I am following the instruction mentioned on Submit to GEO to upload about 83G of RNA-seq data in gzipped form to the GEO FTP server. I was first using the following command, but the connection had a time-out after every file:
ncftpput -B 33554432 -z -u 'username' -p 'password' -v -R \ ftp-private.ncbi.nlm.nih.gov /fasp/ local_folder_to_upload
I then extended this to the following script, such that it retries until all files are uploaded:
#!/bin/bash cd /home/ec2-user try=0 COMPLETE_CONDITION=0 echo "START" until [ "$lastresult" = "$COMPLETE_CONDITION" ]; do let "try+=1" echo "Try $try ..." ncftpput -B 33554432 -z -u 'username' -p 'password' -v -R \ ftp-private.ncbi.nlm.nih.gov /fasp/ local_folder_to_upload let "lastresult=$?" echo "Last Resultcode: $lastresult" done echo "UPLOAD COMPLETED AFTER $try TRY(S)" exit 0
Which worked in principal and after several tries I got all samples uploading correctly on GEO. However the error message persisted:
Could not read reply from control connection -- timed out.
Any thoughts on why this happens and how to resolve it? I does not look to be crucial as all files seem to be uploaded correctly.