Missing build items in conda OR freebayes-parrallel problem

[hughgifford]

Hello,

I hope you're well. I am struggling to get any install of Snippy working.

I've followed all instructions using either Conda or Brew, and both result in errors. I've even re-installed conda and all my environments from scratch.

Conda install

conda list packages in environment at /Users/hughgifford/miniconda3/envs/snippy: Name Version Build Channel any2fasta 0.4.2 hdfd78af_3 bioconda argtable2 2.13 h1de35cc_1001 conda-forge bcftools 1.17 h3bbda8f_1 bioconda bedtools 2.31.0 h6372da2_3 bioconda blast 2.14.1 pl5321h91c44f7_0 bioconda bwa 0.7.17 h45fc8d7_11 bioconda bzip2 1.0.8 h0d85af4_4 conda-forge c-ares 1.19.1 h0dc2134_0 conda-forge ca-certificates 2023.7.22 h8857fd0_0 conda-forge clustalo 1.2.4 h7133b54_7 bioconda clustalw 2.1 h85dcccf_9 bioconda curl 8.3.0 h5f667d7_0 conda-forge entrez-direct 16.2 h193322a_1 bioconda expat 2.5.0 hf0c8a7f_1 conda-forge freebayes 1.3.6 hd0edb90_5 bioconda gettext 0.21.1 h8a4c099_0 conda-forge gsl 2.7 h93259b0_0 conda-forge htslib 1.18 h365c357_0 bioconda k8 0.2.5 hdf58011_4 bioconda krb5 1.21.2 hb884880_0 conda-forge libblas 3.9.0 18_osx64_openblas conda-forge libcblas 3.9.0 18_osx64_openblas conda-forge libcurl 8.3.0 h5f667d7_0 conda-forge libcxx 16.0.6 hd57cbcb_0 conda-forge libdb 6.2.32 he49afe7_0 conda-forge libdeflate 1.18 hac1461d_0 conda-forge libedit 3.1.20191231 h0678c8f_2 conda-forge libev 4.33 haf1e3a3_1 conda-forge libexpat 2.5.0 hf0c8a7f_1 conda-forge libffi 3.4.2 h0d85af4_5 conda-forge libgfortran 5.0.0 13_2_0_h97931a8_1 conda-forge libgfortran5 13.2.0 h2873a65_1 conda-forge libiconv 1.17 hac89ed1_0 conda-forge libidn2 2.3.4 hb7f2c08_0 conda-forge libnghttp2 1.52.0 he2ab024_0 conda-forge libopenblas 0.3.24 openmp_h48a4ad5_0 conda-forge libsqlite 3.43.0 h58db7d2_0 conda-forge libssh2 1.11.0 hd019ec5_0 conda-forge libunistring 0.9.10 h0d85af4_0 conda-forge libzlib 1.2.13 h8a1eda9_5 conda-forge llvm-openmp 16.0.6 hff08bdf_0 conda-forge mafft 7.520 h2413b67_2 bioconda minimap2 2.26 h45fc8d7_1 bioconda muscle 5.1 h7d747a2_3 bioconda ncbi-vdb 3.0.0 pl5321h9722bc1_0 bioconda ncurses 6.4 hf0c8a7f_0 conda-forge openjdk 20.0.2 h7d26f99_1 conda-forge openssl 3.1.3 h8a1eda9_0 conda-forge paml 4.10.6 h2413b67_2 bioconda parallel 20230722 h694c41f_0 conda-forge pcre 8.45 he49afe7_0 conda-forge perl 5.32.1 4_h0dc2134_perl5 conda-forge perl-algorithm-diff 1.201 pl5321hd8ed1ab_0 conda-forge perl-archive-tar 2.40 pl5321hdfd78af_0 bioconda perl-base 2.23 pl5321hd8ed1ab_0 conda-forge perl-bio-asn1-entrezgene 1.73 pl5321hdfd78af_3 bioconda perl-bio-coordinate 1.007001 pl5321hdfd78af_3 bioconda perl-bio-featureio 1.6.905 pl5321hdfd78af_4 bioconda perl-bio-samtools 1.43 pl5321h1f540d2_3 bioconda perl-bio-searchio-hmmer 1.7.3 pl5321hdfd78af_0 bioconda perl-bio-tools-phylo-paml 1.7.3 pl5321hdfd78af_3 bioconda perl-bio-tools-run-alignment-clustalw 1.7.4 pl5321hdfd78af_3 bioconda perl-bio-tools-run-alignment-tcoffee 1.7.4 pl5321hdfd78af_5 bioconda perl-bioperl 1.7.8 hdfd78af_1 bioconda perl-bioperl-core 1.7.8 pl5321hdfd78af_1 bioconda perl-bioperl-run 1.007003 pl5321hdfd78af_0 bioconda perl-business-isbn 3.007 pl5321hd8ed1ab_0 conda-forge perl-business-isbn-data 20210112.006 pl5321hd8ed1ab_0 conda-forge perl-carp 1.50 pl5321hd8ed1ab_0 conda-forge perl-class-data-inheritable 0.09 pl5321h694c41f_0 conda-forge perl-common-sense 3.75 pl5321hd8ed1ab_0 conda-forge perl-compress-raw-bzip2 2.201 pl5321h775f41a_0 conda-forge perl-compress-raw-zlib 2.202 pl5321h775f41a_0 conda-forge perl-constant 1.33 pl5321hd8ed1ab_0 conda-forge perl-data-dumper 2.183 pl5321h775f41a_0 conda-forge perl-db_file 1.858 pl5321hac89ed1_0 conda-forge perl-devel-stacktrace 2.04 pl5321h694c41f_0 conda-forge perl-digest-hmac 1.04 pl5321hdfd78af_0 bioconda perl-digest-md5 2.58 pl5321hb7f2c08_0 conda-forge perl-encode 3.19 pl5321hb7f2c08_0 conda-forge perl-encode-locale 1.05 pl5321hdfd78af_7 bioconda perl-exception-class 1.45 pl5321hdfd78af_0 bioconda perl-exporter 5.74 pl5321hd8ed1ab_0 conda-forge perl-exporter-tiny 1.002002 pl5321hd8ed1ab_0 conda-forge perl-extutils-makemaker 7.70 pl5321hd8ed1ab_0 conda-forge perl-file-listing 6.16 pl5321hdfd78af_0 bioconda perl-file-slurp-tiny 0.004 pl5321hdfd78af_2 bioconda perl-file-sort 1.01 pl5321hdfd78af_3 bioconda perl-file-spec 3.48_01 pl5321hdfd78af_2 bioconda perl-getopt-long 2.54 pl5321hdfd78af_0 bioconda perl-html-parser 3.81 pl5321hb3ea9af_0 bioconda perl-html-tagset 3.20 pl5321hdfd78af_4 bioconda perl-http-cookies 6.10 pl5321hdfd78af_0 bioconda perl-http-daemon 6.16 pl5321hdfd78af_0 bioconda perl-http-date 6.06 pl5321hdfd78af_0 bioconda perl-http-message 6.36 pl5321hdfd78af_0 bioconda perl-http-negotiate 6.01 pl5321hdfd78af_4 bioconda perl-io-compress 2.201 pl5321h7133b54_2 bioconda perl-io-html 1.004 pl5321hdfd78af_0 bioconda perl-io-socket-ssl 2.075 pl5321hd8ed1ab_0 conda-forge perl-io-string 1.08 pl5321hdfd78af_4 bioconda perl-io-tty 1.16 pl5321h775f41a_0 conda-forge perl-io-zlib 1.14 pl5321hdfd78af_0 bioconda perl-ipc-run 20200505.0 pl5321hdfd78af_0 bioconda perl-json 4.10 pl5321hdfd78af_0 bioconda perl-json-xs 2.34 pl5321hcd10b59_5 bioconda perl-libwww-perl 6.67 pl5321hdfd78af_0 bioconda perl-libxml-perl 0.08 pl5321hdfd78af_3 bioconda perl-list-moreutils 0.430 pl5321hdfd78af_0 bioconda perl-list-moreutils-xs 0.430 pl5321ha5712d3_1 bioconda perl-lwp-mediatypes 6.04 pl5321hdfd78af_1 bioconda perl-mime-base64 3.16 pl5321h775f41a_0 conda-forge perl-net-http 6.22 pl5321hdfd78af_0 bioconda perl-net-ssleay 1.92 pl5321h278ddf8_1 conda-forge perl-ntlm 1.09 pl5321hdfd78af_5 bioconda perl-parent 0.241 pl5321hd8ed1ab_0 conda-forge perl-pathtools 3.75 pl5321h775f41a_0 conda-forge perl-scalar-list-utils 1.63 pl5321h775f41a_0 conda-forge perl-socket 2.027 pl5321ha5712d3_3 bioconda perl-storable 3.15 pl5321h775f41a_0 conda-forge perl-sub-uplevel 0.2800 pl5321h775f41a_0 conda-forge perl-test-deep 1.130 pl5321hd8ed1ab_0 conda-forge perl-test-differences 0.70 pl5321h694c41f_0 conda-forge perl-test-exception 0.43 pl5321hd8ed1ab_0 conda-forge perl-test-fatal 0.016 pl5321h694c41f_0 conda-forge perl-test-most 0.38 pl5321hdfd78af_0 bioconda perl-test-warn 0.37 pl5321hd8ed1ab_0 conda-forge perl-test-warnings 0.031 pl5321h694c41f_0 conda-forge perl-text-diff 1.45 pl5321hd8ed1ab_0 conda-forge perl-time-local 1.35 pl5321hdfd78af_0 bioconda perl-timedate 2.33 pl5321hdfd78af_2 bioconda perl-tree-dag_node 1.32 pl5321hdfd78af_0 bioconda perl-try-tiny 0.31 pl5321h694c41f_0 conda-forge perl-types-serialiser 1.01 pl5321hdfd78af_0 bioconda perl-uri 5.17 pl5321h694c41f_0 conda-forge perl-url-encode 0.03 pl5321h527b516_0 bioconda perl-www-robotrules 6.02 pl5321hdfd78af_4 bioconda perl-xml-dom 1.46 pl5321hdfd78af_1 bioconda perl-xml-dom-xpath 0.14 pl5321hdfd78af_2 bioconda perl-xml-parser 2.44_01 pl5321h06ef574_1003 conda-forge perl-xml-regexp 0.04 pl5321hdfd78af_3 bioconda perl-xml-xpathengine 0.14 pl5321hdfd78af_3 bioconda pip 23.2.1 pyhd8ed1ab_0 conda-forge python 3.11.5 h30d4d87_0_cpython conda-forge readline 8.2 h9e318b2_1 conda-forge samclip 0.4.0 hdfd78af_1 bioconda samtools 1.17 h25dfcfb_1 bioconda seqtk 1.4 h45fc8d7_1 bioconda setuptools 68.2.2 pyhd8ed1ab_0 conda-forge snippy 4.6.0 hdfd78af_3 bioconda snp-sites 2.5.1 h45fc8d7_4 bioconda snpeff 5.0 hdfd78af_1 bioconda t-coffee 12.00.7fb08c2 h26a2512_0 bioconda tabixpp 1.1.2 hdc9e95e_1 bioconda tk 8.6.12 h5dbffcc_0 conda-forge tzdata 2023c h71feb2d_0 conda-forge vcflib 1.0.2 h819f6dc_6 bioconda viennarna 2.4.7 h470a237_4 bioconda vt 0.57721 hfd6c91b_9 bioconda wget 1.20.3 hd3787cc_1 conda-forge wheel 0.41.2 pyhd8ed1ab_0 conda-forge xz 5.2.6 h775f41a_0 conda-forge zlib 1.2.13 h8a1eda9_5 conda-forge zstd 1.5.5 h829000d_0 conda-forge

Conda output snps.log

dyld[14593]: Library not loaded: @rpath/libtabixpp.0.dylib Referenced from: <CC39E3FB-E880-3379-9A2C-B8EF798A32A3> /Users/hughgifford/miniconda3/envs/snippy/bin/vcfuniq Reason: tried: '/Users/hughgifford/miniconda3/envs/snippy/bin/../lib/libtabixpp.0.dylib' (no such file), '/Users/hughgifford/miniconda3/envs/snippy/bin/../lib/libtabixpp.0.dylib' (no such file), '/usr/local/lib/libtabixpp.0.dylib' (no such file), '/usr/lib/libtabixpp.0.dylib' (no such file, not in dyld cache) dyld[14591]: Library not loaded: @rpath/libtabixpp.0.dylib Referenced from: <020BDE82-37AD-3A5B-A97B-B1AC787C020D> /Users/hughgifford/miniconda3/envs/snippy/bin/vcfstreamsort Reason: tried: '/Users/hughgifford/miniconda3/envs/snippy/bin/../lib/libtabixpp.0.dylib' (no such file), '/Users/hughgifford/miniconda3/envs/snippy/bin/../lib/libtabixpp.0.dylib' (no such file), '/usr/local/lib/libtabixpp.0.dylib' (no such file), '/usr/lib/libtabixpp.0.dylib' (no such file, not in dyld cache) Traceback (most recent call last): File "/Users/hughgifford/miniconda3/envs/snippy/bin/vcffirstheader", line 17, in print(line.strip()) BrokenPipeError: [Errno 32] Broken pipe Exception ignored in: <_io.TextIOWrapper name='' mode='w' encoding='utf-8'> BrokenPipeError: [Errno 32] Broken pipe /Users/hughgifford/miniconda3/envs/snippy/bin/freebayes-parallel: line 39: 14589 Exit 141 ( cat "$regionsfile" | parallel -k -j "$ncpus" "${command[@]}" --region {} ) 14590 Exit 120 | vcffirstheader 14591 Abort trap: 6 | vcfstreamsort -w 1000 14593 Abort trap: 6 | vcfuniq

Brew install snps.log

dyld[10799]: Library not loaded: @rpath/libcrypto.1.1.dylib Referenced from: <EF7BDB2C-8AE7-3333-A9DA-7076233B266D> /Users/hughgifford/miniconda3/bin/vt Reason: tried: '/Users/hughgifford/miniconda3/bin/../lib/libcrypto.1.1.dylib' (no such file), '/Users/hughgifford/miniconda3/bin/../lib/libcrypto.1.1.dylib' (no such file), '/usr/local/lib/libcrypto.1.1.dylib' (no such file), '/usr/lib/libcrypto.1.1.dylib' (no such file, not in dyld cache)

In this case, I was able to find this file (/Users/hughgifford/miniconda3/pkgs/openssl-1.1.1w-h8a1eda9_0/lib/libcrypto.1.1.dylib) and created a sym link in /usr/lib/. However, the number of bases called was extremely low (well under 1 % of reference genome) compared to other callers.

Plea

I would like to get this working in conda so that it can be implemented across an hpc cluster - please would you advise as to how to get a reliable install of snippy working without these build issues? Thank you again.

I note a similar build issue at

• https://github.com/tseemann/snippy/issues/528
• https://github.com/tseemann/snippy/issues/413 And a similar fault at
• https://github.com/tseemann/snippy/issues/494