-successfully changed directories to /suikou/files/m256y/yoshitake.kazutoshi/work/pp-dev/yoshitake/test/annotation~funannotate/test/fun/predict_misc/EVM/scaffold_17/scaffold_17_465844-679050 -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_17-snap.103-T1 Sorry, intron length (7) is less than minimum required (10) Valid prediction for GlimmerHMM_glimmerT_39636-T1 Valid prediction for snap_scaffold_17-snap.85-T1 Valid prediction for snap_scaffold_17-snap.93-T1 Valid prediction for snap_scaffold_17-snap.117-T1 Valid prediction for GlimmerHMM_glimmerT_39616-T1 Valid prediction for snap_scaffold_17-snap.99-T1 Valid prediction for Augustus_model.g26384.t1 Couldn't classify 67949, 68020 Sorry, prediction pasa_asmbl_18542.p1 fails validation. (ATG) TC 66929-67198 GT CGG (GAC) AG 67336-67473 GT AGG (CCC) AG 67949-68020 CA CCC -recovered pasa_asmbl_18542.p1, initial, 66929, 67198 -recovered pasa_asmbl_18542.p1, internal, 67336, 67473 Valid prediction for snap_scaffold_17-snap.91-T1 Valid prediction for CodingQuarry_transcript_21826-T1 Couldn't classify 33518, 33718 Sorry, prediction pasa_asmbl_18540.p1 fails validation. (CTG) AC 33518-33718 GT AGG (CAA) AG 33973-34170 GT GGG (CTG) AG 34450-34578 GT TGG (TCC) AG 35082-35270 GT AGG (GAC) AG 35384-35557 GT AGG (GTG) AG 35793-35952 GT GGG (ACG) AG 36226-36362 GT TGG (GTT) AG 36527-36760 TA AGT -recovered pasa_asmbl_18540.p1, terminal, 36527, 36760 -recovered pasa_asmbl_18540.p1, internal, 33973, 34170 -recovered pasa_asmbl_18540.p1, internal, 34450, 34578 -recovered pasa_asmbl_18540.p1, internal, 35082, 35270 -recovered pasa_asmbl_18540.p1, internal, 35384, 35557 -recovered pasa_asmbl_18540.p1, internal, 35793, 35952 -recovered pasa_asmbl_18540.p1, internal, 36226, 36362 Valid prediction for Augustus_model.g26379.t1 Valid prediction for GlimmerHMM_glimmerT_39614-T1 Valid prediction for snap_scaffold_17-snap.95-T1 Valid prediction for GlimmerHMM_glimmerT_39625-T1 Valid prediction for Augustus_model.g26394.t1 Valid prediction for snap_scaffold_17-snap.111-T1 Valid prediction for snap_scaffold_17-snap.109-T1 Valid prediction for GlimmerHMM_glimmerT_39618-T1 Valid prediction for snap_scaffold_17-snap.120-T1 Valid prediction for GlimmerHMM_glimmerT_39634-T1 Valid prediction for pasa_asmbl_18553.p1 Valid prediction for Augustus_model.g26378.t1 Valid prediction for snap_scaffold_17-snap.118-T1 Valid prediction for GlimmerHMM_glimmerT_39631-T1 Valid prediction for GlimmerHMM_glimmerT_39635-T1 Valid prediction for snap_scaffold_17-snap.104-T1 Valid prediction for HiQ_model.g26397.t1 Valid prediction for snap_scaffold_17-snap.79-T1 Valid prediction for Augustus_model.g26380.t1 Valid prediction for GlimmerHMM_glimmerT_39620-T1 Valid prediction for snap_scaffold_17-snap.90-T1 Valid prediction for snap_scaffold_17-snap.89-T1 Valid prediction for HiQ_model.g26386.t1 Valid prediction for HiQ_model.g26385.t1 Valid prediction for CodingQuarry_transcript_21829-T1 Valid prediction for pasa_asmbl_18551.p1 Valid prediction for GlimmerHMM_glimmerT_39619-T1 Valid prediction for snap_scaffold_17-snap.88-T1 Couldn't classify 209547, 209672 Sorry, prediction pasa_asmbl_18558.p1 fails validation. (GTG) GT 209547-209672 GT AGG (GTT) AG 210304-210411 GT TGG (GAG) AG 210568-210633 GT AGG (GAG) AG 210866-210977 GT GGG (CTC) AG 211565-211683 GT AGG (GGG) AG 211850-211996 CC AGC -recovered pasa_asmbl_18558.p1, terminal, 211850, 211996 -recovered pasa_asmbl_18558.p1, internal, 210304, 210411 -recovered pasa_asmbl_18558.p1, internal, 210568, 210633 -recovered pasa_asmbl_18558.p1, internal, 210866, 210977 -recovered pasa_asmbl_18558.p1, internal, 211565, 211683 Valid prediction for HiQ_model.g26383.t1 Valid prediction for snap_scaffold_17-snap.83-T1 Valid prediction for snap_scaffold_17-snap.82-T1 Valid prediction for Augustus_model.g26396.t1 Couldn't classify 25512, 25683 Sorry, prediction pasa_asmbl_18539.p1 fails validation. (GAT) TG 25512-25683 GT AGG (TCC) AG 26190-26513 GT AGG (GAT) AG 26983-27099 GT AGG (GCT) AG 27270-27287 GT CAG (TTT) AG 27513-27562 GG GAG -recovered pasa_asmbl_18539.p1, terminal, 27513, 27562 -recovered pasa_asmbl_18539.p1, internal, 26190, 26513 -recovered pasa_asmbl_18539.p1, internal, 26983, 27099 -recovered pasa_asmbl_18539.p1, internal, 27270, 27287 Valid prediction for snap_scaffold_17-snap.84-T1 Valid prediction for pasa_asmbl_18543.p1 Valid prediction for GlimmerHMM_glimmerT_39633-T1 Valid prediction for snap_scaffold_17-snap.115-T1 Valid prediction for snap_scaffold_17-snap.96-T1 Valid prediction for snap_scaffold_17-snap.87-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_39626-T1 Valid prediction for snap_scaffold_17-snap.97-T1 Valid prediction for pasa_asmbl_17634.p1 Valid prediction for Augustus_model.g26392.t1 Valid prediction for Augustus_model.g26381.t1 Valid prediction for snap_scaffold_17-snap.94-T1 Valid prediction for snap_scaffold_17-snap.121-T1 Valid prediction for GlimmerHMM_glimmerT_39621-T1 Valid prediction for snap_scaffold_17-snap.102-T1 Valid prediction for snap_scaffold_17-snap.110-T1 Valid prediction for HiQ_model.g26389.t1 Valid prediction for GlimmerHMM_glimmerT_39632-T1 Couldn't classify 199767, 200031 Sorry, prediction pasa_asmbl_17622.p1 fails validation. (CTG) AG 199767-200031 GT TGG (GAG) AG 200164-200265 GT TGG (ACT) AG 200460-200488 GT AGG (AAG) AG 200812-200823 AG AAA -recovered pasa_asmbl_17622.p1, terminal, 200812, 200823 -recovered pasa_asmbl_17622.p1, internal, 199767, 200031 -recovered pasa_asmbl_17622.p1, internal, 200164, 200265 -recovered pasa_asmbl_17622.p1, internal, 200460, 200488 Couldn't classify 198207, 198384 Couldn't classify 199064, 199368 Sorry, prediction pasa_asmbl_17624.p1 fails validation. (ACT) CG 198207-198384 GT AGG (ACC) AG 198594-198842 GT AGG (TGA) AG 199064-199368 AC GCA -recovered pasa_asmbl_17624.p1, internal, 198594, 198842 Valid prediction for snap_scaffold_17-snap.112-T1 Valid prediction for snap_scaffold_17-snap.107-T1 Valid prediction for Augustus_model.g26393.t1 Valid prediction for Augustus_model.g26390.t1 Valid prediction for GlimmerHMM_glimmerT_39629-T1 Valid prediction for snap_scaffold_17-snap.119-T1 Couldn't classify 119290, 119325 Couldn't classify 120334, 120387 Sorry, prediction pasa_asmbl_17629.p2 fails validation. (GGA) AA 119290-119325 GT AAG (GGA) AG 119506-119559 GT GGG (GGA) AG 119681-119788 GT AGG (GGT) AG 119971-120024 GT AGG (GGA) AG 120334-120387 GT GGG -recovered pasa_asmbl_17629.p2, internal, 119506, 119559 -recovered pasa_asmbl_17629.p2, internal, 119681, 119788 -recovered pasa_asmbl_17629.p2, internal, 119971, 120024 -recovered pasa_asmbl_17629.p2, internal, 120334, 120387 Valid prediction for snap_scaffold_17-snap.80-T1 Couldn't classify 123852, 123905 Couldn't classify 127065, 127220 Sorry, prediction pasa_asmbl_17628.p1 fails validation. (GGA) AG 123852-123905 GT AGG (GGA) AG 124334-124387 GT TGG (GGT) AG 124554-124607 GT ATG (GGT) AG 124842-124895 GT AGG (GGA) AG 125122-125175 GT AAG (GGG) AG 125337-125444 GT CTG (GGC) AG 125543-125596 GT GGG (GGT) AG 125775-125828 GT CTG (GGC) AG 126038-126091 GT GGG (GGT) AG 126198-126251 GT AGG (GGA) AG 126608-126715 GT TGG (GGT) AG 126876-126929 GT TGG (GGT) AG 127065-127220 GA GAG -recovered pasa_asmbl_17628.p1, internal, 123852, 123905 -recovered pasa_asmbl_17628.p1, internal, 124334, 124387 -recovered pasa_asmbl_17628.p1, internal, 124554, 124607 -recovered pasa_asmbl_17628.p1, internal, 124842, 124895 -recovered pasa_asmbl_17628.p1, internal, 125122, 125175 -recovered pasa_asmbl_17628.p1, internal, 125337, 125444 -recovered pasa_asmbl_17628.p1, internal, 125543, 125596 -recovered pasa_asmbl_17628.p1, internal, 125775, 125828 -recovered pasa_asmbl_17628.p1, internal, 126038, 126091 -recovered pasa_asmbl_17628.p1, internal, 126198, 126251 -recovered pasa_asmbl_17628.p1, internal, 126608, 126715 -recovered pasa_asmbl_17628.p1, internal, 126876, 126929 Couldn't classify 128177, 128384 Couldn't classify 129184, 129300 Sorry, prediction pasa_asmbl_17627.p1 fails validation. (CTG) AG 128177-128384 GT TGG (GAG) AG 128609-128721 GT CAG (GTG) AG 128901-128969 GT AGG (CTC) AG 129184-129300 TG CCT -recovered pasa_asmbl_17627.p1, internal, 128177, 128384 -recovered pasa_asmbl_17627.p1, internal, 128609, 128721 -recovered pasa_asmbl_17627.p1, internal, 128901, 128969 Valid prediction for CodingQuarry_transcript_21828-T1 Valid prediction for GlimmerHMM_glimmerT_39623-T1 Valid prediction for GlimmerHMM_glimmerT_39617-T1 Valid prediction for Augustus_model.g26388.t1 Valid prediction for GlimmerHMM_glimmerT_39622-T1 Valid prediction for Augustus_model.g26377.t1 Valid prediction for Augustus_model.g26387.t1 Valid prediction for snap_scaffold_17-snap.78-T1 Valid prediction for Augustus_model.g26382.t1 Valid prediction for snap_scaffold_17-snap.86-T1 Valid prediction for GlimmerHMM_glimmerT_39628-T1 Valid prediction for snap_scaffold_17-snap.98-T1 Valid prediction for pasa_asmbl_17637.p2 Valid prediction for pasa_asmbl_17636.p1 Valid prediction for CodingQuarry_transcript_21831-T1 Valid prediction for GlimmerHMM_glimmerT_39624-T1 Valid prediction for GlimmerHMM_glimmerT_39630-T1 Valid prediction for snap_scaffold_17-snap.100-T1 Valid prediction for snap_scaffold_17-snap.113-T1 Valid prediction for GlimmerHMM_glimmerT_39615-T1 Valid prediction for snap_scaffold_17-snap.101-T1 Valid prediction for snap_scaffold_17-snap.108-T1 Valid prediction for HiQ_model.g26391.t1 Valid prediction for snap_scaffold_17-snap.92-T1 Couldn't classify 68969, 69076 Sorry, prediction pasa_asmbl_17633.p1 fails validation. (CCC) GT 68969-69076 GT AGG (ATC) AG 69579-69735 GT CGG (GTA) AG 70137-70316 GT AGG (TGG) AG 71104-71127 GT ATG (CTG) AG 71715-71875 GT CGG (CCC) AG 72085-72214 GT AGG (GCT) AG 72336-72468 GT AGG (AGT) AG 75152-75243 GT AGG (ATG) AG 75357-75462 GT AGG (GTT) AG 76145-76292 GG AGG add_exon() Sorry, pasa_asmbl_17633.p1 75357-75462-initial-1 is invalid. -recovered pasa_asmbl_17633.p1, initial, 75357, 75462 -recovered pasa_asmbl_17633.p1, terminal, 76145, 76292 -recovered pasa_asmbl_17633.p1, internal, 69579, 69735 -recovered pasa_asmbl_17633.p1, internal, 70137, 70316 -recovered pasa_asmbl_17633.p1, internal, 71104, 71127 -recovered pasa_asmbl_17633.p1, internal, 71715, 71875 -recovered pasa_asmbl_17633.p1, internal, 72085, 72214 -recovered pasa_asmbl_17633.p1, internal, 72336, 72468 -recovered pasa_asmbl_17633.p1, internal, 75152, 75243 -recovered pasa_asmbl_17633.p1, internal, 75357, 75462 Couldn't classify 61515, 61568 Couldn't classify 63073, 63102 Sorry, prediction pasa_asmbl_17635.p1 fails validation. (ATA) TG 61515-61568 GT AGG (ATC) AG 61704-61805 GT AGG (AAA) AG 61900-62041 GT AGG (GCC) AG 62236-62436 GT AGG (GTG) AG 62785-62900 GT AGG (CGT) AG 63073-63102 AA CCA -recovered pasa_asmbl_17635.p1, internal, 61704, 61805 -recovered pasa_asmbl_17635.p1, internal, 61900, 62041 -recovered pasa_asmbl_17635.p1, internal, 62236, 62436 -recovered pasa_asmbl_17635.p1, internal, 62785, 62900 Valid prediction for snap_scaffold_17-snap.105-T1 Valid prediction for HiQ_model.g26395.t1 Valid prediction for snap_scaffold_17-snap.116-T1 Valid prediction for snap_scaffold_17-snap.114-T1 Valid prediction for CodingQuarry_transcript_21827-T1 Valid prediction for snap_scaffold_17-snap.81-T1 Valid prediction for GlimmerHMM_glimmerT_39627-T1 Valid prediction for snap_scaffold_17-snap.106-T1 -loading the search evidence (protein and EST search results, strand: -) -scoring exons (strand: -)Error with prediction: snap lend_intergenic: 27457, rend_intergenic: 23214 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 74441, rend_intergenic: 71391 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 101060, rend_intergenic: 91499 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 116647, rend_intergenic: 113147 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 119104, rend_intergenic: 117800 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 131342, rend_intergenic: 129455 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 142274, rend_intergenic: 136916 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 170320, rend_intergenic: 169562 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 177525, rend_intergenic: 176008 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 208109, rend_intergenic: 205147 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 211996, rend_intergenic: 208664 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: GlimmerHMM lend_intergenic: 136919, rend_intergenic: 136916 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. -building DP trellis -building trellis in range 1 - 213207 -exon list size: 499 building trellis 0.2 0.4 0.6 0.8 1.0 1.2 1.4 1.6 1.8 2.0 2.2 2.4 2.6 2.8 3.0 3.2 3.4 3.6 3.8 4.0 4.2 4.4 4.6 4.8 5.0 5.2 5.4 5.6 5.8 6.0 6.2 6.4 6.6 6.8 7.0 7.2 7.4 7.6 7.8 8.0 8.2 8.4 8.6 8.8 9.0 9.2 9.4 9.6 9.8 10.0 10.2 10.4 10.6 10.8 11.0 11.2 11.4 11.6 11.8 12.0 12.2 12.4 12.6 12.8 13.0 13.2 13.4 13.6 13.8 14.0 14.2 14.4 14.6 14.8 15.0 15.2 15.4 15.6 15.8 16.0 16.2 16.4 16.6 16.8 17.0 17.2 17.4 17.6 17.8 18.0 18.2 18.4 18.6 18.8 19.0 19.2 19.4 19.6 19.8 20.0 20.2 20.4 20.6 20.8 21.0 21.2 21.4 21.6 21.8 22.0 22.2 22.4 22.6 22.8 23.0 23.2 23.4 23.6 23.8 24.0 24.2 24.4 24.6 24.8 25.0 25.1 25.3 25.5 25.7 25.9 26.1 26.3 26.5 26.7 26.9 27.1 27.3 27.5 27.7 27.9 28.1 28.3 28.5 28.7 28.9 29.1 29.3 29.5 29.7 29.9 30.1 30.3 30.5 30.7 30.9 31.1 31.3 31.5 31.7 31.9 32.1 32.3 32.5 32.7 32.9 33.1 33.3 33.5 33.7 33.9 34.1 34.3 34.5 34.7 34.9 35.1 35.3 35.5 35.7 35.9 36.1 36.3 36.5 36.7 36.9 37.1 37.3 37.5 37.7 37.9 38.1 38.3 38.5 38.7 38.9 39.1 39.3 39.5 39.7 39.9 40.1 40.3 40.5 40.7 40.9 41.1 41.3 41.5 41.7 41.9 42.1 42.3 42.5 42.7 42.9 43.1 43.3 43.5 43.7 43.9 44.1 44.3 44.5 44.7 44.9 45.1 45.3 45.5 45.7 45.9 46.1 46.3 46.5 46.7 46.9 47.1 47.3 47.5 47.7 47.9 48.1 48.3 48.5 48.7 48.9 49.1 49.3 49.5 49.7 49.9 50.1 50.3 50.5 50.7 50.9 51.1 51.3 51.5 51.7 51.9 52.1 52.3 52.5 52.7 52.9 53.1 53.3 53.5 53.7 53.9 54.1 54.3 54.5 54.7 54.9 55.1 55.3 55.5 55.7 55.9 56.1 56.3 56.5 56.7 56.9 57.1 57.3 57.5 57.7 57.9 58.1 58.3 58.5 58.7 58.9 59.1 59.3 59.5 59.7 59.9 60.1 60.3 60.5 60.7 60.9 61.1 61.3 61.5 61.7 61.9 62.1 62.3 62.5 62.7 62.9 63.1 63.3 63.5 63.7 63.9 64.1 64.3 64.5 64.7 64.9 65.1 65.3 65.5 65.7 65.9 66.1 66.3 66.5 66.7 66.9 67.1 67.3 67.5 67.7 67.9 68.1 68.3 68.5 68.7 68.9 69.1 69.3 69.5 69.7 69.9 70.1 70.3 70.5 70.7 70.9 71.1 71.3 71.5 71.7 71.9 72.1 72.3 72.5 72.7 72.9 73.1 73.3 73.5 73.7 73.9 74.1 74.3 74.5 74.7 74.9 75.0 75.2 75.4 75.6 75.8 76.0 76.2 76.4 76.6 76.8 77.0 77.2 77.4 77.6 77.8 78.0 78.2 78.4 78.6 78.8 79.0 79.2 79.4 79.6 79.8 80.0 80.2 80.4 80.6 80.8 81.0 81.2 81.4 81.6 81.8 82.0 82.2 82.4 82.6 82.8 83.0 83.2 83.4 83.6 83.8 84.0 84.2 84.4 84.6 84.8 85.0 85.2 85.4 85.6 85.8 86.0 86.2 86.4 86.6 86.8 87.0 87.2 87.4 87.6 87.8 88.0 88.2 88.4 88.6 88.8 89.0 89.2 89.4 89.6 89.8 90.0 90.2 90.4 90.6 90.8 91.0 91.2 91.4 91.6 91.8 92.0 92.2 92.4 92.6 92.8 93.0 93.2 93.4 93.6 93.8 94.0 94.2 94.4 94.6 94.8 95.0 95.2 95.4 95.6 95.8 96.0 96.2 96.4 96.6 96.8 97.0 97.2 97.4 97.6 97.8 98.0 98.2 98.4 98.6 98.8 99.0 99.2 99.4 99.6 99.8 -found 27 predictions from path traversal Error with prediction: snap lend_intergenic: 27457, rend_intergenic: 23214 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 74441, rend_intergenic: 71391 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 101060, rend_intergenic: 91499 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 116647, rend_intergenic: 113147 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 119104, rend_intergenic: 117800 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 131342, rend_intergenic: 129455 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 142274, rend_intergenic: 136916 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 170320, rend_intergenic: 169562 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 177525, rend_intergenic: 176008 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 208109, rend_intergenic: 205147 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: snap lend_intergenic: 211996, rend_intergenic: 208664 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. Error with prediction: GlimmerHMM lend_intergenic: 136919, rend_intergenic: 136916 at /venv/opt/evidencemodeler-1.1.1/evidence_modeler.pl line 3218. GOT 5prime partial gene. -reporting highest scoring path thru the trellis. -found 24 predictions persist after filtering for low support