[maker-devel] Problem with maker_map_ids

[Carson Holt]

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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