Closed hjarnek closed 2 weeks ago
Hi @hjarnek sorry for the delay, I was on vacation.
I've created a small example with the same characteristics as your dataset (mainly, an empty first cell, which mumu
accepts) but I could not reproduce your issue:
sample1
ASV1 10
ASV2 1
ASV1 ASV2 96.8
mumu \
--otu_table <( printf "\tsample1\nASV1\t10\nASV2\t1\n") \
--match_list <(printf "ASV1\tASV2\t96.8\n") \
--new_otu_table /dev/null \
--log /dev/null
mumu
outputs no warning and merges the two ASVs:
parse OTU table... done, 2 entries
parse match list... done
sort lists of matches... done
search for potential parent OTUs... done
merge OTUs... done
update spread values... done
write new OTU table... done, 2 entries
The error message you get indicates that there is somehow a difference between the ASV names in the table and in the match list. I am not sure what that difference could be (non-printable characters maybe?). You could check your files with an hexadecimal viewer such as xxd
or od
:
printf "ASV1\tASV2\t96.8\n" | xxd | head
00000000: 4153 5631 0941 5356 3209 3936 2e38 0a ASV1.ASV2.96.8.
Or if you could share your input files with me, I could run my own tests to find whats wrong.
Frédéric, I'm sorry to bother you, I must have been too tired when I ran mumu, as I have apparently input the FASTA file in place of the ASV table, as also seen in my original post above actually. Your program is working like a charm of course. I'm closing this "issue" now before someone else sees it 🤦♂️
Ah, mumu -o COI.fasta ...
, I should have spotted it too. Thanks for trying mumu
!
Hi @hjarnek I've implemented a test that warns users when the OTU table does not seem to contain samples (e.g.; not a table). That should at least help users understand what's wrong with their data. The test is now included in mumu
(see https://github.com/frederic-mahe/mumu/commit/136d738e46534ff51451f75a56e148b9a1abc8eb).
Great! I promise I won't make this mistake again ;)
Hi @frederic-mahe,
I know there is a similar closed issue, but this case seems to be a different problem.
I have exported an ASV table from DADA2 into a txt file that looks like this:
Neither column names nor row names are quoted, and there is a single leading
\t
on the first line.There are no whitespaces or non-ASCII characters in the ASV names, just "ASV" followed by a number. The FASTA file looks like this:
And the match list is produced with VSEARCH as suggested in the mumu manual:
Still, when I run it (
mumu -o COI.fasta -m match.list -l COI_log.txt -n COI_seqtab_mumu.txt
) I get warnings likewarning: one of these is not in the OTU table: ASV1404 ASV1243 85.3
for every post in the match list. The log file comes out empty. Do you have any idea what's going on? mumu 1.0.2 in native Linux environment.