ITSx ITS Extraction Software Error

Question

[Oliver K.]

Hello. I am using the software ITSx (https://microbiology.se/software/itsx/) in combination with HMMER (http://hmmer.org/) to extract the ITS1 region from my sequences. I am using Ubuntu 18.

When I input my sequence file, I receive the following ERROR message: ERROR: Sequence file ITSx_temp_directory__ITSx_out?main.1.fasta is empty or misformatted

How could I solve this problem? What does this mean? Anyone has ideas where to start looking?

I would be happy if you could use simple language because I am pretty new to Bioinformatics and dont understand much yet.

Greeting, Oliver

[GenoMax]

ERROR: Sequence file ITSx_temp_directory__ITSx_out?main.1.fasta is empty or misformatted

Is there a question mark in your file name? If so remove it by

mv ITSx_temp_directory__ITSx_out?main.1.fasta ITSx_temp_directory__ITSx_out_main.1.fasta

Then show us the output of

head -3 ITSx_temp_directory__ITSx_out_main.1.fasta

[Oliver K.]

Hello genomax Thank you for your answer. If I type the command you wrote:

ITSx_temp_directory__ITSx_out?main.1.fasta ITSx_temp_directory__ITSx_out_main.1.fasta

I receive the answer:

ITSx_temp_directory_ITSx_out?main.1.fasta: command not found

How can I find the file?

Could this problem be related to the attempt of creating a script? A friend tried to edit the software so that it would put the outputs into one folder but we didnt finished that. I typed:

touch_makingfolder.sh
#!/usr/bin/env_bash

and then i deleted these lines in the script again and closed it without saving.

So I have the questions: 1. How do I find the folder: ITS_temp_directory_ITS_out ? 2. Why is the command you send me not working? 3. Could the bash scripting be related to the problems arising?

Thanks, Oliver

[Dunois]

The command is "mv ITSx_temp_directory__ITSx_out?main.1.fasta ITSx_temp_directory__ITSx_out_main.1.fasta" (without the quotes). Is that what you typed? It appears you simply entered "ITSx_temp_directory__ITSx_out?main.1.fasta ITSx_temp_directory__ITSx_out_main.1.fasta", which wouldn't do anything.

[Oliver K.]

Yes, you are right. I didnt typed the mv in the beginning of the command. After typing: mv ITSx_temp_directory__ITSx_out?main.1.fasta ITSx_temp_directory__ITSx_out_main.1.fasta

The output is: mv: cannot stat 'ITSx_temp_directory__ITSx_out?main.1.fasta' : No such file or directory

Also when I type the second command: head -3 ITSx_temp_directory__ITSx_out_main.1.fasta

the output is: head: cannot open 'ITSx_temp_directory__ITSx_out_main.1.fasta' for reading: No such file or directory

Both results would mean, that I dont have an output directory at all?

[GenoMax]

If TSx_temp_directory__ITSx_out_main.1.fasta is a directory name then head command would not work. Based on first error it looks like you don't have a directory/file with that name at all.

[GenoMax]

Oliver K. : If you are new to command line then I suggest that you take the time to spend a day or two learning basics of unix. This would go a long way in making your analyses easier down the road. Here is a simple tutorial that I recommend.