Anomalous results in using RGI bwt for metagenomics #319
Description
Input features:
DNA metagenomic samples sequenced with Illumina (2x150), pre-processed with BBDuk, rendering a median of 262 Mreads (both R1 and R2).
RGI features: RGI v6.0.5 (conda); CARD database v4.0.1, with and without Wildcard (+Wcard, -Wcard, respectively).
Commands used:
rgi bwt -n 24 -1 sample1_R1.fastq.gz -2 sample1_R2.fastq.gz --output_file sample1_output --local
rgi bwt -n 24 -1 sample1_R1.fastq.gz -2 sample1_R2.fastq.gz --output_file sample1_output --local --include_wildcard
Outputs:
a) WARNINGS -Wcard: about 1,300, all of them with text " has few mapped reads to make consensus sequence skipping: 'ARO ID' ".
b) WARNINGS +Wcard: about 14,400; almost all with text " has few mapped reads to make consensus sequence skipping: 'ARO ID' "; a few of them with text Exception: '2219'.
c) File *_output.overall_mapping_stats.txt:
-. Proper-pairs: about 27 Mreads (-Wcard), 107 Mreads (+Wcard), i.e., much more higher than numbers of Mapped reads --> anomalous result!!
-. Mapped reads: about 226,000 reads (-Wcard), 445,000 reads (+Wcard).
-.Both pairs mapped: about 214,000 reads (-Wcard), 424,000 reads (+Wcard).
-.Singletons: about 12,000 reads (-Wcard), 21,000 reads (+Wcard).
d) Files *_output.gene_mapping_data.txt and *_output.allele_mapping_data.txt: values of Completely Mapped Reads (206,000 and 300,000, for -Wcard and +Wcard) and Mapped Reads with Flanking Sequence (0 for both runs) were different from those recorded in the overall statistics --> anomalous results !!
Similar anomalous results were also obtained by using another sample of the same sequence set.
Any idea why these anomalous results were obtained?