ImportError: No module named tabulate

[jonatho...@icloud.com]

```

$ anvi-self-test --version

Anvi'o version ...............................: esther (v6.2-master)

Profile DB version ...........................: 35

Contigs DB version ...........................: 19

Pan DB version ...............................: 14

Genome data storage version ..................: 7

Auxiliary data storage version ...............: 2

Structure DB version .........................: 2

Kegg Modules DB version ......................: 2

tRNA-seq DB version ..........................: 1

```

Hello Anvi'o team, I tried to run a phylogenomics workflow and got the following error message when it gets to the script-reformat-fasta step (it happened for each input fasta):

```

$ anvi-run-workflow -w phylogenomics \

>                 -c phylo-configs.json \

>                 --additional-params \

>                     --cluster 'qsub -P 0718 -cwd -pe threaded 32 -V -j y -N anvio' \

>                     --jobs 20 \

>                     --resources nodes=40

...

...

Error in rule anvi_script_reformat_fasta_prefix_only:

    jobid: 254

    output: 01_FASTA/Candidatus_Saccharibacteria_bacterium_RAAC3_TM7_1/Candidatus_Saccharibacteria_bacterium_RAAC3_TM7_1-contigs-prefix-formatted-only.fa, 01_FASTA/Candidatus_Saccharibacteria_bacterium_RAAC3_TM7_1/Candidatus_Saccharibacteria_bacterium_RAAC3_TM7_1-reformat-report.txt

    log: 00_LOGS/Candidatus_Saccharibacteria_bacterium_RAAC3_TM7_1-anvi_script_reformat_fasta_prefix_only.log (check log file(s) for error message)

    shell:

        anvi-script-reformat-fasta ref-genomes/GCA_000503915.1_ASM50391v1_genomic.fa -o 01_FASTA/Candidatus_Saccharibacteria_bacterium_RAAC3_TM7_1/Candidatus_Saccharibacteria_bacterium_RAAC3_TM7_1-contigs-prefix-formatted-only.fa -r 01_FASTA/Candidatus_Saccharibacteria_bacterium_RAAC3_TM7_1/Candidatus_Saccharibacteria_bacterium_RAAC3_TM7_1-reformat-report.txt --prefix Candidatus_Saccharibacteria_bacterium_RAAC3_TM7_1   --simplify-names  >> 00_LOGS/Candidatus_Saccharibacteria_bacterium_RAAC3_TM7_1-anvi_script_reformat_fasta_prefix_only.log 2>&1

        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

    cluster_jobid: removed environment variable LD_LIBRARY_PATH from submit environment - it is considered a security issue

Error executing rule anvi_script_reformat_fasta_prefix_only on cluster (jobid: 254, external: removed environment variable LD_LIBRARY_PATH from submit environment - it is considered a security issue, jobscript: /local/ifs2_projdata/0718/projects/jon/meren-genomes/.snakemake/tmp.8lhtgsn5/snakejob.anvi_script_reformat_fasta_prefix_only.254.sh). For error details see the cluster log and the log files of the involved rule(s).

...

...

Shutting down, this might take some time.

Exiting because a job execution failed. Look above for error message

Complete log: /local/ifs2_projdata/0718/projects/jon/meren-genomes/.snakemake/log/2020-11-18T152901.513007.snakemake.log

$ cat 00_LOGS/Candidatus_Saccharibacteria_bacterium_RAAC3_TM7_1-anvi_script_reformat_fasta_prefix_only.log

Traceback (most recent call last):

  File "/usr/local/projdata/0718/projects/jon/conda_envs/github/anvio/sandbox/anvi-script-reformat-fasta", line 8, in <module>

    import anvio

  File "/usr/local/projdata/0718/projects/jon/conda_envs/github/anvio/anvio/__init__.py", line 13, in <module>

    from tabulate import tabulate

ImportError: No module named tabulate

```

So it looks like tabulate is missing, but when I try:

```

$ pip install tabulate

Requirement already satisfied: tabulate in /local/ifs2_projdata/0718/projects/jon/conda_envs/github/virtual-envs/anvio-master/lib/python3.6/site-packages (0.8.3)

WARNING: You are using pip version 20.0.2; however, version 20.2.4 is available.

You should consider upgrading via the '/local/ifs2_projdata/0718/projects/jon/conda_envs/github/virtual-envs/anvio-master/bin/python -m pip install --upgrade pip' command.

```

It looks like it's already there?

Thanks very much for your insight!  

Also, if you know how to highlight code syntax with the new Google Groups layout, please let me know...I just spent some time and a google search trying to figure out how, but no luck.

Very Best,

Jon

[A. Murat Eren]

Can you please run this in your anvi'o environment:

python -c "import tabulate"

Best,

--

A. Murat Eren (Meren) | he/him
http://merenlab.org :: twitter

--
Anvi'o Paper: https://peerj.com/articles/1319/
Project Page: http://merenlab.org/projects/anvio/
Code Repository: https://github.com/meren/anvio
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