Software Testing - Stevens workflow-annotation Pipeline

2026
software
annotation
workflow-annotation
Author

Sam White

Published

March 5, 2026

INTRO

Steven asked me to test out his workflow-annotation pipeline (GitHub) after Hannah encountered an issue yesterday and we implemented a potential fix (GitHub Issue).

The pipeline was designed to take nucleotide sequences all the way through gene ontology annotation.

After some back-and-forth attempts at troubleshooting, I resorted to asking the Gemini 3 Flash (preview) gAI agent. The suggestion was the lack of an User-Agent in the URL request header was causing the 403 permission denied error Hannah (and I) encountered.

I implemented the suggested changes and tested them.

METHODS

As input, I used a subset of a FastA file provided by Hannah (see code below).

Set up Conda environment

Create Mamba/Conda environment

Important

Be sure to deactivate any current Python/Conda environments!

deactivate

and/or

conda deactivate

mamba create \
-n sr320-workflow-annotation \
python=3.11 \
diamond \
blast \
requests \
pandas \
goatools \
matplotlib \
-c bioconda \
-c conda-forge \
-y

R setup

Code 
library(reticulate)

Set R variables

Specifically, sets Conda paths/environments to be used throughout this notebook.

Important

This was run on my laptop, so the paths are specific to my system. Adjust as needed for your system.

Code 
# CONDA
conda_env_name <- c("/home/sam/programs/miniforge3/envs/sr320-workflow-annotation")
conda_path <- c("/home/sam/programs/miniforge3/bin/conda")

# WORKING DIRECTORY
working_dir <- c("/home/sam/gitrepos/RobertsLab/sams-notebook/posts/2026/2026-03-05-Software-Testing---Stevens-workflow-annotation-Pipeline/")
Sys.setenv(working_dir = working_dir)

Load worfkflow-annotation conda environment

If this is successful, the first line of output should show that the Python being used is the one in your workflow-annotation conda environment path.

E.g.

python: /home/sam/programs/miniforge3/envs/sr320-workflow-annotation/bin/python

Code 
use_condaenv(condaenv = conda_env_name, conda = conda_path)
py_config()
python:         /home/sam/programs/miniforge3/envs/sr320-workflow-annotation/bin/python
libpython:      /home/sam/programs/miniforge3/envs/sr320-workflow-annotation/lib/libpython3.11.so
pythonhome:     /home/sam/programs/miniforge3/envs/sr320-workflow-annotation:/home/sam/programs/miniforge3/envs/sr320-workflow-annotation
version:        3.11.15 | packaged by conda-forge | (main, Mar  5 2026, 16:45:40) [GCC 14.3.0]
numpy:          /home/sam/programs/miniforge3/envs/sr320-workflow-annotation/lib/python3.11/site-packages/numpy
numpy_version:  2.4.2

NOTE: Python version was forced by use_python() function

Clone the workflow-annotation pipeline

git clone git@github.com:kubu4/workflow-annotation.git

Download the FastA

Note

The full FastA was not utilized. I created a subset for quick testing.

cd "/home/sam/gitrepos/RobertsLab/sams-notebook/posts/2026/2026-03-05-Software-Testing---Stevens-workflow-annotation-Pipeline/"

git clone git@github.com:kubu4/workflow-annotation.git

cd workflow-annotation

wget --quiet --continue https://raw.githubusercontent.com/hannahnowers/Seastar-capstone/refs/heads/main/data/derm-protein.fa
Code 
cd "/home/sam/gitrepos/RobertsLab/sams-notebook/posts/2026/2026-03-05-Software-Testing---Stevens-workflow-annotation-Pipeline/workflow-annotation"

cat subset-derm-protein.fa
>g7941.t1
MQYLPFRGVLCVFWGFLLIETFRPANAGDFALVADLRNGTIYAGSIGQSLADIAPLPLTG
VIRPLAVEYDPVEKMVYWTDVNSLPSPKITRAHVNGSGQMTLVDQLHLPDGLALDVESRL
VYWTDGVLGYIGRTRMNGTGARETIVVGLDQPRAIITDSGFIYWTDWGNSSRIERAGLDG
SNRTTLITGNLVWPNGLFKDGNNLYWCDAKLDKIERSDLLGNNREIVIDLTSYPQIHPFD
LAVYDEYIYWTDWGYTTLIRVHTSGRGEQNYGPSVFQQSGGLHIQKEPNYCNSSPCQNGA
ICIDVINGFSCICPSEHQGITRSENPSGSGPCVNGGTCTTIPGGFTCQCPAGYDGPTCTI
EFIVKKRDREIAGKCKRLH*
>g7942.t1
MVVQVTKTSRDYGKINPELLQNLLDERLRDTFQTEDYPNLLYETYESITTSVLDEICPVT
TRVRTVKPRLPWYDNTIQEERRIPRRLERNWRKSRLDTDYDAFLTQENNV*
>g7943.t1
MKSTSSAILCLFGLFGLGYCGPCETLDPCENGAQCLDFDSIPGYFFCYCPYTFYGTRCEN
RNAACDDNPCMFGGTCLVFNERYECECPSGIYGNHCQANGCANDPCMNGGTCWPFGFSYT
CICSPGYRGENCDE*
>g7944.t1
MATIPIDTCKRHASTKSAETVGVKHLRRRIQTTGPLTIADYMREVLTNPLTGYYMNKDVF
GNKGDFITSPEISQMFGELIALWIIHEWTQLGQMTPLQVVELGPGRGTLADDMLRVFKQF
QHITGNSLSLHLVEVSPKMSQLQEEKLTGQQQSKTDMDQPSVSQDSPAGRCEGDTVAERG
SLSSAYKTSISKTGMPVSWYQSLKEVPKGVSCFIAHEFFDALPIHQFKKTEKGWREVLVD
VDSDDAGSNHLRFVLSPAATPASTVYPQGSDSRGQIEVCPEGGVIVQEMAHRISEHGGMS
LIVDYGHDGTKTDTLRGFKKHKLHDVLCEPGTADLTADVDFSYFRQVVQGKVSTHGPITQ
ESFLKAMGIETRLKMLLKSATGEQRNSLITGCRMLTDPAQMGERFKFFAMMPLNQGTESG
QAKARTPAGFPSVC*

Execute the annotation script

Code 
cd "/home/sam/gitrepos/RobertsLab/sams-notebook/posts/2026/2026-03-05-Software-Testing---Stevens-workflow-annotation-Pipeline/workflow-annotation" && \
export PATH="/home/sam/programs/miniforge3/envs/sr320-workflow-annotation/bin:$PATH" && \
./blast2slim.sh \
-i subset-derm-protein.fa \
--diamond \
--protein \
> blast_run.log 2>&1

RESULTS

Check log

Code 
cat "/home/sam/gitrepos/RobertsLab/sams-notebook/posts/2026/2026-03-05-Software-Testing---Stevens-workflow-annotation-Pipeline/workflow-annotation/blast_run.log"
[INFO] Output directory: output/run_20260310_164133
[INFO] Running DIAMOND BLASTP...
diamond v2.1.23.177 (C) Max Planck Society for the Advancement of Science, Benjamin J. Buchfink, University of Tuebingen
Documentation, support and updates available at http://www.diamondsearch.org
Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021)

#CPU threads: 40
Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1)
Temporary directory: output/run_20260310_164133
#Target sequences to report alignments for: 1
Opening the database...  [0.101s]
Database: blastdb/uniprot_sprot.dmnd (type: Diamond database, sequences: 574627, letters: 208482574)
Block size = 2000000000
Opening the input file...  [0s]
Opening the output file...  [0s]
Loading query sequences...  [0s]
Masking queries...  [0.014s]
Algorithm: Double-indexed
Building query histograms...  [0.006s]
Seeking in database...  [0s]
Loading reference sequences...  [0.565s]
Masking reference...  [3.266s]
Initializing temporary storage...  [0s]
Building reference histograms...  [2.46s]
Allocating buffers...  [0s]
Processing query block 1, reference block 1/1, shape 1/2, index chunk 1/4.
Building reference seed array...  [0.838s]
Building query seed array...  [0.007s]
Computing hash join...  [0.055s]
Masking low complexity seeds...  [0.009s]
Searching alignments...  [0.006s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 1/2, index chunk 2/4.
Building reference seed array...  [1.104s]
Building query seed array...  [0.008s]
Computing hash join...  [0.056s]
Masking low complexity seeds...  [0.006s]
Searching alignments...  [0.005s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 1/2, index chunk 3/4.
Building reference seed array...  [1.153s]
Building query seed array...  [0.009s]
Computing hash join...  [0.058s]
Masking low complexity seeds...  [0.003s]
Searching alignments...  [0.004s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 1/2, index chunk 4/4.
Building reference seed array...  [0.817s]
Building query seed array...  [0.006s]
Computing hash join...  [0.056s]
Masking low complexity seeds...  [0.003s]
Searching alignments...  [0.005s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 2/2, index chunk 1/4.
Building reference seed array...  [0.859s]
Building query seed array...  [0.009s]
Computing hash join...  [0.054s]
Masking low complexity seeds...  [0.003s]
Searching alignments...  [0.005s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 2/2, index chunk 2/4.
Building reference seed array...  [1.106s]
Building query seed array...  [0.006s]
Computing hash join...  [0.049s]
Masking low complexity seeds...  [0.004s]
Searching alignments...  [0.003s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 2/2, index chunk 3/4.
Building reference seed array...  [1.038s]
Building query seed array...  [0.007s]
Computing hash join...  [0.05s]
Masking low complexity seeds...  [0.006s]
Searching alignments...  [0.007s]
Deallocating memory...  [0s]
Processing query block 1, reference block 1/1, shape 2/2, index chunk 4/4.
Building reference seed array...  [0.786s]
Building query seed array...  [0.007s]
Computing hash join...  [0.055s]
Masking low complexity seeds...  [0.005s]
Searching alignments...  [0.011s]
Deallocating memory...  [0s]
Deallocating buffers...  [0.036s]
Clearing query masking...  [0s]
Computing alignments...  [0.098s]
Deallocating reference...  [0.017s]
Loading reference sequences...  [0s]
Deallocating buffers...  [0s]
Deallocating queries...  [0s]
Loading query sequences...  [0s]
Closing the input file...  [0s]
Closing the output file...  [0s]
Closing the database...  [0.005s]
Cleaning up...  [0s]
Total time = 14.878s
Reported 2 pairwise alignments, 2 HSPs.
2 queries aligned.
deps ok
output/run_20260310_164133/go-basic.obo: fmt(1.2) rel(2026-01-23) 42,036 Terms; optional_attrs(relationship)
output/run_20260310_164133/goslim_generic.obo: fmt(1.2) rel(go/2026-01-23/subsets/goslim_generic.owl) 207 Terms; optional_attrs(relationship)
[DONE] Wrote:
 - output/run_20260310_164133/annotation_full_go.tsv
 - output/run_20260310_164133/annotation_with_goslim.tsv
[INFO] Summary stats: 2/2 BLAST hits, 2 GO annotations, 2 GO-Slim mappings
[INFO] Generated GO-Slim chart: goslim_chart.png
[INFO] Generated summary report: summary.md
[OK] All done. See output/run_20260310_164133/annotation_with_goslim.tsv and output/run_20260310_164133/summary.md

Confirm expected output files

Code 
cd "/home/sam/gitrepos/RobertsLab/sams-notebook/posts/2026/2026-03-05-Software-Testing---Stevens-workflow-annotation-Pipeline/workflow-annotation"

ls -ltrh output/run_*
output/run_20260306_113912:
total 31M
-rw-rw-r-- 1 sam sam  339 Mar  6 11:39 subset-derm-protein.blast.tsv
-rw-rw-r-- 1 sam sam 9.0K Mar  6 11:39 postprocess_uniprot_go.py
-rw-rw-r-- 1 sam sam 2.8K Mar  6 11:39 annotation_full_go.tsv
-rw-rw-r-- 1 sam sam  31M Mar  6 11:39 go-basic.obo
-rw-rw-r-- 1 sam sam 122K Mar  6 11:39 goslim_generic.obo
-rw-rw-r-- 1 sam sam 3.2K Mar  6 11:39 annotation_with_goslim.tsv
-rw-rw-r-- 1 sam sam  296 Mar  6 11:39 summary_stats.json
-rw-rw-r-- 1 sam sam  51K Mar  6 11:39 goslim_chart.png
-rw-rw-r-- 1 sam sam 1.2K Mar  6 11:39 summary.md

output/run_20260306_150323:
total 31M
-rw-rw-r-- 1 sam sam  339 Mar  6 15:03 subset-derm-protein.blast.tsv
-rw-rw-r-- 1 sam sam 9.0K Mar  6 15:03 postprocess_uniprot_go.py
-rw-rw-r-- 1 sam sam 2.8K Mar  6 15:03 annotation_full_go.tsv
-rw-rw-r-- 1 sam sam  31M Mar  6 15:03 go-basic.obo
-rw-rw-r-- 1 sam sam 122K Mar  6 15:03 goslim_generic.obo
-rw-rw-r-- 1 sam sam 3.2K Mar  6 15:03 annotation_with_goslim.tsv
-rw-rw-r-- 1 sam sam  296 Mar  6 15:03 summary_stats.json
-rw-rw-r-- 1 sam sam  51K Mar  6 15:03 goslim_chart.png
-rw-rw-r-- 1 sam sam 1.2K Mar  6 15:03 summary.md

output/run_20260310_164133:
total 31M
-rw-rw-r-- 1 sam sam  339 Mar 10 16:41 subset-derm-protein.blast.tsv
-rw-rw-r-- 1 sam sam 9.0K Mar 10 16:41 postprocess_uniprot_go.py
-rw-rw-r-- 1 sam sam 2.8K Mar 10 16:41 annotation_full_go.tsv
-rw-rw-r-- 1 sam sam  31M Mar 10 16:41 go-basic.obo
-rw-rw-r-- 1 sam sam 122K Mar 10 16:41 goslim_generic.obo
-rw-rw-r-- 1 sam sam 3.2K Mar 10 16:41 annotation_with_goslim.tsv
-rw-rw-r-- 1 sam sam  296 Mar 10 16:41 summary_stats.json
-rw-rw-r-- 1 sam sam  51K Mar 10 16:41 goslim_chart.png
-rw-rw-r-- 1 sam sam 1.2K Mar 10 16:41 summary.md

Peek at output files

Code 
cd "/home/sam/gitrepos/RobertsLab/sams-notebook/posts/2026/2026-03-05-Software-Testing---Stevens-workflow-annotation-Pipeline/workflow-annotation/output"

find run_*/ -maxdepth 1 -type f ! -name "*.png" -exec head {} +
==> run_20260306_113912/annotation_with_goslim.tsv <==
query   accession   id  reviewed    protein_name    organism    pident  length  evalue  bitscore    title   go_ids  go_bp   go_cc   go_mf   goslim_ids  goslim_names
g7941.t1    C0HL13  LRP2_PIG        Low-density lipoprotein receptor-related protein 2 (LRP-2) (Glycoprotein 330) (gp330) (Megalin) Sus scrofa (Pig)    28.9    294 2.34e-31    129 sp|C0HL13|LRP2_PIG Low-density lipoprotein receptor-related protein 2 OS=Sus scrofa OX=9823 GN=LRP2 PE=1 SV=1   GO:0001843; GO:0003139; GO:0003148; GO:0003223; GO:0005509; GO:0005905; GO:0006898; GO:0007605; GO:0008584; GO:0009897; GO:0016324; GO:0017124; GO:0030001; GO:0030424; GO:0030425; GO:0030514; GO:0031526; GO:0031904; GO:0043235; GO:0050769; GO:0051087; GO:0060068; GO:0060982; GO:0061156; GO:0070447; GO:0140058; GO:1904447; GO:1905167  coronary artery morphogenesis [GO:0060982]; folate import across plasma membrane [GO:1904447]; male gonad development [GO:0008584]; metal ion transport [GO:0030001]; negative regulation of BMP signaling pathway [GO:0030514]; neural tube closure [GO:0001843]; neuron projection arborization [GO:0140058]; outflow tract septum morphogenesis [GO:0003148]; positive regulation of lysosomal protein catabolic process [GO:1905167]; positive regulation of neurogenesis [GO:0050769]; positive regulation of oligodendrocyte progenitor proliferation [GO:0070447]; pulmonary artery morphogenesis [GO:0061156]; receptor-mediated endocytosis [GO:0006898]; secondary heart field specification [GO:0003139]; sensory perception of sound [GO:0007605]; vagina development [GO:0060068]; ventricular compact myocardium morphogenesis [GO:0003223]   apical plasma membrane [GO:0016324]; axon [GO:0030424]; brush border membrane [GO:0031526]; clathrin-coated pit [GO:0005905]; dendrite [GO:0030425]; endosome lumen [GO:0031904]; external side of plasma membrane [GO:0009897]; receptor complex [GO:0043235]  calcium ion binding [GO:0005509]; protein-folding chaperone binding [GO:0051087]; SH3 domain binding [GO:0017124]   GO:0016192; GO:0022414; GO:0048856; GO:0050877; GO:0055085  vesicle-mediated transport; reproductive process; anatomical structure development; nervous system process; transmembrane transport
g7944.t1    Q7L592  NDUF7_HUMAN     Protein arginine methyltransferase NDUFAF7, mitochondrial (EC 2.1.1.320) (NADH dehydrogenase [ubiquinone] complex I, assembly factor 7) (Protein midA homolog)  Homo sapiens (Human)    51.8    415 8.529999999999999e-141  412 sp|Q7L592|NDUF7_HUMAN Protein arginine methyltransferase NDUFAF7, mitochondrial OS=Homo sapiens OX=9606 GN=NDUFAF7 PE=1 SV=1    GO:0005615; GO:0005739; GO:0005759; GO:0008168; GO:0019899; GO:0019918; GO:0032981; GO:0035243  mitochondrial respiratory chain complex I assembly [GO:0032981]; peptidyl-arginine methylation, to symmetrical-dimethyl arginine [GO:0019918]   extracellular space [GO:0005615]; mitochondrial matrix [GO:0005759]; mitochondrion [GO:0005739] enzyme binding [GO:0019899]; methyltransferase activity [GO:0008168]; protein-arginine omega-N symmetric methyltransferase activity [GO:0035243]    GO:0003824; GO:0005615; GO:0005739; GO:0016740; GO:0043226; GO:0065003; GO:0140096  catalytic activity; extracellular space; mitochondrion; transferase activity; organelle; protein-containing complex assembly; catalytic activity, acting on a protein

==> run_20260306_113912/postprocess_uniprot_go.py <==
import sys, os, time, json, math
import pandas as pd
import requests
from pathlib import Path

BLAST_TSV = sys.argv[1]
OUTDIR = sys.argv[2]

os.makedirs(OUTDIR, exist_ok=True)
hits = pd.read_csv(BLAST_TSV, sep='\t', header=None,

==> run_20260306_113912/summary_stats.json <==
{"total_sequences": 2, "blast_hits": 2, "go_matches": 2, "goslim_matches": 2, "goslim_counts": {"vesicle-mediated transport": 1, "reproductive process": 1, "anatomical structure development": 1, "nervous system process": 1, "transmembrane transport": 1, "protein-containing complex assembly": 1}}
==> run_20260306_113912/subset-derm-protein.blast.tsv <==
g7941.t1    sp|C0HL13|LRP2_PIG  28.9    294 2.34e-31    129 sp|C0HL13|LRP2_PIG Low-density lipoprotein receptor-related protein 2 OS=Sus scrofa OX=9823 GN=LRP2 PE=1 SV=1
g7944.t1    sp|Q7L592|NDUF7_HUMAN   51.8    415 8.53e-141   412 sp|Q7L592|NDUF7_HUMAN Protein arginine methyltransferase NDUFAF7, mitochondrial OS=Homo sapiens OX=9606 GN=NDUFAF7 PE=1 SV=1

==> run_20260306_113912/summary.md <==
# Annotation Summary Report

## Job Information
- **Input file**: subset-derm-protein.fa
- **Start time**: 2026-03-06 11:39:12
- **End time**: 2026-03-06 11:39:39
- **Duration**: 0h 0m 27s
- **CPUs used**: 40
- **Tool**: DIAMOND BLASTP (protein)


==> run_20260306_113912/goslim_generic.obo <==
format-version: 1.2
data-version: go/releases/2026-01-23/subsets/goslim_generic.owl
subsetdef: chebi_ph7_3 "Rhea list of ChEBI terms representing the major species at pH 7.3."
subsetdef: gocheck_do_not_annotate "Term not to be used for direct annotation"
subsetdef: gocheck_obsoletion_candidate "Terms planned for obsoletion"
subsetdef: goslim_agr "AGR slim"
subsetdef: goslim_aspergillus "Aspergillus GO slim"
subsetdef: goslim_candida "Candida GO slim"
subsetdef: goslim_chembl "ChEMBL protein targets summary"
subsetdef: goslim_drosophila "Drosophila GO slim"

==> run_20260306_113912/go-basic.obo <==
format-version: 1.2
data-version: releases/2026-01-23
subsetdef: chebi_ph7_3 "Rhea list of ChEBI terms representing the major species at pH 7.3."
subsetdef: gocheck_do_not_annotate "Term not to be used for direct annotation"
subsetdef: gocheck_obsoletion_candidate "Terms planned for obsoletion"
subsetdef: goslim_agr "AGR slim"
subsetdef: goslim_aspergillus "Aspergillus GO slim"
subsetdef: goslim_candida "Candida GO slim"
subsetdef: goslim_chembl "ChEMBL protein targets summary"
subsetdef: goslim_drosophila "Drosophila GO slim"

==> run_20260306_113912/annotation_full_go.tsv <==
query   accession   pident  length  evalue  bitscore    title   id  Reviewed    protein_name    organism    go_ids  go_bp   go_cc   go_mf
g7941.t1    C0HL13  28.9    294 2.34e-31    129 sp|C0HL13|LRP2_PIG Low-density lipoprotein receptor-related protein 2 OS=Sus scrofa OX=9823 GN=LRP2 PE=1 SV=1   LRP2_PIG    reviewed    Low-density lipoprotein receptor-related protein 2 (LRP-2) (Glycoprotein 330) (gp330) (Megalin) Sus scrofa (Pig)    GO:0001843; GO:0003139; GO:0003148; GO:0003223; GO:0005509; GO:0005905; GO:0006898; GO:0007605; GO:0008584; GO:0009897; GO:0016324; GO:0017124; GO:0030001; GO:0030424; GO:0030425; GO:0030514; GO:0031526; GO:0031904; GO:0043235; GO:0050769; GO:0051087; GO:0060068; GO:0060982; GO:0061156; GO:0070447; GO:0140058; GO:1904447; GO:1905167  coronary artery morphogenesis [GO:0060982]; folate import across plasma membrane [GO:1904447]; male gonad development [GO:0008584]; metal ion transport [GO:0030001]; negative regulation of BMP signaling pathway [GO:0030514]; neural tube closure [GO:0001843]; neuron projection arborization [GO:0140058]; outflow tract septum morphogenesis [GO:0003148]; positive regulation of lysosomal protein catabolic process [GO:1905167]; positive regulation of neurogenesis [GO:0050769]; positive regulation of oligodendrocyte progenitor proliferation [GO:0070447]; pulmonary artery morphogenesis [GO:0061156]; receptor-mediated endocytosis [GO:0006898]; secondary heart field specification [GO:0003139]; sensory perception of sound [GO:0007605]; vagina development [GO:0060068]; ventricular compact myocardium morphogenesis [GO:0003223]   apical plasma membrane [GO:0016324]; axon [GO:0030424]; brush border membrane [GO:0031526]; clathrin-coated pit [GO:0005905]; dendrite [GO:0030425]; endosome lumen [GO:0031904]; external side of plasma membrane [GO:0009897]; receptor complex [GO:0043235]  calcium ion binding [GO:0005509]; protein-folding chaperone binding [GO:0051087]; SH3 domain binding [GO:0017124]
g7944.t1    Q7L592  51.8    415 8.529999999999999e-141  412 sp|Q7L592|NDUF7_HUMAN Protein arginine methyltransferase NDUFAF7, mitochondrial OS=Homo sapiens OX=9606 GN=NDUFAF7 PE=1 SV=1    NDUF7_HUMAN reviewed    Protein arginine methyltransferase NDUFAF7, mitochondrial (EC 2.1.1.320) (NADH dehydrogenase [ubiquinone] complex I, assembly factor 7) (Protein midA homolog)  Homo sapiens (Human)    GO:0005615; GO:0005739; GO:0005759; GO:0008168; GO:0019899; GO:0019918; GO:0032981; GO:0035243  mitochondrial respiratory chain complex I assembly [GO:0032981]; peptidyl-arginine methylation, to symmetrical-dimethyl arginine [GO:0019918]   extracellular space [GO:0005615]; mitochondrial matrix [GO:0005759]; mitochondrion [GO:0005739] enzyme binding [GO:0019899]; methyltransferase activity [GO:0008168]; protein-arginine omega-N symmetric methyltransferase activity [GO:0035243]

==> run_20260306_150323/annotation_with_goslim.tsv <==
query   accession   id  reviewed    protein_name    organism    pident  length  evalue  bitscore    title   go_ids  go_bp   go_cc   go_mf   goslim_ids  goslim_names
g7941.t1    C0HL13  LRP2_PIG        Low-density lipoprotein receptor-related protein 2 (LRP-2) (Glycoprotein 330) (gp330) (Megalin) Sus scrofa (Pig)    28.9    294 2.34e-31    129 sp|C0HL13|LRP2_PIG Low-density lipoprotein receptor-related protein 2 OS=Sus scrofa OX=9823 GN=LRP2 PE=1 SV=1   GO:0001843; GO:0003139; GO:0003148; GO:0003223; GO:0005509; GO:0005905; GO:0006898; GO:0007605; GO:0008584; GO:0009897; GO:0016324; GO:0017124; GO:0030001; GO:0030424; GO:0030425; GO:0030514; GO:0031526; GO:0031904; GO:0043235; GO:0050769; GO:0051087; GO:0060068; GO:0060982; GO:0061156; GO:0070447; GO:0140058; GO:1904447; GO:1905167  coronary artery morphogenesis [GO:0060982]; folate import across plasma membrane [GO:1904447]; male gonad development [GO:0008584]; metal ion transport [GO:0030001]; negative regulation of BMP signaling pathway [GO:0030514]; neural tube closure [GO:0001843]; neuron projection arborization [GO:0140058]; outflow tract septum morphogenesis [GO:0003148]; positive regulation of lysosomal protein catabolic process [GO:1905167]; positive regulation of neurogenesis [GO:0050769]; positive regulation of oligodendrocyte progenitor proliferation [GO:0070447]; pulmonary artery morphogenesis [GO:0061156]; receptor-mediated endocytosis [GO:0006898]; secondary heart field specification [GO:0003139]; sensory perception of sound [GO:0007605]; vagina development [GO:0060068]; ventricular compact myocardium morphogenesis [GO:0003223]   apical plasma membrane [GO:0016324]; axon [GO:0030424]; brush border membrane [GO:0031526]; clathrin-coated pit [GO:0005905]; dendrite [GO:0030425]; endosome lumen [GO:0031904]; external side of plasma membrane [GO:0009897]; receptor complex [GO:0043235]  calcium ion binding [GO:0005509]; protein-folding chaperone binding [GO:0051087]; SH3 domain binding [GO:0017124]   GO:0016192; GO:0022414; GO:0048856; GO:0050877; GO:0055085  vesicle-mediated transport; reproductive process; anatomical structure development; nervous system process; transmembrane transport
g7944.t1    Q7L592  NDUF7_HUMAN     Protein arginine methyltransferase NDUFAF7, mitochondrial (EC 2.1.1.320) (NADH dehydrogenase [ubiquinone] complex I, assembly factor 7) (Protein midA homolog)  Homo sapiens (Human)    51.8    415 8.529999999999999e-141  412 sp|Q7L592|NDUF7_HUMAN Protein arginine methyltransferase NDUFAF7, mitochondrial OS=Homo sapiens OX=9606 GN=NDUFAF7 PE=1 SV=1    GO:0005615; GO:0005739; GO:0005759; GO:0008168; GO:0019899; GO:0019918; GO:0032981; GO:0035243  mitochondrial respiratory chain complex I assembly [GO:0032981]; peptidyl-arginine methylation, to symmetrical-dimethyl arginine [GO:0019918]   extracellular space [GO:0005615]; mitochondrial matrix [GO:0005759]; mitochondrion [GO:0005739] enzyme binding [GO:0019899]; methyltransferase activity [GO:0008168]; protein-arginine omega-N symmetric methyltransferase activity [GO:0035243]    GO:0003824; GO:0005615; GO:0005739; GO:0016740; GO:0043226; GO:0065003; GO:0140096  catalytic activity; extracellular space; mitochondrion; transferase activity; organelle; protein-containing complex assembly; catalytic activity, acting on a protein

==> run_20260306_150323/postprocess_uniprot_go.py <==
import sys, os, time, json, math
import pandas as pd
import requests
from pathlib import Path

BLAST_TSV = sys.argv[1]
OUTDIR = sys.argv[2]

os.makedirs(OUTDIR, exist_ok=True)
hits = pd.read_csv(BLAST_TSV, sep='\t', header=None,

==> run_20260306_150323/summary_stats.json <==
{"total_sequences": 2, "blast_hits": 2, "go_matches": 2, "goslim_matches": 2, "goslim_counts": {"vesicle-mediated transport": 1, "reproductive process": 1, "anatomical structure development": 1, "nervous system process": 1, "transmembrane transport": 1, "protein-containing complex assembly": 1}}
==> run_20260306_150323/subset-derm-protein.blast.tsv <==
g7941.t1    sp|C0HL13|LRP2_PIG  28.9    294 2.34e-31    129 sp|C0HL13|LRP2_PIG Low-density lipoprotein receptor-related protein 2 OS=Sus scrofa OX=9823 GN=LRP2 PE=1 SV=1
g7944.t1    sp|Q7L592|NDUF7_HUMAN   51.8    415 8.53e-141   412 sp|Q7L592|NDUF7_HUMAN Protein arginine methyltransferase NDUFAF7, mitochondrial OS=Homo sapiens OX=9606 GN=NDUFAF7 PE=1 SV=1

==> run_20260306_150323/summary.md <==
# Annotation Summary Report

## Job Information
- **Input file**: subset-derm-protein.fa
- **Start time**: 2026-03-06 15:03:23
- **End time**: 2026-03-06 15:03:42
- **Duration**: 0h 0m 19s
- **CPUs used**: 40
- **Tool**: DIAMOND BLASTP (protein)


==> run_20260306_150323/goslim_generic.obo <==
format-version: 1.2
data-version: go/releases/2026-01-23/subsets/goslim_generic.owl
subsetdef: chebi_ph7_3 "Rhea list of ChEBI terms representing the major species at pH 7.3."
subsetdef: gocheck_do_not_annotate "Term not to be used for direct annotation"
subsetdef: gocheck_obsoletion_candidate "Terms planned for obsoletion"
subsetdef: goslim_agr "AGR slim"
subsetdef: goslim_aspergillus "Aspergillus GO slim"
subsetdef: goslim_candida "Candida GO slim"
subsetdef: goslim_chembl "ChEMBL protein targets summary"
subsetdef: goslim_drosophila "Drosophila GO slim"

==> run_20260306_150323/go-basic.obo <==
format-version: 1.2
data-version: releases/2026-01-23
subsetdef: chebi_ph7_3 "Rhea list of ChEBI terms representing the major species at pH 7.3."
subsetdef: gocheck_do_not_annotate "Term not to be used for direct annotation"
subsetdef: gocheck_obsoletion_candidate "Terms planned for obsoletion"
subsetdef: goslim_agr "AGR slim"
subsetdef: goslim_aspergillus "Aspergillus GO slim"
subsetdef: goslim_candida "Candida GO slim"
subsetdef: goslim_chembl "ChEMBL protein targets summary"
subsetdef: goslim_drosophila "Drosophila GO slim"

==> run_20260306_150323/annotation_full_go.tsv <==
query   accession   pident  length  evalue  bitscore    title   id  Reviewed    protein_name    organism    go_ids  go_bp   go_cc   go_mf
g7941.t1    C0HL13  28.9    294 2.34e-31    129 sp|C0HL13|LRP2_PIG Low-density lipoprotein receptor-related protein 2 OS=Sus scrofa OX=9823 GN=LRP2 PE=1 SV=1   LRP2_PIG    reviewed    Low-density lipoprotein receptor-related protein 2 (LRP-2) (Glycoprotein 330) (gp330) (Megalin) Sus scrofa (Pig)    GO:0001843; GO:0003139; GO:0003148; GO:0003223; GO:0005509; GO:0005905; GO:0006898; GO:0007605; GO:0008584; GO:0009897; GO:0016324; GO:0017124; GO:0030001; GO:0030424; GO:0030425; GO:0030514; GO:0031526; GO:0031904; GO:0043235; GO:0050769; GO:0051087; GO:0060068; GO:0060982; GO:0061156; GO:0070447; GO:0140058; GO:1904447; GO:1905167  coronary artery morphogenesis [GO:0060982]; folate import across plasma membrane [GO:1904447]; male gonad development [GO:0008584]; metal ion transport [GO:0030001]; negative regulation of BMP signaling pathway [GO:0030514]; neural tube closure [GO:0001843]; neuron projection arborization [GO:0140058]; outflow tract septum morphogenesis [GO:0003148]; positive regulation of lysosomal protein catabolic process [GO:1905167]; positive regulation of neurogenesis [GO:0050769]; positive regulation of oligodendrocyte progenitor proliferation [GO:0070447]; pulmonary artery morphogenesis [GO:0061156]; receptor-mediated endocytosis [GO:0006898]; secondary heart field specification [GO:0003139]; sensory perception of sound [GO:0007605]; vagina development [GO:0060068]; ventricular compact myocardium morphogenesis [GO:0003223]   apical plasma membrane [GO:0016324]; axon [GO:0030424]; brush border membrane [GO:0031526]; clathrin-coated pit [GO:0005905]; dendrite [GO:0030425]; endosome lumen [GO:0031904]; external side of plasma membrane [GO:0009897]; receptor complex [GO:0043235]  calcium ion binding [GO:0005509]; protein-folding chaperone binding [GO:0051087]; SH3 domain binding [GO:0017124]
g7944.t1    Q7L592  51.8    415 8.529999999999999e-141  412 sp|Q7L592|NDUF7_HUMAN Protein arginine methyltransferase NDUFAF7, mitochondrial OS=Homo sapiens OX=9606 GN=NDUFAF7 PE=1 SV=1    NDUF7_HUMAN reviewed    Protein arginine methyltransferase NDUFAF7, mitochondrial (EC 2.1.1.320) (NADH dehydrogenase [ubiquinone] complex I, assembly factor 7) (Protein midA homolog)  Homo sapiens (Human)    GO:0005615; GO:0005739; GO:0005759; GO:0008168; GO:0019899; GO:0019918; GO:0032981; GO:0035243  mitochondrial respiratory chain complex I assembly [GO:0032981]; peptidyl-arginine methylation, to symmetrical-dimethyl arginine [GO:0019918]   extracellular space [GO:0005615]; mitochondrial matrix [GO:0005759]; mitochondrion [GO:0005739] enzyme binding [GO:0019899]; methyltransferase activity [GO:0008168]; protein-arginine omega-N symmetric methyltransferase activity [GO:0035243]

==> run_20260310_164133/annotation_with_goslim.tsv <==
query   accession   id  reviewed    protein_name    organism    pident  length  evalue  bitscore    title   go_ids  go_bp   go_cc   go_mf   goslim_ids  goslim_names
g7941.t1    C0HL13  LRP2_PIG        Low-density lipoprotein receptor-related protein 2 (LRP-2) (Glycoprotein 330) (gp330) (Megalin) Sus scrofa (Pig)    28.9    294 2.34e-31    129 sp|C0HL13|LRP2_PIG Low-density lipoprotein receptor-related protein 2 OS=Sus scrofa OX=9823 GN=LRP2 PE=1 SV=1   GO:0001843; GO:0003139; GO:0003148; GO:0003223; GO:0005509; GO:0005905; GO:0006898; GO:0007605; GO:0008584; GO:0009897; GO:0016324; GO:0017124; GO:0030001; GO:0030424; GO:0030425; GO:0030514; GO:0031526; GO:0031904; GO:0043235; GO:0050769; GO:0051087; GO:0060068; GO:0060982; GO:0061156; GO:0070447; GO:0140058; GO:1904447; GO:1905167  coronary artery morphogenesis [GO:0060982]; folate import across plasma membrane [GO:1904447]; male gonad development [GO:0008584]; metal ion transport [GO:0030001]; negative regulation of BMP signaling pathway [GO:0030514]; neural tube closure [GO:0001843]; neuron projection arborization [GO:0140058]; outflow tract septum morphogenesis [GO:0003148]; positive regulation of lysosomal protein catabolic process [GO:1905167]; positive regulation of neurogenesis [GO:0050769]; positive regulation of oligodendrocyte progenitor proliferation [GO:0070447]; pulmonary artery morphogenesis [GO:0061156]; receptor-mediated endocytosis [GO:0006898]; secondary heart field specification [GO:0003139]; sensory perception of sound [GO:0007605]; vagina development [GO:0060068]; ventricular compact myocardium morphogenesis [GO:0003223]   apical plasma membrane [GO:0016324]; axon [GO:0030424]; brush border membrane [GO:0031526]; clathrin-coated pit [GO:0005905]; dendrite [GO:0030425]; endosome lumen [GO:0031904]; external side of plasma membrane [GO:0009897]; receptor complex [GO:0043235]  calcium ion binding [GO:0005509]; protein-folding chaperone binding [GO:0051087]; SH3 domain binding [GO:0017124]   GO:0016192; GO:0022414; GO:0048856; GO:0050877; GO:0055085  vesicle-mediated transport; reproductive process; anatomical structure development; nervous system process; transmembrane transport
g7944.t1    Q7L592  NDUF7_HUMAN     Protein arginine methyltransferase NDUFAF7, mitochondrial (EC 2.1.1.320) (NADH dehydrogenase [ubiquinone] complex I, assembly factor 7) (Protein midA homolog)  Homo sapiens (Human)    51.8    415 8.529999999999999e-141  412 sp|Q7L592|NDUF7_HUMAN Protein arginine methyltransferase NDUFAF7, mitochondrial OS=Homo sapiens OX=9606 GN=NDUFAF7 PE=1 SV=1    GO:0005615; GO:0005739; GO:0005759; GO:0008168; GO:0019899; GO:0019918; GO:0032981; GO:0035243  mitochondrial respiratory chain complex I assembly [GO:0032981]; peptidyl-arginine methylation, to symmetrical-dimethyl arginine [GO:0019918]   extracellular space [GO:0005615]; mitochondrial matrix [GO:0005759]; mitochondrion [GO:0005739] enzyme binding [GO:0019899]; methyltransferase activity [GO:0008168]; protein-arginine omega-N symmetric methyltransferase activity [GO:0035243]    GO:0003824; GO:0005615; GO:0005739; GO:0016740; GO:0043226; GO:0065003; GO:0140096  catalytic activity; extracellular space; mitochondrion; transferase activity; organelle; protein-containing complex assembly; catalytic activity, acting on a protein

==> run_20260310_164133/postprocess_uniprot_go.py <==
import sys, os, time, json, math
import pandas as pd
import requests
from pathlib import Path

BLAST_TSV = sys.argv[1]
OUTDIR = sys.argv[2]

os.makedirs(OUTDIR, exist_ok=True)
hits = pd.read_csv(BLAST_TSV, sep='\t', header=None,

==> run_20260310_164133/summary_stats.json <==
{"total_sequences": 2, "blast_hits": 2, "go_matches": 2, "goslim_matches": 2, "goslim_counts": {"vesicle-mediated transport": 1, "reproductive process": 1, "anatomical structure development": 1, "nervous system process": 1, "transmembrane transport": 1, "protein-containing complex assembly": 1}}
==> run_20260310_164133/subset-derm-protein.blast.tsv <==
g7941.t1    sp|C0HL13|LRP2_PIG  28.9    294 2.34e-31    129 sp|C0HL13|LRP2_PIG Low-density lipoprotein receptor-related protein 2 OS=Sus scrofa OX=9823 GN=LRP2 PE=1 SV=1
g7944.t1    sp|Q7L592|NDUF7_HUMAN   51.8    415 8.53e-141   412 sp|Q7L592|NDUF7_HUMAN Protein arginine methyltransferase NDUFAF7, mitochondrial OS=Homo sapiens OX=9606 GN=NDUFAF7 PE=1 SV=1

==> run_20260310_164133/summary.md <==
# Annotation Summary Report

## Job Information
- **Input file**: subset-derm-protein.fa
- **Start time**: 2026-03-10 16:41:33
- **End time**: 2026-03-10 16:41:54
- **Duration**: 0h 0m 21s
- **CPUs used**: 40
- **Tool**: DIAMOND BLASTP (protein)


==> run_20260310_164133/goslim_generic.obo <==
format-version: 1.2
data-version: go/releases/2026-01-23/subsets/goslim_generic.owl
subsetdef: chebi_ph7_3 "Rhea list of ChEBI terms representing the major species at pH 7.3."
subsetdef: gocheck_do_not_annotate "Term not to be used for direct annotation"
subsetdef: gocheck_obsoletion_candidate "Terms planned for obsoletion"
subsetdef: goslim_agr "AGR slim"
subsetdef: goslim_aspergillus "Aspergillus GO slim"
subsetdef: goslim_candida "Candida GO slim"
subsetdef: goslim_chembl "ChEMBL protein targets summary"
subsetdef: goslim_drosophila "Drosophila GO slim"

==> run_20260310_164133/go-basic.obo <==
format-version: 1.2
data-version: releases/2026-01-23
subsetdef: chebi_ph7_3 "Rhea list of ChEBI terms representing the major species at pH 7.3."
subsetdef: gocheck_do_not_annotate "Term not to be used for direct annotation"
subsetdef: gocheck_obsoletion_candidate "Terms planned for obsoletion"
subsetdef: goslim_agr "AGR slim"
subsetdef: goslim_aspergillus "Aspergillus GO slim"
subsetdef: goslim_candida "Candida GO slim"
subsetdef: goslim_chembl "ChEMBL protein targets summary"
subsetdef: goslim_drosophila "Drosophila GO slim"

==> run_20260310_164133/annotation_full_go.tsv <==
query   accession   pident  length  evalue  bitscore    title   id  Reviewed    protein_name    organism    go_ids  go_bp   go_cc   go_mf
g7941.t1    C0HL13  28.9    294 2.34e-31    129 sp|C0HL13|LRP2_PIG Low-density lipoprotein receptor-related protein 2 OS=Sus scrofa OX=9823 GN=LRP2 PE=1 SV=1   LRP2_PIG    reviewed    Low-density lipoprotein receptor-related protein 2 (LRP-2) (Glycoprotein 330) (gp330) (Megalin) Sus scrofa (Pig)    GO:0001843; GO:0003139; GO:0003148; GO:0003223; GO:0005509; GO:0005905; GO:0006898; GO:0007605; GO:0008584; GO:0009897; GO:0016324; GO:0017124; GO:0030001; GO:0030424; GO:0030425; GO:0030514; GO:0031526; GO:0031904; GO:0043235; GO:0050769; GO:0051087; GO:0060068; GO:0060982; GO:0061156; GO:0070447; GO:0140058; GO:1904447; GO:1905167  coronary artery morphogenesis [GO:0060982]; folate import across plasma membrane [GO:1904447]; male gonad development [GO:0008584]; metal ion transport [GO:0030001]; negative regulation of BMP signaling pathway [GO:0030514]; neural tube closure [GO:0001843]; neuron projection arborization [GO:0140058]; outflow tract septum morphogenesis [GO:0003148]; positive regulation of lysosomal protein catabolic process [GO:1905167]; positive regulation of neurogenesis [GO:0050769]; positive regulation of oligodendrocyte progenitor proliferation [GO:0070447]; pulmonary artery morphogenesis [GO:0061156]; receptor-mediated endocytosis [GO:0006898]; secondary heart field specification [GO:0003139]; sensory perception of sound [GO:0007605]; vagina development [GO:0060068]; ventricular compact myocardium morphogenesis [GO:0003223]   apical plasma membrane [GO:0016324]; axon [GO:0030424]; brush border membrane [GO:0031526]; clathrin-coated pit [GO:0005905]; dendrite [GO:0030425]; endosome lumen [GO:0031904]; external side of plasma membrane [GO:0009897]; receptor complex [GO:0043235]  calcium ion binding [GO:0005509]; protein-folding chaperone binding [GO:0051087]; SH3 domain binding [GO:0017124]
g7944.t1    Q7L592  51.8    415 8.529999999999999e-141  412 sp|Q7L592|NDUF7_HUMAN Protein arginine methyltransferase NDUFAF7, mitochondrial OS=Homo sapiens OX=9606 GN=NDUFAF7 PE=1 SV=1    NDUF7_HUMAN reviewed    Protein arginine methyltransferase NDUFAF7, mitochondrial (EC 2.1.1.320) (NADH dehydrogenase [ubiquinone] complex I, assembly factor 7) (Protein midA homolog)  Homo sapiens (Human)    GO:0005615; GO:0005739; GO:0005759; GO:0008168; GO:0019899; GO:0019918; GO:0032981; GO:0035243  mitochondrial respiratory chain complex I assembly [GO:0032981]; peptidyl-arginine methylation, to symmetrical-dimethyl arginine [GO:0019918]   extracellular space [GO:0005615]; mitochondrial matrix [GO:0005759]; mitochondrion [GO:0005739] enzyme binding [GO:0019899]; methyltransferase activity [GO:0008168]; protein-arginine omega-N symmetric methyltransferase activity [GO:0035243]

DISCUSSION

Looks like the fix worked! Everything is as expected.