Sam’s Notebook - Daily Bits

20230223

Created a genes BED file to use in E5 isoform analysis and added to the Genomic Resources Handbook page:

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. 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 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 and added to Genomic Resources Handbook page.
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 alignments and StringTie analysis using E5 P.verrucosa trimmed RNA-seq data.

20230215

Long Slack chat with Danielle Becker regarding her E5 P.verrucosa RNA-seq data.
- Trimming doesn’t look like it worked (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).
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. Read this notebook entry of hers 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/
  - 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, 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, 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 = <redacted>
secret_access_key = <redacted>
endpoint = https://sdsc.osn.xsede.org
```
  Ran this command to initiate transfer:
```
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 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 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.