New way to build a default candidate SSU database for EMIRGE

[Chris Miller]

The master branch on github has just been updated with a new method to download and build a default EMIRGE database. The new script presents the SILVA license and prompts you to accept it, then

1. downloads the most recent SSU database directly from SILVA,
2. filters it by sequence length
3. clusters at 97% sequence identity
4. replaces ambiguous bases with random characters, and
5. creates a bowtie index.

This is back-ported from something @epruesse wrote for EMIRGE2.

Try out this for more options:
python emirge_makedb.py --help

Let us know if there are any issues.
Chris

[edie...@gmail.com]

Just to clarify a bit, needs vsearch installed and python >= 2.7 at least to run. Tested on python 2.6.9 and did not run with syntax error.

Regards,

[gabi.fra...@gmail.com]

I am running the python emirge_makedb.py command and getting the following error after agreeing to the SILVA terms (see below).  Any insight of things I can try?  I'm running this in a python 2.7 environment, and all the listed dependencies on the github page.  Thank you!

Downloading https://ftp.arb-silva.de/release_128/Exports/SILVA_128_SSURef_Nr99_tax_silva_trunc.fasta.gz

Local filename is "./SILVA_128_SSURef_Nr99_tax_silva_trunc.fasta.gz"

Found existing file matching remote size. Skipping download.

Fetching https://ftp.arb-silva.de/release_128/Exports/SILVA_128_SSURef_Nr99_tax_silva_trunc.fasta.gz.md5

Computing MD5 checksum of SILVA_128_SSURef_Nr99_tax_silva_trunc.fasta.gz...

Verified MD5 sum for SILVA_128_SSURef_Nr99_tax_silva_trunc.fasta.gz

Running:  vsearch --threads 0 --minseqlength 1200 --maxseqlength 2000 --fasta_width 0 --notrunclabels --centroids SILVA_128_SSURef_Nr99_tax_silva_trunc.ge1200bp.le2000bp.0.97.fasta --cluster_fast SILVA_128_SSURef_Nr99_tax_silva_trunc.fasta.gz --id 0.97

Traceback (most recent call last):

  File "emirge_makedb.py", line 431, in <module>

    main()

  File "emirge_makedb.py", line 417, in main

    options.clusterid, options.threads)

  File "emirge_makedb.py", line 260, in cluster_fasta

    subprocess.call(cmd)

  File "/home/gabif/miniconda3/envs/emirge_env/lib/python2.7/subprocess.py", line 523, in call

    return Popen(*popenargs, **kwargs).wait()

  File "/home/gabif/miniconda3/envs/emirge_env/lib/python2.7/subprocess.py", line 711, in __init__

    errread, errwrite)

  File "/home/gabif/miniconda3/envs/emirge_env/lib/python2.7/subprocess.py", line 1343, in _execute_child

    raise child_exception

OSError: [Errno 2] No such file or directory

[jincheng...@gmail.com]

I am not the developer but I think your error is due to vsearch. Have you installed vsearch? You can test if you have installed vsearch or is your vsearch in your PATH? You can test by go to your home directory and type vsearch.