Hey All, I downloaded an 88mb genome from ncbi and tried to use tblastn to find a protein homolog after building the database for the organism. I encountered the following error, and looking for ways to overcome it. By the way, I have done this beofre and it worked fine but not this time. I checked that line and it looked fine. I assume there might be error in my downloaded. I repeated the download twice and still got the same error.
command
tblastn -db genome -query protein.txt -out file2.txt
Error
Error: NCBI C++ Exception: T0 "/private/tmp/blast-20170511-49816-1rw4ib1/ncbi-blast-2.6.0+-src/c++/src/objtools/readers/fasta.cpp", line 2428: Error: CFastaReader: Near line 1, there's a line that doesn't look like plausible data, but it's not marked as defline or comment. (m_Pos = 1)
1 answer
what is the output of
file protein.txt
and
head protein.txt
you have your answer: this is not a fasta file.
the content of the text file looks like this. I believe its a fasta
>Cel-Ego1
MGDEGYRGWIKLEIPCSLPERQMGPIVKCHVAKLEPALNEYNIKVLTKGQVQVVEEQDCEPFYETNYEVATSRFSHDLIA
AIQTYLKDLSTDHLMPFQRGNLVLHSSDFWSSELTCHLVDIPLAAVFFGNIQGGTFINHWEVSFWDDVRRRKSARTRNTE
PTQADKIGMNQIKVEFEFDKIDFMTVHFKHFENDFEVADKDAKRTKQTVTMYYQITVRRTSIRRIIVDPVVQDCNGSDRI
RVHFELNCPVLIRRAYRTAKQESENRHSVPHYRRYLVINRGRSANQYPTAKAITDSPVFTIEFDQSVGLNEIYRLLSRLR
IRTGVSIEFADIPSIDCLIWRENPYNRWTFLNNQHLSPTHFSAPIYRDFITTAFPKKHEVCGSREVDTNRERKFAITYLL
is that a formatting issue in your post the indentation of the sequence?
How did you get to that content? cat tail head?
head returned a binary stream...
exactly, just wanted to know how OP then got any content of that file. And to hint to the fact OP likely edited the file with something other than linux compatible software
it's not, file protein.txt would have return something else.
$ echo -e ">Cel-Ego1\nMGDEGYRGWIKLEIPCSLPERQMGPIVKCHVAKLEPALNEYNIKVLTKGQVQVVEEQDCEPFYETNYEVATSRFSHDLIA\nAIQTYLKDLSTDHLMPFQRGNLVLHSSDFWSSELTCHLVDIPLAAVFFGNIQGGTFINHWEVSFWDDVRRRKSARTRNTE" | file -
/dev/stdin: ASCII text
it's a binary file; Something edited with an exotic text editor ?
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I think the error is rather triggered by your input fasta file. Does that one looks OK?
Yes. the fasta looks fine to me. Anyway to check other than visually scanning through?