Question: FastQC stuck at 95% read sequences forever
0
gravatar for bxia
2.9 years ago by
bxia140
bxia140 wrote:

Hi, I just encounter another problem, after I convert SRA file to FASTQ, and use fastQC to check the quality,

The program stuck at 95% for "read xxx sequences" for over an hour.

Anyone have the similar problem before?

Thanks

rna-seq • 3.3k views
ADD COMMENTlink modified 13 months ago by fadimeoztoprak10 • written 2.9 years ago by bxia140
2

FastQC may have run out of memory. How much RAM do you have and how big is the sequence file you are trying to QC?

ADD REPLYlink modified 2.9 years ago • written 2.9 years ago by genomax65k

I have 8Gb, the fastq file is 8.4Gb, it will use all of them?

ADD REPLYlink written 2.9 years ago by bxia140

Another dumb question, do most software in the RNA-seq pipeline require a large amount of RAM?

Thank you very much

ADD REPLYlink written 2.9 years ago by bxia140
1

You can check memory usage by e.g. top or htop in your terminal.

ADD REPLYlink written 2.9 years ago by WouterDeCoster38k

What OS are you using? @WouterDeCoster's suggestion will work for unix/OS X but not for Windows.
Generally memory usage will be proportional to the analysis you are doing/software you are using. There are specific examples (e.g. STAR aligner with human genome which needs 30+G of RAM for alignments) known to require significant RAM. Most de novo assemblers will need tens to hundreds of GB of RAM for very large datasets.

ADD REPLYlink modified 2.9 years ago • written 2.9 years ago by genomax65k

FastQC should use swap once it runs out of RAM. Is it possible that you may have a corrupt fastq file (based on the other question you had asked)? Did you check the size of the corresponding file on ENA?

ADD REPLYlink written 2.9 years ago by genomax65k

I tracked the usage of mem and cpu, after reach the 95%, everything dropped to 0...

I am using Ubuntu. will check ENA to see whether the fastq file have problem

ADD REPLYlink written 2.9 years ago by bxia140

I am not sure what is the problem, on ENA website, the fastq bytes information is empty, I checked the read number and it is correct.

I download the SRA file from NCBI and use fastq-dump for conversion to fastq file.

ADD REPLYlink written 2.9 years ago by bxia140
1
gravatar for fadimeoztoprak
13 months ago by
fadimeoztoprak10 wrote:

I suffered the same problems. Solution: I realized that the version i was using (and automatically downloaded with sudo apt-get install fastqc) was 0.11.4 (0.11.7 has been released this year). I have installed 0.11.5 referenced here, and completed my analysis without issues. Worth to try :) (I use ubuntu 16.04)

ADD COMMENTlink written 13 months ago by fadimeoztoprak10

While that may have worked for you the latest version is required (v. 0.11.7) if you have NovaSeq 6000 data.

ADD REPLYlink written 13 months ago by genomax65k

i use ubuntu 16.04 and your solution had worked for me. realy thanks for your useful comment

ADD REPLYlink written 10 months ago by tzahra68750
0
gravatar for mmahar
2.2 years ago by
mmahar0
United States
mmahar0 wrote:

I've had this problem as well - I'm not sure what the cause of it is. However, an easy work around is to first uninstall FastQC - "sudo apt-get remove fastqc" in Ubuntu. Next, find and go into the fastqc directory - you can open the application from here without installing it. Just type "./fastqc" and it'll open. I've never had issues running it this way.

ADD COMMENTlink written 2.2 years ago by mmahar0

Running fastqc from the commandline in Linux (usually Ubuntu), I have often had problems when using larger fastq files or settings that use more resources, like --nogroup. The fastqc perl script that runs fastqc has a memory limit of 250Mb (Xmx250m). When I have problems I usually increase the amount of memory.

ADD REPLYlink written 2.2 years ago by mastal5112.0k

I've run into this issue recently, as well. How do you increase memory allocation for the command line? FastQC help only mentions that the default allocated memory is 250Mb, but I don't see an option to change it, and -Xmx isn't recognized as an option.

ADD REPLYlink modified 19 months ago • written 19 months ago by jrhawley0
1

While you could edit the fastqc perl wraper script using a text editor and change the value to a larger one, it may be simpler to use more threads -t on the command line (try 2 or 4 as long as you have the right CPU). FastQC allocates 250Mb RAM per thread. See if that helps.

ADD REPLYlink modified 19 months ago • written 19 months ago by genomax65k

Excellent, changing the number of threads worked for me. Thanks

ADD REPLYlink written 19 months ago by jrhawley0
0
gravatar for yanevski2009
17 months ago by
yanevski20090 wrote:

starting with sudo rights solved the problem for me

ADD COMMENTlink written 17 months ago by yanevski20090
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