fastx quality stats outputting .txt? files

Question

[iaagosch]

Hi!

My first post here, so, sorry for the bad formatting.

I had a bioinformatics subject a year ago and I'm getting into it again.

I'm having some trouble going through fastx quality stats. I got an example from the classes I had, and the command line, was simple, I just want to output .txt files, but the program is outputting .txt? files.

fastx_quality_stats -i A_PE_1.fq -o A_PE_1.txt

The files are coming out as A_PE_1.txt? instead of the intended.

I tried using the rename command without success.

Any help would be appreciated :)

[GenoMax]

Are you saying that the result files have a ? in the name or you are not sure if the output file is in text format?

You can look inside the file by doing less file.txt or cat file.txt.

[iaagosch]

yes. The results have a ? in the file extension.

The outputs are, for example file.txt? instead of file.txt

The files are ok, but with the ? I can't transfer the file to my computer (using FileZilla), and the .txt extensions work just fine to transfer.

[Friederike]

what if you rename the entry for -o when running the tool, e.g. fastx_quality_stats -i A_PE_1.fq -o test.txt? Did you type the command or did you copy and paste it from the class notes?

[iaagosch]

I adapted the script to the files that I have.

I have a lot of samples, so renaming them to something else would make everything super confusing.

[GenoMax]

Did you type the command or did you copy and paste it from the class notes?

Can you answer that question? It is possible that you are copying and pasting some unseen character which is resulting in that additional ? at end of file name. Have you tried to type the command out to see what happens.

[iaagosch]

Yes, I have typed the command manually. Still gives me the .txt? at the end.

[GenoMax]

That is very odd. What OS are you using?

I suggest that you switch to using seqkit stats (https://bioinf.shenwei.me/seqkit/usage/#stats ). Fastx toolkit is a bit outdated at this time anyway.

[iaagosch]

Using Ubuntu 16.04.6.

And I'll take a look at that ! Thanks :)

[Friederike]

does that only happen with that specific tool?

[iaagosch]

Yes, it only happened with FastX quality stats

Answer 1

[iaagosch]

I added ; to the end of every line and, apparently, fixed it. The scripts I had as examples did not have ;. Did that a couple days ago and forgot to post here.

Thanks for the help! :)

[Friederike]

geat that you found a solution! what made you think the addition of ; would fix it?

[iaagosch]

Going through books about Unix/Perl/Python, I noticed a lot of scripts had ; to end a command and start another one in the line below, so I thought I could give it a shot.

[GenoMax]

Just for the record while it worked it does not make logical sense. On a normal ubuntu machine that should not be required.

[Friederike]

I concur with genomax -- while semicolons are used as statement delimiters in perl, they are usually not required in the shell. Unless the code you executed at once involved more than the one line you've shared, it's difficult to fathom why your solution worked

[iaagosch]

I agree, it shouldn't need the semicolons at the end.

None of the examples I had on hand (PI's stuff/Colleagues scripts) had semicolons at the end of the code. They worked as planned when they were used, but when I adapted the scripts to my files, stuff just didn't work out.

The code is eight lines of fastx_quality_stats -i A_PE_1.fq -o A_PE_1.txt but with different inputs and outputs, because I have multiple files.