Seqtk seq fastq to assembled.fa

[Gabriellavp]

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?

[shenwei356]

Please format your code and paste error message.

[Gabriellavp]

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 :(

[Gabriellavp]

Actually it generates the file ".assembled.fa" however with zero bytes

[shenwei356]

It should be seqtk seq -A not -a.

[Gabriellavp]

Sorry, but no change

[shenwei356]

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.

[hliang]

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.

[Gabriellavp]

Thank you very much

[lh3]

Thank you, @hliang and @shenwei356!