Erfan Shekarriz

DEICODE Package for R Programming Language

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Hello! First of all, thank you for clearly addressing the issue of compositionality and the high probability of artifacts in ordination methodology. I wanted to ask if there would be...

Detecting kill signal by server when running on HPC

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Hello! I love snakemake and have been using it to build many projects. One feature I wanted to request is the ability of snakemake to detect when a job has...

[BUG] in writeMPS with open(filename, "w") as f: FileNotFoundError: [Errno 2] No such file or directory: 'tmp/d43ef73e150d46648f4e326813c760da-pulp.mps'

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Hello! I wanted to report a strange bug I'm seeing. When running ``` virsorter run -i output/2__assembly/contigs/CRC_meta.fa -w test/ --db-dir pipeline/database/vs2/ -j 1 --prep-for-dramv --min-length 200 --min-score 0 --include-groups dsDNAphage,ssDNA...

[Enhancement] Improving Multi-sample Parallelisation Strategy

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Hi! I wanted to point out that running ```coverm contig --coupled ....``` with 40+ samples doesn't scale well when compared to running each sample individually and then merging the output...

Hi and hope all is well! I just wanted to jump in and leave a quick recommendation for documentation. Specifically that I think CoverM lacks any real-life example walkthroughs with...

[Feature Request] Internally assigning Z for ```HMM``` class

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Hello! Thank you for the awesome and much-needed package. I wanted to ask if there could be an internal way to determine the Z value or if it can be...

cannot reproduce example for ```pyhmmer.hmmer.hmmsearch```

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Hello and hope all is well. I'm running into issues reproducing this code (https://pyhmmer.readthedocs.io/en/stable/examples/performance_tips.html#Search-and-scan): ```python import time import pyhmmer t1 = time.time() with pyhmmer.plan7.HMMFile("data/hmms/bin/t2pks.h3m") as hmms: with pyhmmer.easel.SequenceFile("data/seqs/938293.PRJEB85.HG003687.faa", digital=True) as...

Model selection for rank/beta penalty criterion of the SLR

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Dear Zachary, I hope all is well. I wanted to inquire about your pre-print and the beta/rank penalty parameter tuning for model selection. Specifically in your manuscript, you've written :...

[Feature Request] Conda Distribution for Taxonomic Identification

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Hi and hope all is well! I wanted to inquire about the conda installation timeline. I know that PPR-Meta is not conda-installable which is why you need to withhold the...

name attribute ValueError when running on the cluster

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Hi and hope all is well! I've caught a bug around the ```name``` attribute in Snakemake rules. Specifically the character ```:``` is not allowed and raises an error, but strangely...