SEA-PHAGES | tRNAScan-SE Down-ish?

Link to this post \| posted 24 Sep, 2020 10:22
scaruso	Hello, Several students have reported to me that they are not getting results from tRNAScan-SE over the last week. So I just tried it, and let it run all night and had the same experience. It just stalled while working on a cluster BE, which has lots, and lots of tRNAs. Does anyone know something about tRNAScan-SE? Thanks, Steve

Link to this post \| posted 24 Sep, 2020 11:46
debbie	Hi Steve, This is likely due to the wild fires in California. It appears that folks can be back on campus, but if the Lowe lab can't get to their servers, tRNA-ScanSE is in jeopardy. debbie

Link to this post \| posted 24 Sep, 2020 12:02
scaruso	Thank you. I am going to advise they use Aragorn for now and revisit with tRNAScan-SE later in the semester, unless you suggest otherwise. Steve

Link to this post \| posted 24 Sep, 2020 20:02
cdshaffer	For those of you that have the SEAVM with pdm utils installed that came out in June 2020, it has version 2.0.5 of tRNA-scan already installed. It is the command line version, not the web page, but it is pretty straightforward to run. First copy the genome fasta file into the VM and put the file on the Desktop. Open a terminal and change the working directory to the Desktop with this command: `cd Desktop` Now use the following command (I tried to use the parameter settings that would mimic the settings recommended on the web interface). You will need to replace the items bounded by the <> with your specific values: `tRNAscan-SE -B -I –max -D -o <name of file with results> <name of fasta file>` Here is an example of the command I used recently on phage Jada where the fasta genome file is called Jada.fasta, and I wanted the results file to be called Jada.tRNAscan.txt. `tRNAscan-SE -B -I –max -D -o Jada.tRNAscan.txt Jada.fasta` the results will be a text file that you can copy back to your computer, it can be opened by textedit on a Mac or Wordpad on Windows. Here are the first few lines of the output for phage Jada: `Sequence tRNA Bounds tRNA Anti Intron Bounds Inf Name tRNA # Begin End Type Codon Begin End Score N ——– —— —– —— —- —– —– —- —— — Jada 1 65495 65565 Pro TGG 0 0 50.1 Jada 2 65734 65808 Pro TGG 0 0 72.6 Jada 3 66800 66873 Gln CTG 0 0 54.6 Jada 4 66926 66996 Trp CCA 0 0 26.0 Jada 5 67273 67347 Ile GAT 0 0 68.1 Jada 6 67752 67835 Ser TGA 0 0 42.0`

Link to this post | posted 24 Sep, 2020 20:02

cdshaffer

For those of you that have the SEAVM with pdm utils installed that came out in June 2020, it has version 2.0.5 of tRNA-scan already installed. It is the command line version, not the web page, but it is pretty straightforward to run.

First copy the genome fasta file into the VM and put the file on the Desktop. Open a terminal and change the working directory to the Desktop with this command:

cd Desktop

Now use the following command (I tried to use the parameter settings that would mimic the settings recommended on the web interface). You will need to replace the items bounded by the <> with your specific values:

tRNAscan-SE -B -I –max -D -o <name of file with results> <name of fasta file>

Here is an example of the command I used recently on phage Jada where the fasta genome file is called Jada.fasta, and I wanted the results file to be called Jada.tRNAscan.txt.

tRNAscan-SE -B -I –max -D -o Jada.tRNAscan.txt Jada.fasta

the results will be a text file that you can copy back to your computer, it can be opened by textedit on a Mac or Wordpad on Windows. Here are the first few lines of the output for phage Jada:

Sequence		tRNA  	Bounds	tRNA	Anti	Intron Bounds	Inf
Name    	tRNA #	Begin 	End   	Type	Codon	Begin	End	Score	N
——–	——	—– 	——	—-	—–	—–	—-	——	—
Jada    	1	65495 	65565 	Pro	TGG	0	0	50.1
Jada    	2	65734 	65808 	Pro	TGG	0	0	72.6
Jada    	3	66800 	66873 	Gln	CTG	0	0	54.6
Jada    	4	66926 	66996 	Trp	CCA	0	0	26.0
Jada    	5	67273 	67347 	Ile	GAT	0	0	68.1
Jada    	6	67752 	67835 	Ser	TGA	0	0	42.0

Link to this post \| posted 24 Sep, 2020 20:07
scaruso	Thank you, Chris. I will give that a try! Steve

Link to this post \| posted 25 Sep, 2020 00:24
scaruso	Chris, Excellent. And thank you for the very clear directions with sample. Worked perfectly. Steve

Link to this post \| posted 04 Feb, 2021 14:58
GregFrederick@letu.edu	It seems that the tRNA-Scan server listed in the Bioinformatics guide is currently broken. (http://trna.ucsc.edu/tRNAscan-SE/) We have been trying for several days to run the program on our four genomes and they all start and then the screen freezes and even if left overnight, they never finish. I can run the script above, but I would like for the students to be able to complete this exercise and have their personally generated files. Is there another tRNA-Scan-SE server available that I can direct them too? Other options they can use. Obviously, tRNA analysis can wait until later. But we have already introduced the concepts and students like to check boxes once they have have completed a task. Thanks. Greg

Link to this post | posted 04 Feb, 2021 14:58

GregFrederick@letu.edu

It seems that the tRNA-Scan server listed in the Bioinformatics guide is currently broken. (http://trna.ucsc.edu/tRNAscan-SE/) We have been trying for several days to run the program on our four genomes and they all start and then the screen freezes and even if left overnight, they never finish.

I can run the script above, but I would like for the students to be able to complete this exercise and have their personally generated files.

Is there another tRNA-Scan-SE server available that I can direct them too? Other options they can use. Obviously, tRNA analysis can wait until later. But we have already introduced the concepts and students like to check boxes once they have have completed a task.

Thanks. Greg

Link to this post \| posted 06 Feb, 2021 19:05
debbie	Hi all, The site is not broken. It just won't run in any timley fashion with the settings we have been using. We did some fiddling with our settings and have modified how to run tRNA Scan SE. Go to the Bioinformatics Guide to get them!

Link to this post \| posted 09 Feb, 2021 12:38
GregFrederick@letu.edu	Thanks Debbie. It has worked for some of our genomes this semester, with the previous settings. But the others start and then just sit there, even if left running for 24-36hrs. Thanks for troubleshooting. We will try to modified tRNA-Scan-SE settings. QUESTION: If the previous settings do run on a given genome, should we use the results obtained with those settings? Or should we rerun the analysis with the currently published settings? Thanks again for all your support! Greg

Link to this post | posted 09 Feb, 2021 12:38

GregFrederick@letu.edu

Thanks Debbie.

It has worked for some of our genomes this semester, with the previous settings. But the others start and then just sit there, even if left running for 24-36hrs.

Thanks for troubleshooting. We will try to modified tRNA-Scan-SE settings.

QUESTION: If the previous settings do run on a given genome, should we use the results obtained with those settings? Or should we rerun the analysis with the currently published settings? Thanks again for all your support! Greg

Link to this post \| posted 09 Feb, 2021 12:38
GregFrederick@letu.edu	Thanks Debbie. It has worked for some of our genomes this semester, with the previous settings. But the others start and then just sit there, even if left running for 24-36hrs. Thanks for troubleshooting. We will try to modified tRNA-Scan-SE settings. QUESTION: If the previous settings do run on a given genome, should we use the results obtained with those settings? Or should we rerun the analysis with the currently published settings? Thanks again for all your support! Greg

Link to this post | posted 09 Feb, 2021 12:38

GregFrederick@letu.edu

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tRNAScan-SE Down-ish?