Hi all, I am new in this forum, so I hope to explain myself well. I am trying to do remote Blast with an input file with 237,805 sequences. I used the next command:
blastn -db nt -query JAL6513ln1.fa -out JAL6513ln1.xml -outfmt 5 -max_target_seqs 10 -remote
But at some point of the execution this give me several error:
Error: (308.5) [blastn] [blast4] Service not found
Error: (301.5) [blastn] [CONN_Open(blast4)] Failed to open connection: Closed
Error: (315.4) [blastn] CConn_Streambuf::overflow(): CONN_Write() failed (blast4): Closed
Error: (315.4) [blastn] CConn_Streambuf::overflow(): CONN_Write() failed (blast4): Closed
Error: (315.4) [blastn] CConn_Streambuf::overflow(): CONN_Write() failed (blast4): Closed
Error: (802.5) [blastn] CObjectOStream: error at byte 52: stack is empty: cannot close output stream
Error: (CIOException::eFlush) [blastn] COStreamBuffer::Flush: failed
Error: (802.4) [blastn] Cannot close serializing output stream (CSerialException::eIoError) byte 52: cannot close output stream
When I try remote Blast with a subset of the previous file with only 100 sequences it since there is no problem. Somebody have any idea of this errors? is possible that I need to "cut" the original file in several more tinny files?
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arturo.marin •
2 answers
Remote blast is not made for so many sequences at once. There is a certain limit and the ncbi will refuse or close the connection if you exceed it. There is a page somewhere that explains it but can't find it right now. I believe they first slow down your blast and after that they close the connection. There is or was also a way to contact the ncbi to temporary white list your ip.
EDIT:
Think this is the page that I mentioned
https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=DeveloperInfo
The best solution is to run blast locally, an other not so recommended solution is to build in breaks of a few seconds between each sequence and if you get an error wait 5 minutes and start it again with the sequence that gave the error. But again that is not so recommended.
Yes, thanks for your help. I think I'll try to use Blastn localy.
This action was restricted on my laptop due to Error Code 0X80071A90. But as I fix Error Code 0X80071A90, it got solved but not with the big file. How can I solve that issue?
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