mothur database issue

[splaisan]

Hi Anna,

I tried to download files from the mothur and decipher sites as suggested in the readme but when I link them in the config, mothur does not seem to work.

for mothur I downloaded from thir wiki link Full-length sequences and taxonomy references and untar'ed to /data/biodata/mothur_taxonomy:

• silva.nr_v138_1.align
• silva.nr_v138_1.fasta
• silva.seed_v138_1.align
• silva.seed_v138_1.tax

these 4 files do not match the command reported in the error log

for decipher I downloaded and unzipped to /data/biodata/decipher_taxonomy

• SILVA_SSU_r138_2019.RData

Then I edited my yaml as:

taxonomy:
  mothur:
    do: true
    db_path: "/data/biodata/mothur_taxonomy"
    tax_db: "silva.nr_v138_1"
  decipher:
    do: false
    db_path: "/data/biodata/decipher_taxonomy"
    tax_db: "SILVA_SSU_r138_2019.RData"
    db_short_names: "SILVA_SSU_r138"

If not correct, would you have a primer on how to install SSU references for mothur. Or at least the listing of your database folder to see which files are expected there.

Thanks in advance

mothur error log

Script Mode

mothur > set.dir(tempdefault=/data/biodata/mothur_taxonomy)
Mothur's directories:
tempDefault=/data/biodata/mothur_taxonomy/

mothur > 
            classify.seqs(fasta=sequenceTables/all.seqs.for_SILVA_138_SSURef_NR99_cut.fasta, template=silva.nr_v138_1.fasta, taxonomy=silva.nr_v138_1.taxonomy, cutoff=60, method=wang, processors=1)

Using 1 processors.
Unable to open silva.nr_v138_1.fasta. Trying default /data/biodata/mothur_taxonomy/silva.nr_v138_1.fasta.
Unable to open /data/biodata/mothur_taxonomy/silva.nr_v138_1.fasta. Trying mothur's executable location /opt/biotools/dadasnake/conda/ec4abc68013d874fa157380f1e65649f/bin/silva.nr_v138_1.fasta.
Unable to open /opt/biotools/dadasnake/conda/ec4abc68013d874fa157380f1e65649f/bin/silva.nr_v138_1.fasta.
Unable to open silva.nr_v138_1.fasta
Unable to open silva.nr_v138_1.taxonomy. Trying default /data/biodata/mothur_taxonomy/silva.nr_v138_1.taxonomy.
Unable to open /data/biodata/mothur_taxonomy/silva.nr_v138_1.taxonomy. Trying mothur's executable location /opt/biotools/dadasnake/conda/ec4abc68013d874fa157380f1e65649f/bin/silva.nr_v138_1.taxonomy.
Unable to open /opt/biotools/dadasnake/conda/ec4abc68013d874fa157380f1e65649f/bin/silva.nr_v138_1.taxonomy.
Unable to open silva.nr_v138_1.taxonomy
[ERROR]: did not complete classify.seqs.

mothur > quit()

[Fred-White94]

If you download this file https://mothur.s3.us-east-2.amazonaws.com/wiki/silva.nr_v138_1.tgz from this site: https://mothur.org/wiki/silva_reference_files/ and untar it you should then have these files:

• silva.nr_v138_1.align
• silva.nr_v138_1.tax

the .align file can be renamed .fasta and the same for the .tax file to .taxonomy. Seemed to solve the problem for me.

[splaisan]

thanks @Fred-White94, this renaming was not mentioned clearly in other pages and I did not think about such a simple edit