Closed jamesdalg closed 10 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.
Your input file is empty. That's the problem. We might fix this.
Operating system Ubuntu 22.04 Package name PBSV Conda environment
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.