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mauranolab / GWAS_plots

Performs enrichment plots of GWAS p-value lists in DHSs (like Fig. 5 of Maurano, Humbert, et al. Science 2012)
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namedFDR5pctHotspots.starch file not exist #1

Open shirleydaidai opened 6 years ago

shirleydaidai commented 6 years ago

Hello, Where can I find "namedFDR5pctHotspots.starch" file? The web page "http://www.uwencode.org/proj/Science_Maurano_Humbert_et_al/data/namedFDR5pctHotspots.starch" seems not exist.
Thanks Shirley

erichaugen commented 6 years ago

Hi Shirley, That file is available at http://resources.altius.org/proj/Science_Maurano_Humbert_et_al/data/namedFDR5pctHotspots.starch Sorry about the outdated Readme. Best regards, Eric

shirleydaidai commented 6 years ago

Thank you, Eric. I guess it's a binary file so I cannot view it. But after running gwasVsRegions.pl, I got several errors. Not sure if it still related to this problem. Can you have a look? Tnx. Here's my code:

epiroot@epi-ubuntu:/media/epiroot/GWAS_plots-master/src$ perl ./gwasVsRegions.pl -p OS.sorted4.bed -s ../hg19/namedFDR5pctHotspots.starch -r ../results_hotspots_nocoding-OS Using starch ../hg19/namedFDR5pctHotspots.starch Output results to ../results_hotspots_nocoding-OS Using pvalues in OS.sorted4.bed Starting run Mon Nov 6 17:05:19 2017 bedmap --ec --echo --echo-map-id OS.sorted4.bed ../hg19/namedFDR5pctHotspots.starch | bedops --ec -n -0% - ../hg19/ccdsGene.Exons.bed May use bedmap --help for more help.

Error: in ../hg19/namedFDR5pctHotspots.starch Fully nested component found. See row: 2 Processing results Mon Nov 6 17:05:20 2017 Making plot Mon Nov 6 17:05:20 2017 Plot command: tail -q -n +2 ../results_hotspots_nocoding-OS/bed/.txt | grep -v -f excluded_samples.txt > $TMPDIR/t.txt; ./GWASPlot.R $TMPDIR/t.txt 1e-20 50 ../results_hotspots_nocoding-OS/bed/bed sh: 1: cannot create /t.txt: Permission denied tail: cannot open ‘../results_hotspots_nocoding-OS/bed/.txt’ for reading: No such file or directory sh: 1: ./GWASPlot.R: Permission denied Finished Mon Nov 6 17:05:20 2017

erichaugen commented 6 years ago

Okay it seems bedmap was made incompatible with this type of file as of v2.4.27 and the developer is on vacation right now. I put up a 2.4.26 version of the Linux BEDOPS programs (including bedmap) here: https://resources.altius.org/proj/Science_Maurano_Humbert_et_al/data/bedops_2.4.26.tar.gz

You can also view the binary starch file with 'unstarch': $ unstarch namedFDR5pctHotspots.starch | head chr1 10132 10463 Jurkat-DS12659 chr1 10135 10452 NB4-DS12543 chr1 10136 10315 HMVEC_dLyAd-DS13261 chr1 10137 10316 HMVEC_LLy-DS13185 chr1 10137 10350 HL60-DS11809 chr1 10139 10354 HUVEC-DS10060 chr1 10141 10314 HVMF-DS13981 chr1 10141 10318 HMVEC_dNeo-DS12937 chr1 10141 10332 Hela-DS10011 chr1 10144 10314 fMuscle_leg-DS19272

The latest bedmap would only work correctly if this were filtered to include only one sample at a time.

For a similar analysis of your GWAS SNPs you might also try http://phase3browser.1000genomes.org/Homo_sapiens/UserData/Forge It actually works as is (last I checked), and tries to account for LD.

Best, Eric

erichaugen commented 6 years ago

Update: This bedmap bug is fixed in the latest BEDOPS development version but that hasn't been incorporated yet in a new binary release.

And apparently just removing the '--ec' in the bedmap call will bypass the error and produce correct output.

shirleydaidai commented 6 years ago

Hello again, I could finally run this after sorting the starch file. Here's another minor error, which said it cannot library ‘directlabels’. But I am sure I have just installed this package which I can run it in R.

epiroot@epi-ubuntu:/media/epiroot/GWAS_plots-master/src$ sudo perl ./gwasVsRegions.pl -p OS.sorted4.bed -s ../hg19/namedFDR5pctHotspots.starch.sorted..txt -r ../results_hotspots_nocoding-OS [sudo] password for epiroot: Using starch ../hg19/namedFDR5pctHotspots.starch.sorted..txt Output results to ../results_hotspots_nocoding-OS Using pvalues in OS.sorted4.bed Starting run Tue Nov 7 09:57:29 2017 bedmap --ec --echo --echo-map-id OS.sorted4.bed ../hg19/namedFDR5pctHotspots.starch.sorted..txt | bedops --ec -n -0% - ../hg19/ccdsGene.Exons.bed Processing results Tue Nov 7 10:01:27 2017 Making plot Tue Nov 7 10:01:27 2017 Plot command: tail -q -n +2 ../results_hotspots_nocoding-OS/bed/*.txt | grep -v -f excluded_samples.txt > $TMPDIR/t.txt; ./GWASPlot.R $TMPDIR/t.txt 1e-20 50 ../results_hotspots_nocoding-OS/bed/bed Reading /t.txt Plotting ../results_hotspots_nocoding-OS/bed/bed at P> 1e-20 Error in library(directlabels) : there is no package called ‘directlabels’ Execution halted Finished Tue Nov 7 10:01:28 2017