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: /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: /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

• Error running snippy  #528
• samtolls faidx #413
  And a similar fault at
• freebayes-parallel #494

[jbrizuelagabaldon]

vcflib 1.0.2 breaks snippy, try specifying version 1.0.1 or 1.0.0.

In issue #561 i left the recipe im using which currently works.

[Alejandro-PI]

your log says
"dyld[14593]: Library not loaded: @rpath/libtabixpp.0.dylib"

I noticed a similar error and found that libtabixpp.so.0 was missing. Installing libtabixxp.0 solved the problem.
sudo apt-get update
sudo apt-get install libtabixpp0

Hope this works.

Alejandro