Blastp Error 303.7

Question

[stamakro]

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!

[Lars Juhl Jensen]

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

Answer 1

[GenoMax]

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.

[stamakro]

That did indeed the trick! Thank you very much!

Answer 2

[st.ph.n]

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

[stamakro]

No, I get the same error.

Answer 3

[henry-keen]

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.

[ntmarshall406]

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?

[GenoMax]

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.

[ntmarshall406]

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.

[GenoMax]

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

Answer 4

[larvalanobium]

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

[dago]

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