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loosolab / TOBIAS

Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal
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Issue with running TOBIAS BINDetect #24

Closed anu-bioinfo closed 4 years ago

anu-bioinfo commented 4 years ago

Hello,

I am having issues running TOBIAS BINDetect. I get the following error --

Traceback (most recent call last): File "/mnt/NewHDD/anaconda3/bin/TOBIAS", line 8, in sys.exit(main()) File "/mnt/NewHDD/anaconda3/lib/python3.7/site-packages/tobias/TOBIAS.py", line 154, in main args.func(args)
File "/mnt/NewHDD/anaconda3/lib/python3.7/site-packages/tobias/tools/bindetect.py", line 684, in run_bindetect fig = plot_bindetect(comparison_motifs, clustering, [cond1, cond2], args) File "/mnt/NewHDD/anaconda3/lib/python3.7/site-packages/tobias/tools/bindetect_functions.py", line 584, in plot_bindetect dendro_dat = dendrogram(cluster_obj.linkage_mat, labels=list(IDS), no_labels=True, orientation="right", ax=ax3, above_threshold_color="black", link_color_func=lambda k: cluster_obj.node_color[k]) File "/mnt/NewHDD/anaconda3/lib/python3.7/site-packages/scipy/cluster/hierarchy.py", line 3278, in dendrogram raise ValueError("Dimensions of Z and labels must be consistent.") ValueError: Dimensions of Z and labels must be consistent.

I am running the following command --

TOBIAS BINDetect --motifs MA0099.3.jaspar --signals inhib_footprints.bw ctrl_footprints.bw --genome genome.fa --peaks peaks.bed --outdir TOBIAS_BINDetect_output --cond_names Inhib Ctrl --motif-pvalue 0.05 --bound-pvalue 0.05 --cores 2

The bigwig files are obtained from 10x genomics scATAC-seq bam files, after running the two previous commands of the pipeline. Could you please hlep me out here ?

Thanks in advance.

msbentsen commented 4 years ago

Hi! Thank you for your report and the error message. Your commandline call looks good, so I don't think that is the problem - could you tell me what version you are running? (TOBIAS --version)

Can you also tell me if you get the same error using the test data? I have some test data available from TOBIAS DownloadData (command here https://github.com/loosolab/TOBIAS/wiki/test-data), and there are some test runs at https://github.com/loosolab/TOBIAS/wiki/BINDetect. Thanks!

I feel like it might be an issue with a certain numpy/scipy version, but I will have a look and see if I can reproduce :-)

anu-bioinfo commented 4 years ago

Thanks for your response. So, I ran TOBIAS on the test data and could not reproduce the error. The following is the version number: TOBIAS --version 0.11.6

Thanks

msbentsen commented 4 years ago

I can reproduce this for input --motifs files with only one motif. I will have a look at fixing this as soon as possible!

Until then, a quick fix for you would be to just add another motif to the --motifs file. This does not affect the results of the first motif, so you would still get the needed results for MA0099.3.jaspar. Sorry for the inconvenience!

anu-bioinfo commented 4 years ago

Thanks for your response. Yes, that was my initial guess. And then I reran TOBIAS BINDetect using all the motifs that I am interested in and it worked fine.

msbentsen commented 4 years ago

This was be fixed in TOBIAS 0.11.7 - closing, but please reopen in case of any issues.