fastx_quality_stats error : input file (-) has unknown file format

[mbk0asis]

Hi.
I was trying to check qualities of my fastq files from RNA-seq using fastx-toolkit, but I kept getting a following error.

$ fastx_quality_stats -Q 33 4.1.fastq

fastx_quality_stats error : input file (-) has unknown file format (not FASTA or FASTQ), first character = (10)

RNA-seq was performed in Hiseq2000 (paired-end), and the guy who ran the sequencing gave me these files when I asked the raw sequencing data. I merged all the fastq files in each sample into one file using 'cat' command since I wated to map them as singe-ends.

Has anyone expreinced this?

Thanks!

[dpryan]

The error means that the first line of the file is blank. If that's true, then the file is screwed up. What does

head 4.1.fastq

show?

[mbk0asis]

The file doesn't seem to have blank at the start.

$ head 4.1.fastq 
@HWI-ST908R:191:D27LWACXX:7:1101:4446:2397 2:N:0:CGATGT
NNNNNNCNTCTTCNNNTGNGNNNNGNNCNTNGGGGAGACCNNGNNAANNNNNTTANNNGNNNANTNCCNNNNNNNNNGNNCNCTNNNNNNNNNNNNNNNNN
+
#####################################################################################################
@HWI-ST908R:191:D27LWACXX:7:1101:4422:2401 2:N:0:CGATGT
NNNNNNTNAGCTTNNNAANCCNNTANNCAACTCATCCGAGNNTNNTTNNNNNGGCNNNGNNNCNGTCCNNNNNNNNNTGNCNCGGNNNNTNNNNNNNNNNN
+
#####################################################################################################
@HWI-ST908R:191:D27LWACXX:7:1101:4557:2387 2:N:0:CGATGT
NNNNNNANTNTCNNNNCGNANNNNCNNNNCNNGNCGCTNCNNNNNNNNNNNNNTANNNNNNNGNNNTNNNNNNNNNNNNNNNNANNNNNNNNNNNNNNNNN

As I mentioned earlier, I used 'cat' command to merge four files.
Could that cause the problem?

[dpryan]

Oh, I actually missed the "input file (-)" part of the error. An input file of "-" typically means stdin, which is the default for that command. Also, there is no "-Q" parameter, so that's likely ignored. The command should be:

fastx_quality_stats -i 4.1.fastq

[mbk0asis]

Thanks, dpryan!
It worked!!!
I didn't add '-i' in front of the input file, so the program couldn't find a input file.
Am I understanding right?

[GenoMax]

That is correct. Some programs require an explicit "-i" to signify input.