Error: "The format could not be recognized!"

[j-a-thia]

Hi there!

I am using SweeD v4.0.0 to analyse input in the SweepFinder format.

I keep getting the error: "ERROR: Please check the input file [MY INPUT FILE]. The format could not be recognized!"

Would it be possible to have a working example input file in this format available in the Git Repo? The manual (v3.0.0) whilst describing the structure does not provide an example of what the data should look like.

Here are the first 10 lines of my input (for a single chromosome):

location x n folded
4058 28 145 1
4381 3 128 1
4665 21 102 1
4684 3 108 1
4685 15 110 1
5032 36 89 1
5059 30 94 1
5122 37 86 1

I have tried both space and tab delimited, but neither works, and the documentation doesn't specify what the delimiter should be.

Thanks for your help. :)

[alachins]

Hi there, Can you replace "location" with "position"? If I remember correctly, the parser recognizes only the word "position" in the case of the SF format. Best regards, Nikos A.

…

On Thu, Aug 18, 2022 at 7:30 AM j-a-thia ***@***.***> wrote: Hi there! I am using SweeD v4.0.0 to analyse input in the SweepFinder format. I keep getting the error: "ERROR: Please check the input file [MY INPUT FILE]. The format could not be recognized!" Would it be possible to have a working example input file in this format available in the Git Repo? The manual (v3.0.0) whilst describing the structure does not provide an example of what the data should look like. Here are the first 10 lines of my input (for a single chromosome): location x n folded 4058 28 145 1 4381 3 128 1 4665 21 102 1 4684 3 108 1 4685 15 110 1 5032 36 89 1 5059 30 94 1 5122 37 86 1 I have tried both space and tab delimited, but neither works, and the documentation doesn't specify what the delimiter should be. Thanks for your help. :) — Reply to this email directly, view it on GitHub <#24>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AALKWCRMJVCFXK5E5JQWAOTVZXDATANCNFSM5632QN2Q> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

-- Nikolaos Alachiotis

[j-a-thia]

Hi there Nikos,

Thank you for that suggestion, I now have a space delimited file that looks like this:

position x n folded
4058 28 145 1
4381 3 128 1
4665 21 102 1
4684 3 108 1
4685 15 110 1
5032 36 89 1
5059 30 94 1
5122 37 86 1
5263 0 87 1

But I am still getting an error. See output below.

Best,

~ JT

$ SweeD -name test -input test.SF -grid 5


                                      _______________

                                           SweeD
                                      _______________



 SweeD version 4.0.0 released by Nikolaos Alachiotis and Pavlos Pavlidis in July 2018.
 Code contributions by Antonis Kioukis and Aggelos Koropoulis.


 Command:

         SweeD -name test -input test.SF -grid 5



 Input file format (0:ms, 1:fasta, 2:macs, 3:vcf, 4:sf, 5:mbs): 4
 Alignment 1

 ERROR: Invalid character (4 - ASCII: 52) in the input file. (Alignment separator: //), last: x,120

SweeD: SweeD_Input.c:4627: readAlignmentSF: Assertion `0' failed.
Aborted (core dumped)