John Urban

Some results. I tested just re-running the GeMoMa command, which failed due to `java.lang.OutOfMemoryError: Java heap space` as expected: ``` GeMoMa AnnotationFinalizer u=YES g=/path/to/genome.fa a=./gushr-NDXOWEYYRLQX/complete_gemoma_like.gff3 i=./gushr-NDXOWEYYRLQX/introns.gff c=UNSTRANDED coverage_unstranded=./gushr-NDXOWEYYRLQX/coverage.bedgraph rename=NO outdir=./gushr-NDXOWEYYRLQX/...

Thanks for your interest in poreminion. Poreminion was designed on older sets of fast5 files. Since ONT changes the internal structure of the fast5 files fairly often, poreminion breaks with...

Can you share a problematic fast5 file?

I can reproduce your issue on files that have no 2D and no 1D information -- but filled out with information otherwise -- and with completely empty fast5 files. It...

In the biorxiv preprint, it shows that I did the following order: ``` $ poreminion uncalled -m -o fail-filter fail/ $ poreminion timetest -m -o fail-filter fail/ ``` Noting that...

Both of the files you sent have "No template data found" in their logs. If poreminion did not label them as such it is almost certainly because ONT has changed...

The fast5stats from fast5tools will give you all seqlen information. However you can also try another fast5tools script: ``` fast5tofastx -r $READTYPE -o details pass/ fail/ > seqlens.txt ```

If you downloaded fast5tools in the past few days or so and had trouble, that is because we made some large packaging changes that broke all the scripts in the...