error bbduk
Can anyone help me, I try to run the command and it gives this error, how can I adjust?
java -ea -Xmx-78m -Xms-78m -cp /home/qiime2/Documents/bbmap/current/ jgi.BBDuk in= /Home/Desktop/Documents/limpeza/S2500_1.fastq out= /Home/Desktop/Documents/limpeza/S2500_1.fastq.clean.fastq trimq=20 minlen=75
Invalid maximum heap size: -Xmx-78m
Error: Could not create the Java Virtual Machine.
Error: A fatal exception has occurred. Program will exit.
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lieven.sterck
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Kárita •
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-Xmx-78m ; your asking for a negative amount of memory. Try:
now it appeared like this
Exception in thread "main" java.lang.RuntimeException: Unknown parameter /Home/Desktop/Documents/limpeza/S2500_1.fastq.clean.fastq at jgi.BBDuk.<init>(BBDuk.java:538)
Provide the actual command you used.
You would normally specify memory using
bbduk.sh -Xmx4gin your command line. BBDuk should need a small amount of memory.There is a blank space between option and argument:
out= /Home/Desktop/Documents/limpeza/S2500_1.fastq.clean.fastq.Correct. No spaces are allowed between
=and file names for all options.Use
78 M might anyway be too small though ;)