[maker-devel] Problem with maker_map_ids

[Carson Holt]

Thanks for the GFF3 file.  The meta character came across in the GFF3 as
well, so I think it's safe to assume they are being introduced by the
e-mail client used to add the attachment (so ignore the last file I sent).

I've attached the fixed maker_map_ids.

Thanks,
Carson





On 12-09-25 9:01 AM, "Carson Holt" <carsonhh at gmail.com> wrote:

>While you are sending me the GFF3 file also try the sort order file
>attached.  I found a number of illegal meta character contaminating the
>file.  Sometimes those can be introduced by text editors or sometimes
>e-mail clients.  In case it wasn't the e-mail client I'm sending you this
>fixed version.
>
>Also I see you are using maker_map_ids from version 2.10.  Try the 2.26
>version.  They are different.
>
>Thanks,
>Carson
>
>
>On 12-09-25 8:44 AM, "Carson Holt" <carsonhh at gmail.com> wrote:
>
>>Could you also provide 34112_3June11Ass.gff?
>>
>>Thanks,
>>Carson
>>
>>
>>On 12-09-25 8:31 AM, "Ian Misner" <ianmisner at my.uri.edu> wrote:
>>
>>>Hello,
>>>
>>>I'm trying to create human friendly ids and I'm getting an error when I
>>>use the -sort_file option. Without the sort file it runs fine just not
>>>numbered from the first contig. I have had some programers at our
>>>cluster 
>>>look at the script and they attempted a fix but it did not work. They
>>>mentioned the script was "buggy" so this might be part of the problem.
>>>I've attached the error as well as the sort file. I can send more files
>>>if necessary. Thanks for you time.
>>>
>>>Cheers
>>>Ian
>>>
>>>$ maker_map_ids --prefix THRCLA_ --justify 5 --sort_order
>>>34112_sort.txt 
>>>34112_3June11Ass.gff > 34112_3June11Ass_named.txt
>>>Can't use string ("34112_sort.txt") as a HASH ref while "strict refs"
>>>in 
>>>use at /gpfs/runtime/opt/maker/2.10/maker/bin/maker_map_ids line 311,
>>><$IN> line 499186._______________________________________________
>>>maker-devel mailing list
>>>maker-devel at box290.bluehost.com
>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

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