fcsgx_mss

FCSgx-related scripts to assist MSS works for quick screening of the sequence contamination

Prerequisites

• a012 node (>512GB RAM, SSD, >48 Cores)
• w3const user (for only the 1st setup)
• This script is expected to be executed by members of w3const group.
• python3
  • The modules (biopython, dictdiffer, ete3, pandas, polars, pydrive2, xlsxwriter) are quired to run, but have already been prepared in python venv, ~/wok-kosuge/mypy/ that is called during the script. Therefore you do not need to install them by yourself.
• Google Workspace (Gdrive, Spreadsheet, and GAS)

Installation

1. ssh login to a012 as w3const user.
2. git clone https://github.com/ddbj/fcsgx_mss.git
3. Prepare symbolic lins for fcsgxmss.sh in /data1/FCS. ln -s ~/fcsgx_mss/fcsgxmss.sh /data1/FCS/fcsgxmss.sh
4. Copy the secret keys to upload the file to Gdrive. Make sure that the owner of the two json files must be w3const:w3const. In addition, file permission is 640 and 660 for client_secrets.json, saved_credentials.json, respectively.
   cp -av ~/work-kosuge/fcsgxmss_secrets/*.json ~/fcsgx_mss/
5. The script depends on the taxonomy data prepared by ete tool. To update ~/work-kosuge/etetoolkit/ncbitaxonomy.sqlite, bash ~/fcsgx_mss/update_taxonomydb.sh should be executeted by w3const user at 6:00 every day.
6. Create the fill_fcslinkMSS.gs (access to the link is restricted to our members) to your google apps project, moreover enable 'Drive v3 API' for it. Set the trigger to run putFCSlink every 5 minutes.

How to use

bash /home/w3const/fcsgx_mss/run_fcs2gsheet.sh -d </home/w3const/submissions/production/NSUB######/YYYYmmdd-HHMMSS>
e.g. bash /home/w3const/fcsgx_mss/run_fcs2gsheet.sh -d /home/w3const/submissions/production/NSUB999999/20261231-012346

Then the result is saved in /home/w3const/fcslog/gx/<NSUB number>. When the contamination is detected, the hyperlink to the contamination report is filled to the cell for corresponding NSUB in MSS working sheet.

When you would like to run only FCS-gx.

ssh a012
/data1/FCS/fcsgxmss.sh -q <NSUB######>|<path to a fasta file> -t <tax ID> [-o <directory name>]

You will find the FCS-GX result in ~/fcsgxmss as default.

e.g. 1

/data1/FCS/fcsgxmss.sh -q ~/w3const/submissions/production/NSUB001887/20240702-151414/SAMD00797160_TA6350.fasta -t 2104

e.g. 2

You can do FCS-GX against the latest submission files when NSUB number is designated at -q option

/data1/FCS/fcsgxmss.sh -q NSUB001972 -t 105296

e.g. 3

Use of -o option can change the output directory to your favorite one. You should prepare the output directory in advance when you use -d option.

/data1/FCS/fcsgxmss.sh -q ~/w3const/submissions/production/NSUB001887/20240702-151414/SAMD00797160_TA6350.fasta -t 2104 -o ~/myresult