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computers:bioinfo_server_configuration [2023/01/11 11:05] – [HTSeq] hychangcomputers:bioinfo_server_configuration [2026/01/22 14:57] (current) – hychang
Line 103: Line 103:
 chkuo@koa[~]$ sudo pip3 install seqmagick chkuo@koa[~]$ sudo pip3 install seqmagick
 Successfully installed seqmagick-0.7.0 Successfully installed seqmagick-0.7.0
 +
 +# install panda package on 2024/07/29
 +hychang@koa[~]$ sudo pip3 install pandas
 +Successfully installed pandas-1.3.5 pytz-2024.1
 +hychang@koa[~]$ sudo pip3 -V
 +pip 22.2.2 from /usr/local/lib/python3.7/dist-packages/pip (python 3.7)
 +
 </code> </code>
  
Line 364: Line 371:
 ===== PAML ===== ===== PAML =====
   * Phylogenetic Analysis by Maximum Likelihood (PAML)   * Phylogenetic Analysis by Maximum Likelihood (PAML)
-  * [[http://abacus.gene.ucl.ac.uk/software/paml.html]]+  * [[http://abacus.gene.ucl.ac.uk/software/]]
  
 <code bash> <code bash>
-chkuo@koa[/usr/local]$ sudo wget http://abacus.gene.ucl.ac.uk/software/paml4.9h.tgz +# 2023/05/19 
-chkuo@koa[/usr/local]$ sudo tar xzf paml4.9h.tgz +chkuo@koa[/usr/local]$ sudo wget https://github.com/abacus-gene/paml/releases/download/v4.10.6/paml-4.10.6-linux-X86_64.tgz 
-chkuo@koa[/usr/local]$ sudo chown -R root:root paml4.9h +chkuo@koa[/usr/local]$ sudo tar xzf paml-4.10.6-linux-X86_64.tgz 
-chkuo@koa[/usr/local]$ sudo chmod -R 755 paml4.9h +chkuo@koa[/usr/local]$ sudo chown -R root:root paml-4.10.6 
-chkuo@koa[/usr/local]$ sudo rm /usr/local/paml4.9h/bin/*exe +chkuo@koa[/usr/local]$ sudo chmod -R 755 paml-4.10.6 
-chkuo@koa[/usr/local]$ cd /usr/local/paml4.9h/src +chkuo@koa[/usr/local]$ cd paml-4.10.6/src 
-chkuo@koa[/usr/local/paml4.9h/src]$ sudo make -f Makefile +chkuo@koa[/usr/local/paml-4.10.6/src]$ sudo make -f Makefile 
-chkuo@koa[/usr/local/paml4.9h/src]$ sudo mv baseml basemlg chi2 codeml evolver mcmctree pamp yn00  ../bin +chkuo@koa[/usr/local/paml-4.10.6/src]$ sudo rm *.o 
-chkuo@koa[/usr/local]$ sudo ln -s /usr/local/paml4.9h /usr/local/paml+chkuo@koa[/usr/local/paml-4.10.6/src]$ sudo mv baseml basemlg chi2 codeml evolver infinitesites mcmctree pamp yn00 ../bin
 </code> </code>
  
Line 482: Line 489:
 chkuo@koa[/usr/local/beagle-lib-3.1.2]$ sudo make install chkuo@koa[/usr/local/beagle-lib-3.1.2]$ sudo make install
 # install mrbayes # install mrbayes
-chkuo@koa[/usr/local]$ sudo wget https://github.com/NBISweden/MrBayes/raw/v3.2.6/mrbayes-3.2.6.tar.gz +# 2024/04/19 
-chkuo@koa[/usr/local]$ sudo tar xzf mrbayes-3.2.6.tar.gz +# 3.2.6 -> 3.2.7 
-chkuo@koa[/usr/local]$ sudo chown -R root:root mrbayes-3.2.6 +chkuo@koa[/usr/local]$ sudo wget https://github.com/NBISweden/MrBayes/releases/download/v3.2.7/mrbayes-3.2.7.tar.gz 
-chkuo@koa[/usr/local]$ cd mrbayes-3.2.6/src +chkuo@koa[/usr/local]$ sudo tar xzf mrbayes-3.2.7.tar.gz 
-chkuo@koa[/usr/local/mrbayes-3.2.6/src]$ sudo autoconf +chkuo@koa[/usr/local]$ sudo chown -R root:root mrbayes-3.2.7 
-chkuo@koa[/usr/local/mrbayes-3.2.6/src]$ sudo ./configure --enable-mpi=yes +chkuo@koa[/usr/local]$ cd mrbayes-3.2.7 
-chkuo@koa[/usr/local/mrbayes-3.2.6/src]$ sudo make +chkuo@koa[/usr/local/mrbayes-3.2.7]$ sudo ./configure --with-mpi 
-chkuo@koa[/usr/local/mrbayes-3.2.6/src]$ sudo make install+chkuo@koa[/usr/local/mrbayes-3.2.7]$ sudo make 
 +chkuo@koa[/usr/local/mrbayes-3.2.7]$ sudo make install 
 +chkuo@koa[/usr/local/mrbayes-3.2.7]$ /usr/local/bin/mb -v 
 +Version:   3.2.7
 </code> </code>
  
Line 663: Line 673:
 ===== bbtools ===== ===== bbtools =====
   * BBMap short-read aligner and a bunch of tools (shell scripts)   * BBMap short-read aligner and a bunch of tools (shell scripts)
-  * [[https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/installation-guide/]]+  * [[https://jgi.doe.gov/data-and-tools/software-tools/bbtools/]]
  
 <code bash> <code bash>
Line 800: Line 810:
   * [[https://htseq.readthedocs.io/en/master/]]   * [[https://htseq.readthedocs.io/en/master/]]
   * HTSeq: High-throughput sequence analysis in Python   * HTSeq: High-throughput sequence analysis in Python
-  * Because using pip install is failed, so using apt install.+  * Using pip install failed, so using apt install.[[https://ubuntu.pkgs.org/20.04/ubuntu-universe-arm64/python3-htseq_0.11.2-2build1_arm64.deb.html|pkgs.org for python3-htseq]]
  
 <code bash> <code bash>
-hychang@koa:~$ sudo apt install python3-htseq +hychang@koa:[~]$ sudo apt install python3-htseq 
-[sudo] password for hychang:  +# [sudo] password for hychang:  
-Reading package lists... Done +# Reading package lists... Done 
-Building dependency tree        +# Building dependency tree        
-Reading state information... Done +# Reading state information... Done 
-E: Unable to locate package python3-htseq +# E: Unable to locate package python3-htseq 
-hychang@koa:~$ htseq-count --version +hychang@koa:[~]$ htseq-count --version 
-2.0.2+# 2.0.2 
 +hychang@koa:[~]$ whereis htseq-count 
 +# htseq-count: /usr/local/bin/htseq-count
 </code> </code>
  
Line 854: Line 866:
 </code> </code>
 ===== SPAdes ===== ===== SPAdes =====
-  * http://cab.spbu.ru/software/spades/+  * [[https://github.com/ablab/spades]]
  
 <code bash> <code bash>
Line 909: Line 921:
  
 ===== Velvet ===== ===== Velvet =====
-  * Sequence assembler for very short reads +  * [[https://github.com/dzerbino/velvet]]
-  * [[http://www.ebi.ac.uk/~zerbino/velvet/]]+
  
 <code bash> <code bash>
Line 954: Line 965:
  
 <code bash> <code bash>
-# updated 2020/04/29 by chkuo; the previous version (also the version first installed on koa) was v0.4.8-beta+# 2023/09/07; v0.4.9b -> v0.5.0; chkuo 
 +# 2020/04/29; v0.4.8b -> v0.4.9b; chkuo
 chkuo@koa[/usr/local]$ sudo git clone https://github.com/rrwick/Unicycler.git chkuo@koa[/usr/local]$ sudo git clone https://github.com/rrwick/Unicycler.git
-chkuo@koa[/usr/local]$ sudo mv Unicycler unicycler-0.4.9b +chkuo@koa[/usr/local]$ sudo mv Unicycler unicycler-0.5.0 
-chkuo@koa[/usr/local]$ cd unicycler-0.4.9b +chkuo@koa[/usr/local]$ cd unicycler-0.5.0 
-chkuo@koa[/usr/local/unicycler-0.4.9b]$ sudo python3 setup.py install +chkuo@koa[/usr/local/unicycler-0.5.0]$ sudo python3 setup.py install 
-chkuo@koa[/usr/local/unicycler-0.4.9b]$ unicycler --version +chkuo@koa[/usr/local/unicycler-0.5.0]$ unicycler --version 
-Unicycler v0.4.9b+Unicycler v0.5.0
 </code> </code>
  
Line 1222: Line 1234:
 chkuo@koa[~]$ checkm chkuo@koa[~]$ checkm
 </code> </code>
 +
 +
 +===== CheckM2 =====
 +  * Rapid assessment of genome bin quality using machine learning.
 +  * [[https://github.com/chklovski/CheckM2]]
 +  * Before installation. CheckM2 requires Python >3.7 (3.8 preferred), but Ubuntu 18.04 usually comes with Python 3.6 (koa have 3.6 and 3.7). Installing it globally isn’t recommended because its heavy dependencies (e.g., TensorFlow, scikit-learn) can interfere with system Python. The official docs also recommend installing CheckM2 via Conda. I’ll set up an isolated, shared Conda environment so everyone can run CheckM2 without affecting the system or needing a personal Conda installation.
 +  * As the official doc mentioned: The easiest way to install is using Conda in a new environment. However, conda can be very slow when processing requirements for the environment. A much faster and better way to install CheckM2 is to install using mamba and creating a new environment.
 +== Usage ==
 +  * Please follow the official website, **Usage** section: [[https://github.com/chklovski/CheckM2?tab=readme-ov-file#usage]]
 +  * Note: the output folder should be an empty folder.
 +
 +<code bash>
 +# 2025/01/07; hychang
 +
 +# Use Mamba to create the Shared CheckM2 Environment
 +(base) hychang@koa[~]$ sudo mkdir -p /opt/conda_envs
 +(base) hychang@koa[~]$ sudo ~/miniconda3/bin/mamba create -p /opt/conda_envs/checkm2 -c bioconda -c conda-forge checkm2 python=3.8
 +
 +# activate CheckM2 Environment and check
 +(base) hychang@koa[~]$ conda activate /opt/conda_envs/checkm2
 +(/opt/conda_envs/checkm2) hychang@koa[~]$ checkm2 -h
 +                ...::: CheckM2 v1.1.0 :::...
 +
 +  General usage:
 +    predict         -> Predict the completeness and contamination of genome bins in a folder. Example usage: 
 +
 + checkm2 predict --threads 30 --input <folder_with_bins> --output-directory <output_folder>
 +    testrun         -> Runs Checkm2 on internal test genomes to ensure it runs without errors. Example usage: 
 +
 + checkm2 testrun --threads 10
 +    database        -> Download and set up required CheckM2 DIAMOND database for annotation
 +
 +  Use checkm2 <command> -h for command-specific help.
 +
 +# Set up the shared Database. Download database.
 +(/opt/conda_envs/checkm2) hychang@koa[~]$ sudo mkdir -p /opt/conda_envs/checkm2/database
 +(/opt/conda_envs/checkm2) hychang@koa[~]$ sudo /opt/conda_envs/checkm2/bin/checkm2 database --download --path /opt/conda_envs/checkm2/database
 +# Failed because the hard-coded 15-second limit, so download manually by wget.
 +(/opt/conda_envs/checkm2) hychang@koa[~]$ cd /opt/conda_envs/checkm2/database
 +(/opt/conda_envs/checkm2) hychang@koa[/opt/conda_envs/checkm2/database]$ sudo wget -c https://zenodo.org/api/records/14897628/files/checkm2_database.tar.gz/content -O checkm2_database.tar.gz
 +# Extract the database
 +(/opt/conda_envs/checkm2) hychang@koa[/opt/conda_envs/checkm2/database]$ sudo tar -xvzf checkm2_database.tar.gz
 +
 +# Set the Permanent Path
 +# Create a small script that will run every time any user logs in. This ensures CheckM2 always knows where its "brain" is
 +(/opt/conda_envs/checkm2) hychang@koa[/opt/conda_envs/checkm2/database]$ sudo vim /etc/profile.d/checkm2.sh
 +
 +# Paste this exact line into the file and save:
 +export CHECKM2DB="/opt/conda_envs/checkm2/database/CheckM2_database/uniref100.KO.1.dmnd"
 +
 +# apply the change to current session
 +(/opt/conda_envs/checkm2) hychang@koa[/opt/conda_envs/checkm2/database]$ source /etc/profile.d/checkm2.sh
 +# Verify with the Test Run
 +(/opt/conda_envs/checkm2) hychang@koa[/opt/conda_envs/checkm2/database]$ /opt/conda_envs/checkm2/bin/checkm2 testrun
 +# Several error need to fix
 +
 +# 1. Since this enviroment is using Python 3.8 on Ubuntu 18.04, we need to ensure it has the exact version of CheckM2 that matches the models it expects.
 +# First need to confirm that we are under (/opt/conda_envs/checkm2) enviroment, and then Force-reinstall CheckM2 via Pip: This will download the missing .keras and .pb model files and place them exactly where the error message is looking.
 +(/opt/conda_envs/checkm2) hychang@koa[/opt/conda_envs/checkm2/database]$ sudo /opt/conda_envs/checkm2/bin/pip install --upgrade --force-reinstall checkm2
 +
 +# Erify the fix
 +(/opt/conda_envs/checkm2) hychang@koa[/opt/conda_envs/checkm2/database]$ /opt/conda_envs/checkm2/bin/checkm2 testrun
 +# There were error
 +
 +# 2. Protobuf version is too new for the TensorFlow version currently in the environment.
 +# Fix the Package Conflict: downgrade the protobuf package to a version that TensorFlow 2.x understands.
 +(/opt/conda_envs/checkm2) hychang@koa[/opt/conda_envs/checkm2/database]$ sudo /opt/conda_envs/checkm2/bin/pip install "protobuf<4.21"
 +# Run the Test Again
 +(/opt/conda_envs/checkm2) hychang@koa[/opt/conda_envs/checkm2/database]$ /opt/conda_envs/checkm2/bin/checkm2 testrun
 +# AttributeError: module 'numpy' has no attribute 'typeDict'
 +
 +# 3. Fix the NumPy Version: In NumPy 1.24, typeDict was officially removed, but older versions of TensorFlow still look for it. To fix this, we need to downgrade NumPy to a stable version (like 1.23.5) that still supports this attribute.
 +(/opt/conda_envs/checkm2) hychang@koa[/opt/conda_envs/checkm2/database]$ sudo /opt/conda_envs/checkm2/bin/pip install "numpy<1.24"
 +# Final Permissions Cleanup
 +(/opt/conda_envs/checkm2) hychang@koa[/opt/conda_envs/checkm2/database]$ sudo chmod -R 755 /opt/conda_envs/checkm2/lib/python3.8/site-packages/
 +# Verify the Fix
 +(/opt/conda_envs/checkm2) hychang@koa[/opt/conda_envs/checkm2/database]$ /opt/conda_envs/checkm2/bin/checkm2 testrun
 +# Due to it took a long time, terminated the run. Use more thread in next test.
 +# There is a note on CheckM2 website in "Test run" section:
 +# It is highly recommended to do a testrun with CheckM2 after installation and database download to ensure everything works successfully. You can test that the CheckM2 # installation was successful using checkm2 testrun. This command should complete in < 5 mins on an average desktop computer.
 +
 +(/opt/conda_envs/checkm2) hychang@koa[/opt/conda_envs/checkm2/database]$ /opt/conda_envs/checkm2/bin/checkm2 testrun --threads 8 --database_path /opt/conda_envs/checkm2/database/CheckM2_database/uniref100.KO.1.dmnd
 +# Error. CheckM2 finally found the database file! However, it failed the "security check" because that file is likely incomplete or corrupted from the earlier failed download attempts (the IncompleteRead errors).
 +
 +# 4. Delete the "Broken" Database, and re-download the database
 +(/opt/conda_envs/checkm2) hychang@koa[/opt/conda_envs/checkm2/database]$ ls -l /opt/conda_envs/checkm2/database/checkm2_database.tar.gz
 +-rwxr-xr-x 1 root root 1735095710 Jan  7 18:20 /opt/conda_envs/checkm2/database/checkm2_database.tar.gz
 +(/opt/conda_envs/checkm2) hychang@koa[/opt/conda_envs/checkm2/database]$ sudo rm -rf /opt/conda_envs/checkm2/database/*
 +(/opt/conda_envs/checkm2) hychang@koa[/opt/conda_envs/checkm2/database]$ sudo wget https://zenodo.org/api/records/14897628/files/checkm2_database.tar.gz/content -O checkm2_database.tar.gz
 +--2026-01-08 10:01:47--  https://zenodo.org/api/records/14897628/files/checkm2_database.tar.gz/content
 +Resolving zenodo.org (zenodo.org)... 188.185.48.75, 188.185.43.153, 137.138.52.235, ...
 +Connecting to zenodo.org (zenodo.org)|188.185.48.75|:443... connected.
 +HTTP request sent, awaiting response... 200 OK
 +Length: 1735095710 (1.6G) [application/octet-stream]
 +Saving to: ‘checkm2_database.tar.gz’
 +
 +checkm2_database.tar.gz             100%[===================================================================>]   1.62G   711KB/s    in 43m 3s  
 +
 +2026-01-08 10:44:51 (656 KB/s) - ‘checkm2_database.tar.gz’ saved [1735095710/1735095710]
 +# Still the same size 1735095710 bytes, not 1862590464 bytes.
 +# Extract
 +(/opt/conda_envs/checkm2) hychang@koa[/opt/conda_envs/checkm2/database]$ sudo tar -xvzf checkm2_database.tar.gz
 +(/opt/conda_envs/checkm2) hychang@koa[/opt/conda_envs/checkm2/database]$ ls -F CheckM2_database/
 +uniref100.KO.1.dmnd
 +(/opt/conda_envs/checkm2) hychang@koa[/opt/conda_envs/checkm2/database]$ source /etc/profile.d/checkm2.sh
 +(/opt/conda_envs/checkm2) hychang@koa[/opt/conda_envs/checkm2/database]$ echo $CHECKM2DB
 +/opt/conda_envs/checkm2/database/CheckM2_database/uniref100.KO.1.dmnd
 +(/opt/conda_envs/checkm2) hychang@koa[/opt/conda_envs/checkm2/database]$ /opt/conda_envs/checkm2/bin/checkm2 testrun --threads 8 --database_path /opt/conda_envs/checkm2/database/CheckM2_database/uniref100.KO.1.dmnd
 +# Error
 +
 +# 6. The version of CheckM2 you have installed (likely 1.1.0) is hard-coded to expect an older version of the database, but Zenodo is now serving a newer one.
 +# The "Surgical" Fix: Disable Checksum Validation
 +# (1) Open the file where the checksum logic lives:
 +(/opt/conda_envs/checkm2) hychang@koa[/opt/conda_envs/checkm2/database]$ sudo vim /opt/conda_envs/checkm2/lib/python3.8/site-packages/checkm2/versionControl.py
 +# (2) Find the validation function: find this block: checksum_version_validate_DIAMOND
 +# (3) Force it to always pass: Change the function so it just says return True immediately. It look like this:
 +
 +     def checksum_version_validate_DIAMOND(self, location=None):
 +        '''Runs to ensure DIAMOND database has correct checksum and is congruent with current CheckM2 version'''
 +
 +        # modify by hychang, to skip "CheckM2's internal code is running a "sanity check" on that .dmnd file and rejecting it because the MD5 hash doesn't match its hard-coded list." problem.
 +        return True  # Add this line here
 +        # (You can leave the rest of the code below it, it will be ignored)
 +
 +        version_hashes = os.path.join(DefaultValues.VERSION_PATH,
 +                                      'version_hashes_{}.json'.format(version.__version__))
 +        ...
 +
 +# Test
 +(/opt/conda_envs/checkm2) hychang@koa[/opt/conda_envs/checkm2/database]$ /opt/conda_envs/checkm2/bin/checkm2 testrun --threads 8
 +# Error again
 +
 +# 7. The Fix: Downgrade Pandas
 +(/opt/conda_envs/checkm2) hychang@koa[/opt/conda_envs/checkm2/database]$ sudo /opt/conda_envs/checkm2/bin/pip install "pandas<2.0.0"
 +# Verify the fix
 +(/opt/conda_envs/checkm2) hychang@koa[/opt/conda_envs/checkm2/database]$ /opt/conda_envs/checkm2/bin/checkm2 testrun --threads 8
 +2026-01-08 11:58:17.598241: I tensorflow/tsl/cuda/cudart_stub.cc:28] Could not find cuda drivers on your machine, GPU will not be used.
 +2026-01-08 11:58:17.722622: I tensorflow/tsl/cuda/cudart_stub.cc:28] Could not find cuda drivers on your machine, GPU will not be used.
 +2026-01-08 11:58:17.723499: I tensorflow/core/platform/cpu_feature_guard.cc:182] This TensorFlow binary is optimized to use available CPU instructions in performance-critical operations.
 +To enable the following instructions: AVX2 AVX512F FMA, in other operations, rebuild TensorFlow with the appropriate compiler flags.
 +2026-01-08 11:58:19.218146: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Could not find TensorRT
 +[01/08/2026 11:58:20 AM] INFO: Test run: Running quality prediction workflow on test genomes with 8 threads.
 +[01/08/2026 11:58:20 AM] INFO: Running checksum on test genomes.
 +[01/08/2026 11:58:20 AM] INFO: Checksum successful.
 +[01/08/2026 11:58:24 AM] INFO: Calling genes in 3 bins with 8 threads:
 +    Finished processing 3 of 3 (100.00%) bins.
 +[01/08/2026 11:59:09 AM] INFO: Calculating metadata for 3 bins with 8 threads:
 +    Finished processing 3 of 3 (100.00%) bin metadata.
 +[01/08/2026 11:59:10 AM] INFO: Annotating input genomes with DIAMOND using 8 threads
 +[01/08/2026 12:01:38 PM] INFO: Processing DIAMOND output
 +[01/08/2026 12:01:38 PM] INFO: Predicting completeness and contamination using ML models.
 +[01/08/2026 12:01:52 PM] INFO: Parsing all results and constructing final output table.
 +[01/08/2026 12:01:52 PM] INFO: CheckM2 finished successfully.
 +[01/08/2026 12:01:52 PM] INFO: Test run successful! See README for details. Results:
 + Name  Completeness  Contamination         Completeness_Model_Used  Translation_Table_Used
 +TEST1        100.00           0.74 Neural Network (Specific Model)                      11
 +TEST2         98.54           0.21 Neural Network (Specific Model)                      11
 +TEST3         98.75           0.51 Neural Network (Specific Model)                      11
 +
 +# Successed
 +
 +# Final step: Create the Wrapper Script
 +# This script acts as a shortcut. When a user types checkm2, it automatically points to the correct Conda environment and the database file we fixed.
 +(/opt/conda_envs/checkm2) hychang@koa[/opt/conda_envs/checkm2/database]$ sudo vim /usr/local/bin/checkm2
 +# Paste this exactly into the editor:
 +
 +#!/bin/bash
 +# CheckM2 Global Wrapper
 +
 +# 1. Add the environment's bin folder to the path so it can find Diamond
 +export PATH="/opt/conda_envs/checkm2/bin:$PATH"
 +
 +# 2. Set the database path
 +export CHECKM2DB="/opt/conda_envs/checkm2/database/CheckM2_database/uniref100.KO.1.dmnd"
 +
 +# 3. Run CheckM2
 +/opt/conda_envs/checkm2/bin/checkm2 "$@"
 +
 +# END this script
 +
 +# Executable and Verification
 +(/opt/conda_envs/checkm2) hychang@koa[/opt/conda_envs/checkm2/database]$ sudo chmod +x /usr/local/bin/checkm2
 +# leave the conda enviroment (/opt/conda_envs/checkm2)
 +(/opt/conda_envs/checkm2) hychang@koa[/opt/conda_envs/checkm2/database]$ conda deactivate
 +# As a normal user, call CheckM2
 +hychang@koa[~]$ checkm2
 +2026-01-22 14:39:47.980496: I tensorflow/tsl/cuda/cudart_stub.cc:28] Could not find cuda drivers on your machine, GPU will not be used.
 +2026-01-22 14:39:48.096168: I tensorflow/tsl/cuda/cudart_stub.cc:28] Could not find cuda drivers on your machine, GPU will not be used.
 +2026-01-22 14:39:48.096930: I tensorflow/core/platform/cpu_feature_guard.cc:182] This TensorFlow binary is optimized to use available CPU instructions in performance-critical operations.
 +To enable the following instructions: AVX2 AVX512F FMA, in other operations, rebuild TensorFlow with the appropriate compiler flags.
 +2026-01-22 14:39:49.245385: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning: Could not find TensorRT
 +      ____ _               _    __  __ ____  
 +     / ___| |__   ___  ___| | _|  \/  |___ \ 
 +    | |   | '_ \ / _ \/ __| |/ / |\/| | __) | 
 +    | |___| | | |  __/ (__|   <| |  | |/ __/  
 +     \____|_| |_|\___|\___|_|\_\_|  |_|_____| 
 + 
 +                ...::: CheckM2 v1.0.1 :::...
 +
 +  General usage:
 +    predict         -> Predict the completeness and contamination of genome bins in a folder.
 +    testrun         -> Runs Checkm2 on internal test genomes to ensure it runs without errors.
 +    database        -> Download and set up required CheckM2 DIAMOND database for annotation
 +
 +  Use checkm2 <command> -h for command-specific help.
 +
 +</code>
 +
  
  
Line 1393: Line 1613:
 ===== SignalP ===== ===== SignalP =====
   * Predicts the presence and location of signal peptide cleavage sites in amino acid sequences.   * Predicts the presence and location of signal peptide cleavage sites in amino acid sequences.
-  * Server: [[http://www.cbs.dtu.dk/services/SignalP/]] +  * [[https://services.healthtech.dtu.dk/services/SignalP-6.0/]]
-  * Download: [[http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?signalp]]+
  
 +
 +
 +<code bash>
 +# 2024/02/07
 +# fast
 +chkuo@koa[/usr/local]$ sudo tar -xzvf signalp-6.0h.fast.tar.gz
 +chkuo@koa[/usr/local]$ sudo chown -R root:root signalp6_fast
 +chkuo@koa[/usr/local]$ sudo pip3 install /usr/local/signalp6_fast/signalp-6-package/
 +# slow
 +chkuo@koa[/usr/local]$ sudo tar -xzvf signalp-6.0h.slow_sequential.tar.gz
 +chkuo@koa[/usr/local]$ sudo chown -R root:root signalp6_slow_sequential
 +chkuo@koa[/usr/local]$ sudo pip3 install /usr/local/signalp6_slow_sequential/signalp-6-package/
 +
 +chkuo@koa[/usr/local]$ which signalp6
 +/usr/local/bin/signalp6
 +chkuo@koa[/usr/local]$ signalp6 --version
 +SignalP 6.0 Signal peptide prediction tool 6.0h
 +</code>
  
 <code bash> <code bash>
Line 1480: Line 1717:
  
 <code bash> <code bash>
-chkuo@koa[/usr/local/bin]$ sudo wget https://github.com/ParBLiSS/FastANI/releases/download/v1.1/fastani-Linux64-v1.1.zip +# 2024/04/02 
-chkuo@koa[/usr/local/bin]$ sudo unzip fastani-Linux64-v1.1.zip  +# note: v1.34 has some error message; use v1.33 for now 
-Archive:  fastani-Linux64-v1.1.zip +chkuo@koa[/usr/local/bin]$ sudo wget https://github.com/ParBLiSS/FastANI/releases/download/v1.33/fastANI-Linux64-v1.33.zip 
-  inflating: fastANI                  +chkuo@koa[/usr/local/bin]$ sudo unzip fastANI-Linux64-v1.33.zip 
-   creating: __MACOSX/ +Archive:  fastANI-Linux64-v1.33.zip 
-  inflating: __MACOSX/._fastANI       +  inflating: fastANI    
-chkuo@koa[/usr/local/bin]$ sudo rm -r __MACOSX+chkuo@koa[/usr/local/bin]$ sudo mv fastANI fastANI_v1.33
 </code> </code>
  
 +
 +===== parallel =====
 +  * GNU parallel is a shell tool for executing jobs in parallel using one or more computers.
 +  * http://www.gnu.org/software/parallel
 +
 +<code bash>
 +# 2024/07/29
 +hychang@koa[~]$ sudo apt install parallel
 +hychang@koa[~]$ parallel --version
 +GNU parallel 20161222
 +Copyright (C) 2007,2008,2009,2010,2011,2012,2013,2014,2015,2016
 +Ole Tange and Free Software Foundation, Inc.
 +License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
 +This is free software: you are free to change and redistribute it.
 +GNU parallel comes with no warranty.
 +
 +Web site: http://www.gnu.org/software/parallel
 +
 +When using programs that use GNU Parallel to process data for publication
 +please cite as described in 'parallel --citation'.
 +
 +</code>
 +
 +
 +===== HH-suite =====
 +  * The HH-suite is an open-source software package for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs).
 +  * https://manpages.ubuntu.com/manpages/lunar/man1/hhsearch.1.html
 +
 +<code bash>
 +# 2024/07/29
 +# note: 
 +hychang@koa[~]$ sudo apt install hhsuite
 +hychang@koa[~]$ hhsearch
 +
 +HHsearch 3.0.0 (15-03-2015)
 +Search a database of HMMs with a query alignment or query HMM
 +(C) Johannes Soeding, Michael Remmert, Andreas Biegert, Andreas Hauser
 +Soding, J. Protein homology detection by HMM-HMM comparison. Bioinformatics 21:951-960 (2005).
 +
 +Usage: hhsearch -i query -d database [options]
 +...
 +
 +</code>
computers/bioinfo_server_configuration.1673406335.txt.gz · Last modified: by hychang