.3-T1, initial, 9012, 9060 -recovered snap_scaffold_137-snap.3-T1, internal, 9355, 9515 -recovered snap_scaffold_137-snap.3-T1, internal, 11770, 11875 -recovered snap_scaffold_137-snap.3-T1, internal, 12454, 12785 -recovered snap_scaffold_137-snap.3-T1, internal, 12948, 13029 Couldn't classify 960, 1278 Sorry, prediction snap_scaffold_137-snap.2-T1 fails validation. (AGA) AG 960-1278 GT AGG (GCC) AG 3392-3475 GT AAG (GCT) AG 3963-4032 GT AGG (CCT) AG 6350-6499 GT GTG (AAG) AG 6608-6710 GT AGG (TGA) AG 6994-7071 GT AGG (CCG) AG 7788-7930 GA GAG add_exon() Sorry, snap_scaffold_137-snap.2-T1 6608-6710-terminal-3 is invalid. -recovered snap_scaffold_137-snap.2-T1, terminal, 6608, 6710 -recovered snap_scaffold_137-snap.2-T1, terminal, 7788, 7930 -recovered snap_scaffold_137-snap.2-T1, internal, 960, 1278 -recovered snap_scaffold_137-snap.2-T1, internal, 3392, 3475 -recovered snap_scaffold_137-snap.2-T1, internal, 3963, 4032 -recovered snap_scaffold_137-snap.2-T1, internal, 6350, 6499 -recovered snap_scaffold_137-snap.2-T1, internal, 6608, 6710 -recovered snap_scaffold_137-snap.2-T1, internal, 6994, 7071 Valid prediction for GeneMark_model.106701_t Couldn't classify 12948, 12983 Sorry, prediction pasa_asmbl_11707.p1 fails validation. (ATG) GA 8970-9060 GT AGG (CGG) AG 9355-9515 GT AGG (CAC) AG 11770-11875 GT AGG (GTA) AG 12454-12785 GT AGG (GTC) AG 12948-12983 GC GGG -recovered pasa_asmbl_11707.p1, initial, 8970, 9060 -recovered pasa_asmbl_11707.p1, internal, 9355, 9515 -recovered pasa_asmbl_11707.p1, internal, 11770, 11875 -recovered pasa_asmbl_11707.p1, internal, 12454, 12785 -recovered pasa_asmbl_11707.p1, internal, 12948, 12983 -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 GeneMark_model.106700_t Couldn't classify 99, 166 Sorry, prediction snap_scaffold_137-snap.4-T1 fails validation. (TAG) AG 99-166 GT AGG (TCC) AG 359-441 GT CGG (AAA) AG 523-548 GT TCG (GCG) AG 599-894 GT AGG (CCG) AG 1748-1786 GT CGG (CCG) AG 1827-1865 GT CGG (CCG) AG 1906-1944 GT CGG (CTT) AG 2070-2109 GT CGG (CCG) AG 2152-2191 GT TGG (CTT) AG 2238-2279 GT CGG (ACC) AG 2656-2695 GT CGG (CCG) AG 2736-2778 GT CGG (CCG) AG 2893-2934 GT CGG (CGT) AG 3057-3094 GT CGG (CCG) AG 3566-3789 CA GAC -recovered snap_scaffold_137-snap.4-T1, terminal, 3566, 3789 -recovered snap_scaffold_137-snap.4-T1, internal, 99, 166 -recovered snap_scaffold_137-snap.4-T1, internal, 359, 441 -recovered snap_scaffold_137-snap.4-T1, internal, 523, 548 -recovered snap_scaffold_137-snap.4-T1, internal, 599, 894 -recovered snap_scaffold_137-snap.4-T1, internal, 1748, 1786 -recovered snap_scaffold_137-snap.4-T1, internal, 1827, 1865 -recovered snap_scaffold_137-snap.4-T1, internal, 1906, 1944 -recovered snap_scaffold_137-snap.4-T1, internal, 2070, 2109 -recovered snap_scaffold_137-snap.4-T1, internal, 2152, 2191 -recovered snap_scaffold_137-snap.4-T1, internal, 2238, 2279 -recovered snap_scaffold_137-snap.4-T1, internal, 2656, 2695 -recovered snap_scaffold_137-snap.4-T1, internal, 2736, 2778 -recovered snap_scaffold_137-snap.4-T1, internal, 2893, 2934 -recovered snap_scaffold_137-snap.4-T1, internal, 3057, 3094 Couldn't classify 9076, 9166 Couldn't classify 10284, 10315 Sorry, prediction pasa_asmbl_11704.p2 fails validation. (TGG) CC 9076-9166 GT AGG (TGC) AG 9654-9832 GT AGG (GAT) AG 9996-10068 GT CGG (CCA) AG 10284-10315 CA ACC -recovered pasa_asmbl_11704.p2, internal, 9654, 9832 -recovered pasa_asmbl_11704.p2, internal, 9996, 10068 Couldn't classify 13084, 13106 Sorry, prediction Augustus_model.g40816.t1 fails validation. (ATG) AC 4270-4283 GT ACG (AGA) AG 5032-5065 GT CTG (CTC) AG 5218-5384 GT AGG (GTA) AG 6070-6178 GT AGG (TTT) AG 6569-6761 GT GGG (GGT) AG 7328-7413 GT AGG (AAT) AG 8394-8477 GT ACG (GAC) AG 8767-8779 GT TGG (GAC) AG 8886-8898 GT TGG (GAC) AG 9021-9166 GT AGG (TGC) AG 9654-9832 GT AGG (GAT) AG 9996-10068 GT CGG (CCA) AG 10284-10360 GT TCG (TCT) AG 10468-10522 GT TGG (TAG) AG 10748-10828 GT CAG (GTG) AG 12021-12161 GT GAG (AGC) AG 13084-13106 CT -recovered Augustus_model.g40816.t1, initial, 4270, 4283 -recovered Augustus_model.g40816.t1, internal, 5032, 5065 -recovered Augustus_model.g40816.t1, internal, 5218, 5384 -recovered Augustus_model.g40816.t1, internal, 6070, 6178 -recovered Augustus_model.g40816.t1, internal, 6569, 6761 -recovered Augustus_model.g40816.t1, internal, 7328, 7413 -recovered Augustus_model.g40816.t1, internal, 8394, 8477 -recovered Augustus_model.g40816.t1, internal, 8767, 8779 -recovered Augustus_model.g40816.t1, internal, 8886, 8898 -recovered Augustus_model.g40816.t1, internal, 9021, 9166 -recovered Augustus_model.g40816.t1, internal, 9654, 9832 -recovered Augustus_model.g40816.t1, internal, 9996, 10068 -recovered Augustus_model.g40816.t1, internal, 10284, 10360 -recovered Augustus_model.g40816.t1, internal, 10468, 10522 -recovered Augustus_model.g40816.t1, internal, 10748, 10828 -recovered Augustus_model.g40816.t1, internal, 12021, 12161 Couldn't classify 12021, 12161 Sorry, prediction snap_scaffold_137-snap.1-T1 fails validation. (ATG) AG 4995-5011 GT ACG (GAT) AG 5262-5384 GT AGG (GTA) AG 6070-6178 GT AGG (TTT) AG 6569-6953 GT AGG (GGT) AG 7328-7413 GT AGG (AAT) AG 8394-8477 GT ACG (GAC) AG 8886-8908 GT AAG (GAC) AG 9021-9166 GT AGG (TGC) AG 9654-9832 GT AGG (GAT) AG 9996-10068 GT CGG (CCA) AG 10284-10394 GT CAG (GTG) AG 12021-12161 GT GAG -recovered snap_scaffold_137-snap.1-T1, initial, 4995, 5011 -recovered snap_scaffold_137-snap.1-T1, terminal, 8886, 8908 -recovered snap_scaffold_137-snap.1-T1, internal, 4995, 5011 -recovered snap_scaffold_137-snap.1-T1, internal, 5262, 5384 -recovered snap_scaffold_137-snap.1-T1, internal, 6070, 6178 -recovered snap_scaffold_137-snap.1-T1, internal, 6569, 6953 -recovered snap_scaffold_137-snap.1-T1, internal, 7328, 7413 -recovered snap_scaffold_137-snap.1-T1, internal, 8394, 8477 -recovered snap_scaffold_137-snap.1-T1, internal, 8886, 8908 -recovered snap_scaffold_137-snap.1-T1, internal, 9021, 9166 -recovered snap_scaffold_137-snap.1-T1, internal, 9654, 9832 -recovered snap_scaffold_137-snap.1-T1, internal, 9996, 10068 -recovered snap_scaffold_137-snap.1-T1, internal, 10284, 10394 -recovered snap_scaffold_137-snap.1-T1, internal, 12021, 12161 Valid prediction for GeneMark_model.106702_t Valid prediction for GlimmerHMM_glimmerT_61364-T1 Valid prediction for GlimmerHMM_glimmerT_61363-T1 Couldn't classify 88, 166 Sorry, prediction GeneMark_model.106703_t fails validation. (CCT) AG 88-166 GT AGG (AAC) AG 407-462 GT ACG (AAA) AG 523-572 GT CAG (GAG) AG 678-701 GT GGG (GAG) AG 727-738 GT GGG (GGA) AG 770-781 GT GGG (GGT) AG 807-848 GT GTG (GAG) AG 880-894 GT AGG (TGG) AG 916-954 GT GGG (GGT) AG 978-989 GT GGG (GGT) AG 1016-1048 GT AGG (AGG) AG 1069-1118 GT GAG (CCG) AG 1748-1786 GT CGG (CCG) AG 1827-1865 GT CGG (CCG) AG 1906-1944 GT CGG (CGT) AG 1992-2030 GT CGG (CTT) AG 2070-2109 GT CGG (GGA) AG 2163-2191 GT TGG (CTT) AG 2238-2279 GT CGG (CCG) AG 2320-2358 GT CGG (CCG) AG 2576-2614 GT CGG (GGA) AG 2667-2695 GT CGG (CCG) AG 2736-2778 GT CGG (CCG) AG 2893-2934 GT CGG (CCG) AG 2977-3022 GT TGG (CGT) AG 3057-3094 GT CGG (GGA) AG 3412-3440 GT CGG (GTC) AG 3480-3523 GT CGG (ACA) AG 3580-3720 GT TTG (TAA) AG 3777-3785 GT GAG (AGA) AG 3811-3819 GC GAG (TGA) AG 3843-3869 GT AAG (AAA) AG 3895-3915 GT AAG (CGA) AG 3943-3973 TT AGT -recovered GeneMark_model.106703_t, terminal, 3943, 3973 -recovered GeneMark_model.106703_t, internal, 88, 166 -recovered GeneMark_model.106703_t, internal, 407, 462 -recovered GeneMark_model.106703_t, internal, 523, 572 -recovered GeneMark_model.106703_t, internal, 678, 701 -recovered GeneMark_model.106703_t, internal, 727, 738 -recovered GeneMark_model.106703_t, internal, 770, 781 -recovered GeneMark_model.106703_t, internal, 807, 848 -recovered GeneMark_model.106703_t, internal, 880, 894 -recovered GeneMark_model.106703_t, internal, 916, 954 -recovered GeneMark_model.106703_t, internal, 978, 989 -recovered GeneMark_model.106703_t, internal, 1016, 1048 -recovered GeneMark_model.106703_t, internal, 1069, 1118 -recovered GeneMark_model.106703_t, internal, 1748, 1786 -recovered GeneMark_model.106703_t, internal, 1827, 1865 -recovered GeneMark_model.106703_t, internal, 1906, 1944 -recovered GeneMark_model.106703_t, internal, 1992, 2030 -recovered GeneMark_model.106703_t, internal, 2070, 2109 -recovered GeneMark_model.106703_t, internal, 2163, 2191 -recovered GeneMark_model.106703_t, internal, 2238, 2279 -recovered GeneMark_model.106703_t, internal, 2320, 2358 -recovered GeneMark_model.106703_t, internal, 2576, 2614 -recovered GeneMark_model.106703_t, internal, 2667, 2695 -recovered GeneMark_model.106703_t, internal, 2736, 2778 -recovered GeneMark_model.106703_t, internal, 2893, 2934 -recovered GeneMark_model.106703_t, internal, 2977, 3022 -recovered GeneMark_model.106703_t, internal, 3057, 3094 -recovered GeneMark_model.106703_t, internal, 3412, 3440 -recovered GeneMark_model.106703_t, internal, 3480, 3523 -recovered GeneMark_model.106703_t, internal, 3580, 3720 -recovered GeneMark_model.106703_t, internal, 3777, 3785 -recovered GeneMark_model.106703_t, internal, 3811, 3819 -recovered GeneMark_model.106703_t, internal, 3843, 3869 -recovered GeneMark_model.106703_t, internal, 3895, 3915 Couldn't classify 7328, 7413 Sorry, prediction pasa_asmbl_11705.p1 fails validation. (ATG) GG 5263-5384 GT AGG (GTA) AG 6070-6178 GT AGG (TTT) AG 6569-6761 GT GGG (GGT) AG 7328-7413 GT AGG -recovered pasa_asmbl_11705.p1, initial, 5263, 5384 -recovered pasa_asmbl_11705.p1, internal, 6070, 6178 -recovered pasa_asmbl_11705.p1, internal, 6569, 6761 -recovered pasa_asmbl_11705.p1, internal, 7328, 7413 -loading the search evidence (protein and EST search results, strand: -) -scoring exons (strand: -)Error with prediction: snap lend_intergenic: 8112, rend_intergenic: 960 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 13029, rend_intergenic: 9318 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -building DP trellis -building trellis in range 1 - 13106 -exon list size: 205 building trellis 0.5 1.0 1.4 1.9 2.4 2.9 3.4 3.9 4.3 4.8 5.3 5.8 6.3 6.8 7.2 7.7 8.2 8.7 9.2 9.7 10.1 10.6 11.1 11.6 12.1 12.6 13.0 13.5 14.0 14.5 15.0 15.5 15.9 16.4 16.9 17.4 17.9 18.4 18.8 19.3 19.8 20.3 20.8 21.3 21.7 22.2 22.7 23.2 23.7 24.2 24.6 25.1 25.6 26.1 26.6 27.1 27.5 28.0 28.5 29.0 29.5 30.0 30.4 30.9 31.4 31.9 32.4 32.9 33.3 33.8 34.3 34.8 35.3 35.7 36.2 36.7 37.2 37.7 38.2 38.6 39.1 39.6 40.1 40.6 41.1 41.5 42.0 42.5 43.0 43.5 44.0 44.4 44.9 45.4 45.9 46.4 46.9 47.3 47.8 48.3 48.8 49.3 49.8 50.2 50.7 51.2 51.7 52.2 52.7 53.1 53.6 54.1 54.6 55.1 55.6 56.0 56.5 57.0 57.5 58.0 58.5 58.9 59.4 59.9 60.4 60.9 61.4 61.8 62.3 62.8 63.3 63.8 64.3 64.7 65.2 65.7 66.2 66.7 67.1 67.6 68.1 68.6 69.1 69.6 70.0 70.5 71.0 71.5 72.0 72.5 72.9 73.4 73.9 74.4 74.9 75.4 75.8 76.3 76.8 77.3 77.8 78.3 78.7 79.2 79.7 80.2 80.7 81.2 81.6 82.1 82.6 83.1 83.6 84.1 84.5 85.0 85.5 86.0 86.5 87.0 87.4 87.9 88.4 88.9 89.4 89.9 90.3 90.8 91.3 91.8 92.3 92.8 93.2 93.7 94.2 94.7 95.2 95.7 96.1 96.6 97.1 97.6 98.1 98.6 99.0 99.5 -found 2 predictions from path traversal Error with prediction: snap lend_intergenic: 8112, rend_intergenic: 960 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 13029, rend_intergenic: 9318 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -reporting highest scoring path thru the trellis. -found 2 predictions persist after filtering for low support