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Old 02-20-2018, 03:54 PM   #1
susanklein
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Location: oceania

Join Date: Feb 2014
Posts: 115
Default Command line Blast.. not as good as it was?

Hi All,

I just have a general question for everyone who regularly uses command line blast with '-remote' i.e. using NCBI online databases. I'm using BLAST 2.6.0+ and I consistently get errors that are related to the NCBI server.. busy, overload, query too big, too many queries.. e.g. below. But the errors are random and its difficult to script repeating a failed blast when its seemingly random and can take a long time before it even errors.

I think these problems have been getting worse and NCBI only tells me to use the browser version or submit fewer / smaller jobs (LOL).

So just wondering what others' thoughts are? I think I'll have to give up and download a local copy of the dbs.

Thanks,

S.

example:
Error: (308.5) [blastn] [blast4] Service not found
Error: (315.2) [blastn] CConn_Streambuf::CConn_Streambuf(): NULL connector: Unknown
Error: (308.5) [blastn] [blast4] Service not found
Error: (315.2) [blastn] CConn_Streambuf::CConn_Streambuf(): NULL connector: Unknown
Error: (802.5) [blastn] CObjectOStream: error at byte 52: stack is empty: write fault
Error: (802.5) [blastn] CObjectOStream: error at byte 0: stack is empty: cannot close output stream
Error: (CIOException::eFlush) [blastn] COStreamBuffer::Flush: failed
Error: (CSerialException::eIoError) [blastn] byte 0: cannot close output stream
Error: (802.4) [blastn] Cannot close serializing output stream (CSerialException::eIoError) byte 0: cannot close output stream

but lots of others too..

Last edited by susanklein; 02-20-2018 at 03:57 PM. Reason: forgot example
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Old 02-20-2018, 05:43 PM   #2
GenoMax
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Location: East Coast USA

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Posts: 7,077
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The remote option is a convenience for those who don't have access to local hardware infrastructure to download copies of blast databases. If you have a need to run scores of jobs regularly then running blast locally should be your first choice. It is a free service after all.
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