I have been downloading data using the SRA toolkit with prefetch + fastq-dump and more recently fasterq-dump. I have had a variety of messages that come up when I was in the troubleshooting process, but I still get this message regularly:
fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned-76 ( NET - Reading information from the socket failed ) - the process continues and eventually I get the readout stating the number of spots and reads read.
I'm now curious about checking the integrity of the downloaded data - I've read that you can use MD5 checksums for the SRA file but not the fastq files. Now that I already have the fastq files, is there another way I can check the integrity? Is having the correct number of "reads read/written" printed out after fasterq-dump is finished enough to confirm correct downloading and processing or is there something I'm not thinking of?