FastX tool :: fastq_quality_filter

[huma Asif]

Dear All,
i am doing quality filtering of my fastq file using fastq_quality_filter
and i am getting this error
Premature End-Of-File (filename ='-')
my code is
nohup fastq_quality_filter ‐v ‐q 20 ‐p 100 -Q33 ‐i GO06_2500_Mate.read2.fastq ‐o Read2.filteredQ20.GO06.fastq > fastq_quality_filterlog &

my fastq look like
@GO06_2500_Mate:1_4_72/2
NGAAGGGTGGGCATGTNATTGNGGGTNATGTNANNTNNNNTNNNNNNNN
+
!%(''(%%&/%%%%'&!)'+%!%&+1!%)'(!%!!(!!!!)!!!!!!!!
@GO06_2500_Mate:1_5_104/2
NGAAAGGAGGGAGAGGNAAGTNAGTTNAGGTNGNNTNNNNTNNNNNNNN
+
!'&(%(*0'&+&%+%%!%*)%!(+%(!'&%(!(!!'!!!!%!!!!!!!!
@GO06_2500_Mate:1_9_50/2
NAAATAAAAAGCCGGAAAAGTNGGGTNAATGNANNTNNNNANNNNNNNN
+
!%'*'%&&%(*%%)1(%)(**!%&),!)%%%!%!!%!!!!(!!!!!!!!

can any body help me with this error i

[Michael.Ante]

I copied your code and had a similar problem.
But writing it in the same style, it worked:
Your '-' symbols look on my bash a bit shorter than mine.

 -v vs. ‐v

Try to re-write your code in a plain text editor and run it again.

[huma Asif]

i corrected that but now getting this error
failed to open input file 'GO06_2500_Mate.read2.fastq': Value too large for defined data type

[Michael.Ante]

How big is your file?
Maybe it is really to big for the old fastx tool-kit.
If that's the case and you need to stick to the program, you can split the file into several smaller ones.

Alternatively, you may have a look at bbduk. Especially, if you are dealing with paired-end data.

[huma Asif]

thank you for your help
i will try that