segmentation fault

[maojn]

Hi, I was following the example here http://www-personal.umich.edu/~xwen/download/qtl_example/geuv.gene.map.gz

but failed when running torus: $ mkdir scan_out $ perl batch_scan.pl > batch_scan.cmd $ openmp_wrapper -d batch_scan.cmd -t 8 $ cat scan_out/*.bf | gzip - > geuv.tsi.bf.gz $ ls -l total 57368 -rw-r----- 1 teacher teacher 899612 Jun 21 12:43 batch_scan.cmd -rw-r----- 1 teacher teacher 125 Jun 21 12:29 batch_scan.pl -rw-r----- 1 teacher teacher 124036 Mar 20 11:52 geuv.gene.map.gz -rw-r----- 1 teacher teacher 15869191 Mar 20 11:52 geuv.snp.map.gz -rw-r----- 1 teacher teacher 39749358 Jun 21 13:43 geuv.tsi.bf.gz drwxr-x--- 3 teacher teacher 4096 Jun 21 14:50 github.com drwxr-x--- 2 teacher teacher 917504 Jun 21 13:46 sbams_data drwxr-x--- 2 teacher teacher 917504 Jun 21 12:52 scan_out

$ torus -d geuv.tsi.bf.gz -smap geuv.snp.map.gz -gmap geuv.gene.map.gz --load_bf -dump_prior priors Segmentation fault

$ torus -h TORUS: QTL Discovery Utilizing Genomic Annotations Usage: torus -est|qtl|dump_prior -d input_data.gz [-smap snp_map.gz] [-gmap gene_map.gz] [-annot annotation_file.gz] [--load_bf | --load_zval] Error: data file unspecified TORUS: QTL Discovery Utilizing Genomic Annotations Usage: torus -est|qtl|dump_prior -d input_data.gz [-smap snp_map.gz] [-gmap gene_map.gz] [-annot annotation_file.gz] [--load_bf | --load_zval]

$ ldd /usr/local/apps/integrative/bin/torus linux-vdso.so.1 => (0x00002aaaaaacb000) libgsl.so.0 => /usr/local/lib64/libgsl.so.0 (0x00002aaaaaccd000) libgslcblas.so.0 => /usr/local/GSL/gcc-6.2.0/2.2.1/lib/libgslcblas.so.0 (0x00002aaaab0f9000) libboost_iostreams.so.5 => /usr/lib64/libboost_iostreams.so.5 (0x00002aaaab336000) libz.so.1 => /lib64/libz.so.1 (0x00002aaaab544000) libstdc++.so.6 => /usr/local/GCC/6.2.0/lib64/libstdc++.so.6 (0x00002aaaab75b000) libm.so.6 => /lib64/libm.so.6 (0x00002aaaabadb000) libgcc_s.so.1 => /usr/local/GCC/6.2.0/lib64/libgcc_s.so.1 (0x00002aaaabd5f000) libc.so.6 => /lib64/libc.so.6 (0x00002aaaabf77000) libbz2.so.1 => /lib64/libbz2.so.1 (0x00002aaaac30b000) /lib64/ld-linux-x86-64.so.2 (0x00002aaaaaaab000)

Thank you.

[xqwen]

The problem seems to be in the input file "geuv.tsi.bf.gz". Can you share the file with me by email? or at least show a few line from the file by

zcat geuv.tsi.bf.gz | head -10 

Best, William

[maojn]

Hi William,

Thank you for your reply and help. Here is the content of input file.

$ zcat geuv.tsi.bf.gz | head -10 chr1.169763807 ENSG00000000457 -0.205 chr1.169763814 ENSG00000000457 -0.205 chr1.169764420 ENSG00000000457 -0.205 chr1.169764568 ENSG00000000457 1.085 chr1.169765052 ENSG00000000457 6.027 chr1.169765139 ENSG00000000457 -0.179 chr1.169765340 ENSG00000000457 1.283 chr1.169765348 ENSG00000000457 -0.205 chr1.169765591 ENSG00000000457 -0.146 chr1.169765899 ENSG00000000457 6.027

On Thu, Jun 22, 2017 at 1:06 AM, Xiaoquan (William) Wen < notifications@github.com> wrote:

The problem seems to be in the input file "geuv.tsi.bf.gz". Can you share the file with me by email? or at least show a few line from the file by

zcat geuv.tsi.bf.gz | head -10

Best, William

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/xqwen/integrative/issues/2#issuecomment-310276531, or mute the thread https://github.com/notifications/unsubscribe-auth/AA2z-7nM0hvygmCoG_3f-S_UjKxxi59rks5sGfZKgaJpZM4OBYch .

[xqwen]

The format looks correct, does torus run at all? The potential problem is that you need to create the directory priors before using -dump_prior option. Nevertheless, you should see output to standard error from the EM algorithm.