Releases: mothur/mothur
Releases · mothur/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
Version 1.41.1
Bug Fix:
- Fixes file mismatch caused by pre.cluster command run with a count file. #556
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
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.linux_64.zip contains a dynamically linked copy of mothur. The Mothur.linux_64.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
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.linux_64.zip contains a dynamically linked copy of mothur. The Mothur.linux_64.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.
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.linux_64.zip contains a dynamically linked copy of mothur. The Mothur.linux_64.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.
Version 1.40.3
Version 1.40.2
Bug Fixes
- Fixes *contigs.report file append issue that resulted in reads missing from report.
Version 1.40.1
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.linux_64.zip contains a dynamically linked copy of mothur. The Mothur.linux_64.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