I have tried to use mrCaNaVar with some sequencing data generated on a SOLiD 4
sequencer. Since mrFAST and mrsFAST only work with Illumina reads, I used the
alignment that I generated with the Bioscope software which comes with the
SOLiD 4 sequencer.
Mode: Read SAM …
Loading reference configuration, hold on … . 25 chromosomes loaded.
Scanning the SAM directory: /Data/bioInfo/SOLiD/sam/
Loading file 1 of 1: SOLiD.sam…
So, I'm wondering if this segfault is caused by the SOLiD alignment I'm using,
or if I did something else wrong.
If it is caused by the BAM file I'm using, should I try to re-align my SOLiD
reads with another mapping software before using mrCaNaVar? If so, which one?
Thanks in advance for your help,
Greetings,
Stéphane Wenric
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First, I suspect mrcanavar would work reliably with BioScape, it definitely
will not if the mapper doesn't return all possible map locations. This is
essential in correctly identifying segmental duplications and multi-copy
segments. It might be possible to detect large deletions, however I never
tried. We do have a beta version of a SOLiD mapper now at drfast.sf.net; which
could be used with mrcanavar.
That being said, the segmentation fault you are getting seems to be the issue
I had with some versions of gcc and Linux kernel. I released an update just
yesterday (v. 0.33). Please download and try with this version, and let me
know if it still fails.
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This happens if I make with gcc 4.3.4, gcc 4.1.1 or icc 12.0 but doesn't occur
(ie runs to completion) with gcc4.1.1
icc gives a possible clue:
icc -c -O2 -g callcnv.c -o callcnv.o
callcnv.c(96): warning #592: variable "fname" is used before its value is
set
sprintf (fname, "%s.cw_norm.bed", out_prefix);
^
(the caret points to 'fname')
Running it through the debugger confirms fname has no value:
idbc -args mrcanavar -call -conf hpr.conf -depth NA19238.depth -o output
Intel(R) Debugger for applications running on Intel(R) 64, Version 12.0,
Build
object file name: mrcanavar
Reading symbols from /home/g/gg78/mrcanavar-0.33/mrcanavar…done.
(idb) run
Starting program: /home/g/gg78/mrcanavar-0.33/mrcanavar
Mode: Call copy numbers …
Loading reference configuration, hold on … . 1 chromosomes loaded.
depth file NA19238.depth is loaded.
Control region cleanup…
CW Normalization completed.
LW Normalization completed.
SW Normalization completed.
Writing normalized CW depth to: output.cw_norm.bed.
Program received signal SIGSEGV
_IO_str_overflow () in /lib64/libc-2.5.so
(idb) bt
#0 0x00000030d146f0f1 in _IO_str_overflow () in /lib64/libc-2.5.so
#1 0x00000030d146e294 in _IO_default_xsputn () in /lib64/libc-2.5.so
#2 0x00000030d1446503 in _IO_vfprintf () in /lib64/libc-2.5.so
#3 0x00000030d1463b49 in vsprintf () in /lib64/libc-2.5.so
#4 0x00000030d144d528 in _IO_sprintf () in /lib64/libc-2.5.so
#5 0x0000000000406c54 in call_cnv (depthFile=0x7fffffffd2e0
"\001\200\255\3730", out_prefix=0x6f (null)) at
/home/g/gg78/mrcanavar-0.33/callcnv.c:96
#6 0x0000000000401a8b in main (argc=-11552, argv=0x6f) at
/home/g/gg78/mrcanavar-0.33/mrcanavar.c:123
(idb) display fname
No symbol "fname" in current context.
Cannot evaluate 'fname'.
1: fname =
(idb) quit
So it looks like fname is declared on line 10 of callcnv.c within
call_cnv(), and is then referred to on line 96 without getting a value
assigned.
I hope this is useful for you.
Regards
Gary
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Hello,
I have tried to use mrCaNaVar with some sequencing data generated on a SOLiD 4
sequencer. Since mrFAST and mrsFAST only work with Illumina reads, I used the
alignment that I generated with the Bioscope software which comes with the
SOLiD 4 sequencer.
Here are the steps I followed:
./mrcanavar -prep -fasta /Data/bioInfo/Genomes/human/UCSC/hg19.fa.masked -gaps /Data/bioInfo/Genomes/human/hg19.gap.bed -conf /home/swe/2011-10-18/hg19.masked.conf
(where /Data/bioInfo/Genomes/human/UCSC/hg19.fa.masked is the concatenation
of masked chr*.fa downloaded from UCSC)
This step seems to have worked correctly, here is the output:
Mode: Prepare genome…
Scanning the reference genome.
…………………….
Total of 25 chromosomes in the reference genome, with 914 gaps.
Longest chromosome is 249250621 bp
Reading the reference genome.
Chromosome chr1 (249250621 bp). Counting windows …
LW: 224778 SW: 225082 CW: 111158
Recalculating windows …
Chromosome chr2 (243199373 bp). Counting windows …
LW: 238021 SW: 238121 CW: 123162
Recalculating windows …
Chromosome chr3 (198022430 bp). Counting windows …
LW: 194572 SW: 194601 CW: 97260
Recalculating windows …
Chromosome chr4 (191154276 bp). Counting windows …
LW: 187460 SW: 187586 CW: 92258
Recalculating windows …
Chromosome chr5 (180915260 bp). Counting windows …
LW: 177346 SW: 177397 CW: 88831
Recalculating windows …
Chromosome chr6 (171115067 bp). Counting windows …
LW: 167231 SW: 167300 CW: 85191
Recalculating windows …
Chromosome chr7 (159138663 bp). Counting windows …
LW: 154713 SW: 154813 CW: 77669
Recalculating windows …
Chromosome chr8 (146364022 bp). Counting windows …
LW: 142357 SW: 142560 CW: 71126
Recalculating windows …
Chromosome chr9 (141213431 bp). Counting windows …
LW: 119553 SW: 119957 CW: 59715
Recalculating windows …
Chromosome chr10 (135534747 bp). Counting windows …
LW: 130852 SW: 130990 CW: 67652
Recalculating windows …
Chromosome chr11 (135006516 bp). Counting windows …
LW: 130599 SW: 130663 CW: 64318
Recalculating windows …
Chromosome chr12 (133851895 bp). Counting windows …
LW: 130087 SW: 130368 CW: 63195
Recalculating windows …
Chromosome chr13 (115169878 bp). Counting windows …
LW: 95549 SW: 95575 CW: 49985
Recalculating windows …
Chromosome chr14 (107349540 bp). Counting windows …
LW: 88283 SW: 88289 CW: 44152
Recalculating windows …
Chromosome chr15 (102531392 bp). Counting windows …
LW: 81611 SW: 81679 CW: 41617
Recalculating windows …
Chromosome chr16 (90354753 bp). Counting windows …
LW: 78632 SW: 78687 CW: 39074
Recalculating windows …
Chromosome chr17 (81195210 bp). Counting windows …
LW: 77679 SW: 77738 CW: 39648
Recalculating windows …
Chromosome chr18 (78077248 bp). Counting windows …
LW: 74581 SW: 74617 CW: 39667
Recalculating windows …
Chromosome chr19 (59128983 bp). Counting windows …
LW: 55475 SW: 55543 CW: 23608
Recalculating windows …
Chromosome chr20 (63025520 bp). Counting windows …
LW: 59377 SW: 59419 CW: 29459
Recalculating windows …
Chromosome chr21 (48129895 bp). Counting windows …
LW: 35009 SW: 35080 CW: 18291
Recalculating windows …
Chromosome chr22 (51304566 bp). Counting windows …
LW: 34836 SW: 34871 CW: 17638
Recalculating windows …
Chromosome chrX (155270560 bp). Counting windows …
LW: 150311 SW: 150771 CW: 59360
Recalculating windows …
Chromosome chrY (59373566 bp). Counting windows …
LW: 25026 SW: 25222 CW: 9582
Recalculating windows …
Chromosome chrM (16571 bp). Counting windows …
LW: 12 SW: 16 CW: 16
Recalculating windows …
Saving the reference configuration.
As the read step takes as input a SAM file, I extracted the BAM file i had,
with samtools.
I then ran the read step:
./mrcanavar -read -conf /home/swe/2011-10-18/hg19.masked.conf -samdir /Data/bioInfo/SOLiD/sam/ -depth /Data/bioInfo/SOLiD/solid-canavar.depth
which also seems to have run properly.
Here is the output:
Mode: Read SAM …
Loading reference configuration, hold on … . 25 chromosomes loaded.
Scanning the SAM directory: /Data/bioInfo/SOLiD/sam/
Loading file 1 of 1: SOLiD.sam…
1 file loaded.
Saving depth file /Data/bioInfo/SOLiD/solid-canavar.depth.lw.txt
Saving depth file /Data/bioInfo/SOLiD/solid-canavar.depth.sw.txt
Saving depth file /Data/bioInfo/SOLiD/solid-canavar.depth.cw.txt
Finally, I ran the call step, which has failed:
./mrcanavar -call -conf /home/swe/2011-10-18/hg19.masked.conf -depth /Data/bioInfo/SOLiD/solid-canavar.depth -o /Data/bioInfo/SOLiD/mrCaNaVar
Here is the output in verbose mode:
Mode: Call copy numbers …
Loading reference configuration, hold on … . 25 chromosomes loaded.
depth file /Data/bioInfo/SOLiD/solid-canavar.depth is loaded.
LW_MEAN: 2059.441895 SW_MEAN: 605.480774 CW_MEAN:351.397430
Control region cleanup…
MEAN: 278.714905 MEAN_X: 176.730011
Autodetect Gender: Male
Control regions CW iteration 1 mean: 257.823975 stdev: 92.366211 max:
529.499268 (cut: 488.739502) min: 27.872284 (cut: 26.908447)
mean_x: 140.258347 stdev_x: 54.233944 max_x: 290.730011 (cut: 248.726227)
min_x: 15.180389 (cut: 31.790459)
Control regions CW iteration 2 mean: 251.361252 stdev: 84.883377 max:
488.738342 (cut: 463.569702) min: 27.872284 (cut: 39.152809)
mean_x: 132.994141 stdev_x: 46.139637 max_x: 248.681839 (cut: 225.273407)
min_x: 31.855011 (cut: 40.714867)
Control regions CW iteration 3 mean: 247.158890 stdev: 79.906769 max:
463.565063 (cut: 446.925812) min: 39.188171 (cut: 47.391968)
mean_x: 128.075455 stdev_x: 41.218159 max_x: 225.234650 (cut: 210.511780)
min_x: 40.730011 (cut: 45.639137)
Control regions CW iteration 4 mean: 244.280853 stdev: 76.582237 max:
446.922882 (cut: 435.736450) min: 47.397064 (cut: 52.825260)
mean_x: 124.884010 stdev_x: 38.129169 max_x: 210.508636 (cut: 201.142349)
min_x: 45.735138 (cut: 48.625671)
Control regions CW iteration 5 mean: 242.206818 stdev: 74.274292 max:
435.732788 (cut: 427.892548) min: 52.868347 (cut: 56.521088)
mean_x: 122.475586 stdev_x: 35.952019 max_x: 201.118179 (cut: 194.379623)
min_x: 48.633850 (cut: 50.571548)
Control regions CW iteration 6 mean: 240.725906 stdev: 72.663239 max:
427.892273 (cut: 422.384003) min: 56.563690 (cut: 59.067810)
mean_x: 120.876892 stdev_x: 34.515820 max_x: 194.347656 (cut: 189.908539)
min_x: 50.621323 (cut: 51.845253)
Control regions CW iteration 7 mean: 239.628845 stdev: 71.502235 max:
422.381989 (cut: 418.384430) min: 59.080688 (cut: 60.873257)
mean_x: 119.588806 stdev_x: 33.356731 max_x: 189.903168 (cut: 186.302277)
min_x: 51.903168 (cut: 52.875343)
Control regions CW iteration 8 mean: 238.835449 stdev: 70.646355 max:
418.381989 (cut: 415.451324) min: 60.876831 (cut: 62.219563)
mean_x: 118.615044 stdev_x: 32.472641 max_x: 186.297668 (cut: 183.560333)
min_x: 52.969009 (cut: 53.669762)
Control regions CW iteration 9 mean: 238.251862 stdev: 70.038078 max:
415.449219 (cut: 413.347046) min: 62.221985 (cut: 63.156666)
mean_x: 117.879059 stdev_x: 31.791397 max_x: 183.527115 (cut: 181.461853)
min_x: 53.681229 (cut: 54.296265)
Control regions CW iteration 10 mean: 237.829895 stdev: 69.595711 max:
413.339111 (cut: 411.819153) min: 63.238556 (cut: 63.840618)
mean_x: 117.183960 stdev_x: 31.222639 max_x: 181.444305 (cut: 179.629242)
min_x: 54.311401 (cut: 54.738682)
Control regions CW iteration 11 mean: 237.529388 stdev: 69.280785 max:
411.814209 (cut: 410.731354) min: 63.946198 (cut: 64.327423)
mean_x: 116.612495 stdev_x: 30.717026 max_x: 179.618896 (cut: 178.046539)
min_x: 54.805710 (cut: 55.178444)
Control regions CW iteration 12 mean: 237.294174 stdev: 69.043617 max:
410.726166 (cut: 409.903198) min: 64.361176 (cut: 64.685135)
mean_x: 116.175842 stdev_x: 30.313696 max_x: 178.037460 (cut: 176.803238)
min_x: 55.180389 (cut: 55.548450)
Control regions CW iteration 13 mean: 237.131149 stdev: 68.873703 max:
409.897766 (cut: 409.315399) min: 64.692932 (cut: 64.946892)
mean_x: 115.862930 stdev_x: 30.045509 max_x: 176.786713 (cut: 175.953949)
min_x: 55.567993 (cut: 55.771912)
Control regions CW iteration 14 mean: 236.990875 stdev: 68.736023 max:
409.312073 (cut: 408.830933) min: 64.960022 (cut: 65.150818)
mean_x: 115.570328 stdev_x: 29.802471 max_x: 175.949402 (cut: 175.175262)
min_x: 55.786713 (cut: 55.965385)
Control regions CW iteration 15 mean: 236.899429 stdev: 68.642593 max:
408.826019 (cut: 408.505920) min: 65.170990 (cut: 65.292946)
mean_x: 115.327652 stdev_x: 29.573811 max_x: 175.158585 (cut: 174.475281)
min_x: 56.009155 (cut: 56.180031)
Control regions CW iteration 16 mean: 236.825867 stdev: 68.568459 max:
408.500000 (cut: 408.247009) min: 65.331451 (cut: 65.404724)
mean_x: 115.127022 stdev_x: 29.408606 max_x: 174.475204 (cut: 173.944229)
min_x: 56.285919 (cut: 56.309811)
Control regions CW iteration 17 mean: 236.775162 stdev: 68.518211 max:
408.245392 (cut: 408.070679) min: 65.424545 (cut: 65.479630)
mean_x: 114.915131 stdev_x: 29.258854 max_x: 173.910110 (cut: 173.432831)
min_x: 56.378525 (cut: 56.397423)
Control regions CW iteration 18 mean: 236.748703 stdev: 68.492752 max:
408.070526 (cut: 407.980591) min: 65.484772 (cut: 65.516823)
mean_x: 114.771347 stdev_x: 29.146822 max_x: 173.430008 (cut: 173.064987)
min_x: 56.401825 (cut: 56.477703)
Control regions CW iteration 19 mean: 236.734482 stdev: 68.475502 max:
407.971008 (cut: 407.923218) min: 65.519531 (cut: 65.545731)
mean_x: 114.619087 stdev_x: 29.050684 max_x: 173.053085 (cut: 172.720459)
min_x: 56.507782 (cut: 56.517719)
Control regions CW iteration 20 mean: 236.722244 stdev: 68.463699 max:
407.922882 (cut: 407.881470) min: 65.545746 (cut: 65.562996)
mean_x: 114.489395 stdev_x: 28.962048 max_x: 172.701447 (cut: 172.413483)
min_x: 56.539871 (cut: 56.565300)
Control regions CW iteration 21 mean: 236.715744 stdev: 68.457222 max:
407.880066 (cut: 407.858795) min: 65.565063 (cut: 65.572693)
mean_x: 114.406250 stdev_x: 28.874161 max_x: 172.400894 (cut: 172.154572)
min_x: 56.571136 (cut: 56.657928)
Control regions CW iteration 22 mean: 236.709259 stdev: 68.448578 max:
407.858063 (cut: 407.830688) min: 65.700470 (cut: 65.587814)
mean_x: 114.333611 stdev_x: 28.807657 max_x: 172.144302 (cut: 171.948929)
min_x: 56.671875 (cut: 56.718296)
Control regions CW iteration 23 mean: 236.702835 stdev: 68.442780 max:
407.826019 (cut: 407.809784) min: 65.700470 (cut: 65.595886)
mean_x: 114.262146 stdev_x: 28.748957 max_x: 171.944290 (cut: 171.760056)
min_x: 56.735138 (cut: 56.764233)
Control regions CW iteration 24 mean: 236.699127 stdev: 68.439606 max:
407.808319 (cut: 407.798157) min: 65.700470 (cut: 65.600113)
mean_x: 114.209328 stdev_x: 28.702429 max_x: 171.739182 (cut: 171.614182)
min_x: 56.805710 (cut: 56.804470)
Control regions CW iteration 25 mean: 236.695175 stdev: 68.436279 max:
407.795074 (cut: 407.785889) min: 65.700470 (cut: 65.604477)
mean_x: 114.178642 stdev_x: 28.674614 max_x: 171.598145 (cut: 171.527863)
min_x: 56.805710 (cut: 56.829414)
Control regions CW iteration 26 mean: 236.691528 stdev: 68.432549 max:
407.785248 (cut: 407.772888) min: 65.700470 (cut: 65.610153)
mean_x: 114.161530 stdev_x: 28.655060 max_x: 171.525467 (cut: 171.471649)
min_x: 56.844482 (cut: 56.851410)
Control regions CW iteration 27 mean: 236.684509 stdev: 68.426155 max:
407.772400 (cut: 407.749878) min: 65.700470 (cut: 65.619125)
mean_x: 114.136337 stdev_x: 28.632793 max_x: 171.465866 (cut: 171.401917)
min_x: 56.869247 (cut: 56.870750)
Control regions CW iteration 28 mean: 236.679733 stdev: 68.420784 max:
407.748230 (cut: 407.731689) min: 65.700470 (cut: 65.627777)
mean_x: 114.124565 stdev_x: 28.622074 max_x: 171.400894 (cut: 171.368713)
min_x: 56.902161 (cut: 56.880417)
Control regions CW iteration 29 mean: 236.676636 stdev: 68.417961 max:
407.726166 (cut: 407.721527) min: 65.700470 (cut: 65.631729)
mean_x: 114.116058 stdev_x: 28.612591 max_x: 171.321671 (cut: 171.341248)
min_x: 56.902161 (cut: 56.890877)
Control regions CW iteration 30 mean: 236.676117 stdev: 68.417267 max:
407.719147 (cut: 407.719299) min: 65.700470 (cut: 65.632950)
mean_x: 114.116058 stdev_x: 28.612587 max_x: 171.321671 (cut: 171.341232)
min_x: 56.902161 (cut: 56.890884)
CW Normalization completed.
Control regions LW iteration 1 mean: 1655.755981 stdev: 528.203247 max:
3457.322754 (cut: 2976.264160) min: 182.162476 (cut: 335.247864)
mean_x: 1119.082886 stdev_x: 465.718994 max_x: 2819.626465 (cut:
2050.520996) min_x: 135.412964 (cut: 187.644897)
Control regions LW iteration 2 mean: 1573.071167 stdev: 445.811371 max:
2976.260010 (cut: 2687.599609) min: 335.573242 (cut: 458.542725)
mean_x: 988.418945 stdev_x: 340.732391 max_x: 2050.113281 (cut:
1669.883789) min_x: 188.436401 (cut: 306.954163)
Control regions LW iteration 3 mean: 1515.306274 stdev: 394.833710 max:
2687.590332 (cut: 2502.390625) min: 460.437988 (cut: 528.221985)
mean_x: 915.875366 stdev_x: 266.793823 max_x: 1669.757812 (cut:
1449.463013) min_x: 307.412964 (cut: 382.287720)
Control regions LW iteration 4 mean: 1474.036743 stdev: 361.605927 max:
2502.376953 (cut: 2378.051514) min: 528.953735 (cut: 570.021912)
mean_x: 870.606323 stdev_x: 219.656021 max_x: 1449.461914 (cut:
1309.918335) min_x: 382.373535 (cut: 431.294281)
Control regions LW iteration 5 mean: 1443.904785 stdev: 338.649780 max:
2378.042969 (cut: 2290.529297) min: 570.513550 (cut: 597.280334)
mean_x: 837.129822 stdev_x: 186.614822 max_x: 1309.779175 (cut:
1210.359497) min_x: 431.505127 (cut: 463.900177)
Control regions LW iteration 6 mean: 1421.731079 stdev: 322.140930 max:
2290.525391 (cut: 2227.083496) min: 597.346436 (cut: 616.378784)
mean_x: 811.565491 stdev_x: 161.093231 max_x: 1210.294678 (cut:
1133.751953) min_x: 464.290283 (cut: 489.379028)
Control regions LW iteration 7 mean: 1404.471680 stdev: 309.779297 max:
2227.063721 (cut: 2178.919922) min: 616.728882 (cut: 630.023438)
mean_x: 792.413330 stdev_x: 142.045624 max_x: 1133.560791 (cut:
1076.504639) min_x: 489.488159 (cut: 508.322083)
Control regions LW iteration 8 mean: 1391.489746 stdev: 300.502808 max:
2178.890137 (cut: 2142.746826) min: 630.024170 (cut: 640.232727)
mean_x: 778.961426 stdev_x: 126.755081 max_x: 1076.446533 (cut:
1032.471558) min_x: 508.362183 (cut: 525.451294)
Control regions LW iteration 9 mean: 1381.462402 stdev: 293.441681 max:
2142.736572 (cut: 2115.066650) min: 640.352783 (cut: 647.858215)
mean_x: 767.725586 stdev_x: 114.445152 max_x: 1032.114990 (cut:
996.615906) min_x: 525.460815 (cut: 538.835266)
Control regions LW iteration 10 mean: 1373.719482 stdev: 288.079803 max:
2115.060303 (cut: 2093.918945) min: 647.955566 (cut: 653.519958)
mean_x: 758.773621 stdev_x: 104.856125 max_x: 996.335815 (cut:
968.485840) min_x: 538.870728 (cut: 549.061401)
Control regions LW iteration 11 mean: 1367.967529 stdev: 283.966888 max:
2093.851562 (cut: 2077.884766) min: 653.535522 (cut: 658.050293)
mean_x: 754.368286 stdev_x: 97.558090 max_x: 968.406616 (cut: 949.484497)
min_x: 549.126709 (cut: 559.252075)
Control regions LW iteration 12 mean: 1363.380371 stdev: 280.869446 max:
2077.884277 (cut: 2065.553955) min: 658.160156 (cut: 661.206787)
mean_x: 749.739441 stdev_x: 91.508064 max_x: 949.297119 (cut: 932.755554)
min_x: 559.333008 (cut: 566.723328)
Control regions LW iteration 13 mean: 1359.717773 stdev: 278.456299 max:
2065.547363 (cut: 2055.858398) min: 661.328491 (cut: 663.577026)
mean_x: 746.642151 stdev_x: 86.925041 max_x: 932.656006 (cut: 920.492249)
min_x: 566.798584 (cut: 572.792053)
Control regions LW iteration 14 mean: 1356.816406 stdev: 276.499695 max:
2055.856934 (cut: 2048.065674) min: 663.695435 (cut: 665.567139)
mean_x: 741.834778 stdev_x: 82.461105 max_x: 919.872559 (cut: 906.756958)
min_x: 572.904175 (cut: 576.912598)
Control regions LW iteration 15 mean: 1354.584106 stdev: 274.980133 max:
2048.060303 (cut: 2042.034424) min: 665.638184 (cut: 667.133789)
mean_x: 738.829712 stdev_x: 79.660446 max_x: 906.738525 (cut: 898.150635)
min_x: 577.119019 (cut: 579.508789)
Control regions LW iteration 16 mean: 1352.786011 stdev: 273.782593 max:
2041.999390 (cut: 2037.242432) min: 667.256592 (cut: 668.329529)
mean_x: 735.819946 stdev_x: 77.636765 max_x: 897.485596 (cut: 891.093506)
min_x: 579.521118 (cut: 580.546387)
Control regions LW iteration 17 mean: 1351.380615 stdev: 272.912598 max:
2037.238159 (cut: 2033.662109) min: 668.337036 (cut: 669.099121)
mean_x: 733.413635 stdev_x: 75.840645 max_x: 891.070190 (cut: 885.094910)
min_x: 580.552124 (cut: 581.732361)
Control regions LW iteration 18 mean: 1350.242554 stdev: 272.155212 max:
2033.653442 (cut: 2030.630615) min: 669.227417 (cut: 669.854492)
mean_x: 731.950439 stdev_x: 74.040131 max_x: 884.687866 (cut: 880.030701)
min_x: 581.828857 (cut: 583.870178)
Control regions LW iteration 19 mean: 1349.320312 stdev: 271.545624 max:
2030.615845 (cut: 2028.184326) min: 669.953735 (cut: 670.456238)
mean_x: 730.085815 stdev_x: 72.384438 max_x: 879.986816 (cut: 874.854675)
min_x: 583.999756 (cut: 585.316956)
Control regions LW iteration 20 mean: 1348.645142 stdev: 271.070831 max:
2028.181396 (cut: 2026.322266) min: 670.489502 (cut: 670.968079)
mean_x: 728.631165 stdev_x: 71.080452 max_x: 874.841675 (cut: 870.792053)
min_x: 585.454712 (cut: 586.470276)
Control regions LW iteration 21 mean: 1348.037842 stdev: 270.692871 max:
2026.284180 (cut: 2024.770020) min: 670.985229 (cut: 671.305664)
mean_x: 727.389709 stdev_x: 70.208054 max_x: 870.535767 (cut: 867.805786)
min_x: 586.623657 (cut: 586.973633)
Control regions LW iteration 22 mean: 1347.583984 stdev: 270.374176 max:
2024.763062 (cut: 2023.519409) min: 671.392212 (cut: 671.648560)
mean_x: 727.001831 stdev_x: 69.589691 max_x: 867.779175 (cut: 866.181213)
min_x: 587.113159 (cut: 587.822449)
Control regions LW iteration 23 mean: 1347.166138 stdev: 270.122620 max:
2023.516357 (cut: 2022.472656) min: 671.661255 (cut: 671.859619)
mean_x: 726.981567 stdev_x: 68.985573 max_x: 865.874390 (cut: 864.952698)
min_x: 587.955200 (cut: 589.010437)
Control regions LW iteration 24 mean: 1346.838745 stdev: 269.895416 max:
2022.469727 (cut: 2021.577271) min: 671.932495 (cut: 672.100220)
mean_x: 726.986816 stdev_x: 68.444878 max_x: 864.923462 (cut: 863.876587)
min_x: 589.012207 (cut: 590.097046)
Control regions LW iteration 25 mean: 1346.595581 stdev: 269.741638 max:
2021.572876 (cut: 2020.949707) min: 672.165283 (cut: 672.241455)
mean_x: 727.284729 stdev_x: 67.835426 max_x: 863.738525 (cut: 862.955566)
min_x: 590.148804 (cut: 591.613892)
Control regions LW iteration 26 mean: 1346.382324 stdev: 269.588257 max:
2020.944458 (cut: 2020.353027) min: 672.261841 (cut: 672.411682)
mean_x: 727.685059 stdev_x: 67.167885 max_x: 862.535767 (cut: 862.020813)
min_x: 591.798584 (cut: 593.349304)
Control regions LW iteration 27 mean: 1346.207642 stdev: 269.477051 max:
2020.351440 (cut: 2019.900269) min: 672.464722 (cut: 672.515015)
mean_x: 728.287537 stdev_x: 66.777534 max_x: 861.928345 (cut: 861.842590)
min_x: 593.577393 (cut: 594.732483)
Control regions LW iteration 28 mean: 1346.122681 stdev: 269.401550 max:
2019.899414 (cut: 2019.626587) min: 672.746460 (cut: 672.618774)
mean_x: 728.466858 stdev_x: 66.355225 max_x: 861.610107 (cut: 861.177307)
min_x: 594.754761 (cut: 595.756409)
Control regions LW iteration 29 mean: 1346.007935 stdev: 269.335815 max:
2019.616333 (cut: 2019.347412) min: 672.746460 (cut: 672.668396)
mean_x: 728.977478 stdev_x: 66.143700 max_x: 861.009888 (cut: 861.264893)
min_x: 595.878906 (cut: 596.690063)
Control regions LW iteration 30 mean: 1345.946045 stdev: 269.297882 max:
2019.344482 (cut: 2019.190674) min: 672.746460 (cut: 672.701355)
mean_x: 729.241089 stdev_x: 66.011330 max_x: 861.009888 (cut: 861.263733)
min_x: 597.265503 (cut: 597.218445)
Control regions LW iteration 31 mean: 1345.883545 stdev: 269.265472 max:
2019.181396 (cut: 2019.047241) min: 672.746460 (cut: 672.719849)
mean_x: 729.241089 stdev_x: 66.011223 max_x: 861.009888 (cut: 861.263550)
min_x: 597.265503 (cut: 597.218628)
Control regions LW iteration 32 mean: 1345.822876 stdev: 269.225769 max:
2019.044189 (cut: 2018.887329) min: 672.746460 (cut: 672.758423)
mean_x: 729.241089 stdev_x: 66.011223 max_x: 861.009888 (cut: 861.263550)
min_x: 597.265503 (cut: 597.218628)
Control regions LW iteration 33 mean: 1345.738647 stdev: 269.169098 max:
2018.877197 (cut: 2018.661377) min: 672.802124 (cut: 672.815918)
mean_x: 729.241089 stdev_x: 66.011223 max_x: 861.009888 (cut: 861.263550)
min_x: 597.265503 (cut: 597.218628)
Control regions LW iteration 34 mean: 1345.670776 stdev: 269.125854 max:
2018.653442 (cut: 2018.485352) min: 672.830444 (cut: 672.856140)
mean_x: 729.241089 stdev_x: 66.011223 max_x: 861.009888 (cut: 861.263550)
min_x: 597.265503 (cut: 597.218628)
Control regions LW iteration 35 mean: 1345.598267 stdev: 269.081726 max:
2018.472778 (cut: 2018.302612) min: 672.895752 (cut: 672.893921)
mean_x: 729.241089 stdev_x: 66.011223 max_x: 861.009888 (cut: 861.263550)
min_x: 597.265503 (cut: 597.218628)
Control regions LW iteration 36 mean: 1345.529785 stdev: 269.040619 max:
2018.257568 (cut: 2018.131348) min: 672.895752 (cut: 672.928223)
mean_x: 729.241089 stdev_x: 66.011223 max_x: 861.009888 (cut: 861.263550)
min_x: 597.265503 (cut: 597.218628)
Control regions LW iteration 37 mean: 1345.504028 stdev: 269.018921 max:
2018.129883 (cut: 2018.051270) min: 673.134155 (cut: 672.956726)
mean_x: 729.241089 stdev_x: 66.011223 max_x: 861.009888 (cut: 861.263550)
min_x: 597.265503 (cut: 597.218628)
Control regions LW iteration 38 mean: 1345.486694 stdev: 269.007721 max:
2018.050171 (cut: 2018.005981) min: 673.134155 (cut: 672.967407)
mean_x: 729.241089 stdev_x: 66.011223 max_x: 861.009888 (cut: 861.263550)
min_x: 597.265503 (cut: 597.218628)
Control regions LW iteration 39 mean: 1345.475830 stdev: 269.000458 max:
2017.997314 (cut: 2017.976929) min: 673.134155 (cut: 672.974670)
mean_x: 729.241089 stdev_x: 66.011223 max_x: 861.009888 (cut: 861.263550)
min_x: 597.265503 (cut: 597.218628)
Control regions LW iteration 40 mean: 1345.456909 stdev: 268.991547 max:
2017.969238 (cut: 2017.935791) min: 673.134155 (cut: 672.978027)
mean_x: 729.241089 stdev_x: 66.011223 max_x: 861.009888 (cut: 861.263550)
min_x: 597.265503 (cut: 597.218628)
Control regions LW iteration 41 mean: 1345.422485 stdev: 268.969055 max:
2017.932495 (cut: 2017.845093) min: 673.134155 (cut: 672.999878)
mean_x: 729.241089 stdev_x: 66.011223 max_x: 861.009888 (cut: 861.263550)
min_x: 597.265503 (cut: 597.218628)
Control regions LW iteration 42 mean: 1345.395508 stdev: 268.953369 max:
2017.834961 (cut: 2017.778931) min: 673.134155 (cut: 673.012085)
mean_x: 729.241089 stdev_x: 66.011223 max_x: 861.009888 (cut: 861.263550)
min_x: 597.265503 (cut: 597.218628)
Control regions LW iteration 43 mean: 1345.369019 stdev: 268.937958 max:
2017.770508 (cut: 2017.713867) min: 673.134155 (cut: 673.024109)
mean_x: 729.241089 stdev_x: 66.011223 max_x: 861.009888 (cut: 861.263550)
min_x: 597.265503 (cut: 597.218628)
Control regions LW iteration 44 mean: 1345.339966 stdev: 268.922241 max:
2017.711792 (cut: 2017.645508) min: 673.134155 (cut: 673.034363)
mean_x: 729.241089 stdev_x: 66.011223 max_x: 861.009888 (cut: 861.263550)
min_x: 597.265503 (cut: 597.218628)
Control regions LW iteration 45 mean: 1345.309204 stdev: 268.903748 max:
2017.638184 (cut: 2017.568604) min: 673.134155 (cut: 673.049805)
mean_x: 729.241089 stdev_x: 66.011223 max_x: 861.009888 (cut: 861.263550)
min_x: 597.265503 (cut: 597.218628)
Control regions LW iteration 46 mean: 1345.284790 stdev: 268.890503 max:
2017.560059 (cut: 2017.510986) min: 673.134155 (cut: 673.058533)
mean_x: 729.241089 stdev_x: 66.011223 max_x: 861.009888 (cut: 861.263550)
min_x: 597.265503 (cut: 597.218628)
Control regions LW iteration 47 mean: 1345.243652 stdev: 268.865997 max:
2017.502075 (cut: 2017.408691) min: 673.134155 (cut: 673.078674)
mean_x: 729.241089 stdev_x: 66.011223 max_x: 861.009888 (cut: 861.263550)
min_x: 597.265503 (cut: 597.218628)
Control regions LW iteration 48 mean: 1345.217163 stdev: 268.848907 max:
2017.403564 (cut: 2017.339355) min: 673.134155 (cut: 673.094910)
mean_x: 729.241089 stdev_x: 66.011223 max_x: 861.009888 (cut: 861.263550)
min_x: 597.265503 (cut: 597.218628)
Control regions LW iteration 49 mean: 1345.199341 stdev: 268.839966 max:
2017.338867 (cut: 2017.299316) min: 673.134155 (cut: 673.099426)
mean_x: 729.241089 stdev_x: 66.011223 max_x: 861.009888 (cut: 861.263550)
min_x: 597.265503 (cut: 597.218628)
Control regions LW iteration 50 mean: 1345.198364 stdev: 268.839996 max:
2017.284180 (cut: 2017.298340) min: 673.134155 (cut: 673.098389)
mean_x: 729.241089 stdev_x: 66.011223 max_x: 861.009888 (cut: 861.263550)
min_x: 597.265503 (cut: 597.218628)
LW Normalization completed.
Control regions SW iteration 1 mean: 304.289062 stdev: 128.999390 max:
743.088989 (cut: 578.149231) min: 39.444641 (cut: 30.428905)
mean_x: 238.727463 stdev_x: 143.803360 max_x: 821.058655 (cut:
453.582184) min_x: 31.626282 (cut: 23.872746)
Control regions SW iteration 2 mean: 277.741547 stdev: 101.510216 max:
578.138428 (cut: 531.517090) min: 39.444641 (cut: 23.966007)
mean_x: 200.120056 stdev_x: 97.614418 max_x: 526.238037 (cut: 395.348877)
min_x: 31.626282 (cut: 4.891220)
Control regions SW iteration 3 mean: 268.261871 stdev: 92.808342 max:
527.708313 (cut: 500.282715) min: 39.444641 (cut: 36.241016)
mean_x: 178.941650 stdev_x: 77.257347 max_x: 395.225098 (cut: 333.456360)
min_x: 31.626282 (cut: 24.426956)
Control regions SW iteration 4 mean: 262.690125 stdev: 87.958450 max:
500.279449 (cut: 482.586243) min: 39.444641 (cut: 42.793999)
mean_x: 166.690201 stdev_x: 67.545319 max_x: 333.447906 (cut: 301.780823)
min_x: 31.626282 (cut: 31.599564)
Control regions SW iteration 5 mean: 258.985565 stdev: 84.845879 max:
482.585510 (cut: 471.100250) min: 42.812195 (cut: 46.870869)
mean_x: 158.526428 stdev_x: 61.959457 max_x: 301.751770 (cut: 282.445343)
min_x: 31.626282 (cut: 34.607513)
Control regions SW iteration 6 mean: 256.493347 stdev: 82.785500 max:
471.099731 (cut: 463.457092) min: 46.894928 (cut: 49.529598)
mean_x: 153.097931 stdev_x: 57.596943 max_x: 282.411316 (cut: 268.291809)
min_x: 34.619812 (cut: 37.904045)
Control regions SW iteration 7 mean: 254.848038 stdev: 81.399231 max:
463.448822 (cut: 458.346130) min: 49.545135 (cut: 51.349960)
mean_x: 149.326553 stdev_x: 54.247608 max_x: 268.254852 (cut: 257.821777)
min_x: 37.919556 (cut: 40.831337)
Control regions SW iteration 8 mean: 253.736710 stdev: 80.455940 max:
458.343262 (cut: 454.876556) min: 51.371185 (cut: 52.596859)
mean_x: 146.553543 stdev_x: 51.664921 max_x: 257.811768 (cut: 249.883392)
min_x: 40.849274 (cut: 43.223701)
Control regions SW iteration 9 mean: 252.984375 stdev: 79.799332 max:
454.876160 (cut: 452.482697) min: 52.608154 (cut: 53.486046)
mean_x: 144.459778 stdev_x: 49.710808 max_x: 249.849274 (cut: 243.881393)
min_x: 43.249146 (cut: 45.038162)
Control regions SW iteration 10 mean: 252.440292 stdev: 79.326973 max:
452.481628 (cut: 450.757721) min: 53.519318 (cut: 54.122860)
mean_x: 142.771912 stdev_x: 48.094547 max_x: 243.868622 (cut: 238.960999)
min_x: 45.056122 (cut: 46.582817)
Control regions SW iteration 11 mean: 252.071960 stdev: 79.008453 max:
450.754669 (cut: 449.593079) min: 54.127777 (cut: 54.550827)
mean_x: 141.410507 stdev_x: 46.899040 max_x: 238.960907 (cut: 235.208588)
min_x: 46.619812 (cut: 47.612427)
Control regions SW iteration 12 mean: 251.806137 stdev: 78.776291 max:
449.590851 (cut: 448.746857) min: 54.557343 (cut: 54.865410)
mean_x: 140.287125 stdev_x: 45.923450 max_x: 235.208099 (cut: 232.134033)
min_x: 47.628784 (cut: 48.440224)
Control regions SW iteration 13 mean: 251.619919 stdev: 78.615845 max:
448.743744 (cut: 448.159546) min: 54.884552 (cut: 55.080307)
mean_x: 139.473297 stdev_x: 45.201511 max_x: 232.121918 (cut: 229.876312)
min_x: 48.459503 (cut: 49.070274)
Control regions SW iteration 14 mean: 251.486984 stdev: 78.502213 max:
448.157135 (cut: 447.742493) min: 55.084686 (cut: 55.231453)
mean_x: 138.712906 stdev_x: 44.603195 max_x: 229.867584 (cut: 227.919296)
min_x: 49.071991 (cut: 49.506516)
Control regions SW iteration 15 mean: 251.398758 stdev: 78.425842 max:
447.731445 (cut: 447.463379) min: 55.286560 (cut: 55.334152)
mean_x: 138.165192 stdev_x: 44.119938 max_x: 227.901215 (cut: 226.405060)
min_x: 49.525146 (cut: 49.925316)
Control regions SW iteration 16 mean: 251.327652 stdev: 78.367210 max:
447.458984 (cut: 447.245667) min: 55.355957 (cut: 55.409626)
mean_x: 137.685150 stdev_x: 43.745193 max_x: 226.382294 (cut: 225.175537)
min_x: 49.953949 (cut: 50.194763)
Control regions SW iteration 17 mean: 251.280945 stdev: 78.328484 max:
447.244781 (cut: 447.102142) min: 55.413696 (cut: 55.459736)
mean_x: 137.316467 stdev_x: 43.457664 max_x: 225.159515 (cut: 224.231796)
min_x: 50.214172 (cut: 50.401138)
Control regions SW iteration 18 mean: 251.257751 stdev: 78.307655 max:
447.099731 (cut: 447.026886) min: 55.464569 (cut: 55.488613)
mean_x: 136.957062 stdev_x: 43.191208 max_x: 224.214172 (cut: 223.339478)
min_x: 50.408752 (cut: 50.574646)
Control regions SW iteration 19 mean: 251.240921 stdev: 78.293686 max:
447.009766 (cut: 446.975128) min: 55.493652 (cut: 55.506706)
mean_x: 136.645645 stdev_x: 42.932125 max_x: 223.331665 (cut: 222.509888)
min_x: 50.619812 (cut: 50.781395)
Control regions SW iteration 20 mean: 251.230301 stdev: 78.284096 max:
446.973175 (cut: 446.940552) min: 55.514893 (cut: 55.520061)
mean_x: 136.348602 stdev_x: 42.732014 max_x: 222.447754 (cut: 221.812622)
min_x: 50.798981 (cut: 50.884575)
Control regions SW iteration 21 mean: 251.212692 stdev: 78.270576 max:
446.926300 (cut: 446.889130) min: 55.544678 (cut: 55.536251)
mean_x: 136.181732 stdev_x: 42.586132 max_x: 221.808777 (cut: 221.354004)
min_x: 50.885010 (cut: 51.009468)
Control regions SW iteration 22 mean: 251.194611 stdev: 78.257889 max:
446.886658 (cut: 446.839325) min: 55.544678 (cut: 55.549889)
mean_x: 136.149719 stdev_x: 42.469685 max_x: 221.351074 (cut: 221.089081)
min_x: 51.058655 (cut: 51.210350)
Control regions SW iteration 23 mean: 251.187286 stdev: 78.251633 max:
446.837372 (cut: 446.816376) min: 55.557343 (cut: 55.558205)
mean_x: 136.048965 stdev_x: 42.387882 max_x: 221.068970 (cut: 220.824738)
min_x: 51.214172 (cut: 51.273201)
Control regions SW iteration 24 mean: 251.183563 stdev: 78.247810 max:
446.812195 (cut: 446.803101) min: 55.560425 (cut: 55.564037)
mean_x: 135.966324 stdev_x: 42.333736 max_x: 220.824158 (cut: 220.633789)
min_x: 51.274811 (cut: 51.298851)
Control regions SW iteration 25 mean: 251.182144 stdev: 78.245529 max:
446.800812 (cut: 446.795959) min: 55.581268 (cut: 55.568321)
mean_x: 135.932205 stdev_x: 42.297146 max_x: 220.628784 (cut: 220.526489)
min_x: 51.310364 (cut: 51.337914)
Control regions SW iteration 26 mean: 251.180313 stdev: 78.244492 max:
446.794739 (cut: 446.791534) min: 55.581268 (cut: 55.569084)
mean_x: 135.900375 stdev_x: 42.272102 max_x: 220.526123 (cut: 220.444580)
min_x: 51.381470 (cut: 51.356171)
Control regions SW iteration 27 mean: 251.179672 stdev: 78.243912 max:
446.788086 (cut: 446.789429) min: 55.581268 (cut: 55.569893)
mean_x: 135.862320 stdev_x: 42.247379 max_x: 220.408020 (cut: 220.357086)
min_x: 51.381470 (cut: 51.367561)
Control regions SW iteration 28 mean: 251.179672 stdev: 78.243927 max:
446.788086 (cut: 446.789490) min: 55.581268 (cut: 55.569855)
mean_x: 135.851318 stdev_x: 42.237152 max_x: 220.355804 (cut: 220.325623)
min_x: 51.381470 (cut: 51.377014)
Control regions SW iteration 29 mean: 251.179672 stdev: 78.243927 max:
446.788086 (cut: 446.789490) min: 55.581268 (cut: 55.569855)
mean_x: 135.792511 stdev_x: 42.207077 max_x: 220.268616 (cut: 220.206665)
min_x: 51.381470 (cut: 51.378357)
Control regions SW iteration 30 mean: 251.179672 stdev: 78.243927 max:
446.788086 (cut: 446.789490) min: 55.581268 (cut: 55.569855)
mean_x: 135.753662 stdev_x: 42.193321 max_x: 220.190247 (cut: 220.140305)
min_x: 51.381470 (cut: 51.367020)
Control regions SW iteration 31 mean: 251.179672 stdev: 78.243927 max:
446.788086 (cut: 446.789490) min: 55.581268 (cut: 55.569855)
mean_x: 135.729080 stdev_x: 42.185062 max_x: 220.134949 (cut: 220.099213)
min_x: 51.381470 (cut: 51.358955)
Control regions SW iteration 32 mean: 251.179672 stdev: 78.243927 max:
446.788086 (cut: 446.789490) min: 55.581268 (cut: 55.569855)
mean_x: 135.715149 stdev_x: 42.180794 max_x: 220.078888 (cut: 220.076736)
min_x: 51.381470 (cut: 51.353561)
Control regions SW iteration 33 mean: 251.179672 stdev: 78.243927 max:
446.788086 (cut: 446.789490) min: 55.581268 (cut: 55.569855)
mean_x: 135.708023 stdev_x: 42.177605 max_x: 220.068970 (cut: 220.063232)
min_x: 51.381470 (cut: 51.352814)
Control regions SW iteration 34 mean: 251.179672 stdev: 78.243927 max:
446.788086 (cut: 446.789490) min: 55.581268 (cut: 55.569855)
mean_x: 135.693008 stdev_x: 42.170464 max_x: 220.063141 (cut: 220.033936)
min_x: 51.381470 (cut: 51.352081)
Control regions SW iteration 35 mean: 251.179672 stdev: 78.243927 max:
446.788086 (cut: 446.789490) min: 55.581268 (cut: 55.569855)
mean_x: 135.654541 stdev_x: 42.148514 max_x: 219.992905 (cut: 219.951569)
min_x: 51.381470 (cut: 51.357513)
Control regions SW iteration 36 mean: 251.179672 stdev: 78.243927 max:
446.788086 (cut: 446.789490) min: 55.581268 (cut: 55.569855)
mean_x: 135.612610 stdev_x: 42.125824 max_x: 219.951447 (cut: 219.864258)
min_x: 51.381470 (cut: 51.360962)
Control regions SW iteration 37 mean: 251.179672 stdev: 78.243927 max:
446.788086 (cut: 446.789490) min: 55.581268 (cut: 55.569855)
mean_x: 135.569824 stdev_x: 42.102119 max_x: 219.814240 (cut: 219.774063)
min_x: 51.381470 (cut: 51.365585)
Control regions SW iteration 38 mean: 251.179672 stdev: 78.243927 max:
446.788086 (cut: 446.789490) min: 55.581268 (cut: 55.569855)
mean_x: 135.567093 stdev_x: 42.093773 max_x: 219.757996 (cut: 219.754639)
min_x: 51.381470 (cut: 51.379547)
Control regions SW iteration 39 mean: 251.179672 stdev: 78.243927 max:
446.788086 (cut: 446.789490) min: 55.581268 (cut: 55.569855)
mean_x: 135.566376 stdev_x: 42.092220 max_x: 219.746033 (cut: 219.750824)
min_x: 51.381470 (cut: 51.381935)
Control regions SW iteration 40 mean: 251.179672 stdev: 78.243927 max:
446.788086 (cut: 446.789490) min: 55.581268 (cut: 55.569855)
mean_x: 135.569977 stdev_x: 42.090569 max_x: 219.746033 (cut: 219.751114)
min_x: 51.430969 (cut: 51.388840)
SW Normalization completed.
Writing normalized CW depth to: /Data/bioInfo/SOLiD/mrCaNaVar.cw_norm.bed.
Segmentation fault
So, I'm wondering if this segfault is caused by the SOLiD alignment I'm using,
or if I did something else wrong.
If it is caused by the BAM file I'm using, should I try to re-align my SOLiD
reads with another mapping software before using mrCaNaVar? If so, which one?
Thanks in advance for your help,
Greetings,
Stéphane Wenric
Hi
First, I suspect mrcanavar would work reliably with BioScape, it definitely
will not if the mapper doesn't return all possible map locations. This is
essential in correctly identifying segmental duplications and multi-copy
segments. It might be possible to detect large deletions, however I never
tried. We do have a beta version of a SOLiD mapper now at drfast.sf.net; which
could be used with mrcanavar.
That being said, the segmentation fault you are getting seems to be the issue
I had with some versions of gcc and Linux kernel. I released an update just
yesterday (v. 0.33). Please download and try with this version, and let me
know if it still fails.
Hi there,
I didn't ask the original question, but am seeing a segmentation fault when
running:
./mrcanavar -call -conf hpr.conf -depth NA19238.depth -o output
This happens if I make with gcc 4.3.4, gcc 4.1.1 or icc 12.0 but doesn't occur
(ie runs to completion) with gcc4.1.1
icc gives a possible clue:
icc -c -O2 -g callcnv.c -o callcnv.o
callcnv.c(96): warning #592: variable "fname" is used before its value is
set
sprintf (fname, "%s.cw_norm.bed", out_prefix);
^
(the caret points to 'fname')
Running it through the debugger confirms fname has no value:
idbc -args mrcanavar -call -conf hpr.conf -depth NA19238.depth -o output
Intel(R) Debugger for applications running on Intel(R) 64, Version 12.0,
Build
object file name: mrcanavar
Reading symbols from /home/g/gg78/mrcanavar-0.33/mrcanavar…done.
(idb) run
Starting program: /home/g/gg78/mrcanavar-0.33/mrcanavar
Mode: Call copy numbers …
Loading reference configuration, hold on … . 1 chromosomes loaded.
depth file NA19238.depth is loaded.
Control region cleanup…
CW Normalization completed.
LW Normalization completed.
SW Normalization completed.
Writing normalized CW depth to: output.cw_norm.bed.
Program received signal SIGSEGV
_IO_str_overflow () in /lib64/libc-2.5.so
(idb) bt
#0 0x00000030d146f0f1 in _IO_str_overflow () in /lib64/libc-2.5.so
#1 0x00000030d146e294 in _IO_default_xsputn () in /lib64/libc-2.5.so
#2 0x00000030d1446503 in _IO_vfprintf () in /lib64/libc-2.5.so
#3 0x00000030d1463b49 in vsprintf () in /lib64/libc-2.5.so
#4 0x00000030d144d528 in _IO_sprintf () in /lib64/libc-2.5.so
#5 0x0000000000406c54 in call_cnv (depthFile=0x7fffffffd2e0
"\001\200\255\3730", out_prefix=0x6f (null)) at
/home/g/gg78/mrcanavar-0.33/callcnv.c:96
#6 0x0000000000401a8b in main (argc=-11552, argv=0x6f) at
/home/g/gg78/mrcanavar-0.33/mrcanavar.c:123
(idb) display fname
No symbol "fname" in current context.
Cannot evaluate 'fname'.
1: fname =
(idb) quit
So it looks like fname is declared on line 10 of callcnv.c within
call_cnv(), and is then referred to on line 96 without getting a value
assigned.
I hope this is useful for you.
Regards
Gary
I omitted to add the actual output when the segfaults occurs and the kernel is
2.6.18-194.11.4.el5
./mrcanavar -call -conf hpr.conf -depth NA19238.depth -o output
Mode: Call copy numbers …
Loading reference configuration, hold on … . 1 chromosomes loaded.
depth file NA19238.depth is loaded.
Control region cleanup…
CW Normalization completed.
LW Normalization completed.
SW Normalization completed.
Writing normalized CW depth to: output.cw_norm.bed.
Segmentation fault
fixed in version 0.34. I wish all bug reports I get were this detailed :-)
Thanks.
And I wish all bugs were fixed this fast - thanks, much appreciated!