AUGUSTUS 3.3 hanging on contig

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PKooij
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Joined: Tue Apr 10, 2018 10:54 am

AUGUSTUS 3.3 hanging on contig

Post by PKooij » Tue Apr 10, 2018 11:01 am

I am trying to do a local gene prediction of my genome assembly with AUGUSTUS 3.3, but the analysis seems to be hanging on the second segment of my second contig:

Code: Select all

###
viterbi algorithm progress:
[%]: ........10........20........30........40........50........60........70........80........90........100
examining piece 165669..329444 (163776 bp)
viterbi algorithm progress:
[%]: ........10........20........30........40........50........60........70........80........90........100
sampling algorithm progress:
[%]: ........10........20........30........40........50........60........70........80........90........100
The first parts it analysed quite quickly, but it was hanging on this for 4 days (and I just canceled the analysis). I had a look into that particular segment of my contig, but I couldn't see any strange things in the sequence (no long stretches of N or repeats or other).

Command submitted was:

Code: Select all

augustus --strand=both --progress=true --gff3=on --uniqueGeneId=true --species=coprinus Ac200942-fast_redundans.scaffolds.reduced.polished.fasta
Any idea what could be happening here?

My computer is running on Ubuntu 18.04.

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katharina
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Re: AUGUSTUS 3.3 hanging on contig

Post by katharina » Thu Apr 12, 2018 8:56 am

I have notified Mario of this bug report. It might take a while to fix it, though.

Best,

Katharina
Katharina

PKooij
Posts: 2
Joined: Tue Apr 10, 2018 10:54 am

Re: AUGUSTUS 3.3 hanging on contig

Post by PKooij » Thu Apr 12, 2018 4:50 pm

Ok thanks! Please let me know if he needs any other details

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