jessicalumian issues

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jessicalumian

`ModuleNotFoundError: No module named 'Cython'` error when install sgc on EC2 instance

hi! I'm having problems installing sgc on a fresh ec2. This could be user error. AMI: Ubuntu Server 20.04 LTS (HVM), SSD Volume Type Instance Type: r4.large Followed installs here:...

questions about sourmash gather and prefetch output `avg_abund` and `match_bp`

From sourmash gather command line output, what is `avg_abund`? (I believe this is `average_abund` in the gather csv output). Is it the depth of coverage of matching hashes between query...

Removing unique k-mers between samples

Hello! I am working on replicating some (amazing) work from Taylor's [IBD project](https://www.biorxiv.org/content/10.1101/2022.06.30.498290v1.full). I have signatures from `sourmash sketch dna` of metagenome samples. I would like to remove k-mers that...

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How will redundant or closely related sequences in a database affect kraken?

I am interested in using RefSeq as a Kraken database and supplementing it with sequences from Genbank. If there are multiple sequences from closely related organisms in the database, will...

Problem with rule extract_leftover_reads_wc (DeprecationWarning: Implementing implicit namespace packages)

Hello! I'm using v0.9.3 I got an error in the `rule extract_leftover_reads_wc` step. yml: ``` samples: - ckd_AA_RX_25_31201053301001_LP_550_C1_L2_R128 outdir: outputs.ckd/ sourmash_databases: - /home/jupyter-jessica/databases/gtdb-rs207.genomic-reps.dna.k31.zip - /home/jupyter-jessica/databases/genbank-2022.03-fungi-k31.zip - /home/jupyter-jessica/databases/genbank-2022.03-protozoa-k31.zip - /home/jupyter-jessica/databases/genbank-2022.03-viral-k31.zip prevent_sra_download:...

maximum number of gather hashes on report graph and finding numbers of hashes that don't match anything

Hello I have some questions! 1. How can I modify the gather hashes vs mapped bp graph to show more than 60 genomes? 2. How can I see the number...

would it be helpful to add ln to configuration instructions?

whenever i have run my own metagenomes following [this](https://dib-lab.github.io/genome-grist/configuring/), I don't move the actual metagenomes into the `trim/` directory because they're already on farm somewhere else and they're big. I...

output directories besides abundtrim and sigs removed after clean_gather

I've been running grist with a custom list of metagenomes. I removed a few metagenomes and ran `clean_gather` but got some errors, and found all the directories in my output...

add pip install screed to instructions?

I ran the following commands while following the page to configure my own [genome-grist project](https://dib-lab.github.io/genome-grist/configuring/) ``` python -m genome_grist.copy_local_genomes databases/antarctic/*.fa -o databases/antarctic.info.csv -d databases/antarctic.d python -m genome_grist.make_info_file databases/antarctic.info.csv ``` I...