Extract a specific gene contig from multiple assemblies

1)  Copy and paste a gene (for example NDM-1) from a database in text file - NDM-1.fa

2) Create blast DB for NDM gene using following command

$ makeblastdb -in NDM-1.fa -dbtype nucl -out NDM-1.fa.DB -parse_seqids

3) BLAST the assemblies against the NDM gene

$ for d in $(ls */assembly.fasta); do \
sample=`echo $d | sed 's/\/assembly.fasta//g'`; \
echo "$sample"; sed -i "s/>/>"$sample"_/g" $d; \
sed -i 's/ /_/g' $d; \
~/sw/ncbi-blast-2.7.1+/bin/blastn -db NDM-1.fa.DB -query $d -outfmt '6 qseqid sseqid pident nident length mismatch gapopen qstart qend sstart send evalue bitscore qlen slen' -num_threads 4 -out "$sample"_vs_NDM_blastresults.txt; done

This would rename all the contigs in the assembly.fasta with the directory name which holds assembly.fasta

4) cat *.txt | column -t

THY1079 NDM-1_JQ080305_1-813_813 100 813 813 0 0 48157 48969 813 1 0 1502 91643 813
THY1219 NDM-1_JQ080305_1-813_813 100 813 813 0 0 4586 5398 813 1 0 1502 13505 813
THY1250 NDM-1_JQ080305_1-813_813 99.754 811 813 2 0 14408 15220 1 813 0 1491 88353 813
THY1357 NDM-1_JQ080305_1-813_813 100 813 813 0 0 78370 79182 813 1 0 1502 177751 813
THY1440 NDM-1_JQ080305_1-813_813 99.754 811 813 2 0 14408 15220 1 813 0 1491 96544 813
THY1669 NDM-1_JQ080305_1-813_813 100 813 813 0 0 6747 7559 813 1 0 1502 118064 813
THY1758 NDM-1_JQ080305_1-813_813 99.754 811 813 2 0 5708 6520 1 813 0 1491 62334 813
THY1916 NDM-1_JQ080305_1-813_813 100 813 813 0 0 19307 20119 813 1 0 1502 278408 813
THY1940 NDM-1_JQ080305_1-813_813 100 813 813 0 0 3171762 3172574 1 813 0 1502 4879405 813
THY1968 NDM-1_JQ080305_1-813_813 100 813 813 0 0 3173593 3174405 1 813 0 1502 4880726 813
THY285 NDM-1_JQ080305_1-813_813 99.754 811 813 2 0 25547 26359 1 813 0 1491 46161 813
THY337 NDM-1_JQ080305_1-813_813 100 813 813 0 0 57706 58518 1 813 0 1502 88057 813
THY708 NDM-1_JQ080305_1-813_813 100 813 813 0 0 302 1114 1 813 0 1502 14280 813
THY807 NDM-1_JQ080305_1-813_813 99.754 811 813 2 0 2469 3281 1 813 0 1491 5469 813
THY924 NDM-1_JQ080305_1-813_813 99.754 811 813 2 0 36917 37729 1 813 0 1491 75214 813
THY924 NDM-1_JQ080305_1-813_813 99.754 811 813 2 0 20047 20859 813 1 0 1491 70472 813

5) extract the NDM_gene from the assemblies

fgrep -A1 -f <(cat *.txt | cut -f1) <(cat */assembly.fasta | awk '/^>/ {printf("\n%s\n",$0);next; } { printf("%s",$0);}  END {printf("\n");}') >NDM_positive_contigs.fasta

<(cat *.txt | cut -f1) -process substitution operator - gives the list of contig names


cat */assembly.fasta | awk '/^>/ {printf("\n%s\n",$0);next; } { printf("%s",$0);}  END {printf("\n");}' - this woud convert all the multiline fasta to single line fasta

-A1 get the single line after the match

Search for a protein in specific genome database

1) Go to NCBI Blast page and select tblastn

2) Select the protein you want to check, for example, I want to check the following protein is present in the database. Select the protein accession and copy it in the query box.

3) Now search for the protein sequence in Database: Whole-genome shotgun contigs (I selected this because Asian Seabass does not have RefSeq Genome) and organism by typing: Asian Seabass

4)  Blast! If you find the protein sequences in the genome, it will appears in the results. 

Note: It will take time, if you are using proteins to search because BLAST has to translate all the 6 frames and search against the database. For faster check of the presence of the sequences in the database, it is better to do a local NCBI blast.

locate: can not open `/var/lib/mlocate/mlocate.db': Permission denied - Solved!

$ locate unicycler
locate: can not open `/var/lib/mlocate/mlocate.db': Permission denied

Changing the permission solved the issue!

$ sudo chmod -R 755 /var/lib/mlocate/mlocate.db

$ locate unicycler
/home/user/Lab_Doc_Share/Assembly/SA3_Noclean_barcode01_unicycler.log

Installing nanopack

$ pip install nanopack

Collecting nanopack

Collecting nanoplotter>=0.16.5 (from nanopack)

Collecting NanoPlot>=0.20.1 (from nanopack)

Collecting NanoLyse>=0.2.1 (from nanopack)

Collecting NanoFilt>=1.5.2 (from nanopack)

Collecting nanomath>=0.13.3 (from nanopack)

Collecting nanoget>=0.15.0 (from nanopack)

Collecting NanoStat>=0.6.1 (from nanopack)

Collecting numpy (from nanoplotter>=0.16.5->nanopack)

  Using cached https://files.pythonhosted.org/packages/e0/b5/63b79fe426433fa1cd110eb04a94ec0c6967e56e5f57c98caf455a5fb6e2/numpy-1.16.1-cp27-cp27mu-manylinux1_x86_64.whl

Collecting seaborn (from nanoplotter>=0.16.5->nanopack)

Collecting pauvre (from nanoplotter>=0.16.5->nanopack)

Collecting pandas (from nanoplotter>=0.16.5->nanopack)

  Using cached https://files.pythonhosted.org/packages/c5/88/b8659eecde0350d37d5b47c1c2a88f39e6153e5809bcfc48bb7fde6f231b/pandas-0.24.1-cp27-cp27mu-manylinux1_x86_64.whl

Collecting matplotlib>=2.0.0 (from nanoplotter>=0.16.5->nanopack)

  Using cached https://files.pythonhosted.org/packages/59/08/04933377dc4500e3698e93f9113dc3624874e0914f4c85767ecb5b389084/matplotlib-2.2.3-cp27-cp27mu-manylinux1_x86_64.whl

Collecting scipy (from nanoplotter>=0.16.5->nanopack)

  Using cached https://files.pythonhosted.org/packages/81/39/f1457091d0a45a84a2bd7815e2cf6bd45d4fe240728e9ed567cbb17c8abe/scipy-1.2.1-cp27-cp27mu-manylinux1_x86_64.whl

Collecting biopython (from NanoPlot>=0.20.1->nanopack)

  Using cached https://files.pythonhosted.org/packages/19/4e/ac487da685e947c56fafd10b2a04c6a09f0051c2e7665a873263f5e303f2/biopython-1.73-cp27-cp27mu-manylinux1_x86_64.whl

Collecting pysam>0.10.0.0 (from NanoPlot>=0.20.1->nanopack)

  Using cached https://files.pythonhosted.org/packages/0f/bd/f5ab828a9ff45a6ca14d5ea2a3580f720134052db258cd7ef929a4ed1d7a/pysam-0.15.2-cp27-cp27mu-manylinux1_x86_64.whl

Collecting python-dateutil (from NanoPlot>=0.20.1->nanopack)

  Using cached https://files.pythonhosted.org/packages/41/17/c62faccbfbd163c7f57f3844689e3a78bae1f403648a6afb1d0866d87fbb/python_dateutil-2.8.0-py2.py3-none-any.whl

Collecting mappy>=2.2 (from NanoLyse>=0.2.1->nanopack)

Collecting pytz>=2011k (from pandas->nanoplotter>=0.16.5->nanopack)

  Using cached https://files.pythonhosted.org/packages/61/28/1d3920e4d1d50b19bc5d24398a7cd85cc7b9a75a490570d5a30c57622d34/pytz-2018.9-py2.py3-none-any.whl

Collecting cycler>=0.10 (from matplotlib>=2.0.0->nanoplotter>=0.16.5->nanopack)

  Using cached https://files.pythonhosted.org/packages/f7/d2/e07d3ebb2bd7af696440ce7e754c59dd546ffe1bbe732c8ab68b9c834e61/cycler-0.10.0-py2.py3-none-any.whl

Collecting backports.functools-lru-cache (from matplotlib>=2.0.0->nanoplotter>=0.16.5->nanopack)

  Using cached https://files.pythonhosted.org/packages/03/8e/2424c0e65c4a066e28f539364deee49b6451f8fcd4f718fefa50cc3dcf48/backports.functools_lru_cache-1.5-py2.py3-none-any.whl

Collecting subprocess32 (from matplotlib>=2.0.0->nanoplotter>=0.16.5->nanopack)

Collecting kiwisolver>=1.0.1 (from matplotlib>=2.0.0->nanoplotter>=0.16.5->nanopack)

  Using cached https://files.pythonhosted.org/packages/3a/62/a8c9bef3059d55ab38e41fe9cba4fad773bfc04e47290bab84db1c18262e/kiwisolver-1.0.1-cp27-cp27mu-manylinux1_x86_64.whl

Collecting six>=1.10 (from matplotlib>=2.0.0->nanoplotter>=0.16.5->nanopack)

  Using cached https://files.pythonhosted.org/packages/73/fb/00a976f728d0d1fecfe898238ce23f502a721c0ac0ecfedb80e0d88c64e9/six-1.12.0-py2.py3-none-any.whl

Collecting pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 (from matplotlib>=2.0.0->nanoplotter>=0.16.5->nanopack)

  Using cached https://files.pythonhosted.org/packages/de/0a/001be530836743d8be6c2d85069f46fecf84ac6c18c7f5fb8125ee11d854/pyparsing-2.3.1-py2.py3-none-any.whl

Collecting setuptools (from kiwisolver>=1.0.1->matplotlib>=2.0.0->nanoplotter>=0.16.5->nanopack)

  Using cached https://files.pythonhosted.org/packages/d1/6a/4b2fcefd2ea0868810e92d519dacac1ddc64a2e53ba9e3422c3b62b378a6/setuptools-40.8.0-py2.py3-none-any.whl

Installing collected packages: numpy, pytz, six, python-dateutil, pandas, scipy, cycler, backports.functools-lru-cache, subprocess32, setuptools, kiwisolver, pyparsing, matplotlib, seaborn, biopython, pauvre, nanoplotter, pysam, nanomath, nanoget, NanoPlot, mappy, NanoLyse, NanoFilt, NanoStat, nanopack

Successfully installed NanoFilt-2.0.0 NanoLyse-0.5.0 NanoPlot-1.8.1 NanoStat-0.8.0 backports.functools-lru-cache-1.5 biopython-1.73 cycler-0.10.0 kiwisolver-1.0.1 mappy-2.15 matplotlib-2.2.3 nanoget-1.2.0 nanomath-0.15.1 nanopack-0.1.4 nanoplotter-0.28.0 numpy-1.16.1 pandas-0.24.1 pauvre-0.1.86 pyparsing-2.3.1 pysam-0.15.2 python-dateutil-2.8.0 pytz-2018.9 scipy-1.2.1 seaborn-0.9.0 setuptools-40.8.0 six-1.12.0 subprocess32-3.5.3


$ NanoPlot

NanoPlot: command not found


$ pip install nanopack

Collecting nanopack

  Downloading https://files.pythonhosted.org/packages/3b/cc/52bdfaa3fb739d6fc26ac9ec55cd63d7db06d73bf0d7d096b37b7b2839bf/nanopack-0.1.4.tar.gz

Collecting NanoPlot>=0.20.1 (from nanopack)

  Downloading https://files.pythonhosted.org/packages/d6/9e/992d05d1e8a72a3de6dd945a6c2fab64ddae0b95657b3263809a4c125ecb/NanoPlot-1.8.1.tar.gz

Collecting NanoStat>=0.6.1 (from nanopack)

  Downloading https://files.pythonhosted.org/packages/5f/58/6555371d9c6fe42c67e64bcf1a4e2a25d237f086292f696a814c12149a68/NanoStat-0.8.0.tar.gz

Collecting NanoFilt>=1.5.2 (from nanopack)

  Downloading https://files.pythonhosted.org/packages/b9/96/6e9025334a704d64140e8d7fc664c0a11e3e98ba16d109ea12dc6ca2d067/NanoFilt-2.0.0.tar.gz

Collecting NanoLyse>=0.2.1 (from nanopack)

  Downloading https://files.pythonhosted.org/packages/37/ec/3ce7573f77a341040f77de0988594d2229522b8a52384f7a29aecf7082b2/NanoLyse-0.5.0.tar.gz

Collecting nanoget>=0.15.0 (from nanopack)

  Downloading https://files.pythonhosted.org/packages/b0/a4/d925390225969242be5e1ff8e019372a3831b3cd71870164c4c95b243449/nanoget-1.2.0.tar.gz

Collecting nanomath>=0.13.3 (from nanopack)

  Downloading https://files.pythonhosted.org/packages/6d/cd/b6ea00834b31c20de01fdaaea334e87bbba04ec47222f6f17d06a47b06d2/nanomath-0.15.1.tar.gz

Collecting nanoplotter>=0.16.5 (from nanopack)

  Downloading https://files.pythonhosted.org/packages/3e/6c/1e0ec0d9eb36ad6ebca1f9be2a388e620c91279987a15a42ad4b2756cd5f/nanoplotter-0.28.0.tar.gz

Collecting biopython (from NanoPlot>=0.20.1->nanopack)

  Downloading https://files.pythonhosted.org/packages/19/4e/ac487da685e947c56fafd10b2a04c6a09f0051c2e7665a873263f5e303f2/biopython-1.73-cp27-cp27mu-manylinux1_x86_64.whl (2.2MB)

    100% |████████████████████████████████| 2.2MB 1.3MB/s

Collecting pysam>0.10.0.0 (from NanoPlot>=0.20.1->nanopack)

  Downloading https://files.pythonhosted.org/packages/0f/bd/f5ab828a9ff45a6ca14d5ea2a3580f720134052db258cd7ef929a4ed1d7a/pysam-0.15.2-cp27-cp27mu-manylinux1_x86_64.whl (8.9MB)

    100% |████████████████████████████████| 8.9MB 1.5MB/s

Collecting pandas (from NanoPlot>=0.20.1->nanopack)

  Downloading https://files.pythonhosted.org/packages/c5/88/b8659eecde0350d37d5b47c1c2a88f39e6153e5809bcfc48bb7fde6f231b/pandas-0.24.1-cp27-cp27mu-manylinux1_x86_64.whl (10.1MB)

    100% |████████████████████████████████| 10.1MB 3.1MB/s

Collecting numpy (from NanoPlot>=0.20.1->nanopack)

  Downloading https://files.pythonhosted.org/packages/e0/b5/63b79fe426433fa1cd110eb04a94ec0c6967e56e5f57c98caf455a5fb6e2/numpy-1.16.1-cp27-cp27mu-manylinux1_x86_64.whl (17.0MB)

    100% |████████████████████████████████| 17.0MB 2.9MB/s

Collecting scipy (from NanoPlot>=0.20.1->nanopack)

  Downloading https://files.pythonhosted.org/packages/81/39/f1457091d0a45a84a2bd7815e2cf6bd45d4fe240728e9ed567cbb17c8abe/scipy-1.2.1-cp27-cp27mu-manylinux1_x86_64.whl (24.8MB)

    100% |████████████████████████████████| 24.8MB 2.4MB/s

Collecting python-dateutil (from NanoPlot>=0.20.1->nanopack)

  Downloading https://files.pythonhosted.org/packages/41/17/c62faccbfbd163c7f57f3844689e3a78bae1f403648a6afb1d0866d87fbb/python_dateutil-2.8.0-py2.py3-none-any.whl (226kB)

    100% |████████████████████████████████| 235kB 1.4MB/s

Collecting seaborn (from NanoPlot>=0.20.1->nanopack)

  Downloading https://files.pythonhosted.org/packages/7a/bf/04cfcfc9616cedd4b5dd24dfc40395965ea9f50c1db0d3f3e52b050f74a5/seaborn-0.9.0.tar.gz (198kB)

    100% |████████████████████████████████| 204kB 1.8MB/s

Collecting mappy>=2.2 (from NanoLyse>=0.2.1->nanopack)

  Downloading https://files.pythonhosted.org/packages/0d/66/8e1170f36283f45743e3e6e923a513e2386d5df93e935daba27e7e0d2ad6/mappy-2.15.tar.gz (195kB)

    100% |████████████████████████████████| 204kB 2.4MB/s

Collecting matplotlib>=2.0.0 (from nanoplotter>=0.16.5->nanopack)

  Downloading https://files.pythonhosted.org/packages/59/08/04933377dc4500e3698e93f9113dc3624874e0914f4c85767ecb5b389084/matplotlib-2.2.3-cp27-cp27mu-manylinux1_x86_64.whl (12.6MB)

    100% |████████████████████████████████| 12.6MB 2.9MB/s

Collecting pauvre (from nanoplotter>=0.16.5->nanopack)

  Downloading https://files.pythonhosted.org/packages/f0/70/b1a2c106128156d2f234964caee3f900733f81b67df51ffa62591e5bba46/pauvre-0.1.86.tar.gz (40kB)

    100% |████████████████████████████████| 40kB 27.8MB/s

Collecting pytz>=2011k (from pandas->NanoPlot>=0.20.1->nanopack)

  Downloading https://files.pythonhosted.org/packages/61/28/1d3920e4d1d50b19bc5d24398a7cd85cc7b9a75a490570d5a30c57622d34/pytz-2018.9-py2.py3-none-any.whl (510kB)

    100% |████████████████████████████████| 512kB 3.5MB/s

Collecting six>=1.5 (from python-dateutil->NanoPlot>=0.20.1->nanopack)

  Downloading https://files.pythonhosted.org/packages/73/fb/00a976f728d0d1fecfe898238ce23f502a721c0ac0ecfedb80e0d88c64e9/six-1.12.0-py2.py3-none-any.whl

Collecting cycler>=0.10 (from matplotlib>=2.0.0->nanoplotter>=0.16.5->nanopack)

  Downloading https://files.pythonhosted.org/packages/f7/d2/e07d3ebb2bd7af696440ce7e754c59dd546ffe1bbe732c8ab68b9c834e61/cycler-0.10.0-py2.py3-none-any.whl

Collecting backports.functools-lru-cache (from matplotlib>=2.0.0->nanoplotter>=0.16.5->nanopack)

  Downloading https://files.pythonhosted.org/packages/03/8e/2424c0e65c4a066e28f539364deee49b6451f8fcd4f718fefa50cc3dcf48/backports.functools_lru_cache-1.5-py2.py3-none-any.whl

Collecting subprocess32 (from matplotlib>=2.0.0->nanoplotter>=0.16.5->nanopack)

  Downloading https://files.pythonhosted.org/packages/be/2b/beeba583e9877e64db10b52a96915afc0feabf7144dcbf2a0d0ea68bf73d/subprocess32-3.5.3.tar.gz (96kB)

    100% |████████████████████████████████| 102kB 2.6MB/s

Collecting kiwisolver>=1.0.1 (from matplotlib>=2.0.0->nanoplotter>=0.16.5->nanopack)

  Downloading https://files.pythonhosted.org/packages/3a/62/a8c9bef3059d55ab38e41fe9cba4fad773bfc04e47290bab84db1c18262e/kiwisolver-1.0.1-cp27-cp27mu-manylinux1_x86_64.whl (951kB)

    100% |████████████████████████████████| 952kB 3.0MB/s

Collecting pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 (from matplotlib>=2.0.0->nanoplotter>=0.16.5->nanopack)

  Downloading https://files.pythonhosted.org/packages/de/0a/001be530836743d8be6c2d85069f46fecf84ac6c18c7f5fb8125ee11d854/pyparsing-2.3.1-py2.py3-none-any.whl (61kB)

    100% |████████████████████████████████| 71kB 35.6MB/s

Collecting setuptools (from kiwisolver>=1.0.1->matplotlib>=2.0.0->nanoplotter>=0.16.5->nanopack)

  Downloading https://files.pythonhosted.org/packages/d1/6a/4b2fcefd2ea0868810e92d519dacac1ddc64a2e53ba9e3422c3b62b378a6/setuptools-40.8.0-py2.py3-none-any.whl (575kB)

    100% |████████████████████████████████| 583kB 2.9MB/s

Installing collected packages: numpy, biopython, pysam, pytz, six, python-dateutil, pandas, scipy, cycler, backports.functools-lru-cache, subprocess32, setuptools, kiwisolver, pyparsing, matplotlib, seaborn, pauvre, nanoplotter, nanomath, nanoget, NanoPlot, NanoStat, NanoFilt, mappy, NanoLyse, nanopack

  Running setup.py install for subprocess32 ... done

  Running setup.py install for seaborn ... done

  Running setup.py install for pauvre ... done

  Running setup.py install for nanoplotter ... done

  Running setup.py install for nanomath ... done

  Running setup.py install for nanoget ... done

  Running setup.py install for NanoPlot ... done

  Running setup.py install for NanoStat ... done

  Running setup.py install for NanoFilt ... done

  Running setup.py install for mappy ... done

  Running setup.py install for NanoLyse ... done

  Running setup.py install for nanopack ... done

Successfully installed NanoFilt-2.0.0 NanoLyse-0.5.0 NanoPlot-1.8.1 NanoStat-0.8.0 backports.functools-lru-cache-1.5 biopython-1.73 cycler-0.10.0 kiwisolver-1.0.1 mappy-2.15 matplotlib-2.2.3 nanoget-1.2.0 nanomath-0.15.1 nanopack-0.1.4 nanoplotter-0.28.0 numpy-1.16.1 pandas-0.24.1 pauvre-0.1.86 pyparsing-2.3.1 pysam-0.15.2 python-dateutil-2.8.0 pytz-2018.9 scipy-1.2.1 seaborn-0.9.0 setuptools-40.8.0 six-1.12.0 subprocess32-3.5.3


$ pip list | grep NanoPlot

NanoPlot (1.8.1)


$ sudo pip install nanopack

[sudo] password for user:

The directory '/home/user/.cache/pip/http' or its parent directory is not owned by the current user and the cache has been disabled. Please check the permissions and owner of that directory. If executing pip with sudo, you may want sudo's -H flag.

The directory '/home/user/.cache/pip' or its parent directory is not owned by the current user and caching wheels has been disabled. check the permissions and owner of that directory. If executing pip with sudo, you may want sudo's -H flag.

Requirement already satisfied: nanopack in /home/user/.local/lib/python2.7/site-packages

Requirement already satisfied: NanoPlot>=0.20.1 in /home/user/.local/lib/python2.7/site-packages (from nanopack)

Requirement already satisfied: NanoStat>=0.6.1 in /home/user/.local/lib/python2.7/site-packages (from nanopack)

Requirement already satisfied: NanoFilt>=1.5.2 in /home/user/.local/lib/python2.7/site-packages (from nanopack)

Requirement already satisfied: NanoLyse>=0.2.1 in /home/user/.local/lib/python2.7/site-packages (from nanopack)


Added the path in bashrc


Still no luck!



Tried this:


$ pip3 install nanopack


Collecting nanopack

  Downloading https://files.pythonhosted.org/packages/54/24/f5b5a96a6a32d1127eb547745ab9572286035058f60a2988bdd2b1673bd7/nanopack-1.0.0.tar.gz

Collecting NanoComp>=0.4.0 (from nanopack)

  Downloading https://files.pythonhosted.org/packages/75/4f/9e8f5c304d1644ab0892e35de294188d99aa8eb3df351d19c199b51f3ae6/NanoComp-1.4.0.tar.gz

Collecting NanoFilt>=1.5.2 (from nanopack)

  Downloading https://files.pythonhosted.org/packages/dc/4a/dacdbbd28973d2d56ad0c0f3bf578f2bdfb68c9d27d7828034ea05cc90bc/NanoFilt-2.2.0.tar.gz

Collecting NanoGUI (from nanopack)

  Downloading https://files.pythonhosted.org/packages/bd/a1/6cf74f2086e4e7215c740c28671337f01d126e9d2f4ec6ebacc47fd792de/NanoGUI-0.1.0.tar.gz

Collecting NanoLyse>=0.2.1 (from nanopack)

  Downloading https://files.pythonhosted.org/packages/e9/52/812e19f50576871e82c0f5e8f188f4a7de99199fe1ceb50c33ac353de408/NanoLyse-1.1.0.tar.gz

Collecting NanoPlot>=0.20.1 (from nanopack)

  Downloading https://files.pythonhosted.org/packages/f2/79/849cda1c7a6a124ccbf9e81d4c2e61ec6d780a841f4b6bb04aa942b47fcc/NanoPlot-1.21.0.tar.gz

Collecting NanoStat>=0.6.1 (from nanopack)

  Downloading https://files.pythonhosted.org/packages/9c/8e/3fd581ebe737d1bf6716e5e8731f6677a84ab71bb0291b0cf8f1a9c6b656/NanoStat-1.1.2.tar.gz

Collecting nanoget>=0.15.0 (from nanopack)

  Downloading https://files.pythonhosted.org/packages/2e/97/f439c3cdb85d99288091b1224460d6b6245ceaa962286744e89006b95aa8/nanoget-1.7.7.tar.gz

Collecting nanomath>=0.13.3 (from nanopack)

  Downloading https://files.pythonhosted.org/packages/19/0b/2cdf6f70b6b7e581b7149b60f9117841326186d44aa62f60ed18280f7515/nanomath-0.22.0.tar.gz

Collecting nanoplotter>=0.16.5 (from nanopack)

  Downloading https://files.pythonhosted.org/packages/0c/85/86e0323e7448c3c96b7cb17cd41c1e99c80336380cdb77b48debbb82772b/nanoplotter-1.3.1.tar.gz

Collecting numpy (from NanoComp>=0.4.0->nanopack)

  Downloading https://files.pythonhosted.org/packages/f5/bf/4981bcbee43934f0adb8f764a1e70ab0ee5a448f6505bd04a87a2fda2a8b/numpy-1.16.1-cp36-cp36m-manylinux1_x86_64.whl (17.3MB)

    100% |████████████████████████████████| 17.3MB 82kB/s

Collecting pandas (from NanoComp>=0.4.0->nanopack)

  Downloading https://files.pythonhosted.org/packages/e6/de/a0d3defd8f338eaf53ef716e40ef6d6c277c35d50e09b586e170169cdf0d/pandas-0.24.1-cp36-cp36m-manylinux1_x86_64.whl (10.1MB)

    100% |████████████████████████████████| 10.1MB 125kB/s

Collecting psutil (from NanoComp>=0.4.0->nanopack)

  Downloading https://files.pythonhosted.org/packages/c7/01/7c30b247cdc5ba29623faa5c8cf1f1bbf7e041783c340414b0ed7e067c64/psutil-5.5.1.tar.gz (426kB)

    100% |████████████████████████████████| 430kB 3.0MB/s

Collecting biopython (from NanoFilt>=1.5.2->nanopack)

  Downloading https://files.pythonhosted.org/packages/28/15/8ac646ff24cfa2588b4d5e5ea51e8d13f3d35806bd9498fbf40ef79026fd/biopython-1.73-cp36-cp36m-manylinux1_x86_64.whl (2.2MB)

    100% |████████████████████████████████| 2.2MB 512kB/s

Collecting mappy>=2.2 (from NanoLyse>=0.2.1->nanopack)

  Using cached https://files.pythonhosted.org/packages/0d/66/8e1170f36283f45743e3e6e923a513e2386d5df93e935daba27e7e0d2ad6/mappy-2.15.tar.gz

Collecting pysam>0.10.0.0 (from NanoPlot>=0.20.1->nanopack)

  Downloading https://files.pythonhosted.org/packages/f1/fc/d2be1a093bd8494ab63e3168aca36c2494753bbff190f3201ce2e7da9cda/pysam-0.15.2-cp36-cp36m-manylinux1_x86_64.whl (9.6MB)

    100% |████████████████████████████████| 9.6MB 126kB/s

Collecting python-dateutil (from NanoPlot>=0.20.1->nanopack)

  Using cached https://files.pythonhosted.org/packages/41/17/c62faccbfbd163c7f57f3844689e3a78bae1f403648a6afb1d0866d87fbb/python_dateutil-2.8.0-py2.py3-none-any.whl

Collecting scipy (from NanoPlot>=0.20.1->nanopack)

  Downloading https://files.pythonhosted.org/packages/7f/5f/c48860704092933bf1c4c1574a8de1ffd16bf4fde8bab190d747598844b2/scipy-1.2.1-cp36-cp36m-manylinux1_x86_64.whl (24.8MB)

    100% |████████████████████████████████| 24.8MB 55kB/s

Collecting seaborn (from NanoPlot>=0.20.1->nanopack)

  Downloading https://files.pythonhosted.org/packages/a8/76/220ba4420459d9c4c9c9587c6ce607bf56c25b3d3d2de62056efe482dadc/seaborn-0.9.0-py3-none-any.whl (208kB)

    100% |████████████████████████████████| 215kB 1.2MB/s

Collecting matplotlib>=2.1.0 (from nanoplotter>=0.16.5->nanopack)

  Downloading https://files.pythonhosted.org/packages/71/07/16d781df15be30df4acfd536c479268f1208b2dfbc91e9ca5d92c9caf673/matplotlib-3.0.2-cp36-cp36m-manylinux1_x86_64.whl (12.9MB)

    100% |████████████████████████████████| 12.9MB 99kB/s

Collecting pauvre==0.1.86 (from nanoplotter>=0.16.5->nanopack)

  Using cached https://files.pythonhosted.org/packages/f0/70/b1a2c106128156d2f234964caee3f900733f81b67df51ffa62591e5bba46/pauvre-0.1.86.tar.gz

Collecting plotly>=3.4.2 (from nanoplotter>=0.16.5->nanopack)

  Downloading https://files.pythonhosted.org/packages/fd/db/003b5cfbc710f4d4982440451185b952269e4080a57ae7e760a2ceb8ce0c/plotly-3.6.1-py2.py3-none-any.whl (38.6MB)

    100% |████████████████████████████████| 38.6MB 35kB/s

Collecting statsmodels>=0.8.0 (from nanoplotter>=0.16.5->nanopack)

  Downloading https://files.pythonhosted.org/packages/85/d1/69ee7e757f657e7f527cbf500ec2d295396e5bcec873cf4eb68962c41024/statsmodels-0.9.0-cp36-cp36m-manylinux1_x86_64.whl (7.4MB)

    100% |████████████████████████████████| 7.4MB 155kB/s

Collecting pytz>=2011k (from pandas->NanoComp>=0.4.0->nanopack)

  Using cached https://files.pythonhosted.org/packages/61/28/1d3920e4d1d50b19bc5d24398a7cd85cc7b9a75a490570d5a30c57622d34/pytz-2018.9-py2.py3-none-any.whl

Collecting six>=1.5 (from python-dateutil->NanoPlot>=0.20.1->nanopack)

  Using cached https://files.pythonhosted.org/packages/73/fb/00a976f728d0d1fecfe898238ce23f502a721c0ac0ecfedb80e0d88c64e9/six-1.12.0-py2.py3-none-any.whl

Collecting pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 (from matplotlib>=2.1.0->nanoplotter>=0.16.5->nanopack)

  Using cached https://files.pythonhosted.org/packages/de/0a/001be530836743d8be6c2d85069f46fecf84ac6c18c7f5fb8125ee11d854/pyparsing-2.3.1-py2.py3-none-any.whl

Collecting kiwisolver>=1.0.1 (from matplotlib>=2.1.0->nanoplotter>=0.16.5->nanopack)

  Downloading https://files.pythonhosted.org/packages/69/a7/88719d132b18300b4369fbffa741841cfd36d1e637e1990f27929945b538/kiwisolver-1.0.1-cp36-cp36m-manylinux1_x86_64.whl (949kB)

    100% |████████████████████████████████| 952kB 1.3MB/s

Collecting cycler>=0.10 (from matplotlib>=2.1.0->nanoplotter>=0.16.5->nanopack)

  Using cached https://files.pythonhosted.org/packages/f7/d2/e07d3ebb2bd7af696440ce7e754c59dd546ffe1bbe732c8ab68b9c834e61/cycler-0.10.0-py2.py3-none-any.whl

Collecting decorator>=4.0.6 (from plotly>=3.4.2->nanoplotter>=0.16.5->nanopack)

  Downloading https://files.pythonhosted.org/packages/f1/cd/7c8240007e9716b14679bc217a1baefa4432aa30394f7e2ec40a52b1a708/decorator-4.3.2-py2.py3-none-any.whl

Collecting retrying>=1.3.3 (from plotly>=3.4.2->nanoplotter>=0.16.5->nanopack)

  Downloading https://files.pythonhosted.org/packages/44/ef/beae4b4ef80902f22e3af073397f079c96969c69b2c7d52a57ea9ae61c9d/retrying-1.3.3.tar.gz

Collecting requests (from plotly>=3.4.2->nanoplotter>=0.16.5->nanopack)

  Downloading https://files.pythonhosted.org/packages/7d/e3/20f3d364d6c8e5d2353c72a67778eb189176f08e873c9900e10c0287b84b/requests-2.21.0-py2.py3-none-any.whl (57kB)

    100% |████████████████████████████████| 61kB 5.9MB/s

Collecting nbformat>=4.2 (from plotly>=3.4.2->nanoplotter>=0.16.5->nanopack)

  Downloading https://files.pythonhosted.org/packages/da/27/9a654d2b6cc1eaa517d1c5a4405166c7f6d72f04f6e7eea41855fe808a46/nbformat-4.4.0-py2.py3-none-any.whl (155kB)

    100% |████████████████████████████████| 163kB 4.5MB/s

Collecting patsy (from statsmodels>=0.8.0->nanoplotter>=0.16.5->nanopack)

  Downloading https://files.pythonhosted.org/packages/ea/0c/5f61f1a3d4385d6bf83b83ea495068857ff8dfb89e74824c6e9eb63286d8/patsy-0.5.1-py2.py3-none-any.whl (231kB)

    100% |████████████████████████████████| 235kB 3.2MB/s

Collecting setuptools (from kiwisolver>=1.0.1->matplotlib>=2.1.0->nanoplotter>=0.16.5->nanopack)

  Using cached https://files.pythonhosted.org/packages/d1/6a/4b2fcefd2ea0868810e92d519dacac1ddc64a2e53ba9e3422c3b62b378a6/setuptools-40.8.0-py2.py3-none-any.whl

Collecting chardet<3.1.0,>=3.0.2 (from requests->plotly>=3.4.2->nanoplotter>=0.16.5->nanopack)

  Downloading https://files.pythonhosted.org/packages/bc/a9/01ffebfb562e4274b6487b4bb1ddec7ca55ec7510b22e4c51f14098443b8/chardet-3.0.4-py2.py3-none-any.whl (133kB)

    100% |████████████████████████████████| 143kB 5.3MB/s

Collecting idna<2.9,>=2.5 (from requests->plotly>=3.4.2->nanoplotter>=0.16.5->nanopack)

  Downloading https://files.pythonhosted.org/packages/14/2c/cd551d81dbe15200be1cf41cd03869a46fe7226e7450af7a6545bfc474c9/idna-2.8-py2.py3-none-any.whl (58kB)

    100% |████████████████████████████████| 61kB 5.1MB/s

Collecting certifi>=2017.4.17 (from requests->plotly>=3.4.2->nanoplotter>=0.16.5->nanopack)

  Downloading https://files.pythonhosted.org/packages/9f/e0/accfc1b56b57e9750eba272e24c4dddeac86852c2bebd1236674d7887e8a/certifi-2018.11.29-py2.py3-none-any.whl (154kB)

    100% |████████████████████████████████| 163kB 4.4MB/s

Collecting urllib3<1.25,>=1.21.1 (from requests->plotly>=3.4.2->nanoplotter>=0.16.5->nanopack)

  Downloading https://files.pythonhosted.org/packages/62/00/ee1d7de624db8ba7090d1226aebefab96a2c71cd5cfa7629d6ad3f61b79e/urllib3-1.24.1-py2.py3-none-any.whl (118kB)

    100% |████████████████████████████████| 122kB 4.7MB/s

Collecting ipython-genutils (from nbformat>=4.2->plotly>=3.4.2->nanoplotter>=0.16.5->nanopack)

  Downloading https://files.pythonhosted.org/packages/fa/bc/9bd3b5c2b4774d5f33b2d544f1460be9df7df2fe42f352135381c347c69a/ipython_genutils-0.2.0-py2.py3-none-any.whl

Collecting jsonschema!=2.5.0,>=2.4 (from nbformat>=4.2->plotly>=3.4.2->nanoplotter>=0.16.5->nanopack)

  Downloading https://files.pythonhosted.org/packages/cd/e6/be1b2a6ebebdaf1f790f1e750bb720fbda0335c2a19601ea9d8bb5059f38/jsonschema-3.0.0-py2.py3-none-any.whl (54kB)

    100% |████████████████████████████████| 61kB 6.3MB/s

Collecting traitlets>=4.1 (from nbformat>=4.2->plotly>=3.4.2->nanoplotter>=0.16.5->nanopack)

  Downloading https://files.pythonhosted.org/packages/93/d6/abcb22de61d78e2fc3959c964628a5771e47e7cc60d53e9342e21ed6cc9a/traitlets-4.3.2-py2.py3-none-any.whl (74kB)

    100% |████████████████████████████████| 81kB 6.3MB/s

Collecting jupyter-core (from nbformat>=4.2->plotly>=3.4.2->nanoplotter>=0.16.5->nanopack)

  Downloading https://files.pythonhosted.org/packages/1d/44/065d2d7bae7bebc06f1dd70d23c36da8c50c0f08b4236716743d706762a8/jupyter_core-4.4.0-py2.py3-none-any.whl (126kB)

    100% |████████████████████████████████| 133kB 4.8MB/s

Collecting pyrsistent>=0.14.0 (from jsonschema!=2.5.0,>=2.4->nbformat>=4.2->plotly>=3.4.2->nanoplotter>=0.16.5->nanopack)

  Downloading https://files.pythonhosted.org/packages/8c/46/4e93ab8a379d7efe93f20a0fb8a27bdfe88942cc954ab0210c3164e783e0/pyrsistent-0.14.11.tar.gz (104kB)

    100% |████████████████████████████████| 112kB 4.6MB/s

Collecting attrs>=17.4.0 (from jsonschema!=2.5.0,>=2.4->nbformat>=4.2->plotly>=3.4.2->nanoplotter>=0.16.5->nanopack)

  Downloading https://files.pythonhosted.org/packages/3a/e1/5f9023cc983f1a628a8c2fd051ad19e76ff7b142a0faf329336f9a62a514/attrs-18.2.0-py2.py3-none-any.whl

Building wheels for collected packages: nanopack, NanoComp, NanoFilt, NanoGUI, NanoLyse, NanoPlot, NanoStat, nanoget, nanomath, nanoplotter, psutil, mappy, pauvre, retrying, pyrsistent

  Running setup.py bdist_wheel for nanopack ... done

  Stored in directory: /home/user/.cache/pip/wheels/03/38/47/12ff3f64dcef32f2a9fcd92e57c3fdf8fb8953db45e083a806

  Running setup.py bdist_wheel for NanoComp ... done

  Stored in directory: /home/user/.cache/pip/wheels/ae/88/53/f817a6e2106e5518ab72a0c9c6193318d84b1ba8de82f279f9

  Running setup.py bdist_wheel for NanoFilt ... done

  Stored in directory: /home/user/.cache/pip/wheels/dd/c0/fb/671cd6f70dc0ef487ce9e155e1c181ad7ee660d66843a0c4c1

  Running setup.py bdist_wheel for NanoGUI ... done

  Stored in directory: /home/user/.cache/pip/wheels/43/da/4a/2e2d1f57a5ad2eacaac123f036096c2be9ce4a996e94551fc4

  Running setup.py bdist_wheel for NanoLyse ... done

  Stored in directory: /home/user/.cache/pip/wheels/68/6d/64/27b22d72fac5d81ed03f70d98c141ce056fdada3d1860132cb

  Running setup.py bdist_wheel for NanoPlot ... done

  Stored in directory: /home/user/.cache/pip/wheels/1b/5b/3e/6c83f4fed51f3960855fad667a1010be1086edcc023207a679

  Running setup.py bdist_wheel for NanoStat ... done

  Stored in directory: /home/user/.cache/pip/wheels/ad/ab/b1/55c9bf3e44f4229d21815a72c729bfa0ddfb502a32a060a9f7

  Running setup.py bdist_wheel for nanoget ... done

  Stored in directory: /home/user/.cache/pip/wheels/b3/6c/58/9455b58b65606ddef508f2eed959a2cd17bfe7ee3b3ff6d79c

  Running setup.py bdist_wheel for nanomath ... done

  Stored in directory: /home/user/.cache/pip/wheels/64/7a/53/59b333f92366f22359fda6aab46098068b42372508748f6173

  Running setup.py bdist_wheel for nanoplotter ... done

  Stored in directory: /home/user/.cache/pip/wheels/6d/f8/45/a2685a78ec02d253bb0e233d8a7901dbd7efc8c6637c9e731f

  Running setup.py bdist_wheel for psutil ... done

  Stored in directory: /home/user/.cache/pip/wheels/b4/9c/85/b73f594568ccc19c310ec6c61564346dd16c96aa2c35c5849a

  Running setup.py bdist_wheel for mappy ... done

  Stored in directory: /home/user/.cache/pip/wheels/16/61/f2/3ab933f528809270525fdf5b4f85d633b9212082a1d120fbd2

  Running setup.py bdist_wheel for pauvre ... done

  Stored in directory: /home/user/.cache/pip/wheels/6e/2b/00/0e4d27ead78a742a19bc4705a54bdcaae9cc456974b234bfad

  Running setup.py bdist_wheel for retrying ... done

  Stored in directory: /home/user/.cache/pip/wheels/d7/a9/33/acc7b709e2a35caa7d4cae442f6fe6fbf2c43f80823d46460c

  Running setup.py bdist_wheel for pyrsistent ... done

  Stored in directory: /home/user/.cache/pip/wheels/83/59/9a/a037b9b3c3e93d9275ea0aff9d6064400f372879dfdab01afe

Successfully built nanopack NanoComp NanoFilt NanoGUI NanoLyse NanoPlot NanoStat nanoget nanomath nanoplotter psutil mappy pauvre retrying pyrsistent

Installing collected packages: numpy, biopython, pytz, six, python-dateutil, pandas, nanomath, pysam, nanoget, pyparsing, setuptools, kiwisolver, cycler, matplotlib, scipy, pauvre, decorator, retrying, chardet, idna, certifi, urllib3, requests, ipython-genutils, pyrsistent, attrs, jsonschema, traitlets, jupyter-core, nbformat, plotly, seaborn, patsy, statsmodels, nanoplotter, NanoPlot, psutil, NanoComp, NanoFilt, NanoGUI, mappy, NanoLyse, NanoStat, nanopack

Successfully installed NanoComp-1.4.0 NanoFilt-2.2.0 NanoGUI-0.1.0 NanoLyse-1.1.0 NanoPlot-1.21.0 NanoStat-1.1.2 attrs-18.2.0 biopython-1.73 certifi-2018.11.29 chardet-3.0.4 cycler-0.10.0 decorator-4.3.2 idna-2.8 ipython-genutils-0.2.0 jsonschema-3.0.0 jupyter-core-4.4.0 kiwisolver-1.0.1 mappy-2.15 matplotlib-3.0.2 nanoget-1.7.7 nanomath-0.22.0 nanopack-1.0.0 nanoplotter-1.3.1 nbformat-4.4.0 numpy-1.16.1 pandas-0.24.1 patsy-0.5.1 pauvre-0.1.86 plotly-3.6.1 psutil-5.5.1 pyparsing-2.3.1 pyrsistent-0.14.11 pysam-0.15.2 python-dateutil-2.8.0 pytz-2018.9 requests-2.21.0 retrying-1.3.3 scipy-1.2.1 seaborn-0.9.0 setuptools-40.8.0 six-1.12.0 statsmodels-0.9.0 traitlets-4.3.2 urllib3-1.24.1


This worked!!



$ NanoComp -h

usage: NanoComp [-h] [-v] [-t THREADS] [-o OUTDIR] [-p PREFIX] [--verbose]

                [--raw] [--readtype {1D,2D,1D2}] [--maxlength N]

                [--minlength N] [--barcoded] [--split_runs TSV_FILE]

                [-f {eps,jpeg,jpg,pdf,pgf,png,ps,raw,rgba,svg,svgz,tif,tiff}]

                [-n names [names ...]] [-c colors [colors ...]]

                [--plot {violin,box,false}] [--title TITLE] [--dpi DPI]

                (--fasta file [file ...] | --fastq files [files ...] | --summary files [files ...] | --bam files [files ...])


Compares long read sequencing datasets.

fastqc -java.lang.OutOfMemoryError: Java heap space - Solved!

$fastqc filename.fastq
Started analysis of filename.fastq
Exception in thread "Thread-1" java.lang.OutOfMemoryError: Java heap space
    at uk.ac.babraham.FastQC.Modules.GCModel.GCModel.<init>(GCModel.java:69)
    at uk.ac.babraham.FastQC.Modules.PerSequenceGCContent.processSequence(PerSequenceGCContent.java:198)
    at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:88)
    at java.base/java.lang.Thread.run(Thread.java:844)


$ grep -n 'Xm' /home/prakki/sw/FastQC/fastqc
167:    unshift @java_args,"-Xmx${memory}m";
170:    unshift @java_args,'-Xmx250m';


$ vi /home/prakki/sw/FastQC/fastqc


Changed the 250m to 10g (depends on the RAM of your computer) in the line 170

$ fastqc filename.fastq
Started analysis of filename.fastq
Approx 5% complete for filename.fastq
Approx 10% complete for filename.fastq
Approx 15% complete for filename.fastq
Approx 20% complete for filename.fastq
Approx 25% complete for filename.fastq
Approx 30% complete for filename.fastq
Approx 35% complete for filename.fastq
Approx 40% complete for filename.fastq
Approx 45% complete for filename.fastq
Approx 50% complete for filename.fastq
Approx 55% complete for filename.fastq
Approx 60% complete for filename.fastq
Approx 65% complete for filename.fastq
Approx 70% complete for filename.fastq
Approx 75% complete for filename.fastq
Approx 80% complete for filename.fastq
Approx 85% complete for filename.fastq
Approx 90% complete for filename.fastq
Approx 95% complete for filename.fastq
Analysis complete for filename.fastq