jsoghigian

My error appears to be related to this error, so posting here. I did reinstall MaSuRCA and still received the error: ``` Attempt to free unreferenced scalar: SV 0x30b6ad8, Perl...

As I remembered previously running masurca some time ago on the cluster I was using, I loaded an earlier perl version that seemed to resolve the issue. May be an...

Hopefully it is okay to say, this would be a feature I would greatly appreciate. Was just coming to look if there was any 'less-interactive' way to do this!

Just as a note, we're getting the same above issue, I believe - Trying to calculate aai as follows, following install into the ezaai conda environment as per instructions. Command...

Great suggestions - I did what you said, and notably I updated the MACSE wrapper to have more memory. That got rid of the heap space error, but now I...

So I tried various things and kept running into the same error... I think the problem is my input file formats. The files from RefSeq have pipes which I think...

I did try to restart the pipeline. I noticed A LOT of the files that are pulled out by single_gene_orthogroups_tree.nf are 80 mb with 40k sequences in them! We've run...

Okay! It was the headers. RefSeq headers for a couple of my species looked like this: >lcl|NC_004818.2_prot_XP_311158.5_1 [gene=KIBRLG] [locus_tag=AgaP_AGAP000002] [db_xref=VectorBase:AGAP000002-PA,GeneID:1272272] [protein=AGAP000002-PA] [protein_id=XP_311158.5] [location=complement(join(582..865,950..3120,3211..3370,3459..3760,15747..15871))] [gbkey=CDS] I found an alternative repository with...

I can take a look! I almost wonder if a "translation table" would be a better optional approach for datasets like mine, where the headers are kind of a mess,...

Hi, I'm looking to train a dataset to test DeepNOG with. Could you provide a bit more information on how to do this? I'm working on a cluster environment if...