DecontaMiner is a tool designed and developed to investigate the presence of contaminating sequences in unmapped NGS data. It can suggest the presence of contaminating organisms in sequenced samples, that might derive either from laboratory contamination or from their biological source, and in both cases can be considered as worthy of further investigation and experimental validation. The novelty of DecontaMiner is mainly represented by its easy integration with the standard procedures of NGS data analysis, while providing a complete, reliable, and automatic pipeline. https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-2684-x
INFO: organism type flag -V not specified. O(thers) assumed (default option).
PROCESSING DETAILS
INFO: processing NON virus data
INFO: filtering with DEFAULT match count threshold 5.
INFO: filtering terminated. Generating data Matrix
Processing sample IgG_S4, with total read counts: 571, valid reads: 571, others reads: 0
... finished.
Output files written in the directory:
/path/to/BACTERIA/COLLECTED_INFO/VALID
Processing sample IgG_S4, with total read counts: 571, valid reads: 571, others reads: 0
... finished.
Output files written in the directory:
/path/to/BACTERIA/COLLECTED_INFO/VALID
INFO: processing terminated. Generating HTML report
ERROR !! NO FILES IN THE DIRECTORY: /path/to/BACTERIA/COLLECTED_INFO/VALID/BACTERIA/COLLECTED_INFO
ERROR !! NO FILES IN THE DIRECTORY: /path/to/BACTERIA/COLLECTED_INFO/VALID/BACTERIA/COLLECTED_INFOINFO: processing terminated. Output files written in the dir /path/to/BACTERIA/COLLECTED_INFO/VALID/BACTERIA/HTML_REPORTS
amarinderthind
commented
1 year ago
./collectInfo.sh -i /path/to/BACTERIA/COLLECTED_INFO/VALID
-- COLLECTING INFO --
INFO: organism type flag -V not specified. O(thers) assumed (default option).
PROCESSING DETAILS INFO: processing NON virus data INFO: filtering with DEFAULT match count threshold 5. INFO: filtering terminated. Generating data Matrix
Processing sample IgG_S4, with total read counts: 571, valid reads: 571, others reads: 0 ... finished. Output files written in the directory: /path/to/BACTERIA/COLLECTED_INFO/VALID
Processing sample IgG_S4, with total read counts: 571, valid reads: 571, others reads: 0 ... finished. Output files written in the directory: /path/to/BACTERIA/COLLECTED_INFO/VALID
INFO: processing terminated. Generating HTML report
ERROR !! NO FILES IN THE DIRECTORY: /path/to/BACTERIA/COLLECTED_INFO/VALID/BACTERIA/COLLECTED_INFO ERROR !! NO FILES IN THE DIRECTORY: /path/to/BACTERIA/COLLECTED_INFO/VALID/BACTERIA/COLLECTED_INFOINFO: processing terminated. Output files written in the dir /path/to/BACTERIA/COLLECTED_INFO/VALID/BACTERIA/HTML_REPORTS