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Old 12-09-2014, 02:08 AM   #1
huma Asif
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Default FastX tool :: fastq_quality_filter

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

Last edited by huma Asif; 12-09-2014 at 03:43 AM.
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Old 12-09-2014, 03:14 AM   #2
Michael.Ante
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Default

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.
Code:
 -v vs. ‐v
Try to re-write your code in a plain text editor and run it again.
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Old 12-09-2014, 03:42 AM   #3
huma Asif
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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
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Old 12-09-2014, 04:28 AM   #4
Michael.Ante
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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.
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Old 12-09-2014, 04:49 AM   #5
huma Asif
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thank you for your help
i will try that
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