MULLER Héloïse

So I realized that by default java writes temporary files in /tmp, no matter where my current directory is and no matter where I direct the ouput. I found how to modify the directory of the temporary files like this: java -Djava.io.tmpdir=path_I_want/tmp -jar ~/Softwares/popte2-v1.10.03.jar se2pe --fastq1 walkthrough-reads/France_1.fq.gz --fastq2 walkthrough-reads/France_2.fq.gz --bam1 map/France_1.sam --bam2 map/France_2.sam --sort --output France.sort.bam

Hi, I have been following the wiki, running the following comment line on my own data: bwa bwasw -t 3 walkthrough-refgenome/2R-603-consensusTE.fasta walkthrough-reads/France_1.fq.gz >map/France_1.sam bwa bwasw -t 3 walkthrough-refgenome/2R-603-consensusTE.fasta walkthrough-reads/France_2.fq.gz >map/France_2.sam java -jar ~pt2/popte2.jar se2pe --fastq1 walkthrough-reads/France_1.fq.gz --fastq2 walkthrough-reads/France_2.fq.gz --bam1 map/France_1.sam --bam2 map/France_2.sam --sort --output France.sort.bam...