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crazyhottommy / phantompeakqualtools

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threshold= Inf, no peak saved #10

Closed zhuchcn closed 4 years ago

zhuchcn commented 4 years ago

Hi, I'm using a pipeline developed by encode (https://github.com/ENCODE-DCC/chip-seq-pipeline2) to run my tf chip-seq data. The pipeline works fine until recently it failed with this error. It looks like spp was able to find some positions (quite a few in chromosomes), but because it calculated the threshold as infinity, so no peak was saved. The pipeline's developer is very helpful but couldn't solve the problem so far. It seems to be an issue of spp, so I'm posting it here to see if I can get any help here. Btw, the same pipeline works fine before with my other data.

The command that called run_spp.R is

Rscript --max-ppsize=500000 $(which run_spp.R) 
    -c=/cromwell-executions/chip/3516233a-e8eb-4cca-9c61-f05ce8c6881e/call-call_peak_ppr1/inputs/1728995192/RORgamma_SR8278.merged.nodup.pr1.pooled.tagAlign.gz 
    -i=/cromwell-executions/chip/3516233a-e8eb-4cca-9c61-f05ce8c6881e/call-call_peak_ppr1/inputs/-1056463068/Input-RORgamma_SR8278.merged.nodup.pooled.tagAlign.gz 
    -npeak=300000 
    -odir=/cromwell-executions/chip/3516233a-e8eb-4cca-9c61-f05ce8c6881e/call-call_peak_ppr1/execution -speak=88 
    -savr=RORgamma_SR8278.merged.nodup.pr1.pooled_x_Input-RORgamma_SR8278.merged.nodup.pooled.300K.regionPeak.gz.tmp 
    -rf

Below is the relevant part extracted from the the stderr.

[2019-12-19 21:19:15,772 INFO] run_shell_cmd: PID=16, PGID=16, CMD=Rscript --max-ppsize=500000 $(which run_spp.R) -c=/cromwell-executions/chip/3516233a-e8eb-4cca-9c61-f05ce8c6881e/call-call_peak_ppr1/inputs/1728995192/RORgamma_SR8278.merged.nodup.pr1.pooled.tagAlign.gz -i=/cromwell-executions/chip/3516233a-e8eb-4cca-9c61-f05ce8c6881e/call-call_peak_ppr1/inputs/-1056463068/Input-RORgamma_SR8278.merged.nodup.pooled.tagAlign.gz -npeak=300000 -odir=/cromwell-executions/chip/3516233a-e8eb-4cca-9c61-f05ce8c6881e/call-call_peak_ppr1/execution -speak=88 -savr=RORgamma_SR8278.merged.nodup.pr1.pooled_x_Input-RORgamma_SR8278.merged.nodup.pooled.300K.regionPeak.gz.tmp -rf 
[2019-12-19 23:15:07,430 INFO] PID=16, PGID=16, RC=0
STDERR=Loading required package: caTools
There were 24 warnings (use warnings() to see them)
There were 50 or more warnings (use warnings() to see the first 50)
STDOUT=################
ChIP data: /cromwell-executions/chip/3516233a-e8eb-4cca-9c61-f05ce8c6881e/call-call_peak_ppr1/inputs/1728995192/RORgamma_SR8278.merged.nodup.pr1.pooled.tagAlign.gz 
Control data: /cromwell-executions/chip/3516233a-e8eb-4cca-9c61-f05ce8c6881e/call-call_peak_ppr1/inputs/-1056463068/Input-RORgamma_SR8278.merged.nodup.pooled.tagAlign.gz 
strandshift(min): -500 
strandshift(step): 5 
strandshift(max) 1500 
user-defined peak shift 88 
exclusion(min): 10 
exclusion(max): NaN 
num parallel nodes: NA 
FDR threshold: 0.01 
NumPeaks Threshold: 3e+05 
Output Directory: /cromwell-executions/chip/3516233a-e8eb-4cca-9c61-f05ce8c6881e/call-call_peak_ppr1/execution 
narrowPeak output file name: NA 
regionPeak output file name: RORgamma_SR8278.merged.nodup.pr1.pooled_x_Input-RORgamma_SR8278.merged.nodup.pooled.300K.regionPeak.gz.tmp 
Rdata filename: NA 
plot pdf filename: NA 
result filename: NA 
Overwrite files?: TRUE

Decompressing ChIP file
Decompressing control file
Reading ChIP tagAlign/BAM file /cromwell-executions/chip/3516233a-e8eb-4cca-9c61-f05ce8c6881e/call-call_peak_ppr1/inputs/1728995192/RORgamma_SR8278.merged.nodup.pr1.pooled.tagAlign.gz 
opened /cromwell-executions/chip/3516233a-e8eb-4cca-9c61-f05ce8c6881e/call-call_peak_ppr1/tmp.89420c28/RtmpHtJFMf/RORgamma_SR8278.merged.nodup.pr1.pooled.tagAlign1255ec619f
done. read 15586545 fragments
ChIP data read length 50 
[1] TRUE
Reading Control tagAlign/BAM file /cromwell-executions/chip/3516233a-e8eb-4cca-9c61-f05ce8c6881e/call-call_peak_ppr1/inputs/-1056463068/Input-RORgamma_SR8278.merged.nodup.pooled.tagAlign.gz 
opened /cromwell-executions/chip/3516233a-e8eb-4cca-9c61-f05ce8c6881e/call-call_peak_ppr1/tmp.89420c28/RtmpHtJFMf/Input-RORgamma_SR8278.merged.nodup.pooled.tagAlign123cd5c1b1
done. read 12301614 fragments
Control data read length 50 
Calculating peak characteristics
Minimum cross-correlation value 0.1761151 
Minimum cross-correlation shift 1500 
Top 3 cross-correlation values 0.176655001491476 
Top 3 estimates for fragment length 88 
Window half size 195 
Phantom peak location 50 
Phantom peak Correlation 0.1776285 
Normalized Strand cross-correlation coefficient (NSC) 1.003066 
Relative Strand cross-correlation Coefficient (RSC) 0.3567363 
Phantom Peak Quality Tag -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= 0.7807313  processing chr11 in 4 steps [....] done ( 45269 positions)
processing chr17 in 3 steps [...] done ( 39589 positions)
processing chr12 in 4 steps [....] done ( 50222 positions)
processing chr1 in 7 steps [.......] done ( 80939 positions)
processing chr4 in 5 steps [.....] done ( 54397 positions)
processing chr20 in 2 steps [..] done ( 24780 positions)
processing chr19 in 2 steps [..] done ( 36115 positions)
processing chr3 in 5 steps [.....] done ( 62629 positions)
processing chr2 in 7 steps [.......] done ( 56991 positions)
processing chr9 in 4 steps [....] done ( 38905 positions)
processing chr7 in 4 steps [....] done ( 55427 positions)
processing chrX in 4 steps [....] done ( 27321 positions)
processing chr15 in 3 steps [...] done ( 29337 positions)
processing chr10 in 4 steps [....] done ( 46148 positions)
processing chr13 in 3 steps [...] done ( 19956 positions)
processing chr6 in 5 steps [.....] done ( 47965 positions)
processing chr16 in 3 steps [...] done ( 35229 positions)
processing chr5 in 5 steps [.....] done ( 55253 positions)
processing chr14 in 3 steps [...] done ( 31831 positions)
processing chr8 in 4 steps [....] done ( 46370 positions)
processing chr18 in 3 steps [...] done ( 22334 positions)
processing chr22 in 2 steps [..] done ( 16787 positions)
processing chr21 in 2 steps [..] done ( 10370 positions)
processing chrY in 2 steps [..] done ( 3152 positions)
processing chrUn_KI270587v1 in 1 steps [.] done ( 4 positions)
processing chr22_KI270736v1_random in 1 steps [.] done ( 185 positions)
processing chr4_GL000008v2_random in 1 steps [.] done ( 22 positions)
processing chrM in 1 steps [.] done ( 43 positions)
processing chrUn_KI270744v1 in 1 steps [.] done ( 14 positions)
processing chrUn_KI270756v1 in 1 steps [.] done ( 17 positions)
processing chrUn_KI270467v1 in 1 steps [.] done ( 9 positions)
processing chrUn_KI270507v1 in 1 steps [.] done ( 4 positions)
processing chr14_KI270724v1_random in 1 steps [.] done ( 4 positions)
processing chr17_KI270729v1_random in 1 steps [.] done ( 193 positions)
processing chrUn_KI270442v1 in 1 steps [.] done ( 398 positions)
processing chrUn_GL000218v1 in 1 steps [.] done ( 16 positions)
processing chrUn_KI270757v1 in 1 steps [.] done ( 34 positions)
processing chrUn_KI270509v1 in 1 steps [.] done ( 2 positions)
processing chrUn_KI270438v1 in 1 steps [.] done ( 116 positions)
processing chrUn_KI270538v1 in 1 steps [.] done ( 65 positions)
processing chr22_KI270735v1_random in 1 steps [.] done ( 9 positions)
processing chrUn_GL000216v2 in 1 steps [.] done ( 147 positions)
processing chrUn_KI270743v1 in 1 steps [.] done ( 8 positions)
processing chr17_GL000205v2_random in 1 steps [.] done ( 92 positions)
processing chrUn_KI270468v1 in 1 steps [.] done ( 4 positions)
processing chrUn_KI270750v1 in 1 steps [.] done ( 6 positions)
processing chr14_KI270722v1_random in 1 steps [.] done ( 31 positions)
processing chr5_GL000208v1_random in 1 steps [.] done ( 53 positions)
processing chrUn_KI270435v1 in 1 steps [.] done ( 46 positions)
processing chrUn_KI270519v1 in 1 steps [.] done ( 118 positions)
processing chrUn_GL000224v1 in 1 steps [.] done ( 28 positions)
processing chrUn_GL000219v1 in 1 steps [.] done ( 30 positions)
processing chr9_KI270718v1_random in 1 steps [.] done ( 1 positions)
processing chrUn_KI270466v1 in 1 steps [.] done ( 3 positions)
processing chrUn_KI270517v1 in 1 steps [.] done ( 3 positions)
processing chr16_KI270728v1_random in 1 steps [.] done ( 41 positions)
processing chrUn_KI270333v1 in 1 steps [.] done ( 6 positions)
processing chr14_GL000225v1_random in 1 steps [.] done ( 180 positions)
processing chr17_KI270730v1_random in 1 steps [.] done ( 38 positions)
processing chrUn_KI270746v1 in 1 steps [.] done ( 10 positions)
processing chr1_KI270706v1_random in 1 steps [.] done ( 11 positions)
processing chrUn_KI270511v1 in 1 steps [.] done ( 7 positions)
processing chr22_KI270738v1_random in 1 steps [.] done ( 111 positions)
processing chr14_KI270725v1_random in 1 steps [.] done ( 5 positions)
processing chr22_KI270733v1_random in 1 steps [.] done ( 32 positions)
processing chrUn_KI270591v1 in 1 steps [.] done ( 7 positions)
processing chrUn_KI270753v1 in 1 steps [.] done ( 0 positions)
processing chrUn_KI270515v1 in 1 steps [.] done ( 12 positions)
processing chr22_KI270732v1_random in 1 steps [.] done ( 11 positions)
processing chr9_KI270720v1_random in 1 steps [.] done ( 4 positions)
processing chr14_KI270726v1_random in 1 steps [.] done ( 6 positions)
processing chr9_KI270719v1_random in 1 steps [.] done ( 8 positions)
processing chrUn_KI270749v1 in 1 steps [.] done ( 10 positions)
processing chrUn_KI270751v1 in 1 steps [.] done ( 13 positions)
processing chr1_KI270711v1_random in 1 steps [.] done ( 1 positions)
processing chr14_GL000194v1_random in 1 steps [.] done ( 8 positions)
processing chr1_KI270712v1_random in 1 steps [.] done ( 11 positions)
processing chr14_GL000009v2_random in 1 steps [.] done ( 9 positions)
processing chrUn_KI270522v1 in 1 steps [.] done ( 4 positions)
processing chrUn_GL000195v1 in 1 steps [.] done ( 13 positions)
processing chrUn_KI270337v1 in 1 steps [.] done ( 3 positions)
processing chrUn_GL000220v1 in 1 steps [.] done ( 4 positions)
processing chr14_KI270723v1_random in 1 steps [.] done ( 10 positions)
processing chr1_KI270709v1_random in 1 steps [.] done ( 27 positions)
processing chrUn_KI270588v1 in 1 steps [.] done ( 7 positions)
processing chrUn_KI270336v1 in 1 steps [.] done ( 3 positions)
processing chr1_KI270708v1_random in 1 steps [.] done ( 10 positions)
processing chr22_KI270739v1_random in 1 steps [.] done ( 3 positions)
processing chrUn_KI270429v1 in 1 steps [.] done ( 2 positions)
processing chr22_KI270737v1_random in 1 steps [.] done ( 11 positions)
processing chrUn_KI270584v1 in 1 steps [.] done ( 9 positions)
processing chrUn_KI270510v1 in 1 steps [.] done ( 4 positions)
processing chrUn_GL000214v1 in 1 steps [.] done ( 3 positions)
processing chr15_KI270727v1_random in 1 steps [.] done ( 1 positions)
processing chrUn_KI270590v1 in 1 steps [.] done ( 9 positions)
processing chrUn_KI270448v1 in 1 steps [.] done ( 10 positions)
processing chrUn_KI270754v1 in 1 steps [.] done ( 1 positions)
processing chrUn_KI270508v1 in 1 steps [.] done ( 2 positions)
processing chrUn_KI270742v1 in 1 steps [.] done ( 5 positions)
processing chrUn_KI270589v1 in 1 steps [.] done ( 6 positions)
processing chrUn_KI270512v1 in 1 steps [.] done ( 13 positions)
processing chrUn_KI270580v1 in 1 steps [.] done ( 1 positions)
processing chrY_KI270740v1_random in 1 steps [.] done ( 0 positions)
processing chrUn_KI270311v1 in 1 steps [.] done ( 1 positions)
processing chrUn_KI270362v1 in 1 steps [.] done ( 1 positions)
processing chrUn_KI270755v1 in 1 steps [.] done ( 0 positions)
processing chrUn_KI270516v1 in 1 steps [.] done ( 2 positions)
processing chrUn_KI270518v1 in 1 steps [.] done ( 2 positions)
processing chrUn_KI270593v1 in 1 steps [.] done ( 2 positions)
processing chr1_KI270710v1_random in 1 steps [.] done ( 7 positions)
processing chr2_KI270716v1_random in 1 steps [.] done ( 13 positions)
processing chrUn_KI270330v1 in 1 steps [.] done ( 0 positions)
processing chrUn_KI270521v1 in 1 steps [.] done ( 3 positions)
processing chr1_KI270707v1_random in 1 steps [.] done ( 1 positions)
processing chrUn_KI270747v1 in 1 steps [.] done ( 5 positions)
processing chrUn_KI270320v1 in 1 steps [.] done ( 1 positions)
processing chr1_KI270713v1_random in 1 steps [.] done ( 3 positions)
processing chr3_GL000221v1_random in 1 steps [.] done ( 3 positions)
processing chrUn_KI270322v1 in 1 steps [.] done ( 0 positions)
processing chr22_KI270731v1_random in 1 steps [.] done ( 0 positions)
processing chrUn_GL000213v1 in 1 steps [.] done ( 0 positions)
processing chrUn_KI270583v1 in 1 steps [.] done ( 1 positions)
processing chrUn_KI270420v1 in 1 steps [.] done ( 0 positions)
processing chrUn_KI270465v1 in 1 steps [.] done ( 1 positions)
processing chr22_KI270734v1_random in 1 steps [.] done ( 0 positions)
processing chr9_KI270717v1_random in 1 steps [.] done ( 1 positions)
processing chrUn_KI270417v1 in 1 steps [.] done ( 2 positions)
processing chr1_KI270714v1_random in 1 steps [.] done ( 0 positions)
processing chr2_KI270715v1_random in 1 steps [.] done ( 1 positions)
processing chrUn_KI270741v1 in 1 steps [.] done ( 0 positions)
excluding systematic background anomalies ... done
determining peaks on real data:
bg.weight= 1.28085  processing chr11 in 4 steps [....] done ( 34251 positions)
processing chr17 in 3 steps [...] done ( 17942 positions)
processing chr12 in 4 steps [....] done ( 34038 positions)
processing chr1 in 7 steps [.......] done ( 57326 positions)
processing chr4 in 5 steps [.....] done ( 46423 positions)
processing chr20 in 2 steps [..] done ( 15476 positions)
processing chr19 in 2 steps [..] done ( 9556 positions)
processing chr3 in 5 steps [.....] done ( 53839 positions)
processing chr2 in 7 steps [.......] done ( 36187 positions)
processing chr9 in 4 steps [....] done ( 28796 positions)
processing chr7 in 4 steps [....] done ( 38976 positions)
processing chrX in 4 steps [....] done ( 10644 positions)
processing chr15 in 3 steps [...] done ( 20804 positions)
processing chr10 in 4 steps [....] done ( 32213 positions)
processing chr13 in 3 steps [...] done ( 14221 positions)
processing chr6 in 5 steps [.....] done ( 35714 positions)
processing chr16 in 3 steps [...] done ( 16237 positions)
processing chr5 in 5 steps [.....] done ( 47970 positions)
processing chr14 in 3 steps [...] done ( 23766 positions)
processing chr8 in 4 steps [....] done ( 38414 positions)
processing chr18 in 3 steps [...] done ( 20487 positions)
processing chr22 in 2 steps [..] done ( 6987 positions)
processing chr21 in 2 steps [..] done ( 6903 positions)
processing chrY in 2 steps [..] done ( 552 positions)
processing chrUn_KI270587v1 in 1 steps [.] done ( 0 positions)
processing chr22_KI270736v1_random in 1 steps [.] done ( 6 positions)
processing chr4_GL000008v2_random in 1 steps [.] done ( 0 positions)
processing chrM in 1 steps [.] done ( 0 positions)
processing chrUn_KI270744v1 in 1 steps [.] done ( 3 positions)
processing chrUn_KI270756v1 in 1 steps [.] done ( 0 positions)
processing chrUn_KI270467v1 in 1 steps [.] done ( 0 positions)
processing chrUn_KI270507v1 in 1 steps [.] done ( 0 positions)
processing chr14_KI270724v1_random in 1 steps [.] done ( 4 positions)
processing chr17_KI270729v1_random in 1 steps [.] done ( 0 positions)
processing chrUn_KI270442v1 in 1 steps [.] done ( 11 positions)
processing chrUn_GL000218v1 in 1 steps [.] done ( 1 positions)
processing chrUn_KI270757v1 in 1 steps [.] done ( 0 positions)
processing chrUn_KI270509v1 in 1 steps [.] done ( 0 positions)
processing chrUn_KI270438v1 in 1 steps [.] done ( 1 positions)
processing chrUn_KI270538v1 in 1 steps [.] done ( 2 positions)
processing chr22_KI270735v1_random in 1 steps [.] done ( 4 positions)
processing chrUn_GL000216v2 in 1 steps [.] done ( 5 positions)
processing chrUn_KI270743v1 in 1 steps [.] done ( 0 positions)
processing chr17_GL000205v2_random in 1 steps [.] done ( 45 positions)
processing chrUn_KI270468v1 in 1 steps [.] done ( 0 positions)
processing chrUn_KI270750v1 in 1 steps [.] done ( 22 positions)
processing chr14_KI270722v1_random in 1 steps [.] done ( 25 positions)
processing chr5_GL000208v1_random in 1 steps [.] done ( 0 positions)
processing chrUn_KI270435v1 in 1 steps [.] done ( 2 positions)
processing chrUn_KI270519v1 in 1 steps [.] done ( 4 positions)
processing chrUn_GL000224v1 in 1 steps [.] done ( 4 positions)
processing chrUn_GL000219v1 in 1 steps [.] done ( 4 positions)
processing chr9_KI270718v1_random in 1 steps [.] done ( 0 positions)
processing chrUn_KI270466v1 in 1 steps [.] done ( 0 positions)
processing chrUn_KI270517v1 in 1 steps [.] done ( 0 positions)
processing chr16_KI270728v1_random in 1 steps [.] done ( 3 positions)
processing chrUn_KI270333v1 in 1 steps [.] done ( 0 positions)
processing chr14_GL000225v1_random in 1 steps [.] done ( 7 positions)
processing chr17_KI270730v1_random in 1 steps [.] done ( 0 positions)
processing chrUn_KI270746v1 in 1 steps [.] done ( 6 positions)
processing chr1_KI270706v1_random in 1 steps [.] done ( 0 positions)
processing chrUn_KI270511v1 in 1 steps [.] done ( 0 positions)
processing chr22_KI270738v1_random in 1 steps [.] done ( 2 positions)
processing chr14_KI270725v1_random in 1 steps [.] done ( 2 positions)
processing chr22_KI270733v1_random in 1 steps [.] done ( 2 positions)
processing chrUn_KI270591v1 in 1 steps [.] done ( 1 positions)
processing chrUn_KI270753v1 in 1 steps [.] done ( 0 positions)
processing chrUn_KI270515v1 in 1 steps [.] done ( 1 positions)
processing chr22_KI270732v1_random in 1 steps [.] done ( 4 positions)
processing chr9_KI270720v1_random in 1 steps [.] done ( 1 positions)
processing chr14_KI270726v1_random in 1 steps [.] done ( 1 positions)
processing chr9_KI270719v1_random in 1 steps [.] done ( 4 positions)
processing chrUn_KI270749v1 in 1 steps [.] done ( 1 positions)
processing chrUn_KI270751v1 in 1 steps [.] done ( 2 positions)
processing chr1_KI270711v1_random in 1 steps [.] done (  positions)
processing chr14_GL000194v1_random in 1 steps [.] done ( 1 positions)
processing chr1_KI270712v1_random in 1 steps [.] done ( 0 positions)
processing chr14_GL000009v2_random in 1 steps [.] done ( 1 positions)
processing chrUn_KI270522v1 in 1 steps [.] done ( 1 positions)
processing chrUn_GL000195v1 in 1 steps [.] done ( 9 positions)
processing chrUn_KI270337v1 in 1 steps [.] done ( 0 positions)
processing chrUn_GL000220v1 in 1 steps [.] done ( 0 positions)
processing chr14_KI270723v1_random in 1 steps [.] done ( 1 positions)
processing chr1_KI270709v1_random in 1 steps [.] done ( 6 positions)
processing chrUn_KI270588v1 in 1 steps [.] done ( 0 positions)
processing chrUn_KI270336v1 in 1 steps [.] done ( 0 positions)
processing chr1_KI270708v1_random in 1 steps [.] done ( 0 positions)
processing chr22_KI270739v1_random in 1 steps [.] done ( 0 positions)
processing chrUn_KI270429v1 in 1 steps [.] done ( 0 positions)
processing chr22_KI270737v1_random in 1 steps [.] done ( 0 positions)
processing chrUn_KI270584v1 in 1 steps [.] done ( 0 positions)
processing chrUn_KI270510v1 in 1 steps [.] done ( 0 positions)
processing chrUn_GL000214v1 in 1 steps [.] done ( 1 positions)
processing chr15_KI270727v1_random in 1 steps [.] done ( 0 positions)
processing chrUn_KI270590v1 in 1 steps [.] done ( 0 positions)
processing chrUn_KI270448v1 in 1 steps [.] done ( 0 positions)
processing chrUn_KI270754v1 in 1 steps [.] done ( 0 positions)
processing chrUn_KI270508v1 in 1 steps [.] done ( 0 positions)
processing chrUn_KI270742v1 in 1 steps [.] done ( 5 positions)
processing chrUn_KI270589v1 in 1 steps [.] done ( 0 positions)
processing chrUn_KI270512v1 in 1 steps [.] done ( 0 positions)
processing chrUn_KI270580v1 in 1 steps [.] done ( 0 positions)
processing chrY_KI270740v1_random in 1 steps [.] done ( 0 positions)
processing chrUn_KI270311v1 in 1 steps [.] done ( 0 positions)
processing chrUn_KI270362v1 in 1 steps [.] done ( 0 positions)
processing chrUn_KI270755v1 in 1 steps [.] done ( 0 positions)
processing chrUn_KI270516v1 in 1 steps [.] done ( 0 positions)
processing chrUn_KI270518v1 in 1 steps [.] done ( 1 positions)
processing chrUn_KI270593v1 in 1 steps [.] done ( 0 positions)
processing chr1_KI270710v1_random in 1 steps [.] done ( 0 positions)
processing chr2_KI270716v1_random in 1 steps [.] done ( 0 positions)
processing chrUn_KI270330v1 in 1 steps [.] done ( 0 positions)
processing chrUn_KI270521v1 in 1 steps [.] done ( 0 positions)
processing chr1_KI270707v1_random in 1 steps [.] done ( 0 positions)
processing chrUn_KI270747v1 in 1 steps [.] done ( 0 positions)
processing chrUn_KI270320v1 in 1 steps [.] done ( 0 positions)
processing chr1_KI270713v1_random in 1 steps [.] done ( 0 positions)
processing chr3_GL000221v1_random in 1 steps [.] done ( 0 positions)
processing chrUn_KI270322v1 in 1 steps [.] done ( 0 positions)
processing chrUn_KI270752v1 in 1 steps [.] done ( 0 positions)
processing chr22_KI270731v1_random in 1 steps [.] done ( 0 positions)
processing chrUn_KI270583v1 in 1 steps [.] done ( 0 positions)
processing chrUn_KI270420v1 in 1 steps [.] done ( 0 positions)
processing chrUn_KI270465v1 in 1 steps [.] done ( 0 positions)
processing chr22_KI270734v1_random in 1 steps [.] done (  positions)
processing chr9_KI270717v1_random in 1 steps [.] done ( 0 positions)
processing chrUn_KI270417v1 in 1 steps [.] done ( 0 positions)
processing chrUn_KI270741v1 in 1 steps [.] done (  positions)
excluding systematic background anomalies ... done
calculating statistical thresholds
FDR 0.99 threshold= Inf 
Detected 0 peaks
zhuchcn commented 4 years ago

I didn't solve my problem, but I think it is related to the data quality so I will close it now.