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DATE 2018-11-01

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MESSAGE
DATE 2018-11-20
FROM Ruben Safir
SUBJECT Subject: [Hangout - NYLXS] [mothur] mothur v1.41.0
Hey mothur users,

We’re happy to announce the release of v.1.41.0! This update includes
a number of bug fixes and new features that we’re confident you will
find useful. First, we’ve added several methods to the pre.cluster
command so you can use the default
version as suggested in the MiSeq SOP or you can use our implementation
of the deblur or unoise3 algorithms. Check out the notes on the wiki
page for the pre.cluster command to see our comments on how the
implementations differ from the original tools. Second, the new release
has an updated version of biom.info
that allows you to read in the newer version of the standard that is
based on hdf5 binary files. You can learn more about these and the
updates listed below at
https://github.com/mothur/mothur/releases/tag/v1.41.0.

In addition to the new version of mothur that we are releasing, we’re
excited to announce that we’ve migrated the user forum to
https://forum.mothur.org. If you had an account on the previous version
of the forum, it was transferred, but you will need to request a new
password by attempting to log in and then indicating that you need to
reset your password. We hope people like the new interface and find it
easier to use. Thanks to all of you that have been playing with it
already and especially to those of you that frequently help out by
answering other people’s questions. Because of the difficulties with
the previous version of the forum, many users have used the GitHub
issues tracker, but it would be best if people could use the new forum
instead.

Finally, I am working on the workshop schedule for 2019, but we still
have one workshop with openings for 2018. This will be a mothur workshop
and it will be offered December
17-19 in Detroit. Please email me for more details on costs and how to
register. I’m sorry, but there isn’t enough bandwidth in the room to
livestream and I’m not able to offer the workshop elsewhere.

As always, thanks for your support of mothur!
Pat




Features
• Add sample info to tax.summary in biom.info command. #531
• Updates biom.info to read hdf5 biom files. #178
• make.contigs change to quality score calculation. #468
• Adds oldfasta and column parameters to pairwise.seqs command.
• Adds testing features
• Adds count file to shared file option in make.shared command. #519
• Updates boost version to 1.68.0.
• Adds fasta, taxonomy, name and count options to merge.files. #506
• Updates get.oturep command to use optiMatrix. Reduces time and
memory needed. #465
• Prevent excessive log file size by limiting errors and warnings for
commands to 10. #420
• Adds relabund to create.database command. #478
• Adds multiple cutoffs to cluster command for opti, agc and dgc. #305
• Adds accnos parameter to filter.shared. #293
• Adds shared and groups parameters to get.rabund command. #325
• Adds unoise, tree, deblur methods to pre.cluster command.
Bugs

• unifrac command crashes with subsample option.
• cluster command nearest neighbor bug fix
• collect.shared "[ERROR]: requesting groups not present in files,
aborting." error #497
• Removes extra "quit()" output. #464
• Fixes make.contigs group file issue with *.gz files. #480
• Fixes pcr.seqs file mismatch. #522
• Tree.shared command results with shared file. #535
• Make.contigs group names.
https://forum.mothur.org/t/make-contigs-with-oligo-creating-new-names/3542
• Fixed 1.40.1 - Mothur's logfile created in mothur's executable
location, instead of current working directory. #436
• Fixed 1.40.1 - Smart distancing hangs if label not found in file. #441
• Fixed 1.40.2 - Fixes *contigs.report file append issue that
resulted in reads missing from report.
• Fixed 1.40.3 - get.coremicrobiome command segfault with shared
option. #445
• Fixed 1.40.3 - merge.files not finding input files. #438
• Fixed 1.40.3 - sparcc improves speed with threaded code and
corrects small bug.
• Fixed 1.40.4 - Cluster commands printing of list file. #454
• Fixed 1.40.4 - Cluster.split merge of list files bug #460
• Fixed 1.40.4 - Cluster commands - method agc and dgc do not require
distance matrix. #456
• Fixed 1.40.4 - Trim.seqs multiple matches error. #427
• Fixed 1.40.4 - Pre.cluster name / group error. #461
• Fixed 1.40.4 - Pre.cluster single sample crash. #451
• Fixed 1.40.4 - pcr.seqs and screen.seqs (with no bad reads
detected), causing accnos file issue.
• Fixed 1.40.5 - get.lineage failing to find taxons. #477
• Fixed 1.40.5 - screen.seqs not making *good.groups or
*good.count_table files. #476
• Fixed 1.40.5 - get.communitytype crash. #472
• Fixed 1.40.5 - Fixes make.contigs gz file read issues. #471
• Fixed 1.40.5 - Solves seq.error crash #463
• Fixed 1.40.5 - Resolves trim.seqs "could not open" error. #444


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