Proper usage of index about sting

[ar0ch]

The VFDB and CARD databases will need to be used with detector not typer, I'll note that in the STing docs.

➜  detector -x vfdb/db/gene_set -1 ERR008581_1.fastq -2 ERR008581_2.fastq -s ERR008581  --print-tidy | tee output.tsv
Sample  Gene    Presence        Total_hits      Total_k-mers    Total_reads     Input_files
ERR008581       vfdb_774        1       2983466 2942836 377323  ERR008581_1.fastq,ERR008581_2.fastq
ERR008581       vfdb_775        1       2983466 2942836 377323  ERR008581_1.fastq,ERR008581_2.fastq
ERR008581       vfdb_776        1       2983466 2942836 377323  ERR008581_1.fastq,ERR008581_2.fastq
ERR008581       vfdb_777        1       2983466 2942836 377323  ERR008581_1.fastq,ERR008581_2.fastq
ERR008581       vfdb_778        1       2983466 2942836 377323  ERR008581_1.fastq,ERR008581_2.fastq
ERR008581       vfdb_779        1       2983466 2942836 377323  ERR008581_1.fastq,ERR008581_2.fastq
ERR008581       vfdb_780        1       2983466 2942836 377323  ERR008581_1.fastq,ERR008581_2.fastq
ERR008581       vfdb_781        1       2983466 2942836 377323  ERR008581_1.fastq,ERR008581_2.fastq
ERR008581       vfdb_782        1       2983466 2942836 377323  ERR008581_1.fastq,ERR008581_2.fastq
ERR008581       vfdb_783        1       2983466 2942836 377323  ERR008581_1.fastq,ERR008581_2.fastq
ERR008581       vfdb_784        1       2983466 2942836 377323  ERR008581_1.fastq,ERR008581_2.fastq
ERR008581       vfdb_785        1       2983466 2942836 377323  ERR008581_1.fastq,ERR008581_2.fastq
ERR008581       vfdb_786        1       2983466 2942836 377323  ERR008581_1.fastq,ERR008581_2.fastq
ERR008581       vfdb_787        1       2983466 2942836 377323  ERR008581_1.fastq,ERR008581_2.fastq
ERR008581       vfdb_788        1       2983466 2942836 377323  ERR008581_1.fastq,ERR008581_2.fastq
ERR008581       vfdb_789        1       2983466 2942836 377323  ERR008581_1.fastq,ERR008581_2.fastq
ERR008581       vfdb_790        1       2983466 2942836 377323  ERR008581_1.fastq,ERR008581_2.fastq
ERR008581       vfdb_791        1       2983466 2942836 377323  ERR008581_1.fastq,ERR008581_2.fastq
ERR008581       vfdb_792        1       2983466 2942836 377323  ERR008581_1.fastq,ERR008581_2.fastq
ERR008581       vfdb_793        1       2983466 2942836 377323  ERR008581_1.fastq,ERR008581_2.fastq
ERR008581       vfdb_794        1       2983466 2942836 377323  ERR008581_1.fastq,ERR008581_2.fastq
ERR008581       vfdb_795        1       2983466 2942836 377323  ERR008581_1.fastq,ERR008581_2.fastq
ERR008581       vfdb_796        1       2983466 2942836 377323  ERR008581_1.fastq,ERR008581_2.fastq
ERR008581       vfdb_797        0       2983466 2942836 377323  ERR008581_1.fastq,ERR008581_2.fastq
ERR008581       vfdb_798        1       2983466 2942836 377323  ERR008581_1.fastq,ERR008581_2.fastq
ERR008581       vfdb_799        1       2983466 2942836 377323  ERR008581_1.fastq,ERR008581_2.fastq
ERR008581       vfdb_800        1       2983466 2942836 377323  ERR008581_1.fastq,ERR008581_2.fastq
ERR008581       vfdb_801        1       2983466 2942836 377323  ERR008581_1.fastq,ERR008581_2.fastq
ERR008581       vfdb_802        1       2983466 2942836 377323  ERR008581_1.fastq,ERR008581_2.fastq
ERR008581       vfdb_803        1       2983466 2942836 377323  ERR008581_1.fastq,ERR008581_2.fastq
ERR008581       vfdb_804        1       2983466 2942836 377323  ERR008581_1.fastq,ERR008581_2.fastq
ERR008581       vfdb_805        1       2983466 2942836 377323  ERR008581_1.fastq,ERR008581_2.fastq
ERR008581       vfdb_806        0       2983466 2942836 377323  ERR008581_1.fastq,ERR008581_2.fastq
ERR008581       vfdb_807        1       2983466 2942836 377323  ERR008581_1.fastq,ERR008581_2.fastq
ERR008581       vfdb_808        1       2983466 2942836 377323  ERR008581_1.fastq,ERR008581_2.fastq
ERR008581       vfdb_1389       0       2983466 2942836 377323  ERR008581_1.fastq,ERR008581_2.fastq

(I also just noticed that I did a horrible job naming the vfdb tar, too much time working with VCFs... I pushed an update to rename the archive)

[ar0ch]

In both applications, --fastq-1-files and --fastq-2-files are accumulators, so they can be given multiple times or a list of files can be given. The ordering of inputs is preserved and they're assumed to be paired between 1 <> 2. However, both applications only operate on one sample at a time -- do not provide reads from multiple samples in one run. The classification problem, as solved by STing, is embarrassingly parallel and parallelism is achieved through additional instances.

[MatteoSchiavinato]

Thanks! That explains the issue.

Maybe another thing that could be clearer is whether I can declare --sample-name item1,item2,...,itemN the same way I would do with --fastq-1-files file1,file2,…,fileN. I did it like that for now and it did not complain but I never got to see an output due to this issue with the index.

[MatteoSchiavinato]

Roger that. Thanks!