about antismash

[sunnycqcn]

Hello Jon, Could you add a command about antismash in local? I find the server of antismash is crashed if we submitted lots of data since the server is updating. I always have to wait for finishing one job more than one day in server. Best, Fuyou

[nextgenusfs]

There are conflicting dependencies so you can just install antiSMASH locally in a different conda environment. Look at their documentation for install instructions.

[sunnycqcn]

Thanks. I did it. Fuyou

发自我的 iPhone

在 2019年10月10日，下午9:25，Jon Palmer notifications@github.com 写道：

There are conflicting dependencies so you can just install antiSMASH locally in a different conda environment. Look at their documentation for install instructions.

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[sunnycqcn]

Hello Jon, If I run antiSMASH locally, what can the file name and format be accepted by funannotate annotate? Since I have about 200 isolates, it takes too long time to get the results from antiSMASH server. Thanks, Fuyou

[nextgenusfs]

I usually run it locally like this (note this is v4):

antismash --outputfolder antismash_output --cpus 24 \
    --smcogs --cassis --asf --knownclusterblast \
   --subclusterblast --taxon fungi funannotate.gbk

Then the output file you would give to funannotate annotate would be located in the antismash_output folder and it is named as the first scaffold/contig in the GBK file + '.final.gbk'

I found the reason why the remote antismash was failing, but it won't help you with that many genomes to run through, you should use a local installation.

[Rob-murphys]

Creating an new environment for antismash (following their conda install instructions) still creates many package conflicts for me:

 conda create -n antismash antismash
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: \
Found conflicts! Looking for incompatible packages.
This can take several minutes.  Press CTRL-C to abort.                                                                                                                                     failed

UnsatisfiableError: The following specifications were found to be incompatible with each other:

Package perl-pathtools conflicts for:
antismash -> perl-pathtools
Package perl conflicts for:
antismash -> perl=5.26
Package python conflicts for:
antismash -> python[version='2.7.*|>=2.7,<2.8.0a0']
Package scipy conflicts for:
antismash -> scipy
Package pandas conflicts for:
antismash -> pandas
Package icu conflicts for:
antismash -> icu[version='>=58.2,<59.0a0']
Package hmmer2 conflicts for:
antismash -> hmmer2
Package bcbiogff conflicts for:
antismash -> bcbiogff
Package scikit-learn conflicts for:
antismash -> scikit-learn[version='0.18.*|0.18.2']
Package openjdk conflicts for:
antismash -> openjdk
Package glimmer conflicts for:
antismash -> glimmer==3.02
Package bcbio-gff conflicts for:
antismash -> bcbio-gff
Package clustalw conflicts for:
antismash -> clustalw
Package matplotlib conflicts for:
antismash -> matplotlib
Package backports.lzma conflicts for:
antismash -> backports.lzma
Package argparse conflicts for:
antismash -> argparse
Package networkx conflicts for:
antismash -> networkx
Package fasttree conflicts for:
antismash -> fasttree[version='2.1.*|2.1.9']
Package hmmer conflicts for:
antismash -> hmmer==3.1b2
Package cssselect conflicts for:
antismash -> cssselect
Package mafft conflicts for:
antismash -> mafft
Package glimmerhmm conflicts for:
antismash -> glimmerhmm[version='3.0.*|3.0.4']
Package diamond conflicts for:
antismash -> diamond[version='0.8.*|0.8.36']
Package pyquery conflicts for:
antismash -> pyquery[version='1.2.*|1.2.9']
Package helperlibs conflicts for:
antismash -> helperlibs
Package biopython conflicts for:
antismash -> biopython[version='>=1.65']
Package meme conflicts for:
antismash -> meme==4.11.2
Package libxml2 conflicts for:
antismash -> libxml2[version='2.9.*|2.9.4']
Package pyexcelerator conflicts for:
antismash -> pyexcelerator
Package prodigal conflicts for:
antismash -> prodigal
Package blast conflicts for:
antismash -> blast[version='2.2.*|2.2.31']
Package muscle conflicts for:
antismash -> muscle
Package perl-bioperl conflicts for:
antismash -> perl-bioperl
Package xz conflicts for:
antismash -> xz[version='5.2.*|5.2.2']
Package pysvg conflicts for:
antismash -> pysvg
Package numpy conflicts for:
antismash -> numpy
Package ete2 conflicts for:
antismash -> ete2
Note that strict channel priority may have removed packages required for satisfiability.

Is there a fix for this?

[nextgenusfs]

Seems like a conda issue not related to funannotate. closing.