Question on: README for the SILVA v138.1 reference files

I am trying to use the built files with dadasnake and they do not comply (maybe just their names?) then trying to reproduce the protocol and it fails:

# typo
gunzip SILVA_138.1_SSURef_NR99_05_01_20_opt.arb.gz 
=>     SILVA_138.1_SSURef_NR99_12_06_20_opt.arb.gz

when I run the first mothur command I get an empty silva.full_v138_1.good set of files (I tried with silva.full_v138.1.fasta and silva.full_v138_1.fasta, no difference)

mothur "#screen.seqs(fasta=silva.full_v138.1.fasta, start=1044, end=43116, maxambig=5);
        pcr.seqs(start=1044, end=43116, keepdots=T);
        degap.seqs();
        unique.seqs();"

I get

Linux version

Using ReadLine,Boost,HDF5,GSL
mothur v.1.47.0
Last updated: 1/21/22
by
Patrick D. Schloss

Department of Microbiology & Immunology

University of Michigan
http://www.mothur.org

When using, please cite:
Schloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.

Distributed under the GNU General Public License

Type 'help()' for information on the commands that are available

For questions and analysis support, please visit our forum at https://forum.mothur.org

Type 'quit()' to exit program

[NOTE]: Setting random seed to 19760620.

Script Mode

mothur > screen.seqs(fasta=silva.full_v138_1.fasta, start=1044, end=43116, maxambig=5)

Using 88 processors.

It took 13 secs to screen 446881 sequences, removed 446881.

Output File Names:
silva.full_v138_1.good.fasta
silva.full_v138_1.bad.accnos

It took 13 secs to screen 446881 sequences.

mothur > 
        pcr.seqs(start=1044, end=43116, keepdots=T)
Using silva.full_v138_1.good.fasta as input file for the fasta parameter.

Using 88 processors.
[ERROR]: silva.full_v138_1.good.fasta is blank. Please correct.
Error in reading your fastafile, at position -1. Blank name.

It took 13 seconds to run 2 commands from your script.

Logfile : mothur.1645605984.logfile

************************************************************
************************************************************
************************************************************
Detected 1 [ERROR] messages, please review.
************************************************************
************************************************************
************************************************************

mothur > summary.seqs(fasta=silva.full_v138_1.fasta)

Using 88 processors.

                Start   End     NBases  Ambigs  Polymer NumSeqs
Minimum:        1       13701   900     0       4       1
2.5%-tile:      996     27397   1210    0       5       11173
25%-tile:       1007    28523   1387    0       5       111721
Median:         1020    29127   1458    0       6       223441
75%-tile:       1056    29212   1516    0       6       335161
97.5%-tile:     2051    29235   1793    5       8       435709
Maximum:        16358   31768   4000    547     540     446881
Mean:   1152    28753   1454    0       5
# of Seqs:      446881

It took 18 secs to summarize 446881 sequences.

Thanks for your help

info

Linux Mothur version=1.47.0 Release Date=1/21/22

arb version 7.0

mothur / mothur.github.io

Question on: README for the SILVA v138.1 reference files #76

info