Segmentation fault

[klmartinez]

Hello,

I am using the static binaries to run phase_common on a ~1 million bp locus on chromosome 9. I am using a cloud environment with 16 CPUs and 104 GB RAM.

When I run phase_common (./phase_common_static --input mt_chr9_serology_subset_locus_srwgs_v7.bcf --filter-maf 0.001 --region chr9 --map chr9.b38.gmap.gz --output tmp/target.scaffold.bcf --thread 16), I get the following output and error:

[SHAPEIT5] phase_common (jointly phase multiple common markers)
  * Author        : Olivier DELANEAU, University of Lausanne
  * Contact       : olivier.delaneau@gmail.com
  * Version       : 5.1.1 / commit = 990ed0d / release = 2023-05-08
  * Run date      : 02/08/2023 - 20:06:51

Files:
  * Input         : [mt_chr9_serology_subset_locus_srwgs_v7.bcf]
  * Genetic Map   : [chr9.b38.gmap.gz]
  * Output        : [tmp/target.scaffold.bcf]
  * Output format : [bcf]

Parameters:
  * Seed    : 15052011
  * Threads : 16 threads
  * MCMC    : 15 iterations [5b + 1p + 1b + 1p + 1b + 1p + 5m]
  * PBWT    : [window = 4cM / depth = auto / modulo = auto / mac = 5 / missing = 0.1]
  * HMM     : [window = 4cM / Ne = 15000 / Recombination rates given by genetic map]
  * FILTERS : [snp only = 0 / MAF = 0.001]

Reading genotype data:
  * VCF/BCF scanning done (3.00s)
      + Variants [#sites=17931 / region=chr9]
         - 25623 sites removed in main panel [below MAF threshold]
      + Samples [#target=18929 / #reference=0]
  * VCF/BCF parsing done (13.97s)
      + Genotypes [0/0=63.313%, 0/1=7.923%, 1/1=3.768%, ./.=24.996%, 0|1=0.000%]

Setting up genetic map:
  * GMAP parsing [n=0] (0.00s)
bash: line 1:  2076 Segmentation fault      (core dumped) ./phase_common_static --input mt_chr9_serology_subset_locus_srwgs_v7.bcf --filter-maf 0.001 --region chr9 --map chr9.b38.gmap.gz --output tmp/target.scaffold.bcf --thread 16
---------------------------------------------------------------------------
CalledProcessError                        Traceback (most recent call last)
/tmp/ipykernel_329/2112237477.py in <module>
----> 1 get_ipython().run_cell_magic('bash', '', './phase_common_static --input mt_chr9_serology_subset_locus_srwgs_v7.bcf --filter-maf 0.001 --region chr9 --map chr9.b38.gmap.gz --output tmp/target.scaffold.bcf --thread 16\n')

/opt/conda/lib/python3.7/site-packages/IPython/core/interactiveshell.py in run_cell_magic(self, magic_name, line, cell)
   2460             with self.builtin_trap:
   2461                 args = (magic_arg_s, cell)
-> 2462                 result = fn(*args, **kwargs)
   2463             return result
   2464 

/opt/conda/lib/python3.7/site-packages/IPython/core/magics/script.py in named_script_magic(line, cell)
    140             else:
    141                 line = script
--> 142             return self.shebang(line, cell)
    143 
    144         # write a basic docstring:

<decorator-gen-103> in shebang(self, line, cell)

/opt/conda/lib/python3.7/site-packages/IPython/core/magic.py in <lambda>(f, *a, **k)
    185     # but it's overkill for just that one bit of state.
    186     def magic_deco(arg):
--> 187         call = lambda f, *a, **k: f(*a, **k)
    188 
    189         if callable(arg):

/opt/conda/lib/python3.7/site-packages/IPython/core/magics/script.py in shebang(self, line, cell)
    243             sys.stderr.flush()
    244         if args.raise_error and p.returncode!=0:
--> 245             raise CalledProcessError(p.returncode, cell, output=out, stderr=err)
    246 
    247     def _run_script(self, p, cell, to_close):

CalledProcessError: Command 'b'./phase_common_static --input mt_chr9_serology_subset_locus_srwgs_v7.bcf --filter-maf 0.001 --region chr9 --map chr9.b38.gmap.gz --output tmp/target.scaffold.bcf --thread 16\n'' returned non-zero exit status 139.

Any suggestions on how to resolve this issue would be greatly appreciated.

[srubinacci]

Hi,

It's likely a problem in your map? The line: * GMAP parsing [n=0] (0.00s) Indicates that there are zero records found int the map file. This should not be the case. Can you check if the path is correctly specified?

Hope this helps.

Simone

[klmartinez]

Hi Simone,

Thank you for your reply. I was making a very silly mistake and instead of actually pulling the map file you offer under resources, I was pulling the path to the HTML site that hosts the raw data. This issue has now been resolved.

Many thanks, Kiana