error bbduk

Question

[Kárita]

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.

[Pierre Lindenbaum]

-Xmx-78m ; your asking for a negative amount of memory. Try:

 -Xmx78m -Xms78m 

[Kárita]

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)

[GenoMax]

Provide the actual command you used.

You would normally specify memory using bbduk.sh -Xmx4g in your command line. BBDuk should need a small amount of memory.

[Kárita]

./bbduk.sh -Xmx2g in= /Home/Desktop/Documents/limpeza/S2500_1.fastq out= /Home/Desktop/Documents/limpeza/S2500_1.fastq.clean.fastq trimq=20 minlen=75
java -ea -Xmx2g -Xms2g -cp /home/qiime2/Documents/bbmap/current/ jgi.BBDuk -Xmx2g in= /Home/Desktop/Documents/limpeza/S2500_1.fastq out= /Home/Desktop/Documents/limpeza/S2500_1.fastq.clean.fastq trimq=20 minlen=75
Executing jgi.BBDuk [-Xmx2g, in=, /Home/Desktop/Documents/limpeza/S2500_1.fastq, out=, /Home/Desktop/Documents/limpeza/S2500_1.fastq.clean.fastq, trimq=20, minlen=75]
Version 39.01

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)
    at jgi.BBDuk.main(BBDuk.java:78)

[Matthias Zepper]

There is a blank space between option and argument: out= /Home/Desktop/Documents/limpeza/S2500_1.fastq.clean.fastq.

[GenoMax]

Correct. No spaces are allowed between = and file names for all options.

Use

./bbduk.sh -Xmx2g in=/Home/Desktop/Documents/limpeza/S2500_1.fastq out=/Home/Desktop/Documents/limpeza/S2500_1.fastq.clean.fastq trimq=20 minlen=75

[lieven.sterck]

78 M might anyway be too small though ;)