Minimal-but-complete set of example files, say, below 1 MB, to work with the supplied config file?

[richelbilderbeek]

Dear MetONTIIME maintainers and fellow users,

To get MetONTIIME running, it would be useful to get a small yet full example dataset to work with the supported config file.

Currently, Zymo-GridION-EVEN-BB-SN_sup_pass_filtered_27F_1492Rw_1000_reads.fastq.gz is supplied (good job!), but what is lacking is:

• Example detabase sequences (.fasta)
• ~Example sample metadata (.tsv)~ [edit: it is not needed]
• Example taxonomy (.tsv)

Is there anyone that has a small but usable dataset to help getting MetONTIIME running?

Thanks and cheers, Richel

[MaestSi]

Hi,

• in the readme you can find a link to preformatted databases;
• the sample metadata file is optional, you don't need to create one, you can specify the path to an empty file, which will be created upon running;
• in the readme you can find the barplot you are supposed to obtain with the test dataset; the tsv taxonomy file is expected to contain the same information.

Simone

[richelbilderbeek]

The example dataset linked by the README at the 'test-dataset' header at URL https://nanopore.s3.climb.ac.uk/Zymo-GridION-EVEN-BB-SN_signal.tar is 260 GB big. I'd say that does not qualify as a minimal-but-full example dataset :-)

Likewise for the others...

Anyone knows a minimal-but-full example dataset, as in below 1 MB?

[MaestSi]

The example test dataset is indeed this one. SM

[richelbilderbeek]

Thanks @MaestSi, indeed this is one of the file. As a set of files to be able to run MetONTIIME, however, as it misses:

• Example detabase sequences (.fasta)
• Example taxonomy (.tsv)

Anyone knows a minimal-but-complete example dataset, below 1 MB (but hey, 10 would be fine too) so anyone can test-run MetONTIIME?

[MaestSi]

For example, you can use a fasta file with B. subtilis 16S sequence:

>NR_116192.1 Bacillus subtilis strain NRRL NRS-744 16S ribosomal RNA, partial sequence
GGATAACTCCGGGAAACCGGGGCTAATACCGGATGGTTGTTTGAACCGCATGGTTCAAACATAAAAGGTG
GCTTCGGCTACCACTTACAGATGGACCCGCGGCGCATTAGCTAGTTGGTGAGGTAACGGCTCACCAAGGC
AACGATGCGTAGCCGACCTGAGAGGGTGATCGGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGG
GAGGCAGCAGTAGGGAATCTTCCGCAATGGACGAAAGTCTGACGGAGCAACGCCGCGTGAGTGATGAAGG
TTTTCGGATCGTAAAGCTCTGTTGTTAGGGAAGAACAAGTACCGTTCGAATAGGGCGGTACCTTGACGGT
ACCTAACCAGAAAGCCACGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGTGGCAAGCGTTGTCC
GGAATTATTGGGCGTAAAGGGCTCGCAGGCGGTTTCTTAAGTCTGATGTGAAAGCCCCCGGCTCAACCGG
GGAGGGTCATTGGAAACTGGGGAACTTGAGTGCAGAAGAGGAGAGTGGAATTCCACGTGTAGCGGTGAAA
TGCGTAGAGATGTGGAGGAACACCAGTGGCGAAGGCGACTCTCTGGTCTGTAACTGACGCTGAGGAGCGA
AAGCGTGGGGAGCGAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGAGTGCTAAGTGTTAG
GGGGTTTCCGCCCCTTAGTGCTGCAGCTAACGCATTAAGCACTCCGCCTGGGGAGTACGGTCGCAAGACT
GAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGAAGCAACGCGAA
GAACCTTACCAGGTCTTGACATCCTCTGACAATCCTAGAGATAGGACGTCCCCTTCGGGGGCAGAGTGAC
AGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCT
TGATCTTAGTTGCCAGCATTCAGTTGGGCACTCTAAGGTGACTGCCGGTGACAAACCGGAGGAAGGTGGG
GATGACGTCAAATCATCATGCCCCTTATGACCTGGGCTACACACGTGCTACAATGGACAGAACAAAGGGC
AGCGAAACCGCGAGGTTAAGCCAATCCCACAAATCTGTTCTCAGTTCG

And the corresponding taxonomy file: NR_116192.1 Bacteria;Bacillota;Bacilli;Bacillales;Bacillaceae;Bacillus;Bacillus subtilis; (the separator between the id and the taxonomy should be a tab) That should be enough for checking everything is working. Best, SM

[richelbilderbeek]

Awesome, thanks!

[richelbilderbeek]

I reopen this Issue as the set of files is still incomplete: it results in the error Ordinations with less than two dimensions are not supported.

I will try to add a line to the FASTA or taxonomy file and see if that solve the problem :innocent:

[MaestSi]

I guess that is due to the fact that beta-diversity analysis is not possible with a single sample. You may consider splitting the fastq in 2 chunks and see if that solves the issue, or setting diversityAnalyses process to false in the config file. SM

[richelbilderbeek]

I reopen this Issue as the set of files is still incomplete, after or setting diversityAnalyses process to false: it results in the error (see in GitHub Actions log here):

All features were filtered, resulting in an empty table

I tried to alleviate this by setting clusteringIdentity to 0.1and minConsensus to 0.51, but still no run that passes.

So, anyone knows a minimal-but-complete example dataset, below 1 MB (but hey, 10 would be fine too) so anyone can test-run MetONTIIME, ideally allowing the diversity analysis?

[MaestSi]

It looks like the reads do not align to Bacillus subtilis 16S gene sequence that I downloaded from NCBI. You may check this by uploading to QIIME2 Viewer the file taxonomy.qzv. If this is the case, you may consider downloading more fasta sequences from NCBI and creating the tsv files with the script I provided - or just using a real database, which you can easily download from QIIME2 website.