Troubleshooting

Once version 1.0 of the pipeline is released after beta-testing this page will contain examples of what we consider good/bad genome assemblies and our reasoning for it.

Errors

For an error with BBDuk like this:

java -ea -Xmx10g -Xms10g -cp /usr/local/opt/bbmap-38.90-1/current/ jgi.BBDuk -Xmx10g in1=SRR12352255_1.fastq.gz in2=SRR12352255_2.fastq.gz out1=SRR12352255_1.fastq.gz out2=SRR12352255_2.fastq.gz threads=6 hdist=1 k=31 ref=phiX.fasta
Executing jgi.BBDuk [-Xmx10g, in1=SRR12352255_1.fastq.gz, in2=SRR12352255_2.fastq.gz, out1=SRR12352255_1.fastq.gz, out2=SRR12352255_2.fastq.gz, threads=6, hdist=1, k=31, ref=phiX.fasta]
Version 38.90

Set threads to 6
Exception in thread "main" java.lang.RuntimeException: File 'SRR12352255_1.fastq.gz' was specified multiple times.
	at shared.Tools.testForDuplicateFiles(Tools.java:219)
	at jgi.BBDuk.<init>(BBDuk.java:918)
	at jgi.BBDuk.main(BBDuk.java:78)

Notice here that the in file names are the same as the out file names and bbduk doesn't like this. To fix this just add something like Sample_ to the beginning of your sample ids in your samplesheet and rerun the program.