Error: reads file does not look like a fastq file

Question

[addilynn.beach]

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?

[Pierre Lindenbaum]

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 ?

[addilynn.beach]

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.

[GenoMax]

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

[GenoMax]

Show us the output of these commands

zcat 1.fastq.gz | head -8
zcat 2.fastq.gz | head -8

[addilynn.beach]

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.

[GenoMax]

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.

[Pierre Lindenbaum]

what is the output of

file  6_GGCTAC_L007_R1_001.fastq.gz 
file  6_GGCTAC_L008_R1_001.fastq.gz

[addilynn.beach]

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

[GenoMax]

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.

[WouterDeCoster]

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?