Question: (Closed) Unable to download Bulk data of sra at once using PREFETCH
0
gravatar for S AR
13 months ago by
S AR50
Pakistan
S AR50 wrote:

Hi i have a list of SRA IDs and im trying to download in one go so im using:

sort sraids.txt | parallel -j 4 "prefetch {}"

Im getting the following error for all sra ids:

2018-11-13T07:06:18 prefetch.2.8.2 err: libs/vfs/resolver.c:3350:VResolverQueryPath: path not found while resolving tree within virtual file system module - 'ERR688043 ' cannot be found.

2018-11-13T07:06:19 prefetch.2.8.2 err: libs/vfs/resolver.c:3350:VResolverQueryPath: path not found while resolving tree within virtual file system module - 'ERR688044 ' cannot be found.

2018-11-13T07:06:19 prefetch.2.8.2 err: libs/vfs/resolver.c:3350:VResolverQueryPath: path not found while resolving tree within virtual file system module - 'ERR688045 ' cannot be found.

2018-11-13T07:06:21 prefetch.2.8.2 err: libs/vfs/resolver.c:3350:VResolverQueryPath: path not found while resolving tree within virtual file system module - 'ERR688046 ' cannot be found.

2018-11-13T07:06:21 prefetch.2.8.2 err: libs/vfs/resolver.c:3350:VResolverQueryPath: path not found while resolving tree within virtual file system module - 'ERR688047 ' cannot be found.

2018-11-13T07:06:21 prefetch.2.8.2 err: libs/vfs/resolver.c:3350:VResolverQueryPath: path not found while resolving tree within virtual file system module - 'ERR688048 ' cannot be found.

2018-11-13T07:06:24 prefetch.2.8.2 err: libs/vfs/resolver.c:3350:VResolverQueryPath: path not found while resolving tree within virtual file system module - 'ERR688049 ' cannot be found.

2018-11-13T07:06:24 prefetch.2.8.2 err: libs/vfs/resolver.c:3350:VResolverQueryPath: path not found

Then i tried to download the individual SRA id:

prefetch ERR133900

It is giving these log messages:

2018-11-13T04:27:21 prefetch.2.8.2: 1) Downloading 'ERR133900'...
2018-11-13T04:27:21 prefetch.2.8.2:  Downloading via https...
2018-11-13T04:40:16 prefetch.2.8.2: 1) 'ERR133900' was downloaded successfully
2018-11-13T04:40:23 prefetch.2.8.2: 'ERR133900' has 1 unresolved dependency
2018-11-13T04:40:27 prefetch.2.8.2: 2) Downloading 'ncbi-acc:AL123456.2?vdb-ctx=refseq'...
2018-11-13T04:40:27 prefetch.2.8.2:  Downloading via https...
2018-11-13T04:40:30 prefetch.2.8.2: 2) 'ncbi-acc:AL123456.2?vdb-ctx=refseq' was downloaded successfully
2018-11-13T04:40:41 prefetch.2.8.2: 'ERR133900' has no remote vdbcache

But no file present if it downloaded? i tried the same command again it says:

2018-11-13T07:12:40 prefetch.2.8.2: 1) 'ERR133900' is found locally
2018-11-13T07:12:47 prefetch.2.8.2: 'ERR133900' has 0 unresolved dependencies
2018-11-13T07:13:09 prefetch.2.8.2: 'ERR133900' has no remote vdbcache

Im confused! Can anyone help.

Thank You

awk prefetch loop sra • 679 views
ADD COMMENTlink written 13 months ago by S AR50

Hello S AR!

We believe that this post does not fit the main topic of this site.

Duplicate of 347050. See answer there. It is a whitespace behind your accession number messing things up.

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

ADD REPLYlink modified 13 months ago • written 13 months ago by ATpoint26k

I did remove whitespaces. Still getting same errors.

ADD REPLYlink written 13 months ago by S AR50

Show the error message in the first question. This one is closed as it would spread informatio over two threads.

ADD REPLYlink modified 13 months ago • written 13 months ago by ATpoint26k

I did replied with the error on the first post. Please see if you can help

ADD REPLYlink modified 13 months ago • written 13 months ago by S AR50
Please log in to add an answer.
The thread is closed. No new answers may be added.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1889 users visited in the last hour