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CostaLab / reg-gen

Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.
https://reg-gen.readthedocs.io/
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rgt-THOR multiple warnings for wigToBigWig #270

Open sunta3iouxos opened 1 month ago

sunta3iouxos commented 1 month ago

Hi all, I created a mamba/conda environment as follows:

mamba create -n rgts -c bioconda rgt
mamba activate rgts

the python version is 3.7.12:

 python
Python 3.7.12 | packaged by conda-forge | (default, Oct 26 2021, 06:08:53)
[GCC 9.4.0] on linux

I am running rgt-THOR with the folloing command:

rgt-THOR KOUT_Vs_WTUT.config --merge --output-dir THOR/ --report --deadzones assemblies/mm39/annotation/blacklist.bed --rmdup --pvalue 0.01  --foldchange 4 --save-input --name THOR_KOUT_Vs_WTUT

and although it seems like it is running it outputs a huge amount of warnings:


wigToBigWig v 4 - Convert ascii format wig file (in fixedStep, variableStep
or bedGraph format) to binary big wig format.
usage:
   wigToBigWig in.wig chrom.sizes out.bw
Where in.wig is in one of the ascii wiggle formats, but not including track lines
and chrom.sizes is two column: <chromosome name> <size in bases>
and out.bw is the output indexed big wig file.
Use the script: fetchChromSizes to obtain the actual chrom.sizes information
from UCSC, please do not make up a chrom sizes from your own information.
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
   -clip - If set just issue warning messages rather than dying if wig
                  file contains items off end of chromosome.
   -unc - If set, do not use compression.
   -fixedSummaries - If set, use a predefined sequence of summary levels.
   -keepAllChromosomes - If set, store all chromosomes in b-tree.
wigToBigWig v 4 - Convert ascii format wig file (in fixedStep, variableStep
or bedGraph format) to binary big wig format.
usage:
   wigToBigWig in.wig chrom.sizes out.bw
Where in.wig is in one of the ascii wiggle formats, but not including track lines
and chrom.sizes is two column: <chromosome name> <size in bases>
and out.bw is the output indexed big wig file.
Use the script: fetchChromSizes to obtain the actual chrom.sizes information
from UCSC, please do not make up a chrom sizes from your own information.
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
   -clip - If set just issue warning messages rather than dying if wig
                  file contains items off end of chromosome.
   -unc - If set, do not use compression.
   -fixedSummaries - If set, use a predefined sequence of summary levels.
   -keepAllChromosomes - If set, store all chromosomes in b-tree.
wigToBigWig v 4 - Convert ascii format wig file (in fixedStep, variableStep
or bedGraph format) to binary big wig format.
usage:
   wigToBigWig in.wig chrom.sizes out.bw
Where in.wig is in one of the ascii wiggle formats, but not including track lines
and chrom.sizes is two column: <chromosome name> <size in bases>
and out.bw is the output indexed big wig file.
Use the script: fetchChromSizes to obtain the actual chrom.sizes information
from UCSC, please do not make up a chrom sizes from your own information.
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
   -clip - If set just issue warning messages rather than dying if wig
                  file contains items off end of chromosome.
   -unc - If set, do not use compression.
   -fixedSummaries - If set, use a predefined sequence of summary levels.
   -keepAllChromosomes - If set, store all chromosomes in b-tree.
wigToBigWig v 4 - Convert ascii format wig file (in fixedStep, variableStep
or bedGraph format) to binary big wig format.
usage:
   wigToBigWig in.wig chrom.sizes out.bw
Where in.wig is in one of the ascii wiggle formats, but not including track lines
and chrom.sizes is two column: <chromosome name> <size in bases>
and out.bw is the output indexed big wig file.
Use the script: fetchChromSizes to obtain the actual chrom.sizes information
from UCSC, please do not make up a chrom sizes from your own information.
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
   -clip - If set just issue warning messages rather than dying if wig
                  file contains items off end of chromosome.
   -unc - If set, do not use compression.
   -fixedSummaries - If set, use a predefined sequence of summary levels.
   -keepAllChromosomes - If set, store all chromosomes in b-tree.
wigToBigWig v 4 - Convert ascii format wig file (in fixedStep, variableStep
or bedGraph format) to binary big wig format.
usage:
   wigToBigWig in.wig chrom.sizes out.bw
Where in.wig is in one of the ascii wiggle formats, but not including track lines
and chrom.sizes is two column: <chromosome name> <size in bases>
and out.bw is the output indexed big wig file.
Use the script: fetchChromSizes to obtain the actual chrom.sizes information
from UCSC, please do not make up a chrom sizes from your own information.
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
   -clip - If set just issue warning messages rather than dying if wig
                  file contains items off end of chromosome.
   -unc - If set, do not use compression.
   -fixedSummaries - If set, use a predefined sequence of summary levels.
   -keepAllChromosomes - If set, store all chromosomes in b-tree.
wigToBigWig v 4 - Convert ascii format wig file (in fixedStep, variableStep
or bedGraph format) to binary big wig format.
usage:
   wigToBigWig in.wig chrom.sizes out.bw
Where in.wig is in one of the ascii wiggle formats, but not including track lines
and chrom.sizes is two column: <chromosome name> <size in bases>
and out.bw is the output indexed big wig file.
Use the script: fetchChromSizes to obtain the actual chrom.sizes information
from UCSC, please do not make up a chrom sizes from your own information.
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
   -clip - If set just issue warning messages rather than dying if wig
                  file contains items off end of chromosome.
   -unc - If set, do not use compression.
   -fixedSummaries - If set, use a predefined sequence of summary levels.
   -keepAllChromosomes - If set, store all chromosomes in b-tree.
wigToBigWig v 4 - Convert ascii format wig file (in fixedStep, variableStep
or bedGraph format) to binary big wig format.
usage:
   wigToBigWig in.wig chrom.sizes out.bw
Where in.wig is in one of the ascii wiggle formats, but not including track lines
and chrom.sizes is two column: <chromosome name> <size in bases>
and out.bw is the output indexed big wig file.
Use the script: fetchChromSizes to obtain the actual chrom.sizes information
from UCSC, please do not make up a chrom sizes from your own information.
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
   -clip - If set just issue warning messages rather than dying if wig
                  file contains items off end of chromosome.
   -unc - If set, do not use compression.
   -fixedSummaries - If set, use a predefined sequence of summary levels.
   -keepAllChromosomes - If set, store all chromosomes in b-tree.
wigToBigWig v 4 - Convert ascii format wig file (in fixedStep, variableStep
or bedGraph format) to binary big wig format.
usage:
   wigToBigWig in.wig chrom.sizes out.bw
Where in.wig is in one of the ascii wiggle formats, but not including track lines
and chrom.sizes is two column: <chromosome name> <size in bases>
and out.bw is the output indexed big wig file.
Use the script: fetchChromSizes to obtain the actual chrom.sizes information
from UCSC, please do not make up a chrom sizes from your own information.
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
   -clip - If set just issue warning messages rather than dying if wig
                  file contains items off end of chromosome.
   -unc - If set, do not use compression.
   -fixedSummaries - If set, use a predefined sequence of summary levels.
   -keepAllChromosomes - If set, store all chromosomes in b-tree.