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sanger-tol / PretextMap

Paired REad TEXTure Mapper. Converts SAM formatted read pairs into genome contact maps.
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pairs from pairtools seem to produce a segfault/stack smashing #6

Open brantfaircloth opened 1 year ago

brantfaircloth commented 1 year ago

Similar to #5, I'm getting a segfault with pairs output from pairtools (following duplicate filtering). Have used two different systems - a linux workstation:

$ PretextMap -o DTG-HiC-732.pretext --sortby length --sortorder descend --mapq 10 < DTG-HiC-732.nodups.pairs
[PretextMap status] :: Running with AVX CPU extensions
[1]    14582 segmentation fault  PretextMap -o DTG-HiC-732.pretext --sortby length --sortorder descend --mapq

as well as our HPC system:

$ PretextMap -o DTG-HiC-732.pretext --sortby length --sortorder descend --mapq 10 < DTG-HiC-732.nodups.pairs
[PretextMap status] :: Running with AVX2 CPU extensions
*** stack smashing detected ***: <unknown> terminated
Aborted (core dumped)

Both packages installed using conda:

$ conda list -n pretextmap
# packages in environment at /project/brant/mike-home/miniconda3/envs/pretextmap:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
libgcc-ng                 12.2.0              h65d4601_19    conda-forge
libgomp                   12.2.0              h65d4601_19    conda-forge
libstdcxx-ng              12.2.0              h46fd767_19    conda-forge
pretext-suite             0.0.2                hdfd78af_1    bioconda
pretextgraph              0.0.6                h9f5acd7_1    bioconda
pretextmap                0.1.9                h9f5acd7_1    bioconda
pretextsnapshot           0.0.4                h9f5acd7_1    bioconda