HI I'm using CNVnator to do some CNV analysis but came across problems of core dump
Basically I first generated .root files from .bam files; then merged those small .root files into larger ones. See below:
This _1, _2, _3 ....represents chromosome number. The interesting here is, for NA12878_1.root and NA12878_2.root, the two largest files (11GB each), somehow two additional files are generated named as NA12878_1_1.root and NA12878_2_1.root (16K). I think this is core dump problem because core.* files are also generated (which I don't show here)
Is it because these two files are too large?
The part of the errors go like this:
And the werid error report about NA12878_1_1 and NA12878_2_1 and dumped core
I then used the generated .root files for further step like make histogram, there are errors (not surprisingly) but not only for NA12878_1 or _2, but also for others like _6
part of errors are shown below:
Anyone has encountered such problems? thx
Basically I first generated .root files from .bam files; then merged those small .root files into larger ones. See below:
Code:
total 139G 6.5G NA12878_10.root 3.7G NA12878_18.root 9.1G NA12878_4.root 16K NA12878_1_1.root 2.8G NA12878_19.root 8.8G NA12878_5.root 6.6G NA12878_11.root 11G NA12878_1.root 8.3G NA12878_6.root 6.5G NA12878_12.root 3.1G NA12878_20.root 7.7G NA12878_7.root 4.6G NA12878_13.root 16K NA12878_2_1.root 7.1G NA12878_8.root 4.4G NA12878_14.root 1.8G NA12878_21.root 6.1G NA12878_9.root 4.1G NA12878_15.root 1.8G NA12878_22.root 7.2G NA12878_X.root 4.1G NA12878_16.root 11G NA12878_2.root 253M NA12878_Y.root 4.0G NA12878_17.root 9.7G NA12878_3.root
Is it because these two files are too large?
The part of the errors go like this:
And the werid error report about NA12878_1_1 and NA12878_2_1 and dumped core
Code:
Fill: Switching to new file: /home/xug/nearline/NA12878root/NA12878_2_1.root Filling and saving tree for 'chr19' ... *** glibc detected *** /home/xug/CNVnator/src/cnvnator: double free or corruption (out): 0xDone with the tree. ======= Backtrace: ========= /share/bin/intel/cc/10.1.015/lib/tls/x86_64/libc.so.6[0x3a17e71834] /share/bin/intel/cc/10.1.015/lib/tls/x86_64/libc.so.6(cfree+0x8c)[0x3a17e74e7c] /home/xug/root/lib/libCore.so(_ZN8TStorage13ObjectDeallocEPv+0x68)[0x2b2e6c2239f8] /home/xug/root/lib/libRIO.so(_ZN5TFileD0Ev+0x217)[0x2b2e6d41cf97] /home/xug/root/lib/libTree.so(_ZN5TTree10ChangeFileEP5TFile+0x449)[0x2b2e6ec35d89] /home/xug/root/lib/libTree.so(_ZN5TTree4FillEv+0x5b2)[0x2b2e6ec31a82] /home/xug/CNVnator/src/cnvnator[0x40aa58] /home/xug/CNVnator/src/cnvnator[0x40e02d] /home/xug/CNVnator/src/cnvnator[0x40782d] /share/bin/intel/cc/10.1.015/lib/tls/x86_64/libc.so.6(__libc_start_main+0xf4)[0x3a17e1d8b4] /home/xug/CNVnator/src/cnvnator[0x4063e9] ======= Memory map: ======== 00400000-0043c000 r-xp 00000000 00:17 2189064480 /home/xug/CNVnator/src/cnvnator 0063c000-0063d000 rw-p 0003c000 00:17 2189064480 /home/xug/CNVnator/src/cnvnator 0063d000-00645000 rw-p 0063d000 00:00 0 19cd6000-1a29b000 rw-p 19cd6000 00:00 0 3a17a00000-3a17a1a000 r-xp 00000000 08:01 6864978 /lib64/ld-2.5.so 3a17c1a000-3a17c1b000 r--p 0001a000 08:01 6864978 /lib64/ld-2.5.so 3a17c1b000-3a17c1c000 rw-p 0001b000 08:01 6864978 /lib64/ld-2.5.so 3a17e00000-3a17f4a000 r-xp 00000000 08:01 6864988 /lib64/libc-2.5.so 3a17f4a000-3a1814a000 ---p 0014a000 08:01 6864988 /lib64/libc-2.5.so 3a1814a000-3a1814e000 r--p 0014a000 08:01 6864988 /lib64/libc-2.5.so
part of errors are shown below:
Code:
SysError in <TFile::Seek>: cannot seek to position -1857646445 in file NA12878_chr6.root, retpos=-1 (Invalid argument) Calculating histogram with bin size of 100 for chromosome 'chr6' ... Calculating histogram with bin size of 100 for chromosome 'chr5' ... Warning in <TFile::Init>: file NA12878_chr6.root probably not closed, cannot read free segments SysError in <TFile::Seek>: cannot seek to position -1857646445 in file NA12878_chr6.root, retpos=-1 (Invalid argument) Error in <TKey::Create>: Cannot allocate 60031 bytes for ID = his_rd_u_chr6_100 Title = Unique read depth for chr6 Error in <TKey::Create>: Cannot allocate 2590048 bytes for ID = his_rd_p_chr6_100 Title = read depth for chr6 Making GC histogram for 'chr6' ... SysError in <TFile::Seek>: cannot seek to position -1857646445 in file NA12878_chr6.root, retpos=-1 (Invalid argument) Making GC histogram for 'chr5' ...
Anyone has encountered such problems? thx
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