# Latest **URL:** https://forum.mothur.org/latest.md?page=3 [Latest](https://forum.mothur.org/latest.md) · [Categories](https://forum.mothur.org/categories.md) **Page:** 4 --- ## [Producing correlation matrix in mothur](https://forum.mothur.org/t/producing-correlation-matrix-in-mothur/22251)
**Author:** [@ritikadev](https://forum.mothur.org/u/ritikadev)\ **Replies:** 1\ **Last updated:** [November 22, 2024, 1:28pm UTC](https://forum.mothur.org/t/producing-correlation-matrix-in-mothur/22251 "2024-11-22T13:28:56Z")
Hi, I am working with a large dataset in Mothur (around 350 samples, each with approximately 10,000 reads), and I need to generate a correlation matrix for the OTUs. I attempted to use the SparCC command in Mothur to ca… --- ## [Error in biom convert with mothur generated biom files](https://forum.mothur.org/t/error-in-biom-convert-with-mothur-generated-biom-files/2426)
**Author:** [@Andre](https://forum.mothur.org/u/Andre)\ **Replies:** 1\ **Last updated:** [June 30, 2015, 1:39pm UTC](https://forum.mothur.org/t/error-in-biom-convert-with-mothur-generated-biom-files/2426 "2015-06-30T13:39:56Z")
Hello, I have generated some biom files with make.biom and have problems to convert these files with the biom convert command. My biom files looks like this: { “id”:“C:\\Users\\afrontzek\\Documents\\Mothur\_Daten\\RV\_Metabi… --- ## [Mothur classify error](https://forum.mothur.org/t/mothur-classify-error/22249)
**Author:** [@Adyasha](https://forum.mothur.org/u/Adyasha)\ **Replies:** 5\ **Last updated:** [November 19, 2024, 4:13pm UTC](https://forum.mothur.org/t/mothur-classify-error/22249 "2024-11-19T16:13:51Z")
Hello , I am getting this error while running classify command mothur \> classify.seqs(fasta=unique\_ASVs.fasta, reference=/home/adyasha/18S/data/silva.seed\_v138\_2.align, taxonomy=/home/adyasha/18S/data/silva.seed\_v138\_2… --- ## [Error with classify.seqs(), " \*\*\*\* Exceeded maximum allowed command errors, quitting \*\*\*\* "](https://forum.mothur.org/t/error-with-classify-seqs-exceeded-maximum-allowed-command-errors-quitting/22235)
**Author:** [@elundin](https://forum.mothur.org/u/elundin)\ **Replies:** 2\ **Last updated:** [November 7, 2024, 9:33pm UTC](https://forum.mothur.org/t/error-with-classify-seqs-exceeded-maximum-allowed-command-errors-quitting/22235 "2024-11-07T21:33:49Z")
Hello, Should probably start off by saying I’m new to this, and I’m trying to follow the MiSeq protocol to completion before diving into details. Running into an error using classify.seqs() command. I’m unsure exactly … --- ## [Strange Mothur in Ubuntu](https://forum.mothur.org/t/strange-mothur-in-ubuntu/22247)
**Author:** [@Alexandre\_Thibodeau](https://forum.mothur.org/u/Alexandre_Thibodeau)\ **Replies:** 1\ **Last updated:** [November 7, 2024, 4:53pm UTC](https://forum.mothur.org/t/strange-mothur-in-ubuntu/22247 "2024-11-07T16:53:51Z")
Hello! I downloaded the latest Ubuntu version. My Ubunu is at the latest version. First step I am doing: unique.seqs(fasta=barcode35chop.fasta) and all is going well. Then I try the following and look at the strange r… --- ## [One of the commands, regarding the "phylotype" is not running](https://forum.mothur.org/t/one-of-the-commands-regarding-the-phylotype-is-not-running/22240)
**Author:** [@1234](https://forum.mothur.org/u/1234)\ **Replies:** 7\ **Last updated:** [November 7, 2024, 9:38am UTC](https://forum.mothur.org/t/one-of-the-commands-regarding-the-phylotype-is-not-running/22240 "2024-11-07T09:38:49Z")
Hi, I’ve just started using Mothur for genomic analysis. Every command ran smoothly until the OTUs analysis. When I give the command: make.shared(list=final.tx.list, count=final.count\_table, label=1), it gives an error … --- ## [Issues running dist.shared with CLR-transformed data](https://forum.mothur.org/t/issues-running-dist-shared-with-clr-transformed-data/22238)
**Author:** [@docp1980](https://forum.mothur.org/u/docp1980)\ **Replies:** 5\ **Last updated:** [November 6, 2024, 2:49pm UTC](https://forum.mothur.org/t/issues-running-dist-shared-with-clr-transformed-data/22238 "2024-11-06T14:49:17Z")
Hi, I am interested in generating a distance matrix file using CLR-transformed data so that it better satisfies the linearity assumptions for plotting the data using PCoA. I can generate the file without issue using mak… --- ## [Issue with Group Files and Count.seqs Command in Mothur](https://forum.mothur.org/t/issue-with-group-files-and-count-seqs-command-in-mothur/22230)
**Author:** [@JJOJ](https://forum.mothur.org/u/JJOJ)\ **Replies:** 2\ **Last updated:** [October 29, 2024, 8:20pm UTC](https://forum.mothur.org/t/issue-with-group-files-and-count-seqs-command-in-mothur/22230 "2024-10-29T20:20:37Z")
I hope you’re doing well. I’m reaching out for assistance regarding persistent errors I’ve encountered when using Mothur for a metabarcoding analysis. I’ve been working through the pipeline in Aylagas et al. (2016) and e… --- ## [Illumina binned Q scores](https://forum.mothur.org/t/illumina-binned-q-scores/22228)
**Author:** [@leocadio](https://forum.mothur.org/u/leocadio)\ **Replies:** 1\ **Last updated:** [October 16, 2024, 8:58pm UTC](https://forum.mothur.org/t/illumina-binned-q-scores/22228 "2024-10-16T20:58:26Z")
A general question; Illumina has launched the new platforms and they are providing binned q scores (every five bases) instead of the base by base. I was wondering if there is a planned update to be able to run those samp… --- ## [Classify.seqs is not running with Silva 138.2](https://forum.mothur.org/t/classify-seqs-is-not-running-with-silva-138-2/22220)
**Author:** [@mshaheen](https://forum.mothur.org/u/mshaheen)\ **Replies:** 1\ **Last updated:** [October 16, 2024, 8:57pm UTC](https://forum.mothur.org/t/classify-seqs-is-not-running-with-silva-138-2/22220 "2024-10-16T20:57:02Z")
Hi, I tried to do classify.seqs with Silva 138.2 but the command did not generate the taxonomy file. I used reference=silva.nr\_v138\_2.align taxonomy=silva.nr\_v138\_2.tax and received many of the following lines: AB515… --- ## [Make.shared error when used after phylotype](https://forum.mothur.org/t/make-shared-error-when-used-after-phylotype/22219)
**Author:** [@nohayoussef](https://forum.mothur.org/u/nohayoussef)\ **Replies:** 1\ **Last updated:** [October 16, 2024, 8:56pm UTC](https://forum.mothur.org/t/make-shared-error-when-used-after-phylotype/22219 "2024-10-16T20:56:06Z")
Hi all, I am working with LSU fungal sequences. I use Blast against an in-house database to classify the sequences and then create a .taxonomy file from the Blast output (long story but classify.seqs against my database… --- ## [Chimera.vsearch not removing chimeras - screen.seqs to blame?](https://forum.mothur.org/t/chimera-vsearch-not-removing-chimeras-screen-seqs-to-blame/22214)
**Author:** [@James146](https://forum.mothur.org/u/James146)\ **Replies:** 7\ **Last updated:** [October 2, 2024, 3:37pm UTC](https://forum.mothur.org/t/chimera-vsearch-not-removing-chimeras-screen-seqs-to-blame/22214 "2024-10-02T15:37:21Z")
Dear Mothur team In the early workflow, the Mothur SOP has users perform make.contigs followed by summary.seqs. The next instruction is then to filter the sequences based on specified criteria (max length, and so on) us… --- ## [Clearcut Syntax Error: Distance Matrix Issue in](https://forum.mothur.org/t/clearcut-syntax-error-distance-matrix-issue-in/22204)
**Author:** [@Jayalal](https://forum.mothur.org/u/Jayalal)\ **Replies:** 8\ **Last updated:** [October 1, 2024, 5:57pm UTC](https://forum.mothur.org/t/clearcut-syntax-error-distance-matrix-issue-in/22204 "2024-10-01T17:57:15Z")
Hi, How can I fix this? Command runs in cluster computer with 400 GB RAM mothur 1.48.0 mothur \> clearcut(phylip=current) Using stability.trim.contigs.good.unique.good.filter.unique.precluster.denovo.vsearch.pick.phyl… --- ## [Removing vs. labelling contaminants](https://forum.mothur.org/t/removing-vs-labelling-contaminants/22215)
**Author:** [@ericalg](https://forum.mothur.org/u/ericalg)\ **Replies:** 1\ **Last updated:** [September 26, 2024, 1:20pm UTC](https://forum.mothur.org/t/removing-vs-labelling-contaminants/22215 "2024-09-26T13:20:43Z")
Hi! Prior to subsampling/rarefaction, I compared my data to my negative controls and realized there were some ASVs in my data that are probably contaminants. I was wondering if I should remove these ASVs from all of my s… --- ## [Code to Remove Unwanted OTUs with decontam (Mothur 1.48.0) or alternative method for remove specific OTU](https://forum.mothur.org/t/code-to-remove-unwanted-otus-with-decontam-mothur-1-48-0-or-alternative-method-for-remove-specific-otu/22212)
**Author:** [@Jayalal](https://forum.mothur.org/u/Jayalal)\ **Replies:** 1\ **Last updated:** [September 24, 2024, 12:58pm UTC](https://forum.mothur.org/t/code-to-remove-unwanted-otus-with-decontam-mothur-1-48-0-or-alternative-method-for-remove-specific-otu/22212 "2024-09-24T12:58:50Z")
Hello, I’m currently using Mothur 1.48.0 for my 16S rRNA analysis, and I have identified some unwanted OTUs, specifically cutibacterium\_otu00011. I would like to remove these OTUs using R with the decontam package. Coul… --- ## [Customizing reference alignment for the V3-V4 region](https://forum.mothur.org/t/customizing-reference-alignment-for-the-v3-v4-region/22211)
**Author:** [@venki09](https://forum.mothur.org/u/venki09)\ **Replies:** 1\ **Last updated:** [September 24, 2024, 12:58pm UTC](https://forum.mothur.org/t/customizing-reference-alignment-for-the-v3-v4-region/22211 "2024-09-24T12:58:26Z")
Hi! I am very new Mothur and want to customize my reference alignment to V3-V4 region. I read the blog post and I don’t know how to trim E.coli 16S rRNA gene sequence in the blog post to start and end with my primers. M… --- ## [Pcr.seqs error. Segmentation fault (core dumped)](https://forum.mothur.org/t/pcr-seqs-error-segmentation-fault-core-dumped/22209)
**Author:** [@venki09](https://forum.mothur.org/u/venki09)\ **Replies:** 1\ **Last updated:** [September 24, 2024, 12:55pm UTC](https://forum.mothur.org/t/pcr-seqs-error-segmentation-fault-core-dumped/22209 "2024-09-24T12:55:45Z")
Hi! I am running the 16S workflow and while running the pcr.seqs command I am getting segmentation fault (core dumped) error. I tried running it on just one processor, 8 processors and all processors but getting the sam… --- ## [Greengenes2 alignment and analysis](https://forum.mothur.org/t/greengenes2-alignment-and-analysis/22207)
**Author:** [@MotherUser](https://forum.mothur.org/u/MotherUser)\ **Replies:** 1\ **Last updated:** [September 19, 2024, 2:19am UTC](https://forum.mothur.org/t/greengenes2-alignment-and-analysis/22207 "2024-09-19T02:19:42Z")
Hi! I am trying to use green genes 2 as my database for assigning 16s sequences. I saw that there is a greengenes reference alignment available in the SOP. Would this reference be sufficient for alignment and then I can… --- ## [Remove.groups - number of sequences removed from fasta table and count has difference of one sequence](https://forum.mothur.org/t/remove-groups-number-of-sequences-removed-from-fasta-table-and-count-has-difference-of-one-sequence/22202)
**Author:** [@DeboraRSilva](https://forum.mothur.org/u/DeboraRSilva)\ **Replies:** 2\ **Last updated:** [September 11, 2024, 4:15pm UTC](https://forum.mothur.org/t/remove-groups-number-of-sequences-removed-from-fasta-table-and-count-has-difference-of-one-sequence/22202 "2024-09-11T16:15:02Z")
Hi, The remove.groups command removes different number of sequences from the fasta file and count table file This is an example: mothur \> remove.groups(count=exp44\_65samples.trim.contigs.subsample.unique.good.filter.u… --- ## [PacBio SOP tutorial](https://forum.mothur.org/t/pacbio-sop-tutorial/22141)
**Author:** [@Emankhalaf](https://forum.mothur.org/u/Emankhalaf)\ **Replies:** 1\ **Last updated:** [September 5, 2024, 6:59am UTC](https://forum.mothur.org/t/pacbio-sop-tutorial/22141 "2024-09-05T06:59:36Z")
Hi, I’m new to the mothur pipeline, having previously relied on other pipelines for microbiome data analysis from both MiSeq and PacBio. Currently, I’m working on a project involving over 1000 16S PacBio sequence sample… --- ## [Screen.seq fail](https://forum.mothur.org/t/screen-seq-fail/22199)
**Author:** [@JuanFrene](https://forum.mothur.org/u/JuanFrene)\ **Replies:** 1\ **Last updated:** [September 3, 2024, 1:58pm UTC](https://forum.mothur.org/t/screen-seq-fail/22199 "2024-09-03T13:58:40Z")
I am having difficulties figuring out why screen.seqs is completely removing \>99% of my reads. As per the SOP, you run screen.seqs to get sequences that start at or before/after the start/end positions. However, instead … --- ## [AVITI vs. MiSeq](https://forum.mothur.org/t/aviti-vs-miseq/22197)
**Author:** [@maivubeauclaire](https://forum.mothur.org/u/maivubeauclaire)\ **Replies:** 1\ **Last updated:** [August 13, 2024, 12:45pm UTC](https://forum.mothur.org/t/aviti-vs-miseq/22197 "2024-08-13T12:45:41Z")
Hi everyone, Our Genomics Center has been advertising using Element Biosciences AVITI system for 16S sequencing. Apparently, it’s cheaper and produce higher quality reads. I’m just checking to see if anyone has analyzin… --- ## [Running mothur as batch job in conda environment](https://forum.mothur.org/t/running-mothur-as-batch-job-in-conda-environment/22194)
**Author:** [@ritikadev](https://forum.mothur.org/u/ritikadev)\ **Replies:** 1\ **Last updated:** [August 9, 2024, 9:26pm UTC](https://forum.mothur.org/t/running-mothur-as-batch-job-in-conda-environment/22194 "2024-08-09T21:26:50Z")
Hello! I have a pretty massive dataset that I am working with, and I suspect that the dist.seqs step will take many hours to run. I want to run this step as a batch job, however, I have mothur installed in a conda enviro… --- ## [Running mothur in R Studio!](https://forum.mothur.org/t/running-mothur-in-r-studio/22193)
**Author:** [@ericalg](https://forum.mothur.org/u/ericalg)\ **Replies:** 1\ **Last updated:** [August 9, 2024, 9:24pm UTC](https://forum.mothur.org/t/running-mothur-in-r-studio/22193 "2024-08-09T21:24:18Z")
I don’t have a question! I’m just super excited because I just realized I could run mothur in Rstudio. So I set up a markdown file where I can alternate between mothur and R and have my whole thought process and coding p… --- ## [When to combine data from two batches?](https://forum.mothur.org/t/when-to-combine-data-from-two-batches/22191)
**Author:** [@ericalg](https://forum.mothur.org/u/ericalg)\ **Replies:** 5\ **Last updated:** [August 1, 2024, 3:15pm UTC](https://forum.mothur.org/t/when-to-combine-data-from-two-batches/22191 "2024-08-01T15:15:29Z")
Hello! I’m sorry if this has been answered, I looked across the forum first and couldn’t find something quite the same. I submitted 2 plates for 6S V4 community profiling at the UMich microbiome core a few months apart. … --- ## [Mothur run aborted](https://forum.mothur.org/t/mothur-run-aborted/22190)
**Author:** [@jrthelusmond](https://forum.mothur.org/u/jrthelusmond)\ **Replies:** 1\ **Last updated:** [July 30, 2024, 1:02pm UTC](https://forum.mothur.org/t/mothur-run-aborted/22190 "2024-07-30T13:02:18Z")
Hello everyone, I have been trying to use Mothur to process 16S rRNA sequence data. Whenever I got to the line of codes below, the run is aborted. Have you encountered this before? Your assistance is highly appreciated. … --- ## [HOMOVA vs AMOVA](https://forum.mothur.org/t/homova-vs-amova/2375)
**Author:** [@Somebodyatthedoor](https://forum.mothur.org/u/Somebodyatthedoor)\ **Replies:** 3\ **Last updated:** [July 30, 2024, 1:01pm UTC](https://forum.mothur.org/t/homova-vs-amova/2375 "2024-07-30T13:01:25Z")
Hi, I am a little bit confused about how AMOVA and HOMOVA differ. I understand that AMOVA tells you whether there is a significant difference between the centroids of groups but I’m struggling to understand what HOMOVA … --- ## [Mothur logfiles not found](https://forum.mothur.org/t/mothur-logfiles-not-found/22188)
**Author:** [@ritikadev](https://forum.mothur.org/u/ritikadev)\ **Replies:** 1\ **Last updated:** [July 24, 2024, 1:22pm UTC](https://forum.mothur.org/t/mothur-logfiles-not-found/22188 "2024-07-24T13:22:03Z")
Hello! I am following the mothur miseq SOP in order to analyze the v3-v4 region of my samples. I am currently using mothur version 1.48.0, and I keep running into the following error every time I run a command: \[ERROR\]:… --- ## [Order lost after degap.seqs and classify.seqs](https://forum.mothur.org/t/order-lost-after-degap-seqs-and-classify-seqs/22185)
**Author:** [@Anouschka](https://forum.mothur.org/u/Anouschka)\ **Replies:** 2\ **Last updated:** [July 22, 2024, 4:24pm UTC](https://forum.mothur.org/t/order-lost-after-degap-seqs-and-classify-seqs/22185 "2024-07-22T16:24:02Z")
Hi! I was hoping to get some help with the issue below. We use the following commands in order to obtain the representative sequences (without gaps) for each OTU, and their taxonomy. get.oturep → degap.seqs → classif… --- ## [Summary.tax and relative abundance per sample](https://forum.mothur.org/t/summary-tax-and-relative-abundance-per-sample/22187)
**Author:** [@jmacnico](https://forum.mothur.org/u/jmacnico)\ **Replies:** 1\ **Last updated:** [July 18, 2024, 6:20pm UTC](https://forum.mothur.org/t/summary-tax-and-relative-abundance-per-sample/22187 "2024-07-18T18:20:53Z")
Hello, I’m wanting to get the relative abundances in each sample for my ASV analysis. I ran the classify.otu and got the counts and am wondering if I can use the summary.tax with the relabund=T to change this into relat… [Previous page](https://forum.mothur.org/latest.md?page=2) [Next page](https://forum.mothur.org/latest.md?page=4)