Comments (4)
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)
from sting.
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.
from sting.
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.
from sting.
Roger that. Thanks!
from sting.
Related Issues (15)
- Rewrite git history for publication
- Could not open the input file 'ERR026529_1.fastq.gz' HOT 3
- cgMLST schemes? HOT 21
- finding rST through rMLST scheme HOT 2
- Profile file for cgMLST HOT 3
- indexer reports "ERROR: The config file does not contain the [loci] section." HOT 1
- Preparing the database missing from README
- Is it possible to use assembly instead of NGS raw reads?
- Check licensing info HOT 1
- Automated STing MLST db
- Indexer throwing ParseError HOT 2
- subprocess.CalledProcessError HOT 5
- db_util.py not able to download data from PubMLST HOT 1
- Missing files HOT 2
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from sting.