Please help to import sequence.fasta file from NCBI

[langse62171]

Hello, first of all thank you for the MetONTIIME pipeline. The script "install.sh" ran without any error message. The import of SILVA_132 with "qiime tools import" also worked wll. If I run the script "Importing_database.sh" now, I get the following error message: # ./Import_database.sh /home/sysadmin/NCBI33175/sequence.fasta # Collecting package metadata (current_repodata.json): done Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source. Collecting package metadata (repodata.json): done Solving environment: done

Package Plan ##

environment location: /home/sysadmin/miniconda3/envs/entrez_qiime_env

added / updated specs:

• gcc
• python=2.7

The following NEW packages will be INSTALLED:

ca-certificates anaconda/linux-64::ca-certificates-2020.1.1-0 certifi anaconda/linux-64::certifi-2019.11.28-py27_0 cloog anaconda/linux-64::cloog-0.18.0-0 gcc anaconda/linux-64::gcc-4.8.5-7 gmp anaconda/linux-64::gmp-6.1.2-hb3b607b_0 isl anaconda/linux-64::isl-0.12.2-0 libedit anaconda/linux-64::libedit-3.1.20181209-hc058e9b_0 libffi anaconda/linux-64::libffi-3.2.1-h4deb6c0_3 libgcc-ng anaconda/linux-64::libgcc-ng-9.1.0-hdf63c60_0 libstdcxx-ng anaconda/linux-64::libstdcxx-ng-9.1.0-hdf63c60_0 mpc anaconda/linux-64::mpc-1.1.0-h10f8cd9_1 mpfr anaconda/linux-64::mpfr-4.0.1-hdf1c602_3 ncurses anaconda/linux-64::ncurses-6.2-he6710b0_0 openssl anaconda/linux-64::openssl-1.1.1-h7b6447c_0 pip anaconda/linux-64::pip-19.3.1-py27_0 python anaconda/linux-64::python-2.7.17-h9bab390_0 readline anaconda/linux-64::readline-7.0-h7b6447c_5 setuptools anaconda/linux-64::setuptools-44.0.0-py27_0 sqlite anaconda/linux-64::sqlite-3.31.1-h7b6447c_0 tk anaconda/linux-64::tk-8.6.8-hbc83047_0 wheel anaconda/linux-64::wheel-0.33.6-py27_0 zlib anaconda/linux-64::zlib-1.2.11-h7b6447c_3

Proceed ([y]/n)? y

Preparing transaction: done Verifying transaction: done Executing transaction: done ERROR conda.core.link:_execute(700): An error occurred while installing package 'anaconda::gcc-4.8.5-7'. Rolling back transaction: done

LinkError: post-link script failed for package anaconda::gcc-4.8.5-7 location of failed script: /home/sysadmin/miniconda3/envs/entrez_qiime_env/bin/.gcc-post-link.sh ==> script messages <==

==> script output <== stdout: Installation failed: gcc is not able to compile a simple 'Hello, World' program. stderr: No LSB modules are available. /home/sysadmin/miniconda3/envs/entrez_qiime_env/bin/../libexec/gcc/x86_64-unknown-linux-gnu/4.8.5/cc1: error while loading shared libraries: libmpfr.so.4: cannot open shared object file: No such file or directory return code: 1 () Requirement already satisfied: numpy in /home/sysadmin/miniconda3/lib/python3.7/site-packages (1.18.2) Collecting cogent Using cached cogent-1.9.tar.gz (1.6 MB) ERROR: Command errored out with exit status 1: command: /home/sysadmin/miniconda3/bin/python -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-x3su186b/cogent/setup.py'"'"'; __file__='"'"'/tmp/pip-install-x3su186b/cogent/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-install-x3su186b/cogent/pip-egg-info cwd: /tmp/pip-install-x3su186b/cogent/ Complete output (6 lines): Traceback (most recent call last): File "", line 1, in File "/tmp/pip-install-x3su186b/cogent/setup.py", line 61 print "Failed to build html due to ImportErrors for sphinx" ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print("Failed to build html due to ImportErrors for sphinx")? ---------------------------------------- ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output. File "./entrez_qiime/entrez_qiime.py", line 192 print "Need to supply either FASTA file or accession number list as input." # should never get here because either -i or -L is a required argument. ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print("Need to supply either FASTA file or accession number list as input." # should never get here because either -i or -L is a required argument.)? Imported /home/sysadmin/NCBI33175/sequence.fasta as DNAFASTAFormat to /home/sysadmin/NCBI33175/sequence_sequence.qza Usage: qiime tools import [OPTIONS] Import data to create a new QIIME 2 Artifact. See https://docs.qiime2.org/ for usage examples and details on the file types and associated semantic types that can be imported. Options: --type TEXT The semantic type of the artifact that will be created upon importing. Use --show-importable-types to see what importable semantic types are available in the current deployment. [required] --input-path PATH Path to file or directory that should be imported. [required] --output-path ARTIFACT Path where output artifact should be written. [required] --input-format TEXT The format of the data to be imported. If not provided, data must be in the format expected by the semantic type provided via --type. --show-importable-types Show the semantic types that can be supplied to --type to import data into an artifact. --show-importable-formats Show formats that can be supplied to --input-format to import data into an artifact. --help Show this message and exit. There was a problem with the command: (1/1) Invalid value for "--input-path": Path "/home/sysadmin/NCBI33175/sequence_accession_taxonomy.txt" does not exist. sysadmin@BI:~/MetONTIIME$ # Even if I try to install gcc separately with "conda install gcc" I get the same error message: # Collecting package metadata (current_repodata.json): done Solving environment: done Package Plan ## environment location: /home/sysadmin/miniconda3 added / updated specs: - gcc The following packages will be downloaded: package | build ---------------------------|----------------- certifi-2019.11.28 | py37_1 156 KB anaconda conda-4.8.3 | py37_0 3.0 MB anaconda ------------------------------------------------------------ Total: 3.2 MB The following NEW packages will be INSTALLED: cloog anaconda/linux-64::cloog-0.18.0-0 gcc anaconda/linux-64::gcc-4.8.5-7 gmp anaconda/linux-64::gmp-6.1.2-hb3b607b_0 isl anaconda/linux-64::isl-0.12.2-0 mpc anaconda/linux-64::mpc-1.1.0-h10f8cd9_1 mpfr anaconda/linux-64::mpfr-4.0.1-hdf1c602_3 The following packages will be UPDATED: openssl pkgs/main::openssl-1.1.1f-h7b6447c_0 --> anaconda::openssl-1.1.1-h7b6447c_0 The following packages will be SUPERSEDED by a higher-priority channel: ca-certificates pkgs/main --> anaconda certifi pkgs/main --> anaconda conda pkgs/main --> anaconda Proceed ([y]/n)? y Downloading and Extracting Packages certifi-2019.11.28 | 156 KB | ############################### | 100% conda-4.8.3 | 3.0 MB | ############################### | 100% Preparing transaction: done Verifying transaction: done Executing transaction: done ERROR conda.core.link:_execute(700): An error occurred while installing package 'anaconda::gcc-4.8.5-7'. Rolling back transaction: done LinkError: post-link script failed for package anaconda::gcc-4.8.5-7 location of failed script: /home/sysadmin/miniconda3/bin/.gcc-post-link.sh ==> script messages <== ==> script output <== stdout: Installation failed: gcc is not able to compile a simple 'Hello, World' program. stderr: No LSB modules are available. /home/sysadmin/miniconda3/bin/../libexec/gcc/x86_64-unknown-linux-gnu/4.8.5/cc1: error while loading shared libraries: libmpfr.so.4: cannot open shared object file: No such file or directory return code: 1 () # when i run "conda env list" i get: # conda environments: base * /home/sysadmin/miniconda3 MetONTIIME_env /home/sysadmin/miniconda3/envs/MetONTIIME_env entrez_qiime_env /home/sysadmin/miniconda3/envs/entrez_qiime_env qiime2-2020.2 /home/sysadmin/miniconda3/envs/qiime2-2020.2 # When I searched the net for this I could not find anything, so I ask for help here. If you need further information please let me know.

[MaestSi]

Hi, I found a similar issue here. Apparently someone solved it by adding line allow_softlinks: False to .condarc file with something like: echo "allow_softlinks: False" | cat - /home/sysadmin/.condarc > /tmp/out && mv /tmp/out /home/sysadmin/.condarc. I tried to reproduce your issue removing entrez_qiime_env environment and repeating the installation from scratch. It installed exactly the same versions you listed, but it worked successfully, so I was not able to reproduce it. My guess is that you may have some environmental variables set that don't allow gcc to work correctly. First of all I would try this: open file Import_database.sh and replace gcc with gcc_linux-64. Then try rerunning the script and let me know. Simone

[langse62171]

Hi Simon. Thanks a lot for your quick response, the change in Import_database.sh to gcc_linux-64 worked. Setting up entrez_qiime_env and creating the files sequence_sequnze.qza and sequence_taxonomy.qza now worked without errors.

Now I have one more question. In the meantime I have run the pipeline with the enclosed test file "Test_BC04_xxx.zip" and the SILVA database. According to logfile.txt the pipeline is finished. All files in the folders "analysis, basecalling, preprocessing and qc" seem to have been created. Only the files taxa-bar-plots.qzv and taxa-bar-plots-no-Unassigned.qzv in the analysis folder are missing. Therefore I ask for help here, too. What could be the reason for this?

In the nohup.out file is several times deposited that no metadata file is present. I did not specify this file in the config_MinION_mobile_lab.R. Could that possibly be the reason?

Best regards, Sebastian

[MaestSi]

Yes, you must specify the path to a file. In the config_MinION_mobile_lab.R file you may set: SAMPLE_METADATA <- "/home/sysadmin/sample-metadata.tsv" Let me know if it works! Simone

[langse62171]

Hi and many thanks again! It works now after just adding a path :-) Best Sebastian

[MaestSi]

Good! I am going to close the issue. Feel free to open another one if you need any other clarifications. Best, Simone