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JAMSalpha_output

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johnmcculloch edited this page Dec 3, 2019 · 1 revision

JAMSalpha output - What you get

Once the JAMSalpha pipeline has completed, five things should have been generated.

  1. A folder containing all the JAMSalpha files pertaining to the sample. This folder is named by the sample prefix followed by JAMS
  2. A tarball of the JAMSalpha sample folder described above, named by the prefix followed by JAMS.tar.gz
  3. A .jams file, which is the only file that must be used for beta-analysis using the JAMSbeta executable
  4. A tarball with any reads (if any) used for contig assembly, if applicable.
  5. A pdf file with the complete report for the JAMSalpha analysis.

The JAMSalpha pdf report gives a bird's eye view of the characteristics of the sample.

#For instance, the command
JAMSalpha -a GCA_000969225.1 -d /path/to/your/JAMSdb -p FCFHV36 -A isolate -n

#will generate the files:
ls FCFHV36*
FCFHV36.jams  FCFHV36_JAMSalpha_report.pdf  FCFHV36_JAMS.tar.gz

#and a folder with the structure
tree -a FCFHV36_JAMS

FCFHV36_JAMS
├── FCFHV36_16SrRNA.fna
├── FCFHV36_assemblystats.tsv
├── FCFHV36_contigsdata.tsv
├── FCFHV36_contigs.fasta
├── FCFHV36_featuredata.tsv
├── FCFHV36_featuredose.tsv
├── FCFHV36_LKTdose.tsv
├── FCFHV36_projinfo.tsv
├── FCFHV36_PROKKA
│   ├── FCFHV36.bed
│   ├── FCFHV36.err
│   ├── FCFHV36.faa
│   ├── FCFHV36.ffn
│   ├── FCFHV36.fna
│   ├── FCFHV36.fsa
│   ├── FCFHV36.gbk
│   ├── FCFHV36.gff
│   ├── FCFHV36.log
│   ├── FCFHV36.sqn
│   ├── FCFHV36.tbl
│   ├── FCFHV36.tsv
│   └── FCFHV36.txt
├── FCFHV36_resfinder.tsv
├── FCFHV36_taxa_16S_cons.tsv
├── FCFHV36_ucobias.tsv
├── FCFHV36_vfdb.tsv
├── GCA_000969225.1.fasta
└── .RData

Note that an R session image (.RData) is saved within the sample folder, meaning that it is possible to access all the intermediate objects for the JAMSalpha run, by just loading the image into an R or RStudio session.

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