Question: Error: reads file does not look like a fastq file
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gravatar for addilynn.beach
3.4 years ago by
addilynn.beach30 wrote:

I am trying to align fastq files using bowtie2, but I am getting a message saying "Error: reads file does not look like a fastq file". Some of the fastq files do align, however, but with extremely low alignment rates. I've been reading posts about this error and it seems the .gz format may be a problem? Any suggestions?

ADD COMMENTlink modified 3.4 years ago • written 3.4 years ago by addilynn.beach30

Error: reads file does not look like a fastq file

so, how does it look like ? what have you tried to look at those files ? what was the result ?

ADD REPLYlink written 3.4 years ago by Pierre Lindenbaum125k

I used this command: bowtie2 -p 2 --no-unal -x /Users/.../bowtie2_index/VZV -U 1.fastq.gz, 2.fastq.gz -S 3.VZV.sam

I've also gotten the error "bowtie2-align exited with value 1" when trying a different format.

ADD REPLYlink written 3.4 years ago by addilynn.beach30

Please use ADD REPLY/ADD COMMENT when responding to existing posts.

ADD REPLYlink written 3.4 years ago by genomax76k

Show us the output of these commands

zcat 1.fastq.gz | head -8
zcat 2.fastq.gz | head -8
ADD REPLYlink modified 3.4 years ago • written 3.4 years ago by genomax76k
zcat 6_GGCTAC_L007_R1_001.fastq.gz | head -8 
zcat 6_GGCTAC_L008_R1_001.fastq.gz | head -8
zcat: can't stat: 6_GGCTAC_L007_R1_001.fastq.gz (6_GGCTAC_L007_R1_001.fastq.gz.Z): No such file or directory
head: zcat: No such file or directory
==> 6_GGCTAC_L008_R1_001.fastq.gz <==
???ˎ?Ȳd9?_Q?? ?M?D*w??t??h???I?%J)= ...followed by a few rows of symbols.
ADD REPLYlink modified 3.4 years ago by Pierre Lindenbaum125k • written 3.4 years ago by addilynn.beach30

Are the files not present in the directory where you are issuing the commands from?

Based on the last line that does not appear to be a FASTQ format file.

If your files do end in .Z then you may need to use uncompress file_name before you can use them.

ADD REPLYlink modified 3.4 years ago • written 3.4 years ago by genomax76k

what is the output of

file  6_GGCTAC_L007_R1_001.fastq.gz 
file  6_GGCTAC_L008_R1_001.fastq.gz
ADD REPLYlink written 3.4 years ago by Pierre Lindenbaum125k

They do end in .gz, how can I uncompress them?

ADD REPLYlink written 3.4 years ago by addilynn.beach30

If they end in .gz then the command I had posted above should have produced proper output which it did not. What is the output of @Pierre's command above?

You do not need to uncompress sequence files to use them with most aligners.

ADD REPLYlink modified 3.4 years ago • written 3.4 years ago by genomax76k

The -U flag expects a comma separated list of fastq files. You listed the files separated by a comma and a space. Does that make a difference?

ADD REPLYlink written 3.4 years ago by WouterDeCoster42k
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