# Infrastructure and utilities **URL:** https://forum.biobakery.org/c/infrastructure-and-utilities/22.md?page=2 [Latest](https://forum.biobakery.org/latest.md) · [Categories](https://forum.biobakery.org/categories.md) **Page:** 3 --- ## [Biobakery\_workflows using SGE hangs after kneaddata completes, gives error for each task](https://forum.biobakery.org/t/biobakery-workflows-using-sge-hangs-after-kneaddata-completes-gives-error-for-each-task/5073)
**Author:** [@Keaton\_Stagaman](https://forum.biobakery.org/u/Keaton_Stagaman)\ **Replies:** 1\ **Last updated:** [August 30, 2024, 5:53pm UTC](https://forum.biobakery.org/t/biobakery-workflows-using-sge-hangs-after-kneaddata-completes-gives-error-for-each-task/5073 "2024-08-30T17:53:24Z")
Hello, I’m trying to set up biobakery\_workflows on a centos 7 cluster. I’m running the following command: biobakery\_workflows wmgx \\ --input $INPUT \\ --output $OUTPUT \\ --threads 20 \\ --taxonomic-profil… --- ## [Kneaddata tossing roughly half of the reads at the trimmomatic step](https://forum.biobakery.org/t/kneaddata-tossing-roughly-half-of-the-reads-at-the-trimmomatic-step/7415)
**Author:** [@gmark](https://forum.biobakery.org/u/gmark)\ **Replies:** 0\ **Last updated:** [August 29, 2024, 4:11pm UTC](https://forum.biobakery.org/t/kneaddata-tossing-roughly-half-of-the-reads-at-the-trimmomatic-step/7415 "2024-08-29T16:11:48Z")
Hi All, I’m running kneaddata v0.12.0 on some libraries generated with truseq barcodes. At the trimmomatic step kneaddata tosses out roughly half of the reads of every sample. However, when I run trimmomatic independent… --- ## [Kneaddata unable to interpret sequencing header format](https://forum.biobakery.org/t/kneaddata-unable-to-interpret-sequencing-header-format/7347)
**Author:** [@brett-vantassel](https://forum.biobakery.org/u/brett-vantassel)\ **Replies:** 4\ **Last updated:** [August 23, 2024, 8:19pm UTC](https://forum.biobakery.org/t/kneaddata-unable-to-interpret-sequencing-header-format/7347 "2024-08-23T20:19:47Z")
kneaddata v0.12.0 After trimming reads, no paired end reads are found. A potential solution exists in a github pull request. I believe there were some issues with the commit, I’m unsure of the best course of action to c… --- ## [Paired End Run output explanation](https://forum.biobakery.org/t/paired-end-run-output-explanation/7335)
**Author:** [@annie](https://forum.biobakery.org/u/annie)\ **Replies:** 1\ **Last updated:** [August 22, 2024, 2:50pm UTC](https://forum.biobakery.org/t/paired-end-run-output-explanation/7335 "2024-08-22T14:50:30Z")
Hi everyone, I get some output files after running Kneaddata, including kneaddata\_paired\_1.fastq and kneaddata\_paired\_2.fastq. I thought these two output files are aligned to the reference database I chose. But in the … --- ## [Installation graphlan](https://forum.biobakery.org/t/installation-graphlan/7236)
**Author:** [@Shwetha\_Kumar](https://forum.biobakery.org/u/Shwetha_Kumar)\ **Replies:** 4\ **Last updated:** [August 17, 2024, 4:42pm UTC](https://forum.biobakery.org/t/installation-graphlan/7236 "2024-08-17T16:42:07Z")
I am not sure this has been quite answered in the previous posts as well. I have this issue with installing graphaln. I get this error. include/python3.12 -c Bio/triemodule.c -o build/temp.macosx-10.9-x86\_64-cpython-312… --- ## [Metaphlan sequence identification](https://forum.biobakery.org/t/metaphlan-sequence-identification/7364)
**Author:** [@Laura\_Brenner](https://forum.biobakery.org/u/Laura_Brenner)\ **Replies:** 0\ **Last updated:** [August 13, 2024, 8:51pm UTC](https://forum.biobakery.org/t/metaphlan-sequence-identification/7364 "2024-08-13T20:51:17Z")
I have completed an analysis on human respiratory samples using metaphlan3 and had a few organisms returned that were halophiles that were both high in prevalence and abundance. I am curious if there is a way to pull ou… --- ## [Bowtie2 removed the entire reads from my fecal metagenomic data](https://forum.biobakery.org/t/bowtie2-removed-the-entire-reads-from-my-fecal-metagenomic-data/7345)
**Author:** [@marvin](https://forum.biobakery.org/u/marvin)\ **Replies:** 2\ **Last updated:** [August 10, 2024, 3:31am UTC](https://forum.biobakery.org/t/bowtie2-removed-the-entire-reads-from-my-fecal-metagenomic-data/7345 "2024-08-10T03:31:26Z")
Hello everyone, I met a very serious problem about the contaminated reads removing using bowtie2 in the kneaddata pipeline (v0.12.0). I want to perform quality control on my giant panda (Ailuropoda\_melanoleuca) fecal m… --- ## [Biobakery\_workflows wmgx ValueError: could not convert string to float: '8.355B'](https://forum.biobakery.org/t/biobakery-workflows-wmgx-valueerror-could-not-convert-string-to-float-8-355b/7079)
**Author:** [@jamoltzau](https://forum.biobakery.org/u/jamoltzau)\ **Replies:** 0\ **Last updated:** [May 22, 2024, 8:41pm UTC](https://forum.biobakery.org/t/biobakery-workflows-wmgx-valueerror-could-not-convert-string-to-float-8-355b/7079 "2024-05-22T20:41:48Z")
Hi, I’m trying to run the wmgx workflow using the following command: biobakery\_workflows wmgx --input $INPUT --output $OUTPUT --grid-jobs 20 --grid sge --threads 20 --grid-partition long.q\` While it will submit a grid … --- ## [Trimmomatic errors](https://forum.biobakery.org/t/trimmomatic-errors/7322)
**Author:** [@kogkog](https://forum.biobakery.org/u/kogkog)\ **Replies:** 2\ **Last updated:** [August 2, 2024, 6:25pm UTC](https://forum.biobakery.org/t/trimmomatic-errors/7322 "2024-08-02T18:25:15Z")
Hi. I am getting an error message during the tutorial when I enter “kneaddata --unpaired input/singleEnd.fastq --reference-db input/demo\_db --output kneaddataOutputSingleEnd” I used the same command lines as the tutor… --- ## [MTX Model IBD Data Processing Pipeline](https://forum.biobakery.org/t/mtx-model-ibd-data-processing-pipeline/7311)
**Author:** [@RodRoss\_TV](https://forum.biobakery.org/u/RodRoss_TV)\ **Replies:** 1\ **Last updated:** [July 26, 2024, 4:10pm UTC](https://forum.biobakery.org/t/mtx-model-ibd-data-processing-pipeline/7311 "2024-07-26T16:10:13Z")
Hey folks, I am currently employing the MTX Model to identify upregulated and downregulated genes within IBD metatranscriptomic data, sourced from the Inflammatory Bowel Disease Multiomics Database. As I am relatively ne… --- ## [Failed building wheel for biopython](https://forum.biobakery.org/t/failed-building-wheel-for-biopython/6149)
**Author:** [@cchin](https://forum.biobakery.org/u/cchin)\ **Replies:** 2\ **Last updated:** [July 5, 2024, 6:42pm UTC](https://forum.biobakery.org/t/failed-building-wheel-for-biopython/6149 "2024-07-05T18:42:57Z")
Hi I am trying to install Graphlan on a Mac. I have chance the shell to Bash, running on M2, Sonoma 14.0, and python 3. However I am getting the following error and hoping someone can help me. Seems to be a problem wit… --- ## [Processes and threads command difference in Kneaddata](https://forum.biobakery.org/t/processes-and-threads-command-difference-in-kneaddata/7215)
**Author:** [@Shuyuan\_Zhang](https://forum.biobakery.org/u/Shuyuan_Zhang)\ **Replies:** 0\ **Last updated:** [July 1, 2024, 1:45pm UTC](https://forum.biobakery.org/t/processes-and-threads-command-difference-in-kneaddata/7215 "2024-07-01T13:45:03Z")
$ Kneaddata Version 0.12.0 --help Dear officer, I have recently started using Kneaddata to quality control my sequencing data. However, I have a question regarding the distinction between the terms “processes” and “thr… --- ## [Paired input to kneaddata resulting in unpaired files](https://forum.biobakery.org/t/paired-input-to-kneaddata-resulting-in-unpaired-files/6281)
**Author:** [@kreigema](https://forum.biobakery.org/u/kreigema)\ **Replies:** 1\ **Last updated:** [June 29, 2024, 3:20am UTC](https://forum.biobakery.org/t/paired-input-to-kneaddata-resulting-in-unpaired-files/6281 "2024-06-29T03:20:39Z")
When running kneaddata, my paired input is ending up as entirely unpaired. I have tried adding “/1” and “/2” as a suffix to the read headers, but the kneaddata\_paired.fastq output files are blank while kneaddata\_unpaired… --- ## [Taxonomic-profiling-options with more than one option](https://forum.biobakery.org/t/taxonomic-profiling-options-with-more-than-one-option/7197)
**Author:** [@imontero](https://forum.biobakery.org/u/imontero)\ **Replies:** 0\ **Last updated:** [June 27, 2024, 8:08am UTC](https://forum.biobakery.org/t/taxonomic-profiling-options-with-more-than-one-option/7197 "2024-06-27T08:08:24Z")
Hi: I woul like to know the way to add more than one metaphlan option to biobakery workflows using the argument “–taxonomic-profiling-options” My default use is --taxonomic-profiling-options=“–add\_viruses”, but I woul… --- ## [Can't change annotation colors on graphlan cladogram](https://forum.biobakery.org/t/cant-change-annotation-colors-on-graphlan-cladogram/7185)
**Author:** [@rachel](https://forum.biobakery.org/u/rachel)\ **Replies:** 0\ **Last updated:** [June 21, 2024, 10:09pm UTC](https://forum.biobakery.org/t/cant-change-annotation-colors-on-graphlan-cladogram/7185 "2024-06-21T22:09:59Z")
Hi, I’m very new to using graphlan. I have a cladogram that was generated with lefse using the Galaxy website. I’ve been asked to format this cladogram a bit differently using graphlan. I’ve installed both export2graphla… --- ## [Paired-end data results in unpaired output](https://forum.biobakery.org/t/paired-end-data-results-in-unpaired-output/928)
**Author:** [@kbobowik](https://forum.biobakery.org/u/kbobowik)\ **Replies:** 27\ **Last updated:** [June 20, 2024, 2:49pm UTC](https://forum.biobakery.org/t/paired-end-data-results-in-unpaired-output/928 "2024-06-20T14:49:44Z")
Hi, After running Kneaddata with Bowtie2 on paired-end data, the output I’m getting from the final output seems to be unpaired (the first read has over 9x the amount of reads as the second). I’m curious to know if there… --- ## [MTX Model Coefficient to Log Fold Change](https://forum.biobakery.org/t/mtx-model-coefficient-to-log-fold-change/7144)
**Author:** [@RodRoss\_TV](https://forum.biobakery.org/u/RodRoss_TV)\ **Replies:** 0\ **Last updated:** [June 10, 2024, 3:12pm UTC](https://forum.biobakery.org/t/mtx-model-coefficient-to-log-fold-change/7144 "2024-06-10T15:12:29Z")
Hi everybody! I’m sorry if this sounds like a silly question but I’m currently trying to do differential expression analysis (using both MTX and MGX data) of a microbial community using MTXmodel v1.2.4. While I understa… --- ## [Metatranscriptomic pre-processing](https://forum.biobakery.org/t/metatranscriptomic-pre-processing/5608)
**Author:** [@garfield](https://forum.biobakery.org/u/garfield)\ **Replies:** 3\ **Last updated:** [June 13, 2024, 6:05pm UTC](https://forum.biobakery.org/t/metatranscriptomic-pre-processing/5608 "2024-06-13T18:05:30Z")
Hi, can I use “wmgx” workflow (change --contaminate-databases) to analyze metatranscriptomic data? I already got the taxonomic and functional profiling from metagenomes and would like to skip this process in " wmgx\_wmtx"… --- ## [Biobakery workflows computational speed](https://forum.biobakery.org/t/biobakery-workflows-computational-speed/3040)
**Author:** [@imontero](https://forum.biobakery.org/u/imontero)\ **Replies:** 8\ **Last updated:** [June 12, 2024, 3:21pm UTC](https://forum.biobakery.org/t/biobakery-workflows-computational-speed/3040 "2024-06-12T15:21:56Z")
Hi I have just installed and tested biobakery workflows with tutorial files and it works for me. It was a bi difficult to install so I created a conda environment file to save my configuration. Now I am trying to us bi… --- ## [Combined MTX/MGX analysis, contamination removal](https://forum.biobakery.org/t/combined-mtx-mgx-analysis-contamination-removal/7099)
**Author:** [@rackajuh](https://forum.biobakery.org/u/rackajuh)\ **Replies:** 0\ **Last updated:** [May 28, 2024, 2:38pm UTC](https://forum.biobakery.org/t/combined-mtx-mgx-analysis-contamination-removal/7099 "2024-05-28T14:38:26Z")
Hello, I am trying to perform combined MTX/MGX analysis. When running the pipeline (Kneaddata/Humann), would it be more reasonable in case of the metatranscriptome to align it to the human genome or the human transcript… --- ## [Limit input file size when running kneaddata](https://forum.biobakery.org/t/limit-input-file-size-when-running-kneaddata/7073)
**Author:** [@Wan-YuLin](https://forum.biobakery.org/u/Wan-YuLin)\ **Replies:** 0\ **Last updated:** [May 20, 2024, 8:47am UTC](https://forum.biobakery.org/t/limit-input-file-size-when-running-kneaddata/7073 "2024-05-20T08:47:44Z")
Hello, I’m running shotgun samples through kneaddata v0.12.0. However, 4 of those samples failed running kneaddata. Their fastq files have a larger size (7-15GB) than the rest of the samples (~2GB) Wondering is there a… --- ## [Bug for TRF Download](https://forum.biobakery.org/t/bug-for-trf-download/7019)
**Author:** [@pkubruce](https://forum.biobakery.org/u/pkubruce)\ **Replies:** 1\ **Last updated:** [May 8, 2024, 3:30pm UTC](https://forum.biobakery.org/t/bug-for-trf-download/7019 "2024-05-08T15:30:11Z")
While following the installation instructions for KneadData from the BioBakery GitHub page (GitHub - biobakery/kneaddata: Quality control tool on metagenomic and metatranscriptomic sequencing data, especially data from m… --- ## [KneadData critical error in bowtie2\_discordant\_pairs](https://forum.biobakery.org/t/kneaddata-critical-error-in-bowtie2-discordant-pairs/2625)
**Author:** [@EmilyB](https://forum.biobakery.org/u/EmilyB)\ **Replies:** 12\ **Last updated:** [April 17, 2024, 3:51pm UTC](https://forum.biobakery.org/t/kneaddata-critical-error-in-bowtie2-discordant-pairs/2625 "2024-04-17T15:51:49Z")
I’m running KneadData on a HPC cluster and parallelizing with GNU Parallel. I’m getting an error at the discordant pairs step but the log does not contain any information about what’s causing this. I’ve already fixed the… --- ## [Kneaddata stringent bowtie2 filtering](https://forum.biobakery.org/t/kneaddata-stringent-bowtie2-filtering/6889)
**Author:** [@ym2877](https://forum.biobakery.org/u/ym2877)\ **Replies:** 0\ **Last updated:** [April 3, 2024, 4:35pm UTC](https://forum.biobakery.org/t/kneaddata-stringent-bowtie2-filtering/6889 "2024-04-03T16:35:28Z")
Hi all! I had a question about kneaddata filtering using the bowtie2 --un-conc option (which I noticed kneaddata uses when running on paired-end reads). From my understanding, this option writes out reads for which one … --- ## [Biobakery workflows absolute reads](https://forum.biobakery.org/t/biobakery-workflows-absolute-reads/6911)
**Author:** [@imontero](https://forum.biobakery.org/u/imontero)\ **Replies:** 0\ **Last updated:** [April 9, 2024, 7:45am UTC](https://forum.biobakery.org/t/biobakery-workflows-absolute-reads/6911 "2024-04-09T07:45:38Z")
Hello: I would like to know if there is any way to have Metaphlan4 absolute reads instead of normalized relative abundances. I tried --t rel\_ab\_w\_read\_stats option, but I can not run together with --add\_viruses. I need… --- ## [\`pip install kneaddata\` doesn't install dependencies](https://forum.biobakery.org/t/pip-install-kneaddata-doesnt-install-dependencies/2967)
**Author:** [@crusher083](https://forum.biobakery.org/u/crusher083)\ **Replies:** 2\ **Last updated:** [April 2, 2024, 8:14pm UTC](https://forum.biobakery.org/t/pip-install-kneaddata-doesnt-install-dependencies/2967 "2024-04-02T20:14:46Z")
When using pip dependencies such as trimmomatic or bowtie2 aren’t installed. The docker biobakery/Dockerfile at master · biobakery/biobakery · GitHub will not run kneaddata, as it fails to find trimmomatic and bowtie2 i… --- ## [Error with bowtie2: Saw ASCII character 10 but expected 33-based Phred qual](https://forum.biobakery.org/t/error-with-bowtie2-saw-ascii-character-10-but-expected-33-based-phred-qual/6867)
**Author:** [@mojiefei](https://forum.biobakery.org/u/mojiefei)\ **Replies:** 0\ **Last updated:** [March 29, 2024, 9:03am UTC](https://forum.biobakery.org/t/error-with-bowtie2-saw-ascii-character-10-but-expected-33-based-phred-qual/6867 "2024-03-29T09:03:36Z")
kneaddata v0.10.0 Issue 1: I installed kneaddata v0.10.0 through conda. When I used one database as an index for bowtie2, everything ran fine except deleting the intermediate files containing the index name. Following … --- ## [BIOBAKERY\_WORKFLOWS\_DATABASES: command not found](https://forum.biobakery.org/t/biobakery-workflows-databases-command-not-found/6787)
**Author:** [@Wan-YuLin](https://forum.biobakery.org/u/Wan-YuLin)\ **Replies:** 0\ **Last updated:** [March 12, 2024, 9:34am UTC](https://forum.biobakery.org/t/biobakery-workflows-databases-command-not-found/6787 "2024-03-12T09:34:24Z")
Hi all, I’ve installed biobakery3 today using following command: conda config --add channels biobakery mamba install -c biobakery biobakery\_workflows I think I have succesfully install biobakery3 cuz I can execute th… --- ## [Biobakey tools version for data reproducibility](https://forum.biobakery.org/t/biobakey-tools-version-for-data-reproducibility/6683)
**Author:** [@Adi](https://forum.biobakery.org/u/Adi)\ **Replies:** 0\ **Last updated:** [February 22, 2024, 9:55pm UTC](https://forum.biobakery.org/t/biobakey-tools-version-for-data-reproducibility/6683 "2024-02-22T21:55:13Z")
Hi I’ve used kneaddata version 0.12.0 (with the human genome hg37) for quality control on WGS data from a study, but noticed the authors originally used kneaddata version 0.7.2 with the same human genome. Should I redo … --- ## [Accessing the MGX-normalized MTX feature expression data in MTX\_model?](https://forum.biobakery.org/t/accessing-the-mgx-normalized-mtx-feature-expression-data-in-mtx-model/6560)
**Author:** [@j.ryou](https://forum.biobakery.org/u/j.ryou)\ **Replies:** 1\ **Last updated:** [March 5, 2024, 4:40pm UTC](https://forum.biobakery.org/t/accessing-the-mgx-normalized-mtx-feature-expression-data-in-mtx-model/6560 "2024-03-05T16:40:18Z")
Hi All, I am using MTX\_model to analyze microbiome metatranscriptomic (MTX) pathway expression data with paired metagenomic (MGX) pathway data as covariates. Is there a way to access the MGX-normalized MTX feature expre… [Previous page](https://forum.biobakery.org/c/infrastructure-and-utilities/22.md?page=1) [Next page](https://forum.biobakery.org/c/infrastructure-and-utilities/22.md?page=3)