How do I resolve this error when using tblastn -db?

Question

[jaqx008]

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)

[lieven.sterck]

I think the error is rather triggered by your input fasta file. Does that one looks OK?

[jaqx008]

Yes. the fasta looks fine to me. Anyway to check other than visually scanning through?

Answer 1

[Pierre Lindenbaum]

what is the output of

file protein.txt

and

head protein.txt

[jaqx008]

file protein.txt gave protein.txt: data head protein.txt gave a binary looking file as outbut (just jagons inside I guess)

[Pierre Lindenbaum]

you have your answer: this is not a fasta file.

[jaqx008]

the content of the text file looks like this. I believe its a fasta

 >Cel-Ego1
    MGDEGYRGWIKLEIPCSLPERQMGPIVKCHVAKLEPALNEYNIKVLTKGQVQVVEEQDCEPFYETNYEVATSRFSHDLIA
    AIQTYLKDLSTDHLMPFQRGNLVLHSSDFWSSELTCHLVDIPLAAVFFGNIQGGTFINHWEVSFWDDVRRRKSARTRNTE
    PTQADKIGMNQIKVEFEFDKIDFMTVHFKHFENDFEVADKDAKRTKQTVTMYYQITVRRTSIRRIIVDPVVQDCNGSDRI
    RVHFELNCPVLIRRAYRTAKQESENRHSVPHYRRYLVINRGRSANQYPTAKAITDSPVFTIEFDQSVGLNEIYRLLSRLR
    IRTGVSIEFADIPSIDCLIWRENPYNRWTFLNNQHLSPTHFSAPIYRDFITTAFPKKHEVCGSREVDTNRERKFAITYLL

[Pierre Lindenbaum]

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 ?

[jaqx008]

You were right. I copied the content into a new text file and got something out. thanks for your sugestion

[Pierre Lindenbaum]

If an answer was helpful you should upvote it, if the answer resolved your question you should mark it as accepted.

[jaqx008]

I did upvoted it.

[lieven.sterck]

is that a formatting issue in your post the indentation of the sequence?

How did you get to that content? cat tail head?

[Pierre Lindenbaum]

head returned a binary stream...

[lieven.sterck]

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