bam2hints created an empty gff file

Discussions about predicting genes with AUGUSTUS. Not covered here: WebAUGUSTUS and BRAKER1

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Jung
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Joined: Mon May 08, 2017 4:25 am

bam2hints created an empty gff file

Postby Jung » Mon May 08, 2017 4:35 am

Dear all,
I am trying ab-initio gene prediction on my species.

According to this page (http://bioinf.uni-greifswald.de/bioinf/ ... seq.Tophat), I attempted to get intron hints from several sets of RNAseq data, but at step 11, bam2hints created an empty .gff file.

I think it's not error because there was no on terminal and it just said like:

Wait a moment, calculating maximum block size that needs to be allocated... .. done

I suspected I happened to make some mistakes at previous steps, but I could not figure out.
Please Help.

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katharina
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Re: bam2hints created an empty gff file

Postby katharina » Mon Jan 29, 2018 9:07 am

Is it possible that you maxed the memory of your computer? If the bam file is huge, this might happen.
Katharina


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