In the corresponding .err file fanc recognizes the inputs as the 2 fastqs, goes through various checks for the regions within the $redigest file (a digest I created with genome_digester.py from HiCPro using the motifs from the Arima kit), and begins task Process Process-1, then returns the following traceback:
Traceback (most recent call last):
File "/common/software/install/spack/linux-centos7-ivybridge/gcc-13.1.0/python-3.10.10-ucftoxtxmvazes7lcobwhishhspudjbq/lib/python3.10/multiprocessing/process.py", line 314, in _bootstrap
self.run()
File "/common/software/install/spack/linux-centos7-ivybridge/gcc-13.1.0/python-3.10.10-ucftoxtxmvazes7lcobwhishhspudjbq/lib/python3.10/multiprocessing/process.py", line 108, in run
self._target(*self._args, *self._kwargs)
File "/home/largaesp/stehn007/bin/venv/fanc/lib/python3.10/site-packages/fanc/commands/auto.py", line 58, in _run_task
res = subprocess.call(task.command)
File "/common/software/install/spack/linux-centos7-ivybridge/gcc-13.1.0/python-3.10.10-ucftoxtxmvazes7lcobwhishhspudjbq/lib/python3.10/subprocess.py", line 345, in call
with Popen(popenargs, **kwargs) as p:
File "/common/software/install/spack/linux-centos7-ivybridge/gcc-13.1.0/python-3.10.10-ucftoxtxmvazes7lcobwhishhspudjbq/lib/python3.10/subprocess.py", line 971, in init
self._execute_child(args, executable, preexec_fn, close_fds,
File "/common/software/install/spack/linux-centos7-ivybridge/gcc-13.1.0/python-3.10.10-ucftoxtxmvazes7lcobwhishhspudjbq/lib/python3.10/subprocess.py", line 1780, in _execute_child
self.pid = _posixsubprocess.fork_exec(
TypeError: expected str, bytes or os.PathLike object, not NoneType
I installed fanc 0.9.28 using pip with python 3.10.10. Does anyone have any clue why this is occurring?
Hello,
I have 2 fastq.gz files from Arima HiC+ kit I am trying to process with fanc auto from start to finish. My call is as follows
fanc -vvv auto ${fastq}/${sample}.R1.fastq.gz ${fastq}/${sample}.R2.fastq.gz $outdir -g $redigest -n ${sample} --split-fastq -i $hg38 -tmp --split-ligation-junction
In the corresponding .err file fanc recognizes the inputs as the 2 fastqs, goes through various checks for the regions within the $redigest file (a digest I created with genome_digester.py from HiCPro using the motifs from the Arima kit), and begins task Process Process-1, then returns the following traceback:
Traceback (most recent call last): File "/common/software/install/spack/linux-centos7-ivybridge/gcc-13.1.0/python-3.10.10-ucftoxtxmvazes7lcobwhishhspudjbq/lib/python3.10/multiprocessing/process.py", line 314, in _bootstrap self.run() File "/common/software/install/spack/linux-centos7-ivybridge/gcc-13.1.0/python-3.10.10-ucftoxtxmvazes7lcobwhishhspudjbq/lib/python3.10/multiprocessing/process.py", line 108, in run self._target(*self._args, *self._kwargs) File "/home/largaesp/stehn007/bin/venv/fanc/lib/python3.10/site-packages/fanc/commands/auto.py", line 58, in _run_task res = subprocess.call(task.command) File "/common/software/install/spack/linux-centos7-ivybridge/gcc-13.1.0/python-3.10.10-ucftoxtxmvazes7lcobwhishhspudjbq/lib/python3.10/subprocess.py", line 345, in call with Popen(popenargs, **kwargs) as p: File "/common/software/install/spack/linux-centos7-ivybridge/gcc-13.1.0/python-3.10.10-ucftoxtxmvazes7lcobwhishhspudjbq/lib/python3.10/subprocess.py", line 971, in init self._execute_child(args, executable, preexec_fn, close_fds, File "/common/software/install/spack/linux-centos7-ivybridge/gcc-13.1.0/python-3.10.10-ucftoxtxmvazes7lcobwhishhspudjbq/lib/python3.10/subprocess.py", line 1780, in _execute_child self.pid = _posixsubprocess.fork_exec( TypeError: expected str, bytes or os.PathLike object, not NoneType
I installed fanc 0.9.28 using pip with python 3.10.10. Does anyone have any clue why this is occurring?