ITSx ITS Extraction Software Error
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
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Is there a question mark in your file name? If so remove it by
Then show us the output of
Hello genomax Thank you for your answer. If I type the command you wrote:
I receive the answer:
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:
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
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.
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?
If
TSx_temp_directory__ITSx_out_main.1.fastais a directory name thenheadcommand would not work. Based on first error it looks like you don't have a directory/file with that name at all.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.