fail to run set up

[xushaoyi]

dear author, I used install manual in this website (https://zenodo.org/record/3697265#.XykIRigzbic) and create the backblast env by conda. but when I want to use backblast setup command, it was failed. and the error was as follows:

I don't know how to solve it, so maybe do you have any suggestions? thanks !

[jmtsuji]

Hello @xushaoyi ,

Thanks for your interest in BackBLAST. Version 2 is still under development and is not yet stable or fully documented, but I'm happy to hear that you'd like to give it a try.

I think the easiest first course of action is to see if you can get the built-in test data to run successfully. Would you mind giving that a try? Here is how:

1. Go to the backblast install folder (e.g., cd /public/home/luhuijie/lib/miniconda2/share/BackBLAST)
2. Run the test code as mentioned on the README:

   mkdir -p testing/outputs
   # Make sure your backblast conda env is activated before you run the test
   backblast run testing/inputs/config.yaml testing/outputs --notemp

3. See if the output file looks as expected

   cmp testing/outputs/blast/combine_blast_tables/blast_tables_combined.csv \
   testing/outputs_expected/blast/combine_blast_tables/blast_tables_combined.csv
   # You will get an error message if the two files do not perfectly match

4. Clean up the test if everything looks good: rm -r testing/outputs

Let me know if this works, or if it fails, then send me a screenshot, and we can troubleshoot from there. Thanks.

[xushaoyi]

Hello @xushaoyi ,

Thanks for your interest in BackBLAST. Version 2 is still under development and is not yet stable or fully documented, but I'm happy to hear that you'd like to give it a try.

I think the easiest first course of action is to see if you can get the built-in test data to run successfully. Would you mind giving that a try? Here is how:

1. Go to the backblast install folder (e.g., `cd /public/home/luhuijie/lib/miniconda2/share/BackBLAST`)

2. Run the test code as mentioned on the README:

mkdir -p testing/outputs
# Make sure your backblast conda env is activated before you run the test
backblast run testing/inputs/config.yaml testing/outputs --notemp

1. See if the output file looks as expected

cmp testing/outputs/blast/combine_blast_tables/blast_tables_combined.csv \
  testing/outputs_expected/blast/combine_blast_tables/blast_tables_combined.csv
# You will get an error message if the two files do not perfectly match

1. Clean up the test if everything looks good: `rm -r testing/outputs`

Let me know if this works, or if it fails, then send me a screenshot, and we can troubleshoot from there. Thanks.

thanks for your reply！ I tried what you suggessted, and at 2nd step, it was failed. the detail was as follows：

[jmtsuji]

Hi @xushaoyi ,

This is really helpful -- thanks. It looks like your BackBLAST install folder is not being recognized properly. Can you confirm if realpath is installed on your system? Try typing realpath . in command line and see if it gives you the name of your present directory.

Thanks!

[xushaoyi]

Hi @xushaoyi ,

This is really helpful -- thanks. It looks like your BackBLAST install folder is not being recognized properly. Can you confirm if realpath is installed on your system? Try typing realpath . in command line and see if it gives you the name of your present directory.

Thanks!

oh,it seems it was not installed, since the output is:"-bash: realpath: command not found". so, how can install it? thanks very much!

[jmtsuji]

@xushaoyi What type of linux system are you running? For example, are you using debian? Also, are you using a HPC cluster or on an individual server? I had not realized that realpath was not included in some base linux installations, but it appears that is the case.

For now, try running readlink -f . in your command line. Does that work? It looks like readlink might be a more common built-in shell function than realpath, based on some reading. If that works, I will update the code base to rely on readlink instead of realpath.

[jmtsuji]

P.S. Otherwise, you can just install realpath through your Linux distro's installation manager, e.g., apt

[xushaoyi]

@xushaoyi What type of linux system are you running? For example, are you using debian? Also, are you using a HPC cluster or on an individual server? I had not realized that realpath was not included in some base linux installations, but it appears that is the case.

For now, try running readlink -f . in your command line. Does that work? It looks like readlink might be a more common built-in shell function than realpath, based on some reading. If that works, I will update the code base to rely on readlink instead of realpath.

hi,readlink seems work,so would you mind update the code? thanks so much !

[jmtsuji]

@xushaoyi Thanks for your prompt response. I did some more background reading and found that readlink is not a good cross-platform solution either -- the issue is a bit more complex than initially thought. I'll keep looking into this and hope to have a solution for you tomorrow (Thursday in Canada). Sorry for the delay.

Until then, I'd recommend trying to install realpath on your system if you want to use the tool.

[xushaoyi]

@xushaoyi Thanks for your prompt response. I did some more background reading and found that readlink is not a good cross-platform solution either -- the issue is a bit more complex than initially thought. I'll keep looking into this and hope to have a solution for you tomorrow (Thursday in Canada). Sorry for the delay.

Until then, I'd recommend trying to install realpath on your system if you want to use the tool.

dear author, finally I was successfully installed, and the test finished, details as follows:

but when I run my data, something again seems wrong, it was so sad... can you help me ? thansk so much!

[jmtsuji]

Hi @xushaoyi ,

My apologies for the delayed response -- other deadlines came up on this end that prevented me from getting to the code. I'm glad you found the -U and -T flags as manual workaround for locating the script path.

Are you using BackBLAST version 2.0.0-alpha3? There was an environment path issue in that version that caused issues with phylogenetic tree generation. The issue was corrected in version 2.0.0-alpha4 (https://github.com/LeeBergstrand/BackBLAST_Reciprocal_BLAST/releases)

You might need to update to the latest version to continue.

[xushaoyi]

Hi @xushaoyi ,

My apologies for the delayed response -- other deadlines came up on this end that prevented me from getting to the code. I'm glad you found the -U and -T flags as manual workaround for locating the script path.

Are you using BackBLAST version 2.0.0-alpha3? There was an environment path issue in that version that caused issues with phylogenetic tree generation. The issue was corrected in version 2.0.0-alpha4 (https://github.com/LeeBergstrand/BackBLAST_Reciprocal_BLAST/releases)

You might need to update to the latest version to continue.

ok.I will try, thanks! also, I have a non-technonical quetion, how can I get the faa file for the reference genome? it seems the data on NCBI was very limited. only few representive genomes were availble for that data.

[xushaoyi]

Hi @xushaoyi ,

My apologies for the delayed response -- other deadlines came up on this end that prevented me from getting to the code. I'm glad you found the -U and -T flags as manual workaround for locating the script path.

Are you using BackBLAST version 2.0.0-alpha3? There was an environment path issue in that version that caused issues with phylogenetic tree generation. The issue was corrected in version 2.0.0-alpha4 (https://github.com/LeeBergstrand/BackBLAST_Reciprocal_BLAST/releases)

You might need to update to the latest version to continue.

hi，sorry to disturb you again, I updated the software as you suggested, but when I run the code, something still wrong...so sad.. here is the details:

[jmtsuji]

Hi @xushaoyi ,

It looks like the script is failing with a cryptic error message when loading the phylogenetic tree. Based on the log, it must be failing when running the ape::read.tree() function.

I assume this must be due to an issue with the conda environment.

From Bash, can you activate your backblast conda environment and then run conda list ? Could you please then paste the output of conda list into this Github issue so I can check your software versions?

Based on the log, you are going to run into a second error later because of not having realpath on your system. The gene_metadata.tsv and genome_metdata.tsv files are currently relative paths that are not accurate based on the fact that the script is running from within the backblast output directory. Can you please edit your config.yaml file to provide the absolute system path to your gene_metadata.tsv and genome_metadata.tsv files before proceeding?

Sorry you've had issues with the code so far, but I'm happy to see that you are close to getting it to work end-to-end. Only one step left to go.

[xushaoyi]

Hi @xushaoyi ,

It looks like the script is failing with a cryptic error message when loading the phylogenetic tree. Based on the log, it must be failing when running the ape::read.tree() function.

I assume this must be due to an issue with the conda environment.

From Bash, can you activate your backblast conda environment and then run conda list ? Could you please then paste the output of conda list into this Github issue so I can check your software versions?

Based on the log, you are going to run into a second error later because of not having realpath on your system. The gene_metadata.tsv and genome_metdata.tsv files are currently relative paths that are not accurate based on the fact that the script is running from within the backblast output directory. Can you please edit your config.yaml file to provide the absolute system path to your gene_metadata.tsv and genome_metadata.tsv files before proceeding?

Sorry you've had issues with the code so far, but I'm happy to see that you are close to getting it to work end-to-end. Only one step left to go.

sorry to reply you late, here is the details of conda list: for the second question, I have changed the path to the absolute system path, but the error seems still occur. please help me, thanks sooo much!

Name Version Build Channel

_libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 1_llvm conda-forge _r-mutex 1.0.1 anacondar_1 conda-forge aioeasywebdav 2.4.0 py37_1000 conda-forge aiohttp 3.6.2 py37h516909a_0 conda-forge appdirs 1.4.3 py_1 conda-forge async-timeout 3.0.1 py_1000 conda-forge attrs 19.3.0 py_0 conda-forge bcrypt 3.1.7 py37h8f50634_1 conda-forge binutils_impl_linux-64 2.34 h53a641e_7 conda-forge binutils_linux-64 2.34 hc952b39_20 conda-forge bioconductor-ggtree 1.14.4 r351_0 bioconda bioconductor-treeio 1.6.1 r351_0 bioconda biopython 1.74 py37h516909a_0 conda-forge blas 2.17 openblas conda-forge blast 2.9.0 pl526h3066fca_4 bioconda boto3 1.14.39 pyh9f0ad1d_0 conda-forge botocore 1.17.39 pyh9f0ad1d_0 conda-forge brotlipy 0.7.0 py37h8f50634_1000 conda-forge bwidget 1.9.14 0 conda-forge bzip2 1.0.8 h516909a_2 conda-forge c-ares 1.16.1 h516909a_0 conda-forge ca-certificates 2020.6.20 hecda079_0 conda-forge cachetools 4.1.1 py_0 conda-forge cairo 1.16.0 h18b612c_1001 conda-forge certifi 2020.6.20 py37hc8dfbb8_0 conda-forge cffi 1.14.1 py37h2b28604_0 conda-forge chardet 3.0.4 py37hc8dfbb8_1006 conda-forge configargparse 1.2.3 pyh9f0ad1d_0 conda-forge cryptography 3.0 py37hb09aad4_0 conda-forge curl 7.68.0 hf8cf82a_0 conda-forge datrie 0.8.2 py37h8f50634_0 conda-forge decorator 4.4.2 py_0 conda-forge docutils 0.15.2 py37_0 conda-forge dropbox 10.1.1 pyh9f0ad1d_0 conda-forge entrez-direct 13.3 pl526h375a9b1_0 bioconda expat 2.2.9 he1b5a44_2 conda-forge ffmpeg 4.3.1 h167e202_0 conda-forge fftw 3.3.8 mpi_mpich_h3f9e1be_1011 conda-forge filechunkio 1.8 py_2 conda-forge fontconfig 2.13.1 he4413a7_1000 conda-forge freetype 2.10.2 he06d7ca_0 conda-forge ftputil 4.0.0 py_0 conda-forge gcc_impl_linux-64 7.5.0 hd420e75_6 conda-forge gcc_linux-64 7.5.0 h09487f9_20 conda-forge gdk-pixbuf 2.36.12 h3f25603_1005 conda-forge gettext 0.19.8.1 hc5be6a0_1002 conda-forge gfortran_impl_linux-64 7.5.0 hdf63c60_6 conda-forge gfortran_linux-64 7.5.0 h09487f9_20 conda-forge ghostscript 9.22 hf484d3e_1001 conda-forge giflib 5.1.7 h516909a_1 conda-forge gitdb 4.0.5 py_0 conda-forge gitpython 3.1.7 py_0 conda-forge glib 2.65.0 h6f030ca_0 conda-forge gmp 6.2.0 he1b5a44_2 conda-forge gnutls 3.6.13 h79a8f9a_0 conda-forge gobject-introspection 1.64.1 py37h619baee_1 conda-forge google-api-core 1.22.0 py37hc8dfbb8_1 conda-forge google-auth 1.20.1 py_0 conda-forge google-cloud-core 1.4.1 pyh9f0ad1d_0 conda-forge google-cloud-storage 1.30.0 pyh9f0ad1d_0 conda-forge google-crc32c 1.0.0 py37h193935f_0 conda-forge google-resumable-media 0.7.0 pyh9f0ad1d_0 conda-forge googleapis-common-protos 1.51.0 py37hc8dfbb8_2 conda-forge graphite2 1.3.13 he1b5a44_1001 conda-forge graphviz 2.38.0 hf68f40c_1011 conda-forge grpcio 1.31.0 py37hb0870dc_0 conda-forge gsl 2.5 h294904e_1 conda-forge gxx_impl_linux-64 7.5.0 hdf63c60_6 conda-forge gxx_linux-64 7.5.0 h09487f9_20 conda-forge harfbuzz 2.4.0 h37c48d4_1 conda-forge icu 58.2 hf484d3e_1000 conda-forge idna 2.10 pyh9f0ad1d_0 conda-forge imagemagick 7.0.8_54 pl526h39023e4_0 conda-forge importlib-metadata 1.7.0 py37hc8dfbb8_0 conda-forge importlib_metadata 1.7.0 0 conda-forge jbig 2.1 h516909a_2002 conda-forge jinja2 2.11.2 pyh9f0ad1d_0 conda-forge jmespath 0.10.0 pyh9f0ad1d_0 conda-forge jpeg 9d h516909a_0 conda-forge jsonschema 3.2.0 py37hc8dfbb8_1 conda-forge krb5 1.16.4 h2fd8d38_0 conda-forge lame 3.100 h14c3975_1001 conda-forge ld_impl_linux-64 2.34 h53a641e_7 conda-forge libblas 3.8.0 17_openblas conda-forge libcblas 3.8.0 17_openblas conda-forge libcrc32c 1.1.1 he1b5a44_2 conda-forge libcroco 0.6.13 h8d621e5_0 conda-forge libcurl 7.68.0 hda55be3_0 conda-forge libedit 3.1.20191231 h46ee950_1 conda-forge libffi 3.2.1 he1b5a44_1007 conda-forge libgcc-ng 9.3.0 h24d8f2e_14 conda-forge libgfortran-ng 7.5.0 hdf63c60_14 conda-forge libgomp 9.3.0 h24d8f2e_14 conda-forge libiconv 1.15 h516909a_1006 conda-forge liblapack 3.8.0 17_openblas conda-forge liblapacke 3.8.0 17_openblas conda-forge libopenblas 0.3.10 pthreads_hb3c22a3_4 conda-forge libpng 1.6.37 hed695b0_1 conda-forge libprotobuf 3.12.4 h8b12597_0 conda-forge librsvg 2.44.14 h11c8777_0 conda-forge libssh2 1.9.0 hab1572f_5 conda-forge libstdcxx-ng 9.3.0 hdf63c60_14 conda-forge libtiff 4.1.0 hc3755c2_3 conda-forge libtool 2.4.6 h516909a_1003 conda-forge libuuid 2.32.1 h14c3975_1000 conda-forge libwebp 1.0.2 hf4e8a37_4 conda-forge libxcb 1.13 h14c3975_1002 conda-forge libxml2 2.9.9 h13577e0_2 conda-forge llvm-openmp 10.0.1 hc9558a2_0 conda-forge lz4-c 1.9.2 he1b5a44_1 conda-forge make 4.3 h516909a_0 conda-forge markupsafe 1.1.1 py37h8f50634_1 conda-forge mpi 1.0 mpich conda-forge mpich 3.3.2 hc856adb_0 conda-forge multidict 4.7.5 py37h8f50634_1 conda-forge ncurses 6.2 he1b5a44_1 conda-forge nettle 3.4.1 h1bed415_1002 conda-forge networkx 2.4 py_1 conda-forge numpy 1.17.0 py37h99e49ec_0 r numpy-base 1.17.0 py37h2f8d375_0 r openh264 2.1.1 h8b12597_0 conda-forge openjpeg 2.3.1 h981e76c_3 conda-forge openssl 1.1.1g h516909a_1 conda-forge pandas 1.1.0 py37h3340039_0 conda-forge pango 1.40.14 he7ab937_1005 conda-forge paramiko 2.7.1 pyh9f0ad1d_1 conda-forge pcre 8.44 he1b5a44_0 conda-forge perl 5.26.2 h516909a_1006 conda-forge perl-app-cpanminus 1.7044 pl526_1 bioconda perl-archive-tar 2.32 pl526_0 bioconda perl-base 2.23 pl526_1 bioconda perl-business-isbn 3.004 pl526_0 bioconda perl-business-isbn-data 20140910.003 pl526_0 bioconda perl-carp 1.38 pl526_3 bioconda perl-common-sense 3.74 pl526_2 bioconda perl-compress-raw-bzip2 2.087 pl526he1b5a44_0 bioconda perl-compress-raw-zlib 2.087 pl526hc9558a2_0 bioconda perl-constant 1.33 pl526_1 bioconda perl-data-dumper 2.173 pl526_0 bioconda perl-digest-hmac 1.03 pl526_3 bioconda perl-digest-md5 2.55 pl526_0 bioconda perl-encode 2.88 pl526_1 bioconda perl-encode-locale 1.05 pl526_6 bioconda perl-exporter 5.72 pl526_1 bioconda perl-exporter-tiny 1.002001 pl526_0 bioconda perl-extutils-makemaker 7.36 pl526_1 bioconda perl-file-listing 6.04 pl526_1 bioconda perl-file-path 2.16 pl526_0 bioconda perl-file-temp 0.2304 pl526_2 bioconda perl-html-parser 3.72 pl526h6bb024c_5 bioconda perl-html-tagset 3.20 pl526_3 bioconda perl-html-tree 5.07 pl526_1 bioconda perl-http-cookies 6.04 pl526_0 bioconda perl-http-daemon 6.01 pl526_1 bioconda perl-http-date 6.02 pl526_3 bioconda perl-http-message 6.18 pl526_0 bioconda perl-http-negotiate 6.01 pl526_3 bioconda perl-io-compress 2.087 pl526he1b5a44_0 bioconda perl-io-html 1.001 pl526_2 bioconda perl-io-socket-ssl 2.066 pl526_0 bioconda perl-io-zlib 1.10 pl526_2 bioconda perl-json 4.02 pl526_0 bioconda perl-json-xs 2.34 pl526h6bb024c_3 bioconda perl-libwww-perl 6.39 pl526_0 bioconda perl-list-moreutils 0.428 pl526_1 bioconda perl-list-moreutils-xs 0.428 pl526_0 bioconda perl-lwp-mediatypes 6.04 pl526_0 bioconda perl-lwp-protocol-https 6.07 pl526_4 bioconda perl-mime-base64 3.15 pl526_1 bioconda perl-mozilla-ca 20180117 pl526_1 bioconda perl-net-http 6.19 pl526_0 bioconda perl-net-ssleay 1.88 pl526h90d6eec_0 bioconda perl-ntlm 1.09 pl526_4 bioconda perl-parent 0.236 pl526_1 bioconda perl-pathtools 3.75 pl526h14c3975_1 bioconda perl-scalar-list-utils 1.52 pl526h516909a_0 bioconda perl-socket 2.027 pl526_1 bioconda perl-storable 3.15 pl526h14c3975_0 bioconda perl-test-requiresinternet 0.05 pl526_0 bioconda perl-time-local 1.28 pl526_1 bioconda perl-try-tiny 0.30 pl526_1 bioconda perl-types-serialiser 1.0 pl526_2 bioconda perl-uri 1.76 pl526_0 bioconda perl-www-robotrules 6.02 pl526_3 bioconda perl-xml-namespacesupport 1.12 pl526_0 bioconda perl-xml-parser 2.44_01 pl526ha1d75be_1002 conda-forge perl-xml-sax 1.02 pl526_0 bioconda perl-xml-sax-base 1.09 pl526_0 bioconda perl-xml-sax-expat 0.51 pl526_3 bioconda perl-xml-simple 2.25 pl526_1 bioconda perl-xsloader 0.24 pl526_0 bioconda pip 20.2.1 py_0 conda-forge pixman 0.38.0 h516909a_1003 conda-forge pkg-config 0.29.2 h516909a_1006 conda-forge prettytable 0.7.2 py_3 conda-forge protobuf 3.12.4 py37h3340039_0 conda-forge psutil 5.7.2 py37h8f50634_0 conda-forge pthread-stubs 0.4 h14c3975_1001 conda-forge pyasn1 0.4.8 py_0 conda-forge pyasn1-modules 0.2.7 py_0 conda-forge pycparser 2.20 pyh9f0ad1d_2 conda-forge pygments 2.6.1 py_0 conda-forge pygraphviz 1.5 py37h8f50634_1002 conda-forge pynacl 1.3.0 py37h516909a_1001 conda-forge pyopenssl 19.1.0 py_1 conda-forge pyrsistent 0.16.0 py37h8f50634_0 conda-forge pysftp 0.2.9 py_1 conda-forge pysocks 1.7.1 py37hc8dfbb8_1 conda-forge python 3.7.8 h6f2ec95_1_cpython conda-forge python-dateutil 2.8.1 py_0 conda-forge python-irodsclient 0.8.2 py_0 conda-forge python_abi 3.7 1_cp37m conda-forge pytz 2020.1 pyh9f0ad1d_0 conda-forge pyyaml 5.3.1 py37h8f50634_0 conda-forge r 3.5.1 r351_0 r r-animation 2.6 r35h6115d3f_2 conda-forge r-ape 5.2 r351h29659fb_0 conda-forge r-argparser 0.4 r35_1001 conda-forge r-assertthat 0.2.0 r351h6115d3f_0 r r-backports 1.1.2 r351h96ca727_0 r r-base 3.5.1 h08e1455_1008 conda-forge r-bh 1.66.0_1 r351h6115d3f_0 r r-bindr 0.1.1 r351h6115d3f_0 r r-bindrcpp 0.2.2 r351h29659fb_0 r r-biocmanager 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[jmtsuji]

@xushaoyi Sorry for the delay, and thanks for sending these details! I'll take a look at this soon and will get back to you. -Jackson

[jmtsuji]

@xushaoyi I apologize for not being able to get back to you about BackBLAST yet -- I am busy preparing for my PhD defence next week, and debugging this issue could take some time. I hope to get back to you after my defence and revisions are complete.

[xushaoyi]

@xushaoyi I apologize for not being able to get back to you about BackBLAST yet -- I am busy preparing for my PhD defence next week, and debugging this issue could take some time. I hope to get back to you after my defence and revisions are complete.

thanks for your kind help! it's ok, do it when if it's convinent for you, I can do other analysis first! thanks again for your patience! Wish you all the best!

[jmtsuji]

Thanks, I appreciate it. :-)