maker_functional_gff

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maker_functional_gff

nathan.ricks
I've been working with maker and trying to use the maker_functional_gff to create an annotated .gff file. However, whenever I run the command, the following pops up, and just continues for a long time.
Use of uninitialized value $qid in hash element at ./maker_functional_gff line 165, <$IN> line 58363.
Use of uninitialized value $qid in hash element at ./maker_functional_gff line 170, <$IN> line 58363.
Use of uninitialized value $qid in hash element at ./maker_functional_gff line 165, <$IN> line 58367.
Use of uninitialized value $qid in hash element at ./maker_functional_gff line 170, <$IN> line 58367.
^CUse of uninitialized value $qid in hash element at ./maker_functional_gff line 165, <$IN> line 58368.


Nathan Ricks

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Re: maker_functional_gff

Ence,daniel
Hi Nathan, can you send the command line that you’re using and is giving the error?

Thanks,
Daniel Ence

> On May 23, 2017, at 5:23 PM, Nathan Ricks <[hidden email]> wrote:
>
> I've been working with maker and trying to use the maker_functional_gff to create an annotated .gff file. However, whenever I run the command, the following pops up, and just continues for a long time.
> Use of uninitialized value $qid in hash element at ./maker_functional_gff line 165, <$IN> line 58363.
> Use of uninitialized value $qid in hash element at ./maker_functional_gff line 170, <$IN> line 58363.
> Use of uninitialized value $qid in hash element at ./maker_functional_gff line 165, <$IN> line 58367.
> Use of uninitialized value $qid in hash element at ./maker_functional_gff line 170, <$IN> line 58367.
> ^CUse of uninitialized value $qid in hash element at ./maker_functional_gff line 165, <$IN> line 58368.
>
>
> Nathan Ricks
> _______________________________________________
> maker-devel mailing list
> [hidden email]
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

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Re: maker_functional_gff

Carson Holt-2
In reply to this post by nathan.ricks
The blast report you gave it is in the wrong format, it is partial/truncated, or you provided the files in the wrong order. Basically it receive an empty line from the file at some point.

The blast report format must in tabular foramt which is "wu-blast -mformat 2” or "ncbi-blast -outfmt 6"

Also the script only supports blast results against UniProt/Swiss-prot.

—Carson


> On May 23, 2017, at 3:23 PM, Nathan Ricks <[hidden email]> wrote:
>
> I've been working with maker and trying to use the maker_functional_gff to create an annotated .gff file. However, whenever I run the command, the following pops up, and just continues for a long time.
> Use of uninitialized value $qid in hash element at ./maker_functional_gff line 165, <$IN> line 58363.
> Use of uninitialized value $qid in hash element at ./maker_functional_gff line 170, <$IN> line 58363.
> Use of uninitialized value $qid in hash element at ./maker_functional_gff line 165, <$IN> line 58367.
> Use of uninitialized value $qid in hash element at ./maker_functional_gff line 170, <$IN> line 58367.
> ^CUse of uninitialized value $qid in hash element at ./maker_functional_gff line 165, <$IN> line 58368.
>
>
> Nathan Ricks
> _______________________________________________
> maker-devel mailing list
> [hidden email]
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org


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