problem on simulation of tumor reads

[arthuryxt]

Hi, first of all, thanks for the tool!

I met a problem in simulating reads with CNV, where normal reads are generated nicely but no tumor reads. I tried setting the "region file" to include "chr1" to reduce memory use (the machine I use have 32G mem). Could you suggest a way through?

The "SIMULATION_IS_COMPLETE.txt" file reads:
/========================
SIMULATION STARTED WITH THE FOLLOWING PARAMETERS

SNP Rate: 0.05
Indel Rate: 0.001
Transition/Transversion Ratio: 2
CNV Rate: 0
CNV Minimum Size: 0
CNV Maximum Size: 0
Ploidy: 2
Subclones: 1
Number of Reads: 1000000
Read Length: 100

Copying temporary files for normal reads ..
Copying temporary files for tumor reads ..

Generating normal reads ..

Generating fasta file for given regions...

---

Reference: /ref/my_sim/normal/GRCh37.fa
Region file: /ref/my_sim/normal/target.chr1.bed
Fragment: 200 +- 50 > 120
Paired-end mode? True
Sequencing model: /easyscnvsim_lib/Wessim/models/ill100v4_p.gzip
Read length: 100 Read number: 10000
Output File: /ref/my_sim/normal/normal
Gzip compress? False
Quality base: 33
Thread number: 2
Job started at: 2018-07-13 04:43:37
/-------------------------------------------

exiting subprocess 2
exiting subprocess 1
Done generating 10000 reads in 18.700755 secs
Merging subresults...
Finished generating normal reads ..

Simulating tumor variations in subclone 1 ..
This step takes some time. Be patient and don't terminate the Docker container :)

Wait! Wait! Simulating the variations in subclone 1 is complete. But it's still generating reads ..

Cleaning temporary files ..

Traceback (most recent call last):
File "cnv-sim.py", line 103, in
main()
File "cnv-sim.py", line 65, in main
args = parser.parse_args()
File "/usr/lib/python2.7/argparse.py", line 1690, in parse_args
args, argv = self.parse_known_args(args, namespace)
File "/usr/lib/python2.7/argparse.py", line 1722, in parse_known_args
namespace, args = self._parse_known_args(args, namespace)
File "/usr/lib/python2.7/argparse.py", line 1931, in _parse_known_args
stop_index = consume_positionals(start_index)
File "/usr/lib/python2.7/argparse.py", line 1887, in consume_positionals
take_action(action, args)
File "/usr/lib/python2.7/argparse.py", line 1780, in take_action
argument_values = self._get_values(action, argument_strings)
File "/usr/lib/python2.7/argparse.py", line 2220, in _get_values
value = self._get_value(action, arg_string)
File "/usr/lib/python2.7/argparse.py", line 2249, in _get_value
result = type_func(arg_string)
IOError: [Errno 2] No such file or directory: '/ref/my_sim/tumor/subclone_1/allele_1.fa'
/========================