Question: Blastp Error 303.7
0
gravatar for stamakro
10 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 • 1.1k views
ADD COMMENTlink modified 4 months ago by larvalanobium20 • written 10 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 10 months ago by Lars Juhl Jensen11k
3
gravatar for genomax
10 months ago by
genomax37k
United States
genomax37k 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 10 months ago • written 10 months ago by genomax37k

That did indeed the trick! Thank you very much!

ADD REPLYlink written 10 months ago by stamakro20
0
gravatar for st.ph.n
10 months ago by
st.ph.n1.9k
Philadelphia, PA
st.ph.n1.9k 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 10 months ago by st.ph.n1.9k

No, I get the same error.

ADD REPLYlink written 10 months ago by stamakro20
0
gravatar for henry-keen
10 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 10 months ago • written 10 months ago by henry-keen10
0
gravatar for larvalanobium
4 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 4 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 4 months ago by dago2.3k
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