--- author: Sam White toc-title: Contents toc-depth: 5 toc-location: left layout: post title: Daily Bits - February 2023 date: '2023-02-01 08:22' tags: - daily bits categories: - 2023 - Daily Bits --- 20230223 - Created a genes BED file to use in E5 isoform analysis and added to the [Genomic Resources Handbook page](https://robertslab.github.io/resources/Genomic-Resources/): ```shell bedops_linux_x86_64-v2.4.40/gff2bed \ < Pver_genome_assembly_v1.0-valid.genes.gff3 \ | awk -F"\t" 'BEGIN {OFS="\t"} {print $1, $2, $3, $4, $5, $6}' \ > Pver_genome_assembly_v1.0-valid.genes.bed ``` 20230222 - Managed to fix missing "Edit" icon from the [The Roberts Lab Handbook](https://robertslab.github.io/resources/). Not sure which of the following was the final fix, but here's what was done after I noticed that the MkDocs "Material" theme had been updated: - New update requires explicit declaration for "edit" button. Added this to the `mkdocs.yml`: ``` features: - content.action.edit ``` - Updated GitHub action (`github_actions.yml`) to match "Material" theme documentation: # Runs mkdocs-material theme for readthedocs documentation # Automatically deploys documentation to https://robertslab.github.io/resources name: ci on: push: branches: - master - main permissions: contents: write jobs: deploy: runs-on: ubuntu-latest steps: - uses: actions/checkout@v3 - uses: actions/setup-python@v4 with: python-version: 3.x - uses: actions/cache@v2 with: key: ${{ github.ref }} path: .cache - run: pip install mkdocs-material - run: mkdocs gh-deploy --force 20230221 - Initiated MEGAN6 taxonomic classification on _P.verrucosa_ E5 RNA-seq reads. - Updated [Genomic Resources Handbook page](https://robertslab.github.io/resources/Genomic-Resources/) with the updated _P.verrucosa_ GFFs and GTFs, along with corresponding notebook links, etc. 20230220 - Discovered (after HiSat2/Stringtie analysis failed) that the _P.verrucosa_ GFF3 file is not a valid GFF. A number of rows had more than nine fields, which is not a valid GFF. So, had to deal with figuring out how to fix that. Will re-run the analysis using the fixed GFF, and the corresponding updated GTF... 20230217 - Science Hour - [Created _C.goreaui_ (_P.verrucosa_ endosymbiont) GTF](https://robertslab.github.io/sams-notebook/posts/2023/2023-02-17-Data-Wrangling---C.goreaui-Genome-GFF-to-GTF-Using-gffread/) and added to [Genomic Resources Handbook page](https://robertslab.github.io/resources/Genomic-Resources/). - Read a lot about container usage in order to be able to effectively use `coenv` node on Klone... 20230216 - Pub-a-thon - Long meeting with Emma Strand trying to troubleshoot conda install of EpiDiverse/snp on her HPC cluster. No luck. Advised her to talk with her IT dept. - Downloaded _P.verrucosa_ endosymbiont genome and GFF files. - Began [`HISAT2`](https://daehwankimlab.github.io/hisat2/) alignments and StringTie analysis using E5 _P.verrucosa_ [trimmed RNA-seq data]((https://robertslab.github.io/sams-notebook/posts/2023/2023-02-15-FastQ-Trimming-and-QC---P.verrucosa-RNA-seq-Data-from-Danielle-Becker-in-Hollie-Putnam-Lab-Using-fastp-FastQC-and-MultiQC-on-Mox/)). 20230215 - Long Slack chat with Danielle Becker regarding her E5 _P.verrucosa_ RNA-seq data. - [Trimming doesn't look like it worked](https://gannet.fish.washington.edu/Atumefaciens/hputnam-Becker_E5/Becker_RNASeq/data/trimmed/trimmed_qc/multiqc_report.html) (MultiQC Report; HTML). - I trimmed raw data: - [https://robertslab.github.io/sams-notebook/posts/2023/2023-02-15-FastQ-Trimming-and-QC---P.verrucosa-RNA-seq-Data-from-Danielle-Becker-in-Hollie-Putnam-Lab-Using-fastp-FastQC-and-MultiQC-on-Mox//robertslab.github.io/sams-notebook/2023/02/15/FastQ-Trimming-and-QC-P.verrucosa-RNA-seq-Data-from-Danielle-Becker-in-Hollie-Putnam-Lab-Using-fastp-FastQC-and-MultiQC-on-Mox/) 20230214 - Helped with an issue that Marta Gomez-Buckley [was having trying to install RAxML-NG on the UW HPC (Klone)](https://github.com/RobertsLab/resources/issues/1578). - Continued to help Emma Strand with her issue getting EpiDiverse/snp installed on their HPC at URI. 20230213 - Lab meeting. - CEABIGR meeting w/Yaamini. - Just worked on adding text (Methods) to manuscript. - Continued to help Emma Strand with her issue getting EpiDiverse/snp installed on their HPC at URI. 20230210 - Worked a lot with Emma Strand from URI to try to troubleshoot her usage of the Nextflow [EpiDiverse/snp pipeline](https://github.com/EpiDiverse/snp). Read [this notebook entry of hers](https://github.com/emmastrand/EmmaStrand_Notebook/blob/master/_posts/2023-02-06-EpiDiverse-Bleaching-Pairs-Analysis.md#troubleshooting) for some details on the error. Seems to be related to use of Singularity (now Apptainer) container; particularly after she ran the pipeline using the `test` command and got the same error message as when she ran with her own data set. - Transferred Danielle Becker Coral E5 data from Mox to Gannet: - [hputnam-Becker_E5/](https://gannet.fish.washington.edu/Atumefaciens/hputnam-Becker_E5/) - NOTE: There are no README files, so I can only glean info regarding contents from directory names. Will potentially discuss contents in more detail with Danielle at a later date. 20230209 - Worked with Danielle Becker, as part of the Coral E5 project, to transfer data related to [this repo](https://github.com/hputnam/Becker_E5), from her HPC (Univ. of Rhode Island; Andromeda) to ours (Univ. of Washington; Mox) in order to eventually transfer to Gannet so that these files are publicly accessible to all members of the Coral E5 project. - GlobusConnect did not work. Couldn't figure out how to make URI endpoint accessible. - URI IT provide a solution via [rclone](https://rclone.org/), involving transferring the data from an Amazon S3 bucket. `rclone` setup info is below, but I've removed the access key info: ``` [becker] type = s3 provider = Ceph access_key_id = secret_access_key = endpoint = https://sdsc.osn.xsede.org ``` Ran this command to initiate transfer: ```shell rclone --progress copy becker:uri-inbre/Becker/ ./Becker ``` This copied all of the data (~1.1TB!!)to this directory on Mox: `/gscratch/srlab/sam/data/Becker` Transfer was estimated to take ~12hrs, so I just let it run. Will transfer to Gannet tomorrow... - Pub-a-thon. 20230208 - Worked on Ariana's [Tidy Tuesday assignment](https://github.com/RobertsLab/resources/discussions/1574) for lab meeting next week. 20230207 - In lab helping Laura & Steven get supplies ready for cod sampling in Oregon tomorrow. - Worked on Ariana's [Tidy Tuesday assignment](https://github.com/RobertsLab/resources/discussions/1574) for lab meeting next week. 20230206 - Read Ch. 13 of "The Disordered Cosmos." - Lab meeting. - Weekly CEABIGR meeting. - Decision is to spend time on manuscript. 20230203 - Comlete and total lack of motivation. Ugh. 20230202 - Pub-a-thon. 20230201 - Added CEABIGR mean gene methylation coefficients of variation (CoV) scatter plots to [our Miro board](https://miro.com/app/board/uXjVPYZDgxw=/).