BOL: Owner

Install Packages in Python

LEGE — Fri, 17 Sep 2021 02:02:14 -0500

#Create a conda environment.
#Install a Python package in the terminal using conda.

$ conda create -n myenv

$ conda create -n myenv Python=3.7

$ conda env create -f environment.yml

#List Available Conda Environments

$ conda env list

#Activate an Environment for Use
$ conda activate myenv

#Update Conda Environments Using a YAML File
$ conda activate earth-analytics-python
$ conda env update -f environment.yml

#Adding a Package to your YAML File

name: genome-analytics-python
channels:
  - conda-forge
  - defaults

dependencies:
  - python=3.7
  - matplotlib
  # Core scientific python
  - numpy

#List Installed Dependencies Within an Environment
(myenv) $ conda list

Run multiple bash command in screen !

LEGE — Thu, 16 Sep 2021 15:04:21 -0500

#login to screen 
screen -r 123

#bash.sh
srun --partition=compute --nodes=1 --ntasks-per-node=40 --pty bash.sh

#Run and check the status in screen
contol +A +D

Install Nexflow on Linux !

LEGE — Wed, 15 Sep 2021 20:47:11 -0500

# Make sure that Java v8+ is installed:
java -version

# Install Nextflow
curl -fsSL get.nextflow.io | bash

# Add Nextflow binary to your PATH:
mv nextflow ~/bin/
# OR system-wide installation:
# sudo mv nextflow /usr/local/bin

Tadpole is 250x faster than SPADes assembler !

LEGE — Thu, 02 Sep 2021 08:30:43 -0500

lege@jit-Lenovo-ideapad-320-15ISK:~/Downloads/MyTools/Vir$ tadpole.sh 

Written by Brian Bushnell
Last modified July 16, 2018

Description:  Uses kmer counts to assemble contigs, extend sequences, 
or error-correct reads.  Tadpole has no upper bound for kmer length,
but some values are not supported.  Specifically, it allows 1-31,
multiples of 2 from 32-62, multiples of 3 from 63-93, etc.
Please read bbmap/docs/guides/TadpoleGuide.txt for more information.

Usage:
Assembly:     tadpole.sh in= out=
Extension:    tadpole.sh in= out= mode=extend
Correction:   tadpole.sh in= out= mode=correct

Extension and correction may be done simultaneously.  Error correction on 
multiple files may be done like this:

tadpole.sh in=libA_r1.fq,libA_merged.fq in2=libA_r2.fq,null extra=libB_r1.fq out=ecc_libA_r1.fq,ecc_libA_merged.fq out2=ecc_libA_r2.fq,null mode=correct

Extending contigs with reads could be done like this:

tadpole.sh in=contigs.fa out=extended.fa el=100 er=100 mode=extend extra=reads.fq k=62


Input parameters:
in=           Primary input file for reads to use as kmer data.
in2=          Second input file for paired data.
extra=        Extra files for use as kmer data, but not for error-
                    correction or extension.
reads=-1            Only process this number of reads, then quit (-1 means all).
NOTE: in, in2, and extra may also be comma-delimited lists of files.

Output parameters:
out=          Write contigs (in contig mode) or corrected/extended 
                    reads (in other modes).
out2=         Second output file for paired output.
outd=         Write discarded reads, if using junk-removal flags.
dot=          Write a contigs connectivity graph (partially implemented)
dump=         Write kmers and their counts.
fastadump=t         Write kmers and counts as fasta versus 2-column tsv.
mincounttodump=1    Only dump kmers with at least this depth.
showstats=t         Print assembly statistics after writing contigs.

Prefiltering parameters:
prefilter=0         If set to a positive integer, use a countmin sketch
                    to ignore kmers with depth of that value or lower.
prehashes=2         Number of hashes for prefilter.
prefiltersize=0.2   (pff) Fraction of memory to use for prefilter.
minprobprefilter=t  (mpp) Use minprob for the prefilter.
prepasses=1         Use this many prefiltering passes; higher be more thorough
                    if the filter is very full.  Set to 'auto' to iteratively 
                    prefilter until the remaining kmers will fit in memory.
onepass=f           If true, prefilter will be generated in same pass as kmer
                    counts.  Much faster but counts will be lower, by up to
                    prefilter's depth limit.

Hashing parameters:
k=31                Kmer length (1 to infinity).  Memory use increases with K.
prealloc=t          Pre-allocate memory rather than dynamically growing; 
                    faster and more memory-efficient.  A float fraction (0-1)
                    may be specified; default is 1.
minprob=0.5         Ignore kmers with overall probability of correctness below this.
minprobmain=t       (mpm) Use minprob for the primary kmer counts.
threads=X           Spawn X hashing threads (default is number of logical processors).
rcomp=t             Store and count each kmer together and its reverse-complement.
coremask=t          All kmer extensions share the same hashcode.
fillfast=t          Speed up kmer extension lookups.

Assembly parameters:
mincountseed=3      (mcs) Minimum kmer count to seed a new contig or begin extension.
mincountextend=2    (mce) Minimum kmer count continue extension of a read or contig.
                    It is recommended that mce=1 for low-depth metagenomes.
mincountretain=0    (mincr) Discard kmers with count below this.
maxcountretain=INF  (maxcr) Discard kmers with count above this.
branchmult1=20      (bm1) Min ratio of 1st to 2nd-greatest path depth at high depth.
branchmult2=3       (bm2) Min ratio of 1st to 2nd-greatest path depth at low depth.
branchlower=3       (blc) Max value of 2nd-greatest path depth to be considered low.
minextension=2      (mine) Do not keep contigs that did not extend at least this much.
mincontig=auto      (minc) Do not write contigs shorter than this.
mincoverage=1       (mincov) Do not write contigs with average coverage below this.
trimends=0          (trim) Trim contig ends by this much.  Trimming by K/2 
                    may yield more accurate genome size estimation.
contigpasses=16     Build contigs with decreasing seed depth for this many iterations.
contigpassmult=1.7  Ratio between seed depth of two iterations.
ownership=auto      For concurrency; do not touch.
processcontigs=f    Explore the contig connectivity graph. (partially implemented)

Processing modes:
mode=contig         contig: Make contigs from kmers.
                    extend: Extend sequences to be longer, and optionally
                            perform error correction.
                    correct: Error correct only.
                    insert: Measure insert sizes.
                    discard: Discard low-depth reads, without error correction.

Extension parameters:
extendleft=100      (el) Extend to the left by at most this many bases.
extendright=100     (er) Extend to the right by at most this many bases.
ibb=t               (ignorebackbranches) Do not stop at backward branches.
extendrollback=3    Trim a random number of bases, up to this many, on reads
                    that extend only partially.  This prevents the creation
                    of sharp coverage discontinuities at branches.

Error-correction parameters:
ecc=f               Error correct via kmer counts.
reassemble=t        If ecc is enabled, use the reassemble algorithm.
pincer=f            If ecc is enabled, use the pincer algorithm.
tail=f              If ecc is enabled, use the tail algorithm.
eccfull=f           If ecc is enabled, use tail over the entire read.
aggressive=f        (aecc) Use aggressive error correction settings.
                    Overrides some other flags like errormult1 and deadzone.
conservative=f      (cecc) Use conservative error correction settings.
                    Overrides some other flags like errormult1 and deadzone.
rollback=t          Undo changes to reads that have lower coverage for
                    any kmer after correction.
markbadbases=0      (mbb) Any base fully covered by kmers with count below 
                    this will have its quality reduced.
markdeltaonly=t     (mdo) Only mark bad bases adjacent to good bases.
meo=t               (markerrorreadsonly) Only mark bad bases in reads 
                    containing errors.
markquality=0       (mq) Set quality scores for marked bases to this.
                    A level of 0 will also convert the base to an N.
errormult1=16       (em1) Min ratio between kmer depths to call an error.
errormult2=2.6      (em2) Alternate ratio between low-depth kmers.
errorlowerconst=3   (elc) Use mult2 when the lower kmer is at most this deep.
mincountcorrect=3   (mcc) Don't correct to kmers with count under this.
pathsimilarityfraction=0.45(psf) Max difference ratio considered similar.
                           Controls whether a path appears to be continuous.
pathsimilarityconstant=3   (psc) Absolute differences below this are ignored.
errorextensionreassemble=5 (eer) Verify this many kmers before the error as
                           having similar depth, for reassemble.
errorextensionpincer=5     (eep) Verify this many additional bases after the
                           error as matching current bases, for pincer.
errorextensiontail=9       (eet) Verify additional bases before and after 
                           the error as matching current bases, for tail.
deadzone=0          (dz) Do not try to correct bases within this distance of
                    read ends.
window=12           (w) Length of window to use in reassemble mode.
windowcount=6       (wc) If more than this many errors are found within a
                    a window, halt correction in that direction.
qualsum=80          (qs) If the sum of the qualities of corrected bases within
                    a window exceeds this, halt correction in that direction.
rbi=t               (requirebidirectional) Require agreement from both 
                    directions when correcting errors in the middle part of 
                    the read using the reassemble algorithm.
errorpath=1         (ep) For debugging purposes.

Junk-removal parameters (to only remove junk, set mode=discard):
tossjunk=f          Remove reads that cannot be used for assembly.
                    This means they have no kmers above depth 1 (2 for paired
                    reads) and the outermost kmers cannot be extended.
                    Pairs are removed only if both reads fail.
tossdepth=-1        Remove reads containing kmers at or below this depth.
                    Pairs are removed if either read fails.
lowdepthfraction=0  (ldf) Require at least this fraction of kmers to be
                    low-depth to discard a read; range 0-1. 0 still
                    requires at least 1 low-depth kmer.
requirebothbad=f    (rbb) Only discard pairs if both reads are low-depth.
tossuncorrectable   (tu) Discard reads containing uncorrectable errors.
                    Requires error-correction to be enabled.

Shaving parameters:
shave=t             Remove dead ends (aka hair).
rinse=t             Remove bubbles.
wash=               Set shave and rinse at the same time.
maxshavedepth=1     (msd) Shave or rinse kmers at most this deep.
exploredist=300     (sed) Quit after exploring this far.
discardlength=150   (sdl) Discard shavings up to this long.
Note: Shave and rinse can produce substantially better assemblies
for low-depth data, but they are very slow for large metagenomes.

Overlap parameters (for overlapping paired-end reads only):
merge=f             Attempt to merge overlapping reads prior to 
                    kmer-counting, and again prior to correction.  Output
                    will still be unmerged pairs.
ecco=f              Error correct via overlap, but do not merge reads.
testmerge=t         Test kmer counts around the read merge junctions.  If
                    it appears that the merge created new errors, undo it.

Java Parameters:
-Xmx                This will be passed to Java to set memory usage, overriding the program's automatic memory detection.
                    -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs.  The max is typically 85% of physical memory.
-eoom               This flag will cause the process to exit if an out-of-memory exception occurs.  Requires Java 8u92+.
-da                 Disable assertions.

Remove dupcates in multifasta file !

LEGE — Thu, 02 Sep 2021 06:48:43 -0500

#Using seqkit for duplicate sequence removal

seqkit rmdup -n seqs.fa -o seqs_without_duplicate.fa

#Awk for duplicate sequence removal

awk '/^>/ { f = !a[$0]++ } f' seqs.fa

Python script to read FASTA and FASTQ file !

LEGE — Thu, 02 Sep 2021 02:01:39 -0500

# !/usr/bin/env python3
 
# -*- coding: utf-8 -*-
 
from pysam import FastxFile
 
 
def read_fasta_q_file(fasta_q_file):
    """Parse FASTA/Q file using `pysam.FastxFile`.
 
    Args:
 
        fasta_q_file (str): Path to FASTA/Q file.
 
    """
    with FastxFile(fasta_q_file) as fh:
        for entry in fh:
            sequence_id = entry.name
            sequence = entry.sequence

Install grabseqs using conda !

LEGE — Wed, 16 Jun 2021 02:34:39 -0500

vik@vik-Lenovo-ideapad-320-15ISK:~/Downloads/setu/setu$ conda install grabseqs -c louiejtaylor -c bioconda -c conda-forge
Collecting package metadata (current_repodata.json): done
Solving environment: done


==> WARNING: A newer version of conda exists. <==
  current version: 4.9.2
  latest version: 4.10.1

Please update conda by running

    $ conda update -n base -c defaults conda



## Package Plan ##

  environment location: /home/vik/anaconda3/envs/vikENV

  added / updated specs:
    - grabseqs


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    _openmp_mutex-4.5          |            1_gnu          22 KB  conda-forge
    beautifulsoup4-4.9.3       |     pyhb0f4dca_0          86 KB  conda-forge
    c-ares-1.17.1              |       h7f98852_1         109 KB  conda-forge
    ca-certificates-2021.5.30  |       ha878542_0         136 KB  conda-forge
    certifi-2021.5.30          |   py37h89c1867_0         141 KB  conda-forge
    cffi-1.14.5                |   py37hc58025e_0         225 KB  conda-forge
    cryptography-3.4.7         |   py37h5d9358c_0         1.1 MB  conda-forge
    cssselect-1.1.0            |             py_0          18 KB  conda-forge
    curl-7.77.0                |       hea6ffbf_0         149 KB  conda-forge
    fake-useragent-0.1.11      |           py37_0          19 KB  louiejtaylor
    grabseqs-0.7.0             |           py37_0          22 KB  louiejtaylor
    hdf5-1.10.6                |nompi_h6a2412b_1114         3.1 MB  conda-forge
    icu-68.1                   |       h58526e2_0        13.0 MB  conda-forge
    krb5-1.19.1                |       hcc1bbae_0         1.4 MB  conda-forge
    libblas-3.9.0              |       9_openblas          11 KB  conda-forge
    libcblas-3.9.0             |       9_openblas          11 KB  conda-forge
    libcurl-7.77.0             |       h2574ce0_0         334 KB  conda-forge
    libgcc-ng-9.3.0            |      h2828fa1_19         7.8 MB  conda-forge
    libgfortran-ng-9.3.0       |      hff62375_19          22 KB  conda-forge
    libgfortran5-9.3.0         |      hff62375_19         2.0 MB  conda-forge
    libgomp-9.3.0              |      h2828fa1_19         376 KB  conda-forge
    libidn2-2.3.1              |       h7f98852_0          97 KB  conda-forge
    liblapack-3.9.0            |       9_openblas          11 KB  conda-forge
    libopenblas-0.3.15         |pthreads_h8fe5266_1         9.2 MB  conda-forge
    libssh2-1.9.0              |       ha56f1ee_6         226 KB  conda-forge
    libstdcxx-ng-9.3.0         |      h6de172a_19         4.0 MB  conda-forge
    libxml2-2.9.12             |       h72842e0_0         772 KB  conda-forge
    libxslt-1.1.33             |       h15afd5d_2         522 KB  conda-forge
    lxml-4.6.3                 |   py37h77fd288_0         1.5 MB  conda-forge
    ncbi-ngs-sdk-2.11.0        |       hff44eed_0         167 KB  bioconda
    numpy-1.20.3               |   py37h038b26d_1         5.7 MB  conda-forge
    openssl-1.1.1k             |       h7f98852_0         2.1 MB  conda-forge
    ossuuid-1.6.2              |    hf484d3e_1000          56 KB  conda-forge
    pandas-1.2.4               |   py37h219a48f_0        11.8 MB  conda-forge
    parse-1.19.0               |     pyh44b312d_0          22 KB  conda-forge
    perl-xml-libxml-2.0132     |  pl526h7ec2d77_1         260 KB  bioconda
    pigz-2.6                   |       h27826a3_0          87 KB  conda-forge
    pip-21.1.2                 |     pyhd8ed1ab_0         1.1 MB  conda-forge
    pyee-7.0.4                 |     pyh9f0ad1d_0          14 KB  conda-forge
    pyppeteer-0.2.2            |             py_1         104 KB  conda-forge
    pyquery-1.4.3              |     pyhd8ed1ab_0          23 KB  conda-forge
    python-3.7.10              |hffdb5ce_100_cpython        57.3 MB  conda-forge
    pytz-2021.1                |     pyhd8ed1ab_0         239 KB  conda-forge
    readline-8.1               |       h46c0cb4_0         295 KB  conda-forge
    requests_html-0.10.0       |           py37_1          23 KB  louiejtaylor
    six-1.16.0                 |     pyh6c4a22f_0          14 KB  conda-forge
    soupsieve-2.0.1            |             py_1          30 KB  conda-forge
    sqlite-3.35.5              |       h74cdb3f_0         1.4 MB  conda-forge
    sra-tools-2.11.0           | pl5262h314213e_0        64.5 MB  bioconda
    tqdm-4.61.1                |     pyhd8ed1ab_0          79 KB  conda-forge
    urllib3-1.26.5             |     pyhd8ed1ab_0          99 KB  conda-forge
    w3lib-1.22.0               |     pyh9f0ad1d_0          21 KB  conda-forge
    websockets-8.1             |   py37h5e8e339_3          90 KB  conda-forge
    ------------------------------------------------------------
                                           Total:       191.9 MB

The following NEW packages will be INSTALLED:

  _libgcc_mutex      conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge
  _openmp_mutex      conda-forge/linux-64::_openmp_mutex-4.5-1_gnu
  appdirs            conda-forge/noarch::appdirs-1.4.4-pyh9f0ad1d_0
  beautifulsoup4     conda-forge/noarch::beautifulsoup4-4.9.3-pyhb0f4dca_0
  brotlipy           conda-forge/linux-64::brotlipy-0.7.0-py37h5e8e339_1001
  c-ares             conda-forge/linux-64::c-ares-1.17.1-h7f98852_1
  ca-certificates    conda-forge/linux-64::ca-certificates-2021.5.30-ha878542_0
  certifi            conda-forge/linux-64::certifi-2021.5.30-py37h89c1867_0
  cffi               conda-forge/linux-64::cffi-1.14.5-py37hc58025e_0
  chardet            conda-forge/linux-64::chardet-4.0.0-py37h89c1867_1
  cryptography       conda-forge/linux-64::cryptography-3.4.7-py37h5d9358c_0
  cssselect          conda-forge/noarch::cssselect-1.1.0-py_0
  curl               conda-forge/linux-64::curl-7.77.0-hea6ffbf_0
  fake-useragent     louiejtaylor/linux-64::fake-useragent-0.1.11-py37_0
  gettext            conda-forge/linux-64::gettext-0.19.8.1-h0b5b191_1005
  grabseqs           louiejtaylor/linux-64::grabseqs-0.7.0-py37_0
  hdf5               conda-forge/linux-64::hdf5-1.10.6-nompi_h6a2412b_1114
  icu                conda-forge/linux-64::icu-68.1-h58526e2_0
  idna               conda-forge/noarch::idna-2.10-pyh9f0ad1d_0
  krb5               conda-forge/linux-64::krb5-1.19.1-hcc1bbae_0
  ld_impl_linux-64   conda-forge/linux-64::ld_impl_linux-64-2.35.1-hea4e1c9_2
  libblas            conda-forge/linux-64::libblas-3.9.0-9_openblas
  libcblas           conda-forge/linux-64::libcblas-3.9.0-9_openblas
  libcurl            conda-forge/linux-64::libcurl-7.77.0-h2574ce0_0
  libedit            conda-forge/linux-64::libedit-3.1.20191231-he28a2e2_2
  libev              conda-forge/linux-64::libev-4.33-h516909a_1
  libffi             conda-forge/linux-64::libffi-3.3-h58526e2_2
  libgcc-ng          conda-forge/linux-64::libgcc-ng-9.3.0-h2828fa1_19
  libgfortran-ng     conda-forge/linux-64::libgfortran-ng-9.3.0-hff62375_19
  libgfortran5       conda-forge/linux-64::libgfortran5-9.3.0-hff62375_19
  libgomp            conda-forge/linux-64::libgomp-9.3.0-h2828fa1_19
  libiconv           conda-forge/linux-64::libiconv-1.16-h516909a_0
  libidn2            conda-forge/linux-64::libidn2-2.3.1-h7f98852_0
  liblapack          conda-forge/linux-64::liblapack-3.9.0-9_openblas
  libnghttp2         conda-forge/linux-64::libnghttp2-1.43.0-h812cca2_0
  libopenblas        conda-forge/linux-64::libopenblas-0.3.15-pthreads_h8fe5266_1
  libssh2            conda-forge/linux-64::libssh2-1.9.0-ha56f1ee_6
  libstdcxx-ng       conda-forge/linux-64::libstdcxx-ng-9.3.0-h6de172a_19
  libunistring       conda-forge/linux-64::libunistring-0.9.10-h14c3975_0
  libxml2            conda-forge/linux-64::libxml2-2.9.12-h72842e0_0
  libxslt            conda-forge/linux-64::libxslt-1.1.33-h15afd5d_2
  lxml               conda-forge/linux-64::lxml-4.6.3-py37h77fd288_0
  ncbi-ngs-sdk       bioconda/linux-64::ncbi-ngs-sdk-2.11.0-hff44eed_0
  ncurses            conda-forge/linux-64::ncurses-6.2-h58526e2_4
  numpy              conda-forge/linux-64::numpy-1.20.3-py37h038b26d_1
  openssl            conda-forge/linux-64::openssl-1.1.1k-h7f98852_0
  ossuuid            conda-forge/linux-64::ossuuid-1.6.2-hf484d3e_1000
  pandas             conda-forge/linux-64::pandas-1.2.4-py37h219a48f_0
  parse              conda-forge/noarch::parse-1.19.0-pyh44b312d_0
  perl               conda-forge/linux-64::perl-5.26.2-h36c2ea0_1008
  perl-app-cpanminus bioconda/linux-64::perl-app-cpanminus-1.7044-pl526_1
  perl-business-isbn bioconda/linux-64::perl-business-isbn-3.004-pl526_0
  perl-business-isb~ bioconda/linux-64::perl-business-isbn-data-20140910.003-pl526_0
  perl-carp          bioconda/linux-64::perl-carp-1.38-pl526_3
  perl-constant      bioconda/linux-64::perl-constant-1.33-pl526_1
  perl-data-dumper   bioconda/linux-64::perl-data-dumper-2.173-pl526_0
  perl-encode        bioconda/linux-64::perl-encode-2.88-pl526_1
  perl-exporter      bioconda/linux-64::perl-exporter-5.72-pl526_1
  perl-extutils-mak~ bioconda/linux-64::perl-extutils-makemaker-7.36-pl526_1
  perl-file-path     bioconda/linux-64::perl-file-path-2.16-pl526_0
  perl-file-temp     bioconda/linux-64::perl-file-temp-0.2304-pl526_2
  perl-mime-base64   bioconda/linux-64::perl-mime-base64-3.15-pl526_1
  perl-parent        bioconda/linux-64::perl-parent-0.236-pl526_1
  perl-uri           bioconda/linux-64::perl-uri-1.76-pl526_0
  perl-xml-libxml    bioconda/linux-64::perl-xml-libxml-2.0132-pl526h7ec2d77_1
  perl-xml-namespac~ bioconda/linux-64::perl-xml-namespacesupport-1.12-pl526_0
  perl-xml-sax       bioconda/noarch::perl-xml-sax-1.02-pl526_0
  perl-xml-sax-base  bioconda/linux-64::perl-xml-sax-base-1.09-pl526_0
  perl-xsloader      bioconda/linux-64::perl-xsloader-0.24-pl526_0
  pigz               conda-forge/linux-64::pigz-2.6-h27826a3_0
  pip                conda-forge/noarch::pip-21.1.2-pyhd8ed1ab_0
  pycparser          conda-forge/noarch::pycparser-2.20-pyh9f0ad1d_2
  pyee               conda-forge/noarch::pyee-7.0.4-pyh9f0ad1d_0
  pyopenssl          conda-forge/noarch::pyopenssl-20.0.1-pyhd8ed1ab_0
  pyppeteer          conda-forge/noarch::pyppeteer-0.2.2-py_1
  pyquery            conda-forge/noarch::pyquery-1.4.3-pyhd8ed1ab_0
  pysocks            conda-forge/linux-64::pysocks-1.7.1-py37h89c1867_3
  python             conda-forge/linux-64::python-3.7.10-hffdb5ce_100_cpython
  python-dateutil    conda-forge/noarch::python-dateutil-2.8.1-py_0
  python_abi         conda-forge/linux-64::python_abi-3.7-1_cp37m
  pytz               conda-forge/noarch::pytz-2021.1-pyhd8ed1ab_0
  readline           conda-forge/linux-64::readline-8.1-h46c0cb4_0
  requests           conda-forge/noarch::requests-2.25.1-pyhd3deb0d_0
  requests_html      louiejtaylor/linux-64::requests_html-0.10.0-py37_1
  setuptools         conda-forge/linux-64::setuptools-49.6.0-py37h89c1867_3
  six                conda-forge/noarch::six-1.16.0-pyh6c4a22f_0
  soupsieve          conda-forge/noarch::soupsieve-2.0.1-py_1
  sqlite             conda-forge/linux-64::sqlite-3.35.5-h74cdb3f_0
  sra-tools          bioconda/linux-64::sra-tools-2.11.0-pl5262h314213e_0
  tk                 conda-forge/linux-64::tk-8.6.10-h21135ba_1
  tqdm               conda-forge/noarch::tqdm-4.61.1-pyhd8ed1ab_0
  urllib3            conda-forge/noarch::urllib3-1.26.5-pyhd8ed1ab_0
  w3lib              conda-forge/noarch::w3lib-1.22.0-pyh9f0ad1d_0
  websockets         conda-forge/linux-64::websockets-8.1-py37h5e8e339_3
  wget               conda-forge/linux-64::wget-1.20.1-h22169c7_0
  wheel              conda-forge/noarch::wheel-0.36.2-pyhd3deb0d_0
  xz                 conda-forge/linux-64::xz-5.2.5-h516909a_1
  zlib               conda-forge/linux-64::zlib-1.2.11-h516909a_1010


Proceed ([y]/n)? y


Downloading and Extracting Packages
libblas-3.9.0        | 11 KB     | ################################################################################################################################################################## | 100% 
certifi-2021.5.30    | 141 KB    | ################################################################################################################################################################## | 100% 
pip-21.1.2           | 1.1 MB    | ################################################################################################################################################################## | 100% 
pandas-1.2.4         | 11.8 MB   | ################################################################################################################################################################## | 100% 
requests_html-0.10.0 | 23 KB     | ################################################################################################################################################################## | 100% 
sra-tools-2.11.0     | 64.5 MB   | ################################################################################################################################################################## | 100% 
ossuuid-1.6.2        | 56 KB     | ################################################################################################################################################################## | 100% 
libxml2-2.9.12       | 772 KB    | ################################################################################################################################################################## | 100% 
websockets-8.1       | 90 KB     | ################################################################################################################################################################## | 100% 
lxml-4.6.3           | 1.5 MB    | ################################################################################################################################################################## | 100% 
w3lib-1.22.0         | 21 KB     | ################################################################################################################################################################## | 100% 
python-3.7.10        | 57.3 MB   | ################################################################################################################################################################## | 100% 
openssl-1.1.1k       | 2.1 MB    | ################################################################################################################################################################## | 100% 
libcblas-3.9.0       | 11 KB     | ################################################################################################################################################################## | 100% 
soupsieve-2.0.1      | 30 KB     | ################################################################################################################################################################## | 100% 
urllib3-1.26.5       | 99 KB     | ################################################################################################################################################################## | 100% 
grabseqs-0.7.0       | 22 KB     | ################################################################################################################################################################## | 100% 
libstdcxx-ng-9.3.0   | 4.0 MB    | ################################################################################################################################################################## | 100% 
libopenblas-0.3.15   | 9.2 MB    | ################################################################################################################################################################## | 100% 
pigz-2.6             | 87 KB     | ################################################################################################################################################################## | 100% 
_openmp_mutex-4.5    | 22 KB     | ################################################################################################################################################################## | 100% 
readline-8.1         | 295 KB    | ################################################################################################################################################################## | 100% 
libgcc-ng-9.3.0      | 7.8 MB    | ################################################################################################################################################################## | 100% 
tqdm-4.61.1          | 79 KB     | ################################################################################################################################################################## | 100% 
ca-certificates-2021 | 136 KB    | ################################################################################################################################################################## | 100% 
cssselect-1.1.0      | 18 KB     | ################################################################################################################################################################## | 100% 
hdf5-1.10.6          | 3.1 MB    | ################################################################################################################################################################## | 100% 
libgfortran-ng-9.3.0 | 22 KB     | ################################################################################################################################################################## | 100% 
pyppeteer-0.2.2      | 104 KB    | ################################################################################################################################################################## | 100% 
c-ares-1.17.1        | 109 KB    | ################################################################################################################################################################## | 100% 
pytz-2021.1          | 239 KB    | ################################################################################################################################################################## | 100% 
sqlite-3.35.5        | 1.4 MB    | ################################################################################################################################################################## | 100% 
libxslt-1.1.33       | 522 KB    | ################################################################################################################################################################## | 100% 
numpy-1.20.3         | 5.7 MB    | ################################################################################################################################################################## | 100% 
fake-useragent-0.1.1 | 19 KB     | ################################################################################################################################################################## | 100% 
libidn2-2.3.1        | 97 KB     | ################################################################################################################################################################## | 100% 
parse-1.19.0         | 22 KB     | ################################################################################################################################################################## | 100% 
cryptography-3.4.7   | 1.1 MB    | ################################################################################################################################################################## | 100% 
cffi-1.14.5          | 225 KB    | ################################################################################################################################################################## | 100% 
perl-xml-libxml-2.01 | 260 KB    | ################################################################################################################################################################## | 100% 
icu-68.1             | 13.0 MB   | ################################################################################################################################################################## | 100% 
ncbi-ngs-sdk-2.11.0  | 167 KB    | ################################################################################################################################################################## | 100% 
libcurl-7.77.0       | 334 KB    | ################################################################################################################################################################## | 100% 
libgomp-9.3.0        | 376 KB    | ################################################################################################################################################################## | 100% 
libssh2-1.9.0        | 226 KB    | ################################################################################################################################################################## | 100% 
beautifulsoup4-4.9.3 | 86 KB     | ################################################################################################################################################################## | 100% 
curl-7.77.0          | 149 KB    | ################################################################################################################################################################## | 100% 
six-1.16.0           | 14 KB     | ################################################################################################################################################################## | 100% 
krb5-1.19.1          | 1.4 MB    | ################################################################################################################################################################## | 100% 
liblapack-3.9.0      | 11 KB     | ################################################################################################################################################################## | 100% 
pyee-7.0.4           | 14 KB     | ################################################################################################################################################################## | 100% 
pyquery-1.4.3        | 23 KB     | ################################################################################################################################################################## | 100% 
libgfortran5-9.3.0   | 2.0 MB    | ################################################################################################################################################################## | 100% 
Preparing transaction: done
Verifying transaction: done
Executing transaction: done

Install trimmomatic using Conda !

LEGE — Wed, 16 Jun 2021 02:32:43 -0500

vik@vik-Lenovo-ideapad-320-15ISK:~/Downloads/setu/setu$ conda install -c bioconda trimmomatic
Collecting package metadata (current_repodata.json): done
Solving environment: done


==> WARNING: A newer version of conda exists. <==
  current version: 4.9.2
  latest version: 4.10.1

Please update conda by running

    $ conda update -n base -c defaults conda



## Package Plan ##

  environment location: /home/vik/anaconda3/envs/vikENV

  added / updated specs:
    - trimmomatic


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    certifi-2021.5.30          |   py37h06a4308_0         139 KB
    openjdk-8.0.152            |       h7b6447c_3        57.4 MB
    trimmomatic-0.39           |       hdfd78af_2         144 KB  bioconda
    ------------------------------------------------------------
                                           Total:        57.6 MB

The following NEW packages will be INSTALLED:

  openjdk            pkgs/main/linux-64::openjdk-8.0.152-h7b6447c_3
  trimmomatic        bioconda/noarch::trimmomatic-0.39-hdfd78af_2

The following packages will be SUPERSEDED by a higher-priority channel:

  certifi            conda-forge::certifi-2021.5.30-py37h8~ --> pkgs/main::certifi-2021.5.30-py37h06a4308_0


Proceed ([y]/n)? y


Downloading and Extracting Packages
certifi-2021.5.30    | 139 KB    | ################################################################################################################################################################## | 100% 
openjdk-8.0.152      | 57.4 MB   | ################################################################################################################################################################## | 100% 
trimmomatic-0.39     | 144 KB    | ################################################################################################################################################################## | 100% 
Preparing transaction: done
Verifying transaction: done
Executing transaction: done

Install R in Linux !

LEGE — Wed, 16 Jun 2021 02:30:47 -0500

vik@vik-Lenovo-ideapad-320-15ISK:~/Downloads/setu/setu$ sudo apt install r-base-core
[sudo] password for vik:     
Reading package lists... Done
Building dependency tree       
Reading state information... Done
The following additional packages will be installed:
  autoconf automake autopoint autotools-dev build-essential bzip2-doc cdbs debhelper dh-autoreconf dh-strip-nondeterminism dh-translations dpkg-dev fakeroot g++ g++-7 gcc gcc-7 gfortran gfortran-7
  gir1.2-harfbuzz-0.0 icu-devtools intltool jq libalgorithm-merge-perl libarchive-cpio-perl libasan4 libatomic1 libblas-dev libblas3 libbz2-dev libc-dev-bin libc6-dev libcc1-0 libcilkrts5 libfakeroot
  libfile-stripnondeterminism-perl libfile-which-perl libgcc-7-dev libgfortran-7-dev libglib2.0-dev libglib2.0-dev-bin libgraphite2-dev libharfbuzz-dev libharfbuzz-gobject0 libicu-dev libicu-le-hb-dev
  libicu-le-hb0 libiculx60 libitm1 libjpeg-dev libjpeg-turbo8-dev libjpeg8-dev libjq1 liblapack-dev liblapack3 liblsan0 libltdl-dev liblzma-dev libmail-sendmail-perl libmpx2 libncurses5-dev libonig4
  libpcre16-3 libpcre3-dev libpcre32-3 libpcrecpp0v5 libpng-dev libpng-tools libreadline-dev libstdc++-7-dev libsys-hostname-long-perl libtcl8.6 libtinfo-dev libtk8.6 libtool libtsan0 libubsan0
  linux-libc-dev m4 manpages-dev pkg-config po-debconf python3-distutils python3-lib2to3 python3-scour r-base-dev r-cran-boot r-cran-class r-cran-cluster r-cran-codetools r-cran-foreign r-cran-kernsmooth
  r-cran-lattice r-cran-mass r-cran-matrix r-cran-mgcv r-cran-nlme r-cran-nnet r-cran-rpart r-cran-spatial r-cran-survival r-doc-html r-recommended scour zlib1g-dev
Suggested packages:
  autoconf-archive gnu-standards autoconf-doc devscripts dh-make dwz debian-keyring g++-multilib g++-7-multilib gcc-7-doc libstdc++6-7-dbg gcc-multilib flex bison gdb gcc-doc gcc-7-multilib gcc-7-locales
  libgcc1-dbg libgomp1-dbg libitm1-dbg libatomic1-dbg libasan4-dbg liblsan0-dbg libtsan0-dbg libubsan0-dbg libcilkrts5-dbg libmpx2-dbg libquadmath0-dbg gfortran-multilib gfortran-doc gfortran-7-multilib
  gfortran-7-doc libgfortran4-dbg libcoarrays-dev liblapack-doc glibc-doc libglib2.0-doc libgraphite2-utils icu-doc libtool-doc liblzma-doc ncurses-doc readline-doc libstdc++-7-doc tcl8.6 tk8.6 gcj-jdk
  m4-doc libmail-box-perl ess r-doc-info | r-doc-pdf r-mathlib r-base-html texlive-base texlive-latex-base texlive-generic-recommended texlive-fonts-recommended texlive-fonts-extra texlive-extra-utils
  texlive-latex-recommended texlive-latex-extra texinfo gir1.2-rsvg-2.0
The following NEW packages will be installed:
  autoconf automake autopoint autotools-dev build-essential bzip2-doc cdbs debhelper dh-autoreconf dh-strip-nondeterminism dh-translations dpkg-dev fakeroot g++ g++-7 gcc gcc-7 gfortran gfortran-7
  gir1.2-harfbuzz-0.0 icu-devtools intltool jq libalgorithm-merge-perl libarchive-cpio-perl libasan4 libatomic1 libblas-dev libblas3 libbz2-dev libc-dev-bin libc6-dev libcc1-0 libcilkrts5 libfakeroot
  libfile-stripnondeterminism-perl libfile-which-perl libgcc-7-dev libgfortran-7-dev libglib2.0-dev libglib2.0-dev-bin libgraphite2-dev libharfbuzz-dev libharfbuzz-gobject0 libicu-dev libicu-le-hb-dev
  libicu-le-hb0 libiculx60 libitm1 libjpeg-dev libjpeg-turbo8-dev libjpeg8-dev libjq1 liblapack-dev liblapack3 liblsan0 libltdl-dev liblzma-dev libmail-sendmail-perl libmpx2 libncurses5-dev libonig4
  libpcre16-3 libpcre3-dev libpcre32-3 libpcrecpp0v5 libpng-dev libpng-tools libreadline-dev libstdc++-7-dev libsys-hostname-long-perl libtcl8.6 libtinfo-dev libtk8.6 libtool libtsan0 libubsan0
  linux-libc-dev m4 manpages-dev pkg-config po-debconf python3-distutils python3-lib2to3 python3-scour r-base-core r-base-dev r-cran-boot r-cran-class r-cran-cluster r-cran-codetools r-cran-foreign
  r-cran-kernsmooth r-cran-lattice r-cran-mass r-cran-matrix r-cran-mgcv r-cran-nlme r-cran-nnet r-cran-rpart r-cran-spatial r-cran-survival r-doc-html r-recommended scour zlib1g-dev
0 upgraded, 106 newly installed, 0 to remove and 0 not upgraded.
Need to get 104 MB of archives.
After this operation, 315 MB of additional disk space will be used.
Do you want to continue? [Y/n] y
Get:1 http://in.archive.ubuntu.com/ubuntu bionic/main amd64 m4 amd64 1.4.18-1 [197 kB]
Get:2 http://in.archive.ubuntu.com/ubuntu bionic/main amd64 autoconf all 2.69-11 [322 kB]
Get:3 http://in.archive.ubuntu.com/ubuntu bionic/main amd64 autotools-dev all 20180224.1 [39.6 kB]
Get:4 http://in.archive.ubuntu.com/ubuntu bionic/main amd64 automake all 1:1.15.1-3ubuntu2 [509 kB]
Get:5 http://in.archive.ubuntu.com/ubuntu bionic-updates/main amd64 autopoint all 0.19.8.1-6ubuntu0.3 [426 kB]
Get:6 http://in.archive.ubuntu.com/ubuntu bionic-updates/main amd64 libc-dev-bin amd64 2.27-3ubuntu1.4 [71.8 kB]
Get:7 http://in.archive.ubuntu.com/ubuntu bionic-updates/main amd64 linux-libc-dev amd64 4.15.0-144.148 [1,003 kB]
Get:8 http://in.archive.ubuntu.com/ubuntu bionic-updates/main amd64 libc6-dev amd64 2.27-3ubuntu1.4 [2,585 kB]
Get:9 http://in.archive.ubuntu.com/ubuntu bionic-updates/main amd64 libcc1-0 amd64 8.4.0-1ubuntu1~18.04 [39.4 kB]
Get:10 http://in.archive.ubuntu.com/ubuntu bionic-updates/main amd64 libitm1 amd64 8.4.0-1ubuntu1~18.04 [27.9 kB]
Get:11 http://in.archive.ubuntu.com/ubuntu bionic-updates/main amd64 libatomic1 amd64 8.4.0-1ubuntu1~18.04 [9,192 B]
Get:12 http://in.archive.ubuntu.com/ubuntu bionic-updates/main amd64 libasan4 amd64 7.5.0-3ubuntu1~18.04 [358 kB]
Get:13 http://in.archive.ubuntu.com/ubuntu bionic-updates/main amd64 liblsan0 amd64 8.4.0-1ubuntu1~18.04 [133 kB]
Get:14 http://in.archive.ubuntu.com/ubuntu bionic-updates/main amd64 libtsan0 amd64 8.4.0-1ubuntu1~18.04 [288 kB]
Get:15 http://in.archive.ubuntu.com/ubuntu bionic-updates/main amd64 libubsan0 amd64 7.5.0-3ubuntu1~18.04 [126 kB]
Get:16 http://in.archive.ubuntu.com/ubuntu bionic-updates/main amd64 libcilkrts5 amd64 7.5.0-3ubuntu1~18.04 [42.5 kB]
Get:17 http://in.archive.ubuntu.com/ubuntu bionic-updates/main amd64 libmpx2 amd64 8.4.0-1ubuntu1~18.04 [11.6 kB]
Get:18 http://in.archive.ubuntu.com/ubuntu bionic-updates/main amd64 libgcc-7-dev amd64 7.5.0-3ubuntu1~18.04 [2,378 kB]
Get:19 http://in.archive.ubuntu.com/ubuntu bionic-updates/main amd64 gcc-7 amd64 7.5.0-3ubuntu1~18.04 [9,381 kB]
Get:20 http://in.archive.ubuntu.com/ubuntu bionic-updates/main amd64 gcc amd64 4:7.4.0-1ubuntu2.3 [5,184 B]                                                                                                 
Get:21 http://in.archive.ubuntu.com/ubuntu bionic-updates/main amd64 libstdc++-7-dev amd64 7.5.0-3ubuntu1~18.04 [1,471 kB]                                                                                  
Get:22 http://in.archive.ubuntu.com/ubuntu bionic-updates/main amd64 g++-7 amd64 7.5.0-3ubuntu1~18.04 [9,697 kB]                                                                                            
Get:23 http://in.archive.ubuntu.com/ubuntu bionic-updates/main amd64 g++ amd64 4:7.4.0-1ubuntu2.3 [1,568 B]                                                                                                 
Get:24 http://in.archive.ubuntu.com/ubuntu bionic-updates/main amd64 dpkg-dev all 1.19.0.5ubuntu2.3 [607 kB]                                                                                                
Get:25 http://in.archive.ubuntu.com/ubuntu bionic/main amd64 build-essential amd64 12.4ubuntu1 [4,758 B]                                                                                                    
Get:26 http://in.archive.ubuntu.com/ubuntu bionic-updates/main amd64 bzip2-doc all 1.0.6-8.1ubuntu0.2 [294 kB]                                                                                              
Get:27 http://in.archive.ubuntu.com/ubuntu bionic/main amd64 libtool all 2.4.6-2 [194 kB]                                                                                                                   
Get:28 http://in.archive.ubuntu.com/ubuntu bionic/main amd64 dh-autoreconf all 17 [15.8 kB]                                                                                                                 
Get:29 http://in.archive.ubuntu.com/ubuntu bionic/main amd64 libfile-stripnondeterminism-perl all 0.040-1.1~build1 [13.8 kB]                                                                                
Get:30 http://in.archive.ubuntu.com/ubuntu bionic/main amd64 dh-strip-nondeterminism all 0.040-1.1~build1 [5,208 B]                                                                                         
Get:31 http://in.archive.ubuntu.com/ubuntu bionic/main amd64 po-debconf all 1.0.20 [232 kB]                                                                                                                 
Get:32 http://in.archive.ubuntu.com/ubuntu bionic-updates/main amd64 debhelper all 11.1.6ubuntu2 [902 kB]                                                                                                   
Get:33 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 intltool all 0.51.0-5ubuntu1 [44.6 kB]                                                                                                     
Get:34 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 libonig4 amd64 6.7.0-1 [119 kB]                                                                                                            
Get:35 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 libjq1 amd64 1.5+dfsg-2 [111 kB]                                                                                                           
Get:36 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 jq amd64 1.5+dfsg-2 [45.6 kB]                                                                                                              
Get:37 http://in.archive.ubuntu.com/ubuntu bionic/main amd64 libfile-which-perl all 1.21-1 [11.8 kB]                                                                                                        
Get:38 http://in.archive.ubuntu.com/ubuntu bionic-updates/universe amd64 dh-translations all 138.18.04.1 [24.6 kB]                                                                                          
Get:39 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 python3-scour all 0.36-2 [44.8 kB]                                                                                                         
Get:40 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 scour all 0.36-2 [7,372 B]                                                                                                                 
Get:41 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 cdbs all 0.4.156ubuntu4 [45.4 kB]                                                                                                          
Get:42 http://in.archive.ubuntu.com/ubuntu bionic/main amd64 libfakeroot amd64 1.22-2ubuntu1 [25.9 kB]                                                                                                      
Get:43 http://in.archive.ubuntu.com/ubuntu bionic/main amd64 fakeroot amd64 1.22-2ubuntu1 [62.3 kB]                                                                                                         
Get:44 http://in.archive.ubuntu.com/ubuntu bionic-updates/main amd64 libgfortran-7-dev amd64 7.5.0-3ubuntu1~18.04 [530 kB]                                                                                  
Get:45 http://in.archive.ubuntu.com/ubuntu bionic-updates/main amd64 gfortran-7 amd64 7.5.0-3ubuntu1~18.04 [9,014 kB]                                                                                       
Get:46 http://in.archive.ubuntu.com/ubuntu bionic-updates/main amd64 gfortran amd64 4:7.4.0-1ubuntu2.3 [1,356 B]                                                                                            
Get:47 http://in.archive.ubuntu.com/ubuntu bionic/main amd64 gir1.2-harfbuzz-0.0 amd64 1.7.2-1ubuntu1 [18.6 kB]                                                                                             
Get:48 http://in.archive.ubuntu.com/ubuntu bionic-updates/main amd64 icu-devtools amd64 60.2-3ubuntu3.1 [179 kB]                                                                                            
Get:49 http://in.archive.ubuntu.com/ubuntu bionic/main amd64 libalgorithm-merge-perl all 0.08-3 [12.0 kB]                                                                                                   
Get:50 http://in.archive.ubuntu.com/ubuntu bionic/main amd64 libarchive-cpio-perl all 0.10-1 [9,644 B]                                                                                                      
Get:51 http://in.archive.ubuntu.com/ubuntu bionic/main amd64 libblas3 amd64 3.7.1-4ubuntu1 [140 kB]                                                                                                         
Get:52 http://in.archive.ubuntu.com/ubuntu bionic/main amd64 libblas-dev amd64 3.7.1-4ubuntu1 [143 kB]                                                                                                      
Get:53 http://in.archive.ubuntu.com/ubuntu bionic-updates/main amd64 libbz2-dev amd64 1.0.6-8.1ubuntu0.2 [30.0 kB]                                                                                          
Get:54 http://in.archive.ubuntu.com/ubuntu bionic-updates/main amd64 python3-lib2to3 all 3.6.9-1~18.04 [77.4 kB]                                                                                            
Get:55 http://in.archive.ubuntu.com/ubuntu bionic-updates/main amd64 python3-distutils all 3.6.9-1~18.04 [144 kB]                                                                                           
Get:56 http://in.archive.ubuntu.com/ubuntu bionic-updates/main amd64 libglib2.0-dev-bin amd64 2.56.4-0ubuntu0.18.04.8 [102 kB]                                                                              
Get:57 http://in.archive.ubuntu.com/ubuntu bionic/main amd64 libpcre16-3 amd64 2:8.39-9 [147 kB]                                                                                                            
Get:58 http://in.archive.ubuntu.com/ubuntu bionic/main amd64 libpcre32-3 amd64 2:8.39-9 [138 kB]                                                                                                            
Get:59 http://in.archive.ubuntu.com/ubuntu bionic/main amd64 libpcrecpp0v5 amd64 2:8.39-9 [15.3 kB]                                                                                                         
Get:60 http://in.archive.ubuntu.com/ubuntu bionic/main amd64 libpcre3-dev amd64 2:8.39-9 [537 kB]                                                                                                           
Get:61 http://in.archive.ubuntu.com/ubuntu bionic/main amd64 pkg-config amd64 0.29.1-0ubuntu2 [45.0 kB]                                                                                                     
Get:62 http://in.archive.ubuntu.com/ubuntu bionic/main amd64 zlib1g-dev amd64 1:1.2.11.dfsg-0ubuntu2 [176 kB]                                                                                               
Get:63 http://in.archive.ubuntu.com/ubuntu bionic-updates/main amd64 libglib2.0-dev amd64 2.56.4-0ubuntu0.18.04.8 [1,386 kB]                                                                                
Get:64 http://in.archive.ubuntu.com/ubuntu bionic/main amd64 libgraphite2-dev amd64 1.3.11-2 [14.5 kB]                                                                                                      
Get:65 http://in.archive.ubuntu.com/ubuntu bionic/main amd64 libharfbuzz-gobject0 amd64 1.7.2-1ubuntu1 [13.4 kB]                                                                                            
Get:66 http://in.archive.ubuntu.com/ubuntu bionic/main amd64 libicu-le-hb0 amd64 1.0.3+git161113-4 [14.3 kB]                                                                                                
Get:67 http://in.archive.ubuntu.com/ubuntu bionic-updates/main amd64 libiculx60 amd64 60.2-3ubuntu3.1 [19.0 kB]                                                                                             
Get:68 http://in.archive.ubuntu.com/ubuntu bionic/main amd64 libicu-le-hb-dev amd64 1.0.3+git161113-4 [29.5 kB]                                                                                             
Get:69 http://in.archive.ubuntu.com/ubuntu bionic-updates/main amd64 libicu-dev amd64 60.2-3ubuntu3.1 [8,889 kB]                                                                                            
Get:70 http://in.archive.ubuntu.com/ubuntu bionic/main amd64 libharfbuzz-dev amd64 1.7.2-1ubuntu1 [302 kB]                                                                                                  
Get:71 http://in.archive.ubuntu.com/ubuntu bionic-updates/main amd64 libjpeg-turbo8-dev amd64 1.5.2-0ubuntu5.18.04.4 [225 kB]                                                                               
Get:72 http://in.archive.ubuntu.com/ubuntu bionic/main amd64 libjpeg8-dev amd64 8c-2ubuntu8 [1,552 B]                                                                                                       
Get:73 http://in.archive.ubuntu.com/ubuntu bionic/main amd64 libjpeg-dev amd64 8c-2ubuntu8 [1,546 B]                                                                                                        
Get:74 http://in.archive.ubuntu.com/ubuntu bionic/main amd64 liblapack3 amd64 3.7.1-4ubuntu1 [2,112 kB]                                                                                                     
Get:75 http://in.archive.ubuntu.com/ubuntu bionic/main amd64 liblapack-dev amd64 3.7.1-4ubuntu1 [2,140 kB]                                                                                                  
Get:76 http://in.archive.ubuntu.com/ubuntu bionic/main amd64 libltdl-dev amd64 2.4.6-2 [162 kB]                                                                                                             
Get:77 http://in.archive.ubuntu.com/ubuntu bionic/main amd64 libsys-hostname-long-perl all 1.5-1 [11.7 kB]                                                                                                  
Get:78 http://in.archive.ubuntu.com/ubuntu bionic/main amd64 libmail-sendmail-perl all 0.80-1 [22.6 kB]                                                                                                     
Get:79 http://in.archive.ubuntu.com/ubuntu bionic-updates/main amd64 libtinfo-dev amd64 6.1-1ubuntu1.18.04 [81.3 kB]                                                                                        
Get:80 http://in.archive.ubuntu.com/ubuntu bionic-updates/main amd64 libncurses5-dev amd64 6.1-1ubuntu1.18.04 [174 kB]                                                                                      
Get:81 http://in.archive.ubuntu.com/ubuntu bionic-updates/main amd64 libpng-dev amd64 1.6.34-1ubuntu0.18.04.2 [177 kB]                                                                                      
Get:82 http://in.archive.ubuntu.com/ubuntu bionic-updates/main amd64 libpng-tools amd64 1.6.34-1ubuntu0.18.04.2 [25.6 kB]                                                                                   
Get:83 http://in.archive.ubuntu.com/ubuntu bionic/main amd64 libreadline-dev amd64 7.0-3 [133 kB]                                                                                                           
Get:84 http://in.archive.ubuntu.com/ubuntu bionic/main amd64 libtcl8.6 amd64 8.6.8+dfsg-3 [881 kB]                                                                                                          
Get:85 http://in.archive.ubuntu.com/ubuntu bionic/main amd64 libtk8.6 amd64 8.6.8-4 [693 kB]                                                                                                                
Get:86 http://in.archive.ubuntu.com/ubuntu bionic/main amd64 manpages-dev all 4.15-1 [2,217 kB]                                                                                                             
Get:87 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 r-base-core amd64 3.4.4-1ubuntu1 [23.2 MB]                                                                                                 
Get:88 http://in.archive.ubuntu.com/ubuntu bionic/main amd64 liblzma-dev amd64 5.2.2-1.3 [145 kB]                                                                                                           
Get:89 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 r-base-dev all 3.4.4-1ubuntu1 [4,532 B]                                                                                                    
Get:90 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-boot all 1.3-20-1.1 [613 kB]                                                                                                        
Get:91 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-mass amd64 7.3-49-1 [1,100 kB]                                                                                                      
Get:92 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-class amd64 7.3-14-2build1 [85.9 kB]                                                                                                
Get:93 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-cluster amd64 2.0.6-2build1 [502 kB]                                                                                                
Get:94 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-codetools all 0.2-15-1.1 [46.1 kB]                                                                                                  
Get:95 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-foreign amd64 0.8.69-1build1 [228 kB]                                                                                               
Get:96 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-kernsmooth amd64 2.23-15-3build1 [89.4 kB]                                                                                          
Get:97 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-lattice amd64 0.20-35-1build1 [713 kB]                                                                                              
Get:98 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-matrix amd64 1.2-12-1 [2,334 kB]                                                                                                    
Get:99 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-nlme amd64 3.1.131-3build1 [2,186 kB]                                                                                               
Get:100 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-mgcv amd64 1.8-23-1 [2,496 kB]                                                                                                     
Get:101 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-nnet amd64 7.3-12-2build1 [110 kB]                                                                                                 
Get:102 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-survival amd64 2.41-3-2build1 [5,156 kB]                                                                                           
Get:103 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-rpart amd64 4.1-13-1 [878 kB]                                                                                                      
Get:104 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 r-cran-spatial amd64 7.3-11-2build1 [127 kB]                                                                                              
Get:105 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 r-doc-html all 3.4.4-1ubuntu1 [527 kB]                                                                                                    
Get:106 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 r-recommended all 3.4.4-1ubuntu1 [2,820 B]                                                                                                
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Install Spades using conda !

LEGE — Wed, 16 Jun 2021 02:28:04 -0500

vik@vik-Lenovo-ideapad-320-15ISK:~/Downloads/setu/setu$ conda install -c bioconda spades 
Collecting package metadata (current_repodata.json): done
Solving environment: done


==> WARNING: A newer version of conda exists. <==
  current version: 4.9.2
  latest version: 4.10.1

Please update conda by running

    $ conda update -n base -c defaults conda



## Package Plan ##

  environment location: /home/vik/anaconda3/envs/vikENV

  added / updated specs:
    - spades


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    spades-3.13.0              |                0        13.7 MB  bioconda
    ------------------------------------------------------------
                                           Total:        13.7 MB

The following NEW packages will be INSTALLED:

  spades             bioconda/linux-64::spades-3.13.0-0


Proceed ([y]/n)? y


Downloading and Extracting Packages
spades-3.13.0        | 13.7 MB   | ################################################################################################################################################################## | 100% 
Preparing transaction: done
Verifying transaction: done
Executing transaction: done