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Error when downloading database #88

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liangjinsong opened this issue Aug 16, 2019 · 1 comment
Closed

Error when downloading database #88

liangjinsong opened this issue Aug 16, 2019 · 1 comment

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@liangjinsong
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First I installed enrichM via conda following the steps below.
conda create -n enrichm_0.5.0 python=3
conda activate enrichm_0.5.0
conda install -c bioconda mcl R hmmer diamond prodigal parallel openmp mmseqs2 moreutils
conda install -c geronimp enrichm
R
install.packages('gridExtra')
install.packages('optparse')
q()

After the installation steps above, I downloaded the database using "enrichm data" command, then a error happened, which was showed below. Can you help to solve the problem? Thank you!

(enrichm_0.5.0) jinsong@server:/data/liangjinsong/N_update/single_group_assembly_bin/5_N_genes_usearch$ enrichm data
Traceback (most recent call last):
File "/data/software/miniconda3/envs/enrichm_0.5.0/bin/enrichm", line 357, in
r.main(args, sys.argv)
File "/data/software/miniconda3/envs/enrichm_0.5.0/lib/python3.7/site-packages/enrichm/run.py", line 283, in main
self._check_general(args)
File "/data/software/miniconda3/envs/enrichm_0.5.0/lib/python3.7/site-packages/enrichm/run.py", line 116, in _check_general
raise Exception('The following dependencies need to be installed to run enrichm:\n%s' % (dependency_string))
Exception: The following dependencies need to be installed to run enrichm:
seqmagick https://fhcrc.github.io/seqmagick

@liangjinsong
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Installing 'seqmagick' using 'conda install -c bioconda seqmagick' command fixed the error.

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