weird fastqc error

[frankyue50]

Here is how I run it: fastqc file.fastq -o output

Results:
....
Approx 95% complete for 1.fastq
Approx 100% complete for 1.fastq
Analysis complete for 1.fastq
Failed to process file 1.fastq

Why it says "failed" while the analysis is also marked as complete? so confused ... can someone help?

[frankyue50]

Since this is a pair-ended seq, I run the fastqc on both fastqs at the same time, still errors ...

[GenoMax]

Are you getting any results in "output" irrespective of the "failed' message?

[frankyue50]

Are you getting any results in "output" irrespective of the "failed' message?

Thanks for the response. I did get a *fastq.zip file, but when I failed to unzip it, it gave me this error msg:
End-of-central-directory signature not found. Either this file is not
a zipfile, or it constitutes one disk of a multi-part archive. In the
latter case the central directory and zipfile comment will be found on
the last disk(s) of this archive.

[GenoMax]

Are you able to run the GUI for FastQC to test (just run fastqc without any other options)? Are you running this on a server or a local machine (what OS)?

[frankyue50]

Are you able to run the GUI for FastQC to test (just run fastqc without any other options)? Are you running this on a server or a local machine (what OS)?

I am thinking the same thing. I run my fastqc on a linux server ... maybe I should fire up GUI and directly run it on my iMAC

[mastal]

I have had similar problems recently, when I have been analysing Illumina 150 or 250 bp PE samples, and using the --nogroup option.

FastQC seemed to have completed the analysis, but then the output file didn't get printed.

I can't remember whether I also got a Java out of memory error message.

I solved my problem by modifying the fastqc perl script that is used
to run fastqc from the commandline, and increasing the amount of memory.
The default is Xmx250m.