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kundajelab / phantompeakqualtools

This package computes informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. It can also be used to obtain robust estimates of the predominant fragment length or characteristic tag shift values in these assays.
BSD 3-Clause "New" or "Revised" License
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run_spp, not tag.lwcc error #13

Closed KunFang93 closed 4 years ago

KunFang93 commented 5 years ago

Hi,

I have a problem when I run run_spp.R: Error in argfun(job) : object 'tag.lwcc' not found Calls: find.binding.positions ... sendData -> sendData.SOCKnode -> serialize -> argfun Execution halted Thanks a lot!

Kun

leepc12 commented 5 years ago

Please post your full command line and any helpful error logs.

KunFang93 commented 5 years ago

my full command is: run_spp.R -p=20 -c=ENCFF000ZLI.filt.nodup.srt.SE.tagAlign.gz -i=ENCFF162ZAB.filt.nodup.srt.SE.tagAlign.gz -npeak=300000 -odir=test2 -speak=205 -savr -savp -rf -out=test2/test.ccscores

log: ChIP data: ENCFF000ZLI.filt.nodup.srt.SE.tagAlign.gz Control data: ENCFF162ZAB.filt.nodup.srt.SE.tagAlign.gz strandshift(min): -500 strandshift(step): 5 strandshift(max) 1500 user-defined peak shift 205 exclusion(min): 10 exclusion(max): NaN num parallel nodes: 20 FDR threshold: 0.01 NumPeaks Threshold: 3e+05 Output Directory: test2 narrowPeak output file name: NA regionPeak output file name: test2/ENCFF000ZLI.filt.nodup.srt.SE.tagAlign_VS_ENCFF162ZAB.filt.nodup.srt.SE.tagAlign.regionPeak Rdata filename: NA plot pdf filename: test2/ENCFF000ZLI.filt.nodup.srt.SE.tagAlign.pdf result filename: test2/test.ccscores Overwrite files?: TRUE

Decompressing ChIP file Decompressing control file Loading required package: Rcpp Reading ChIP tagAlign/BAM file ENCFF000ZLI.filt.nodup.srt.SE.tagAlign.gz opened /tmp/Rtmpvb55A1/ENCFF000ZLI.filt.nodup.srt.SE.tagAlign6cc93f9df68a done. read 18492897 fragments ChIP data read length 32 [1] TRUE Reading Control tagAlign/BAM file ENCFF162ZAB.filt.nodup.srt.SE.tagAlign.gz opened /tmp/Rtmpvb55A1/ENCFF162ZAB.filt.nodup.srt.SE.tagAlign6cc94cf5b177 done. read 10043693 fragments Control data read length 32 Calculating peak characteristics Minimum cross-correlation value 0.2042988 Minimum cross-correlation shift 1500 Top 3 cross-correlation values 0.220347194048325 Top 3 estimates for fragment length 205 Window half size 505 Phantom peak location 30 Phantom peak Correlation 0.21713 Normalized Strand cross-correlation coefficient (NSC) 1.078554 Relative Strand cross-correlation Coefficient (RSC) 1.250731 Phantom Peak Quality Tag 1 null device 1 Removing read stacks Finding peaks finding background exclusion regions ... done determining peaks on provided 1 control datasets: using reversed signal for FDR calculations bg.weight= 0.543123 Error in argfun(job) : object 'tag.lwcc' not found Calls: find.binding.positions ... sendData -> sendData.SOCKnode -> serialize -> argfun Execution halted

Thanks!

leepc12 commented 5 years ago

Did you install all R requirements including spp package?

KunFang93 commented 5 years ago

I used conda install -c bioconda phantompeakqualtools to install the software. It installed the dependence r-spp.

leepc12 commented 5 years ago

I think you also have ENCODE pipeline's conda environment. Can you try with that?

$ source activate encode-atac-seq-pipeline
$ Rscript run_spp.R ...
KunFang93 commented 5 years ago

Unfortunately, I don't have the pipeline now....I run tutorial successfully once but when I try to run tutorial again. It failed again. And after I reinstall couple of times, my conda environment even doesn't use its own R but use the base environment's R. I completely screwed up my old conda environment so I reinstall a new miniconda3 and decided manually follow the pipeline in the google doc.... By the way, before this error, there is another error when I run the run_spp.R: no function runmean, but this can be solved by add library(caTools) before line 718: cc$y <-runmean(cc$y,sbw,alg="fast").

So sorry for bothering you a lot, thanks!

leepc12 commented 5 years ago

I got the same tag.lwcc error with R 3.6 with spp 1.16. I downgraded them to R 3.4.4 with spp 1.15 worked fine for me.

Until we fix this issue, downgrade your R to <=3.4.4 and R spp package to <=1.15.

KunFang93 commented 5 years ago

Hi, Lee

Thanks for your reply~ I will do that

Best, Kun

On Sep 17, 2019, at 7:01 PM, Jin Lee notifications@github.com wrote:

I got the same tag.lwcc error with R 3.6 with spp 1.16. I downgraded them to R 3.4.4 with spp 1.15 worked fine for me.

Until we fix this issue, downgrade your R to <=3.4.4 and R spp package to <=1.15.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/kundajelab/phantompeakqualtools/issues/13?email_source=notifications&email_token=ADXLIA4F6S4QOXJJ4YWRV7DQKFVXFA5CNFSM4IH5EEM2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD66IMQQ#issuecomment-532448834, or mute the thread https://github.com/notifications/unsubscribe-auth/ADXLIAY2K5TDCZZPI4W2O5TQKFVXFANCNFSM4IH5EEMQ.

leepc12 commented 4 years ago

Fixed in 1.2.2. Closing this.

annashcherbina commented 4 years ago

Hi Jin, I'm still seeing this issue. what do you mean by "fixed in 1.2.2?" 1.2.2 of phantompeaktools?

ChIP data: mouse_chipseq-ChIP_G1E_307C.2x36mers.mm10.unique.dedup.merged.sorted.bam Control data: mouse_chipseq-Input_G1E_307C.2x36mers.mm10.unique.dedup.bam strandshift(min): -100 strandshift(step): 5 strandshift(max) 600 user-defined peak shift NA exclusion(min): 10 exclusion(max): NaN num parallel nodes: 20 FDR threshold: 0.01 NumPeaks Threshold: 3e+05 Output Directory: SPP-300K-mouse_chipseq-ChIP_G1E_307C.2x36mers.mm10.unique.dedup.merged.sorted narrowPeak output file name: NA regionPeak output file name: SPP-300K-mouse_chipseq-ChIP_G1E_307C.2x36mers.mm10.unique.dedup.merged.sorted/mouse_chipseq-ChIP_G1E_307C.2x36mers.mm10.unique.dedup.merged.sorted_VS_mouse_chipseq-Input_G1E_307C.2x36mers.mm10.unique.dedup.regionPeak Rdata filename: NA plot pdf filename: SPP-300K-mouse_chipseq-ChIP_G1E_307C.2x36mers.mm10.unique.dedup.merged.sorted/mouse_chipseq-ChIP_G1E_307C.2x36mers.mm10.unique.dedup.merged.sorted.pdf result filename: NA Overwrite files?: TRUE

[1] TRUE [1] TRUE Loading required package: Rcpp Reading ChIP tagAlign/BAM file mouse_chipseq-ChIP_G1E_307C.2x36mers.mm10.unique.dedup.merged.sorted.bam opened /tmp/RtmpVejf8I/mouse_chipseq-ChIP_G1E_307C.2x36mers.mm10.unique.dedup.merged.sorted.tagAlign46c112d661c done. read 64702726 fragments ChIP data read length 36 [1] TRUE Reading Control tagAlign/BAM file mouse_chipseq-Input_G1E_307C.2x36mers.mm10.unique.dedup.bam opened /tmp/RtmpVejf8I/mouse_chipseq-Input_G1E_307C.2x36mers.mm10.unique.dedup.tagAlign46c459054c6 done. read 67907542 fragments Control data read length 36 Calculating peak characteristics Minimum cross-correlation value 0.4602906 Minimum cross-correlation shift -100 Peak cross-correlation value 0.657640058078151 Peak strand shift 235 Window half size 470 Phantom peak location 40 Phantom peak Correlation 0.5083081 Normalized cross-correlation coefficient (NCCC) 1.42875 Relative Cross correlation Coefficient (RCCC) 4.109946 Phantom Peak Quality Tag 2 null device 1 Removing read stacks Finding peaks finding background exclusion regions ... done determining peaks on provided 1 control datasets: using reversed signal for FDR calculations bg.weight= 2.039481 Error in argfun(job) : object 'tag.lwcc' not found Calls: find.binding.positions ... sendData -> sendData.SOCKnode -> serialize -> argfun Execution halted

annashcherbina commented 4 years ago

sorry, I believe I had the wrong tag. seems fine in 1.2.2. Closing again.