Error: Genome did not load

[prashanti patel]

Hi everyone

I am using the IGV web server and trying to load the genome FASTA file (467 MB) for banana (Musa acuminata v4) with the following name : Musa_acuminata_pahang_v4.fasta. I downloaded this file from the banana genome hub https://banana-genome-hub.southgreen.fr/  and tried to upload it using the "local folder" option in the drop down menu. However it gives me an error message as follows: "Genome did not load - invalid file". Will be grateful for any guidance

Thanks

Prashanti

[James Robinson]

How exactly are you trying to load it?  Please be specific.   Are you using the "File" or "Genomes" menu?

[kpshgv]

--

---
You received this message because you are subscribed to the Google Groups "igv-help" group.
To unsubscribe from this group and stop receiving emails from it, send an email to igv-help+u...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/cfbb0470-e9aa-4843-99e7-e6c0f82a017bn%40googlegroups.com.

Hello Prashanti.

In addition to the possibility that there is a problem with IGV, there could be a real problem with the downloaded file. If the error message "Genome did not load - invalid file" has any  meaning, then you should check the format of the file you downloaded. Open it in a pure text editor tool (not word processing) preferably on a UNIX (-like) machine. Then go to the first line, delete the ">" sign of the first line using the "backspace-delete" and keep on deleting whatever is before that symbol. Even if all characters have been removed, keep on pushing the backspace key a few more times. Then place in a new ">" character. During downloading and opening a file in some word/text processor programmes, some hidden characters may have been added to the document and they could interfere with the proper reading of the file in IGV.

Similarly at the end of the file, there might be hidden characters, so delete them. Scan through the file to check if you might spot some strange characters in the file. Then save the file again, maybe best with a new name.

You might also look at the top and bottom parts of the file in UNIX: head -n 5 file_name.fa   and tail -n 5 file_name.fa to check if there are any bits before the first ">" or after the last nucleotide and remove them.

I have downloaded and locally installed a copy of the banana genome file myself and it works in IGV on my computer.

I have had such problem before with some downloads in some applications and hidden characters caused the trouble.

Good luck,

Hugo

--

Hugo A. Volkaert
Center for Agricultural Biotechnology
Kasetsart University Kamphaengsaen Campus
Kamphaengsaen, Nakhonpathom
Thailand 73140
phone: +66 34353217
fax: +66 34353222

[prashanti patel]

Hi James

I am trying to load the file through the local files options under the "Genomes" tab. I don't find any "File" tab apart from the "Genome, Tracks, Sessions" options

Thank you

--

---
You received this message because you are subscribed to a topic in the Google Groups "igv-help" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/igv-help/TaOA3ynelio/unsubscribe.
To unsubscribe from this group and all its topics, send an email to igv-help+u...@googlegroups.com.

[Helga Thorvaldsdottir]

Hi Prashanti,

In the IGV-Web app, you have to load both the fasta file and the corresponding index file; both at the same time. 

I have confirmed that the Musa_acuminata_pahang_v4.fasta file does load for me if I index it and then load both the file and the index. (I've attached the index file that  I created)

Unfortunately, the app presents that non-informative message when you don't load both. Now that we are aware of it, we will fix the message in a future release.

FYI, the IGV desktop application does not have the same restriction, and you can load the fasta file directly into the application without an index. In fact, it will create an index file for you, which you can use for the IGV-Web app. Because IGV-Web is an app that runs in a web browser, for security reasons it does not have the same access to the local file system as the IGV Java desktop application.

Helga

[prashanti patel]

Hi Helga

Thank you so much for the timely assistance! Yes it's working now but I have a question: What are the column names of the index file you sent me? Also how to prepare this file on my own? Additionally, I don't see any gene annotations when I mouse over the chromosomes so what should I do?

Thank you very much

Prashanti

--

---
You received this message because you are subscribed to a topic in the Google Groups "igv-help" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/igv-help/TaOA3ynelio/unsubscribe.
To unsubscribe from this group and all its topics, send an email to igv-help+u...@googlegroups.com.

To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/4f23b677-d385-47a2-831a-6104ca7e2121n%40googlegroups.com.

[Helga Thorvaldsdottir]

Hi Prashanti,

You can create index files, for example with the faidx command of the samtools utility (see http://www.htslib.org). Or, you can have the IGV desktop application automatically create it for you when you load the fasta file via the Genome menu (Download IGV desktop from our downloads page).

The fasta file just has the genome sequence - it does not include any gene annotations. Perhaps you can find a gene annotation file at the same website where you downloaded the fasta. Gene annotations can be loaded into IGV-Web via the Tracks menu, or into IGV desktop via the File menu.

Helga