Fastq_screen reported that results files where present and skipping tests for bowtie1. Forcing cleanup.
The addition of psutil might have introduced a regression on memory_profiler logic:
Processing /pica/h1/roman/dev/facs/tests/data/synthetic_fastq/simngs_eschColi_K12_1000000.fastq
Counting sequences in /pica/h1/roman/dev/facs/tests/data/synthetic_fastq/simngs_eschColi_K12_1000000.fastq
Searching /pica/h1/roman/dev/facs/tests/data/synthetic_fastq/simngs_eschColi_K12_1000000.fastq against phiX
Process MemTimer-3:
Traceback (most recent call last):
File "/usr/lib64/python2.6/multiprocessing/process.py", line 232, in _bootstrap
self.run()
File "/pica/h1/roman/.virtualenvs/facs/lib/python2.6/site-packages/memory_profiler.py", line 123, in run
include_children=self.include_children)
File "/pica/h1/roman/.virtualenvs/facs/lib/python2.6/site-packages/memory_profiler.py", line 51, in _get_memory
mem += p.get_memory_info()[0] / _TWO_20
File "/pica/h1/roman/.virtualenvs/facs/lib/python2.6/site-packages/psutil/__init__.py", line 758, in get_memory_info
return self._platform_impl.get_memory_info()
File "/pica/h1/roman/.virtualenvs/facs/lib/python2.6/site-packages/psutil/_pslinux.py", line 470, in wrapper
raise NoSuchProcess(self.pid, self._process_name)
NoSuchProcess: process no longer exists (pid=17523)
psutil
might have introduced a regression onmemory_profiler
logic: