# Infrastructure and utilities **URL:** https://forum.biobakery.org/c/infrastructure-and-utilities/22.md?page=1 [Latest](https://forum.biobakery.org/latest.md) · [Categories](https://forum.biobakery.org/categories.md) **Page:** 2 --- ## [Kneaddata\_database --download human\_genome bowtie2](https://forum.biobakery.org/t/kneaddata-database-download-human-genome-bowtie2/8047)
**Author:** [@BlueK77](https://forum.biobakery.org/u/BlueK77)\ **Replies:** 1\ **Last updated:** [May 9, 2025, 3:35pm UTC](https://forum.biobakery.org/t/kneaddata-database-download-human-genome-bowtie2/8047 "2025-05-09T15:35:15Z")
Dear all, I was try to download human\_genome bowtie2 database and it replays with this: kneaddata\_database --download human\_genome bowtie2 ./ Download URL: https://huttenhower.sph.harvard.edu/kneadData\_databases/Homo\_s… --- ## [Conda for biobakery\_workflow for 4.0.0a1](https://forum.biobakery.org/t/conda-for-biobakery-workflow-for-4-0-0a1/8018)
**Author:** [@xie186](https://forum.biobakery.org/u/xie186)\ **Replies:** 1\ **Last updated:** [May 9, 2025, 3:23pm UTC](https://forum.biobakery.org/t/conda-for-biobakery-workflow-for-4-0-0a1/8018 "2025-05-09T15:23:56Z")
Hi I am trying to install the latest version for biobakery\_workflow (v4.0.0a1). But it seems that it is not available on anaconda.org/ Biobakery Workflows | Anaconda.org It’s not availble on biobakery-workflows · PyPI … --- ## [Annotation with phyla data](https://forum.biobakery.org/t/annotation-with-phyla-data/8046)
**Author:** [@apoosakkannu](https://forum.biobakery.org/u/apoosakkannu)\ **Replies:** 0\ **Last updated:** [May 8, 2025, 11:55am UTC](https://forum.biobakery.org/t/annotation-with-phyla-data/8046 "2025-05-08T11:55:37Z")
Hello, I have generated a tree of metagenome assembled genomes with latest Phylophlan software. I am interested in adding taxonomy data in the tree with different colours and also if possible some other details such as h… --- ## [Issue with humann\_regroup\_table in biobakery\_workflows wmgx](https://forum.biobakery.org/t/issue-with-humann-regroup-table-in-biobakery-workflows-wmgx/5047)
**Author:** [@Keaton\_Stagaman](https://forum.biobakery.org/u/Keaton_Stagaman)\ **Replies:** 4\ **Last updated:** [April 9, 2025, 9:15am UTC](https://forum.biobakery.org/t/issue-with-humann-regroup-table-in-biobakery-workflows-wmgx/5047 "2025-04-09T09:15:40Z")
Issue with biobakery\_workflows wmgx Task 23 failed Name: humann\_regroup\_UniRef2EC\_\_\_\_22002010590008.gz Original error: Error executing action 0. Original Exception: Traceback (most recent call last): File "/… --- ## [Unable to download and install Kneaddata database](https://forum.biobakery.org/t/unable-to-download-and-install-kneaddata-database/1358)
**Author:** [@DEEPCHANDA7](https://forum.biobakery.org/u/DEEPCHANDA7)\ **Replies:** 21\ **Last updated:** [March 19, 2025, 5:50pm UTC](https://forum.biobakery.org/t/unable-to-download-and-install-kneaddata-database/1358 "2025-03-19T17:50:43Z")
HI, I have insttalled kneaddata via pip install. Now, I am trying to download and install kneaddata database by the following command: kneaddata\_database --download human\_genome bowtie2 ~/Desktop/ But, it reverts follo… --- ## [Kneaddata - a non very explicit error message](https://forum.biobakery.org/t/kneaddata-a-non-very-explicit-error-message/3334)
**Author:** [@miguensblanco](https://forum.biobakery.org/u/miguensblanco)\ **Replies:** 4\ **Last updated:** [February 19, 2025, 10:02am UTC](https://forum.biobakery.org/t/kneaddata-a-non-very-explicit-error-message/3334 "2025-02-19T10:02:06Z")
Hi guys, I have been working in the past with kneaddata and I did not see this error before. I also checked in the forum before posting. Any tip is appreciated: I ran kneaddata in my server, as usual. The log file from… --- ## [bioBakery workflows (wmgx) failing tasks](https://forum.biobakery.org/t/biobakery-workflows-wmgx-failing-tasks/7811)
**Author:** [@Applebeb](https://forum.biobakery.org/u/Applebeb)\ **Replies:** 0\ **Last updated:** [February 10, 2025, 4:46am UTC](https://forum.biobakery.org/t/biobakery-workflows-wmgx-failing-tasks/7811 "2025-02-10T04:46:43Z")
Hi all, I am a beginner in using Biobakery Workflows. I encountered an issue where tasks fail while running the wmgx Biobakery Workflow with tutorial files in Docker. Command: biobakery\_workflows wmgx --input Tutorial… --- ## [groups: invalid choice: 'uniref90\_level4ec' (choose from 'uniref90\_rxn', 'uniref50\_rxn')\\n"\`](https://forum.biobakery.org/t/groups-invalid-choice-uniref90-level4ec-choose-from-uniref90-rxn-uniref50-rxn-n/2515)
**Author:** [@Mavlarn](https://forum.biobakery.org/u/Mavlarn)\ **Replies:** 7\ **Last updated:** [February 6, 2025, 2:13pm UTC](https://forum.biobakery.org/t/groups-invalid-choice-uniref90-level4ec-choose-from-uniref90-rxn-uniref50-rxn-n/2515 "2025-02-06T14:13:29Z")
There is an error to run “biobakery\_workflows wmgx xxx”. Error message is as below. It looks like humann3 should use “uniref90\_rxn” but in the shotgun.py code, it use uniref90\_level4ec. Task 29 failed Name: humann\_renor… --- ## [Wmgx\_wmgt ERROR: task 17](https://forum.biobakery.org/t/wmgx-wmgt-error-task-17/7792)
**Author:** [@Theda-sys](https://forum.biobakery.org/u/Theda-sys)\ **Replies:** 0\ **Last updated:** [February 6, 2025, 8:19am UTC](https://forum.biobakery.org/t/wmgx-wmgt-error-task-17/7792 "2025-02-06T08:19:28Z")
So i am trying to run the rna/dna biobackery workflow and run into the following issue - this seems to be commen - however i cannot figure out how to solve it. THANKS humann v3.9 MetaPhlAn version 4.1.1 (11 Mar 2024) h… --- ## [The output of KneadData differs when threads are used](https://forum.biobakery.org/t/the-output-of-kneaddata-differs-when-threads-are-used/7693)
**Author:** [@weichi](https://forum.biobakery.org/u/weichi)\ **Replies:** 3\ **Last updated:** [February 6, 2025, 7:11am UTC](https://forum.biobakery.org/t/the-output-of-kneaddata-differs-when-threads-are-used/7693 "2025-02-06T07:11:00Z")
KneadData Version: commit 90c05f3cd25a8c74a4d804f27dd0ce52718007d8 The size of the output FASTQ file is different when the -t argument is added. e.g. # t=8 -rw-r--r-- 1 root root 6126995024 Dec 24 06:13 sample1136\_t… --- ## [Biobakery\_workflows : Broken hand-off of handling fastq compression between Kneaddata and MetaPhlan](https://forum.biobakery.org/t/biobakery-workflows-broken-hand-off-of-handling-fastq-compression-between-kneaddata-and-metaphlan/7785)
**Author:** [@Kborg000](https://forum.biobakery.org/u/Kborg000)\ **Replies:** 1\ **Last updated:** [February 5, 2025, 3:39pm UTC](https://forum.biobakery.org/t/biobakery-workflows-broken-hand-off-of-handling-fastq-compression-between-kneaddata-and-metaphlan/7785 "2025-02-05T15:39:24Z")
Although the fastq.gz files are accepted by the biobakery\_workflows initially, there’s a breakdown in the handoff between Kneaddata and MetaPhlan that produces the error: Error, input data has to be in fastq or fasta f… --- ## [AttributeError: Can't pickle local object 'ArgumentParser.\_\_init\_\_.\.identity'](https://forum.biobakery.org/t/attributeerror-cant-pickle-local-object-argumentparser-init-locals-identity/7763)
**Author:** [@Kborg000](https://forum.biobakery.org/u/Kborg000)\ **Replies:** 1\ **Last updated:** [January 22, 2025, 5:08pm UTC](https://forum.biobakery.org/t/attributeerror-cant-pickle-local-object-argumentparser-init-locals-identity/7763 "2025-01-22T17:08:32Z")
Hello, I just tried to setup biobakery workflows yesterday for the first time, and when I attempt to run the command below (modified pathways for privacy), I get the error " AttributeError: Can’t pickle local object ‘Ar… --- ## [There are small unmatched reads in paired reads of kneaddata result](https://forum.biobakery.org/t/there-are-small-unmatched-reads-in-paired-reads-of-kneaddata-result/7731)
**Author:** [@Kirby](https://forum.biobakery.org/u/Kirby)\ **Replies:** 1\ **Last updated:** [January 14, 2025, 9:02am UTC](https://forum.biobakery.org/t/there-are-small-unmatched-reads-in-paired-reads-of-kneaddata-result/7731 "2025-01-14T09:02:03Z")
Dear bioBakery team, I am using the kneaddata-v0.12.0 from bioconda for QC of my metagenomic raw data. To date, kneaddata has worked perfectly for all my purposes. However, when I recently tried profiling my QCed data… --- ## [Running biobakery wmgx with custom databases](https://forum.biobakery.org/t/running-biobakery-wmgx-with-custom-databases/7720)
**Author:** [@Maddie\_Krieger](https://forum.biobakery.org/u/Maddie_Krieger)\ **Replies:** 0\ **Last updated:** [January 7, 2025, 1:32am UTC](https://forum.biobakery.org/t/running-biobakery-wmgx-with-custom-databases/7720 "2025-01-07T01:32:12Z")
I have installed the biobakery workflow and want to run the wmgx pipeline on some metagenomic samples. I have the standard chocophlan, uniref90 diamond and utility mapping DBs and can get everything to work just fine wit… --- ## [The output of KneadData differs when threads are used](https://forum.biobakery.org/t/the-output-of-kneaddata-differs-when-threads-are-used/7730)
**Author:** [@weichi](https://forum.biobakery.org/u/weichi)\ **Replies:** 0\ **Last updated:** [January 9, 2025, 3:55am UTC](https://forum.biobakery.org/t/the-output-of-kneaddata-differs-when-threads-are-used/7730 "2025-01-09T03:55:41Z")
The size of the output FASTQ file is different when the -t argument is greater then 1. I found that it might be caused by line 124 in kneaddata/trf\_parallel.py Since file\_handle\_write is always not None after the file … --- ## [Citation please](https://forum.biobakery.org/t/citation-please/7239)
**Author:** [@madlam-tech](https://forum.biobakery.org/u/madlam-tech)\ **Replies:** 2\ **Last updated:** [December 31, 2024, 9:59pm UTC](https://forum.biobakery.org/t/citation-please/7239 "2024-12-31T21:59:41Z")
Is there a citation for the Kneaddata pipeline please --- ## [Kneaddata final pair output is 0](https://forum.biobakery.org/t/kneaddata-final-pair-output-is-0/7548)
**Author:** [@nchari](https://forum.biobakery.org/u/nchari)\ **Replies:** 1\ **Last updated:** [December 25, 2024, 3:41am UTC](https://forum.biobakery.org/t/kneaddata-final-pair-output-is-0/7548 "2024-12-25T03:41:45Z")
When running biobakery workflows with paired end reads, my paired end reads are recognized by kneaddata, but the final pair values are 0 across the board, with all the reads showing up as orphan reads? Any info on why th… --- ## [All paired-end read unmatched](https://forum.biobakery.org/t/all-paired-end-read-unmatched/2895)
**Author:** [@wang](https://forum.biobakery.org/u/wang)\ **Replies:** 34\ **Last updated:** [December 25, 2024, 3:32am UTC](https://forum.biobakery.org/t/all-paired-end-read-unmatched/2895 "2024-12-25T03:32:42Z")
Kneaddata (v0.10.0) result I checked the log file, seemed as no error : 12/10/2021 04:46:24 PM - kneaddata.knead\_data - INFO: Running kneaddata v0.10.0 12/10/2021 04:46:24 PM - kneaddata.knead\_data - INFO: Output fi… --- ## [Biobakery\_workflow wmgx\_vis not generating several plot (using toyset)](https://forum.biobakery.org/t/biobakery-workflow-wmgx-vis-not-generating-several-plot-using-toyset/7560)
**Author:** [@JooyoungPark](https://forum.biobakery.org/u/JooyoungPark)\ **Replies:** 0\ **Last updated:** [November 7, 2024, 9:46pm UTC](https://forum.biobakery.org/t/biobakery-workflow-wmgx-vis-not-generating-several-plot-using-toyset/7560 "2024-11-07T21:46:46Z")
I am currently using an example data that is illustrated here: Installing the workflows with pip · biobakery/biobakery\_workflows Wiki · GitHub and run biobakery\_workflow wmgx\_vis. However, the result pdf file does not … --- ## [Java error after new install](https://forum.biobakery.org/t/java-error-after-new-install/6852)
**Author:** [@drelo](https://forum.biobakery.org/u/drelo)\ **Replies:** 1\ **Last updated:** [December 6, 2024, 6:56am UTC](https://forum.biobakery.org/t/java-error-after-new-install/6852 "2024-12-06T06:56:22Z")
Hi all, I am using kneaddata v0.12.0, I recently created a new environment and installed it via mamba/conda. I just downloaded the database and I get the same error either with the input.zip data or using the custom d… --- ## [Do I have to remove overlapping reads from paire\_end data before Metahplan?](https://forum.biobakery.org/t/do-i-have-to-remove-overlapping-reads-from-paire-end-data-before-metahplan/7615)
**Author:** [@Michela\_Francesconi](https://forum.biobakery.org/u/Michela_Francesconi)\ **Replies:** 0\ **Last updated:** [November 27, 2024, 3:55pm UTC](https://forum.biobakery.org/t/do-i-have-to-remove-overlapping-reads-from-paire-end-data-before-metahplan/7615 "2024-11-27T15:55:32Z")
I have paired\_end files from shoutgun metagenomics analysis (251 bp). Before starting with Metaphan, I run fastqc and fastq\_screen to check how my files are. I used KneadData to delete the human genome, and now it is ok… --- ## [Graphlan error: Classes not implemented](https://forum.biobakery.org/t/graphlan-error-classes-not-implemented/7578)
**Author:** [@KaushikRaman](https://forum.biobakery.org/u/KaushikRaman)\ **Replies:** 4\ **Last updated:** [November 25, 2024, 7:32pm UTC](https://forum.biobakery.org/t/graphlan-error-classes-not-implemented/7578 "2024-11-25T19:32:10Z")
Issue with GraPhlAn Annotations: I have been using GraPhlAn (version 1.1.4) to generate a phylogenetic figure for a project involving 9907 samples. The goal is to annotate each clade and add ring colors based on specifi… --- ## [Invalid or corrupt jar file error from Trimmomatic](https://forum.biobakery.org/t/invalid-or-corrupt-jar-file-error-from-trimmomatic/7540)
**Author:** [@Nitty\_Gritty](https://forum.biobakery.org/u/Nitty_Gritty)\ **Replies:** 0\ **Last updated:** [November 1, 2024, 9:04am UTC](https://forum.biobakery.org/t/invalid-or-corrupt-jar-file-error-from-trimmomatic/7540 "2024-11-01T09:04:56Z")
When I run a command as follows mkdir -p $OUTPUT\_DIR for i in {2..45} do if \[ $i -eq 6 \] || \[ $i -eq 30 \]; then continue fi INPUT1=“./${i}\_1.fq.gz” INPUT2=“./${i}\_2.fq.gz” kneaddata --input1 $INPUT1 --input2 $I… --- ## [KneadData, starting with BAM files](https://forum.biobakery.org/t/kneaddata-starting-with-bam-files/7521)
**Author:** [@maringa](https://forum.biobakery.org/u/maringa)\ **Replies:** 0\ **Last updated:** [October 24, 2024, 10:27pm UTC](https://forum.biobakery.org/t/kneaddata-starting-with-bam-files/7521 "2024-10-24T22:27:10Z")
I’m using kneaddata version 0.12.0 and I can’t find any information on how to input bam files in the documentation. I have samtools installed as well as indicated in the requirements. Could you please assist. Thank you. … --- ## [Size of the paired Kneaddata output file is 0](https://forum.biobakery.org/t/size-of-the-paired-kneaddata-output-file-is-0/7418)
**Author:** [@rocilia](https://forum.biobakery.org/u/rocilia)\ **Replies:** 3\ **Last updated:** [October 23, 2024, 9:23am UTC](https://forum.biobakery.org/t/size-of-the-paired-kneaddata-output-file-is-0/7418 "2024-10-23T09:23:35Z")
Hi everyone, I have run kneaddata (v0.12.0) with paired-end data and it generated a 15GB-output file with the command “–cat-final-output”, and Metaphlan and Humann run suceesfully. But when I remove the command “–cat-fi… --- ## [Is there a way to look for kneaddata version without log file?](https://forum.biobakery.org/t/is-there-a-way-to-look-for-kneaddata-version-without-log-file/7477)
**Author:** [@eo24a](https://forum.biobakery.org/u/eo24a)\ **Replies:** 0\ **Last updated:** [October 5, 2024, 6:01pm UTC](https://forum.biobakery.org/t/is-there-a-way-to-look-for-kneaddata-version-without-log-file/7477 "2024-10-05T18:01:20Z")
Hi, I have some trimmed files from kneaddata. I do not have the log files so I wonder if there is a way to determine the version of kneaddata was used from the trimmed fastq files. Thank you --- ## [Problem with paired end demo on new install](https://forum.biobakery.org/t/problem-with-paired-end-demo-on-new-install/1004)
**Author:** [@lowk](https://forum.biobakery.org/u/lowk)\ **Replies:** 15\ **Last updated:** [October 4, 2024, 12:49am UTC](https://forum.biobakery.org/t/problem-with-paired-end-demo-on-new-install/1004 "2024-10-04T00:49:24Z")
I have a strange and jarring error. I have just installed kneaaddata on a new cluster for the first time, and I am seeing some strange behaviour. I installed with pip install kneaddata. This is kneaddata v0.7.10, running… --- ## [Kneaddata installed with conda is not available](https://forum.biobakery.org/t/kneaddata-installed-with-conda-is-not-available/4147)
**Author:** [@Roy\_Cheng](https://forum.biobakery.org/u/Roy_Cheng)\ **Replies:** 9\ **Last updated:** [October 1, 2024, 12:58am UTC](https://forum.biobakery.org/t/kneaddata-installed-with-conda-is-not-available/4147 "2024-10-01T00:58:07Z")
hi! I used conda to install KneadData, but it didn’t work. The error message appears to be related to Trimmomatic. I’ve left the necessary code below. Thank you. (kneaddata) t010208@bio3-Horsea-12U:~/Chengtao/meta/test$… --- ## [Kneaddata paired output have different names](https://forum.biobakery.org/t/kneaddata-paired-output-have-different-names/7454)
**Author:** [@guo](https://forum.biobakery.org/u/guo)\ **Replies:** 0\ **Last updated:** [September 19, 2024, 4:43am UTC](https://forum.biobakery.org/t/kneaddata-paired-output-have-different-names/7454 "2024-09-19T04:43:25Z")
I have run kneaddata 0.12.0 on my metagenomics data. The data do not need to removed host-genome-contaminated reads, thus only use the trimmomatic options. kneaddata -i1 sample\_1.fq.gz -i2 sample\_2.fq.gz -o kneadd… --- ## [Kneaddata fails with message: Killed](https://forum.biobakery.org/t/kneaddata-fails-with-message-killed/7031)
**Author:** [@BioByron](https://forum.biobakery.org/u/BioByron)\ **Replies:** 1\ **Last updated:** [September 5, 2024, 2:49pm UTC](https://forum.biobakery.org/t/kneaddata-fails-with-message-killed/7031 "2024-09-05T14:49:53Z")
It’s my first time using Kneaddata and I’m not sure about the memory requirements for paired end shotgun data. I have tried installs using conda and pip into a conda environment, both result in the same error. I’m not su… [Previous page](https://forum.biobakery.org/c/infrastructure-and-utilities/22.md) [Next page](https://forum.biobakery.org/c/infrastructure-and-utilities/22.md?page=2)