search

ncbi / sra-tools

SRA Tools
Other
1.07k stars 243 forks source link

Prefetch finished with no error #855

Closed Wang0293 closed 8 months ago

Wang0293 commented 9 months ago

“Current preference is set to retrieve SRA Normalized Format files with full base quality scores.” displayed and then prefetch finished directly. Who knows what's the wrong?

bvaldebenitom commented 9 months ago

Hi,

are you running this through a job scheduling system? I was getting the same message, but running prefetch on a clean terminal worked.

Wang0293 commented 9 months ago

Hi,

are you running this through a job scheduling system? I was getting the same message, but running prefetch on a clean terminal worked.

I have tried it but failed, may be different question.

klymenko commented 9 months ago

@Wang0293, what is your prefetch command line?

Wang0293 commented 9 months ago

@Wang0293, what is your prefetch command line?

I used the simplest command: prefetch SRR1173821 but failed too.

klymenko commented 9 months ago

What is the output of the following? curl https://locate.ncbi.nlm.nih.gov/sdl/2/retrieve?acc=SRR1173821

Wang0293 commented 9 months ago

What is the output of the following? curl https://locate.ncbi.nlm.nih.gov/sdl/2/retrieve?acc=SRR1173821

{ "version": "2", "result": [ { "bundle": "SRR1173821", "status": 200, "msg": "ok", "files": [ { "object": "srapub|SRR1173821", "accession": "SRR1173821", "type": "sra", "name": "SRR1173821", "size": 13227449800, "md5": "a58577a516c12c6e1cfb50ca1259e291", "modificationDate": "2014-02-20T20:24:27Z", "locations": [ { "service": "s3", "region": "us-east-1", "link": "https://sra-pub-run-odp.s3.amazonaws.com/sra/SRR1173821/SRR1173821" } ] } ] } ] } That's the output.

klymenko commented 9 months ago

What is the output of the following? srapath SRR1173821

Wang0293 commented 9 months ago

What is the output of the following? srapath SRR1173821

Surprisingly, it works well now, and prefetch also works well. However, in my memory, this command outputted nothing when I tried it after failed download some days ago. And the same commands (prefetch and srapath) were tried on a clean terminal and I got the same output. In fact, I downloaded 132 samples by accession number using --option-file that day, and got 11 *.sra files successfully. Others finished just showed Current preference is set to retrieve SRA Normalized Format files with full base quality scores.. I can't understand what happened but I can use it normally now. I didn't do anything after opened this issue !!! Do you have some opinions? Very thanks for your time.

klymenko commented 9 months ago

Now it is difficult to say what was the exact reason of failure. Most likely you had problems in network connections to NCBI resources.

Wang0293 commented 9 months ago

Now it is difficult to say what was the exact reason of failure. Most likely you had problems in network connections to NCBI resources.

Probably, yes. Network of our server is so unstable. I'll try curl in the first place to confirm the network connections to NCBI resources if I repeated this case again. Truly appreciate for your help.