Download or put following 2 files from official site to current directory or create symbolic link.
- fcs.py
- fcs-gx.sif
Usage: ./fcs-wrapper.sh [--outdir /path/to/outdirdir] fasta_file_path taxid
--outdir output directory Default: same path of fasta file
this script create directory which name is 'fcx-gx'
all output files will be output to 'fcs-gx'
- fasta_file_path
- Input FASTA file
- taxid
- taxid for Input FASTA file
Input file (fasta_file_path) is located following
$ tree NSUB000020/
NSUB000020/
└── 20240527-105300
└── GCA_012927515.1_ASM1292751v1_genomic.fna.gz
1 directory, 1 file
Execute fcs-wrapper.sh
./fcs-wrapper.sh /home/xxx/NSUB000020/20240527-105300/GCA_012927515.1_ASM1292751v1_genomic.fna.gz 40001
Result is following
$ tree NSUB000020/
NSUB000020/
├── 20240527-105300
│ └── GCA_012927515.1_ASM1292751v1_genomic.fna.gz
└── fcs-gx
├── GCA_012927515.1_ASM1292751v1_genomic.fna.40001.fcs_gx_report.txt
├── GCA_012927515.1_ASM1292751v1_genomic.fna.40001.taxonomy.rpt
├── status.txt
├── stderr.txt
└── stdout.txt
2 directories, 6 files
Input file (fasta_file_path) is located following
$ tree NSUB000020/
NSUB000020/
└── 20240527-105300
└── GCA_012927515.1_ASM1292751v1_genomic.fna.gz
1 directory, 1 file
Execute fcs-wrapper.sh with --outdir option
./fcs-wrapper.sh --outdir 40001_outputdir \
/home/xxx/NSUB000020/20240527-105300/GCA_012927515.1_ASM1292751v1_genomic.fna.gz 40001
After execution, no directories and files are created under input directory.
$ tree NSUB000020/
NSUB000020/
└── 20240527-105300
└── GCA_012927515.1_ASM1292751v1_genomic.fna.gz
1 directory, 1 file
40001_ouputdir looks like this.
fcs-gx is created and all output files are located there.
$ tree 40001_outputdir/
40001_outputdir/
└── fcs-gx
├── GCA_012927515.1_ASM1292751v1_genomic.fna.40001.fcs_gx_report.txt
├── GCA_012927515.1_ASM1292751v1_genomic.fna.40001.taxonomy.rpt
├── status.txt
├── stderr.txt
└── stdout.txt
1 directory, 5 files