DANPOS Profile not working

[amitjavilaventura]

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.