error running shortbred-identify

[Daniel Barich]

Hello,

I'm trying to run shortbred_identify.  It runs for a while and then I get this error:

(python2) barichd@JOAN9000:~/mouse/shortbred$ shortbred_identify.py  --goi protein_fasta_protein_homolog_model.adjusted.fasta --ref ../uniref-filtered-identity_0.9.fasta.gz

...

00:00:00   21 MB(100%)  Iter   8  100.00%  Refine biparts

00:00:00   21 MB(100%)  Iter   9  100.00%  Refine biparts
Making BLAST database for the family consensus sequences...
Making BLAST database for the reference protein sequences...
Traceback (most recent call last):
  File "/home/barichd/miniconda3/envs/python2/bin/shortbred_identify.py", line 298, in <module>
    "-dbtype", "prot", "-logfile", dirTmp + os.sep +  "refdb.log"])
  File "/home/barichd/miniconda3/envs/python2/lib/python2.7/subprocess.py", line 190, in check_call    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['makeblastdb', '-in', '../uniref-filtered-identity_0.9.fasta.gz', '-out', 'tmp93601575385787556/refdb/refdb', '-dbtype', 'prot', '-logfile', 'tmp93601575385787556/refdb.log']' returned non-zero exit status 1

--

Daniel Barich

Barich Assistive Technology

Gambier, OH 43022

[Daniel Barich]

FYI, I did some digging and tried decompressing the markers file.  Shortbred-identifyruns fine now.

Daniel

[Eric Franzosa]

Hi Daniel,

Sorry for not catching this before the break. Glad you were able to work out the problem. You can direct future ShortBRED questions to the ShortBRED tag on our new help forum: https://forum.biobakery.org/ (we are consolidating all help there and deprecating the tool-specific Google Groups).

Thanks,

Eric

On Fri, Dec 20, 2019 at 9:45 PM Daniel Barich <bar...@kenyon.edu> wrote:

FYI, I did some digging and tried decompressing the markers file.  Shortbred-identifyruns fine now.

Daniel

On Tue, Dec 3, 2019 at 11:03 AM Daniel Barich <bar...@kenyon.edu> wrote:

--
You received this message because you are subscribed to the Google Groups "shortbred-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to shortbred-use...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/shortbred-users/CAE3pVRb95JE%3DNWne%2BfHUk_CMuMzAemxuOoFDUZbSymjrmQddGA%40mail.gmail.com.

[Joan Slonczewski]

Thanks, Eric.

However, I'm having trouble accessing the forum. When I go there, it just says "All categories" with an orange square. Then it freezes--nothing else appears.

We do have questions about the default settings. For instance, percent identity is set at 0.95.  Is there a reason for that particular cutoff?

Also the number of marker hits allowed, and the length of marker alignment. Is the basis of these dependent on conditions? Has it been tested somewhere?

Joan

Joan L. Slonczewski
Professor of Biology
Higley Hall, 202 N. College Road
Kenyon College
Gambier, OH 43022
http://biology.kenyon.edu/slonc/slonc.htm
slonc...@kenyon.edu
Phone: 740-427-5397

Text: 740-504-2215

To view this discussion on the web visit https://groups.google.com/d/msgid/shortbred-users/CAC%3DWeKos%3DQeePN5zB9jaTqkVB7gbOei9rcj%2BdYPtdCBMGnfyWg%40mail.gmail.com.

[Eric Franzosa]

Hi Joan,

Is it possible to include a screenshot of the error you're seeing with the forum? That's not something I've heard of before (but the system is new, so it could be something unexpected that we need to fix).

Jim Kaminski (original ShortBRED developer and first-author on the ShortBRED paper) did a bunch of parameter "sweeps" using synthetic data. The ShortBRED defaults are based on settings that provided a good balance of sensitivity and specificity in our test cases (spiking antibiotic resistance / virulence factors into gut metagenomes). I could provide guidance on performing similar optimizations for your application if you'd like to fine-tune the behavior?

The basic idea is to make synthetic reads from your proteins of interest (using a tool like ART) and then spike them into a metagenome where they aren't expected to occur. The spiking can be done at a range of intensities/abundances (including 0 as a negative control) and then you can pick parameter settings that most accurately reproduce the known spiked values. This is the process we're illustrating in Fig. 2 of the ShortBRED paper:

https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004557

Thanks,

Eric

On Thu, Jan 2, 2020 at 3:55 PM Joan Slonczewski <slonc...@kenyon.edu> wrote:

Thanks, Eric.

However, I'm having trouble accessing the forum. When I go there, it just says "All categories" with an orange square. Then it freezes--nothing else appears.

We do have questions about the default settings. For instance, percent identity is set at 0.95.  Is there a reason for that particular cutoff?

Also the number of marker hits allowed, and the length of marker alignment. Is the basis of these dependent on conditions? Has it been tested somewhere?

Joan

Joan L. Slonczewski
Professor of Biology
Higley Hall, 202 N. College Road
Kenyon College
Gambier, OH 43022
http://biology.kenyon.edu/slonc/slonc.htm
slonc...@kenyon.edu
Phone: 740-427-5397

Text: 740-504-2215

On Thu, Jan 2, 2020 at 3:47 PM Eric Franzosa <fran...@hsph.harvard.edu> wrote:

To view this discussion on the web visit https://groups.google.com/d/msgid/shortbred-users/CAC%3DWeKos%3DQeePN5zB9jaTqkVB7gbOei9rcj%2BdYPtdCBMGnfyWg%40mail.gmail.com.

--
You received this message because you are subscribed to the Google Groups "shortbred-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to shortbred-use...@googlegroups.com.

To view this discussion on the web visit https://groups.google.com/d/msgid/shortbred-users/CAAzKrdLtEd9VKfRiD5Y3jhZ61TQoFRMa3xLa3O%2Ba9MXGhg4Hgw%40mail.gmail.com.

[Joan Slonczewski]

Eric,

This is what the error page looked like.

However, that was in Edge browser. When I switched to Chrome, the correct page came up.

Thanks for your comments on optimization. We'll look into that.

Joan

[Joan Slonczewski]

Besides CARD (for drug resistance) what other databases do you find produce good markers for ShortBRED? Anything for mobile elements? Metabolic categories?

Joan L. Slonczewski (they/them/theirs)
Professor of Biology