Closed Gabriellavp closed 6 years ago
Please format your code and paste error message.
Hi Shenwei356, thanks for the reply
the command is: seqtk seq -a "$i"-trimmed.fastq > “$i".assembled.fa; and the "$i" means my samples (files) from 1 to 36.
No error message appears, but no new files are generated either.
I dont know what to do :(
Actually it generates the file ".assembled.fa" however with zero bytes
It should be seqtk seq -A
not -a
.
Sorry, but no change
Which version are your using?
And run seqtk seq -h
to print help message.
And try to test the command on one file.
Also, run ls -lh 1-trimmed.fastq
to check the input file.
Before the seqtk command, try using ls
to check if variables/files are valid:
for i in {1..36};
do
echo i = $i
ls -l "$i"-trimmed.fastq
seqtk seq -A "$i"-trimmed.fastq > "$i".assembled.fa;
done;
BTW, doesn't seem to be an issue of seqtk.
Thank you very much
Thank you, @hliang and @shenwei356!
Hello, I am trying to run the command: for i in {1..36};
do
seqtk seq -a "$i"-trimmed.fastq > “$i".assembled.fa;
done;
However it doesn't seems it is working. Does someone can help me with that?