FastQC after read sequences, nothing happened...
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7.8 years ago
bxia ▴ 180

After I converted SRA file to fastq file by fastq-dump,

it stuck at 95% read sequences forever for FastQC.

After I trimmed the fastq file by trimmomatic, it could finish the read sequences, it said read xxxx sequences and nothing happened.....

No usage of CPU and MEM.... looks like the fastqc went to sleep...anyone have the same problem before?

Thanks

RNA-Seq • 2.7k views
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Entering edit mode
7.7 years ago
Ar ★ 1.1k

What is the size of the file and what is the memory of your computer ? There is a good possibility that fastqc does not have the required memory to read the whole file.

Try using Terminal or command line : fastqc --extract <fastq file=""> -q --outdir <output directory="">

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