Closed climbandseq closed 6 years ago
The command seqtk seq -A file.fq.gz > out.fa
looks correct.
Maybe you file.fq.gz
is empty?
What does gzip -c -d file.fq.gz | head -n 4
say?
What version are you using?
seqtk 2>&1 | grep Version
Version: 1.2-r94
Thanks for the response! I am using Version: 1.0-r31. I am running it on Ubuntu in Windows 10 bash shell. I just installed all of that yesterday. I have a single fastq file on my Desktop called test.fq (but it says it is test.fq.gz in Properties). First, I ran this command: cd /mnt/c/Users/"sequencer PC"/Desktop Then I ran: seqtk seq -A test.fq.gz > out.fa That puts an empty file on my Desktop called out.fa. The test.fq.gz file has content, as I can open it in FastQC and see the quality etc. When I run gzip -c -d file.fq.gz | head -n 4 I get this message: "gzip: test.fq.gz: No such file or directory". Thanks for your help!!
Try committing the .gz ending.
On 3 May 2018 at 15:52:51, climbandseq (notifications@github.com) wrote:
.gz
Thanks guys! I think I figured it out, though. When I created the test.fq.gz file, I copied one of my fastq files out of another folder and renamed it to make it simple. This morning I tried the following commands to see if maybe renaming the file was a problem. I did the following: cd /mnt/c/Users/"sequencer PC"/Documents/Location/Run1/Fastq seqtk seq -A 2_S1_L001_R1_001.fastq.gz > out.fa And it worked! I got my fasta file with content. Not sure if renaming the file had something to do with that.
Is there a single command to convert every fastq file in that folder to fasta? For example, can I say:
seqtk seq -A *.fastq.gz > out.fa
Or something similar to convert all files in that folder that end in fastq.gz to fasta.
Thanks for your help! Not sure if renaming the file caused the problem.
Great you got it sorted.
Look at for loops
to do it for every file in your folder.
On 3 May 2018 at 17:45:31, climbandseq (notifications@github.com) wrote:
Thanks guys! I think I figured it out, though. When I created the test.fq.gz file, I copied one of my fastq files out of another folder and renamed it to make it simple. This morning I tried the following commands to see if maybe renaming the file was a problem. I did the following: cd /mnt/c/Users/"sequencer PC"/Documents/Location/Run1/Fastq seqtk seq -A 2_S1_L001_R1_001.fastq.gz > out.fa And it worked! I got my fasta file with content. Not sure if renaming the file had something to do with that.
Is there a single command to convert every fastq file in that folder to fasta? For example, can I say: seqtk seq -A *.fastq.gz > out.fa Or something similar to convert all files in that folder that end in fastq.gz to fasta.
Thanks for your help! Not sure if renaming the file caused the problem.
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@climbandseq can you close this issue now please? thanks!
Thanks for your help guys!
Hello, I am very (!) new to working with sequencing files as well as Linux command line.
I used the command seqtk seq -a test.fq.gz > out.fa to try to convert a fastq file to fasta. I created the out.fa file but there is nothing in it. I also tried seqtk seq -A test.fq.gz > out.fa but with the same result.
I am sure it is something simple. I get no errors, and a .fa file is created, but there is nothing in the file. Thanks for your help!