Sequence does not Match Current Genome: Error

[Auz LoPinto]

When I try to upload the following .bam files, I get this error. I'm using the attached reference genome.


"File: C:\Users\austi\OneDrive\Desktop\A1S24_-_GFP_OP50_Sequencing-415149741\BWA_Aligner_05_06_2024_3_27_54_2-734032312\G2GFP-ds.cac99ac126f948fbbdc7d0ff4a0d7be8\G2GFP.bam
does not contain any sequence names which match the current genome.

File:      chr,
Genome: gi|49175990|ref|NC_000913.2|     "

Please help! I used Illumina BWA Aligner, aligned to E. Coli MG1655.

[Auz LoPinto]

Also, I'm using windows 11.

[igv-help]

Hi, the message means the sequence (chromosome) names in your BAM file do not match the sequence names in the reference fasta.   Did you load the fasta yourself?  

[Auz LoPinto]

I did not, I used one from the server. I fixed this though! I uninstalled everything, downloaded IGV without java included (i had included before), and then downloaded Java 11 SE. Everything worked after that.

[James Robinson]

I'm glad you solved it, but what version of IGV did you install, and from where did you get it?  The current version requires Java 17.

[Auz LoPinto]

From here:
https://igv.org/download/html/download.html

Then, I downloaded java from here:
https://www.oracle.com/java/technologies/javase/jdk11-archive-downloads.html

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[igv-help]

Thanks,  that page shouldn't exist.   I'm not sure how you found it but this is the correct download page

https://igv.org/doc/desktop/#DownloadPage/

[Auz LoPinto]

Oh what? Is it possible that this is a fake website then?

To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/cf6177d8-acc9-4ed0-8283-b1cebc95b7fbn%40googlegroups.com.

[James Robinson]

No it's our website, but that page is not linked to by any of our current pages.   So how did you find it?  A Google search, or old bookmark?

To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/CAFoZpXVAC1%3DJ4rP5gJAp-cw_sbZR%3Dx2Go%2Bd8kr5ueQKE%3D2um_g%40mail.gmail.com.

[Auz LoPinto]

One of my classmates sent it to me. I don’t know where he got it from, could be from some old lecture or old course materials. 

To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/CACOP%2BpvNSnNvg%3Dgan_4BtSD%2BStwhntYKXP2dU31vO4mMFWk85A%40mail.gmail.com.

[igv-help]

Thanks for letting us know. In case others also try to use that link, it now redirects to the latest IGV download page.