sklasfeld / danpos3 Goto Github PK

Dear Samantha,

Thank you for the update of DANPOS to DANPOS3.

I have been running DANPOS to calculate the nuclosome occupancy over certain regions I have.

The DANPOS dpos command have worked well. However, the DANPOS profile is getting some errors and not writting an output.

The command I am running is the following one:

python $DANPOSDIR/danpos.py profile <wigfile> --bed3file_paths <bedfile> --genomic_sites center --flank_up 1500 --flank_dn 1500 --heatmap 1 --periodicity 1 --name <name>

And the stderr has the following message:

Traceback (most recent call last):
  File "/mnt/beegfs/amitjavila/src/tools/DANPOS3//danpos.py", line 1370, in <module>
    elif sys.argv[1]=='profile':profile()
  File "/mnt/beegfs/amitjavila/src/tools/DANPOS3//danpos.py", line 894, in profile
    dic=batchOccPSD(wgs,outname=args.name+'.signalPeriodicity')
  File "/mnt/beegfs/amitjavila/src/tools/DANPOS3/lib.py", line 159, in batchOccPSD
    for k in keys:dic[k]=occPSD(wgs.get(k),outname=None)
  File "/mnt/beegfs/amitjavila/src/tools/DANPOS3/lib.py", line 1198, in occPSD
    v=float(str(v).split()[1])
ValueError: could not convert string to float: 'NA'
R[write to console]: Warning message:

R[write to console]: In cor(q1, q2) :
R[write to console]:  the standard deviation is zero

I have done a test with a "subset of some BAM files" and another one with a full BAM. Both have the same error, although the test with subset BAM writes the expected output.

On the other hand, I have previously run DANPOS profile before and when I run it with different regions in a for loop, it only runs the first iteration, like it was giving an "exit" at the end of the command.

Do you know what could be happening?

Thanks.

Adrià.

Hello

When I am using DANPOS, some tasks have the following bug, is there any solution for it?

Gratefully, siteng

Traceback (most recent call last):
File "/public/home/stbi/task/xxt/sequence/DANPOS3/danpos.py", line 1365, in
if sys.argv[1]=='dpos':runDANPOS(command='dpos')
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/public/home/stbi/task/xxt/sequence/DANPOS3/danpos.py", line 396, in runDANPOS
danpos(
File "/public/home/stbi/task/xxt/sequence/DANPOS3/functions.py", line 506, in danpos
allPositionsInOneFile(controlPositionFile=os.path.join(opath,'pooled',groupnames[1]+addname+"positions.ref_adjust.xls"),
File "/public/home/stbi/task/xxt/sequence/DANPOS3/functions.py", line 1172, in allPositionsInOneFile
temp=log10fuztest(pc=p1,pt=p2,cr=cr,cwig=cwig,twig=twig,rd=rd)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/public/home/stbi/task/xxt/sequence/DANPOS3/functions.py", line 1342, in log10fuztest
else:p=pf(unnumpy(div(vt,vc)),
^^^^^^^^^^^^^^^^^^^^^^^
File "/public/home/stbi/task/xxt/sequence/DANPOS3/functions.py", line 66, in pf
answer = log(answer)
^^^^^^^^^^^
ValueError: math domain error

Dear @sklasfeld,

I got an error when I use the DNAPOS3. Could you please give me some suggestion?

The command "python /home/yilei/biosoftware/DANPOS3/danpos.py dpos 29434_WT1-mono_S21_L999_R1_001.fastq_novoaligned.bam"

The error:

Thank you very much!

Best,
Andy

Hello, I am having a bit a of problem with the above-mentionned -b parameter.

I apologize if this is not strictly appropriate use of the git issue system, but as I tried asking questions over at the relevant google group for DANPOS and did not get a response, I thought I would try my luck here.

I am using ChIP-seq data and would like to know if the -b parameter can/should be used to provide the ChIP-seq input (by which I mean the results for a sample just like the IP, except it does not undergo immunoprecipitation). After reading the documentation on this parameter I am sadly still uncertain.

Thanks in advance for any help you can provide,
Gilles

hello,
cmd: python ~/software/DANPOS3/danpos.py dpos S8_MN_merge.bam:S24_MN_merge.bam -m 1 -t 1e-5
I have just ran into an error using DANPOS3:

The end of the log file

97000 simulated...
98000 simulated...
99000 simulated...
99931 simulated.
analyzing...
combining nucleosome and differential positions...
calculating differential values for positions...
chr1

Traceback (most recent call last):
File "DANPOS3/danpos.py", line 1365, in

if sys.argv[1]=='dpos':runDANPOS(command='dpos')

File "DANPOS3/danpos.py", line 424, in runDANPOS
pcfer=0)#args.pcfer)#0)
File "/D_test/DANPOS3/functions.py", line 511, in danpos
dis=distance,rd=rd,test=test,fdrsimu=0,fdrRegions=peaks,occFDRlist=occFDRlist,fuzFDRlist=fuzFDRlist,fdr=fdr)
File "/D_test/DANPOS3/functions.py", line 1172, in allPositionsInOneFile
temp=log10fuztest(pc=p1,pt=p2,cr=cr,cwig=cwig,twig=twig,rd=rd)
File "/D_test/DANPOS3/functions.py", line 1341, in log10fuztest
if vc<vt:p=pf(unnumpy(div(vc,vt)),unnumpy(cc),unnumpy(ct), log_bool=True)
File "/D_test/DANPOS3/functions.py", line 66, in pf

answer = log(answer)

ValueError: math domain error