How to check SRA file download possible corrupted?

Question

[xqyn]

Hi all,

I tried to use the tool https://sra-explorer.info/ to download direct fastq.gz files. After downloading without any error reported, I did the trimming and it turns out the some file are corrupted, for e.g.:

Error in FASTQ file at line 86591: Line expected to start with '+', but found 'G'


Cutadapt terminated with exit signal: '256'.
Terminating Trim Galore run, please check error message(s) to get an idea what went wrong...

or

Error in FASTQ file at line 6804: Length of sequence and qualities differ


Cutadapt terminated with exit signal: '256'.
Terminating Trim Galore run, please check error message(s) to get an idea what went wrong...

I re-downloaded those error files using the extract same curl command, and this time the files are good that the trimming works fine without any error.

Anyone has experience this problem before that some downloads had just has some random error and is there a way to check the validation of the downloaded files?

Answer 1

[GenoMax]

You can run vdb-validate program included in the SRA toolkit. You may need to prefetch the file. https://open.bioqueue.org/home/knowledge/showKnowledge/sig/vdb-validate-file

that some downloads had just has some random error

If you have a deep packet inspecting firewall at your institution something like this can happen.

[Istvan Albert]

what a curse SRA really is

as time passes it becomes more and more ridiculous

I have installed Red Dead Redemption 2 game the other day; the download was over 100 GB and finished in a few hours, contains tens of thousands of files all working together.

but getting a single fastq file from SRA is still incredibly tedious and flaky - may or may not work

[xqyn]

that seems to be happened. Thank you!