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Old 01-20-2014, 02:19 AM   #1
mbk0asis
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Default fastx_quality_stats error : input file (-) has unknown file format

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

Code:
$ 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!
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Old 01-20-2014, 02:31 AM   #2
dpryan
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The error means that the first line of the file is blank. If that's true, then the file is screwed up. What does
Code:
head 4.1.fastq
show?
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Old 01-20-2014, 06:34 AM   #3
mbk0asis
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The file doesn't seem to have blank at the start.

Code:
$ 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?
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Old 01-20-2014, 06:41 AM   #4
dpryan
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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:

Code:
fastx_quality_stats -i 4.1.fastq
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Old 01-20-2014, 04:45 PM   #5
mbk0asis
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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?
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Old 01-20-2014, 05:03 PM   #6
GenoMax
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That is correct. Some programs require an explicit "-i" to signify input.
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