BBMap Error

[Phage Hunter]

Hi guys,

When attempting to build an index or carry out any mapping with BBMap I always get the following error: Could not find or load main class Drive. I suspect this is may be purely a Java error, but I am not sure as I am new to all this.

Could any of you shed light on this or maybe suggest equivalent programs if no solution can be found?

Thanks

[GenoMax]

Can you tell us what OS are you running this on and the command you are using?

[Phage Hunter]

I am running Ubuntu 14.04 with Java version 1.8.0_25. I have tried multiple commands and each produces the same error. I tried running: ./bbmap.sh ref=T3.fasta k=10

With that command I get the following output:

java -Djava.library.path=/media/damian/Hard Drive - Hyb/bbmap/bbmap/jni/ -ea -Xmx25537m -cp /media/damian/Hard Drive - Hyb/bbmap/bbmap/current/ align2.BBMap build=1 overwrite=true fastareadlen=500 ref=T3.fasta k=10
Error: Could not find or load main class Drive

[GenoMax]

Did you move any of the folders inside the BBMap directory after you downloaded BBMap?

[Phage Hunter]

No I did not move or edit anything. After decompressing, I simply tried to run the program immediately from the script.

[Phage Hunter]

The problem has been sorted out. It was simply because my main drive name has a space in it and the script was unable to locate the path because of it. I changed it and things are working now.

Thanks for your help.

[Xtina]

Can someone help me to understand this message? I'm new to bioinformatic and don't quite understand all the error message meaning. Thanks

Max memory cannot be determined. Attempting to use 2000 MB.
If this fails, please add the -Xmx flag (e.g. -Xmx24g) to your command,
or run this program qsubbed or from a qlogin session on Genepool, or set ulimit to an appropriate value.
java -ea -Xmx2000m -cp /Users/labmac2/Desktop/Lib23/bbmap/current/ jgi.FuseSequence in1=./Trimmed_Reads/Paired/F4259_R1.fastq.gz in2=./Trimmed_Reads/Paired/F4259_R2.fastq.gz pad=7 out=./Paired_Merged/F4259_merged.fastq fusepairs
Executing jgi.FuseSequence [in1=./Trimmed_Reads/Paired/F4259_R1.fastq.gz, in2=./Trimmed_Reads/Paired/F4259_R2.fastq.gz, pad=7, out=./Paired_Merged/F4259_merged.fastq, fusepairs]

Set INTERLEAVED to false
Input is being processed as paired
Writing interleaved

[GenoMax]

BBMap suite programs try to auto detect memory available on your system. If they are not able to do that they will fall back to using a safe 2GB using the option mentioned "-Xmx2000m". This is Java way of specifying the maximum amount of memory to use.

If you have more memory available then you can explicitly choose the amount to use by adding -XmxNNg to any bbmap suite tool. For example

 bbmap.sh -Xmx30g in1=blah ...

[Ahmer]

I am trying to run bbmap but i cannot can anyone tell me where the error is??

~/bbmap$ bash stats.sh /root@wch7p102-04:/home/szweda/bbmap/resources/phix174_ill.ref.fa.gz
Exception in thread "main" java.lang.RuntimeException: Input file does not appear to be valid: /root@wch7p102-04:/home/szweda/bbmap/resources/phix174_ill.ref.fa.gz
at jgi.AssemblyStats2.process(AssemblyStats2.java:248)
at jgi.AssemblyStats2.main(AssemblyStats2.java:40)

[Ahmer]

I am trying to run BBmap with this command but I am getting this error can anyone help??

bash bbmap.sh in=PY53_contigs.fasta out=PY53_bbmapped.sam bamscript=bs.sh java -ea -Xmx4393m -Xms4393m -cp /home/szweda/bbmap/current/ align2.BBMap build=1 overwrite=true fastareadlen=500 in=PY53_contigs.fasta out=PY53_bbmapped.sam bamscript=bs.sh Executing align2.BBMap [build=1, overwrite=true, fastareadlen=500, in=PY53_contigs.fasta, out=PY53_bbmapped.sam, bamscript=bs.sh] Version 38.95 Retaining first best site only for ambiguous mappings. Found samtools 1.10 Exception in thread "main" java.lang.RuntimeException: Can't find file ref/genome/1/summary.txt at fileIO.ReadWrite.getRawInputStream(ReadWrite.java:933) at fileIO.ReadWrite.getInputStream(ReadWrite.java:898) at fileIO.TextFile.open(TextFile.java:280) at fileIO.TextFile.<init>(TextFile.java:123) at dna.Data.setGenome2(Data.java:823) at dna.Data.setGenome(Data.java:769) at align2.BBMap.loadIndex(BBMap.java:316) at align2.BBMap.main(BBMap.java:32)