https://bioinformaticsonline.com/snippets?offset=180 https://bioinformaticsonline.com/snippets/view/42638/install-gffread-using-conda Sun, 17 Jan 2021 00:37:14 -0600 https://bioinformaticsonline.com/snippets/view/42638/install-gffread-using-conda #GffRead: GFF/GTF utility providing format conversions, filtering, FASTA sequence extraction and more. https://github.com/gpertea/gffread (jitENV) jitendra@Bathymodiolus:~$ conda install -c bioconda gffread Collecting package metadata (current_repodata.json): done Solving environment: done ## Package Plan ## environment location: /home/jitendra/.conda/envs/jitENV added / updated specs: - gffread The following packages will be downloaded: package | build ---------------------------|----------------- _libgcc_mutex-0.1 | main 3 KB gffread-0.12.1 | h8b12597_0 635 KB bioconda libgcc-ng-9.1.0 | hdf63c60_0 5.1 MB libstdcxx-ng-9.1.0 | hdf63c60_0 3.1 MB zlib-1.2.11 | h7b6447c_3 103 KB ------------------------------------------------------------ Total: 8.9 MB The following NEW packages will be INSTALLED: _libgcc_mutex pkgs/main/linux-64::_libgcc_mutex-0.1-main gffread bioconda/linux-64::gffread-0.12.1-h8b12597_0 libgcc-ng pkgs/main/linux-64::libgcc-ng-9.1.0-hdf63c60_0 libstdcxx-ng pkgs/main/linux-64::libstdcxx-ng-9.1.0-hdf63c60_0 zlib pkgs/main/linux-64::zlib-1.2.11-h7b6447c_3 Proceed ([y]/n)? y Downloading and Extracting Packages zlib-1.2.11 | 103 KB | ##################################### | 100% _libgcc_mutex-0.1 | 3 KB | ##################################### | 100% libstdcxx-ng-9.1.0 | 3.1 MB | ##################################### | 100% libgcc-ng-9.1.0 | 5.1 MB | ##################################### | 100% gffread-0.12.1 | 635 KB | ##################################### | 100% Preparing transaction: done Verifying transaction: done Executing transaction: done #Run as follows (jitENV) jitendra@Bathymodiolus:~$ gffread -w cds.fa -g ed.clean.fasta gene_structures_post_PASA_updates.19157.gff3 #There are also another good option python gff2fa.py -t CDS ../../GCF_0355.2_L0_genomic.gff ../../GCF_001039355.2_L0_genomic.fna > La.cds.fa #Find more at http://blog.shenwei.me/extract-cds-fastas-from-a-gff-annotation-reference-sequence/]]> Jit https://bioinformaticsonline.com/snippets/view/42617/install-wgd-cli-on-linux Wed, 13 Jan 2021 18:34:19 -0600 https://bioinformaticsonline.com/snippets/view/42617/install-wgd-cli-on-linux (JitMetaENV) ➜ wgd git:(master) pip install --user ERROR: You must give at least one requirement to install (see "pip help install") (JitMetaENV) ➜ wgd git:(master) pip install --user . Processing /home/urbe/sahil_data/novoKorea/comparativeGenomics/wgd Requirement already satisfied: numpy>=1.16 in /home/urbe/.local/lib/python3.6/site-packages (from wgd==1.2) (1.19.0) Requirement already satisfied: scipy>=1.2 in /home/urbe/.local/lib/python3.6/site-packages (from wgd==1.2) (1.5.1) Requirement already satisfied: matplotlib>=3.0.2 in /home/urbe/.local/lib/python3.6/site-packages (from wgd==1.2) (3.2.2) Collecting bokeh==1.4.0 Downloading bokeh-1.4.0.tar.gz (32.4 MB) |████████████████████████████████| 32.4 MB 60 kB/s Requirement already satisfied: six>=1.5.2 in /home/urbe/.local/lib/python3.6/site-packages (from bokeh==1.4.0->wgd==1.2) (1.15.0) Requirement already satisfied: python-dateutil>=2.1 in /home/urbe/.local/lib/python3.6/site-packages (from bokeh==1.4.0->wgd==1.2) (2.8.1) Requirement already satisfied: pillow>=4.0 in /home/urbe/anaconda3/envs/JitMetaENV/lib/python3.6/site-packages (from bokeh==1.4.0->wgd==1.2) (8.1.0) Requirement already satisfied: tornado>=4.3 in /home/urbe/anaconda3/envs/JitMetaENV/lib/python3.6/site-packages (from bokeh==1.4.0->wgd==1.2) (6.1) Collecting fastcluster==1.1.25 Downloading fastcluster-1.1.25-cp36-cp36m-manylinux1_x86_64.whl (153 kB) |████████████████████████████████| 153 kB 44.3 MB/s Collecting joblib==0.11 Downloading joblib-0.11-py2.py3-none-any.whl (176 kB) |████████████████████████████████| 176 kB 63.7 MB/s Collecting pandas==0.24.1 Downloading pandas-0.24.1-cp36-cp36m-manylinux1_x86_64.whl (10.1 MB) |████████████████████████████████| 10.1 MB 38.9 MB/s Requirement already satisfied: pytz>=2011k in /home/urbe/.local/lib/python3.6/site-packages (from pandas==0.24.1->wgd==1.2) (2020.1) Collecting biopython>=1.75 Downloading biopython-1.78-cp36-cp36m-manylinux1_x86_64.whl (2.3 MB) |████████████████████████████████| 2.3 MB 50.3 MB/s Collecting click>=7.0 Downloading click-7.1.2-py2.py3-none-any.whl (82 kB) |████████████████████████████████| 82 kB 164 kB/s Collecting coloredlogs>=10.0 Downloading coloredlogs-15.0-py2.py3-none-any.whl (45 kB) |████████████████████████████████| 45 kB 727 kB/s Collecting ete3>=3.1 Downloading ete3-3.1.2.tar.gz (4.7 MB) |████████████████████████████████| 4.7 MB 47 kB/s Collecting humanfriendly>=9.1 Downloading humanfriendly-9.1-py2.py3-none-any.whl (86 kB) |████████████████████████████████| 86 kB 890 kB/s Collecting Jinja2>=2.7 Downloading Jinja2-2.11.2-py2.py3-none-any.whl (125 kB) |████████████████████████████████| 125 kB 57.8 MB/s Collecting MarkupSafe>=0.23 Downloading MarkupSafe-1.1.1-cp36-cp36m-manylinux1_x86_64.whl (27 kB) Requirement already satisfied: kiwisolver>=1.0.1 in /home/urbe/.local/lib/python3.6/site-packages (from matplotlib>=3.0.2->wgd==1.2) (1.2.0) Requirement already satisfied: cycler>=0.10 in /home/urbe/.local/lib/python3.6/site-packages (from matplotlib>=3.0.2->wgd==1.2) (0.10.0) Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /home/urbe/.local/lib/python3.6/site-packages (from matplotlib>=3.0.2->wgd==1.2) (2.4.7) Collecting packaging>=16.8 Downloading packaging-20.8-py2.py3-none-any.whl (39 kB) Collecting plumbum>=1.6.7 Downloading plumbum-1.6.9-py2.py3-none-any.whl (115 kB) |████████████████████████████████| 115 kB 71.8 MB/s Collecting progressbar2>=3.39 Downloading progressbar2-3.53.1-py2.py3-none-any.whl (25 kB) Collecting python-utils>=2.3.0 Downloading python_utils-2.4.0-py2.py3-none-any.whl (12 kB) Collecting PyYAML>=3.10 Downloading PyYAML-5.3.1.tar.gz (269 kB) |████████████████████████████████| 269 kB 67.9 MB/s Collecting seaborn>=0.9.0 Downloading seaborn-0.11.1-py3-none-any.whl (285 kB) |████████████████████████████████| 285 kB 40.2 MB/s Collecting sklearn Using cached sklearn-0.0.tar.gz (1.1 kB) Collecting scikit-learn Downloading scikit_learn-0.24.0-cp36-cp36m-manylinux2010_x86_64.whl (22.2 MB) |████████████████████████████████| 22.2 MB 83 kB/s Collecting threadpoolctl>=2.0.0 Downloading threadpoolctl-2.1.0-py3-none-any.whl (12 kB) Building wheels for collected packages: wgd, bokeh, ete3, PyYAML, sklearn Building wheel for wgd (setup.py) ... done Created wheel for wgd: filename=wgd-1.2-py3-none-any.whl size=75291 sha256=ebd89070a2b46f55c1191d4daf130d0b1c5d3591d17d7e52020c8c5eccc14863 Stored in directory: /tmp/pip-ephem-wheel-cache-qyjwpfd6/wheels/86/33/fd/c4ff61fc6fbf977d32a25a1c29fc170d9c2e2f15ec4ab06bb8 Building wheel for bokeh (setup.py) ... done Created wheel for bokeh: filename=bokeh-1.4.0-py3-none-any.whl size=23689200 sha256=5109a280afc85f01827c33d14f705cff39975bc24cd852a3c9efa0bdfb10e403 Stored in directory: /home/urbe/.cache/pip/wheels/b6/72/72/a6a223f72a9b02a4922a3c2fec55b2f65567254d398f6c5f74 Building wheel for ete3 (setup.py) ... done Created wheel for ete3: filename=ete3-3.1.2-py3-none-any.whl size=2272998 sha256=f8375eb7814bf43d0a0b5289f7508d2ed4c758ba5ee72927afae2ce846b68a0d Stored in directory: /home/urbe/.cache/pip/wheels/1f/17/0f/fbcffa83fcfad717d040f4de35752ea86cc9106e38c9341f21 Building wheel for PyYAML (setup.py) ... done Created wheel for PyYAML: filename=PyYAML-5.3.1-cp36-cp36m-linux_x86_64.whl size=44621 sha256=8e0904dc4b0fd5c91d07835dcdec3b8798f39ae0f984b196004d3b9852d0953a Stored in directory: /home/urbe/.cache/pip/wheels/e5/9d/ad/2ee53cf262cba1ffd8afe1487eef788ea3f260b7e6232a80fc Building wheel for sklearn (setup.py) ... done Created wheel for sklearn: filename=sklearn-0.0-py2.py3-none-any.whl size=1316 sha256=a5e80e28bbeac53b7a74d810d197415125d63fcf98ccb88172e55e2234396651 Stored in directory: /home/urbe/.cache/pip/wheels/23/9d/42/5ec745cbbb17517000a53cecc49d6a865450d1f5cb16dc8a9c Successfully built wgd bokeh ete3 PyYAML sklearn Installing collected packages: threadpoolctl, MarkupSafe, joblib, scikit-learn, PyYAML, python-utils, pandas, packaging, Jinja2, humanfriendly, sklearn, seaborn, progressbar2, plumbum, fastcluster, ete3, coloredlogs, click, bokeh, biopython, wgd Attempting uninstall: joblib Found existing installation: joblib 0.13.2 Uninstalling joblib-0.13.2: Successfully uninstalled joblib-0.13.2 Attempting uninstall: pandas Found existing installation: pandas 1.0.5 Uninstalling pandas-1.0.5: Successfully uninstalled pandas-1.0.5 WARNING: The script humanfriendly is installed in '/home/urbe/.local/bin' which is not on PATH. Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location. WARNING: The script ete3 is installed in '/home/urbe/.local/bin' which is not on PATH. Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location. WARNING: The script coloredlogs is installed in '/home/urbe/.local/bin' which is not on PATH. Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location. WARNING: The script bokeh is installed in '/home/urbe/.local/bin' which is not on PATH. Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location. Attempting uninstall: biopython Found existing installation: biopython 1.73 Uninstalling biopython-1.73: Successfully uninstalled biopython-1.73 WARNING: The script wgd is installed in '/home/urbe/.local/bin' which is not on PATH. Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location. Successfully installed Jinja2-2.11.2 MarkupSafe-1.1.1 PyYAML-5.3.1 biopython-1.78 bokeh-1.4.0 click-7.1.2 coloredlogs-15.0 ete3-3.1.2 fastcluster-1.1.25 humanfriendly-9.1 joblib-0.11 packaging-20.8 pandas-0.24.1 plumbum-1.6.9 progressbar2-3.53.1 python-utils-2.4.0 scikit-learn-0.24.0 seaborn-0.11.1 sklearn-0.0 threadpoolctl-2.1.0 wgd-1.2 Then (JitMetaENV) ➜ wgd git:(master) export PATH=$PATH:/home/urbe/.local/bin (JitMetaENV) ➜ wgd git:(master) wgd]]> Jit https://bioinformaticsonline.com/snippets/view/42595/create-random-2-translocations-in-genome Sun, 10 Jan 2021 10:20:41 -0600 https://bioinformaticsonline.com/snippets/view/42595/create-random-2-translocations-in-genome (base) ➜ dupStudy git:(master) ✗ perl ../simuG.pl -refseq simuINV.simseq.genome.fa -translocation_count 2 -prefix simuTRANS [Sun Jan 10 17:12:58 2021] Starting simuG .. [Sun Jan 10 17:12:58 2021] Check specified options .. Running simuG for translocation simulation >> This simulation use the random seed: 1925195826 The option translocation_count has been specified: translocation_count = 2 [Sun Jan 10 17:12:58 2021] Introducing random Translocations based on the following parameters: > translocation_count = 2 [Sun Jan 10 17:12:58 2021] Simulation completed! :) [Sun Jan 10 17:12:58 2021] Generating output files .. Generating the correspondance map for genomic variants introduced during simulation: simuTRANS.refseq2simseq.map.txt Generating reference-based vcf file for genomic variants introduced during simulation: simuTRANS.refseq2simseq.translocation.vcf [Sun Jan 10 17:12:58 2021] Done! :)]]> Jit https://bioinformaticsonline.com/snippets/view/42594/create-random-5-inversions-in-genome Sun, 10 Jan 2021 09:33:37 -0600 https://bioinformaticsonline.com/snippets/view/42594/create-random-5-inversions-in-genome (base) ➜ dupStudy git:(master) ✗ perl ../simuG.pl -refseq simuCNV.simseq.genome.fa -inversion_count 5 -prefix simuINV [Sun Jan 10 16:30:40 2021] Starting simuG .. [Sun Jan 10 16:30:40 2021] Check specified options .. Running simuG for inversion simulation >> Ignore all options for translocation simulation. This simulation use the random seed: 639103429 The option inversion_count has been specified: inversion_count = 5 The option inversion_min_size has been specified: inversion_min_size = 1000 The option inversion_max_size has been specified: inversion_max_size = 100000 [Sun Jan 10 16:30:40 2021] Introducing random Inversions based on the following parameters: > inversion_count = 5 > inversion_min_size = 1000 > inversion_max_size = 100000 [Sun Jan 10 16:30:40 2021] Simulation completed! :) [Sun Jan 10 16:30:40 2021] Generating output files .. Generating the correspondance map for genomic variants introduced during simulation: simuINV.refseq2simseq.map.txt Generating reference-based vcf file for genomic variants introduced during simulation: simuINV.refseq2simseq.inversion.vcf [Sun Jan 10 16:30:40 2021] Done! :)]]> Jit https://bioinformaticsonline.com/snippets/view/42593/create-random-1000-cnvs-in-genome Sun, 10 Jan 2021 09:27:42 -0600 https://bioinformaticsonline.com/snippets/view/42593/create-random-1000-cnvs-in-genome (base) ➜ dupStudy git:(master) ✗ perl ../simuG.pl -refseq simuINDEL.simseq.genome.fa -cnv_count 100 -prefix simuCNV [Sun Jan 10 16:24:20 2021] Starting simuG .. [Sun Jan 10 16:24:20 2021] Check specified options .. Running simuG for CNV simulation >> Ignore all options for inversion/translocation simulation. This simulation use the random seed: 678641233 The option cnv_count has been specified: cnv_count = 100 The option duplication_tandem_dispersed_ratio has been specified: duplication_tandem_dispersed_ratio = 1 The option cnv_max_copy_number has been specified: cnv_max_copy_number = 10 The option cnv_min_size has been specified: cnv_min_size = 100 The option cnv_min_size has been specified: cnv_max_size = 10000 [Sun Jan 10 16:24:20 2021] Introducing random CNVs with the following parameters: > cnv_count = 100 > cnv_gain_loss_ratio = 1 > duplication_tandem_dispersed_ratio = 1 > cnv_max_copy_number = 10 > cnv_min_size = 100 > cnv_max_size = 10000 [Sun Jan 10 16:24:20 2021] Simulation completed! :) [Sun Jan 10 16:24:20 2021] Generating output files .. Generating the correspondance map for genomic variants introduced during simulation: simuCNV.refseq2simseq.map.txt Generating reference-based vcf file for genomic variants introduced during simulation: simuCNV.refseq2simseq.CNV.vcf [Sun Jan 10 16:24:20 2021] Done! :)]]> Jit https://bioinformaticsonline.com/snippets/view/42592/create-random-1000-indel-in-genome Sun, 10 Jan 2021 09:15:26 -0600 https://bioinformaticsonline.com/snippets/view/42592/create-random-1000-indel-in-genome (base) ➜ dupStudy git:(master) ✗ perl ../simuG.pl -refseq simuSNP.simseq.genome.fa -indel_count 1000 -prefix simuINDEL [Sun Jan 10 16:14:00 2021] Starting simuG .. [Sun Jan 10 16:14:00 2021] Check specified options .. Running simuG for SNP/INDEL simulation >> Ignore all options for CNV/inversion/translocation simulation. This simulation use the random seed: 1678440514 The option indel_count has been specified: indel_count = 1000 The option ins_del_ratio has been specified: ins_del_ratio = 1 The option indel_size_powerlaw_alpha has been specified: indel_size_powerlaw_alpha = 2 The option indel_size_powerlaw_constant has been specified: indel_size_powerlaw_constant = 0.5 [Sun Jan 10 16:14:00 2021] Introducing random INDELs based on the following parameters: > indel_count = 1000 > ins_del_ratio = 1 > indel_size_powerlaw_alpha = 2 > indel_size_powerlaw_constant = 0.5 [Sun Jan 10 16:14:00 2021] Simulation completed! :) [Sun Jan 10 16:14:00 2021] Generating output files .. Generating the correspondance map for genomic variants introduced during simulation: simuINDEL.refseq2simseq.map.txt Generating reference-based vcf file for genomic variants introduced during simulation: simuINDEL.refseq2simseq.INDEL.vcf [Sun Jan 10 16:14:00 2021] Done! :)]]> Jit https://bioinformaticsonline.com/snippets/view/42591/create-random-10000-snps-in-genome Sun, 10 Jan 2021 09:10:07 -0600 https://bioinformaticsonline.com/snippets/view/42591/create-random-10000-snps-in-genome (base) ➜ dupStudy git:(master) ✗ perl ../simuG.pl -refseq SGDref.R64-2-1.dups.fa -snp_count 10000 -prefix simuSNP [Sun Jan 10 16:05:57 2021] Starting simuG .. [Sun Jan 10 16:05:57 2021] Check specified options .. Running simuG for SNP/INDEL simulation >> Ignore all options for CNV/inversion/translocation simulation. This simulation use the random seed: 811014067 The option snp_count has been specified: snp_count = 10000 The option titv_ratio has been specified: titv_ratio = 0.5 [Sun Jan 10 16:05:57 2021] Introducing random SNPs based on the following parameters: > snp_count = 10000 > titv_ratio = 0.5 [Sun Jan 10 16:05:57 2021] Simulation completed! :) [Sun Jan 10 16:05:57 2021] Generating output files .. Generating the correspondance map for genomic variants introduced during simulation: simuSNP.refseq2simseq.map.txt Generating reference-based vcf file for genomic variants introduced during simulation: simuSNP.refseq2simseq.SNP.vcf [Sun Jan 10 16:05:57 2021] Done! :)]]> Jit https://bioinformaticsonline.com/snippets/view/42579/install-maxbin2-using-conda Thu, 07 Jan 2021 04:27:03 -0600 https://bioinformaticsonline.com/snippets/view/42579/install-maxbin2-using-conda (JitMetaENV) ➜ day3 conda install -c bioconda maxbin2 Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source. Collecting package metadata (repodata.json): done Solving environment: done ==> WARNING: A newer version of conda exists. <== current version: 4.9.0 latest version: 4.9.2 Please update conda by running $ conda update -n base -c defaults conda ## Package Plan ## environment location: /home/urbe/anaconda3/envs/JitMetaENV added / updated specs: - maxbin2 The following packages will be downloaded: package | build ---------------------------|----------------- bowtie2-2.4.2 | py36h5202f60_1 12.7 MB bioconda fraggenescan-1.31 | h516909a_2 1.3 MB bioconda idba-1.1.3 | 1 35.5 MB bioconda maxbin2-2.2.1 | 0 43 KB bioconda tbb-2020.2 | h4bd325d_2 1.5 MB conda-forge ------------------------------------------------------------ Total: 51.1 MB The following NEW packages will be INSTALLED: bowtie2 bioconda/linux-64::bowtie2-2.4.2-py36h5202f60_1 fraggenescan bioconda/linux-64::fraggenescan-1.31-h516909a_2 idba bioconda/linux-64::idba-1.1.3-1 maxbin2 bioconda/linux-64::maxbin2-2.2.1-0 tbb conda-forge/linux-64::tbb-2020.2-h4bd325d_2 Proceed ([y]/n)? y Downloading and Extracting Packages fraggenescan-1.31 | 1.3 MB | ###################################################################################################################### | 100% idba-1.1.3 | 35.5 MB | ###################################################################################################################### | 100% tbb-2020.2 | 1.5 MB | ###################################################################################################################### | 100% bowtie2-2.4.2 | 12.7 MB | ###################################################################################################################### | 100% maxbin2-2.2.1 | 43 KB | ###################################################################################################################### | 100% Preparing transaction: done Verifying transaction: done Executing transaction: done]]> Jit https://bioinformaticsonline.com/snippets/view/42578/install-krona-using-conda Thu, 07 Jan 2021 02:20:39 -0600 https://bioinformaticsonline.com/snippets/view/42578/install-krona-using-conda (JitMetaENV) ➜ day3 conda install -c bioconda krona Collecting package metadata (current_repodata.json): done Solving environment: done ==> WARNING: A newer version of conda exists. <== current version: 4.9.0 latest version: 4.9.2 Please update conda by running $ conda update -n base -c defaults conda ## Package Plan ## environment location: /home/urbe/anaconda3/envs/JitMetaENV added / updated specs: - krona The following packages will be downloaded: package | build ---------------------------|----------------- certifi-2020.12.5 | py36h5fab9bb_1 143 KB conda-forge krona-2.7.1 | pl526_3 189 KB bioconda ------------------------------------------------------------ Total: 332 KB The following NEW packages will be INSTALLED: krona bioconda/noarch::krona-2.7.1-pl526_3 The following packages will be UPDATED: certifi 2020.12.5-py36h5fab9bb_0 --> 2020.12.5-py36h5fab9bb_1 Proceed ([y]/n)?]]> Jit https://bioinformaticsonline.com/snippets/view/42577/download-minikraken-database Thu, 07 Jan 2021 02:05:24 -0600 https://bioinformaticsonline.com/snippets/view/42577/download-minikraken-database (JitMetaENV) ➜ day3 curl -O ftp://ftp.ccb.jhu.edu/pub/data/kraken2_dbs/old/minikraken2_v2_8GB_201904.tgz % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 5661M 100 5661M 0 0 25.3M 0 0:03:43 0:03:43 --:--:-- 29.5M (JitMetaENV) ➜ day3 ls minikraken2_v2_8GB_201904.tgz (JitMetaENV) ➜ day3 mkdir krakenDB (JitMetaENV) ➜ day3 cd krakenDB (JitMetaENV) ➜ krakenDB ls (JitMetaENV) ➜ krakenDB mv ../minikraken2_v2_8GB_201904.tgz . (JitMetaENV) ➜ krakenDB tar -xvzf minikraken2_v2_8GB_201904.tgz minikraken2_v2_8GB_201904_UPDATE/ minikraken2_v2_8GB_201904_UPDATE/taxo.k2d minikraken2_v2_8GB_201904_UPDATE/opts.k2d minikraken2_v2_8GB_201904_UPDATE/database100mers.kmer_distrib minikraken2_v2_8GB_201904_UPDATE/database150mers.kmer_distrib minikraken2_v2_8GB_201904_UPDATE/database200mers.kmer_distrib minikraken2_v2_8GB_201904_UPDATE/hash.k2d #Check for pe reads #kraken2 --use-names --threads 4 --db minikraken2_v2_8GB_201904_UPDATE --fastq-input --report evol1 --gzip-compressed --paired ../mappings/evol1.sorted.unmapped.R1.fastq.gz ../mappings/evol1.sorted.unmapped.R2.fastq.gz > evol1.kraken]]> Jit