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smirarab
PASTA (Practical Alignment using SATe and Transitivity)
Hello Siavash. Hoping you are well. I'm reaching the final steps to build a tree from the Silva 13.8 dataset. Unfortunately, it crashed during the tree inference step. The only...
after installing bioconda package, PASTA repeatedly returns errors because it looks for `mafft`, `hmmeralign`, `opal.jar`, `fasttree`, and `raxml` not in the conda environment's binary directory, but in its Python version's...
Installed Docker, image installs fine, help and --exportconfig work fine, runs fine under mafft. Switched the config "aligner =" option to "muscle" and get this error: ``` Unknown option "build_mst"...
While running the PASTA GUI I receive the following error when I add the "Extra RAxML Search" ```PASTA INFO: Performing post-processing tree search in RAxML… Process Process-2: Traceback (most recent...
I ran 3 PASTA commands, only 2 of which were successful: 1. PASTA with default parameters (SUCCESS) _run_pasta.py -d PROTEIN -i protein_sequences.txt -o pasta_job_ 2. PASTA with RaxML (SUCCESS) _run_pasta.py...
I'm running PASTA thus: ` python pasta/run_pasta.py --num-cpus=6 --aligner=HOMOLOGS --merger=MUSCLE --tree-estimator=RAXML -i simulated_reads/x.fa --alignment-suffix=HOMOLOGS.MUSCLE.RAXML.x -j HOMOLOGS.MUSCLE.RAXML.x` and getting this output: ``` PASTA INFO: Reading input sequences from 'simulated_reads/x.fa'... PASTA INFO:...
I'm confused by the available aligners with the Pasta GUI, why isn't Saté listed as a possible aligner? Also https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4424971/ seems to indicate that PASTA is another aligner itself, instead...
In the README, in step 5 (run `sudo python setup.py develop`), I think the `setup.py` script is expecting Python 3, because I get the following error message: ```bash Traceback (most...
I don't think you're involved with the recipe for Pasta on Bioconductor, and of course you are under no obligation to support that install method. But I thought I would...
The `--treeshrink-filter` help does not fully describe what it does. Does it remove sequences from the final alignment? How about individual steps?
