search

waveygang / wfmash

base-accurate DNA sequence alignments using WFA and mashmap3
MIT License
177 stars 19 forks source link

Segmentation fault #166

Open shenwei356 opened 1 year ago

shenwei356 commented 1 year ago

Hi all, thanks for developing these pan-genome graph tools.

wfmash v0.10.0-4-gcf9bfb0 was installed as a dependency of pggb 0.5.1 via Conda, both in my workstation (manjaro/arch with a relatively new environment) and a server (centos 7.9.2009).

I've successfully run pggb in the workstation with 28 bacterial genomes, while it failed with the same input and command.

pggb -i $seqs \
    -o output \
    -n $ngenomes \
    -t 160 \
    -p 90 \
    -s 500 \
    -V 'ref:#:1' 

Command terminated by signal 11
wfmash -s 500 -l 25000 -p 90 -n 27 -k 19 -H 0.001 -X -t 160 --tmp-base output akk.fasta --approx-map
0.91s user 7.87s system 117% cpu 7.47s total 14264Kb max memory

Then I directly ran the wfmash command, and it reported:

wfmash -s 500 -l 25000 -p 90 -n 27 -k 19 -H 0.001 -X -t 160 --tmp-base output akk.fasta --approx-map
Segmentation fault (core dumped)

I also reran with only two genomes (t.fasta.gz), while the same error occurred. The same command with the same input ran successfully and only take 1.5s in the workstation.

time wfmash -s 5k -l 25000 -p 90 -n 1 -k 19 -H 0.001 -X -t 16 --tmp-base t t.fasta --approx-map
Segmentation fault (core dumped)

real    0m8.537s
user    0m0.940s
sys     0m8.488s

The environment of the server

$ uname -a
Linux gys-svr 3.10.0-1160.11.1.el7.x86_64 #1 SMP Fri Dec 18 16:34:56 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux

$ gcc --version
gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-44)    # yes it's an old version, but Conda did not complain.

$ cmake --version
cmake version 2.8.12.2

I noticed that the date of the wfmash binary file is Nov 13 , not today (date: Thu Dec 1 23:17:17 CST 2022) nor the day of the bioconda recipe being updated (Nov 15). How's that possible? I doubt that conda did not compile from the source at all following the compiling steps.

I also tried to compile from the source but failed both in the workstation and server due to the lack of dependencies or other issues.

I'd recommend specifying the version of cmake, gcc in the conda meta.yaml files of wfmash, seqwish and other tools.

It would be wonderful if a statically-linked binary file is released along with the source code. :)

Wei

AndreaGuarracino commented 1 year ago

Hi @shenwei356, could you please run conda list on your system? It will tell you the exact conda-versions of all tools in your environment. However, if you have wfmash v0.10.0-4-gcf9bfb0 (this is not a conda-version), it means that you have a version not fully portable that can break in older systems.

I am not a conda guru, so I can't properly answer about the versioning problem. If you get more information about it, I will be apply to improve the bioconda recipes' for all pggb's tools.

Why do you recommend specifying the version for cmake and gcc in the meta.yaml? I see that a few tools specify the version of cmake, but not for gcc. Do you know examples of that?

shenwei356 commented 1 year ago

Hi Andrea, thanks for your reply.

conda list details $ conda activate pggb $ conda list # packages in environment at /home/shenwei/app/miniconda3/envs/pggb: # # Name Version Build Channel _libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 2_gnu conda-forge bc 1.07.1 h7f98852_0 conda-forge bcftools 1.16 hfe4b78e_1 bioconda brotli 1.0.9 h166bdaf_8 conda-forge brotli-bin 1.0.9 h166bdaf_8 conda-forge brotlipy 0.7.0 py310h5764c6d_1005 conda-forge bzip2 1.0.8 h7f98852_4 conda-forge c-ares 1.18.1 h7f98852_0 conda-forge ca-certificates 2022.9.24 ha878542_0 conda-forge certifi 2022.9.24 pyhd8ed1ab_0 conda-forge cffi 1.15.1 py310h255011f_2 conda-forge charset-normalizer 2.1.1 pyhd8ed1ab_0 conda-forge click 8.1.3 unix_pyhd8ed1ab_2 conda-forge coloredlogs 15.0.1 pyhd8ed1ab_3 conda-forge colormath 3.0.0 py_2 conda-forge commonmark 0.9.1 py_0 conda-forge contourpy 1.0.6 py310hbf28c38_0 conda-forge cryptography 38.0.4 py310h597c629_0 conda-forge cycler 0.11.0 pyhd8ed1ab_0 conda-forge dataclasses 0.8 pyhc8e2a94_3 conda-forge fonttools 4.38.0 py310h5764c6d_1 conda-forge freetype 2.12.1 hca18f0e_1 conda-forge future 0.18.2 pyhd8ed1ab_6 conda-forge gfaffix 0.1.4 hec16e2b_0 bioconda gsl 2.7 he838d99_0 conda-forge htslib 1.16 h6bc39ce_0 bioconda humanfriendly 10.0 py310hff52083_4 conda-forge idna 2.10 pyh9f0ad1d_0 conda-forge importlib-metadata 5.1.0 pyha770c72_0 conda-forge jinja2 3.1.2 pyhd8ed1ab_1 conda-forge jpeg 9e h166bdaf_2 conda-forge keyutils 1.6.1 h166bdaf_0 conda-forge kiwisolver 1.4.4 py310hbf28c38_1 conda-forge krb5 1.19.3 h3790be6_0 conda-forge lcms2 2.14 h6ed2654_0 conda-forge ld_impl_linux-64 2.39 hcc3a1bd_1 conda-forge lerc 4.0.0 h27087fc_0 conda-forge libblas 3.9.0 16_linux64_openblas conda-forge libbrotlicommon 1.0.9 h166bdaf_8 conda-forge libbrotlidec 1.0.9 h166bdaf_8 conda-forge libbrotlienc 1.0.9 h166bdaf_8 conda-forge libcblas 3.9.0 16_linux64_openblas conda-forge libcurl 7.86.0 h7bff187_1 conda-forge libdeflate 1.13 h166bdaf_0 conda-forge libedit 3.1.20191231 he28a2e2_2 conda-forge libev 4.33 h516909a_1 conda-forge libffi 3.4.2 h7f98852_5 conda-forge libgcc-ng 12.2.0 h65d4601_19 conda-forge libgfortran-ng 12.2.0 h69a702a_19 conda-forge libgfortran5 12.2.0 h337968e_19 conda-forge libgomp 12.2.0 h65d4601_19 conda-forge libjemalloc 5.2.1 h9c3ff4c_6 conda-forge liblapack 3.9.0 16_linux64_openblas conda-forge libnghttp2 1.47.0 hdcd2b5c_1 conda-forge libnsl 2.0.0 h7f98852_0 conda-forge libopenblas 0.3.21 pthreads_h78a6416_3 conda-forge libpng 1.6.39 h753d276_0 conda-forge libsqlite 3.40.0 h753d276_0 conda-forge libssh2 1.10.0 haa6b8db_3 conda-forge libstdcxx-ng 12.2.0 h46fd767_19 conda-forge libtiff 4.4.0 h0e0dad5_3 conda-forge libuuid 2.32.1 h7f98852_1000 conda-forge libwebp-base 1.2.4 h166bdaf_0 conda-forge libxcb 1.13 h7f98852_1004 conda-forge libzlib 1.2.13 h166bdaf_4 conda-forge lzstring 1.0.4 py_1001 conda-forge markdown 3.4.1 pyhd8ed1ab_0 conda-forge markupsafe 2.1.1 py310h5764c6d_2 conda-forge matplotlib-base 3.6.2 py310h8d5ebf3_0 conda-forge multiqc 1.13 pyhdfd78af_0 bioconda munkres 1.1.4 pyh9f0ad1d_0 conda-forge ncurses 6.3 h27087fc_1 conda-forge networkx 2.8.8 pyhd8ed1ab_0 conda-forge numpy 1.23.5 py310h53a5b5f_0 conda-forge odgi 0.8.1 py310hc8f18ef_0 bioconda openjpeg 2.5.0 h7d73246_1 conda-forge openssl 1.1.1s h166bdaf_0 conda-forge packaging 21.3 pyhd8ed1ab_0 conda-forge perl 5.32.1 2_h7f98852_perl5 conda-forge pggb 0.5.1 hdfd78af_1 bioconda pigz 2.6 h27826a3_0 conda-forge pillow 9.2.0 py310h454ad03_3 conda-forge pip 22.3.1 pyhd8ed1ab_0 conda-forge pthread-stubs 0.4 h36c2ea0_1001 conda-forge pycparser 2.21 pyhd8ed1ab_0 conda-forge pygments 2.13.0 pyhd8ed1ab_0 conda-forge pyopenssl 22.1.0 pyhd8ed1ab_0 conda-forge pyparsing 3.0.9 pyhd8ed1ab_0 conda-forge pysocks 1.7.1 pyha2e5f31_6 conda-forge python 3.10.8 h257c98d_0_cpython conda-forge python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge python_abi 3.10 3_cp310 conda-forge pyyaml 6.0 py310h5764c6d_5 conda-forge readline 8.1.2 h0f457ee_0 conda-forge requests 2.28.1 pyhd8ed1ab_1 conda-forge rich 12.6.0 pyhd8ed1ab_0 conda-forge rich-click 1.5.2 pyhd8ed1ab_0 conda-forge seqwish 0.7.7 h5b5514e_1 bioconda setuptools 65.5.1 pyhd8ed1ab_0 conda-forge simplejson 3.18.0 py310h5764c6d_0 conda-forge six 1.16.0 pyh6c4a22f_0 conda-forge smoothxg 0.6.7 hfb1f815_1 bioconda spectra 0.0.11 py_1 conda-forge tabix 1.11 hdfd78af_0 bioconda time 1.8 h516909a_0 conda-forge tk 8.6.12 h27826a3_0 conda-forge typing_extensions 4.4.0 pyha770c72_0 conda-forge tzdata 2022g h191b570_0 conda-forge unicodedata2 15.0.0 py310h5764c6d_0 conda-forge urllib3 1.26.13 pyhd8ed1ab_0 conda-forge vg 1.40.0 h9ee0642_0 bioconda wfmash 0.10.0 hfdddef0_2 bioconda wheel 0.38.4 pyhd8ed1ab_0 conda-forge xorg-libxau 1.0.9 h7f98852_0 conda-forge xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge xz 5.2.6 h166bdaf_0 conda-forge yaml 0.2.5 h7f98852_2 conda-forge zipp 3.11.0 pyhd8ed1ab_0 conda-forge zlib 1.2.13 h166bdaf_4 conda-forge zstd 1.5.2 h6239696_4 conda-forge

However, if you have wfmash v0.10.0-4-gcf9bfb0 (this is not a conda-version), it means that you have a version not fully portable that can break in older systems.

wfmash v0.10.0-4-gcf9bfb0 indeed does not match the commit of the v0.10.0 (e7ab130). Did you draft the release page on Oct 5, 2022 (e7ab130) and tag the release on Oct 28, 2022 (cf9bfb0)? That might be the cause.

$ git clone https://github.com/waveygang/wfmash
cd wfmash
$ git describe --always --tags --long
v0.10.0-9-gcb0ce95

$ git checkout git checkout cf9bfb0ef9fe5b973b91ee3aa649533df7521557
$ git describe --always --tags --long
v0.10.0-4-gcf9bfb0

$ git checkout e7ab130
$ git describe --always --tags --long
v0.10.0-0-ge7ab130

$ which wfmash 
/home/shenwei/Public/app/miniconda3/envs/pggb/bin/wfmash

$ wfmash --version
v0.10.0-4-gcf9bfb0

$ ls -lh $(which wfmash)
-rwxrwxr-x 2 shenwei shenwei 3.9M 11月13日 05:45 /home/shenwei/Public/app/miniconda3/envs/pggb/bin/wfmash

$ tar -jtvf pkgs/wfmash-0.10.0-hfdddef0_2.tar.bz2
-rw-r--r-- 1001/1001        11 2022-11-13 05:45 info/files
-rw-r--r-- 1001/1001        34 2022-11-13 05:45 info/test/run_test.sh
-rw-r--r-- 1001/1001       229 2022-11-13 05:45 info/paths.json
-rw-r--r-- 1001/1001       265 2022-11-13 05:45 info/hash_input.json
-rw-r--r-- 1001/1001       391 2022-11-13 05:45 info/index.json
-rw-r--r-- 1001/1001       482 2022-11-13 05:36 info/recipe/build.sh
-rw-r--r-- 1001/1001       824 2022-11-13 05:36 info/recipe/meta.yaml.template
-rw-rw-r-- 1001/1001      1079 2022-10-28 10:26 info/licenses/LICENSE
-rw-r--r-- 1001/1001      3273 2022-11-13 05:45 info/recipe/meta.yaml
-rw-r--r-- 1001/1001      6497 2022-11-13 05:45 info/recipe/conda_build_config.yaml
-rw-r--r-- 1001/1001      9435 2022-11-13 05:45 info/about.json
-rw-r--r-- 1001/1001         0 2022-11-13 05:45 info/git
-rwxrwxr-x 1001/1001   4051256 2022-11-13 05:45 bin/wfmash

The meta.yaml is the latest. And the compilation environment has a GCC 10.4. 

$ cat  pkgs/wfmash-0.10.0-hfdddef0_2/info/recipe/meta.yaml
# This file created by conda-build 3.21.8
# meta.yaml template originally from:
# /opt/recipe, last modified Sat Nov 12 21:36:58 2022
# ------------------------------------------------

package:
  name: wfmash
  version: 0.10.0
source:
  sha256: f7635d306f7b436b837f01fcb11aa503d939915a1b18e601e0f50fc496ab6632
  url: https://github.com/waveygang/wfmash/releases/download/v0.10.0/wfmash-v0.10.0.tar.gz
build:
  number: '2'
  string: hfdddef0_2
full content $ cat pkgs/wfmash-0.10.0-hfdddef0_2/info/recipe/meta.yaml # This file created by conda-build 3.21.8 # meta.yaml template originally from: # /opt/recipe, last modified Sat Nov 12 21:36:58 2022 # ------------------------------------------------ package: name: wfmash version: 0.10.0 source: sha256: f7635d306f7b436b837f01fcb11aa503d939915a1b18e601e0f50fc496ab6632 url: https://github.com/waveygang/wfmash/releases/download/v0.10.0/wfmash-v0.10.0.tar.gz build: number: '2' string: hfdddef0_2 requirements: build: - _libgcc_mutex 0.1 conda_forge - _openmp_mutex 4.5 2_gnu - binutils_impl_linux-64 2.39 h6ceecb4_0 - binutils_linux-64 2.39 h5fc0e48_11 - bzip2 1.0.8 h7f98852_4 - c-ares 1.18.1 h7f98852_0 - ca-certificates 2022.9.24 ha878542_0 - cmake 3.24.3 h816a3e0_0 - expat 2.5.0 h27087fc_0 - gcc_impl_linux-64 10.4.0 h5231bdf_19 - gcc_linux-64 10.4.0 h9215b83_11 - gxx_impl_linux-64 10.4.0 h5231bdf_19 - gxx_linux-64 10.4.0 h6e491c6_11 - kernel-headers_linux-64 2.6.32 he073ed8_15 - keyutils 1.6.1 h166bdaf_0 - krb5 1.19.3 h08a2579_0 - ld_impl_linux-64 2.39 hc81fddc_0 - libcurl 7.86.0 h2283fc2_1 - libedit 3.1.20191231 he28a2e2_2 - libev 4.33 h516909a_1 - libgcc-devel_linux-64 10.4.0 hd38fd1e_19 - libgcc-ng 12.2.0 h65d4601_19 - libgomp 12.2.0 h65d4601_19 - libnghttp2 1.47.0 hff17c54_1 - libsanitizer 10.4.0 h5246dfb_19 - libssh2 1.10.0 hf14f497_3 - libstdcxx-devel_linux-64 10.4.0 hd38fd1e_19 - libstdcxx-ng 12.2.0 h46fd767_19 - libuv 1.44.2 h166bdaf_0 - libzlib 1.2.13 h166bdaf_4 - make 4.3 hd18ef5c_1 - ncurses 6.3 h27087fc_1 - openssl 3.0.7 h166bdaf_0 - rhash 1.4.3 h166bdaf_0 - sysroot_linux-64 2.12 he073ed8_15 - xz 5.2.6 h166bdaf_0 - zlib 1.2.13 h166bdaf_4 - zstd 1.5.2 h6239696_4 host: - _libgcc_mutex 0.1 conda_forge - _openmp_mutex 4.5 2_gnu - bzip2 1.0.8 h7f98852_4 - c-ares 1.18.1 h7f98852_0 - ca-certificates 2022.9.24 ha878542_0 - gsl 2.7 he838d99_0 - htslib 1.16 h6bc39ce_0 - jemalloc 5.2.1 h9c3ff4c_6 - keyutils 1.6.1 h166bdaf_0 - krb5 1.19.3 h3790be6_0 - libblas 3.9.0 16_linux64_openblas - libcblas 3.9.0 16_linux64_openblas - libcurl 7.86.0 h7bff187_1 - libdeflate 1.13 h166bdaf_0 - libedit 3.1.20191231 he28a2e2_2 - libev 4.33 h516909a_1 - libgcc-ng 12.2.0 h65d4601_19 - libgfortran-ng 12.2.0 h69a702a_19 - libgfortran5 12.2.0 h337968e_19 - libgomp 12.2.0 h65d4601_19 - libjemalloc 5.2.1 h9c3ff4c_6 - libnghttp2 1.47.0 hdcd2b5c_1 - libopenblas 0.3.21 pthreads_h78a6416_3 - libssh2 1.10.0 haa6b8db_3 - libstdcxx-ng 12.2.0 h46fd767_19 - libzlib 1.2.13 h166bdaf_4 - ncurses 6.3 h27087fc_1 - openssl 1.1.1s h166bdaf_0 - xz 5.2.6 h166bdaf_0 - zlib 1.2.13 h166bdaf_4 run: - gsl >=2.7,<2.8.0a0 - htslib >=1.16,<1.17.0a0 - libgcc-ng >=12 - libjemalloc >=5.2.1 - libstdcxx-ng >=12 - libzlib >=1.2.13,<1.3.0a0 test: commands: - wfmash --help about: home: https://github.com/waveygang/wfmash license: MIT license_file: LICENSE summary: a pangenome-scale aligner extra: copy_test_source_files: true final: true recipe-maintainers: - AndreaGuarracino skip-lints: - uses_vcs_url

Why do you recommend specifying the version for cmake and gcc in the meta.yaml? I see that a few tools specify the version of cmake, but not for gcc. Do you know examples of that?

Sorry, I can't find an example via searching the bioconda repo. I'm not familiar with C/C++ ecosystem, but I've met tools that failed to run due to dependencies with versions too new, like sourmash and some other python packages incompatible to Python 3.10 due to the change of stdlib APIs.

I didn't dive into the mechanism of conda. But now I'm pretty sure it caches some files in their server, including binaries (my tools) and packages supposed to be compiled from the source like wfmash. It may check and compare the local environment with that of the cache server; if they matched, the cached binary is downloaded to avoid compiling from the source. Since the readme explicitly requires "At least GCC version 9.3.0 is required for the compilation", it would be better to specify the version.

I also tried to recreate the conda env and installed the latest cmake and GCC before installing pggb (with conda --use-local), but wfmash still failed to run.

shenwei356 commented 1 year ago

This might be the way: Building conda packages from scratch.

# create a new conda environment with new cmake and GCC
conda create -n pggb 
conda activate pggb
mamba install cmake gcc

# copy the build.sh and meta.yaml file to some where
# https://github.com/bioconda/bioconda-recipes/tree/7ba6e417f2b7b31b84c98641214624f961ab2a49/recipes/wfmash

# install conda-build
mamba install conda-build

# cd where build.sh existes.
conda-biuld .

# remove the old one
mamba remove wfmash

# install the locally compiled one
conda install --use-local wfmash

It did compile from scratch. Unfortunately, it still failed to run:

$ ll  $(which wfmash)
-rwxrwxr-x 2 shenwei shenwei 3.7M Dec  2 14:36 /home/shenwei/app/miniconda3/envs/pggb/bin/wfmash

$ wfmash --version
v0.10.0-4-gcf9bfb0

$ wfmash -s 500 -l 25000 -p 90 -n 27 -k 19 -H 0.001 -X -t 16 --tmp-base output akk.fasta --approx-map
Segmentation fault (core dumped)
build log $ conda-build . No numpy version specified in conda_build_config.yaml. Falling back to default numpy value of 1.16 WARNING:conda_build.metadata:No numpy version specified in conda_build_config.yaml. Falling back to default numpy value of 1.16 Adding in variants from internal_defaults INFO:conda_build.variants:Adding in variants from internal_defaults Attempting to finalize metadata for wfmash INFO:conda_build.metadata:Attempting to finalize metadata for wfmash Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... done Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... done Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... done BUILD START: ['wfmash-0.10.0-h3fd9d12_2.tar.bz2'] Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... done ## Package Plan ## environment location: /home/shenwei/app/miniconda3/envs/pggb2/conda-bld/wfmash_1669967869518/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho The following NEW packages will be INSTALLED: _libgcc_mutex: 0.1-conda_forge conda-forge _openmp_mutex: 4.5-2_gnu conda-forge bzip2: 1.0.8-h7f98852_4 conda-forge c-ares: 1.18.1-h7f98852_0 conda-forge ca-certificates: 2022.9.24-ha878542_0 conda-forge gsl: 2.7-he838d99_0 conda-forge htslib: 1.16-h6bc39ce_0 bioconda jemalloc: 5.2.1-h9c3ff4c_6 conda-forge keyutils: 1.6.1-h166bdaf_0 conda-forge krb5: 1.19.3-h3790be6_0 conda-forge libblas: 3.9.0-16_linux64_openblas conda-forge libcblas: 3.9.0-16_linux64_openblas conda-forge libcurl: 7.86.0-h7bff187_1 conda-forge libdeflate: 1.13-h166bdaf_0 conda-forge libedit: 3.1.20191231-he28a2e2_2 conda-forge libev: 4.33-h516909a_1 conda-forge libgcc-ng: 12.2.0-h65d4601_19 conda-forge libgfortran-ng: 12.2.0-h69a702a_19 conda-forge libgfortran5: 12.2.0-h337968e_19 conda-forge libgomp: 12.2.0-h65d4601_19 conda-forge libjemalloc: 5.2.1-h9c3ff4c_6 conda-forge libnghttp2: 1.47.0-hdcd2b5c_1 conda-forge libopenblas: 0.3.21-pthreads_h78a6416_3 conda-forge libssh2: 1.10.0-haa6b8db_3 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: 1.1.1s-h166bdaf_0 conda-forge xz: 5.2.6-h166bdaf_0 conda-forge zlib: 1.2.13-h166bdaf_4 conda-forge Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... done Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... done Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... done ## Package Plan ## environment location: /home/shenwei/app/miniconda3/envs/pggb2/conda-bld/wfmash_1669967869518/_build_env The following NEW packages will be INSTALLED: _libgcc_mutex: 0.1-conda_forge conda-forge _openmp_mutex: 4.5-2_gnu conda-forge binutils_impl_linux-64: 2.39-he00db2b_1 conda-forge binutils_linux-64: 2.39-h5fc0e48_11 conda-forge bzip2: 1.0.8-h7f98852_4 conda-forge c-ares: 1.18.1-h7f98852_0 conda-forge ca-certificates: 2022.9.24-ha878542_0 conda-forge cmake: 3.25.1-h816a3e0_0 conda-forge expat: 2.5.0-h27087fc_0 conda-forge gcc_impl_linux-64: 12.2.0-hcc96c02_19 conda-forge gcc_linux-64: 12.2.0-h4798a0e_11 conda-forge gxx_impl_linux-64: 12.2.0-hcc96c02_19 conda-forge gxx_linux-64: 12.2.0-hb41e900_11 conda-forge kernel-headers_linux-64: 2.6.32-he073ed8_15 conda-forge keyutils: 1.6.1-h166bdaf_0 conda-forge krb5: 1.19.3-h08a2579_0 conda-forge ld_impl_linux-64: 2.39-hcc3a1bd_1 conda-forge libcurl: 7.86.0-h2283fc2_1 conda-forge libedit: 3.1.20191231-he28a2e2_2 conda-forge libev: 4.33-h516909a_1 conda-forge libgcc-devel_linux-64: 12.2.0-h3b97bd3_19 conda-forge libgcc-ng: 12.2.0-h65d4601_19 conda-forge libgomp: 12.2.0-h65d4601_19 conda-forge libnghttp2: 1.47.0-hff17c54_1 conda-forge libsanitizer: 12.2.0-h46fd767_19 conda-forge libssh2: 1.10.0-hf14f497_3 conda-forge libstdcxx-devel_linux-64: 12.2.0-h3b97bd3_19 conda-forge libstdcxx-ng: 12.2.0-h46fd767_19 conda-forge libuv: 1.44.2-h166bdaf_0 conda-forge libzlib: 1.2.13-h166bdaf_4 conda-forge make: 4.3-hd18ef5c_1 conda-forge ncurses: 6.3-h27087fc_1 conda-forge openssl: 3.0.7-h166bdaf_0 conda-forge rhash: 1.4.3-h166bdaf_0 conda-forge sysroot_linux-64: 2.12-he073ed8_15 conda-forge xz: 5.2.6-h166bdaf_0 conda-forge zlib: 1.2.13-h166bdaf_4 conda-forge zstd: 1.5.2-h6239696_4 conda-forge Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... done Source cache directory is: /home/shenwei/app/miniconda3/envs/pggb2/conda-bld/src_cache INFO:conda_build.source:Source cache directory is: /home/shenwei/app/miniconda3/envs/pggb2/conda-bld/src_cache Downloading source to cache: wfmash-v0.10.0_f7635d306f.tar.gz INFO:conda_build.source:Downloading source to cache: wfmash-v0.10.0_f7635d306f.tar.gz Downloading https://github.com/waveygang/wfmash/releases/download/v0.10.0/wfmash-v0.10.0.tar.gz INFO:conda_build.source:Downloading https://github.com/waveygang/wfmash/releases/download/v0.10.0/wfmash-v0.10.0.tar.gz DEBUG:urllib3.util.retry:Incremented Retry for (url='/waveygang/wfmash/releases/download/v0.10.0/wfmash-v0.10.0.tar.gz'): Retry(total=2, connect=None, read=None, redirect=None, status=None) WARNING:urllib3.connectionpool:Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ProxyError('Cannot connect to proxy.', TimeoutError('_ssl.c:980: The handshake operation timed out'))': /waveygang/wfmash/releases/download/v0.10.0/wfmash-v0.10.0.tar.gz DEBUG:urllib3.util.retry:Incremented Retry for (url='/waveygang/wfmash/releases/download/v0.10.0/wfmash-v0.10.0.tar.gz'): Retry(total=1, connect=None, read=None, redirect=None, status=None) WARNING:urllib3.connectionpool:Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ProxyError('Cannot connect to proxy.', TimeoutError('_ssl.c:980: The handshake operation timed out'))': /waveygang/wfmash/releases/download/v0.10.0/wfmash-v0.10.0.tar.gz DEBUG:urllib3.util.retry:Incremented Retry for (url='/github-production-release-asset-2e65be/294910326/0c6c7541-1c13-4816-af0b-b620b25137f0?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20221202%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20221202T075520Z&X-Amz-Expires=300&X-Amz-Signature=10c1e3864e9fd4e2ad3366e9fe8f018839018744f5928b49390df79f94b5d15d&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=294910326&response-content-disposition=attachment%3B%20filename%3Dwfmash-v0.10.0.tar.gz&response-content-type=application%2Foctet-stream'): Retry(total=2, connect=None, read=None, redirect=None, status=None) WARNING:urllib3.connectionpool:Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ProxyError('Cannot connect to proxy.', TimeoutError('_ssl.c:980: The handshake operation timed out'))': /github-production-release-asset-2e65be/294910326/0c6c7541-1c13-4816-af0b-b620b25137f0?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20221202%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20221202T075520Z&X-Amz-Expires=300&X-Amz-Signature=10c1e3864e9fd4e2ad3366e9fe8f018839018744f5928b49390df79f94b5d15d&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=294910326&response-content-disposition=attachment%3B%20filename%3Dwfmash-v0.10.0.tar.gz&response-content-type=application%2Foctet-stream Success INFO:conda_build.source:Success Extracting download source tree in: /home/shenwei/app/miniconda3/envs/pggb2/conda-bld/wfmash_1669967869518/work export PREFIX=/home/shenwei/app/miniconda3/envs/pggb2/conda-bld/wfmash_1669967869518/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho export BUILD_PREFIX=/home/shenwei/app/miniconda3/envs/pggb2/conda-bld/wfmash_1669967869518/_build_env export SRC_DIR=/home/shenwei/app/miniconda3/envs/pggb2/conda-bld/wfmash_1669967869518/work INFO: activate-binutils_linux-64.sh made the following environmental changes: +ADDR2LINE=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-addr2line +AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ar +AS=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-as +CXXFILT=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c++filt +ELFEDIT=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-elfedit +GPROF=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gprof +LD_GOLD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld.gold +LD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld +NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-nm +OBJCOPY=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-objcopy +OBJDUMP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-objdump +RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib +READELF=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-readelf +SIZE=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-size +STRINGS=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strings +STRIP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip INFO: activate-gcc_linux-64.sh made the following environmental changes: +build_alias=x86_64-conda-linux-gnu -BUILD=x86_64-conda_cos6-linux-gnu +BUILD=x86_64-conda-linux-gnu +CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc +CC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc +CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/wfmash-0.10.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix +CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip -DCMAKE_FIND_ROOT_PATH_MODE_PROGRAM=NEVER -DCMAKE_FIND_ROOT_PATH_MODE_LIBRARY=ONLY -DCMAKE_FIND_ROOT_PATH_MODE_INCLUDE=ONLY -DCMAKE_FIND_ROOT_PATH=$PREFIX;$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin +CMAKE_PREFIX_PATH=$PREFIX:$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot/usr +CONDA_BUILD_SYSROOT=$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot +_CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_conda_cos6_linux_gnu +CONDA_TOOLCHAIN_BUILD=x86_64-conda-linux-gnu +CONDA_TOOLCHAIN_HOST=x86_64-conda-linux-gnu +CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include +CPP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cpp +DEBUG_CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/wfmash-0.10.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix +DEBUG_CPPFLAGS=-D_DEBUG -D_FORTIFY_SOURCE=2 -Og -isystem $PREFIX/include +GCC_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar +GCC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc +GCC_NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-nm +GCC_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib +host_alias=x86_64-conda-linux-gnu +HOST=x86_64-conda-linux-gnu +LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib INFO: activate-gxx_linux-64.sh made the following environmental changes: +CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/wfmash-0.10.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix +CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c++ +CXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c++ +DEBUG_CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/wfmash-0.10.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix +GXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-g++ -- The C compiler identification is GNU 12.2.0 -- The CXX compiler identification is GNU 12.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- CMAKE_BUILD_TYPE: Generic -- CMAKE_BUILD_TYPE: Generic -- Configuring done -- Generating done -- Build files have been written to: $SRC_DIR/build In file included from profiler_timer.c:33: profiler_timer.h: In function 'timer_stop': profiler_timer.h:42:38: warning: 'end_timer.tv_sec' is used uninitialized [-Wuninitialized] 42 | #define TIME_DIFF_NS(start,end) ((end.tv_sec*1000000000 + end.tv_nsec) - (start.tv_sec*1000000000 + start.tv_nsec)) | ^ profiler_timer.c:70:19: note: 'end_timer' declared here 70 | struct timespec end_timer; | ^~~~~~~~~ profiler_timer.h:42:62: warning: 'end_timer.tv_nsec' is used uninitialized [-Wuninitialized] 42 | #define TIME_DIFF_NS(start,end) ((end.tv_sec*1000000000 + end.tv_nsec) - (start.tv_sec*1000000000 + start.tv_nsec)) | ^ profiler_timer.c:70:19: note: 'end_timer' declared here 70 | struct timespec end_timer; | ^~~~~~~~~ profiler_timer.h: In function 'timer_pause': profiler_timer.h:42:38: warning: 'end_timer.tv_sec' is used uninitialized [-Wuninitialized] 42 | #define TIME_DIFF_NS(start,end) ((end.tv_sec*1000000000 + end.tv_nsec) - (start.tv_sec*1000000000 + start.tv_nsec)) | ^ profiler_timer.c:70:19: note: 'end_timer' declared here 70 | struct timespec end_timer; | ^~~~~~~~~ profiler_timer.h:42:62: warning: 'end_timer.tv_nsec' is used uninitialized [-Wuninitialized] 42 | #define TIME_DIFF_NS(start,end) ((end.tv_sec*1000000000 + end.tv_nsec) - (start.tv_sec*1000000000 + start.tv_nsec)) | ^ profiler_timer.c:70:19: note: 'end_timer' declared here 70 | struct timespec end_timer; | ^~~~~~~~~ profiler_timer.h: In function 'timer_get_current_lap_ns': profiler_timer.h:42:38: warning: 'end_timer.tv_sec' is used uninitialized [-Wuninitialized] 42 | #define TIME_DIFF_NS(start,end) ((end.tv_sec*1000000000 + end.tv_nsec) - (start.tv_sec*1000000000 + start.tv_nsec)) | ^ profiler_timer.c:82:19: note: 'end_timer' declared here 82 | struct timespec end_timer; | ^~~~~~~~~ profiler_timer.h:42:62: warning: 'end_timer.tv_nsec' is used uninitialized [-Wuninitialized] 42 | #define TIME_DIFF_NS(start,end) ((end.tv_sec*1000000000 + end.tv_nsec) - (start.tv_sec*1000000000 + start.tv_nsec)) | ^ profiler_timer.c:82:19: note: 'end_timer' declared here 82 | struct timespec end_timer; | ^~~~~~~~~ profiler_timer.h: In function 'timer_get_current_total_ns': profiler_timer.h:42:38: warning: 'end_timer.tv_sec' is used uninitialized [-Wuninitialized] 42 | #define TIME_DIFF_NS(start,end) ((end.tv_sec*1000000000 + end.tv_nsec) - (start.tv_sec*1000000000 + start.tv_nsec)) | ^ profiler_timer.c:82:19: note: 'end_timer' declared here 82 | struct timespec end_timer; | ^~~~~~~~~ profiler_timer.h:42:62: warning: 'end_timer.tv_nsec' is used uninitialized [-Wuninitialized] 42 | #define TIME_DIFF_NS(start,end) ((end.tv_sec*1000000000 + end.tv_nsec) - (start.tv_sec*1000000000 + start.tv_nsec)) | ^ profiler_timer.c:82:19: note: 'end_timer' declared here 82 | struct timespec end_timer; | ^~~~~~~~~ [ 0%] Built target wfa_lib [ 9%] Building CXX object src/common/wflign/CMakeFiles/libwflign_static.dir/deps/atomic_image.cpp.o [ 18%] Building CXX object src/common/wflign/CMakeFiles/libwflign_static.dir/deps/lodepng/lodepng.cpp.o [ 27%] Building CXX object src/common/wflign/CMakeFiles/libwflign_static.dir/src/wflign.cpp.o [ 36%] Building CXX object src/common/wflign/CMakeFiles/libwflign_static.dir/src/wflign_alignment.cpp.o [ 45%] Building CXX object src/common/wflign/CMakeFiles/libwflign_static.dir/src/wflign_patch.cpp.o [ 54%] Building CXX object src/common/wflign/CMakeFiles/libwflign_static.dir/src/rkmh.cpp.o [ 63%] Building CXX object src/common/wflign/CMakeFiles/libwflign_static.dir/src/murmur3.cpp.o [ 72%] Linking CXX static library ../../../lib/libwflign.a [ 72%] Built target libwflign_static [ 81%] Building CXX object CMakeFiles/wfmash.dir/src/common/utils.cpp.o [ 90%] Building CXX object CMakeFiles/wfmash.dir/src/interface/main.cpp.o [100%] Linking CXX executable bin/wfmash [100%] Built target wfmash Resource usage statistics from building wfmash: Process count: 10 CPU time: Sys=0:00:00.6, User=0:00:06.4 Memory: 424.4M Disk usage: 24.3K Time elapsed: 0:00:24.7 Packaging wfmash INFO:conda_build.build:Packaging wfmash Packaging wfmash-0.10.0-h3fd9d12_2 INFO:conda_build.build:Packaging wfmash-0.10.0-h3fd9d12_2 number of files: 1 Warning: rpath /home/shenwei/app/miniconda3/envs/pggb2/conda-bld/wfmash_1669967869518/work/src/common/wflign/deps/WFA2-lib/lib is outside prefix /home/shenwei/app/miniconda3/envs/pggb2/conda-bld/wfmash_1669967869518/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho (removing it) Warning: rpath /home/shenwei/app/miniconda3/envs/pggb2/conda-bld/wfmash_1669967869518/_build_env/lib is outside prefix /home/shenwei/app/miniconda3/envs/pggb2/conda-bld/wfmash_1669967869518/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho (removing it) WARNING :: Failed to get_static_lib_exports(/home/shenwei/app/miniconda3/envs/pggb2/conda-bld/wfmash_1669967869518/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/libbz2.a) Unknown format WARNING :: Failed to get_static_lib_exports(/home/shenwei/app/miniconda3/envs/pggb2/conda-bld/wfmash_1669967869518/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/libkeyutils.a) Unknown format WARNING :: Failed to get_static_lib_exports(/home/shenwei/app/miniconda3/envs/pggb2/conda-bld/wfmash_1669967869518/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/libncurses++.a) Unknown format WARNING :: Failed to get_static_lib_exports(/home/shenwei/app/miniconda3/envs/pggb2/conda-bld/wfmash_1669967869518/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/libncurses++w.a) Unknown format WARNING :: Failed to get_static_lib_exports(/home/shenwei/app/miniconda3/envs/pggb2/conda-bld/wfmash_1669967869518/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/libz.a) Unknown format WARNING :: Failed to get_static_lib_exports(/home/shenwei/app/miniconda3/envs/pggb2/conda-bld/wfmash_1669967869518/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/libgsl.a) Unknown format WARNING :: Failed to get_static_lib_exports(/home/shenwei/app/miniconda3/envs/pggb2/conda-bld/wfmash_1669967869518/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/libgslcblas.a) Unknown format WARNING :: Failed to get_static_lib_exports(/home/shenwei/app/miniconda3/envs/pggb2/conda-bld/wfmash_1669967869518/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/libhts.a) Unknown format WARNING :: Failed to get_static_lib_exports(/home/shenwei/app/miniconda3/envs/pggb2/conda-bld/wfmash_1669967869518/_build_env/x86_64-conda-linux-gnu/sysroot/usr/lib64/libBrokenLocale.a) Unknown format WARNING :: Failed to get_static_lib_exports(/home/shenwei/app/miniconda3/envs/pggb2/conda-bld/wfmash_1669967869518/_build_env/x86_64-conda-linux-gnu/sysroot/usr/lib64/libanl.a) Unknown format WARNING :: Failed to get_static_lib_exports(/home/shenwei/app/miniconda3/envs/pggb2/conda-bld/wfmash_1669967869518/_build_env/x86_64-conda-linux-gnu/sysroot/usr/lib64/libbsd-compat.a) Unknown format WARNING :: Failed to get_static_lib_exports(/home/shenwei/app/miniconda3/envs/pggb2/conda-bld/wfmash_1669967869518/_build_env/x86_64-conda-linux-gnu/sysroot/usr/lib64/libc.a) Unknown format WARNING :: Failed to get_static_lib_exports(/home/shenwei/app/miniconda3/envs/pggb2/conda-bld/wfmash_1669967869518/_build_env/x86_64-conda-linux-gnu/sysroot/usr/lib64/libc_nonshared.a) Unknown format WARNING :: Failed to get_static_lib_exports(/home/shenwei/app/miniconda3/envs/pggb2/conda-bld/wfmash_1669967869518/_build_env/x86_64-conda-linux-gnu/sysroot/usr/lib64/libcrypt.a) Unknown format WARNING :: Failed to get_static_lib_exports(/home/shenwei/app/miniconda3/envs/pggb2/conda-bld/wfmash_1669967869518/_build_env/x86_64-conda-linux-gnu/sysroot/usr/lib64/libdl.a) Unknown format WARNING :: Failed to get_static_lib_exports(/home/shenwei/app/miniconda3/envs/pggb2/conda-bld/wfmash_1669967869518/_build_env/x86_64-conda-linux-gnu/sysroot/usr/lib64/libm.a) Unknown format WARNING :: Failed to get_static_lib_exports(/home/shenwei/app/miniconda3/envs/pggb2/conda-bld/wfmash_1669967869518/_build_env/x86_64-conda-linux-gnu/sysroot/usr/lib64/libpthread.a) Unknown format WARNING :: Failed to get_static_lib_exports(/home/shenwei/app/miniconda3/envs/pggb2/conda-bld/wfmash_1669967869518/_build_env/x86_64-conda-linux-gnu/sysroot/usr/lib64/libpthread_nonshared.a) Unknown format WARNING :: Failed to get_static_lib_exports(/home/shenwei/app/miniconda3/envs/pggb2/conda-bld/wfmash_1669967869518/_build_env/x86_64-conda-linux-gnu/sysroot/usr/lib64/libresolv.a) Unknown format WARNING :: Failed to get_static_lib_exports(/home/shenwei/app/miniconda3/envs/pggb2/conda-bld/wfmash_1669967869518/_build_env/x86_64-conda-linux-gnu/sysroot/usr/lib64/librpcsvc.a) Unknown format WARNING :: Failed to get_static_lib_exports(/home/shenwei/app/miniconda3/envs/pggb2/conda-bld/wfmash_1669967869518/_build_env/x86_64-conda-linux-gnu/sysroot/usr/lib64/librt.a) Unknown format WARNING :: Failed to get_static_lib_exports(/home/shenwei/app/miniconda3/envs/pggb2/conda-bld/wfmash_1669967869518/_build_env/x86_64-conda-linux-gnu/sysroot/usr/lib64/libutil.a) Unknown format WARNING :: Failed to get_static_lib_exports(/home/shenwei/app/miniconda3/envs/pggb2/conda-bld/wfmash_1669967869518/_build_env/lib/libbfd.a) Unknown format WARNING :: Failed to get_static_lib_exports(/home/shenwei/app/miniconda3/envs/pggb2/conda-bld/wfmash_1669967869518/_build_env/lib/libctf-nobfd.a) Unknown format WARNING :: Failed to get_static_lib_exports(/home/shenwei/app/miniconda3/envs/pggb2/conda-bld/wfmash_1669967869518/_build_env/lib/libctf.a) Unknown format WARNING :: Failed to get_static_lib_exports(/home/shenwei/app/miniconda3/envs/pggb2/conda-bld/wfmash_1669967869518/_build_env/lib/libopcodes.a) Unknown format WARNING :: Failed to get_static_lib_exports(/home/shenwei/app/miniconda3/envs/pggb2/conda-bld/wfmash_1669967869518/_build_env/lib/libexpat.a) Unknown format WARNING :: Failed to get_static_lib_exports(/home/shenwei/app/miniconda3/envs/pggb2/conda-bld/wfmash_1669967869518/_build_env/lib/libuv.a) Unknown format WARNING :: Failed to get_static_lib_exports(/home/shenwei/app/miniconda3/envs/pggb2/conda-bld/wfmash_1669967869518/_build_env/lib/gcc/x86_64-conda-linux-gnu/12.2.0/libgcc.a) Unknown format WARNING :: Failed to get_static_lib_exports(/home/shenwei/app/miniconda3/envs/pggb2/conda-bld/wfmash_1669967869518/_build_env/lib/gcc/x86_64-conda-linux-gnu/12.2.0/libgcc_eh.a) Unknown format WARNING :: Failed to get_static_lib_exports(/home/shenwei/app/miniconda3/envs/pggb2/conda-bld/wfmash_1669967869518/_build_env/lib/gcc/x86_64-conda-linux-gnu/12.2.0/libgcov.a) Unknown format WARNING :: Failed to get_static_lib_exports(/home/shenwei/app/miniconda3/envs/pggb2/conda-bld/wfmash_1669967869518/_build_env/lib/gcc/x86_64-conda-linux-gnu/12.2.0/libstdc++.a) Unknown format WARNING :: Failed to get_static_lib_exports(/home/shenwei/app/miniconda3/envs/pggb2/conda-bld/wfmash_1669967869518/_build_env/lib/gcc/x86_64-conda-linux-gnu/12.2.0/libstdc++fs.a) Unknown format WARNING :: Failed to get_static_lib_exports(/home/shenwei/app/miniconda3/envs/pggb2/conda-bld/wfmash_1669967869518/_build_env/lib/gcc/x86_64-conda-linux-gnu/12.2.0/libsupc++.a) Unknown format WARNING :: Failed to get_static_lib_exports(/home/shenwei/app/miniconda3/envs/pggb2/conda-bld/wfmash_1669967869518/_build_env/lib/gcc/x86_64-conda-linux-gnu/12.2.0/libiberty.a) Unknown format INFO: sysroot: '/home/shenwei/app/miniconda3/envs/pggb2/conda-bld/wfmash_1669967869518/_build_env/x86_64-conda-linux-gnu/sysroot/' files: '['/home/shenwei/app/miniconda3/envs/pggb2/conda-bld/wfmash_1669967869518/_build_env/x86_64-conda-linux-gnu/sysroot/usr/share/zoneinfo/zone.tab', '/home/shenwei/app/miniconda3/envs/pggb2/conda-bld/wfmash_1669967869518/_build_env/x86_64-conda-linux-gnu/sysroot/usr/share/zoneinfo/tzdata.zi', '/home/shenwei/app/miniconda3/envs/pggb2/conda-bld/wfmash_1669967869518/_build_env/x86_64-conda-linux-gnu/sysroot/usr/share/zoneinfo/right/Zulu', '/home/shenwei/app/miniconda3/envs/pggb2/conda-bld/wfmash_1669967869518/_build_env/x86_64-conda-linux-gnu/sysroot/usr/share/zoneinfo/right/WET']' INFO (wfmash,bin/wfmash): Needed DSO lib/libgsl.so.25 found in conda-forge::gsl-2.7-he838d99_0 WARNING (wfmash,bin/wfmash): Needed DSO lib/libopenblas.so.0 found in ['libopenblas'] WARNING (wfmash,bin/wfmash): .. but ['libopenblas'] not in reqs/run, (i.e. it is overlinking) (likely) or a missing dependency (less likely) INFO (wfmash,bin/wfmash): Needed DSO x86_64-conda-linux-gnu/sysroot/lib64/libpthread.so.0 found in CDT/compiler package conda-forge::sysroot_linux-64-2.12-he073ed8_15 INFO (wfmash,bin/wfmash): Needed DSO lib/libhts.so.3 found in bioconda::htslib-1.16-h6bc39ce_0 INFO (wfmash,bin/wfmash): Needed DSO lib/libjemalloc.so.2 found in conda-forge::libjemalloc-5.2.1-h9c3ff4c_6 INFO (wfmash,bin/wfmash): Needed DSO lib/libz.so.1 found in conda-forge::libzlib-1.2.13-h166bdaf_4 INFO (wfmash,bin/wfmash): Needed DSO lib/libstdc++.so.6 found in conda-forge::libstdcxx-ng-12.2.0-h46fd767_19 INFO (wfmash,bin/wfmash): Needed DSO x86_64-conda-linux-gnu/sysroot/lib64/libm.so.6 found in CDT/compiler package conda-forge::sysroot_linux-64-2.12-he073ed8_15 INFO (wfmash,bin/wfmash): Needed DSO lib/libgcc_s.so.1 found in conda-forge::libgcc-ng-12.2.0-h65d4601_19 INFO (wfmash,bin/wfmash): Needed DSO x86_64-conda-linux-gnu/sysroot/lib64/libc.so.6 found in CDT/compiler package conda-forge::sysroot_linux-64-2.12-he073ed8_15 Fixing permissions Packaged license file/s. INFO :: Time taken to mark (prefix) 0 replacements in 0 files was 0.02 seconds Importing conda-verify failed. Please be sure to test your packages. conda install conda-verify to make this message go away. WARNING:conda_build.build:Importing conda-verify failed. Please be sure to test your packages. conda install conda-verify to make this message go away. TEST START: /home/shenwei/app/miniconda3/envs/pggb2/conda-bld/linux-64/wfmash-0.10.0-h3fd9d12_2.tar.bz2 Renaming work directory '/home/shenwei/app/miniconda3/envs/pggb2/conda-bld/wfmash_1669967869518/work' to '/home/shenwei/app/miniconda3/envs/pggb2/conda-bld/wfmash_1669967869518/work_moved_wfmash-0.10.0-h3fd9d12_2_linux-64' INFO:conda_build.utils:Renaming work directory '/home/shenwei/app/miniconda3/envs/pggb2/conda-bld/wfmash_1669967869518/work' to '/home/shenwei/app/miniconda3/envs/pggb2/conda-bld/wfmash_1669967869518/work_moved_wfmash-0.10.0-h3fd9d12_2_linux-64' shutil.move(work)=/home/shenwei/app/miniconda3/envs/pggb2/conda-bld/wfmash_1669967869518/work, dest=/home/shenwei/app/miniconda3/envs/pggb2/conda-bld/wfmash_1669967869518/work_moved_wfmash-0.10.0-h3fd9d12_2_linux-64) INFO:conda_build.utils:shutil.move(work)=/home/shenwei/app/miniconda3/envs/pggb2/conda-bld/wfmash_1669967869518/work, dest=/home/shenwei/app/miniconda3/envs/pggb2/conda-bld/wfmash_1669967869518/work_moved_wfmash-0.10.0-h3fd9d12_2_linux-64) Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... done ## Package Plan ## environment location: /home/shenwei/app/miniconda3/envs/pggb2/conda-bld/wfmash_1669967869518/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl The following NEW packages will be INSTALLED: _libgcc_mutex: 0.1-conda_forge conda-forge _openmp_mutex: 4.5-2_gnu conda-forge bzip2: 1.0.8-h7f98852_4 conda-forge c-ares: 1.18.1-h7f98852_0 conda-forge ca-certificates: 2022.9.24-ha878542_0 conda-forge gsl: 2.7-he838d99_0 conda-forge htslib: 1.16-h6bc39ce_0 bioconda keyutils: 1.6.1-h166bdaf_0 conda-forge krb5: 1.19.3-h3790be6_0 conda-forge libblas: 3.9.0-16_linux64_openblas conda-forge libcblas: 3.9.0-16_linux64_openblas conda-forge libcurl: 7.86.0-h7bff187_1 conda-forge libdeflate: 1.13-h166bdaf_0 conda-forge libedit: 3.1.20191231-he28a2e2_2 conda-forge libev: 4.33-h516909a_1 conda-forge libgcc-ng: 12.2.0-h65d4601_19 conda-forge libgfortran-ng: 12.2.0-h69a702a_19 conda-forge libgfortran5: 12.2.0-h337968e_19 conda-forge libgomp: 12.2.0-h65d4601_19 conda-forge libjemalloc: 5.2.1-h9c3ff4c_6 conda-forge libnghttp2: 1.47.0-hdcd2b5c_1 conda-forge libopenblas: 0.3.21-pthreads_h78a6416_3 conda-forge libssh2: 1.10.0-haa6b8db_3 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: 1.1.1s-h166bdaf_0 conda-forge wfmash: 0.10.0-h3fd9d12_2 local xz: 5.2.6-h166bdaf_0 conda-forge zlib: 1.2.13-h166bdaf_4 conda-forge Preparing transaction: ...working... done Verifying transaction: ...working... done Executing transaction: ...working... done export PREFIX=/home/shenwei/app/miniconda3/envs/pggb2/conda-bld/wfmash_1669967869518/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl export SRC_DIR=/home/shenwei/app/miniconda3/envs/pggb2/conda-bld/wfmash_1669967869518/test_tmp + wfmash --help wfmash [target] [queries...] {OPTIONS} wfmash: a pangenome-scale aligner, v0.10.0-4-gcf9bfb0 OPTIONS: [ MANDATORY OPTIONS ] target alignment target/reference sequence file [ Files IO Options ] queries... query sequences file -Q[queries], --query-file-list=[queries] alignment queries files list [ Mapping Options ] -s[N], --segment-length=[N] segment seed length for mapping [default: 5k] -l[N], --block-length=[N] keep merged mappings supported by homologies of this total length [default: 5*segment-length] -c[N], --chain-gap=[N] chain mappings closer than this distance in query and target, retaining mappings in best chain [default: 100k] -k[N], --kmer=[N] kmer size [default: 19] -H[%], --kmer-threshold=[%] ignore the top % most-frequent kmers [default: 0.001] -n[N], --num-mappings-for-segment=[N] number of mappings to retain for each segment [default: 1] -S[N], --num-mappings-for-short-seq=[N] number of mappings to retain for each sequence shorter than segment length [default: 1] -X, --skip-self skip self mappings when the query and target name is the same (for all-vs-all mode) -Y[C], --skip-prefix=[C] skip mappings when the query and target have the same prefix before the last occurrence of the given character C -m, --approx-map skip base-level alignment, producing an approximate mapping in PAF -N, --no-split disable splitting of input sequences during mapping [default: enabled] -p[%], --map-pct-id=[%] percent identity in the mashmap step [default: 90] -K, --drop-low-map-id drop mappings with estimated identity below --map-pct-id=% -O, --keep-low-align-id keep alignments with gap-compressed identity below --map-pct-id=% x 0.75 -f, --no-filter disable mapping filtering -x[FACTOR], --sparsify-mappings=[FACTOR] keep this fraction of mappings -M, --no-merge don't merge consecutive segment-level mappings (NOT FULLY IMPLEMENTED) -w[N], --window-size=[N] window size for sketching. If 0, it computes the best window size automatically [default: 0, minimum -k] -U, --window-minimizers Use window minimizers rather than world minimizers -e[spaced-seeds], --spaced-seeds=[spaced-seeds] Params to generate spaced seeds e.g "10 5 0.75 20" [ Alignment Options ] -i[FILE], --input-paf=[FILE] derive precise alignments for this input PAF -W[N], --wflamda-segment=[N] wflambda segment length: size (in bp) of segment mapped in hierarchical WFA problem [default: 256] -g[mismatch,gap1,ext1], --wfa-params=[mismatch,gap1,ext1] score parameters for the wfa alignment (affine); match score is fixed at 0 [default: adaptive with respect to the estimated identity] -G[mismatch,gap1,ext1], --wflign-params=[mismatch,gap1,ext1] score parameters for the wflign alignment (affine); match score is fixed at 0 [default: adaptive with respect to the estimated identity] -b[N], --max-mash-dist=[N] maximum mash distance to perform the alignment in a wflambda segment [default: adaptive with respect to the estimated identity] -C[N], --max-patch-major=[N] maximum length to patch in the major axis [default: 512*segment-length] -F[N], --max-patch-minor=[N] maximum length to patch in the minor axis [default: 128*segment-length] -E[N], --erode-match-mismatch=[N] maximum length of match/mismatch islands to erode before patching [default: adaptive] [ Output Format Options ] -d, --md-tag output the MD tag -a, --sam-format output in the SAM format (PAF by default) -q, --no-seq-in-sam do not fill the sequence field in the SAM format [ General Options ] -B[PATH], --tmp-base=[PATH] base name for temporary files [default: `pwd`] -Z, --keep-temp keep intermediate files [ Threading ] -t[N], --threads=[N] use this many threads during parallel steps [ Program Information ] -v, --version show version number and github commit hash -h, --help display this help menu + exit 0 Resource usage statistics from testing wfmash: Process count: 1 CPU time: Sys=-, User=- Memory: 1.2M Disk usage: 12B Time elapsed: 0:00:02.1 TEST END: /home/shenwei/app/miniconda3/envs/pggb2/conda-bld/linux-64/wfmash-0.10.0-h3fd9d12_2.tar.bz2 Renaming work directory '/home/shenwei/app/miniconda3/envs/pggb2/conda-bld/wfmash_1669967869518/work' to '/home/shenwei/app/miniconda3/envs/pggb2/conda-bld/wfmash_1669967869518/work_moved_wfmash-0.10.0-h3fd9d12_2_linux-64_main_build_loop' INFO:conda_build.utils:Renaming work directory '/home/shenwei/app/miniconda3/envs/pggb2/conda-bld/wfmash_1669967869518/work' to '/home/shenwei/app/miniconda3/envs/pggb2/conda-bld/wfmash_1669967869518/work_moved_wfmash-0.10.0-h3fd9d12_2_linux-64_main_build_loop' shutil.move(work)=/home/shenwei/app/miniconda3/envs/pggb2/conda-bld/wfmash_1669967869518/work, dest=/home/shenwei/app/miniconda3/envs/pggb2/conda-bld/wfmash_1669967869518/work_moved_wfmash-0.10.0-h3fd9d12_2_linux-64_main_build_loop) INFO:conda_build.utils:shutil.move(work)=/home/shenwei/app/miniconda3/envs/pggb2/conda-bld/wfmash_1669967869518/work, dest=/home/shenwei/app/miniconda3/envs/pggb2/conda-bld/wfmash_1669967869518/work_moved_wfmash-0.10.0-h3fd9d12_2_linux-64_main_build_loop) # Automatic uploading is disabled # If you want to upload package(s) to anaconda.org later, type: # To have conda build upload to anaconda.org automatically, use # conda config --set anaconda_upload yes anaconda upload \ /home/shenwei/app/miniconda3/envs/pggb2/conda-bld/linux-64/wfmash-0.10.0-h3fd9d12_2.tar.bz2 anaconda_upload is not set. Not uploading wheels: [] INFO :: The inputs making up the hashes for the built packages are as follows: { "wfmash-0.10.0-h3fd9d12_2": { "recipe": { "c_compiler": "gcc", "cxx_compiler": "gxx", "target_platform": "linux-64" } } } #################################################################################### Resource usage summary: Total time: 0:08:10.6 CPU usage: sys=0:00:00.6, user=0:00:06.4 Maximum memory usage observed: 424.4M Total disk usage observed (not including envs): 24.3K
conda list $ conda list # packages in environment at /home/shenwei/app/miniconda3/envs/pggb2: # # Name Version Build Channel _libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 2_gnu conda-forge beautifulsoup4 4.11.1 pyha770c72_0 conda-forge binutils_impl_linux-64 2.39 he00db2b_1 conda-forge brotlipy 0.7.0 py310h5764c6d_1005 conda-forge bzip2 1.0.8 h7f98852_4 conda-forge c-ares 1.18.1 h7f98852_0 conda-forge ca-certificates 2022.9.24 ha878542_0 conda-forge certifi 2022.9.24 pyhd8ed1ab_0 conda-forge cffi 1.15.1 py310h255011f_2 conda-forge chardet 5.0.0 py310hff52083_1 conda-forge charset-normalizer 2.1.1 pyhd8ed1ab_0 conda-forge cmake 3.25.1 h816a3e0_0 conda-forge colorama 0.4.6 pyhd8ed1ab_0 conda-forge conda 22.9.0 py310hff52083_2 conda-forge conda-build 3.23.2 py310hff52083_0 conda-forge conda-package-handling 2.0.2 pyh38be061_0 conda-forge conda-package-streaming 0.7.0 pyhd8ed1ab_1 conda-forge cryptography 38.0.4 py310h597c629_0 conda-forge expat 2.5.0 h27087fc_0 conda-forge filelock 3.8.0 pyhd8ed1ab_0 conda-forge gcc 12.2.0 h26027b1_11 conda-forge gcc_impl_linux-64 12.2.0 hcc96c02_19 conda-forge glob2 0.7 py_0 conda-forge gsl 2.7 he838d99_0 conda-forge htslib 1.16 h6bc39ce_0 bioconda icu 70.1 h27087fc_0 conda-forge idna 3.4 pyhd8ed1ab_0 conda-forge jinja2 3.1.2 pyhd8ed1ab_1 conda-forge kernel-headers_linux-64 2.6.32 he073ed8_15 conda-forge keyutils 1.6.1 h166bdaf_0 conda-forge krb5 1.19.3 h3790be6_0 conda-forge ld_impl_linux-64 2.39 hcc3a1bd_1 conda-forge libarchive 3.6.1 hc6fc967_0 conda-forge libblas 3.9.0 16_linux64_openblas conda-forge libcblas 3.9.0 16_linux64_openblas conda-forge libcurl 7.86.0 h7bff187_1 conda-forge libdeflate 1.13 h166bdaf_0 conda-forge libedit 3.1.20191231 he28a2e2_2 conda-forge libev 4.33 h516909a_1 conda-forge libffi 3.4.2 h7f98852_5 conda-forge libgcc-devel_linux-64 12.2.0 h3b97bd3_19 conda-forge libgcc-ng 12.2.0 h65d4601_19 conda-forge libgfortran-ng 12.2.0 h69a702a_19 conda-forge libgfortran5 12.2.0 h337968e_19 conda-forge libgomp 12.2.0 h65d4601_19 conda-forge libiconv 1.17 h166bdaf_0 conda-forge libjemalloc 5.2.1 h9c3ff4c_6 conda-forge liblief 0.12.3 h27087fc_0 conda-forge libnghttp2 1.47.0 hdcd2b5c_1 conda-forge libnsl 2.0.0 h7f98852_0 conda-forge libopenblas 0.3.21 pthreads_h78a6416_3 conda-forge libsanitizer 12.2.0 h46fd767_19 conda-forge libsqlite 3.40.0 h753d276_0 conda-forge libssh2 1.10.0 haa6b8db_3 conda-forge libstdcxx-ng 12.2.0 h46fd767_19 conda-forge libuuid 2.32.1 h7f98852_1000 conda-forge libuv 1.44.2 h166bdaf_0 conda-forge libxml2 2.10.3 h7463322_0 conda-forge libzlib 1.2.13 h166bdaf_4 conda-forge lz4-c 1.9.3 h9c3ff4c_1 conda-forge lzo 2.10 h516909a_1000 conda-forge markupsafe 2.1.1 py310h5764c6d_2 conda-forge ncurses 6.3 h27087fc_1 conda-forge openssl 1.1.1s h166bdaf_0 conda-forge patch 2.7.6 h7f98852_1002 conda-forge patchelf 0.17.0 h58526e2_0 conda-forge pip 22.3.1 pyhd8ed1ab_0 conda-forge pkginfo 1.9.2 pyhd8ed1ab_0 conda-forge psutil 5.9.4 py310h5764c6d_0 conda-forge py-lief 0.12.3 py310hd8f1fbe_0 conda-forge pycosat 0.6.4 py310h5764c6d_1 conda-forge pycparser 2.21 pyhd8ed1ab_0 conda-forge pyopenssl 22.1.0 pyhd8ed1ab_0 conda-forge pysocks 1.7.1 py310hff52083_5 conda-forge python 3.10.8 h257c98d_0_cpython conda-forge python-libarchive-c 4.0 py310hff52083_2 conda-forge python_abi 3.10 3_cp310 conda-forge pytz 2022.6 pyhd8ed1ab_0 conda-forge pyyaml 6.0 py310h5764c6d_5 conda-forge readline 8.1.2 h0f457ee_0 conda-forge requests 2.28.1 pyhd8ed1ab_1 conda-forge rhash 1.4.3 h166bdaf_0 conda-forge ripgrep 13.0.0 h2f28480_2 conda-forge ruamel_yaml 0.15.80 py310h5764c6d_1008 conda-forge setuptools 65.5.1 pyhd8ed1ab_0 conda-forge six 1.16.0 pyh6c4a22f_0 conda-forge soupsieve 2.3.2.post1 pyhd8ed1ab_0 conda-forge sysroot_linux-64 2.12 he073ed8_15 conda-forge tk 8.6.12 h27826a3_0 conda-forge toml 0.10.2 pyhd8ed1ab_0 conda-forge toolz 0.12.0 pyhd8ed1ab_0 conda-forge tqdm 4.64.1 pyhd8ed1ab_0 conda-forge tzdata 2022g h191b570_0 conda-forge urllib3 1.26.13 pyhd8ed1ab_0 conda-forge wfmash 0.10.0 h3fd9d12_2 file:///home/shenwei/app/miniconda3/envs/pggb2/conda-bld wheel 0.38.4 pyhd8ed1ab_0 conda-forge xz 5.2.6 h166bdaf_0 conda-forge yaml 0.2.5 h7f98852_2 conda-forge zlib 1.2.13 h166bdaf_4 conda-forge zstandard 0.19.0 py310hdeb6495_1 conda-forge zstd 1.5.2 h6239696_4 conda-forge
AndreaGuarracino commented 1 year ago

Looking at your first conda list output, you have the correct bioconda-version of wfmash, that is hfdddef0_2. This does not point to the current version of the master branch on GitHub because bioconda takes the buildable tarball from the release here. Not sure if this information helps or if it was obvious to you.

Could you please share more information on your system? I am wondering if your CPU architecture is older than Sandy Bridge. Usually, wfmash breaks during the alignment due to portability issues, but in your case, it breaks earlier, during the mapping. That is more unusual.

shenwei356 commented 1 year ago

The CPU is Intel Xeon Gold 6248 (Cascade Lake), released in April 2, 2019.