Unexpected error while opening bed-file

[konstak...@gmail.com]

Hello,

I'm running IGV v2.5.0 in Windows 10 Enterprise. I'm getting this error message when trying to open a bed file:

 
    Unexpected error: Error parsing line at byte position:
    LineIteratorImpl(SynchronousLineReader), for input source:
    C:\Users\me\path\to\my\bed\my_bed.bed.
See
    igv.log for more details
 

It's a basic BED3 format file, and other files I prepared similarly can open fine. Any idea what would be the most common cause for this? I tried to find potential causes for this in the internet and this group, but couldn't find any. Any help would be much appreciate.

On a separate note, I cannot view the igv.log file sinse windows doesn't acknowledge that it exists. I can see through IGV open session dialog where it is, but the whole folder is missing when I go to the folder where it is supposed to be in. So that's why I'm not posting my log info with the problem.

Best,

-Konsta

[James Robinson]

Hi,

The error message indicates there is a problem with the format of the bed file.   Apologies that is is not more helpful.    If you can zip and attach your bed file I will look at it.

Jim

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[konstak...@gmail.com]

Hi,

Thanks for the help. I modified the file a bit, by adding the region names and strand, but that didn't affect the error message, and the other files processed similarly open fine in IGV as before. I was not sure how to share the file here directly, so I'm giving you a link for the file in my google drive: https://drive.google.com/open?id=1FQbfKc-t9cMn7RGqgLq0WdkRga85KCz4 Hopefully you can download it.

Best,

-Konsta

torstai 12. maaliskuuta 2020 18.53.35 UTC+2 James Robinson kirjoitti:

Hi,

The error message indicates there is a problem with the format of the bed file.   Apologies that is is not more helpful.    If you can zip and attach your bed file I will look at it.

Jim

On Thu, Mar 12, 2020 at 8:01 AM <konstak...@gmail.com> wrote:

Hello,

I'm running IGV v2.5.0 in Windows 10 Enterprise. I'm getting this error message when trying to open a bed file:

 
    Unexpected error: Error parsing line at byte position:
    LineIteratorImpl(SynchronousLineReader), for input source:
    C:\Users\me\path\to\my\bed\my_bed.bed.
See
    igv.log for more details
 

It's a basic BED3 format file, and other files I prepared similarly can open fine. Any idea what would be the most common cause for this? I tried to find potential causes for this in the internet and this group, but couldn't find any. Any help would be much appreciate.

On a separate note, I cannot view the igv.log file sinse windows doesn't acknowledge that it exists. I can see through IGV open session dialog where it is, but the whole folder is missing when I go to the folder where it is supposed to be in. So that's why I'm not posting my log info with the problem.

Best,

-Konsta

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[James Robinson]

Hi, the problem is this line, which uses scientific notation for the integer start position.  Apologies for the obtuse error message,  I am going to see if I can improve that for the next release.

chr19 8e+05 800500 ARHI0A_peak_75576 . *

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[konstak...@gmail.com]

Hi,

Thank you very much! I need to take a look at my code then.

Cheers,

-Konsta

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