fastx toolkit error

Question

[ieie]

Hi, I know that there are some posts that already dealt with this problem but even following them I could not solve my problem. i am running this command line fastx_quality_stats -i C1P1.fastq -o C1P1_stats.txt and I get this error: fastx_quality_stats: input file (-) has unknown file format (not FASTA or FASTQ), first character = f (102) I checked the head of the fastq file and there is no blank line, plus I have followed the instruction on the fastx toolkit web site. does somebody know what might be the cause of the problem? thanks a lot

[glihm]

Can you please provide the header of you fastq file? Also, did you try renaming '.fastq' to '.fq' (some old programs only rely on extension name)?

Did you try the -Q33 option as mentioned here?

Which version of fastx toolkit are you using?

[ATpoint]

input file (-)

This suggests that you read from STDIN instead of reading the file directly, as your post states. Please provide the original and full command line.

[ieie]

head C1P1.fastq
@SG0S1:00008:00195
CCTCCGCTTATTGA
+
A6;5/-:<)--(--
@SG0S1:00011:00155
CCTCCGCTTT
+
;6;@60-//(
@SG0S1:00012:00173
CCTCCGCTT

I had tried to change it in fq but nothing and I am using the latest version released in 2014. this is the original:

$ fastx_quality_stats -h
    usage: fastx_quality_stats [-h] [-i INFILE] [-o OUTFILE]
 [-h] = This helpful help screen.
       [-i INFILE]  = FASTA/Q input file. default is STDIN.
                      If FASTA file is given, only nucleotides
              distribution is calculated (there's no quality info).
       [-o OUTFILE] = TEXT output file. default is STDOUT.

I am really new to these tools so thanks again for any help!

[glihm]

Think about using "Add comment" for such replies. ;) It keeps the post well organized. Thanks for these details. Also, when pasting fastq sequence, use the "code" formatting instead.

[ieie]

Sorry, I will keep it in mind :) they were the first posts for me.