trying to count a pattern in my fastq file using bbduk

I'm using bbduk to count a specific pattern in my fastq file. The pattern is quite long and contain three barcodes with spacers.

the command looks like that

$ bbduk.sh -Xmx100g in=10_ID_mRNA_S1_L002_R1_001.fastq outm=10_ID_mRNA_pattern_found.fastq literal=NNNNNNNNNNCAGCTACTGCNNNNNNNNNNCGAGTACCCTNNNNNNNNNN k=19 copyundefined mm=f

java -ea -Xmx100g -Xms100g -cp /fs/home/yeroslaviz/miniconda3/envs/bbmap/opt/bbmap-39.06-1/current/ jgi.BBDuk -Xmx100g in=10_ID_mRNA_S1_L002_R1_001.fastq outm=10_ID_mRNA_pattern_found.fastq literal=NNNNNNNNNNCAGCTACTGCNNNNNNNNNNCGAGTACCCTNNNNNNNNNN k=19 copyundefined mm=f
Executing jgi.BBDuk [-Xmx100g, in=10_ID_mRNA_S1_L002_R1_001.fastq, outm=10_ID_mRNA_pattern_found.fastq, literal=NNNNNNNNNNCAGCTACTGCNNNNNNNNNNCGAGTACCCTNNNNNNNNNN, k=19, copyundefined, mm=f]
Version 39.06

0.067 seconds.
Initial:
Memory: max=107374m, total=107374m, free=107272m, used=102m
...

But then I get this java heap space error

Exception in thread "main" java.lang.OutOfMemoryError: Java heap space
        at java.base/java.util.Arrays.copyOf(Arrays.java:3481)
        at java.base/java.util.ArrayList.toArray(ArrayList.java:370)
        at java.base/java.util.ArrayList.addAll(ArrayList.java:753)
        at shared.Tools.makeReplicates(Tools.java:1306)
        at shared.Tools.makeReplicates(Tools.java:1306)
        at shared.Tools.makeReplicates(Tools.java:1306)
        at shared.Tools.makeReplicates(Tools.java:1306)
        at shared.Tools.makeReplicates(Tools.java:1306)
        at shared.Tools.makeReplicates(Tools.java:1306)
        at shared.Tools.makeReplicates(Tools.java:1306)
        at shared.Tools.makeReplicates(Tools.java:1306)
        at shared.Tools.makeReplicates(Tools.java:1306)
        at shared.Tools.makeReplicates(Tools.java:1306)
        at shared.Tools.makeReplicates(Tools.java:1306)
        at shared.Tools.makeReplicates(Tools.java:1306)
        at shared.Tools.makeReplicates(Tools.java:1306)
        at shared.Tools.makeReplicates(Tools.java:1306)
        at shared.Tools.makeReplicates(Tools.java:1306)
        at shared.Tools.makeReplicates(Tools.java:1306)
        at shared.Tools.makeReplicates(Tools.java:1306)
        at shared.Tools.makeReplicates(Tools.java:1306)
        at shared.Tools.makeReplicates(Tools.java:1306)
        at shared.Tools.replicateAmbiguous(Tools.java:1261)
        at jgi.BBDuk.spawnLoadThreads(BBDuk.java:1851)
        at jgi.BBDuk.process2(BBDuk.java:1171)
        at jgi.BBDuk.process(BBDuk.java:1121)
        at jgi.BBDuk.main(BBDuk.java:81)

any idea how to overcome it?

thanks

Assa

java bbduk bbmap fastq

• 1,130 views • link

updated 2.3 years ago by GenoMax

• written 2.3 years ago by Assa Yeroslaviz

I don't think you can use N's in literal= since the match is literal as the option says. Depending where in the read this pattern is you may be able to run three independent operations to add up the read numbers.

I assume this is related to UMI-Tools knee-method has great influence on the results of white list ?

• 0 views • link

written 2.3 years ago by GenoMax

yes it does.

As far as I understand it, you can use N here. I took it from this example Brian posted a few years ago

This is why the degenerate parameter is used here.

Am I wrong thinking this way?

Is it possible, that this pattern is just too long for bbduk to handle?

• 0 views • link

written 2.3 years ago by Assa Yeroslaviz

Thanks for that link. As noted in that example, you can try seal.sh instead of bbduk.sh.

Is it possible, that this pattern is just too long for bbduk to handle?

With those many N's your will likely need a lot more RAM which is what is happening with original command line i.e. 100G is not enough.

• 0 views • link

written 2.3 years ago by GenoMax

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