error when concantenating eggNog hmmer file

Question

[mwanerhi erfgtr]

I am trying to find orthologs between my 6000 functionally annotated protein sequences using the eggNOG database, http://eggnogdb.embl.de/#/app/seqscan, I have followed that step by step protocol but when I came to concatenating I got an error /bin/cat: Argument list too long. how can I concatenate these files before I run the analysis?

I am the super user so not denial

[Ram]

Th exact command (as you typed it in your terminal, not what's on a tutorial) would help.

Answer 1

[mwanerhi erfgtr]

The command i typed is cat bactNOG_hmm/*.hmm>bactDB.hmmer

Answer 2

[James Ashmore]

If you're listing files using ls and a wildcard statement then it's important to note that there is a limit to the number of arguments that can be supplied to a command. Instead use the commands find and xargs to find all the files you want and xargs to supply them to your command. For your specific example:

find bactNOG_hmm -name "*.hmm" | xargs cat > bactDB.hmmer

Also, I recommend you pick up a copy of Bioinformatics Data Skills by Vince Buffalo, this is where I learnt about find and xargs, lots of useful information.

[mwanerhi erfgtr]

I have tried your command, but it gives me an error permission denied, so i rerun the command as super user, but it still tells me bactNOG: is a directory,

what am i doing wrong?

Thanks for the book, i will get it

[James Ashmore]

Either try running the command in the directory above the bactNOG_hmm directory, or provide the full directory path in place of just bactNOG_hmm

[mwanerhi erfgtr]

Thanks , that seems to have worked. i am quite new to the ubuntu environment.

[mwanerhi erfgtr]

I have another problem, i have been trying figure oout for the whole eveining, i am trying to identify otholgs between four strains a,b,c,d, using thier protein sequences, i looked around internet and out of the so many options i went with proteinortho https://www.bioinf.uni-leipzig.de/Software/proteinortho/manual.html, i have done everything. but i when i try to run the .pl command, i get an error that its not there, but i can see it. i have tried using the full path but still nothing has happened. what do i seem to be doing wrong?

tx

[James Ashmore]

Can you show me which commands you used to run the perl script, and is the perl script in the same directory where you run the command?

[mwanerhi erfgtr]

so download the tar file, untar and in the folder containing the perl scripts i copy a folder - samuel containing the fasta files for analysis, which are a,b,c,d and c. so then in the same folder i call the script from the terminal with this command $ proteinortho5.pl -project= samuel/*.faa.

it returns an error : command not found

i tried writing the whole path but still not found. but even when i try using the tab on the key board to auto complete the proteinortho5.pl, it doesnt . so i am not sure what i am doing wrong

Thanks for trying to help me

[James Ashmore]

Okay, first you need to make sure you have permission to run the proteinortho5.pl file, you can set these using:

chmod u+x  proteinortho5.pl

After that try running the script using:

perl proteinortho5.pl

[mwanerhi erfgtr]

You are an absolute genius, it worked after so many times, requiring to change names

[mwanerhi erfgtr]

tx very much

[mwanerhi erfgtr]

Hi, so the process worked and it produced a graph, and a table called myproject.proteinortho. I want to to produce another file of orthologous proteins separated for each individual strain a,b,c, d. according to the manual I thought it could be grab_proteins.pl

So the command was perl grab_proteins.pl samuel/*.faa myproject.proteinortho

It gives me an error:

fasta2hash(): could not open file: .//L228plasmid.faa

but nothing has changed from the previous files used

What am I doing wrong here?

nb: manual command:

perl grab_proteins.pl [options] proteinortho_output_table
options: -path=path to protein files