Question: Blastp Error 303.7
0
gravatar for stamakro
13 months ago by
stamakro20
Netherlands
stamakro20 wrote:

I'm trying to run remote blast, but I keep getting this error:

**-bash-4.2$ blastp -remote -db swissprot -query test.txt -out outfile.txt -outfmt 7

Error: (303.7) [URL_Connect] Failed to connect to www.ncbi.nlm.nih.gov:443: Not supported

Error: (303.7) [URL_Connect] Failed to connect to www.ncbi.nlm.nih.gov:443: Not supported

Error: (303.7) [URL_Connect] Failed to connect to www.ncbi.nlm.nih.gov:443: Not supported

Error: (310.5) [blast4] Service not found

Error: (315.2) CConn_Streambuf::CConn_Streambuf(): NULL connector: Unknown

Error: (303.7) [URL_Connect] Failed to connect to www.ncbi.nlm.nih.gov:443: Not supported

Error: (303.7) [URL_Connect] Failed to connect to www.ncbi.nlm.nih.gov:443: Not supported

Error: (303.7) [URL_Connect] Failed to connect to www.ncbi.nlm.nih.gov:443: Not supported

Error: (310.5) [blast4] Service not found

Error: (315.2) CConn_Streambuf::CConn_Streambuf(): NULL connector: Unknown

Error: (802.5) CObjectOStream: error at byte 14: stack is empty: write fault

Error: (303.7) [URL_Connect] Failed to connect to www.ncbi.nlm.nih.gov:443: Not supported

Error: (303.7) [URL_Connect] Failed to connect to www.ncbi.nlm.nih.gov:443: Not supported

Error: (303.7) [URL_Connect] Failed to connect to www.ncbi.nlm.nih.gov:443: Not supported

Error: (310.5) [blast4] Service not found

Error: (315.2) CConn_Streambuf::CConn_Streambuf(): NULL connector: Unknown

Error: (802.5) CObjectOStream: error at byte 14: stack is empty: write fault

Error: (303.7) [URL_Connect] Failed to connect to www.ncbi.nlm.nih.gov:443: Not supported

Error: (303.7) [URL_Connect] Failed to connect to www.ncbi.nlm.nih.gov:443: Not supported

Error: (303.7) [URL_Connect] Failed to connect to www.ncbi.nlm.nih.gov:443: Not supported

Error: (310.5) [blast4] Service not found

Error: (315.2) CConn_Streambuf::CConn_Streambuf(): NULL connector: Unknown

Error: (802.5) CObjectOStream: error at byte 0: stack is empty: cannot close output stream

Error: (CIOException::eFlush) COStreamBuffer::Flush: failed

Error: (CSerialException::eIoError) byte 0: cannot close output stream

Error: (802.4) Cannot close serializing output stream(CSerialException::eIoError) byte 0: cannot close output stream

Error: (802.5) CObjectOStream: error at byte 14: stack is empty: write fault

Error: NCBI C++ Exception:

"/opt/insy/env.el7/src/ncbi-blast-2.2.27+-src/c++/src/util/strbuffer.cpp", line 794: Error: ncbi::COStreamBuffer::FlushBuffer() - write fault

"/opt/insy/env.el7/src/ncbi-blast-2.2.27+-src/c++/src/serial/objostr.cpp", line 571: Error: ncbi::CObjectOStream::Write() -  Frame type= eFrameNamed, Object type= Blast4-request*

I am pretty sure that my command is correct and I have a working internet connection. Any ideas? Thanks!

blastp ncbi • 1.4k views
ADD COMMENTlink modified 7 months ago by larvalanobium20 • written 13 months ago by stamakro20

I get the same error. My best guess is that NCBI broke something on the server side, which they will hopefully soon fix.

ADD REPLYlink written 13 months ago by Lars Juhl Jensen11k
3
gravatar for GenoMax
13 months ago by
GenoMax42k
United States
GenoMax42k wrote:

Have you downloaded the latest blast+ package (v.2.5.0)? If not that should be the first thing to try.

NCBI has moved to https-only connections, which are only supported in the latest versions of their software (e.g. blast, sratoolkit etc). You appear to be using blast+ v.2.2.27.

ADD COMMENTlink modified 13 months ago • written 13 months ago by GenoMax42k

That did indeed the trick! Thank you very much!

ADD REPLYlink written 13 months ago by stamakro20
0
gravatar for st.ph.n
13 months ago by
st.ph.n2.1k
Philadelphia, PA
st.ph.n2.1k wrote:

Can you do a local blast? wget ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.fasta.gz

ADD COMMENTlink written 13 months ago by st.ph.n2.1k

No, I get the same error.

ADD REPLYlink written 13 months ago by stamakro20
0
gravatar for henry-keen
13 months ago by
henry-keen10
United States
henry-keen10 wrote:

As others have answered, upgrading to a newer version of Blast+ should solve the problem. The error went away for me once I upgraded to version 2.6.0.

ADD COMMENTlink modified 13 months ago • written 13 months ago by henry-keen10

This is probably a simple answer, but I am having this same issue. I have downloaded the newest version of blast (v.2.7.1) but when ever I use blastn I get Error: (303.7) [URL_Connect]......It looks like I am still using BLAST 2.2.25+, but I downloaded and installed BLAST 2.7.1. So how do I switch over to the new version?

ADD REPLYlink written 11 weeks ago by ntmarshall40610

Find out the path of the location where you installed the new version. Use that full path when you run the search. Not optimal but will get you past the error for now.

ADD REPLYlink written 11 weeks ago by GenoMax42k

I am sorry but I do not know how I am supposed to do this. I have downloaded the newest version just onto my Desktop for now, as I have been having problems getting it to work. So even if I move my files into ncbi-blast-2.7.1+ folder, and then run the blastn command from there, I get the same error.

I am just trying a simple blast command for now: $blastn -db nr -query test.fasta -remote >out.txt

And my directory location of the new blast+ download is: /Users/natemarshall/Desktop/ncbi-blast-2.7.1+/

But I do not know where I should add this directory location into the command. And like I said, even if place the test.fasta file into the ncbi-blast-2.7.1+/ or into the ncbi-blast-2.7.1+/bin folder and do the blastn command from inside these directories, it still gives me the same error.

ADD REPLYlink written 11 weeks ago by ntmarshall40610

It appears that you have another version of blast that is in your default path. You can add the directory with the new blast to your $PATH by doing export PATH=/Users/natemarshall/Desktop/ncbi-blast-2.7.1+/:$PATH (if the actual executables are in a bin directory then do export PATH=/Users/natemarshall/Desktop/ncbi-blast-2.7.1+/bin:$PATH).

You could try and run the blastn with this command (before doing the $PATH change): $ /Users/natemarshall/Desktop/ncbi-blast-2.7.1+/blastn -db nr -query test.fasta -remote >out.txt

ADD REPLYlink modified 11 weeks ago • written 11 weeks ago by GenoMax42k
0
gravatar for larvalanobium
7 months ago by
larvalanobium20 wrote:

Hi there

I'm having essentially a similar error output to the original asker, but mine has something to with GnuTLS, so my output starts with:

Warning: [blastn] Unavailable feature GNUTLS Critical: [blastn] Unavailable feature GNUTLS Error: (303.7) [blastn] [URL_Connect; https://www.ncbi.nlm.nih.gov:443/Service/dispd.cgi?service=blast4&address=10.1.153.186&platform=x86_64-apple-darwin15.6.0] Failed to connect: Not supported ... etc.

My input line is:

blastn -db nt -query $FILE -out theten -entrez_query "$EQ" -outfmt 17 -max_target_seqs 10 -remote

I've used brew to double check the the most recent versions of blast+, GnuTLS (and its dependencies; GMP and nettle) are up to date.

Does anyone have any ideas where I'm going wrong?

Thanks and kind regards Crystal

ADD COMMENTlink written 7 months ago by larvalanobium20
1

I would suggest you to open a new post with this issue, you will have more chance to get noticed then.

ADD REPLYlink written 7 months ago by dago2.5k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1305 users visited in the last hour