Sra file download path not exists

I successfully downloaded the files for accession number ERR 20 minutes ago, but now when I try I get:. The exact same thing also happened to me earlier today when I was doing a trial download of SRR It would also be great to have a fix to so this error can be caught easily. I did notice that this error tends to happen when the sample has been downloaded before and is cached on the system. It appears work if you force redownload with prefetch before running fasterq-dump.

In our Snakemake pipeline the code looks like this, including a section to check the log if the download was actually successful:. I downloaded the Sra files with prefetch command, and now doing the sra to fastq conversion with fasterq-dump.

My command worked fine half hour ago, but the temp files were stored at home directory which does not have enough space. So I used -t parameter to changed to the scratch place, then re-run it with the same script, and it gives me error message of this: fasterq-dump. Do you think it is the same intermittent issue as the previous post described it? I think there is a misunderstanding here: Maybe I am wrong, but it looks to me like you moved the sra-file into the scratch-space. That is not what the scratch-space is, it is an directory where the tool can put temporary stuff while it is working on the conversion.

After the work is done the tool will clean up this scratch-space. In order to tell you what went wrong - please copy the complete command-line into this thread. So I run the job on my uni cluster, and it has GB home space and 1TB space on a scratch directory. I stored all the prefetched SRA files in the scratch directory, and ran the fasterq-dump command from my home directory with giving the path to fasterq-dump to find where the SRA files are.

And it gave me the error messages I posted earlier. I have a feeling that the path i gave to fasterq-dump could not find where the SRA files are, and went on to dbGaP to download the files again.

Because it was talking a quite long time to do one file. So I think I must be really unfamiliar with how to use fasterq-dump and whether my path writing was correct, and whether it could only work under the directory where the SRA files are easily found? Could you recommend how to use fasterq-dump commend to let it find the SRA files and do the SRA conversion regardless of where my current directory is?

Let me take it apart: fasterq-dump I have been having the same issue intermittently over the past several days. I have been experiencing errors like the following:. I am using sratoolkit version 2. I'm pretty sure the accessions are valid because when I rerun the command they are able to retrieve the files without issue, seems like some sort of intermittent network issue.

I'm also getting this but only on my local machine, not on the Biowulf cluster. That makes me think its some sort of network issue as well. Happy to help or provide more info. We improved tolerance against network failures.

Thanks for the tip. I managed to get what I needed just naively retrying but if I need to download more files I'll definitely try using prefetch as you suggest. Skip to content. Star New issue. Jump to bottom. Copy link. Running on a cluster, so that could be the source of error, not sure The text was updated successfully, but these errors were encountered:. The accession is valid. We'll investigate. This is a brief tutorial about methods of downloading sra, sam and fastq files, mainly focusing on Aspera Connect.

Repost by indicating the source please! Almost all HTS data in published publications will be asked uploading to here, and stored as. Mostly, we download sra files for the purpose of getting corresponding fastq or sam files, so as to use them in our own pipeline for downstream analysis. If not, go to SRA database. First Choice — Aspera Connect. It is a commercial high speed file transfer software produced by IBM. Many sites can transfer data at Mbps.