BenjaminSchwessinger

Great. We had the same issue! On 6/27/17 3:04 AM, Philipp Rescheneder wrote: > > Thank you for the feedback! > > Instead of commenting out the line you could...

Okay I fixed it now as follows e.g. in the clean.py script I added the following around 160: if not os.path.dirname(args.out) == "": os.chdir(os.path.dirname(args.out)) [needed to add an 'import os'...

Thanks Jon. So for clean a temp folder would be good as snakemake executes all the runs in the same folder so the "minimap_tmp*" "query_*" and "reference_*" of different runs...

Yes pretty much. I found a work around with tweaking your code a tine bit specific for our cluster that works really well. Makes a huge difference being able to...

Sure thing. Jason. Let me clean it up and I put it on github next week with a bit of instructions. I also adapted the code from funannotate minimally to...

Hi there. It took me a while to clean stuff up and our HPC was down as well. So here is a very basic snakemake pipeline for funannotate in w/o...

I could reproduce the same issue when using bam files converted from bax.h5 files generated by an RSII machine in the latest FALCON unzip version [Latest commit 7ebc99c on Dec...

Two related questions. #1 Is unzip also compatible with smrtlink_3.1.0.180439 as I am always getting the error 'Failure: The Quiver algorithm requires an alignment file containing standard (non-CCS) reads.' when...

Apologies badly worded at the end. so the p_ctg.xxx.fa in 1-hasm/xxx file for these two cases, where sum(h_ctg length) > p_ctg length, only contains a header and no actual contig...

sure what all do you want? the whole unzip or only the 1-hasm folder? On 6/17/16 4:12 PM, Jason Chin wrote: > I will need to see the content of...