mothur - 1.48.2

Enhancements: * dist.shared can calculate a euclidean distance matrix using a clr file.

Bug Fixes: * Rarefaction.shared labels incorrect. #729 * Fixes bug with optimization of maxhomop in screen.seqs. #857 * Fixes bug with Optimatrix phylip file read. * Fixes bug with remove.groups #861 * Fixes bug with make.clr calculation of zero OTUs.

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Published by mothur-westcott over 1 year ago

mothur - Version 1.48.1

Enhancements: * Adds fasta type to make.file. This allows you to generate a count or group file for a set of fasta files. For example: make.file(inputdir=./, type=fasta). Mothur will create a 2 or 3 column file file. If there are paired fasta files, a 3 column file file will be generated. group forwardFastaFileName reverseFastaFileName If there are single fasta files, a 2 column file file will be generated. group fastaFileName * Adds file option to make.count. The file used as input here must the 2 or 3 column fasta file file created by the make.file command with fasta as the input type. (described above) Using a fastq file file will result in a read error as make.count is only designed to be used with fasta files.
* Adds constaxonomy and contigsreport files to set.current

Bug Fixes: * Restores ability to escape '-' characters in parameters. * Fixes segfault with pcr.seqs when all seqs are bad and keepdots=f * Fixes bug with get.oturep if invalid cutoff given * Fixes bug with count file compress flag * Fixes bug in fastq.info when using checkorient with barcodes. The barcodes were ignored. * Fixes bug in sequence class that flagged 'U' as ambiguous.

Binaries System Requirements:

Mac Version requires OSX 10.14 or higher Windows 10 or higher Centos 7 RHEL 8 or greater / Ubuntu 20. Binaries include:

Mac version - includes boost, readline, gsl, hdf5 Windows - includes boost Ubuntu - includes boost Linux - includes boost, readline, hdf5, gsl NOTE: Mothur's external tools (vsearch, uchime, prefetch and fasterq-dump) are included with mothur's binary. They are also available separately for our users who build from source in the Mothur.tools* files.

External library requirements (if building from source):

Boost 1.75.0 GSL 2.6 HDF5 1.12.0

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Published by mothur-westcott about 2 years ago

mothur - Version 1.48.0

Enhancements: * Adds translate.seqs command. #789 * Adds make.count command to assign groups to fasta files. * Adds format parameter to make.group command. * Updates fastq.info, trim.seqs, trim.flows to output count file by default. * Significant speed improvements to commands that split by sample. ie, pre.cluster, chimera commands * Significant speed Improvements to unifrac.weighted. * Adds group name check to update sample names with illegal characters. * Adds flow file to get.groups * General speed improvement with sequence commands.

Bug Fixes:

• Fixes bug with chimera.vsearch with no groups and denovo
• Fixes bug with clearcut sequence name copy
• Fixes bug with make.contigs screening parameters if maxlength not set
• Fixes bug with split.groups flow file option with count table
  
• Fixes bug with sets parameter not passing to pairwise lefse calc
• Fixes bug with make.sra single-end reads

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Published by mothur-westcott about 4 years ago

mothur - Version 1.47.0

Hello mothur users!

We are happy to announce the release of mothur v.1.47.0. There are a few significant thigns to report with this release...

First, we are happy to announce that this release is the first announced version of a mothur-based approach to open and closed reference clustering that doesn't suffer from the same problems found with other algorithms. This can be achieved using the cluster.fit function. You can read more about it in a paper we recently had accepted in mSphere. A preprint version of the paper can be found here while we wait for the official publication.

Second, over the past few months we’ve incorporated a number of significant improvements to mothur to make it easier to work with by consolidating commands. For example, we have included the ability to use screen.seqs arguments within make.contigs. This means that you can now do "make.contigs(file=stability.files, maxambig=0, maxlength=275, maxhomop=8)" as a single command rather than two commands. We are also trying to phase out the names and groups files  in place of a count file since they add confusion and extra steps. Another notable change is that, by default, the chimera commands will remove the sequences from the fasta file so that you no longer need to use the subsequent remove.seqs command. 

Third, if you've been to one of my workshops you know that the hardest step can often be getting to the correct place using the command prompt. Now, if you double click on the mothur executable it should start mothur in the directory where the executable was found. We are calling this the 'mothurhome' argument Fourth, we found a small bug in pcr.seqs that inadvertently removed the first base from the outputted sequences. You may notice a one-base difference in the start/end coordinate positions between versions.

Finally, I continue to put a lot of effort into developing educational content that should be of interest to mothur users. I am posting two videos each week to YouTube that often uses mothur-based files as input to work within R. You can find these at the Riffomonas YouTube channel. If you are interested in upcoming R and mothur workshops be sure to check out the schedule for virtual workshops; I'll be teaching an R workshop in a couple of weeks! If you're looking for more updates on Riffomonas and resources for strengthening your R skills, I have a free weekly newsletter that you can subscribe to. I've been encouraged by the positive feedback I've received from the content on Riffomonas - let me know if there's anything you'd like me to be sure to cover.

Enhancements: * Updated SOP to reflect change brought with this version of mothur * Adds cluster.fit command. OptiFit: an Improved Method for Fitting Amplicon Sequences to Existing OTUs #415 * make.contigs now outputs count file instead of group file. #793 * Adds maxambig, maxhomop, maxlength parameters to make.contigs. #793 * Sets default output for unique.seqs to count file. * Adds removechimeras parameter to chimera commands to auto remove chimeras from files. Default=t. #795 * Adds auto name fix for sample names that include special characters like '-'. * MOTHURFILES can now contain multiple paths separated by ';' #799 * Updates MOTHURTOOLS to allow for multiple locations separated by ';' #799 * Allows for multiple input directories separated by ';' #799 * Adds 'mothurhome' keyword #800 * Adds qfile to list.seqs #802 * Adds ability to input multiple files to list.seqs, remove.seqs and get.seqs to help resolve file mismatches. #803 * Adds ability to read *.gz fastq files in list.seqs. #804 * Adds fastq and format parameters to chop.seqs #790 * Removes BLAST from mothur. #801 * Removes search and blastlocation parameters from chimera.slayer. #801 * Removes blastlocation parameter from set.dir. #801 * Forces lefse pairwise comparisons.

Bug Fixes:

• Fixes crash with split.groups when running with fasta and group files without a names file. Effects allfiles options in other commands.
• Fixes bug with pcr.seqs If keepdots=f, and start and end are used, then first base was removed by mistake.
• Fixes bug with get.sharedseqs if no groups are provided.
• Fixes bug with remove.groups phylip file option.
• Fixes formatting issue with chimera.vsearch with a reference
• Fixes bug in sens.spec when name file is used
• Fixes crash with sort.seqs if multiple seqs present with the same name
• Fixed segfault caused by logger.

Amazon Machine Image: * 1.47.0_ID = ami-097205064a488a028

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Published by mothur-westcott over 4 years ago

mothur - Version 1.46.1

Bug Fixes:

• Fixes crash with split.groups when running with fasta and group files without a names file. Effects allfiles options in other commands.
• Fixes pcr.seqs crash when run without oligos file.

Binaries System Requirements:

Mac Version requires OSX 10.14 or higher Windows 10 or higher Centos 7 RHEL 8 or greater / Ubuntu 20. Binaries include:

Mac version - includes boost, readline, gsl, hdf5 Windows - includes boost Ubuntu - includes boost Linux - includes boost, readline, hdf5, gsl NOTE: Mothur's external tools (blast, vsearch, uchime, prefetch and fasterq-dump) are included with mothur's binary. They are also available separately for our users who build from source in the Mothur.tools* files. External library requirements (if building from source):

Boost 1.75.0 GSL 2.6 HDF5 1.12.0

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Published by mothur-westcott almost 5 years ago

mothur - Version 1.46.0

Enhancements:

• Reduces time to run pairwise.seqs by up to 99% using kmer distances. #763
• Adds ability to cluster unaligned sequences in cluster.split. #763
• Reduces time of cluster.split through improvements in the splitting process. #778
• Removes split by distance option from cluster.split.
• Adds jtt, pmb, pam and kimura calculators to dist.seqs to find distances between protein sequences. #776
• Adds pairwise parameter to lefse command. #781
• Adds checkorient parameter to pcr.seqs. Change Includes functions to reorient and reverse unpaired primers. #768
• Rework of rename.seqs file option. #772
• Simplifies system command. #782
• Adds ASV to OTU mapping for otu.hierarchy command. #777
• Adds check to shared file read for incorrect numOtus column. This error can occur if the shared file is modified outside of mothur.
• Adds warning in remove.seqs for dereplicate. See http://mothur.org/wiki/chimeradereplicateexample/ for detailed explanation.

Bug Fixes:

• Fixes uchime command construction. (v.1.45.2)
• Fixes bug with sra.info threads option. (v.1.45.3)
• Fixes bug with OTU priority printing with file option in cluster.split
• Fixes segfault in metasats if abundance of one treatment is 0
• Fixes bug with get.sharedseqs shared file option
• Removes duplicate column headers for align.report #785
• Adds error message for missing headers in design file. Prevents addition of dummy group or removal of valid group. #779

Binaries System Requirements:

Mac Version requires OSX 10.14 or higher Windows 10 or higher Centos 7 RHEL 8 or greater / Ubuntu 20. Binaries include:

Mac version - includes boost, readline, gsl, hdf5 Windows - includes boost Ubuntu - includes boost Linux - includes boost, readline, hdf5, gsl NOTE: Mothur's external tools (blast, vsearch, uchime, prefetch and fasterq-dump) are included with mothur's binary. They are also available separately for our users who build from source in the Mothur.tools* files. External library requirements (if building from source):

Boost 1.75.0 GSL 2.6 HDF5 1.12.0

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Published by mothur-westcott almost 5 years ago

mothur - Version 1.45.3

Fixes bug with sra.info threads option.

Binaries System Requirements:

• Mac Version requires OSX 10.14 or higher
• Windows 10 or higher
• Centos 7
• RHEL 8 or greater / Ubuntu 20.

Binaries include:

• Mac version - includes boost, readline, gsl, hdf5
• Windows - includes boost
• Ubuntu - includes boost
• Linux - includes boost, readline, hdf5, gsl NOTE: Mothur's external tools (blast, vsearch, uchime, prefetch and fasterq-dump) are included with mothur's binary. They are also available separately for our users who build from source in the Mothur.tools* files.

External library requirements (if building from source):

• Boost 1.75.0
• GSL 2.6
• HDF5 1.12.0

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Published by mothur-westcott about 5 years ago

mothur - Version 1.45.2

Bug Fixes:

• Fixes uchime command construction.

Binaries System Requirements:

• Mac Version requires OSX 10.14 or higher
• Windows 10 or higher
• Centos 7
• RHEL 8 or greater / Ubuntu 20.

Binaries include:

• Mac version - includes boost, readline, gsl, hdf5
• Windows - includes boost
• Ubuntu - includes boost, readline
• Linux - includes boost, readline, hdf5, gsl NOTE: Mothur's external tools (blast, vsearch, uchime, prefetch and fasterq-dump) are included with mothur's binary. They are also available separately for our users who build from source in the Mothur.tools* files.

External library requirements (if building from source):

• Boost 1.75.0
• GSL 2.6
• HDF5 1.12.0

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Published by mothur-westcott over 5 years ago

mothur - Version 1.45.1

Bug Fixes:

• Fixes bug with assembly of command string for chimera.uchime and chimera.vsearch. #771

Binaries System Requirements:

• Mac Version requires OSX 10.14 or higher
• Windows 10 or higher
• Centos 7
• RHEL 8 or greater / Ubuntu 20.

Binaries include:

• Mac version - includes boost, readline, gsl, hdf5
• Windows - includes boost
• Ubuntu - includes boost, readline
• Linux - includes boost, readline, hdf5, gsl NOTE: Mothur's external tools (blast, vsearch, uchime, prefetch and fasterq-dump) are included with mothur's binary. They are also available separately for our users who build from source in the Mothur.tools* files.

External library requirements (if building from source):

• Boost 1.75.0
• GSL 2.6
• HDF5 1.12.0

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Published by mothur-westcott over 5 years ago

mothur - Version 1.45.0

Enhancements: * Adds shared file conversion to make.shared #716 * Updates uchime makefile and adds uchime build to mothur #711 * Adds clump parameter to pre.cluster #749 * Rework of rename.seqs for added flexibility * Removes requirement for inputdir to be writable #747 * Adds multiple processors for chimera.vsearch when using reference instead of denovo. #757 * Adds functions to read and write HDF5 biom files. #752 * Adds RELEASE_DATE to makefiles. #761 * Removes "paired" tag from make.file. * Adds ability to run batch files from interactive mode. * Rebuilds uchime for Catalina. * Removes clear screen command from mothur's initial startup. #748 * Updates vsearch to 2.16.0. https://github.com/torognes/vsearch/releases/tag/v2.16.0

Bugs:

• Fixes bug with split.abund when run with names file. #715
• Fixes bug with sff.info parsing with oligos. Effects make.sra command as well because make.sra calls sff.info with an oligos file. #726 #727
• Fixes bug with chimera.uchime assembly of accnos file.
• Fixes trim.flows empty *flow.files issue.
• rarefaction.shared groups output bug. #729
• indicator command pvalues off. #729
• Fixes bug with qfile option in make.contigs. #745
• Fixes bug with pre.cluster's unoise method.
• Fixes Windows mkDir bug. Use boost filesystems if available. #754
• Fixes bug with make.contigs not making group file for *.gz files with oligos file. #753
• Fixes bug where inputdir is attached to the floworder parameter.
• Fixes lefse screen output.
• Fixes bug with trim.seqs that required name or count file.
• Fixes make.contigs segfault.
• Fixes bug with oligos file trimming when several barcodes match same read.
• Fixes bug with align.seqs segfault.
• Fixes bug with remove.lineage and get.lineage not handling taxon definitions with multiple levels.
• Fixes bug with spaces in path.

Binaries System Requirements:

• Mac Version requires OSX 10.14 or higher
• Windows 10 or higher
• Centos 7
• RHEL 8 or greater / Ubuntu 20.

Binaries include:

• Mac version - includes boost, readline, gsl, hdf5
• Windows - includes boost
• Ubuntu - includes boost, readline
• Linux - includes boost, readline, hdf5, gsl NOTE: Mothur's external tools (blast, vsearch, uchime, prefetch and fasterq-dump) are included with mothur's binary. They are also available separately for our users who build from source in the Mothur.tools* files.

External library requirements (if building from source):

• Boost 1.75.0
• GSL 2.6
• HDF5 1.12.0

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Published by mothur-westcott over 5 years ago

mothur - Version 1.44.3

Bugs:

• Fixes bug with trim.seqs that required name or count file.
• Fixes make.contigs segfault.

Binaries:

• Mac Version requires OSX 10.14 or higher
• Windows 10 or higher
• RHEL 7 or greater / Ubuntu 18.

Binaries include:

• Mac version - includes boost, readline, gsl, hdf5
• Windows - includes boost
• Ubuntu - includes boost, readline (version 7), gsl
• Linux - includes boost, readline (version 6), hdf5 NOTE: Mothur's external tools (blast, vsearch, uchime, prefetch and fasterq-dump) are included with mothur's binary. They are also available separately for our users who build from source in the Mothur.tools* files.

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Published by mothur-westcott almost 6 years ago

mothur - Version 1.44.2

Enhancements:

• Adds shared file conversion to make.shared #716
• Updates uchime makefile and adds uchime build to mothur #711

Bugs:

• Fixes bug with split.abund when run with names file. #715
• Fixes bug with sff.info parsing with oligos. Effects make.sra command as well because make.sra calls sff.info with an oligos file. #726 #727
• Fixes trim.flows empty *flow.files issue.
• Fixes rarefaction.shared groups output bug. #729
• Fixes indicator command pvalues. #729
• Removes "paired" tag from make.file command.
• Fixes bug with oligos file trimming when several barcodes match same read.
• Fixes bug with align.seqs segfault.

Binaries:

• Mac Version requires OSX 10.14 or higher
• Windows 10 or higher
• RHEL 7 or greater / Ubuntu 18.

Binaries include:

• Mac version - includes boost, readline, gsl, hdf5
• Windows - includes boost
• Ubuntu - includes boost, readline (version 7), gsl
• Linux - includes boost, readline (version 6), hdf5 NOTE: Mothur's external tools (blast, vsearch, uchime, prefetch and fasterq-dump) are included with mothur's binary. They are also available separately for our users who build from source in the Mothur.tools* files.

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Published by mothur-westcott about 6 years ago

mothur - Version 1.44.1

Enhancements:

• Adds ability to run batch files from interactive mode.

Bugs:

• Fixes segfault crash.
• Fixes bug with remove.lineage and get.lineage not handling taxon definitions with multiple levels.
• Fixes bug with spaces in path.
• Rebuilds uchime for Catalina.

Binaries:

• Mac Version requires OSX 10.14 or higher
• Windows 10 or higher
• RHEL 7 or greater / Ubuntu 18.

Binaries include:

• Mac version - includes boost, readline, gsl, hdf5
• Windows - includes boost
• Ubuntu - includes boost, readline (version 7), gsl
• Linux - includes boost, readline (version 6), hdf5

NOTE: Mothur's external tools (blast, vsearch, uchime, prefetch and fasterq-dump) are included with mothur's binary. They are also available separately for our users who build from source in the Mothur.tools* files.

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Published by mothur-westcott about 6 years ago

mothur - Version 1.44.0

Enhancements:

• Adds sra.info command to download and extract samples from NCBI using prefetch and fasterq-dump written by NCBI. #27
• Adds make.clr command. #695
• Adds clr file type to metastats command. #695
• Expands batch files. #601 #658
• Adds environment variables to mothur. #601
• Adds MOTHUR_TOOLS option to allow you to set the location of mothur's external tools at compile time or through the set.dir command at run time. #682
• Adds uchime parameter to chimera.uchime. #682
• Adds vsearch parameter to chimera.vsearch, cluster, cluster.split commands. #682
• Improves mothur's checkorient option in make.contigs. Also sets checkorient=t by default.
• split.abund command 's cutoff parameter can now be a percentage. Removes fasta file requirement. #263
• Adds contigsreport to get.seqs and remove.seqs commands. #660
• Adds processors option to split.groups. #685
• Adds sets to remove.groups and get.groups commands. #277
• Adds parallelization to chimera.vsearch when using denovo method. #700
• Changes filter.seqs fasta file delimantor from '-' to '|' to allow for '-''s in filenames.
• Adds list file output for make.shared with count table.

Bugs:

• Fixes tree.shared distance being used instead of similarity.
• Fixes bug with remove.seqs not removing empty groups from the count table. #675
• Fixes bug with trim.seqs if no name file is given and allfiles=T. #696
• Fixes corr.axes bug when metadata files contain zeroed columns.

Binaries:

• Mac Version requires OSX 10.14 or higher
• Windows 10 or higher
• RHEL 7 or greater / Ubuntu 18.

Binaries include:

• Mac version - includes boost, readline, gsl, hdf5
• Windows - includes boost
• Ubuntu - includes boost, readline (version 7), gsl
• Linux - includes boost, readline (version 6), hdf5

NOTE: Mothur's external tools (blast, vsearch, uchime, prefetch and fasterq-dump) are included with mothur's binary. They are also available separately for our users who build from source in the Mothur.tools* files.

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Published by mothur-westcott over 6 years ago

mothur - Version 1.43.0

• Adds list to split.groups #624
• Adds estimator.single command. #164
• Passes CXX variables to uchime makefile. #614
• Modifies output files from dist.shared, summary.single and summary.shared. You may run with or without rareification, but not both. #607
• Improves speed and resource management for align.seqs command. #647
• Improves mothur's logging features.
• Adds qfile option to make.contigs. #650
• Adds auto decompress feature to make.contigs if gz read fails. #634
• Improves speed of dist.seqs and pairwise.seqs. #653
• Adds 2 column pacbio file option to fastq.info. #649
• Windows users can now run make.contigs with *.gz files.

Bugs: * Removes empty groups before printing count table. #641 * Changes datatype for opti method to correct overflow. * Makes current file class thread safe. Caused random crashes in pre.cluster. #643 * get.oturep command wasn't handling multiple labels. Removed labels parameter and modifies cutoff to act like cluster commands. ie. cutoff=0.01-0.03. Also failing with abundance method using count file without group information #656 #575
* Trim.seqs was not removing paired primers. #667 * get/remove.lineage not producing a accnos file.

Binaries:

• Mac Version requires OSX 10.14 or higher
• Windows 10 or higher
• RHEL 7 or greater / Ubuntu 18.

Binaries include:

• Mac version - includes boost, readline, gsl, hdf5
• Windows - includes boost
• Ubuntu - includes boost, readline (version 7), gsl
• Linux - includes boost, readline (version 6), hdf5

NOTE: Mothur's external tools (blast, vsearch and uchime) are included with mothur's binary. They are also available separately for our users who build from source in the Mothur.tools* files.

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Published by mothur-westcott over 6 years ago

mothur - Version 1.42.3

• BUG FIX: Issues with count files

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Published by mothur-westcott about 7 years ago

mothur - Version 1.42.2

• Fixes bug in count table removeGroups functions #626
• Fixes definitions #633

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Published by mothur-westcott about 7 years ago

mothur - Version 1.42.1

• Updates vsearch version to resolve Windows output format bug.
• Improves removeOTU functions to increase processing speed.

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Published by mothur-westcott about 7 years ago

mothur - Version 1.42.0

Enhancements: * Sets random seed to 19760620 at start of mothur. #600 * Adds constaxonomy file to list.otus command. #581 * Adds rename option to the get.oturep command. #555 * Adds ability to comment out lines in the file file. #560 * Adds merge.otus command. #558 * Adds processors option to rarefaction.single and rarefaction.shared. #544 * Expands make.shared to allow for count files with no groups. #563 * Adds fastq to split.groups command. #499 * Adds Oligos class and split.groups commands fastq.info. #499 * Merge.count command ignores duplicate names. #259 * Removes catchall dependency. #164 * Improves help command. #183 * Adds tree parameter to sub.sample command. * Adds withreplacement parameter to sub.sample command. #262 * Adds withreplacement parameter to get.communitytype, dist.shared, rarefaction.shared, summary.single, summary.shared, tree.shared, unifrac.unweighted, unifrac.weighted. #262 * Adds map file to make.shared output from count file. This mapping file can then be used with the rename.seqs command to modify the associated files. #583 * Adds taxonomy parameter to rename.seqs. * Removes multiple inputs from mothur. #379 * Reduces memory needed for pre.cluster #589 * Adds count parameter to count.seqs to inflate or deflate count tables. * Updates vsearch version to 2.11.1 #585 * Adds vsearch parameter to chimera.vsearch so that you can specify location of vsearch executable. #586 * Adds constaxonomy file to subsample command. #582

Bug Fixes: * Adds isEqual functions for floats and doubles. Fixes Ubuntu error with filter.shared (-0.01 != -0.01) returned true. * Fixes file extensions of output files in pcr.seqs. * Fixes sub.sample with multiple labels bug. #559 * Fixes bug with otu.association metadata file. * Fixes pcr.seqs end issue with keepdots=f. * Fixes bug in remove.lineage with cons.taxonomy and shared files. #580 * Removes extra space from output. #603 * Fixes output filename for make.group. #602

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Published by mothur-westcott about 7 years ago

mothur - Version 1.42.0 Beta Release

Enhancements: * Adds rename option to the get.oturep command. #555 * Adds ability to comment out lines in the file file. #560 * Adds merge.otus command. #558 * Adds processors option to rarefaction.single and rarefaction.shared. #544 * Expands make.shared to allow for count files with no groups. #563 * Adds fastq to split.groups command. #499 * Adds Oligos class and split.groups commands fastq.info. #499 * Merge.count command ignores duplicate names. #259 * Removes catchall dependency. #164 * Improves help command. #183 * Adds tree parameter to sub.sample command. * Adds withreplacement parameter to sub.sample command. #262 * Adds withreplacement parameter to get.communitytype, dist.shared, rarefaction.shared, summary.single, summary.shared, tree.shared, unifrac.unweighted, unifrac.weighted. #262 * Adds map file to make.shared output from count file. This mapping file can then be used with the rename.seqs command to modify the associated files. #583 * Adds taxonomy parameter to rename.seqs. * Removes multiple inputs from mothur. #379 * Reduces memory needed for pre.cluster #589 * Adds count parameter to count.seqs to inflate or deflate count tables. * Updates vsearch version to 2.11.1 #585 * Adds vsearch parameter to chimera.vsearch so that you can specify location of vsearch executable. #586 * Adds constaxonomy file to subsample command. #582

Bug Fixes: * Adds isEqual functions for floats and doubles. Fixes Ubuntu error with filter.shared (-0.01 != -0.01) returned true. * Fixes file extensions of output files in pcr.seqs. * Fixes sub.sample with multiple labels bug. #559 * Fixes bug with otu.association metadata file. * Fixes pcr.seqs end issue with keepdots=f. * Fixes bug in remove.lineage with cons.taxonomy and shared files. #580

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Published by mothur-westcott over 7 years ago

mothur - Version 1.41.3

Enhancements * Adds timing to pre.cluster deconvolute steps.

Bug Fixes * classify.seqs and filter.seqs command may eliminate reads causing file mismatches. * get.oturep bug with abundance method.

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Published by mothur-westcott over 7 years ago

mothur - Version 1.41.2

• Updated on 1.23.19 to include get.oturep fix

Enhancements: * Adds rename option to the get.oturep command. #555 * Adds ability to comment out lines in the file file. #560 * Adds merge.otus command. #558 * Adds processors option to rarefaction.single and rarefaction.shared. #544 * Expands make.shared to allow for count files with no groups. #563 * Adds fastq to split.groups command. #499 * Adds Oligos class and split.groups commands fastq.info. #499 * Merge.count command ignores duplicate names. #259 * Removes catchall dependency. #164 * Improves help command. #183

Bug Fixes: * Adds isEqual functions for floats and doubles. Fixes Ubuntu error with filter.shared. * Fixes file extensions of output files in pcr.seqs. * Fixes sub.sample with multiple labels bug. #559 * Fixes bug with otu.association metadata file. * Fixes pcr.seqs end issue with keepdots=f. * Fixes get.oturep crash with abundance method. #575

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Published by mothur-westcott over 7 years ago

mothur - Version 1.41.1

Bug Fix: * Fixes file mismatch caused by pre.cluster command run with a count file. #556

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Published by mothur-westcott over 7 years ago

mothur - Version 1.41.0

• 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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Published by mothur-westcott over 7 years ago

mothur - Version 1.41.0

Feature Updates * 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

Bug Fixes * unifrac command crashes with subsample option. * cluster command nearest neighbor bug fix * collect.shared "[ERROR]: requesting groups not present in files, aborting." error #497 * Adds location to merge.files. #438 * Removes extra "quit()" output. #464 * Fixes make.contigs group file issue with *.gz files. #480 * Fixes pcr.seqs file mismatch. #522

Binaries * Mac Version requires OSX 10.13 or higher * Windows 10 or higher * All linux versions contain the same files with the exception of the mothur executable. The Mothur.linux64.zip contains a dynamically linked copy of mothur. The Mothur.linux64.noReadLine.zip contains a dynamically linked copy of mothur built without the readline library. The readline library allows you to use the arrow keys to scroll through previous commands within mothur in interactive mode. To use the regular linux version you must have the readline libraries installed. A few of our mothur enthusiasts do not have readline and don’t want to install it so we made a version without that feature.

AMI * You can run mothur 1.41.0 on Amazon with the following instructions, Mothur_AMI

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Published by mothur-westcott almost 8 years ago

mothur - Version 1.40.5

Enhancements * make.contigs change to quality score calculation. #468

Bug Fixes

• get.lineage failing to find taxons. #477
• screen.seqs not making *good.groups or *good.count_table files. #476
• get.communitytype crash. #472
• Fixes make.contigs gz file read issues. #471
• Solves seq.error crash #463
• Resolves trim.seqs "could not open" error. #444

Binaries

Mac Version requires OSX 10.13 or higher Windows 10 or higher All linux versions contain the same files with the exception of the mothur executable. The Mothur.linux64.zip contains a dynamically linked copy of mothur. The Mothur.linux64.noReadLine.zip contains a dynamically linked copy of mothur built without the readline library. The readline library allows you to use the arrow keys to scroll through previous commands within mothur in interactive mode. To use the regular linux version you must have the readline libraries installed. A few of our mothur enthusiasts do not have readline and don’t want to install it so we made a version without that feature.

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Published by mothur-westcott about 8 years ago

mothur - Version 1.40.4

Bug Fixes:

• Cluster commands printing of list file. #454
• Cluster.split merge of list files bug #460
• Cluster commands - method agc and dgc do not require distance matrix. #456
• Trim.seqs multiple matches error. #427
• Pre.cluster name / group error. #461
• Pre.cluster single sample crash. #451
• pcr.seqs and screen.seqs (with no bad reads detected), causing accnos file issue.

Binaries * Mac Version requires OSX 10.13 or higher * Windows 10 or higher * All linux versions contain the same files with the exception of the mothur executable. The Mothur.linux64.zip contains a dynamically linked copy of mothur. The Mothur.linux64.noReadLine.zip contains a dynamically linked copy of mothur built without the readline library. The readline library allows you to use the arrow keys to scroll through previous commands within mothur in interactive mode. To use the regular linux version you must have the readline libraries installed. A few of our mothur enthusiasts do not have readline and don’t want to install it so we made a version without that feature.

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Published by mothur-westcott about 8 years ago

mothur - Version 1.40.3

Bug Fixes: * get.coremicrobiome command segfault with shared option. #445 * merge.files not finding input files. #438 * sparcc improves speed with threaded code and corrects small bug.

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Published by mothur-westcott about 8 years ago

mothur - Version 1.40.2

Bug Fixes * Fixes *contigs.report file append issue that resulted in reads missing from report.

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Published by mothur-westcott about 8 years ago

mothur - Version 1.40.1

Bug Fixes * Mothur's logfile created in mothur's executable location, instead of current working directory. #436 * Smart distancing hangs if label not found in file. #441

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Published by mothur-westcott about 8 years ago

mothur - Version 1.40.0

Feature Updates * Adds summary, contigsreport, alignreport parameters to summary.seqs command. #319 * Reduces memory usage for screen.seqs #319 * Changes align.seqs flip parameter default to true. This means if you sequence produces a poor alignment in the forward direction, mothur will align the reverse compliment and choose the better alignment. * Adds unique method to cluster command. #340 * Adds opti method to mgcluster command. #342 * Speed and memory improvements for commands that use shared files. #357 #347 * Allow for () characters in taxonomy definitions. #350 * Autodetect number of available processors and use all available. * Removes processors parameter from chimera.bellerophon * Updates to mothur's log file management. #377 * Improves randomization in unifrac commands. * Rewrite of all of mothur's threaded code. * Adds flow parameter to split.groups command. * Fixes blast path issue in classify.seqs. #403 * Adds additional format checks for make.sra command inputs. #410

Bug Fixes * make.file group names incorrect when full path names are in file file. * pcr.seqs command was trimming extra base when using the start and end parameters. #348 * pcr.seqs command "name mismatch" error when using paired primers and keepdots=f. * Fixes segfault error for commands that use subsampling. #357 #347 * Fixes chimera.vsearch screen output. #309 * Fixes out of bounds error in heatmap commands. #363 * Missing '/' and '\' dividing filename and directory in default places to look for files. This caused files not to be found. #364 * Fixes seq.error seg fault. #280 * Adds deliminator to make.groups output file for multiple groups. mergegroups -> merge.groups. #384 * Fixes seeded random issue with classify.seqs and lefse. #416 * Fixes get.lineage and remove.lineage partial match bug. #399 * Fixes pvalue bug in homova command for Windows. #408 * Updates help and fixes redirect bug. #387

Binaries * Mac Version requires OSX 10.13 or higher * Windows 10 or higher * All linux versions contain the same files with the exception of the mothur executable. The Mothur.linux64.zip contains a dynamically linked copy of mothur. The Mothur.linux64.noReadLine.zip contains a dynamically linked copy of mothur built without the readline library. The readline library allows you to use the arrow keys to scroll through previous commands within mothur in interactive mode. To use the regular linux version you must have the readline libraries installed. A few of our mothur enthusiasts do not have readline and don’t want to install it so we made a version without that feature.

AMI * You can run mothur 1.40.0 on Amazon with the following instructions, Mothur_AMI

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Published by mothur-westcott over 8 years ago

mothur - Version 1.39.5

Feature Updates * Adds contigsreport to current files saved by mothur. #291 * Improves randomization functions * Sets method driven cutoffs in cluster commands. For methods opti, agc and dgc (cutoff=0.03) which will create OTU for distance 0.03. For methods average, nearest, furthest and weighted (cutoff=0.15) which may be adjusted down due to the sparse matrix, Why does the cutoff change?

Bug Fixes * Fixes make.lefse output. #314 * Fixes make.file segfault. #316 * Fixes "couldn't find OTUID" make.biom error. * Fixes Windows subsampling issue. #317

Binaries * Mac Version requires OSX 10.12 or higher * Windows 10 or higher * All linux versions contain the same files with the exception of the mothur executable. The Mothur.linux64static.zip contains a statically linked copy of mothur. The Mothur.linux64.zip contains a dynamically linked copy of mothur. The Mothur.linux64.noReadLine.zip contains a dynamically linked copy of mothur built without the readline library. The readline library allows you to use the arrow keys to scroll through previous commands within mothur in interactive mode. To use the regular linux version you must have the readline libraries installed. A few of our mothur enthusiasts do not have readline and don’t want to install it so we made a version without that feature.

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Published by mothur-westcott over 9 years ago

mothur - Version 1.39.4

Feature Updates - Updates mothur to use seeded mersennetwisterengine to randomize. This improves random distribution and resolves the Windows subsampling discrepancies. #311

Binaries - Mac Version requires OSX 10.12 or higher - Windows 10 or higher - Both linux versions contain the same files with the exception of the mothur executable. The Mothur.linux_64.noReadLine.zip contains a copy of mothur built without the readline library. The readline library allows you to use the arrow keys to scroll through previous commands within mothur in interactive mode. To use the regular linux version you must have the readline libraries installed. A few of our mothur enthusiasts do not have readline and don’t want to install it so we made a version without that feature.

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Published by mothur-westcott over 9 years ago

mothur - Version 1.39.3

Feature Updates - Adds contigsreport to current files saved by mothur. #291

Bug Fixes - Fixes bug with shortcut files in classify.seqs command. #307

Binaries - Mac Version requires OSX 10.12 or higher - Windows 10 or higher - Both linux versions contain the same files with the exception of the mothur executable. The Mothur.linux_64.noReadLine.zip contains a copy of mothur built without the readline library. The readline library allows you to use the arrow keys to scroll through previous commands within mothur in interactive mode. To use the regular linux version you must have the readline libraries installed. A few of our mothur enthusiasts do not have readline and don’t want to install it so we made a version without that feature.

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Published by mothur-westcott over 9 years ago

mothur - Version 1.39.2

Feature Updates: - Adds file mismatch check to summary.seqs

Bug Fixes: - chimera.vsearch removing last character of sequence names when processing with a reference. Not an issue with denovo method. #306
- Fixes summary.tax summary file printing issue. - Fixes bug on start "[ERROR]: basicstring::substr: _pos (which is 18446744073709551615) > this->size()..." - Fixes bug with the rename.file command that occurs if outputdir is used and multiple files are provided. - Fixes ls bug for Windows users in make.file command.

Binaries - Mac Version requires OSX 10.12 or higher - Windows 10 or higher - Both linux versions contain the same files with the exception of the mothur executable. The Mothur.linux_64.noReadLine.zip contains a copy of mothur built without the readline library. The readline library allows you to use the arrow keys to scroll through previous commands within mothur in interactive mode. To use the regular linux version you must have the readline libraries installed. A few of our mothur enthusiasts do not have readline and don’t want to install it so we made a version without that feature.

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Published by mothur-westcott over 9 years ago

mothur - Version 1.39.1

Feature Updates: - Adds runsensspec parameter to cluster.split. Default=T.

Bug Fixes: - pre.cluster (without groups) not clustering properly. #301 - make.contigs fixes "off by one" name mismatch error. #303 - rename.file unable to automatically rename with output directory specified. - cluster and cluster.split improper printing of list file when using name file option. Does not effect printing of the list file when clustered with count file. - cluster and cluster.split improper printing of list file when using phylip file option. Does not effect printing of the list file when clustered with column file. - Incorrect taxlevel printed in *.tax.summary file.

Binaries - Mac Version requires OSX 10.12 or higher - Windows 10 or higher

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Published by mothur-westcott over 9 years ago

mothur - Version 1.39.0

New Commands

Feature Updates - Changes default clustering method to opti. - Adds agc and dgc vsearch clustering methods for Windows users. #215 - Adds chimera.vsearch command for Windows users. #215 - Major speed improvement for pre.cluster command with aligned files. #220 - Major memory requirement reduction for pre.cluster command with by group option. #220
- Adds constaxonomy file to current files saved by mothur. - Control-C handling: In script or batch mode exit mothur. In interactive mode exit command. #212 http://www.mothur.org/forum/viewtopic.php?f=5&t=4102&p=12431#p12431 - Adds blastdir parameter to set.dir command. #223 - Taxonomy files can now contain spaces in the taxon names. #265 - Makes refasta and repnames parameters optional for create.database command. #32 - Removes cutoff adjust in dist.seqs command. #274 - Adds trim parameter to make.sra command for use with sff files.

Bug Fixes - Fixes Windows multiple processors with groups crash - chimera.uchime command. - Fixes Windows bug with make.file command. #255 - Creates unique group names for 3 column format make.file command. #270 - Fixes bug with number of "taxon"_unclassifeds appended to taxonomy in classify.seqs. - Eliminates zero abundance OTUs created by some floating point biom files converted to shared files make.shared. - Floating point exception in sparcc command. - Fixes bug where mothur was not finding matches for sequence names "off by one character" in the name. make.contigs - Fixes bug with "find" command for Linux user in make.file - Fixes bug with optimize parameter using alignreport file in screen.seqs command. #288

Download

Registered Users

Binaries - Mac Version requires OSX 10.12 or higher

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Published by mothur-westcott over 9 years ago

mothur - Version 1.38.1

New Commands - merge.count command combines count files. #259

Feature Updates - Removes hard parameter from cluster, cluster.classic and cluster.split commands. All commands now use hard=T. - Improved help command. #257 - Make.file command is more flexible with filenames. #243 - Adds prefix parameter to Make.file command. #251 - Changes bad character in group names error to warning. Modifies group names with '-' characters in output filenames to avoid downstream issues.

Bug Fixes - Fixes bug with output directory in make.group command. - Fixes filename expansion issue make.contigs. http://www.mothur.org/forum/viewtopic.php?f=3&t=5869&p=14857#p14857 - Fixes group name issue with oligos file option in get.mimarkspackage command.

Download

Registered Users

Binaries - Mac Version requires OSX 10.11 or higher

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Published by mothur-westcott almost 10 years ago

mothur - Version 1.38.0

Hey mothur users,

We’re happy to announce the release of v.1.38.0! This release primarily has a bunch of random bug fixes that we were anxious to get out to you. Two new commands should strike your interest. First, we have introduced rename.file, which renames files so that you don't have to worry about using your system commands and updates the "current" files. Second, building off the introduction of VSEARCH functionality in the last release, we've created chimera.vsearch to detect chimeras using VSEARCH. Their benchmarking indicates that it performs similar to UCHIME, which is available as chimera.uchime.

In addition to improvements to mothur, since the last release we've also published several papers and blog posts that you should definitely check out.

Blog: - The mothur AMI for work on Amazon's Web Server - How to customize your reference alignment for non-V4 data

New Commands - rename.file - renames file and updates current files saved by mothur. - chimera.vsearch - detects chimeras using vsearch software package. #239

Feature Updates - Removes hcluster command. It is really really slow and we don't recommend it. #208 - Removes save option which kept references in memory. #208 - Removes clear.memory command which worked with the save option. #208 - Removes pds.pipeline command. #208 - Command line mode returns exit-code to indicate failure. #151 - Removes reftaxonomy parameter from classify.otu and summary.tax. #241 - Removes large parameter from count.seqs command. #203 - Allows make.biom with picrust option to handle mothur's new parentTaxon_unclassified format. #241 - Adds mothur's location as a default file location to check. Reduces unable to open file errors. #231 - Adds count parameter to sens.spec command. #225 - Clarifies seq.error command output. #175 - Adds sets parameter to lefse command. #234 - Removes indexFile requirement for using NONE option in oligos file. make.contigs. #193 - make.contigs command will skip blank file pairs. #233 - Warn about illegal characters in group names to prevent downstream analysis issues. #37 - Adds rdiffs to pcr.seqs command to allow for setting different diffs for the forward and reverse primers. #244

Bug Fixes - Mothur can handle whitespace in command lines. #191 - Fixes gradient bar on heatmap.sim command. #237
- Fixes bug with classify.otu persample option. - Fixes bug with agc method in cluster and cluster.split - Fixes bug with summary.tax command not including name file counts in *tax.summary. - Fixes RAM output for linux get.current. #232 - Error generated when filenames are too long for uchime program. #226 - Fixes cutoff adjust for agc and dgc clustering methods. #254

Binaries - Mac Version requires OSX 10.11 or higher

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Published by mothur-westcott almost 10 years ago

mothur - Version 1.37.6

• Fixes make.contigs gz file error - http://www.mothur.org/forum/viewtopic.php?f=4&t=4210&sid=8303c7614b85114d0587fc03fa3fefce

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Published by mothur-westcott about 10 years ago

mothur - Version 1.37.5

Fixes file divide bug with make.contigs for certain sequence name types.

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Published by mothur-westcott about 10 years ago

mothur - Version 1.37.4

• Fixes chimera.uchime size= instead of ab= for datasets run without references or groups. #236

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Published by mothur-westcott about 10 years ago

mothur - Version 1.37.3

• Fixes bug with agc and dgc methods in the cluster.split and cluster commands that added one duplicate names to OTUs.
  

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Published by mothur-westcott about 10 years ago

mothur - Version 1.37.2

Bug Fixes - Stops sort of user created list file. - Fixes bug introduced in 1.37 that removed barcodes and primers from fastq files instead of simply identifying samples for make.sra command. - Fixes bug with merge.groups initialization of the shared file. - Cleans up makefile. - Removes extra unclassified level from taxonomy files - Fixes make.contigs gz file error - http://www.mothur.org/forum/viewtopic.php?f=4&t=4210&sid=8303c7614b85114d0587fc03fa3fefce

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Published by mothur-westcott about 10 years ago

mothur - Version 1.37.0

Hey mothur users,

We’re happy to announce the long awaited v.1.37.0! There are some pretty sweet features in the new release that I’d like to highlight for you. First, for the mac and unix users, we’ve added two methods to cluster and cluster.split to allow you to use abundance and distance-based greedy clustering using the free and open source VSEARCH program. This release was a bit delayed because we’ve been trying to get the windows version to work, but haven’t gotten as far as we’d like. The next release should include it. I would point out that if you are doing 16S rRNA gene sequencing you want to stick with the defaults - this is mostly for those doing ITS. You can see two of our recent papers published in PeerJ and mSystems for more discussion of this. Second, we’ve added a make.file command that will allow you to generate a files file for use in make.contigs. This command should significantly simplify the process of generating the file. Third, we've created a biom.info command that will convert a biom formatted file to mothur-formatted shared and assorted taxonomy files. There have also been a number of other new features and bug fixes that you should check out on the release page.

In addition to improvements to mothur, since the last release we've also published several papers and blog posts that you should definitely check out.

Blog: - mothur and QIIME - No, greengenes' reference alignment hasn't improved - README for SILVA v123 reference files - Suck until you don't

Papers: - Application of database-independent approach to assess the quality of OTU picking methods - De novo clustering methods outperform reference-based methods for assigning 16S rRNA gene sequences to operational taxonomic units - Sequencing 16S rRNA gene fragments using the PacBio SMRT DNA sequencing system

That's all until next time, enjoy! As always, feel free to let us know what you think or if there are additional features you'd like to see in mothur...

New Commands

• biom.info - reads biom file and creates shared, taxonomy, constaxonomy and tax.summary files. #82

Feature Updates

• Adds agc and dgc methods to the cluster.split and cluster commands from the vsearch software package. Not available for Windows. #169
• merge.groups - adds count option. http://www.mothur.org/forum/viewtopic.php?f=5&t=3698 #88. Adds method and fasta parameter. Method options are sum, average and median. Default=sum. #105
• get.groups / remove.groups - adds phylip and column options. #79
• get.seqs / remove.seqs - Checks for repeat sequences names and eliminates them. Allows users creating their own templates to easily remove duplicate sequences from their reference files. #159
• Remove MPI source code - MPI version is slower than non-MPI version. No advantage to using it. #144
• unique.seqs - adds format parameter. Options are name and count. #125
• Simplify makefile #157
• make.file - adds numcols parameter. Options 2 or 3. Default=3, meaning groupName forwardFastq reverseFastq. The groupName is made from the beginning part of the forwardFastq file. Everything up to the first '' or if no '' is found then the root of the forwardFastq filename. #162
• Output number of warning and errors detected.
• rename.seqs - adds file, map, qfile and contigsreport parameters. The map file allows you to revert sequence names back to original. Works with make.contigs to automatically rename sequences. #132
• make.contigs - adds rename parameter, default=t. Renames sequences to reduce file sizes and greatly reduce the size of the column formatted distance matrix downstream. Uses the rename.seqs command to rename which creates a map file so you can revert to original names at any time. #132
• classify.seqs - Changes cutoff parameter default to 80. This change in the bootstrap threshold reflects the default values in the 454 and MiSeq SOPs. #192
• get.current - Adds current RAM usage and total RAM available.
• Replaces '-' characters in sequences names with '_' characters to avoid downstream issues. #205
• Changes default on minlength to 10 for the screen.seqs command. #160
• Removed load.logfile command. Added output file to get.current and input/output file to set.current . These changes allow the commands to work together to keep track of current files between instances of mothur in a more direct and easy to edit manner. You can input the output file of the get.current command into the set.current command using the new current parameter.
• Adds includescrap parameter to the make.sra command. Default=True. http://www.mothur.org/forum/viewtopic.php?f=3&t=3750&p=11122#p11122
• get.otulabels removed. Functions added to get.otus command.
• remove.otulabels removed. Functions added to remove.otus command.
• Adds output and printlevel parameters to classify.seqs, classify.otu, biom.info and summary.tax commands. Output options simple and detail. Default=detail. #204 #158
  
• Adds relabund parameter to classify.otu command. #101
• Adds threshold parameter to summary.tax command. #31
• Adds parent taxons to unclassified taxons for outputs of classify.seqs, classify.otu, biom.info commands. http://www.mothur.org/forum/viewtopic.php?f=3&t=3183&p=9003#p9003 #29
• Adds count parameter to get.sharedseqs #133

Bug Fixes

• filter.shared - modifies rareOtus label to prevent mothurConvert error. #137
• make.contigs - File mismatch error with certain sequence name formats and multiple processors. Three column format gz file not producing group file.
• Fixes mothurConvert error if "seed" was part of filename.
• Removes OS limit on open files for cluster.split #142
• make.sra - Fastq.info error about no inputs selected when running make.sra with single fastq file and oligos file.
• cluster.split - removes limit on number of files that can be split by cluster.split. Limit caused "[ERROR]: Cannot open yourFasta.xxx.temp" file error.
• "Illegal Instruction" error on Linux machines. Fixed in 1.29.16 release. #179
• Updates Xcode project file to fix collaboration issues.
• Fixes filter.seqs issue where sequences are not the same length by setting default minlength to 10 in the screen.seqs command. #160
• Windows version - if files were used with less sequences than processors specified then empty file error. #195
• Fixes make.contigs name mismatch bug and gives a slight speed boost. #167
• Fixes lefse "Skipping x iter..." warning.

Registered Users

3663

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Published by mothur-westcott over 10 years ago

mothur - Version 1.36.1

Version 1.36.0 with 2 Bug Fixes - make.file - Linux version only bug. Caused error messages about find command -maxdepth parameter. - classify.rf - Design file change caused results to be all zeros.

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Published by mothur-westcott over 10 years ago

mothur - Version 1.36.0

New commands - set.seed - allows you to seed random. - make.file- creates a file containing list of fastq or gz files for input to make.contigs.

Feature updates - pre.cluster - added cluster method for unaligned sequences. Added align, mismatch, match, gapopen, gapextend parameters. - set.dir - if output directory does not exist mothur will create it for you. - chimera.uchime - adds method tag to output files. - http://www.mothur.org/forum/viewtopic.php?f=5&t=3636&p=10748#p10748 - chop.seqs - adds qfile option to allows for chopping quality files. - classify.otu - adds threshold parameter. The threshold parameter allows you to specify a cutoff for the taxonomy file that is being inputted. - rename.seqs - adds count, delim, and placement parameters. - seed parameter added to all commands to allow you to easily seed random while running commands. - make.shared - mothur no longer checks for biom matrix type to allow for more flexibility. - make.shared - rabund files are no longer outputted. Mothur will create a rabund file with the [[get.rabund]] command. - set.dir - if output directory does not exist it will be created. - no longer create a log file simple command line option runs of mothur - make.sra - allow for assigning multiple sets of files to the same group in 3 column format. - make.contigs - allow for missing reads in files. - metastats - remove qvalues. Also removes fortran source from mothur. - automatically adjust number of processors when fork() fails - Removes extra white spaces from mothur's print to make output files more compatible with other software packages. - http://www.mothur.org/forum/viewtopic.php?f=4&t=3703 - degap.seqs - adds the processors option. - Adds column headers to Design File - phylo.diversity - adds sampledepth parameter. - http://www.mothur.org/forum/viewtopic.php?f=3&t=3320 - set.dir - Sets tempdefault location to mothur's executable location to help reduce "unable to find file" errors. - make.contigs - allow for gzipped version for fastq files as inputs. - Added file parameter to saved files by mothur. file=current can now be used.

Bug fixes - metastats - infinite loop with certain datasets - http://www.mothur.org/forum/viewtopic.php?f=3&t=3701 - cluster.split - did not allow you to use the classic option with the file option. - make.biom - repeat labels when combining mothur OTU labels with non mothur OTU labels, this can results in a duplicate "simple" label. This causes an incorrect taxonomy to be assigned to the OTU. - remove.groups - not creating a list file for each label. - make.biom - remove paths from filenames to make compliant with qiime parser. - http://www.mothur.org/forum/viewtopic.php?f=3&t=3781&p=11241#p11241 - sffinfo - off by one in right side trimming. http://www.mothur.org/forum/viewtopic.php?f=4&t=3764 - make.contigs - Bug Fix - when using index files in version 1.35 quality data was over trimmed by the length of the barcode.

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Published by mothur-westcott almost 11 years ago

mothur - Version 1.35.1

Fixes mismatch name issue with make.contigs in v1.35.0

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Published by mothur-westcott over 11 years ago

mothur - Version 1.35.0

http://www.mothur.org/wiki/Mothur_v.1.35.0

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Published by mothur-westcott over 11 years ago