sub_wessim1 numpy error

[menzel]

I'm trying to create reads with CNV's using the following command:

python2 ./SECNVs/SECNVs.py -G ~/hg19.fa -T ~/regions.bed -o test -e_tol 10 -ssr -sb -picard ~/Downloads/picard -GATK /usr/bin/gatk

I had to edit two files to call python2 instead of 3, as '3' is the default python for me. However, now it fails in the __sub_wessim1.py script. This Error message comes for each thread:

Traceback (most recent call last):
File "__sub_wessim1.py", line 834, in
main(sys.argv[1:])
File "__sub_wessim1.py", line 137, in main
insDict=mkInserts(mx1,insD1)
File "__sub_wessim1.py", line 429, in mkInserts
posKeys=insD.keys()
AttributeError: 'numpy.ndarray' object has no attribute 'keys'
exiting subprocess 1

Subsequently SECNVs.py fails with:

Traceback (most recent call last):
File "./SECNVs/SECNVs.py", line 349, in
main()
File "./SECNVs/SECNVs.py", line 334, in main
simulate_WES(param, iin_seqs, iin_chrs, iin_st, iin_ed, args.sim_control, 0, iin_ran_m)
File "/home/menzel/Desktop/uniklinik/ddr/artificial_reads/SECNVs/WES_simulator.py", line 892, in simulate_WES
subprocess.call(['bwa', 'index', ref_genome])
File "/usr/lib/python2.7/subprocess.py", line 172, in call
return Popen(*popenargs, **kwargs).wait()
File "/usr/lib/python2.7/subprocess.py", line 394, in init
errread, errwrite)
File "/usr/lib/python2.7/subprocess.py", line 1047, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory