AUGUSTUS 3.3 hanging on contig
Posted: 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:
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:
Any idea what could be happening here?
My computer is running on Ubuntu 18.04.
Code: Select all
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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........100Command submitted was:
Code: Select all
augustus --strand=both --progress=true --gff3=on --uniqueGeneId=true --species=coprinus Ac200942-fast_redundans.scaffolds.reduced.polished.fastaMy computer is running on Ubuntu 18.04.