-bash: indexdb_rna: command not found
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7 weeks ago
Dude • 0

I've been trying to go through RNA-seq upstream flow work in a Linux cluster. Miniconda has been installed, bin path has been added to the system path. But the command indexdb_rna still can not be found when using it to generate indexes.

ps: the command "sortmerna" is available. And inside the folder "miniconda/bin", sortmerna can be found, but not indexdb_rna.

I would appreciate it if someone could point out to me the solution to this problem. Thank you!! The following code trunks contain the related code that may be needed to identify and solve this problem.

wget https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -O ~/miniconda.sh
# Download the Miniconda3 installer to your home directory (Only for LINUX or Cluster)
wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O ~/miniconda.sh
# Run the miniconda installation
bash miniconda.sh -b -f -p ~/miniconda
# Add miniconda to the system path
echo 'PATH="$HOME/my student id/miniconda/bin:$PATH' >> ~/.bash_profile
# Source system file to activate miniconda
source ~/.bash_profile
# Add bioinformatic channels for downloading required packages
conda config --add channels conda-forge
conda config --add channels defaults
conda config --add channels r
conda config --add channels bioconda

conda install -c bioconda sortmerna --yes
# Download the sortmerna package (~2min) into sortmerna_db folder
wget -P sortmerna_db https://github.com/biocore/sortmerna/archive/2.1b.zip
# Decompress folder 
unzip sortmerna_db/2.1b.zip -d sortmerna_db
# Move the database into the correct folder
mv sortmerna_db/sortmerna-2.1b/rRNA_databases/ sortmerna_db/
# Remove unnecessary folders
rm sortmerna_db/2.1b.zip
rm -r sortmerna_db/sortmerna-2.1b
# Save the location of all the databases into one folder
sortmernaREF=sortmerna_db/rRNA_databases/silva-arc-16s-id95.fasta,sortmerna_db/index/silva-arc-16s-id95:\
sortmerna_db/rRNA_databases/silva-arc-23s-id98.fasta,sortmerna_db/index/silva-arc-23s-id98:\
sortmerna_db/rRNA_databases/silva-bac-16s-id90.fasta,sortmerna_db/index/silva-bac-16s-id95:\
sortmerna_db/rRNA_databases/silva-bac-23s-id98.fasta,sortmerna_db/index/silva-bac-23s-id98:\
sortmerna_db/rRNA_databases/silva-euk-18s-id95.fasta,sortmerna_db/index/silva-euk-18s-id95:\
sortmerna_db/rRNA_databases/silva-euk-28s-id98.fasta,sortmerna_db/index/silva-euk-28s-id98
# Run the indexing command (~8 minutes)
indexdb_rna --ref $sortmernaREF
sortmerna miniconda linux conda fasta • 184 views
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The indexdb_rna binary has been removed from version 4.0.

https://github.com/biocore/sortmerna/wiki/User-manual-v4.0#Usage

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uhhhh.... I see, thank you so much!!

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