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Old 01-24-2020, 10:04 AM   #1
Robo
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Exclamation FastQC problems

Greetings to every one. Here we have another newbie who made the reckless decision to throw himself in bioinformatics . I was given certain sequences from nanopore and pacbio, so really long sequences. Managed the program to work correctly in the server as a perl script but when I run it with the data as an argument I get the following error

Exception in thread "Thread-1" java. lang. Out Of Memory Error: Java heap space
at uk.ac.babraham.FastQC.Utilities.QualityCount.<init>(QualityCount.java:33)
at
uk.ac.babraham.FastQC.Modules.Per Base Quality Scores. process Sequence (Per Base Quality Scores. jaVA:141)
at uk.ac.graham. FastQC.Analysis.Analysis Runner.run(Analysis Runner.java:89)
at java. lang.Thread.run(Thread.java:748)


The strange thing is that thru the same data it worked ones so either I have somehow damaged the data or I am doing something wrong without realizing it.

I would really appreciate some help and I thank you for stopping by and reading my post

Last edited by Robo; 01-25-2020 at 06:08 AM.
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Old 01-24-2020, 02:17 PM   #2
GenoMax
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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.
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Old 01-25-2020, 01:16 AM   #3
Robo
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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 06:29 AM.
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Old 01-26-2020, 04:22 AM   #4
GenoMax
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If you feel your files have become corrupt you can use "validateFiles" utility from Jim Kent to verify the files. Add execute permissions after you download the program. "chmod u+x validateFiles".
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Old 01-29-2020, 01:09 AM   #5
Robo
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Dear GenoMax, Thank you for the help my files do not have errors despite one being an inode/symlink. at this point, I do not know what the error maybe and I'll write to my supervisor for an appointment.
Thank you again, and all the best.
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