Closed udube closed 5 years ago
Dear @udube,
would you have some more program output for me, i.e. the full log of the run? In the beginning there should be some statistics about the BED input files. Additionally, if possible, the predictions.hg19.bed-hg38 would be useful (I assume that's where the warning are coming from). The bedtools warnings may point out some issues while reading the bed files, thus yielding the error you got.
Cheers, Tobias
Sure, please find the files you requested attached.
EDIT: Including logs from a run with no output and a run with the error.
Thanks!
Thank you for providing the files. I'll take a look at the issue - I suspect something in conjunction with the chromosome names may be not correctly handled. The test data usually had "1" instead of "chr1", so that may be the problem.
Dear @udube,
I tried to reproduce the issue with mock CircCoordinates files and do not get errors while using the same GTF and BED file than in you example. Would it be possible to also provide the CircCoordinates file?
Cheers, Tobias
Thank you for continuing to look into this issue. Please find the CircCoordinates file as well as all output produced, including a text file with the program's output to screen.
Dear @udube,
Thank you for providing the files. I used the NPHP4 file as input and still cannot reproduce the error. However my output is also empty. Could you please check your Python3 environment for me and run pip3 list
to see what package versions you have installed right now. Specifically pybedtools
would be interesting (I'm running pybedtools 0.8.0).
Cheers, Tobias
To clarify, I only receive the error when I do not include "-I exon". When I include "-I exon" I have the empty output.
Please find the information you requested below:
biopython (1.73) circtools (1.1.0.7) HTSeq (0.11.2) numpy (1.16.0) pandas (0.23.4) patsy (0.5.1) Pillow (5.4.1) pip (9.0.1) pybedtools (0.8.0) pysam (0.15.2) python-dateutil (2.7.5) pytz (2018.9) reportlab (3.5.13) scipy (1.2.0) setuptools (33.1.1) six (1.12.0) statsmodels (0.9.0) wheel (0.32.3)
Dear @udube,
I could trace back the error to some old code that I have not used for months. Basically, I changed the default to "gene" mode for -I
in the latest commit, meaning that shuffling will take place over all annotated gene regions (which more or less mirrors not specifying -I
in earlier versions). Please update circtools to the latest version from the repository to get the updated code.
That should fix your problem. In a related note, the warning of bedtools is generated by the genome.sizes file that contains "chr1" etc as IDs whereas circtools internally converts everything to "1". I will add an auto conversion of the genome.sizes file in a later release to also address that issue. for now you may use sed and therefore get rid of that warning.
Cheers, Tobias
Thank you. I am able to run the command without any errors. I appreciate your perseverance.
Hello,
I receive the following errors when running the circtools enrichment module using a gencode GTF file.
Input command:
circtools enrich -c circCoordinates-b predictions.hg19.bed-hg38 -a gencode.v26.primary_assembly.annotation.gtf -g sizes.genome -i 10 -p 20 -P 1 -T 1
Warnings and error:
Input command:
circtools enrich -c circCoordinates-b predictions.hg19.bed-hg38 -a gencode.v26.primary_assembly.annotation.gtf -g sizes.genome -i 10 -p 20 -P 1 -T 1 -I exon
This command runs through, but the .csv file output only has a header (output_10_2019_01_23__20_43.zip)
Thanks,