create error model (IndexError)

Encountered errors when running iss model:

DEBUG:iss.app:iss version 1.3.3 DEBUG:iss.app:Using verbose logger INFO:iss.app:Starting iss model INFO:iss.app:Using KDE ErrorModel INFO:iss.bam:Reading bam file: sortedRef.bam INFO:iss.bam:Calculating insert size distribution /home/anting/.local/lib/python3.6/site-packages/numpy/core/_methods.py:140: RuntimeWarning: Degrees of freedom <= 0 for slice keepdims=keepdims) /home/anting/.local/lib/python3.6/site-packages/numpy/core/_methods.py:110: RuntimeWarning: invalid value encountered in true_divide arrmean, rcount, out=arrmean, casting=‘unsafe’, subok=False) /home/anting/.local/lib/python3.6/site-packages/numpy/core/_methods.py:132: RuntimeWarning: invalid value encountered in double_scalars ret = ret.dtype.type(ret / rcount) Traceback (most recent call last): File “/home/anting/.local/bin/iss”, line 11, in <module> sys.exit(main()) File “/home/anting/.local/lib/python3.6/site-packages/iss/app.py”, line 489, in main args.func(args) File “/home/anting/.local/lib/python3.6/site-packages/iss/app.py”, line 263, in model_from_bam bam.to_model(args.bam, args.output) File “/home/anting/.local/lib/python3.6/site-packages/iss/bam.py”, line 189, in to_model hist_insert_size = modeller.insert_size(insert_size_dist) File “/home/anting/.local/lib/python3.6/site-packages/iss/modeller.py”, line 28, in insert_size bw_method=0.2 / np.std(insert_size_distribution, ddof=1)) File “/home/anting/.local/lib/python3.6/site-packages/scipy/stats/kde.py”, line 195, in init raise ValueError(“dataset input should have multiple elements.”) ValueError: dataset input should have multiple elements.

[HadrienG]

In that case I’d advise against using insilicoseq as it will not accurately model homopolymers errors

[antingH]

Hi Hadrien, the bam files are at https://drive.google.com/file/d/1PhGeyhw6zo77pmy8SjoibfD8hyIUcRVL/view?usp=sharing Thanks for working on this!