Gani
Gani
Hi, When I run: `download_genomes.sh "Methanosarcina"` It gives me: `find: refseq/bacteria: No such file or directory` Any tips on downloading from an archaeal genus? Many thanks! Gaofeng
Hello, Hope it's not a very obvious mistake from my side. I used the following command: ``` phylophlan \ --input_folder /home/gnii0001/rp24/gaofeng/projects/02_acidic_nitritation/data/faa \ --output_folder /home/gnii0001/rp24/gaofeng/projects/02_acidic_nitritation/result/phylophlan \ --nproc 24 \ --diversity medium...
Hi, I'm to check my usage of DRAM is appropriate, in terms of maximizing computational efficiency. I specified using 32 threads for annotate on HPC, and I used `htop` to...
Hi @fasnicar It's related to a couple of posts I made [link1](https://github.com/biobakery/phylophlan/issues/107) [link2](https://forum.biobakery.org/t/optimize-run-time-in-phylophlan3/5210/2), and also a [post](https://forum.biobakery.org/t/phylophlan-is-running-too-slow-when-mapping-dna/4152/2) from you on biobakery forum. I was wondering if down grading diamond to...
Hi, I have encountered this error: multiprocessing.pool.RemoteTraceback: """ Traceback (most recent call last): File "/30days/uqgni1/tools/Miniconda3/envs/enrichm_0.5.0/lib/python3.6/multiprocessing/pool.py", line 119, in worker result = (True, func(*args, **kwds)) File "/30days/uqgni1/tools/Miniconda3/envs/enrichm_0.5.0/lib/python3.6/multiprocessing/pool.py", line 44, in mapstar...
Hello, I have 2 genomes in fna, this is my script: source activate enrichm_0.5.0 export ENRICHM_DB=/path_to_enrichm_db enrichm annotate \ --output /path_to_output \ --genome_directory /path_to_genomes \ --ko_hmm \ --ec \ --pfam...
Hey, thank you for the cool script. However, I cannot work this out. I'm trying do download the genomic sequence from: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/762/265/GCF_000762265.1_ASM76226v1 Pretty sure the fna files are available, and...
Hi, Thank you for the nice work. I had run stage one successfully, however, I'm not sure how to troubleshoot an error at stage 2. My script is: ``` perl...