Interpreting the output
tseemann opened this issue · 1 comments
tseemann commented
When I run it i get a lot of output:
<SNIP>
**
rep2.1_ORF(E.faeciumContig1183)_JDOE 100
rep2.2_repR(pEF1)_DQ198088* 99
rep11.1_repA(pB82)_AB178871 100
rep14.3_ORF(pRI1)_EU327398* 99
rep17.1_CDS29(pRUM)_AF507977 100
repUS15._ORF(E.faecium287)_NZAAAK010000287* 89
****
I think this is 'progressive' output as you go through reads? print_interval ?
Do I just focus on the "final" section (see above) ?
What are the numbers?
How many plasmids should I expect given the above output? Six?
What are the numbers? coverage?
% abricate --db plasmidfinder E.faecium/canu/canu.contigs.fasta | cut -f 2,5,6 | column -t
SEQUENCE GENE COVERAGE
tig00000002 rep2_1_ORF(E.faeciumContig1183)_JDOE 1-1494/1494
tig00000002 rep2_1_ORF(E.faeciumContig1183)_JDOE 1-1494/1494
tig00000010 repUS15__ORF(E.faecium287) 1-1041/1041
tig00000011 rep17_1_CDS29(pRUM) 537-1041/1041
tig00000012 rep6_1_repA(p703/5) 14-663/723
tig00000012 rep17_1_CDS29(pRUM) 1-1041/1041
tig00000012 rep6_1_repA(p703/5) 14-663/723
tig00000013 rep18_1_repA(p200B) 413-931/933
tig00000013 rep18_1_repA(p200B) 413-931/933
tig00000013 rep18_1_repA(p200B) 413-931/933
tig00000016 rep14_3_ORF(pRI1) 1-951/951
tig00000016 rep14_3_ORF(pRI1) 772-951/951
tig00000026 rep2_1_ORF(E.faeciumContig1183)_JDOE 1-1494/1494
tig00000027 rep2_1_ORF(E.faeciumContig1183)_JDOE 1-1494/1494
tig00000028 rep2_1_ORF(E.faeciumContig1183)_JDOE 1-1494/1494
andrewjpage commented
I've changed the output to be a bit clearer and documented it in the readme. By default it now only prints the final information at the end rather than intermediate results. I dont know how many plasmids there are since it cant detect where there are multiple different plasmids with the same rep/inc sequence. The categories do seem to overlap between the 2 results, so thats a good sign.