Troubles with motiffinder

[Matt Romero]

Hi All,

I have been trying to run motiffinder on my dataset and I am having some issues. I've tried multiple commands, but here is the standard one I tried from the wiki:

java -jar /opt/juicer/scripts/juicer_tools.7.0.jar motifs hg19 /opt/juicer/references/motif/ /opt/juicer/work/H9Std/aligned/merged_loops.bedpe

And it got the following output:

WARN [2021-03-30T20:25:42,469]  [Globals.java:138] [main]  Development mode is enabled

Exception in thread "main" java.lang.NullPointerException

at juicebox.data.feature.GenomeWideList.addAll(GenomeWideList.java:134)

at juicebox.data.feature.GenomeWideList.<init>(GenomeWideList.java:70)

at juicebox.data.anchor.MotifAnchorParser.loadFromBEDFile(MotifAnchorParser.java:255)

at juicebox.tools.clt.juicer.MotifFinder.getIntersectionOfBEDFiles(MotifFinder.java:64)

at juicebox.tools.clt.juicer.MotifFinder.getThreeTierFilteredProteinTrack(MotifFinder.java:187)

at juicebox.tools.clt.juicer.MotifFinder.findUniqueMotifs(MotifFinder.java:240)

at juicebox.tools.clt.juicer.MotifFinder.run(MotifFinder.java:113)

at juicebox.tools.HiCTools.main(HiCTools.java:94)

I have checked the motif folders and they contain both the inferred and unique folders and both have .bed files for CTCF, SMC3 and RAD21:

/opt/juicer/references/motif/unique> ls

CTCF_collapsed.narrowpeak.bed  RAD21_collapsed.narrowpeak.bed  SMC3_wgEncodeAwgTfbsSydhGm12878Smc3ab9263IggmusUniPk.narrowPeak.bed

I've also tried specifying the directory for hg19, but still no luck. 

Any info would be great and appreciated!

Thanks!

-Matt 

[Muhammad Saad Shamim]

Are both the unique and inferred folders set up properly?

See this colab notebook with an example run of Motif Finder:

https://colab.research.google.com/drive/1ucttsmbfJ7_HVw3VkWPSy-xqNKYF_VDh

- Muhammad Saad Shamim

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[Matt Romero]

Hi Muhammad,

Thanks so much for the response. 

Yes, I believe the folders are set up properly. Here's an "ls" printout of the unique and inferred folders in the motif directory:

/opt/juicer/references/motif> ls

inferred  unique

Now, within those folders they do contain the CTCF, SMC3, and RAD21 .bed files, but their names are different than just CTCF.bed, SMC3.bed and RAD21.bed:

inferred/

CTCF_wgEncodeAwgTfbsSydhGm12878Ctcfsc15914c20UniPk.narrowPeak.bed

unique/

CTCF_collapsed.narrowpeak.bed

RAD21_collapsed.narrowpeak.bed

SMC3_wgEncodeAwgTfbsSydhGm12878Smc3ab9263IggmusUniPk.narrowPeak.bed

I don't know if this would cause a problem - I tried changing the names to just CTCF.bed, for example, using the "cp" command, but permission was not permitted for some reason.

If the names are a problem, I'm assuming I can download the files from the colab notebook you pasted above and rename the files accordingly and retry my motifs command?

Hope this makes sense!

-Matt

[Muhammad Saad Shamim]

Can you try running without including the '/' after the folder name in the java command?

Alternatively, you could try running in the colab notebook / upload your files there.

It's strange that you're not able to cp - perhaps a file system issue if the files aren't readable?

- Muhammad Saad Shamim

To view this discussion on the web visit https://groups.google.com/d/msgid/3d-genomics/9689ffd9-ba56-4ae5-ab12-a372351d87e4n%40googlegroups.com.

[Matt Romero]

Hi Muhammad, 

So I removed the "/" after the motif folder name and it still did not work. I also used the sudo cp command to change the file names of the .bed files and the name change was successful, but running command with new filenames still didn't work. 

Either way I am still getting the same output:

WARN [2021-03-30T23:49:03,541]  [Globals.java:138] [main]  Development mode is enabled

Exception in thread "main" java.lang.NullPointerException

at juicebox.data.feature.GenomeWideList.addAll(GenomeWideList.java:134)

at juicebox.data.feature.GenomeWideList.<init>(GenomeWideList.java:70)

at juicebox.data.anchor.MotifAnchorParser.loadFromBEDFile(MotifAnchorParser.java:255)

at juicebox.tools.clt.juicer.MotifFinder.getIntersectionOfBEDFiles(MotifFinder.java:64)

at juicebox.tools.clt.juicer.MotifFinder.getThreeTierFilteredProteinTrack(MotifFinder.java:187)

at juicebox.tools.clt.juicer.MotifFinder.findUniqueMotifs(MotifFinder.java:240)

at juicebox.tools.clt.juicer.MotifFinder.run(MotifFinder.java:113)

at juicebox.tools.HiCTools.main(HiCTools.java:94)

Not sure what I am doing wrong. Any other suggestions would be greatly appreciated!

-Matt

[Muhammad Saad Shamim]

Are you using the same version of the jar as the notebook?

You could upload your files to colab and try there as well, just substituting the appropriate bed files/loop list/genome.

- Muhammad Saad Shamim

To view this discussion on the web visit https://groups.google.com/d/msgid/3d-genomics/12478ad7-5cc3-4447-bdd6-d91e986ae50bn%40googlegroups.com.

[Matt Romero]

Hi Muhammad, 

I was using the 1.22 version of juicer tools. I downloaded the version from the colab and it seemed to have worked! I haven't checked the data yet, but it ran.

Follow-up question: 

I have motif, pearson and eigenvector data in .txt format after using juicer tools. It's my understanding that those must be converted to .wig files - I found where Neva gave a link for converting to .wig (https://genome.ucsc.edu/goldenPath/help/wiggle.html), but I am a little confused on the layout. 

Am I just adding a header? 

A bit confused by the process.

Thanks again!

-Matt