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Hello
I am getting a segmentation fault. Any idea on what is going wrong ?
#command: rsicnv rsi -f ../ref/NC_012967.fas -c NC_012967.1 -b ../mapping/SRR098036.sorted.bam -o test.out #bamfile: ../mapping/SRR098036.sorted.bam #rdfile: #reffile: ../ref/NC_012967.fas #cnvfile: #chrom: NC_012967.1 #min_mapq: 0 #min_baseQ: 13 #binsize: 101 #adjustGC: 1 #plots: cnv_plots #output: test.out #Check bam header for 1-22XY #BAM has reads on : #processing NC_012967.1 #Noseq regions excluded #processed 1M reads^M#processed 2M reads^M#processed 3M reads 4629812 25.1553 RD mean before GC adjust = 25.8185 RD mean after GC adjust = 26.4944 4629812 25.8139 applying cap 4 times of mean 25 cap = 100 region : NC_012967.1:1-4629812 median : 25 rs::m : 101 rs::cap : 4 RD median : 25 RD median absolute deviation : 5 Negative binormial transformation : median of transformations : 25.19 sigma : 1.48357 median/sigma : 16.9793 rsifactor: 10.4534 lamda : 15.5083 target_tlamda : 7.93142 Max L needed : 38 DEL- 1 1357 45839 0.0296036 DEL- 2 1391 45839 0.0303453 DEL- 3 1398 45839 0.030498 DEL- 4 1400 45839 0.0305417 DEL- 5 1401 45839 0.0305635 DEL- 6 1407 45839 0.0306944 DEL- 7 1413 45839 0.0308253 DEL- 8 1413 45839 0.0308253 DEL- 9 1418 45839 0.0309344 DEL- 10 1421 45839 0.0309998 DEL- 11 1432 45839 0.0312398 DEL- 12 1433 45839 0.0312616 DEL- 13 1433 45839 0.0312616 DEL- 14 1447 45839 0.031567 DEL- 15 1454 45839 0.0317197 DEL- 16 1462 45839 0.0318942 DEL- 17 1464 45839 0.0319379 DEL- 18 1473 45839 0.0321342 DEL- 19 1473 45839 0.0321342 DEL- 20 1484 45839 0.0323742 DEL- 21 1484 45839 0.0323742 DEL- 22 1496 45839 0.032636 DEL- 23 1496 45839 0.032636 DEL- 24 1498 45839 0.0326796 DEL- 25 1507 45839 0.0328759 DEL- 26 1541 45839 0.0336177 DEL- 27 1541 45839 0.0336177 DEL- 28 1556 45839 0.0339449 DEL- 29 1571 45839 0.0342721 DEL- 30 1571 45839 0.0342721 DEL- 31 1571 45839 0.0342721 DEL- 32 1585 45839 0.0345775 DEL- 33 1585 45839 0.0345775 DEL- 34 1585 45839 0.0345775 DEL- 35 1585 45839 0.0345775 DEL- 36 1585 45839 0.0345775 DEL- 37 1599 45839 0.034883 DEL- 38 1599 45839 0.034883 DEL- 39 1599 45839 0.034883 DEL- 40 1620 45839 0.0353411 DEL- 41 1620 45839 0.0353411 DEL- 42 1620 45839 0.0353411 DEL- 43 1620 45839 0.0353411 DEL- 44 1620 45839 0.0353411 DEL- 45 1634 45839 0.0356465 DEL- 46 1645 45839 0.0358865 DEL- 47 1645 45839 0.0358865 DEL- 48 1645 45839 0.0358865 DEL- 49 1645 45839 0.0358865 DEL- 50 1645 45839 0.0358865 DEL- 51 1645 45839 0.0358865 DEL- 52 1672 45839 0.0364755 DEL- 53 1691 45839 0.03689 DEL- 54 1691 45839 0.03689 DEL- 55 1691 45839 0.03689 DEL- 56 1707 45839 0.037239 DEL- 57 1707 45839 0.037239 DEL- 58 1714 45839 0.0373917 DEL- 59 1714 45839 0.0373917 DEL- 60 1714 45839 0.0373917 DEL- 61 1732 45839 0.0377844 DEL- 62 1752 45839 0.0382207 DEL- 63 1752 45839 0.0382207 DEL- 64 1752 45839 0.0382207 DEL- 65 1752 45839 0.0382207 DEL- 66 1772 45839 0.038657 DEL- 67 1784 45839 0.0389188 DEL- 68 1784 45839 0.0389188 DEL- 69 1784 45839 0.0389188 DEL- 70 1808 45839 0.0394424 DEL- 71 1808 45839 0.0394424 DEL- 72 1847 45839 0.0402932 DEL- 73 1847 45839 0.0402932 DEL- 74 1849 45839 0.0403368 DEL- 75 1849 45839 0.0403368 DEL- 76 1849 45839 0.0403368 DEL- 77 1849 45839 0.0403368 DEL- 78 1922 45839 0.0419294 DEL- 79 1942 45839 0.0423657 DEL- 80 1944 45839 0.0424093 DEL- 81 1944 45839 0.0424093 DEL- 82 1953 45839 0.0426056 DEL- 83 1953 45839 0.0426056 DEL- 84 1960 45839 0.0427583 DEL- 85 1960 45839 0.0427583 DEL- 86 1960 45839 0.0427583 DEL- 87 1960 45839 0.0427583 DEL- 88 1985 45839 0.0433037 DEL- 89 1986 45839 0.0433256 DEL- 90 1986 45839 0.0433256 DEL- 91 1986 45839 0.0433256 DEL- 92 1986 45839 0.0433256 DEL- 93 1986 45839 0.0433256 DEL- 94 1993 45839 0.0434783 DEL- 95 2008 45839 0.0438055 DEL- 96 2008 45839 0.0438055 DEL- 97 2008 45839 0.0438055 DEL- 98 2030 45839 0.0442854 DEL- 99 2030 45839 0.0442854 DUP+ 1 0 45839 0 DUP+ 2 0 45839 0 DUP+ 3 80 45839 0.00174524 DUP+ 4 85 45839 0.00185432 DUP+ 5 92 45839 0.00200702 DUP+ 6 140 45839 0.00305417 DUP+ 7 249 45839 0.00543206 DUP+ 8 491 45839 0.0107114 DUP+ 9 668 45839 0.0145727 DUP+ 10 904 45839 0.0197212 DUP+ 11 1018 45839 0.0222082 DUP+ 12 1105 45839 0.0241061 DUP+ 13 1153 45839 0.0251533 DUP+ 14 1176 45839 0.025655 DUP+ 15 1184 45839 0.0258295 DUP+ 16 1197 45839 0.0261131 DUP+ 17 1199 45839 0.0261568 DUP+ 18 1211 45839 0.0264186 DUP+ 19 1216 45839 0.0265276 DUP+ 20 1217 45839 0.0265494 DUP+ 21 1225 45839 0.026724 DUP+ 22 1231 45839 0.0268549 DUP+ 23 1232 45839 0.0268767 DUP+ 24 1237 45839 0.0269858 DUP+ 25 1243 45839 0.0271166 DUP+ 26 1243 45839 0.0271166 DUP+ 27 1243 45839 0.0271166 DUP+ 28 1278 45839 0.0278802 DUP+ 29 1290 45839 0.028142 DUP+ 30 1297 45839 0.0282947 DUP+ 31 1297 45839 0.0282947 DUP+ 32 1301 45839 0.0283819 DUP+ 33 1301 45839 0.0283819 DUP+ 34 1304 45839 0.0284474 DUP+ 35 1324 45839 0.0288837 DUP+ 36 1326 45839 0.0289273 DUP+ 37 1327 45839 0.0289491 DUP+ 38 1327 45839 0.0289491 DUP+ 39 1345 45839 0.0293418 DUP+ 40 1367 45839 0.0298218 DUP+ 41 1367 45839 0.0298218 DUP+ 42 1376 45839 0.0300181 DUP+ 43 1376 45839 0.0300181 DUP+ 44 1384 45839 0.0301926 DUP+ 45 1384 45839 0.0301926 DUP+ 46 1392 45839 0.0303672 DUP+ 47 1397 45839 0.0304762 DUP+ 48 1405 45839 0.0306508 DUP+ 49 1405 45839 0.0306508 DUP+ 50 1407 45839 0.0306944 DUP+ 51 1411 45839 0.0307816 DUP+ 52 1438 45839 0.0313707 DUP+ 53 1466 45839 0.0319815 DUP+ 54 1466 45839 0.0319815 DUP+ 55 1468 45839 0.0320251 DUP+ 56 1468 45839 0.0320251 DUP+ 57 1468 45839 0.0320251 DUP+ 58 1472 45839 0.0321124 DUP+ 59 1480 45839 0.0322869 DUP+ 60 1480 45839 0.0322869 DUP+ 61 1480 45839 0.0322869 DUP+ 62 1480 45839 0.0322869 DUP+ 63 1484 45839 0.0323742 DUP+ 64 1484 45839 0.0323742 DUP+ 65 1484 45839 0.0323742 DUP+ 66 1502 45839 0.0327669 DUP+ 67 1502 45839 0.0327669 DUP+ 68 1502 45839 0.0327669 DUP+ 69 1508 45839 0.0328978 DUP+ 70 1508 45839 0.0328978 DUP+ 71 1508 45839 0.0328978 DUP+ 72 1508 45839 0.0328978 DUP+ 73 1508 45839 0.0328978 DUP+ 74 1508 45839 0.0328978 DUP+ 75 1508 45839 0.0328978 DUP+ 76 1519 45839 0.0331377 DUP+ 77 1519 45839 0.0331377 DUP+ 78 1519 45839 0.0331377 DUP+ 79 1519 45839 0.0331377 DUP+ 80 1519 45839 0.0331377 DUP+ 81 1519 45839 0.0331377 DUP+ 82 1519 45839 0.0331377 DUP+ 83 1519 45839 0.0331377 DUP+ 84 1519 45839 0.0331377 DUP+ 85 1519 45839 0.0331377 DUP+ 86 1519 45839 0.0331377 DUP+ 87 1519 45839 0.0331377 DUP+ 88 1519 45839 0.0331377 DUP+ 89 1519 45839 0.0331377 DUP+ 90 1519 45839 0.0331377 DUP+ 91 1519 45839 0.0331377 DUP+ 92 1519 45839 0.0331377 DUP+ 93 1519 45839 0.0331377 DUP+ 94 1519 45839 0.0331377 DUP+ 95 1519 45839 0.0331377 DUP+ 96 1519 45839 0.0331377 DUP+ 97 1519 45839 0.0331377 DUP+ 98 1519 45839 0.0331377 DUP+ 99 1519 45839 0.0331377 -98 22 25.6541 -95 15 25.0852 -94 7 24.1852 -89 1 23.745 -88 25 25.2581 -84 7 23.1048 -82 9 24.1393 -80 2 22.2336 -79 20 25.5836 -78 73 25.208 -74 2 22.969 -72 39 28.5041 -70 24 24.45 -67 12 25.0488 -66 20 25.0643 -62 20 24.7228 -61 18 25.3744 -58 7 25.6353 -56 16 24.845 -53 19 25.5631 -52 27 24.8275 -46 11 24.2564 -45 14 24.9035 -40 21 25.7255 -37 14 25.3961 -32 14 25.2771 -29 15 24.8332 -28 15 23.9649 -26 34 25.3391 -25 9 24.3998 -24 2 21.8626 -22 12 24.537 -20 11 25.0785 -18 9 24.567 -17 2 23.3972 -16 8 24.2729 -15 7 25.6046 -14 14 24.5476 -12 1 20.6101 -11 11 24.6055 -10 3 22.9904 -9 5 23.9026 -7 6 23.305 -6 6 22.8829 -5 1 18.032 -4 2 20.7306 -3 7 20.4444 -2 34 14.6752 -1 1357 1.7212 0 42290 25.1296 3 80 35.3729 4 5 32.0393 5 7 30.6344 6 48 31.5691 7 109 30.7205 8 242 30.4773 9 177 29.7848 10 236 29.7871 11 114 29.0977 12 87 28.8537 13 48 28.7972 14 23 28.2323 15 8 27.6667 16 13 28.6291 17 2 29.4031 18 12 25.5337 19 5 26.0755 20 1 27.7492 21 8 25.3753 22 6 25.5228 23 1 27.0083 24 5 27.6667 25 6 22.4512 28 35 25.6374 29 12 25.6531 30 7 25.9535 32 4 26.9973 34 3 23.8562 35 20 25.4919 36 2 29.2933 37 1 27.4446 39 18 24.6836 40 22 23.8548 42 9 25.7421 44 8 25.1196 46 8 25.5785 47 5 24.4833 48 8 25.2524 50 2 26.709 51 4 26.5397 52 27 24.82 53 28 25.3735 55 2 26.7717 58 4 25.5641 59 8 25.6822 63 4 25.7852 66 18 24.6047 69 6 25.1265 76 11 25.6693 -97 0 10 29.7871 second pass Negative binormial transformation : median of transformations : 25.1956 sigma : 1.38007 median/sigma : 18.2568 lamda : 14.4264 arget_tlamda : 7.93142 DEL- 1 1363 45839 0.0297345 DEL- 2 1393 45839 0.030389 DEL- 3 1399 45839 0.0305199 DEL- 4 1400 45839 0.0305417 DEL- 5 1401 45839 0.0305635 DEL- 6 1411 45839 0.0307816 DEL- 7 1413 45839 0.0308253 DEL- 8 1413 45839 0.0308253 DEL- 9 1418 45839 0.0309344 DEL- 10 1421 45839 0.0309998 DEL- 11 1433 45839 0.0312616 DEL- 12 1433 45839 0.0312616 DEL- 13 1433 45839 0.0312616 DEL- 14 1447 45839 0.031567 DEL- 15 1454 45839 0.0317197 DEL- 16 1462 45839 0.0318942 DEL- 17 1464 45839 0.0319379 DEL- 18 1473 45839 0.0321342 DEL- 19 1473 45839 0.0321342 DEL- 20 1484 45839 0.0323742 DEL- 21 1484 45839 0.0323742 DEL- 22 1496 45839 0.032636 DEL- 23 1496 45839 0.032636 DEL- 24 1498 45839 0.0326796 DEL- 25 1507 45839 0.0328759 DEL- 26 1541 45839 0.0336177 DEL- 27 1541 45839 0.0336177 DEL- 28 1556 45839 0.0339449 DEL- 29 1571 45839 0.0342721 DEL- 30 1571 45839 0.0342721 DEL- 31 1571 45839 0.0342721 DEL- 32 1585 45839 0.0345775 DEL- 33 1585 45839 0.0345775 DEL- 34 1585 45839 0.0345775 DEL- 35 1585 45839 0.0345775 DEL- 36 1585 45839 0.0345775 DEL- 37 1599 45839 0.034883 DEL- 38 1599 45839 0.034883 DEL- 39 1599 45839 0.034883 DEL- 40 1620 45839 0.0353411 DEL- 41 1620 45839 0.0353411 DEL- 42 1620 45839 0.0353411 DEL- 43 1620 45839 0.0353411 DEL- 44 1620 45839 0.0353411 DEL- 45 1634 45839 0.0356465 DEL- 46 1645 45839 0.0358865 DEL- 47 1645 45839 0.0358865 DEL- 48 1645 45839 0.0358865 DEL- 49 1645 45839 0.0358865 DEL- 50 1645 45839 0.0358865 DEL- 51 1645 45839 0.0358865 DEL- 52 1672 45839 0.0364755 DEL- 53 1691 45839 0.03689 DEL- 54 1691 45839 0.03689 DEL- 55 1691 45839 0.03689 DEL- 56 1707 45839 0.037239 DEL- 57 1707 45839 0.037239 DEL- 58 1714 45839 0.0373917 DEL- 59 1714 45839 0.0373917 DEL- 60 1714 45839 0.0373917 DEL- 61 1732 45839 0.0377844 DEL- 62 1752 45839 0.0382207 DEL- 63 1752 45839 0.0382207 DEL- 64 1752 45839 0.0382207 DEL- 65 1752 45839 0.0382207 DEL- 66 1772 45839 0.038657 DEL- 67 1784 45839 0.0389188 DEL- 68 1784 45839 0.0389188 DEL- 69 1784 45839 0.0389188 DEL- 70 1808 45839 0.0394424 DEL- 71 1808 45839 0.0394424 DEL- 72 1847 45839 0.0402932 DEL- 73 1847 45839 0.0402932 DEL- 74 1849 45839 0.0403368 DEL- 75 1849 45839 0.0403368 DEL- 76 1849 45839 0.0403368 DEL- 77 1849 45839 0.0403368 DEL- 78 1922 45839 0.0419294 DEL- 79 1942 45839 0.0423657 DEL- 80 1944 45839 0.0424093 DEL- 81 1944 45839 0.0424093 DEL- 82 1953 45839 0.0426056 DEL- 83 1953 45839 0.0426056 DEL- 84 1960 45839 0.0427583 DEL- 85 1960 45839 0.0427583 DEL- 86 1960 45839 0.0427583 DEL- 87 1960 45839 0.0427583 DEL- 88 1985 45839 0.0433037 DEL- 89 1986 45839 0.0433256 DEL- 90 1986 45839 0.0433256 DEL- 91 1986 45839 0.0433256 DEL- 92 1986 45839 0.0433256 DEL- 93 1986 45839 0.0433256 DEL- 94 1993 45839 0.0434783 DEL- 95 2008 45839 0.0438055 DEL- 96 2008 45839 0.0438055 DEL- 97 2008 45839 0.0438055 DEL- 98 2030 45839 0.0442854 DEL- 99 2030 45839 0.0442854 DUP+ 1 0 45839 0 DUP+ 2 61 45839 0.00133074 DUP+ 3 84 45839 0.0018325 DUP+ 4 85 45839 0.00185432 DUP+ 5 136 45839 0.00296691 DUP+ 6 262 45839 0.00571566 DUP+ 7 496 45839 0.0108205 DUP+ 8 706 45839 0.0154017 DUP+ 9 921 45839 0.0200921 DUP+ 10 1030 45839 0.0224699 DUP+ 11 1121 45839 0.0244552 DUP+ 12 1161 45839 0.0253278 DUP+ 13 1206 45839 0.0263095 DUP+ 14 1222 45839 0.0266585 DUP+ 15 1226 45839 0.0267458 DUP+ 16 1226 45839 0.0267458 DUP+ 17 1235 45839 0.0269421 DUP+ 18 1244 45839 0.0271385 DUP+ 19 1245 45839 0.0271603 DUP+ 20 1252 45839 0.027313 DUP+ 21 1258 45839 0.0274439 DUP+ 22 1259 45839 0.0274657 DUP+ 23 1264 45839 0.0275748 DUP+ 24 1264 45839 0.0275748 DUP+ 25 1270 45839 0.0277057 DUP+ 26 1277 45839 0.0278584 DUP+ 27 1283 45839 0.0279893 DUP+ 28 1306 45839 0.028491 DUP+ 29 1324 45839 0.0288837 DUP+ 30 1324 45839 0.0288837 DUP+ 31 1324 45839 0.0288837 DUP+ 32 1332 45839 0.0290582 DUP+ 33 1336 45839 0.0291455 DUP+ 34 1338 45839 0.0291891 DUP+ 35 1361 45839 0.0296909 DUP+ 36 1361 45839 0.0296909 DUP+ 37 1368 45839 0.0298436 DUP+ 38 1401 45839 0.0305635 DUP+ 39 1401 45839 0.0305635 DUP+ 40 1401 45839 0.0305635 DUP+ 41 1404 45839 0.0306289 DUP+ 42 1413 45839 0.0308253 DUP+ 43 1413 45839 0.0308253 DUP+ 44 1421 45839 0.0309998 DUP+ 45 1427 45839 0.0311307 DUP+ 46 1434 45839 0.0312834 DUP+ 47 1452 45839 0.0316761 DUP+ 48 1455 45839 0.0317415 DUP+ 49 1455 45839 0.0317415 DUP+ 50 1457 45839 0.0317852 DUP+ 51 1458 45839 0.031807 DUP+ 52 1485 45839 0.032396 DUP+ 53 1510 45839 0.0329414 DUP+ 54 1510 45839 0.0329414 DUP+ 55 1512 45839 0.032985 DUP+ 56 1517 45839 0.0330941 DUP+ 57 1517 45839 0.0330941 DUP+ 58 1521 45839 0.0331814 DUP+ 59 1524 45839 0.0332468 DUP+ 60 1524 45839 0.0332468 DUP+ 61 1528 45839 0.0333341 DUP+ 62 1528 45839 0.0333341 DUP+ 63 1528 45839 0.0333341 DUP+ 64 1528 45839 0.0333341 DUP+ 65 1528 45839 0.0333341 DUP+ 66 1546 45839 0.0337267 DUP+ 67 1546 45839 0.0337267 DUP+ 68 1546 45839 0.0337267 DUP+ 69 1552 45839 0.0338576 DUP+ 70 1552 45839 0.0338576 DUP+ 71 1552 45839 0.0338576 DUP+ 72 1552 45839 0.0338576 DUP+ 73 1552 45839 0.0338576 DUP+ 74 1563 45839 0.0340976 DUP+ 75 1563 45839 0.0340976 DUP+ 76 1563 45839 0.0340976 DUP+ 77 1563 45839 0.0340976 DUP+ 78 1563 45839 0.0340976 DUP+ 79 1563 45839 0.0340976 DUP+ 80 1563 45839 0.0340976 DUP+ 81 1563 45839 0.0340976 DUP+ 82 1563 45839 0.0340976 DUP+ 83 1563 45839 0.0340976 DUP+ 84 1563 45839 0.0340976 DUP+ 85 1563 45839 0.0340976 DUP+ 86 1563 45839 0.0340976 DUP+ 87 1563 45839 0.0340976 DUP+ 88 1563 45839 0.0340976 DUP+ 89 1563 45839 0.0340976 DUP+ 90 1563 45839 0.0340976 DUP+ 91 1563 45839 0.0340976 DUP+ 92 1563 45839 0.0340976 DUP+ 93 1563 45839 0.0340976 DUP+ 94 1563 45839 0.0340976 DUP+ 95 1563 45839 0.0340976 DUP+ 96 1563 45839 0.0340976 DUP+ 97 1563 45839 0.0340976 DUP+ 98 1563 45839 0.0340976 DUP+ 99 1563 45839 0.0340976 Selected 19 segments for testing Done checking overlaps, after merging, 19 segments left Found 19 CNVs : 10 DEL + 9 DUP Segmentation Fault
Tristan
The text was updated successfully, but these errors were encountered:
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Hello
I am getting a segmentation fault. Any idea on what is going wrong ?
Thanks,
Tristan
The text was updated successfully, but these errors were encountered: