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torognes / vsearch

Versatile open-source tool for microbiome analysis
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sintax output is sometimes 4 columns and other times 5 columns #532

Closed todd-desantis closed 8 months ago

todd-desantis commented 10 months ago

Within a single output file, most rows are 4 columns, as expected, but some of the query sequences that presumably match nothing in the database result in rows with 5 columns. The first column is the sequence header and the next 4 are empty. Here's real output notice the row for ASV1964 has more tabs then the other two rows (might be able to see with this formatting).

ASV1956 d:Bacteria(1.00),p:Firmicutes_A(1.00),c:Clostridia(1.00),o:Lachnospirales(1.00),f:Lachnospiraceae(1.00),g:Anaerobutyricum(1.00),s:Anaerobutyricum__soehngenii(1.00)     +       d:Bacteria,p:Firmicutes_A,c:Clostridia,o:Lachnospirales,f:Lachnospiraceae,g:Anaerobutyricum,s:Anaerobutyricum__soehngenii
ASV1964                         
ASV1931 d:Bacteria(1.00),p:Firmicutes(1.00),c:Bacilli(1.00),o:Lactobacillales(1.00),f:Lactobacillaceae(1.00),g:Lactobacillus(1.00),s:Lactobacillus__delbrueckii(1.00)   +       d:Bacteria,p:Firmicutes,c:Bacilli,o:Lactobacillales,f:Lactobacillaceae,g:Lactobacillus,s:Lactobacillus__delbrueckii
torognes commented 10 months ago

Thanks for reporting this issue. Could you please check which vsearch version you are running? I think this issue have been reported and fixed earlier, but it may have returned. See issue #493.

todd-desantis commented 10 months ago

Thank for the response. I encountered the problem on v2.21.1.

$ vsearch
vsearch v2.21.1_linux_x86_64, 251.5GB RAM, 40 cores

I now see that you've released later versions. I'll upgrade and see if the problem persists.

todd-desantis commented 8 months ago

I'm now running vsearch v2.23. Thanks. I'll close this issue.