# KneadData **URL:** https://forum.biobakery.org/c/infrastructure-and-utilities/kneaddata/8.md?page=1 [Latest](https://forum.biobakery.org/latest.md) · [Categories](https://forum.biobakery.org/categories.md) **Page:** 2 --- ## [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… --- ## [Adapters options](https://forum.biobakery.org/t/adapters-options/7417)
**Author:** [@farmer2020](https://forum.biobakery.org/u/farmer2020)\ **Replies:** 0\ **Last updated:** [August 31, 2024, 7:53am UTC](https://forum.biobakery.org/t/adapters-options/7417 "2024-08-31T07:53:34Z")
Dear Developers, May I ask a question about the TruSeq3 adapter from KneadData? There are one pair adapters in the fasta once installed, i.e., PrefixPE/1 and PrefixPE/2, however, I found more adapters from Trimmomatic a… --- ## [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 … --- ## [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… --- ## [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… --- ## [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… --- ## [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… --- ## [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 … --- ## [\`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 … --- ## [ERROR kneaddata output files](https://forum.biobakery.org/t/error-kneaddata-output-files/6638)
**Author:** [@Enkabloza](https://forum.biobakery.org/u/Enkabloza)\ **Replies:** 0\ **Last updated:** [February 12, 2024, 8:28pm UTC](https://forum.biobakery.org/t/error-kneaddata-output-files/6638 "2024-02-12T20:28:42Z")
Hi!! I am trying to run kneadData on bash but I got the following output files after processing my raw files (3158\_R1.fastq.gz and 3158\_R2.fastq.gz) ) on Paired-End-Run mode: Output files obtained: -reformatted\_identi… --- ## ["Clarification on Trimommatic Default Parameters in Kneaddata: Understanding MINLEN Checks for 2x150 bp Data"](https://forum.biobakery.org/t/clarification-on-trimommatic-default-parameters-in-kneaddata-understanding-minlen-checks-for-2x150-bp-data/6532)
**Author:** [@Anupam\_Gautam](https://forum.biobakery.org/u/Anupam_Gautam)\ **Replies:** 0\ **Last updated:** [January 26, 2024, 8:26pm UTC](https://forum.biobakery.org/t/clarification-on-trimommatic-default-parameters-in-kneaddata-understanding-minlen-checks-for-2x150-bp-data/6532 "2024-01-26T20:26:31Z")
Dear Biobakery team, I am trying to understand the default parameters of Trimmomatic when running KneadData with default parameter for 2x150 bp data: java -jar trimmomatic-0.39.jar PE R\_1.fastq R\_2.fastq R\_1\_kneaddata… --- ## [Find TRF version within KneadData](https://forum.biobakery.org/t/find-trf-version-within-kneaddata/6388)
**Author:** [@ebeirns](https://forum.biobakery.org/u/ebeirns)\ **Replies:** 1\ **Last updated:** [January 19, 2024, 3:24pm UTC](https://forum.biobakery.org/t/find-trf-version-within-kneaddata/6388 "2024-01-19T15:24:43Z")
Hi. I’m running KneadData version 0.12.0 and I’d like to find out which version of TRF is running within it. I believe it was installed automatically so I don’t know which version I have. I’ve check the TRF website and g… --- ## [Error when using kneaddata from anaconda](https://forum.biobakery.org/t/error-when-using-kneaddata-from-anaconda/5762)
**Author:** [@danpal](https://forum.biobakery.org/u/danpal)\ **Replies:** 2\ **Last updated:** [January 2, 2024, 7:08pm UTC](https://forum.biobakery.org/t/error-when-using-kneaddata-from-anaconda/5762 "2024-01-02T19:08:02Z")
kneaddata v0.12.0 When installing kneaddata from anaconda there are two errors that occur when using it: trimmomatic in anaconda is a python wrapper script, so it gives the next error: Error: Invalid or corrupt jarfil… --- ## [ERROR: Unable to find trf](https://forum.biobakery.org/t/error-unable-to-find-trf/773)
**Author:** [@elhenawy](https://forum.biobakery.org/u/elhenawy)\ **Replies:** 5\ **Last updated:** [December 26, 2023, 9:14pm UTC](https://forum.biobakery.org/t/error-unable-to-find-trf/773 "2023-12-26T21:14:50Z")
Hi, I am trying to run kneaddata on bash but I got the following error, although TRF is optional: ERROR: Unable to find trf. Please provide the full path to trf with --trf. These are the steps I followed: 1-I install… --- ## [About memory usage of Kneaddata](https://forum.biobakery.org/t/about-memory-usage-of-kneaddata/6360)
**Author:** [@biostatyu](https://forum.biobakery.org/u/biostatyu)\ **Replies:** 0\ **Last updated:** [December 22, 2023, 8:05am UTC](https://forum.biobakery.org/t/about-memory-usage-of-kneaddata/6360 "2023-12-22T08:05:52Z")
Dear team, I’m running kneedata on a small workstation (80 cores, 256 ram). I have about 155 samples. How should I allocate tasks reasonably? Because in my actual test, the running of one sample almost filled up my cach… --- ## [Kneaddata databases download issue](https://forum.biobakery.org/t/kneaddata-databases-download-issue/6346)
**Author:** [@ari](https://forum.biobakery.org/u/ari)\ **Replies:** 3\ **Last updated:** [December 22, 2023, 12:26am UTC](https://forum.biobakery.org/t/kneaddata-databases-download-issue/6346 "2023-12-22T00:26:11Z")
Dear All, I’m using Kneaddata on a HPC cluster and I have issues downloading the following databases : ribosomal\_RNA : bowtie2 = http://huttenhower.sph.harvard.edu/kneadData\_databases/SILVA\_128\_LSUParc\_SSUParc\_ribosoma… --- ## [TRF: Total number of sequences with repeats removed from file](https://forum.biobakery.org/t/trf-total-number-of-sequences-with-repeats-removed-from-file/6116)
**Author:** [@ebeirns](https://forum.biobakery.org/u/ebeirns)\ **Replies:** 0\ **Last updated:** [October 24, 2023, 4:51pm UTC](https://forum.biobakery.org/t/trf-total-number-of-sequences-with-repeats-removed-from-file/6116 "2023-10-24T16:51:06Z")
Could someone please clarify something from the kneaddata log file? I’m using version 0.12.0 and I’m confused (and alarmed) at the number of reads/sequences removed from my metagenomic files by TRF. Input 1&2 read count… --- ## [Single-end or Paired-end?](https://forum.biobakery.org/t/single-end-or-paired-end/6097)
**Author:** [@gsidhu](https://forum.biobakery.org/u/gsidhu)\ **Replies:** 0\ **Last updated:** [October 20, 2023, 2:22pm UTC](https://forum.biobakery.org/t/single-end-or-paired-end/6097 "2023-10-20T14:22:10Z")
I want to run Kneaddata on bacterial shotgun sequences and then Humann 3 on filtered sequences. I have paired-end FASTQ files. I understand that Humann will not pair the reads and analyze paired-end reads as single-end … --- ## [Updated kneaddata to fix issue with paired-end reads?](https://forum.biobakery.org/t/updated-kneaddata-to-fix-issue-with-paired-end-reads/5719)
**Author:** [@fquerdasi](https://forum.biobakery.org/u/fquerdasi)\ **Replies:** 9\ **Last updated:** [October 12, 2023, 11:30am UTC](https://forum.biobakery.org/t/updated-kneaddata-to-fix-issue-with-paired-end-reads/5719 "2023-10-12T11:30:27Z")
Hello, I wanted to ask if an updated version of kneaddata v0.12.0 has been released? When I go to this site: Files :: Anaconda.org I see that a new file, called " noarch/kneaddata-0.12.0-pyhdfd78af\_1.tar.bz2" was upload… --- ## [Kneaddata trf error](https://forum.biobakery.org/t/kneaddata-trf-error/3611)
**Author:** [@cazzlewazzle89](https://forum.biobakery.org/u/cazzlewazzle89)\ **Replies:** 6\ **Last updated:** [September 25, 2023, 8:44pm UTC](https://forum.biobakery.org/t/kneaddata-trf-error/3611 "2023-09-25T20:44:36Z")
Hi, I am having an issue with trf when running kneaddata. It only happens with this one sample (a negative sequencing control, the true samples all run without any issues). The error in the log file isn’t particularly … [Previous page](https://forum.biobakery.org/c/infrastructure-and-utilities/kneaddata/8.md) [Next page](https://forum.biobakery.org/c/infrastructure-and-utilities/kneaddata/8.md?page=2)