Isoseq3 Error: Segmentation fault

[BenSamy2020]

Operating system Which operating system and version are you using?

OS: Linux Architecture: x86_64 CPU op-mode(s): 32-bit, 64-bit Byte Order: Little Endian CPU(s): 48 On-line CPU(s) list: 0-47 Thread(s) per core: 1 Core(s) per socket: 24 Socket(s): 2 NUMA node(s): 2 Vendor ID: GenuineIntel CPU family: 6 Model: 85 Model name: Intel(R) Xeon(R) Platinum 8268 CPU @ 2.90GHz Stepping: 7 CPU MHz: 3500.093 CPU max MHz: 3900.0000 CPU min MHz: 1200.0000 BogoMIPS: 5800.00 Virtualization: VT-x L1d cache: 32K L1i cache: 32K L2 cache: 1024K L3 cache: 36608K NUMA node0 CPU(s): 0-23 NUMA node1 CPU(s): 24-47

Package name Which package / tool is causing the problem? Which version are you using, use tool --version. Have you updated to the latest version conda update package? Have you updated the complete env by running conda update --all? Have you ensured that your channel priorities are set up according to the bioconda recommendations at https://bioconda.github.io/#set-up-channels?

Name Version Build Channel

isoseq3 3.8.2 h9ee0642_0 bioconda

Additionally, I have set-up channel priorities as per instructions.

Conda environment What is the result of conda list? (Try to paste that between triple backticks.)

_libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 2_gnu conda-forge ca-certificates 2022.12.7 ha878542_0 conda-forge certifi 2019.11.28 py27h8c360ce_1 conda-forge isoseq3 3.8.2 h9ee0642_0 bioconda ld_impl_linux-64 2.40 h41732ed_0 conda-forge libffi 3.2.1 he1b5a44_1007 conda-forge libgcc-ng 12.2.0 h65d4601_19 conda-forge libgomp 12.2.0 h65d4601_19 conda-forge libsqlite 3.40.0 h753d276_0 conda-forge libstdcxx-ng 12.2.0 h46fd767_19 conda-forge libzlib 1.2.13 h166bdaf_4 conda-forge ncurses 6.3 h27087fc_1 conda-forge openssl 1.1.1t h0b41bf4_0 conda-forge pip 20.1.1 pyh9f0ad1d_0 conda-forge python 2.7.15 h5a48372_1011_cpython conda-forge python_abi 2.7 1_cp27mu conda-forge readline 8.2 h8228510_1 conda-forge setuptools 44.0.0 py27_0 conda-forge sqlite 3.40.0 h4ff8645_0 conda-forge tk 8.6.12 h27826a3_0 conda-forge wheel 0.37.1 pyhd8ed1ab_0 conda-forge zlib 1.2.13 h166bdaf_4 conda-forge

Describe the bug A clear and concise description of what the bug is.

When I invoke the command isoseq3 --help, I hit the error of Segmentation fault

Error message Paste the error message / stack.

Segmentation fault

Expected behavior A clear and concise description of what you expected to happen.

It is suppose to provide with all the possible isoseq3 commands when isoseq3 --help is entered.

Regards, Ben

[philoel]

Happening for me too, any solutions incoming?

[greensii]

Same here.

fwiw isoseq3 3.8.0 and 3.8.1 both work fine on the same machine in an otherwise identical conda environment

mamba list

────────────────────────────────────────────────────
  _libgcc_mutex  0.1      conda_forge  conda-forge
  _openmp_mutex  4.5      2_gnu        conda-forge
  isoseq3        3.8.1    h9ee0642_0   bioconda   
  libgcc-ng      13.1.0   he5830b7_0   conda-forge
  libgomp        13.1.0   he5830b7_0   conda-forge
  libstdcxx-ng   13.1.0   hfd8a6a1_0   conda-forge
  pbpigeon       1.0.0    h4ac6f70_2   bioconda  

isoseq3 --version

Using:
  pbbam     : 2.2.0 (commit v2.2.0-1-g8c081f6)
  pbcopper  : 2.1.0 (commit v2.1.0)
  pbmm2     : 1.9.0 (commit v1.9.0-2-gbec8e28)
  minimap2  : 2.15
  parasail  : 2.1.3
  boost     : 1.77
  htslib    : 1.14
  zlib      : 1.2.11

mamba remove isoseq3 --> mamba install -c bioconda isoseq3=3.8.2 --> mamba list

────────────────────────────────────────────────────
  _libgcc_mutex  0.1      conda_forge  conda-forge
  _openmp_mutex  4.5      2_gnu        conda-forge
  isoseq3        3.8.2    h9ee0642_0   bioconda   
  libgcc-ng      13.1.0   he5830b7_0   conda-forge
  libgomp        13.1.0   he5830b7_0   conda-forge
  libstdcxx-ng   13.1.0   hfd8a6a1_0   conda-forge
  pbpigeon       1.0.0    h4ac6f70_2   bioconda  

isoseq3 --version

Segmentation fault

[armintoepfer]

I have uploaded a new version. If that still segfaults, but not the github binary itself, then conda is corrupting the binary.