Beginner help with ClustalW error: could not open sequence file

Question

[anstuteville]

Hi all,

Please forgive me if I don't ask my question with the correct terms/syntax/etc.; I am in an introduction to bioinformatics class so this is all still very new to me given that I've had no experience with computers in this way whatsoever (have never even opened a terminal until this class).

I am having issues with the ClustalW program. I am running version 1.82. I am using PuTTY on a Windows computer.

I keep getting the error:

ERROR: Could not open sequence file INFILE=1P30Sr.faaGbl

This is what I'm running (it's actually in a bash script, but I get the same error in the command line): clustalw INFILE=1P30Sr.faaGbl -bootstrap=1000 -output=tree-CLW_1P30Sr.faaGbl -tree

This file is in fasta format (conversion to phylip did not fix anyway). My script does not look any different than fellow classmates' but theirs works and mine does not.

Can anyone please help me figure out why this is happening? I realize this is very simple, basic bioinformatics, but search engines did not help me find a resolution. The help flag also does not work for me for ClustalW (gives same error "cannot open help file"). I have used ClustalW before for alignments instead of trees, and it worked just fine.

[GenoMax]

You are using PuTTY on windows but are connecting to a server where you are running this command? These types of issues are generally due to $PATH not being set correctly. You could try clustalw INFILE=./1P30Sr.faaGbl -bootstrap=1000 -output=tree-CLW_1P30Sr.faaGbl -tree assuming you are trying to run clustalw in the directory where that file exists. BTW: Is your input file actually called 1P30Sr.faaGbl? That seems like a strange name.

In unix clustalW is not the same as clustalw (see case difference for w/W). Make sure you are using the correct case for the program name.

[anstuteville]

Thank you so much for the quick response!

I am connecting to my university's HPC from my home laptop. I don't think it's an issue with my keys because I used ClustalW for alignments last week, and it didn't give me any problems. I double-checked and my file name is correct. When I send my script to the HPC, I get the same error as in the command line (when I run it in the command line I am running it in the same directory where 1P30Sr.faaGbl exists).

[Andrzej Zielezinski]

The error you get is because ClustalW can't find your input file 1P30Sr.faaGbl in your working/current directory. Make sure your file exists in this directory. Type the command ls to see a list of all files in your directory.

[anstuteville]

Thank you for responding so quickly! I'm not sure why it can't locate it because it is in my current/working directory.

Answer 1

[GenoMax]

It looks like you are missing a leading - before your INFILE option. Try the following:

clustalw -INFILE=1P30Sr.faaGbl -bootstrap=1000 -output=tree-CLW_1P30Sr.faaGbl -tree

[anstuteville]

Thank you! That and a missing key fixed my problems. Thank you again!

[lieven.sterck]

what do you mean with 'a missing key'? (just curious)

[anstuteville]

I didn't have the key in my .soft file to execute clustalw