Daily Bits - April 2024 – Sam’s Notebook

20240430

In lab

Helped Eric get started with qPCR analysis.
EH&S disposal of mercuric chloride waste in FTR 228 (GitHub Issue).
Replaced Owl’s UPS battery (APCRBC123).
Dealt with Owl dying (GitHub Issue).
Shipped Pacific cod tissues for WGNS (Notebook).

20240429

DuMOAR (GitHub repo)

Continued to look into Trinotate annotation [issue where BLASTp results do not have SwissProt IDs(https://github.com/laurahspencer/DuMOAR/issues/44#issuecomment-1977588065)].
- Issue is related to built-in BLASTp database. FastA headers do not contain SwissProt IDs, Thus, they don’t end up in the final annotation report file.
- Considering “custom” BLASTp database created from the full UniProt protein FastA, since I belive the Trinotate parsing is based on column numbers in the BLASTp output format 6 (which would contain the SwisProt IDs), as opposed to specifically parsing specifically formatted strings within that output format.

Singularity Containers

Related to above, started to explore the use of containers - specifically the Trinotate Singularity image.
- Most confusing aspect is the fact that there are two programs which cannot be included with Trinotate, due to licensing issues:
  - signalp6
  - tmhmmv2
  The main question: How do I access/run these programs if they’re not in the container? To do so, I downloaded/installed them on Raven and then I added them to the container’s system $PATH when starting the container, like so:
```
singularity shell -e \
--env PREPEND_PATH="/home/sam/programs/mambaforge/envs/singalp6_env/bin:/home/shared/tmhmm-2.0c/bin:/home/shared/infernal-1.1.5-linux-intel-gcc/binaries:/home/shared/hmmer-3.4/src" \
/home/shared/containers/trinotate.v4.0.2.simg
```
  This appended the programs on my computer to the beginning of the container’s system $PATH, thus allowing these programs to be called.
- Another confusing aspect was how to access locations on my local computer once I was in the container. For example, the user’s $HOME directory is mounted/bound (i.e. accessible) by default. However, I also needed access to /home/shared, but I didn’t want to bind this to a directory within the container because then it would superseded the contents of the specified directory in the container. Since I wasn’t terribly familiar with the container’s structure, nor how to add a directory when starting the container image, I managed to figure out that the current directory from which the user starts the container image is automatically bound. So, I navigated to /home/shared first, then started the container with the command shown above. This permitted me to access /home/shared and all its subdirectories.

20240426

DuMOAR (GitHub repo)

Continued to look into Trinotate annotation [issue where BLASTp results do not have SwissProt IDs(https://github.com/laurahspencer/DuMOAR/issues/44#issuecomment-1977588065)].
- Started to explore newer version of Trinotate to see if the issue could be resolved.

20240425

DuMOAR (GitHub repo)

Started to look into Trinotate annotation [issue where BLASTp results do not have SwissProt IDs(https://github.com/laurahspencer/DuMOAR/issues/44#issuecomment-1977588065)].

20240424

Coral E5 (GitHub repo)

Finished up P.meandrina miRDeep2 with cnidarian miRBase.

20240423

Miscellaneous

Resolved degarded storage pool issue with Gannet.

20240422

Coral E5 (GitHub repo)

Worked on P.meandrina stuff:
- BLASTn with cnidarin miRBase.
- miRDeep2 with cnidarian miRBase.

Miscellaneous

ProCard reconcilation junk.

20240402

In lab

Filled LN₂ dry shipper and dewar for Arianna (GitHub Issue).
Showed Zach how to use the plate reader (GitHub Issue).

Coral E5 (GitHub repo)

Worked on running pipeline for A.pulchra with agreed upon trimming/merging params.

20240401

CEABIGR (GitHub repo)

Looked up Freebayes parameters (GitHub Issue).

Coral E5 (GitHub repo)

Worked on running pipeline for A.pulchra with agreed upon trimming/merging params.

Miscellaneous

Submitted PO request for cod WGBS at Psomagen (GitHub Issue).