Error: could nome open genometable.txt about drompaplus HOT 9 CLOSED

Dear fffletcher,

• makegenometable.pl is in script folder.
• Please provide the exact command of parse2wig+. Did you specify the exact file name that you made by the script?

from drompaplus.

Hi rnakato, thank you for getting back to me.

I'm sorry, maybe I am missing it, but I cannot seem to find the right script folder. I do see a folder named scripts, but with an icon different from the rest of the folders, this icon has a folder with an arrow, and takes me to a page with one line on it "submodules/SSP/scripts/". If I am in the wrong place could you please tell me where to find makegenometable.pl.

The command I used was
docker run -it --rm rnakato/ssp_drompa parse2wig+ -i ../ahy.bam -o ahy --gt genometable.txt -n GR

I installed via Docker. I named the makegenometable.pl output from the DROMPA3 script genometable.txt.

Any help would be very much appreciated. Thank you.

from drompaplus.

Dear fffletcher,

• Sorry it is scripts folder, not script folder. Actually, it is a symbolic link to submodules/SSP/scripts/ so you can also access the script with the path submodules/SSP/scripts/makegenometable.pl.
• Because you are using the docker command, it is necessary to mount the directory by -v option to access the input files as follows:
  docker run -it --rm -v $(pwd):/mnt rnakato/ssp_drompa parse2wig+ -i /mnt/ahy.bam -o ahy --gt /mnt/genometable.txt -n GR
  This command mounts the current directory to /mnt directory in the container. when you use this command, please move the bam file to the current directory. Please see also the document of Docker: https://docs.docker.com/storage/volumes/

from drompaplus.

Hi thank you for this, the command seem to be working now. I am however having an issue with writing the output files to the host directory.

I can find the files in the Docker container if it take out the -rm from the command you've given, which allows me to see the container contents, find the parse2wig+dir and the files inside.

Do you have any idea what the issue is here?

Thank you for all your help with this!

from drompaplus.

You can use --odir option to change the path of the output directory:
docker run -it --rm -v $(pwd):/mnt rnakato/ssp_drompa parse2wig+ -i /mnt/ahy.bam -o ahy --odir /mnt/parse2wigdir+ --gt /mnt/genometable.txt -n GR
I hope this command will generate the output data you want :)

from drompaplus.

Hi, thank you for this. The command you gave works perfectly for parse2wig+

But now I am having the same issue with the drompa+ PC_SHARP command. I cannot get the files to write to the host directory, I cannot find an option in the --help to specify the output directory for the files, and I can't seem to use the work around I described before by actually pulling the files out of the Docker container.

Would you be able to help with this?

Thank you!

from drompaplus.

Dear fffletcher,

You can specify the output filename by -o.

docker run -it --rm -v $(pwd):/mnt rnakato/ssp_drompa drompa+ PC_SHARP -o /mnt/drompa --gt /mnt/genometable.txt

from drompaplus.

This is my command docker run -it --rm -v $(pwd):/mnt rnakato/ssp_drompa drompa+ PC_SHARP -i /mnt/ahy.100.bw -o /mnt/drompa1 --gftype 1 -g /mnt/GCF_000182965.3_ASM18296v3_genomic.gtf --gt /mnt/genometable.txt --chr NC_032089.1

I am not getting any error when I execute, but it is not creating any files in my working directory. Where should these files be found?

from drompaplus.

Possibly you specified a chromosome name that is not in your genometable file with --chr option. Please try to remove --chr NC_032089.1.

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