# \--run-trim-repetitive and --sequencer-source not part of Docker, Conda, or Pip **URL:** \ **Category:** KneadData\ **Created:** [November 22, 2020, 8:47pm UTC](https://forum.biobakery.org/t/run-trim-repetitive-and-sequencer-source-not-part-of-docker-conda-or-pip/1321 "2020-11-22T20:47:53Z")\ **Posts on this page:** 2\ **Page:** 1
**Author:** ![djbradshaw2](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/djbradshaw2/32/1050_2.png) [@djbradshaw2](https://forum.biobakery.org/u/djbradshaw2)\ **Post date:** [November 22, 2020, 8:47pm UTC](https://forum.biobakery.org/t/run-trim-repetitive-and-sequencer-source-not-part-of-docker-conda-or-pip/1321/1 "2020-11-22T20:47:53Z")
Dear Kneaddata Developers, Thank you for such a great product. I have been following the tutorial from [https://github.com/biobakery/kneaddata](https://github.com/biobakery/kneaddata). I have tried using Docker, Conda, and Pip to download kneaddata, all had versions 0.7.10, but none of them have the --run-trim-repetitive or –sequencer-source options mentioned in the tutorial, as seen below with the Conda version. Is this going to be added a an upcoming version of kneaddata, or am I missing something in my downloading process? Thank you for your time and help. Sincerely, David (base) microbiology@Willow:~ kneaddata --version kneaddata v0.7.10 (base) microbiology@Willow:~ kneaddata --help usage: kneaddata [-h] [–version] [-v] -i INPUT -o OUTPUT\_DIR [-db REFERENCE\_DB] [–bypass-trim] [–output-prefix OUTPUT\_PREFIX] [-t \<1\>] [-p \<1\>] [-q {phred33,phred64}] [–run-bmtagger] [–bypass-trf] [–run-fastqc-start] [–run-fastqc-end] [–store-temp-output] [–remove-intermediate-output] [–cat-final-output] [–log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL}] [–log LOG] [–trimmomatic TRIMMOMATIC\_PATH] [–max-memory MAX\_MEMORY] [–trimmomatic-options TRIMMOMATIC\_OPTIONS] [–sequencer-source {NexteraPE,TruSeq2,TruSeq3}] [–bowtie2 BOWTIE2\_PATH] [–bowtie2-options BOWTIE2\_OPTIONS] [–no-discordant] [–reorder] [–serial] [–bmtagger BMTAGGER\_PATH] [–trf TRF\_PATH] [–match MATCH] [–mismatch MISMATCH] [–delta DELTA] [–pm PM] [–pi PI] [–minscore MINSCORE] [–maxperiod MAXPERIOD] [–fastqc FASTQC\_PATH] KneadData optional arguments: -h, --help show this help message and exit -v, --verbose additional output is printed global options: –version show program’s version number and exit -i INPUT, --input INPUT input FASTQ file (add a second argument instance to run with paired input files) -o OUTPUT\_DIR, --output OUTPUT\_DIR directory to write output files -db REFERENCE\_DB, --reference-db REFERENCE\_DB location of reference database (additional arguments add databases) –bypass-trim bypass the trim step –output-prefix OUTPUT\_PREFIX prefix for all output files [DEFAULT : $SAMPLE\_kneaddata] -t \<1\>, --threads \<1\> number of threads [Default : 1] -p \<1\>, --processes \<1\> number of processes [Default : 1] -q {phred33,phred64}, --quality-scores {phred33,phred64} quality scores [DEFAULT : phred33] –run-bmtagger run BMTagger instead of Bowtie2 to identify contaminant reads –bypass-trf option to bypass the removal of tandem repeats –run-fastqc-start run fastqc at the beginning of the workflow –run-fastqc-end run fastqc at the end of the workflow –store-temp-output store temp output files [DEFAULT : temp output files are removed] –remove-intermediate-output remove intermediate output files [DEFAULT : intermediate output files are stored] –cat-final-output concatenate all final output files [DEFAULT : final output is not concatenated] –log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL} level of log messages [DEFAULT : DEBUG] –log LOG log file [DEFAULT : $OUTPUT\_DIR/$SAMPLE\_kneaddata.log] trimmomatic arguments: –trimmomatic TRIMMOMATIC\_PATH path to trimmomatic [DEFAULT : $PATH] –max-memory MAX\_MEMORY max amount of memory [DEFAULT : 500m] –trimmomatic-options TRIMMOMATIC\_OPTIONS options for trimmomatic [DEFAULT : ILLUMINACLIP:/-SE.fa:2:30:10 SLIDINGWINDOW:4:20 MINLEN:50] MINLEN is set to 50 percent of total input read length –sequencer-source {NexteraPE,TruSeq2,TruSeq3} options for sequencer-source [DEFAULT : NexteraPE] bowtie2 arguments: –bowtie2 BOWTIE2\_PATH path to bowtie2 [DEFAULT : $PATH] –bowtie2-options BOWTIE2\_OPTIONS options for bowtie2 [DEFAULT : --very-sensitive] –no-discordant do not include discordant alignments for pairs (ie one of the two pairs aligns) [DEFAULT : Discordant alignments are included] –reorder order the sequences in the same order as the input [DEFAULT : With discordant paired alignments sequences are not ordered] –serial filter the input in serial for multiple databases so a subset of reads are processed in each database search bmtagger arguments: –bmtagger BMTAGGER\_PATH path to BMTagger [DEFAULT : $PATH] trf arguments: –trf TRF\_PATH path to TRF [DEFAULT : $PATH] –match MATCH matching weight [DEFAULT : 2] –mismatch MISMATCH mismatching penalty [DEFAULT : 7] –delta DELTA indel penalty [DEFAULT : 7] –pm PM match probability [DEFAULT : 80] –pi PI indel probability [DEFAULT : 10] –minscore MINSCORE minimum alignment score to report [DEFAULT : 50] –maxperiod MAXPERIOD maximum period size to report [DEFAULT : 500] fastqc arguments: –fastqc FASTQC\_PATH path to fastqc [DEFAULT : $PATH] ---
**Author:** ![djbradshaw2](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/djbradshaw2/32/1050_2.png) [@djbradshaw2](https://forum.biobakery.org/u/djbradshaw2)\ **Post date:** [November 24, 2020, 8:18pm UTC](https://forum.biobakery.org/t/run-trim-repetitive-and-sequencer-source-not-part-of-docker-conda-or-pip/1321/2 "2020-11-24T20:18:42Z")
Oops, sorry missed that -sequencer-source was there.