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tseemann / nullarbor

:floppy_disk: :page_with_curl: "Reads to report" for public health and clinical microbiology
GNU General Public License v2.0
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Report not displaying Resistome or Virulome data #286

Closed sdhair closed 3 years ago

sdhair commented 3 years ago

Hi, The pipeline completes and generates the html report however the resistome and virulome data is not displaying. The data is generated but it does not appear to be in the final resistome.csv though is in the individual sample resistome.tab file. Any assistance would be most appreciated! Log attached; nullarbor.log

$ cat resistome.csv Isolate,Found,+,- Sample2,2,✔,? Sample4,2,✔,? Sample3,2,✔,? Sample1,2,✔,?

`$ cat ../Sample1/resistome.tab

FILE SEQUENCE START END STRAND GENE COVERAGE COVERAGE_MAP GAPS %COVERAGE %IDENTITY DATABASE ACCESSION PRODUCT RESISTANCE

Sample1/contigs.fa Contig_193_16.3655 10140 11345 + tet(B) 1-1206/1206 =============== 0/0 100.00 100.00 ncbi NG_048163.1 tetracycline ......... `

sdhair commented 3 years ago

Nuking the conda environment and starting again solved the issue...