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Hi,

This issue is just to inform you that the readDNAStringSet function from Biostrings has been updated to allow very large FASTA headers (see Bioconductor/Biostrings#59). This should make it easier to work with large numbers of samples in MJOLNIR :-)

Best,

Eva

Hi ! Running my data, and then the tutorial data (example_MJOLNIR_demultiplexed_data) just to check whether I had made an error - I am getting this.

> mjolnir6_FRIGGA(lib)
FRYGGA will produce a combined file.
FRYGGA is reading the ecotag-annotated database from THOR...
FRYGGA has read the taxonomy database, with 133 total MOTUs.
FRYGGA is reading the abundances database from ODIN...
Error in read.table(abundances, sep = substr(sept, 2, 2), head = T, stringsAsFactors = F) :
more columns than column names
Calls: mjolnir6_FRIGGA -> read.table
Execution halted

Looking that the abundance database there does seem to be a double ;; in there. Removing one of those unblocks it - but then you get

FRYGGA will produce a combined file.
FRYGGA is reading the ecotag-annotated database from THOR...
FRYGGA has read the taxonomy database, with 3775 total MOTUs.
FRYGGA is reading the abundances database from ODIN...
FRYGGA has read the abundances database, including 133 total MOTUs and 10 samples.
FRYGGA is done. File BATS.All_MOTUs.csv written, including 0 MOTUs with 0 total reads in 10 samples.
(0 non-singletons MOTUs).

So the outfile BATS.All_MOTUs.csv is empty and the next step (Lokki) won't run

Please help !

Many thanks

Martin

Great work as ussual. I have tried to use MJOLNIR. But I am stuck on the mjolnir4_ODIN (ODIN will generate now a list of ESVs for every non-singleton MOTU, using DnoisE). I have install DenoisE and modified the path (mjolnir4_ODIN.R) where I installed DnoisE, but it reported back that the DenoisE wasn't found or permission denied. Please your suggestion. Thank you

Hi! The documentation of ODIN says generate_ESV=TRUE is the default, but in the function this is set to FALSE?

Hello,

I am trying to use Mjolnir for the analysis of gut microbiomes of antarctic fishes but I have a problem when using the first command (mjolnir2_FREYJA). I end up with this error:

FREYJA will do paired-end alignment, demultiplexing and length filter.
sh: 1: illuminapairedend: not found
sh: 1: obigrep: not found
sh: 1: ngsfilter: not found
sh: 1: obigrep: not found
Error in checkForRemoteErrors(val) : 
  one node produced an error: error in running command

I think they're might be a problem with my installation of OBItools because I couldn't installed it the way you suggested, I had to create a miniconda3 environment to install it and I am not sure that your R package is able to recognize this installation.

Thank you in advance for your help

Hi Owen,
I was an online student of yours a while back and I want to use mjolnir for my metabarcoding data. I'm running this on a Mac with an M2 chip, and I keep getting an error involving the sed command.

"Warning messages:
1: In system(paste0("sed -i 's/size/ count/g'", lib, "_no_chimeras.fasta),: running commang 'sed -i 's/size/count/g BATS_no_chimeras.fasta had status 1"

I've run into this before and I've fixed it by changing the code from sed to gsed in a script, but I can't figure out how to do this for the Rcode. Can you please advise me?

Thanks!