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BINDetect not reading motif files correctly #78
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Tried it with a meme format motif database and receive this error: TOBIAS BINDetect --motifs /rds/user/cjr78/hpc-work/Motifs/gimme.vertebrate.v5.0.meme --signals /rds/user/cjr78/hpc-work/ATAC/tobias/ATAC_peaks/FootprintScores/merged_7_8_9_corrected.bw /rds/user/cjr78/hpc-work/ATAC/tobias/ATAC_peaks/FootprintScores/merged_1_2_3_corrected.bw --genome /rds/user/cjr78/hpc-work/References/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa --peaks /rds/user/cjr78/hpc-work/ATAC/DEseq2/Alluvial_open_activated.bed --outdir /rds/user/cjr78/hpc-work/ATAC/tobias/Alluvial_gimmemotifs/Open_activated/
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Hi, thank you for this issue! The first errors with
I would love to add the option to read more formats, but I haven't been able to find a good source for the file format convention. Sometimes
So that is unfortunately a bit hard.... But for the error with the .meme file, this is definitely a bug from my side :-) In the letter-probability matrix-line, you probably have a float number nsites: And the error arises because this can't be directly transformed into int. So changing nsites to an integer will also clear the error. I have made a small fix on the development branch (e5251cc), so you might also fetch and install that. I like to collect a few bugfixes before I release a new version, so I can't say when it will be officially 'out'. But I hope this helps you out! Mette |
Hi I'm getting another error unfortunately. This is my meme file: MEME version 3.0 ALPHABET= ACGT strands: + - Background letter frequencies The run output is: TOBIAS 0.12.12 BINDetect (run started 2021-06-25 16:50:29.791082)Working directory: /rds/user/cjr78/hpc-work/ATAC/tobiasCommand line call: TOBIAS BINDetect --motifs /rds/user/cjr78/hpc-work/Motifs/gimme.vertebrate.v5.0.meme --signals /rds/user/cjr78/hpc-work/ATAC/tobias/ATAC_peaks/FootprintScores/merged_7_8_9_corrected.bw /rds/user/cjr78/hpc-work/ATAC/tobias/ATAC_peaks/FootprintScores/merged_1_2_3_corrected.bw --genome /rds/user/cjr78/hpc-work/References/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa --peaks /rds/user/cjr78/hpc-work/ATAC/DEseq2/Alluvial_open_activated.bed --outdir /rds/user/cjr78/hpc-work/ATAC/tobias/Alluvial_gimmemotifs/Open_activated/----- Input parameters -----signals: ['/rds/user/cjr78/hpc-work/ATAC/tobias/ATAC_peaks/FootprintScores/merged_7_8_9_corrected.bw', '/rds/user/cjr78/hpc-work/ATAC/tobias/ATAC_peaks/FootprintScores/merged_1_2_3_corrected.bw']peaks: /rds/user/cjr78/hpc-work/ATAC/DEseq2/Alluvial_open_activated.bedmotifs: ['/rds/user/cjr78/hpc-work/Motifs/gimme.vertebrate.v5.0.meme']genome: /rds/user/cjr78/hpc-work/References/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.facond_names: ['merged_7_8_9_corrected', 'merged_1_2_3_corrected']peak_header: Nonenaming: name_idmotif_pvalue: 0.0001bound_pvalue: 0.001pseudo: Nonetime_series: Falseskip_excel: Falseoutput_peaks: Noneprefix: bindetectoutdir: /rds/user/cjr78/hpc-work/ATAC/tobias/Alluvial_gimmemotifs/Open_activatedcores: 1split: 100verbosity: 3----- Output files -----/rds/user/cjr78/hpc-work/ATAC/tobias/Alluvial_gimmemotifs/Open_activated//beds/_merged_7_8_9_corrected_bound.bed/rds/user/cjr78/hpc-work/ATAC/tobias/Alluvial_gimmemotifs/Open_activated//beds/_merged_7_8_9_corrected_unbound.bed/rds/user/cjr78/hpc-work/ATAC/tobias/Alluvial_gimmemotifs/Open_activated//beds/_merged_1_2_3_corrected_bound.bed/rds/user/cjr78/hpc-work/ATAC/tobias/Alluvial_gimmemotifs/Open_activated//beds/_merged_1_2_3_corrected_unbound.bed/rds/user/cjr78/hpc-work/ATAC/tobias/Alluvial_gimmemotifs/Open_activated//beds/_all.bed/rds/user/cjr78/hpc-work/ATAC/tobias/Alluvial_gimmemotifs/Open_activated//plots/_log2fcs.pdf/rds/user/cjr78/hpc-work/ATAC/tobias/Alluvial_gimmemotifs/Open_activated//_overview.txt/rds/user/cjr78/hpc-work/ATAC/tobias/Alluvial_gimmemotifs/Open_activated//_overview.xlsx/rds/user/cjr78/hpc-work/ATAC/tobias/Alluvial_gimmemotifs/Open_activated/bindetect_distances.txt/rds/user/cjr78/hpc-work/ATAC/tobias/Alluvial_gimmemotifs/Open_activated/bindetect_results.txt/rds/user/cjr78/hpc-work/ATAC/tobias/Alluvial_gimmemotifs/Open_activated/bindetect_results.xlsx/rds/user/cjr78/hpc-work/ATAC/tobias/Alluvial_gimmemotifs/Open_activated/bindetect_figures.pdf2021-06-25 16:50:29 (127630) [INFO] ----- Processing input data ----- |
Hi Connor, This was a small oversight from my end - I falsely assumed there would always be at least one line between two motifs, e.g.:
The above motifs work with version |
Hi team,
I'm recently re-running some analyses and BINDetect is not reading the motif file correctly.
My original run was using the JASPAR2020 motif database. If we head the file:
However, I've been trying to get TOBIAS to read the motif database that comes with Gimmemotifs (https://github.com/vanheeringen-lab/gimmemotifs), just for consistency. If we head the file:
When I try and run this, I get the errror:
I edited the motif file to remove # items. Head of the edited motif file:
However when I try and run BINDetect, I get this error:
Somehow it reads over 5000 motifs? Any ideas would be appreciated!
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