FCS is a toolset to elimate contaminant sequences from a genome assembly. Currently, there are two tools in this toolset: fcs-adaptor and fcs-gx.

References:

• Astashyn A, Tvedte ES, Sweeney D, Sapojnikov V, Bouk N, Joukov V, Mozes E, Strope PK, Sylla PM, Wagner L, Bidwell SL, Clark K, Davis EW, Smith-White B, Hlavina W, Pruitt KD, Schneider VA, Murphy TD Rapid and sensitive detection of genome contamination at scale with FCS-GX. bioRxiv [Preprint]. 2023 Jun 6:2023.06.02.543519. doi: 10.1101/2023.06.02.543519.

• FCS Main Site: Github site

• Module Name: fcs (see the modules page for more information)
• Test data can be found in ${FCS_TEST_DATA}

Allocate an interactive session and run the program. From the FCS tutorials at the FCS Github site:

[user@biowulf]$ sinteractive --mem=3g --cpus-per-task=4 --gres=lscratch:100
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn4224 are ready for job

[user@cn4224 ~]$ module load fcs
[+] Loading fcs  0.4.0  on cn4285
[+] Loading singularity  3.10.5  on cn4285

[user@cn4244 ~]$ cd /lscratch/${SLURM_JOB_ID}
[user@cn4224 ~]$ cp ${FCS_TEST_DATA}/fcsadaptor_prok_test.fa.gz inputdir/.
[user@cn4224 ~]$ mkdir inputdir outputdir
[user@cn4224 ~]$ run_fcsadaptor.sh --fasta-input ./inputdir/fcsadaptor_prok_test.fa.gz --output-dir ./outputdir --prok --container-engine singularity --image ${FCS_HOME}/fcs-adaptor.sif
[WARN  tini (2647065)] Tini is not running as PID 1 and isn't registered as a child subreaper.
Zombie processes will not be re-parented to Tini, so zombie reaping won't work.
To fix the problem, use the -s option or set the environment variable TINI_SUBREAPER to register Tini as a child subreaper, or run Tini as PID 1.
Output will be placed in: /output-volume
Executing the workflow
Resolved '/app/fcs/progs/ForeignContaminationScreening.cwl' to 'file:///app/fcs/progs/ForeignContaminationScreening.cwl'
[workflow ] start
[workflow ] starting step ValidateInputSequences
[step ValidateInputSequences] start

[..]

[job all_skipped_trims] completed success
[step all_skipped_trims] completed success
[workflow ] starting step all_cleaned_fasta
[step all_cleaned_fasta] start
[step all_cleaned_fasta] completed success
[workflow ] completed success

[user@cn4224 ~]$ cp ${FCS_TEST_DATA}/fcsgx_test.fa.gz .
[user@cn4224 ~]$ SOURCE_DB_MANIFEST="https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/FCS/database/test-only/test-only.manifest"
[user@cn4224 ~]$ LOCAL_DB=/lscratch/${SLURM_JOB_ID}/gxdb
[user@cn4224 ~]$ fcs.py db get --mft "$SOURCE_DB_MANIFEST" --dir "$LOCAL_DB/test-only"
[user@cn4224 ~]$ fcs.py db check --mft "$SOURCE_DB_MANIFEST" --dir "$LOCAL_DB/gxdb"
===============================================================================
Source:      https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/FCS/database/test-only
Destination: /app/db/gxdb
Resuming failed transfer in /app/db/gxdb...
Space check: Available:15.71GiB; Existing:0B; Incoming:4.29GiB; Delta:4.29GiB

Requires transfer: 56B test-only.meta.jsonl

Requires transfer: 5.92KiB test-only.taxa.tsv

Requires transfer: 21.33KiB test-only.seq_info.tsv.gz

Requires transfer: 7.85MiB test-only.blast_div.tsv.gz

Requires transfer: 67.56MiB test-only.gxs

Requires transfer: 4.21GiB test-only.gxi

[user@cn4224 ~]$ GXDB_LOC=/lscratch/${SLURM_JOB_ID}/gxdb
[user@cn4224 ~]$ fcs.py screen genome --fasta ./fcsgx_test.fa.gz --out-dir ./gx_out/ --gx-db "$GXDB_LOC/test-only"  --tax-id 6973
--------------------------------------------------------------------

tax-id    : 6973
fasta     : /sample-volume/fcsgx_test.fa.gz
size      : 8.55 MiB
split-fa  : True
BLAST-div : roaches
gx-div    : anml:insects
w/same-tax: True
bin-dir   : /app/bin
gx-db     : /app/db/gxdb/test-only/test-only.gxi
gx-ver    : Mar 10 2023 15:34:33; git:v0.4.0-3-g8096f62
output    : /output-volume//fcsgx_test.fa.6973.taxonomy.rpt

--------------------------------------------------------------------

 [...]

fcs_gx_report.txt contamination summary:
----------------------------------------
                                seqs      bases
                               ----- ----------
TOTAL                            243   27170378
-----                          ----- ----------
prok:CFB group bacteria          243   27170378

--------------------------------------------------------------------

fcs_gx_report.txt action summary:
---------------------------------
                                seqs      bases
                               ----- ----------
TOTAL                            243   27170378
-----                          ----- ----------
EXCLUDE                          214   25795430
REVIEW                            29    1374948

--------------------------------------------------------------------

[user@cn4224 ~]$ zcat fcsgx_test.fa.gz | fcs.py clean genome --action-report ./gx_out/fcsgx_test.fa.6973.fcs_gx_report.txt --output clean.fasta --contam-fasta-out contam.fasta
Applied 214 actions; 25795430 bps dropped; 0 bps hardmasked.

[user@cn4224 ~]$ ls gx_out
fcsgx_test.fa.6973.fcs_gx_report.txt  fcsgx_test.fa.6973.taxonomy.rpt

Create a batch input file (e.g. fcsadaptor.sh) similar to the following.

#! /bin/bash

module load fcs
cd /lscratch/${SLURM_JOB_ID}
mkdir inputdir outputdir
cp ${FCS_TEST_DATA}/fcsadaptor_prok_test.fa.gz inputdir/.

run_fcsadaptor.sh --fasta-input ./inputdir/fcsadaptor_prok_test.fa.gz --output-dir ./outputdir --prok --container-engine singularity --image ${FCS_HOME}/fcs-adaptor.sif

cp -r outputdir /data/${USER}/.

Submit these jobs using the Slurm sbatch command.

Create a swarmfile to run fcs-adaptor (e.g. fcsadaptor.swarm). For example:

run_fcsadaptor.sh --fasta-input ./inputdir/fcsadaptor_prok_test1.fa.gz --output-dir ./outputdir1 --prok --container-engine singularity --image ${FCS_HOME}/fcs-adaptor.sif; cp -r outputdir1 /data/${USER}/. 
run_fcsadaptor.sh --fasta-input ./inputdir/fcsadaptor_prok_test2.fa.gz --output-dir ./outputdir2 --prok --container-engine singularity --image ${FCS_HOME}/fcs-adaptor.sif; cp -r outputdir2 /data/${USER}/.
run_fcsadaptor.sh --fasta-input ./inputdir/fcsadaptor_prok_test3.fa.gz --output-dir ./outputdir3 --prok --container-engine singularity --image ${FCS_HOME}/fcs-adaptor.sif; cp -r outputdir3 /data/${USER}/.

Submit this job using the swarm command.

swarm -f fcsadaptor.swarm [-g #] --module fcs