Alignment with bbmap.sh

Question

[Hayler Edu]

Hello everyone.

I'm writing because I want to do an alignment with bbmap.sh but have a problem.

This is my scrip:

 bbmap.sh ref=GCF_001660625.2_IpCoco_1.2_genomic.fna -I pimm1_Pg594_il.fastq.gz -O pimm1_Pg594_il.sam

When I try to execute the script I have this error:

/home/hayler99/miniconda3/envs/bbtools/bin/bbmap.sh: line 347: java: command not found

I tried to put the PATH in the bashrc but it didn't work, so I don't know what to do.

I hope that someone can help me :)

I wish a happy new year to everyone in this excellent community.

[GenoMax]

The alignment command also needs to be

bbmap.sh -XmxNNg ref=GCF_001660625.2_IpCoco_1.2_genomic.fna in=pimm1_Pg594_il.fastq.gz out=pimm1_Pg594_il.sam

Use an appropriate value for memory (NN depending on the size of your genome e.g. 30G for human genome)

Answer 1

[ATpoint]

java: command not found

Install Java, be it java.com, OpenJDK or via any of the common package managers such as conda or brew (the latter for Mac mainly.