Thread: FastQC problems
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Old 01-25-2020, 12:16 AM   #3
Robo
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Location: Germany.Frankfurt

Join Date: Jan 2020
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Quote:
Originally Posted by GenoMax View Post
How are you running the fastqc program? You re running out of memory.

If you are using the bat file on windows then be sure to edit that and increase the value for memory allocation by changing the number in "Xmx2g" to say "Xmx8g". Do not use > 80% of RAM that you actually have.
Thank you for the quick reply I am running fastqc in a Ubuntu server from the terminal, the resources are allocated based on the needs of the program. Normally it was not giving problems for resources even because the server is quite powerful.
______total __|__used___|__free___|shared____|_buff/cache__|_available|
Mem: |503909_| 283348__|__8718_|__296_____| 211842_____|___217920 |
Swap:_____0______0________0_____
the free -m command is giving me the up stated results. I read in a previous topic in here regarding fastqc that sometimes (when you have damaged the data some how) it tries to read files as a single line and thou runes out of memory but I do not know if this is my case.
Thank you very much

Last edited by Robo; 01-25-2020 at 05:29 AM.
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