search

PacificBiosciences / pbbioconda

PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.
BSD 3-Clause Clear License
247 stars 43 forks source link

segfault with PBSV #609

Closed jamesdalg closed 10 months ago

jamesdalg commented 11 months ago

Operating system Ubuntu 22.04 Package name PBSV Conda environment

$ conda list
# packages in environment at /home/jd/mambaforge/envs/nf-pacbio:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
bzip2                     1.0.8                h7b6447c_0  
c-ares                    1.19.1               h5eee18b_0  
ca-certificates           2023.08.22           h06a4308_0  
coreutils                 8.25                          1    bioconda
curl                      8.2.1                hdbd6064_0  
dbus                      1.13.18              hb2f20db_0  
expat                     2.5.0                h6a678d5_0  
freetype                  2.12.1               h4a9f257_0  
glib                      2.69.1               he621ea3_2  
htslib                    1.18                 h81da01d_0    bioconda
krb5                      1.20.1               h143b758_1  
libcurl                   8.2.1                h251f7ec_0  
libdeflate                1.18                 h0b41bf4_0    conda-forge
libedit                   3.1.20221030         h5eee18b_0  
libev                     4.33                 h7f8727e_1  
libffi                    3.4.4                h6a678d5_0  
libgcc                    7.2.0                h69d50b8_2  
libgcc-ng                 13.2.0               h807b86a_0    conda-forge
libgomp                   13.2.0               h807b86a_0    conda-forge
libnghttp2                1.52.0               h2d74bed_1  
libpng                    1.6.39               h5eee18b_0  
libssh2                   1.10.0               hdbd6064_2  
libstdcxx-ng              11.2.0               h1234567_1  
libxcb                    1.15                 h7f8727e_0  
libzlib                   1.2.13               hd590300_5    conda-forge
ncurses                   6.4                  h6a678d5_0  
nextflow                  23.04.3              h2a3209d_0    bioconda
openjdk                   11.0.13              h87a67e3_0  
openssl                   3.1.2                hd590300_0    conda-forge
pbmm2                     1.13.0               h9ee0642_0    bioconda
pbsv                      2.9.0                h9ee0642_0    bioconda
pcre                      8.45                 h295c915_0  
samtools                  1.17                 hd87286a_1    bioconda
xz                        5.4.2                h5eee18b_0  
zlib                      1.2.13               hd590300_5    conda-forge

Describe the bug A segmentation fault instantly stops execution and leaves a 0 size tmp file.

Error message $ pbsv discover HG03452_chr22.chm13.pb_aligned_sorted.bam HG03452_chr22_pbsv_chm13.svsig.gz Segmentation fault (core dumped)

[Uploading HG03452_chr22.chm13.pb_aligned_sorted.bam.bai…]()

To Reproduce HG03452_chr22.zip

Just type: pbsv discover HG03452_chr22.chm13.pb_aligned_sorted.bam HG03452_chr22_pbsv_chm13.svsig.gz

Expected behavior No segfault, finished sv calls.

armintoepfer commented 10 months ago

Your input file is empty. That's the problem. We might fix this.