bedGraphToBigWig Install error

Question

[ek699]

Hi I am trying to convert BAM file to BedGraph and ultimately to BigWig file. To install bedGraphToBigWig on cluster system, I did:

URL=http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64
curl $URL/bedGraphToBigWig > ~/bin/bedGraphToBigWig
chmod +x ~/bin/bedGraphToBigWig
curl $URL/faToTwoBit > ~/bin/faToTwoBit
chmod +x ~/bin/faToTwoBit

And to see if bedGraphToBigWig command worked, I typed "bedGraphToBigWig" in the directory, ~/bin, but I got this error:

bedGraphToBigWig: /lib64/libz.so.1: version `ZLIB_1.2.3.3' not found (required by bedGraphToBigWig)
bedGraphToBigWig: /lib64/libc.so.6: version `GLIBC_2.17' not found (required by bedGraphToBigWig)
bedGraphToBigWig: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by bedGraphToBigWig)

Is there any way that I can install bedGraphToBigWig properly? I am using company's cluster system so I am not system administrator. I really appreciate any assistance for this. Thank you very much.

[ATpoint]

You can try pulling the version from conda (https://anaconda.org/bioconda/ucsc-bedgraphtobigwig) as this should take full care of all dependencies and libraries.

[ek699]

Thanks, I removed all the previously downloaded files and followed the instruction in the website, using the code:

conda install -c bioconda ucsc-bedgraphtobigwig

I also added the PATH: /home/id/anaconda2/bin, and I typed "bedGraphToBigWig", I still got this error:

bedGraphToBigWig: error while loading shared libraries: libssl.so.1.0.0: cannot open shared object file: No such file or directory

Do you think it's because I downloaded it through bioconda??

[Jianyu]

Are you directly installing the package without creating an environment? If that is the case, it will mess up the base environment (which conda works on) and cause unexpected problems.

If you have installed the package in the base environment, you should reinstall the conda, install ucsc-bedgraphtobigwig by

conda create -n ucsc -c bioconda ucsc-bedgraphtobigwig

then activate the envrionment containing your package

conda activate ucsc

see if the error will show again

[ek699]

Thanks! I can try this. Since my bash shell shows (base)id@clustername:~$ , so I might install it in the base environment. Should I uninstall "bedgraphtobigwig" first and try your codes?

[Jianyu]

I think you should reinstall the whole conda, since install packages in base environment will cause many problems. Reinstall is simple and you only need to remove the whole conda directory like uninstall conda

Alternatively, you can rollback to the last revision by

conda list --revisions
conda install --revision [revision number]

the revision number should be that before you install packages

[ek699]

Thanks so much for the information. I did :

conda list --revisions
conda install --revision 0
conda create -n ucsc -c bioconda ucsc-bedgraphtobigwig
conda activate ucsc

And now it shows (ucsc)id@clustername:~$, and I also added the PATH:/home/id/anaconda2/envs/ucsc/bin, but when I typed "bedGraphToBigWig", it still says,

bedGraphToBigWig: error while loading shared libraries: libssl.so.1.0.0: cannot open shared object file: No such file or directory

Since I am using server (cluster system), I am not system admin and I am not able to use "sudo" codes as in the recommended website by Kevin above.. I am still stuck..

[Jianyu]

Okay... Seems strange, it works on my server

conda doesn't use the libraries in /lib directory, instead, those files like libxxx.so.x.x lies in the envs/ucsc/lib folder.

try

conda install -n ucsc openssl=1.0

See if it can work

[ek699]

Thanks.. what is "conda root directory"?? Sorry I am very new to this environment.. When I am in the directory, ~/anaconda2/envs/ucsc/lib, I can see below:

(base) id@cluster:~/anaconda2/envs/ucsc/lib$ ls
engines-1.1           libgomp.so.1.0.0            libpng16.so           libtsan.so.0
libasan.so            libitm.so                   libpng16.so.16        libtsan.so.0.0.0
libasan.so.5          libitm.so.1                 libpng16.so.16.37.0   libubsan.so
libasan.so.5.0.0      libitm.so.1.0.0             libpng.a              libubsan.so.1
libatomic.so          liblsan.so                  libpng.so             libubsan.so.1.0.0
libatomic.so.1        liblsan.so.0                libquadmath.so        libuuid.a
libatomic.so.1.2.0    liblsan.so.0.0.0            libquadmath.so.0      libuuid.la
libcrypto.a           libmysqlclient.a            libquadmath.so.0.0.0  libuuid.so
libcrypto.so          libmysqlclient_r.a          libssl.a              libuuid.so.1
libcrypto.so.1.1      libmysqlclient_r.so         libssl.so             libuuid.so.1.0.0
libgcc_s.so           libmysqlclient_r.so.18      libssl.so.1.1         libz.a
libgcc_s.so.1         libmysqlclient_r.so.18.3.0  libstdc++.so          libz.so
libgfortran.so.3      libmysqlclient.so           libstdc++.so.6        libz.so.1
libgfortran.so.3.0.0  libmysqlclient.so.18        libstdc++.so.6.0.21   libz.so.1.2.11
libgomp.so            libmysqlclient.so.18.3.0    libstdc++.so.6.0.26   pkgconfig
libgomp.so.1          libpng16.a                  libtsan.so

I can see there is libssl.so.1.1 above. is it what we are looking for?

[Jianyu]

Yes, you have libssl.so.1.1, but you need libssl.so.1.0.0, so try to install openssl version 1.0 to see it can give you a libssl.so.1.0.0 in ~/anaconda2/envs/ucsc/lib

I realized the old answer is too complex, you just need to try

conda install -n ucsc openssl=1.0

to see if it can fix

[ek699]

Wowwwww! I think it's working now!! I followed as you guided and now I can see:

(base) id@cluster:~/anaconda2/envs/ucsc/bin$ bedGraphToBigWig
bedGraphToBigWig v 4 - Convert a bedGraph file to bigWig format.
usage:
   bedGraphToBigWig in.bedGraph chrom.sizes out.bw
where in.bedGraph is a four column file in the format:
      <chrom> <start> <end> <value>
and chrom.sizes is a two-column file/URL: <chromosome name=""> <size in="" bases="">
and out.bw is the output indexed big wig file.
If the assembly <db> is hosted by UCSC, chrom.sizes can be a URL like
  http://hgdownload.cse.ucsc.edu/goldenPath/<db>/bigZips/<db>.chrom.sizes
or you may use the script fetchChromSizes to download the chrom.sizes file.
If not hosted by UCSC, a chrom.sizes file can be generated by running
twoBitInfo on the assembly .2bit file.
The input bedGraph file must be sorted, use the unix sort command:
  sort -k1,1 -k2,2n unsorted.bedGraph > sorted.bedGraph
options:
   -blockSize=N - Number of items to bundle in r-tree.  Default 256
   -itemsPerSlot=N - Number of data points bundled at lowest level. Default 1024
   -unc - If set, do not use compression.

This means the command is ready to use, right? But, as you can see, I am still in "base" environment though, is it okay??

[Jianyu]

Emm... Actually I think you can use this command because you are in the bin/ directory of this environment, if you are in another dir it should not work. If you need to use it all the time, you still need to activate the ucsc environment first

anyway, cheers!

Answer 1

[geocarvalho]

There is a docker file available on biocontainers:

$ docker pull quay.io/biocontainers/ucsc-bigwigtobedgraph:448--h2a80c09_0
# example
$ wget http://hgdownload.cse.ucsc.edu/goldenpath/hg19/encodeDCC/wgEncodeMapability/wgEncodeDukeMapabilityUniqueness35bp.bigWig
$ docker run -v $PWD:$PWD quay.io/biocontainers/ucsc-bigwigtobedgraph:448--h2a80c09_0 bigWigToBedGraph $PWD/wgEncodeDukeMapabilityUniqueness35bp.bigWig $PWD/wgEncodeDukeMapabilityUniqueness35bp_hg19.bed