Hisat2 --sra-acc option (redirect sra file to a desired directory)

Question

[Chvatil]

Hello, I'm actually using Hisat2 and its option --sra-acc

/beegfs/data/mycount/TOOLS/hisat2-2.1.0/hisat2 -k 1 -q -x mapping_index --sra-acc SRR5074460 | $SAMTOOLS/samtools view -o mapping.bam 2> stats_mapping.txt

But the probleme is here, the sra files are savec to the wroung desired directory:

/beegfs/home/mycount/ncbi/public/sra
mycount@pbil-deb:~/ncbi/public/sra$ ls -ltr
total 1156
-rw-r--r-- 1 mycount abc 52270906 Dec 22 21:01 SRR5074460.sra.cache

But I would need help in order to redirect the sra files output in another path:

I'm using BEEGFS where I have two principal directories;

• /beegfs/data/mycount (with 2To of memory)
• /beegfs/home/mycont (with 60GB of memory where are actually saved the sra files)

so the idea would be to redirect the sra file into /beegfs/data/mycount/TOOLS/ncbi instead of /beegfs/home/mycount/ncbi/

Does anyone have an idea ?

Thank you for your help

[vkkodali_ncbi]

Run vdb-config -i and change the path there?