No clear tutorial for the installation and using command line

[B-1991-ing]

Dear tRNAscan-SE development team,

I downloaded the "trnascan-se-2.0.12.tar" from the web link --- "http://trna.ucsc.edu/tRNAscan-SE/", but not sure how to install on my linux directory correctly and how to use it through linux command line ?

Could you give me a hint?

Thank you very much.

Best,

Bing

[patriciaplchan]

Please read the INSTALL file in the downloaded tRNAscan-SE on how to install the software.

The following paper provides information on how to use the software. Chan, P.P. and Lowe, T. M. (2019) tRNAscan-SE: Searching for tRNA Genes in Genomic Sequences. Methods Mol Biol. 1962:1-14.

[B-1991-ing]

Thank you very much for your suggestion.

The HPC admin installed it publicly on our HPC platform through tar -xvf tRNAscan-SE-2.0.12.tar.gz ./configure # make && make install

Then, I ran the following command line on 330 prokaryotic genomes. tRNAscan-SE final.fa -o final.out -f final.ss -s final.iso -m final.stats -b final.bed -c tRNAscan-SE.conf

But, how long would it take to finish the scanning on 330 assembled genomes normally?

[patriciaplchan]

The required time will depend on the speed of your computing system and the number of processing cores used for the run. It took our lab's system less 1 minute to scan a prokaryotic genome. Table 3 in our paper below provides the benchmark.

Chan, P.P., Lin, B.Y., Mak, A.J., and Lowe, T.M. (2021) tRNAscan-SE 2.0: Improved Detection and Functional Classification of Transfer RNA Genes. Nucl. Acids Res. 49:9077–9096.

[B-1991-ing]

I ran on the thinnode as below, qsub -W group_list=env_10000 -A env_10000 -l nodes=1:ppn=32:thinnode,walltime=240:00:00 MAGtRNA.sh Already 330 minutes passed with 32 HPC cores, 192 GB memory consuming. My genome size is around 1-5 MB.

[patriciaplchan]

As every computing system including hardcore and software configuration is different, I would not be able to provide any estimation of the run time on the system you are using. I can only provide reference to the systems in our lab. If you are interested in obtaining run time estimation of your computing environment, I would suggest that you contact your local support staff and provide the benchmark in our paper as reference.

[B-1991-ing]

Okay, thank you very much. If it runs more than one week, I will email our HPC admin.

[B-1991-ing]

Running the command line below gave me one error

Command line /services/tools/trnascan-se/2.0.12/bin/tRNAscan-SE final.fa -o final.out -f final.ss -s final.iso -m final.stats -c /services/tools/trnascan-se/2.0.12/bin/tRNAscan-SE.conf

Error FATAL: Unable to find /services/tools/trnascan-se/2.0.12/bin/cmsearch executable

What does it mean?

[patriciaplchan]

As stated in the INSTALL file of the tRNAscan-SE package and the first publication I mentioned before, Infernal is a required dependency and has to be installed in the same directory as tRNAscan-SE. Please read the documentation.

[B-1991-ing]

But the tRNAscan-SE and Infernal were already installed under two different directories by the HPC admin.

[patriciaplchan]

As mentioned above, Infernal has to be installed in the SAME directory as tRNAscan-SE. If it is in a different directory, you will need to update the file path for the value of "infernal_dir" in tRNAscan-SE.conf.

[B-1991-ing]

I can't update the tRNAscan-SE.conf myself. Can I specify the value of "infernal_dir" in the command line?

[patriciaplchan]

No. You will have to update tRNAscan-SE.conf or reinstall infernal in the SAME directory as tRNAscan-SE.

[darked89]

One can also install tRNAscan-SE with included infernal using conda: https://anaconda.org/bioconda/trnascan-se

[B-1991-ing]

Thank you for your reply.

The HPC admin installed the cmsearch under the directory --- /services/tools/trnascan-se/2.0.12/bin/ finally.