QuestionsCategory: BIOSTARError using parallel tool for fast-dump
thomasjor@nih.gov asked 5 months ago

Hi,
I tried to run the following command

cat runids.txt | parallel fastq-dump -X 10000 --split-files

and got an error message about int: buffer insufficient / cannot get cloud location / timeout exhausted (see attached screen grab). Is it something to do with my PC memory or bandwidth perhaps?
Thanks, Jo
 

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1 Answers
stonelakeak@nih.gov Staff answered 5 months ago

Hi,
This error message is indicating that the connection timed out before all the data was retrieved. It was able to retrieve all 10000 spots for SRR1972926 and SRR1972925 but failed on SRR1972924. This is a network connection problem that has been reported to SRA/NCBI before. 
The short fix is to try the download again, maybe starting at the one that failed rather than repeating the whole search. 
It can also be helpful to read the error report, which is in /Users/thomasjor/ncbi_error_report.txt
Can you send that to ncbibtep@nih.gov?
Thanks