pachterlab/ffq

Connection reset

Jigyasa3 opened this issue · 2 comments

Jigyasa3 commented

Hi all!

Thank you for a great resource! I am using it to download the R1 reads of multiple bioprojects. I have created a text file with all the SRR ids associated with a bioproject, and feed that to ffq for download.

Code-
while read line;do ffq --ftp ${line} | xargs curl -O ;done < 2-accession_list_PRJNA730929.txt

where the 2-accession_list_PRJNA730929.txt consists of -
SRR14583629
SRR14583630
SRR14583631
SRR14583632
SRR14583633

After generating output for ~100 SRR ids (out of 316 ids), I get the following error. Any suggestions?

Error-
curl: (56) Recv failure: Connection reset by peer curl: (56) Recv failure: Connection reset by peer % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- 0:02:11 --:--:-- 0 curl: (28) Failed to connect to ftp.sra.ebi.ac.uk port 21: Connection timed out

sbooeshaghi commented

This looks to me like a connection timeout for one of the files that curl is trying to download, and not an ffq issue. Do you know which SRR generates an ftp link that results in the timeout?

sbooeshaghi commented

Closing since this is an issue with cURL and not ffq.