Entering edit mode
5.2 years ago
lin97868
•
0
Hello all: I have been trying to download data from sratoolkit using a submission script:
for i in SraAccList;
do
/scratch/lindsawi/PROJECT-ONE/quant/sratoolkit.2.9.4-ubuntu64/bin/prefetch.2.9.4 --option-file /scratch/lindsawi/PROJECT-ONE/quant/SraAccList.txt/ --output-directory ../raw/SRA_files/;
done
And I get the following message in my .o file: prefetch.2.9.4: 'SRR3194428' is a local non-kart file prefetch.2.9.4: 'SRR3194428' has 0 unresolved dependencies
for all items in SraAccList
No additional information is being written to my machine file or error file when I run the job, but there is no data downloaded to my output location. I am not sure what I am doing wrong?
I'm not sure why you are using a loop when
$i
is never used in the prefetch command and remove/
afterSraAccList.txt
.