/var/spool/slurm/d/job1231397/slurm_script: line 28: fg: no job control
Begin flipping the strand of read 2
Mon Aug 26 08:33:59 2019

Traceback (most recent call last):
  File "/gscratch/srlab/strigg/bin/anaconda3/bin/methylpy", line 4, in <module>
    __import__('pkg_resources').run_script('methylpy==1.3.7', 'methylpy')
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 666, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 1453, in run_script
    exec(code, namespace, namespace)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/EGG-INFO/scripts/methylpy", line 5, in <module>
    parse_args()
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/parser.py", line 221, in parse_args
    min_base_quality=args.min_base_quality)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1343, in call_methylated_sites_pe
    path_to_samtools=path_to_samtools)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1259, in flip_read2_strand
    output_handle = open(output_file,'w')
PermissionError: [Errno 13] Permission denied: '/gscratch/scrubbed/sr320/0807/EPI-151_S2_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam.read2flipped.bam'
Begin flipping the strand of read 2
Mon Aug 26 08:34:00 2019

Traceback (most recent call last):
  File "/gscratch/srlab/strigg/bin/anaconda3/bin/methylpy", line 4, in <module>
    __import__('pkg_resources').run_script('methylpy==1.3.7', 'methylpy')
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 666, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 1453, in run_script
    exec(code, namespace, namespace)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/EGG-INFO/scripts/methylpy", line 5, in <module>
    parse_args()
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/parser.py", line 221, in parse_args
    min_base_quality=args.min_base_quality)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1343, in call_methylated_sites_pe
    path_to_samtools=path_to_samtools)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1259, in flip_read2_strand
    output_handle = open(output_file,'w')
PermissionError: [Errno 13] Permission denied: '/gscratch/scrubbed/sr320/0807/EPI-152_S3_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam.read2flipped.bam'
Begin flipping the strand of read 2
Mon Aug 26 08:34:00 2019

Traceback (most recent call last):
  File "/gscratch/srlab/strigg/bin/anaconda3/bin/methylpy", line 4, in <module>
    __import__('pkg_resources').run_script('methylpy==1.3.7', 'methylpy')
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 666, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 1453, in run_script
    exec(code, namespace, namespace)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/EGG-INFO/scripts/methylpy", line 5, in <module>
    parse_args()
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/parser.py", line 221, in parse_args
    min_base_quality=args.min_base_quality)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1343, in call_methylated_sites_pe
    path_to_samtools=path_to_samtools)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1259, in flip_read2_strand
    output_handle = open(output_file,'w')
PermissionError: [Errno 13] Permission denied: '/gscratch/scrubbed/sr320/0807/EPI-153_S4_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam.read2flipped.bam'
Begin flipping the strand of read 2
Mon Aug 26 08:34:00 2019

Traceback (most recent call last):
  File "/gscratch/srlab/strigg/bin/anaconda3/bin/methylpy", line 4, in <module>
    __import__('pkg_resources').run_script('methylpy==1.3.7', 'methylpy')
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 666, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 1453, in run_script
    exec(code, namespace, namespace)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/EGG-INFO/scripts/methylpy", line 5, in <module>
    parse_args()
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/parser.py", line 221, in parse_args
    min_base_quality=args.min_base_quality)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1343, in call_methylated_sites_pe
    path_to_samtools=path_to_samtools)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1259, in flip_read2_strand
    output_handle = open(output_file,'w')
PermissionError: [Errno 13] Permission denied: '/gscratch/scrubbed/sr320/0807/EPI-154_S5_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam.read2flipped.bam'
Begin flipping the strand of read 2
Mon Aug 26 08:34:01 2019

Traceback (most recent call last):
  File "/gscratch/srlab/strigg/bin/anaconda3/bin/methylpy", line 4, in <module>
    __import__('pkg_resources').run_script('methylpy==1.3.7', 'methylpy')
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 666, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 1453, in run_script
    exec(code, namespace, namespace)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/EGG-INFO/scripts/methylpy", line 5, in <module>
    parse_args()
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/parser.py", line 221, in parse_args
    min_base_quality=args.min_base_quality)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1343, in call_methylated_sites_pe
    path_to_samtools=path_to_samtools)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1259, in flip_read2_strand
    output_handle = open(output_file,'w')
PermissionError: [Errno 13] Permission denied: '/gscratch/scrubbed/sr320/0807/EPI-159_S6_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam.read2flipped.bam'
Begin flipping the strand of read 2
Mon Aug 26 08:34:01 2019

Traceback (most recent call last):
  File "/gscratch/srlab/strigg/bin/anaconda3/bin/methylpy", line 4, in <module>
    __import__('pkg_resources').run_script('methylpy==1.3.7', 'methylpy')
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 666, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 1453, in run_script
    exec(code, namespace, namespace)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/EGG-INFO/scripts/methylpy", line 5, in <module>
    parse_args()
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/parser.py", line 221, in parse_args
    min_base_quality=args.min_base_quality)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1343, in call_methylated_sites_pe
    path_to_samtools=path_to_samtools)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1259, in flip_read2_strand
    output_handle = open(output_file,'w')
PermissionError: [Errno 13] Permission denied: '/gscratch/scrubbed/sr320/0807/EPI-160_S7_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam.read2flipped.bam'
Begin flipping the strand of read 2
Mon Aug 26 08:34:02 2019

Traceback (most recent call last):
  File "/gscratch/srlab/strigg/bin/anaconda3/bin/methylpy", line 4, in <module>
    __import__('pkg_resources').run_script('methylpy==1.3.7', 'methylpy')
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 666, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 1453, in run_script
    exec(code, namespace, namespace)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/EGG-INFO/scripts/methylpy", line 5, in <module>
    parse_args()
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/parser.py", line 221, in parse_args
    min_base_quality=args.min_base_quality)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1343, in call_methylated_sites_pe
    path_to_samtools=path_to_samtools)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1259, in flip_read2_strand
    output_handle = open(output_file,'w')
PermissionError: [Errno 13] Permission denied: '/gscratch/scrubbed/sr320/0807/EPI-161_S8_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam.read2flipped.bam'
Begin flipping the strand of read 2
Mon Aug 26 08:34:02 2019

Traceback (most recent call last):
  File "/gscratch/srlab/strigg/bin/anaconda3/bin/methylpy", line 4, in <module>
    __import__('pkg_resources').run_script('methylpy==1.3.7', 'methylpy')
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 666, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 1453, in run_script
    exec(code, namespace, namespace)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/EGG-INFO/scripts/methylpy", line 5, in <module>
    parse_args()
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/parser.py", line 221, in parse_args
    min_base_quality=args.min_base_quality)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1343, in call_methylated_sites_pe
    path_to_samtools=path_to_samtools)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1259, in flip_read2_strand
    output_handle = open(output_file,'w')
PermissionError: [Errno 13] Permission denied: '/gscratch/scrubbed/sr320/0807/EPI-162_S9_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam.read2flipped.bam'
Begin flipping the strand of read 2
Mon Aug 26 08:34:02 2019

Traceback (most recent call last):
  File "/gscratch/srlab/strigg/bin/anaconda3/bin/methylpy", line 4, in <module>
    __import__('pkg_resources').run_script('methylpy==1.3.7', 'methylpy')
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 666, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 1453, in run_script
    exec(code, namespace, namespace)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/EGG-INFO/scripts/methylpy", line 5, in <module>
    parse_args()
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/parser.py", line 221, in parse_args
    min_base_quality=args.min_base_quality)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1343, in call_methylated_sites_pe
    path_to_samtools=path_to_samtools)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1259, in flip_read2_strand
    output_handle = open(output_file,'w')
PermissionError: [Errno 13] Permission denied: '/gscratch/scrubbed/sr320/0807/EPI-167_S10_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam.read2flipped.bam'
Begin flipping the strand of read 2
Mon Aug 26 08:34:03 2019

Traceback (most recent call last):
  File "/gscratch/srlab/strigg/bin/anaconda3/bin/methylpy", line 4, in <module>
    __import__('pkg_resources').run_script('methylpy==1.3.7', 'methylpy')
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 666, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 1453, in run_script
    exec(code, namespace, namespace)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/EGG-INFO/scripts/methylpy", line 5, in <module>
    parse_args()
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/parser.py", line 221, in parse_args
    min_base_quality=args.min_base_quality)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1343, in call_methylated_sites_pe
    path_to_samtools=path_to_samtools)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1259, in flip_read2_strand
    output_handle = open(output_file,'w')
PermissionError: [Errno 13] Permission denied: '/gscratch/scrubbed/sr320/0807/EPI-168_S11_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam.read2flipped.bam'
Begin flipping the strand of read 2
Mon Aug 26 08:34:03 2019

Traceback (most recent call last):
  File "/gscratch/srlab/strigg/bin/anaconda3/bin/methylpy", line 4, in <module>
    __import__('pkg_resources').run_script('methylpy==1.3.7', 'methylpy')
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 666, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 1453, in run_script
    exec(code, namespace, namespace)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/EGG-INFO/scripts/methylpy", line 5, in <module>
    parse_args()
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/parser.py", line 221, in parse_args
    min_base_quality=args.min_base_quality)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1343, in call_methylated_sites_pe
    path_to_samtools=path_to_samtools)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1259, in flip_read2_strand
    output_handle = open(output_file,'w')
PermissionError: [Errno 13] Permission denied: '/gscratch/scrubbed/sr320/0807/EPI-169_S12_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam.read2flipped.bam'
Begin flipping the strand of read 2
Mon Aug 26 08:34:04 2019

Traceback (most recent call last):
  File "/gscratch/srlab/strigg/bin/anaconda3/bin/methylpy", line 4, in <module>
    __import__('pkg_resources').run_script('methylpy==1.3.7', 'methylpy')
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 666, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 1453, in run_script
    exec(code, namespace, namespace)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/EGG-INFO/scripts/methylpy", line 5, in <module>
    parse_args()
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/parser.py", line 221, in parse_args
    min_base_quality=args.min_base_quality)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1343, in call_methylated_sites_pe
    path_to_samtools=path_to_samtools)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1259, in flip_read2_strand
    output_handle = open(output_file,'w')
PermissionError: [Errno 13] Permission denied: '/gscratch/scrubbed/sr320/0807/EPI-170_S13_L002_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam.read2flipped.bam'
/var/spool/slurm/d/job1231397/slurm_script: line 40: fg: no job control
Begin flipping the strand of read 2
Mon Aug 26 08:34:04 2019

Traceback (most recent call last):
  File "/gscratch/srlab/strigg/bin/anaconda3/bin/methylpy", line 4, in <module>
    __import__('pkg_resources').run_script('methylpy==1.3.7', 'methylpy')
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 666, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 1453, in run_script
    exec(code, namespace, namespace)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/EGG-INFO/scripts/methylpy", line 5, in <module>
    parse_args()
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/parser.py", line 221, in parse_args
    min_base_quality=args.min_base_quality)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1343, in call_methylated_sites_pe
    path_to_samtools=path_to_samtools)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1257, in flip_read2_strand
    universal_newlines=True)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/subprocess.py", line 775, in __init__
    restore_signals, start_new_session)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/subprocess.py", line 1522, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'samtools': 'samtools'
Begin flipping the strand of read 2
Mon Aug 26 08:34:04 2019

Traceback (most recent call last):
  File "/gscratch/srlab/strigg/bin/anaconda3/bin/methylpy", line 4, in <module>
    __import__('pkg_resources').run_script('methylpy==1.3.7', 'methylpy')
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 666, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 1453, in run_script
    exec(code, namespace, namespace)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/EGG-INFO/scripts/methylpy", line 5, in <module>
    parse_args()
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/parser.py", line 221, in parse_args
    min_base_quality=args.min_base_quality)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1343, in call_methylated_sites_pe
    path_to_samtools=path_to_samtools)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1257, in flip_read2_strand
    universal_newlines=True)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/subprocess.py", line 775, in __init__
    restore_signals, start_new_session)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/subprocess.py", line 1522, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'samtools': 'samtools'
Begin flipping the strand of read 2
Mon Aug 26 08:34:05 2019

Traceback (most recent call last):
  File "/gscratch/srlab/strigg/bin/anaconda3/bin/methylpy", line 4, in <module>
    __import__('pkg_resources').run_script('methylpy==1.3.7', 'methylpy')
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 666, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 1453, in run_script
    exec(code, namespace, namespace)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/EGG-INFO/scripts/methylpy", line 5, in <module>
    parse_args()
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/parser.py", line 221, in parse_args
    min_base_quality=args.min_base_quality)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1343, in call_methylated_sites_pe
    path_to_samtools=path_to_samtools)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1257, in flip_read2_strand
    universal_newlines=True)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/subprocess.py", line 775, in __init__
    restore_signals, start_new_session)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/subprocess.py", line 1522, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'samtools': 'samtools'
Begin flipping the strand of read 2
Mon Aug 26 08:34:05 2019

Traceback (most recent call last):
  File "/gscratch/srlab/strigg/bin/anaconda3/bin/methylpy", line 4, in <module>
    __import__('pkg_resources').run_script('methylpy==1.3.7', 'methylpy')
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 666, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 1453, in run_script
    exec(code, namespace, namespace)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/EGG-INFO/scripts/methylpy", line 5, in <module>
    parse_args()
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/parser.py", line 221, in parse_args
    min_base_quality=args.min_base_quality)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1343, in call_methylated_sites_pe
    path_to_samtools=path_to_samtools)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1257, in flip_read2_strand
    universal_newlines=True)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/subprocess.py", line 775, in __init__
    restore_signals, start_new_session)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/subprocess.py", line 1522, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'samtools': 'samtools'
Begin flipping the strand of read 2
Mon Aug 26 08:34:06 2019

Traceback (most recent call last):
  File "/gscratch/srlab/strigg/bin/anaconda3/bin/methylpy", line 4, in <module>
    __import__('pkg_resources').run_script('methylpy==1.3.7', 'methylpy')
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 666, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 1453, in run_script
    exec(code, namespace, namespace)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/EGG-INFO/scripts/methylpy", line 5, in <module>
    parse_args()
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/parser.py", line 221, in parse_args
    min_base_quality=args.min_base_quality)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1343, in call_methylated_sites_pe
    path_to_samtools=path_to_samtools)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1257, in flip_read2_strand
    universal_newlines=True)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/subprocess.py", line 775, in __init__
    restore_signals, start_new_session)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/subprocess.py", line 1522, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'samtools': 'samtools'
Begin flipping the strand of read 2
Mon Aug 26 08:34:06 2019

Traceback (most recent call last):
  File "/gscratch/srlab/strigg/bin/anaconda3/bin/methylpy", line 4, in <module>
    __import__('pkg_resources').run_script('methylpy==1.3.7', 'methylpy')
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 666, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 1453, in run_script
    exec(code, namespace, namespace)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/EGG-INFO/scripts/methylpy", line 5, in <module>
    parse_args()
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/parser.py", line 221, in parse_args
    min_base_quality=args.min_base_quality)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1343, in call_methylated_sites_pe
    path_to_samtools=path_to_samtools)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1257, in flip_read2_strand
    universal_newlines=True)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/subprocess.py", line 775, in __init__
    restore_signals, start_new_session)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/subprocess.py", line 1522, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'samtools': 'samtools'
Begin flipping the strand of read 2
Mon Aug 26 08:34:06 2019

Traceback (most recent call last):
  File "/gscratch/srlab/strigg/bin/anaconda3/bin/methylpy", line 4, in <module>
    __import__('pkg_resources').run_script('methylpy==1.3.7', 'methylpy')
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 666, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 1453, in run_script
    exec(code, namespace, namespace)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/EGG-INFO/scripts/methylpy", line 5, in <module>
    parse_args()
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/parser.py", line 221, in parse_args
    min_base_quality=args.min_base_quality)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1343, in call_methylated_sites_pe
    path_to_samtools=path_to_samtools)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1257, in flip_read2_strand
    universal_newlines=True)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/subprocess.py", line 775, in __init__
    restore_signals, start_new_session)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/subprocess.py", line 1522, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'samtools': 'samtools'
Begin flipping the strand of read 2
Mon Aug 26 08:34:07 2019

Traceback (most recent call last):
  File "/gscratch/srlab/strigg/bin/anaconda3/bin/methylpy", line 4, in <module>
    __import__('pkg_resources').run_script('methylpy==1.3.7', 'methylpy')
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 666, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 1453, in run_script
    exec(code, namespace, namespace)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/EGG-INFO/scripts/methylpy", line 5, in <module>
    parse_args()
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/parser.py", line 221, in parse_args
    min_base_quality=args.min_base_quality)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1343, in call_methylated_sites_pe
    path_to_samtools=path_to_samtools)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1257, in flip_read2_strand
    universal_newlines=True)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/subprocess.py", line 775, in __init__
    restore_signals, start_new_session)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/subprocess.py", line 1522, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'samtools': 'samtools'
Begin flipping the strand of read 2
Mon Aug 26 08:34:07 2019

Traceback (most recent call last):
  File "/gscratch/srlab/strigg/bin/anaconda3/bin/methylpy", line 4, in <module>
    __import__('pkg_resources').run_script('methylpy==1.3.7', 'methylpy')
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 666, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 1453, in run_script
    exec(code, namespace, namespace)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/EGG-INFO/scripts/methylpy", line 5, in <module>
    parse_args()
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/parser.py", line 221, in parse_args
    min_base_quality=args.min_base_quality)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1343, in call_methylated_sites_pe
    path_to_samtools=path_to_samtools)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1257, in flip_read2_strand
    universal_newlines=True)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/subprocess.py", line 775, in __init__
    restore_signals, start_new_session)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/subprocess.py", line 1522, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'samtools': 'samtools'
Begin flipping the strand of read 2
Mon Aug 26 08:34:08 2019

Traceback (most recent call last):
  File "/gscratch/srlab/strigg/bin/anaconda3/bin/methylpy", line 4, in <module>
    __import__('pkg_resources').run_script('methylpy==1.3.7', 'methylpy')
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 666, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 1453, in run_script
    exec(code, namespace, namespace)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/EGG-INFO/scripts/methylpy", line 5, in <module>
    parse_args()
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/parser.py", line 221, in parse_args
    min_base_quality=args.min_base_quality)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1343, in call_methylated_sites_pe
    path_to_samtools=path_to_samtools)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1257, in flip_read2_strand
    universal_newlines=True)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/subprocess.py", line 775, in __init__
    restore_signals, start_new_session)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/subprocess.py", line 1522, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'samtools': 'samtools'
Begin flipping the strand of read 2
Mon Aug 26 08:34:08 2019

Traceback (most recent call last):
  File "/gscratch/srlab/strigg/bin/anaconda3/bin/methylpy", line 4, in <module>
    __import__('pkg_resources').run_script('methylpy==1.3.7', 'methylpy')
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 666, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 1453, in run_script
    exec(code, namespace, namespace)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/EGG-INFO/scripts/methylpy", line 5, in <module>
    parse_args()
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/parser.py", line 221, in parse_args
    min_base_quality=args.min_base_quality)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1343, in call_methylated_sites_pe
    path_to_samtools=path_to_samtools)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1257, in flip_read2_strand
    universal_newlines=True)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/subprocess.py", line 775, in __init__
    restore_signals, start_new_session)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/subprocess.py", line 1522, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'samtools': 'samtools'
Begin flipping the strand of read 2
Mon Aug 26 08:34:08 2019

Traceback (most recent call last):
  File "/gscratch/srlab/strigg/bin/anaconda3/bin/methylpy", line 4, in <module>
    __import__('pkg_resources').run_script('methylpy==1.3.7', 'methylpy')
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 666, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 1453, in run_script
    exec(code, namespace, namespace)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/EGG-INFO/scripts/methylpy", line 5, in <module>
    parse_args()
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/parser.py", line 221, in parse_args
    min_base_quality=args.min_base_quality)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1343, in call_methylated_sites_pe
    path_to_samtools=path_to_samtools)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1257, in flip_read2_strand
    universal_newlines=True)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/subprocess.py", line 775, in __init__
    restore_signals, start_new_session)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/subprocess.py", line 1522, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'samtools': 'samtools'
/var/spool/slurm/d/job1231397/slurm_script: line 51: fg: no job control
Begin flipping the strand of read 2
Mon Aug 26 08:34:09 2019

Traceback (most recent call last):
  File "/gscratch/srlab/strigg/bin/anaconda3/bin/methylpy", line 4, in <module>
    __import__('pkg_resources').run_script('methylpy==1.3.7', 'methylpy')
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 666, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 1453, in run_script
    exec(code, namespace, namespace)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/EGG-INFO/scripts/methylpy", line 5, in <module>
    parse_args()
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/parser.py", line 221, in parse_args
    min_base_quality=args.min_base_quality)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1343, in call_methylated_sites_pe
    path_to_samtools=path_to_samtools)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1257, in flip_read2_strand
    universal_newlines=True)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/subprocess.py", line 775, in __init__
    restore_signals, start_new_session)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/subprocess.py", line 1522, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'samtools': 'samtools'
Begin flipping the strand of read 2
Mon Aug 26 08:34:09 2019

Traceback (most recent call last):
  File "/gscratch/srlab/strigg/bin/anaconda3/bin/methylpy", line 4, in <module>
    __import__('pkg_resources').run_script('methylpy==1.3.7', 'methylpy')
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 666, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 1453, in run_script
    exec(code, namespace, namespace)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/EGG-INFO/scripts/methylpy", line 5, in <module>
    parse_args()
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/parser.py", line 221, in parse_args
    min_base_quality=args.min_base_quality)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1343, in call_methylated_sites_pe
    path_to_samtools=path_to_samtools)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1257, in flip_read2_strand
    universal_newlines=True)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/subprocess.py", line 775, in __init__
    restore_signals, start_new_session)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/subprocess.py", line 1522, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'samtools': 'samtools'
Begin flipping the strand of read 2
Mon Aug 26 08:34:10 2019

Traceback (most recent call last):
  File "/gscratch/srlab/strigg/bin/anaconda3/bin/methylpy", line 4, in <module>
    __import__('pkg_resources').run_script('methylpy==1.3.7', 'methylpy')
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 666, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 1453, in run_script
    exec(code, namespace, namespace)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/EGG-INFO/scripts/methylpy", line 5, in <module>
    parse_args()
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/parser.py", line 221, in parse_args
    min_base_quality=args.min_base_quality)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1343, in call_methylated_sites_pe
    path_to_samtools=path_to_samtools)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1257, in flip_read2_strand
    universal_newlines=True)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/subprocess.py", line 775, in __init__
    restore_signals, start_new_session)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/subprocess.py", line 1522, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'samtools': 'samtools'
Begin flipping the strand of read 2
Mon Aug 26 08:34:10 2019

Traceback (most recent call last):
  File "/gscratch/srlab/strigg/bin/anaconda3/bin/methylpy", line 4, in <module>
    __import__('pkg_resources').run_script('methylpy==1.3.7', 'methylpy')
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 666, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 1453, in run_script
    exec(code, namespace, namespace)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/EGG-INFO/scripts/methylpy", line 5, in <module>
    parse_args()
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/parser.py", line 221, in parse_args
    min_base_quality=args.min_base_quality)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1343, in call_methylated_sites_pe
    path_to_samtools=path_to_samtools)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1257, in flip_read2_strand
    universal_newlines=True)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/subprocess.py", line 775, in __init__
    restore_signals, start_new_session)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/subprocess.py", line 1522, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'samtools': 'samtools'
Begin flipping the strand of read 2
Mon Aug 26 08:34:10 2019

Traceback (most recent call last):
  File "/gscratch/srlab/strigg/bin/anaconda3/bin/methylpy", line 4, in <module>
    __import__('pkg_resources').run_script('methylpy==1.3.7', 'methylpy')
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 666, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 1453, in run_script
    exec(code, namespace, namespace)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/EGG-INFO/scripts/methylpy", line 5, in <module>
    parse_args()
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/parser.py", line 221, in parse_args
    min_base_quality=args.min_base_quality)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1343, in call_methylated_sites_pe
    path_to_samtools=path_to_samtools)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1257, in flip_read2_strand
    universal_newlines=True)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/subprocess.py", line 775, in __init__
    restore_signals, start_new_session)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/subprocess.py", line 1522, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'samtools': 'samtools'
Begin flipping the strand of read 2
Mon Aug 26 08:34:11 2019

Traceback (most recent call last):
  File "/gscratch/srlab/strigg/bin/anaconda3/bin/methylpy", line 4, in <module>
    __import__('pkg_resources').run_script('methylpy==1.3.7', 'methylpy')
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 666, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 1453, in run_script
    exec(code, namespace, namespace)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/EGG-INFO/scripts/methylpy", line 5, in <module>
    parse_args()
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/parser.py", line 221, in parse_args
    min_base_quality=args.min_base_quality)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1343, in call_methylated_sites_pe
    path_to_samtools=path_to_samtools)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1257, in flip_read2_strand
    universal_newlines=True)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/subprocess.py", line 775, in __init__
    restore_signals, start_new_session)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/subprocess.py", line 1522, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'samtools': 'samtools'
Begin flipping the strand of read 2
Mon Aug 26 08:34:11 2019

Traceback (most recent call last):
  File "/gscratch/srlab/strigg/bin/anaconda3/bin/methylpy", line 4, in <module>
    __import__('pkg_resources').run_script('methylpy==1.3.7', 'methylpy')
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 666, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 1453, in run_script
    exec(code, namespace, namespace)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/EGG-INFO/scripts/methylpy", line 5, in <module>
    parse_args()
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/parser.py", line 221, in parse_args
    min_base_quality=args.min_base_quality)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1343, in call_methylated_sites_pe
    path_to_samtools=path_to_samtools)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1257, in flip_read2_strand
    universal_newlines=True)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/subprocess.py", line 775, in __init__
    restore_signals, start_new_session)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/subprocess.py", line 1522, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'samtools': 'samtools'
Begin flipping the strand of read 2
Mon Aug 26 08:34:12 2019

Traceback (most recent call last):
  File "/gscratch/srlab/strigg/bin/anaconda3/bin/methylpy", line 4, in <module>
    __import__('pkg_resources').run_script('methylpy==1.3.7', 'methylpy')
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 666, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 1453, in run_script
    exec(code, namespace, namespace)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/EGG-INFO/scripts/methylpy", line 5, in <module>
    parse_args()
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/parser.py", line 221, in parse_args
    min_base_quality=args.min_base_quality)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1343, in call_methylated_sites_pe
    path_to_samtools=path_to_samtools)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1257, in flip_read2_strand
    universal_newlines=True)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/subprocess.py", line 775, in __init__
    restore_signals, start_new_session)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/subprocess.py", line 1522, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'samtools': 'samtools'
Begin flipping the strand of read 2
Mon Aug 26 08:34:12 2019

Traceback (most recent call last):
  File "/gscratch/srlab/strigg/bin/anaconda3/bin/methylpy", line 4, in <module>
    __import__('pkg_resources').run_script('methylpy==1.3.7', 'methylpy')
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 666, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 1453, in run_script
    exec(code, namespace, namespace)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/EGG-INFO/scripts/methylpy", line 5, in <module>
    parse_args()
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/parser.py", line 221, in parse_args
    min_base_quality=args.min_base_quality)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1343, in call_methylated_sites_pe
    path_to_samtools=path_to_samtools)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1257, in flip_read2_strand
    universal_newlines=True)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/subprocess.py", line 775, in __init__
    restore_signals, start_new_session)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/subprocess.py", line 1522, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'samtools': 'samtools'
Begin flipping the strand of read 2
Mon Aug 26 08:34:12 2019

Traceback (most recent call last):
  File "/gscratch/srlab/strigg/bin/anaconda3/bin/methylpy", line 4, in <module>
    __import__('pkg_resources').run_script('methylpy==1.3.7', 'methylpy')
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 666, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 1453, in run_script
    exec(code, namespace, namespace)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/EGG-INFO/scripts/methylpy", line 5, in <module>
    parse_args()
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/parser.py", line 221, in parse_args
    min_base_quality=args.min_base_quality)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1343, in call_methylated_sites_pe
    path_to_samtools=path_to_samtools)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1257, in flip_read2_strand
    universal_newlines=True)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/subprocess.py", line 775, in __init__
    restore_signals, start_new_session)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/subprocess.py", line 1522, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'samtools': 'samtools'
Begin flipping the strand of read 2
Mon Aug 26 08:34:13 2019

Traceback (most recent call last):
  File "/gscratch/srlab/strigg/bin/anaconda3/bin/methylpy", line 4, in <module>
    __import__('pkg_resources').run_script('methylpy==1.3.7', 'methylpy')
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 666, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 1453, in run_script
    exec(code, namespace, namespace)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/EGG-INFO/scripts/methylpy", line 5, in <module>
    parse_args()
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/parser.py", line 221, in parse_args
    min_base_quality=args.min_base_quality)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1343, in call_methylated_sites_pe
    path_to_samtools=path_to_samtools)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1257, in flip_read2_strand
    universal_newlines=True)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/subprocess.py", line 775, in __init__
    restore_signals, start_new_session)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/subprocess.py", line 1522, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'samtools': 'samtools'
Begin flipping the strand of read 2
Mon Aug 26 08:34:13 2019

Traceback (most recent call last):
  File "/gscratch/srlab/strigg/bin/anaconda3/bin/methylpy", line 4, in <module>
    __import__('pkg_resources').run_script('methylpy==1.3.7', 'methylpy')
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 666, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 1453, in run_script
    exec(code, namespace, namespace)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/EGG-INFO/scripts/methylpy", line 5, in <module>
    parse_args()
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/parser.py", line 221, in parse_args
    min_base_quality=args.min_base_quality)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1343, in call_methylated_sites_pe
    path_to_samtools=path_to_samtools)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1257, in flip_read2_strand
    universal_newlines=True)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/subprocess.py", line 775, in __init__
    restore_signals, start_new_session)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/subprocess.py", line 1522, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'samtools': 'samtools'
/var/spool/slurm/d/job1231397/slurm_script: line 62: fg: no job control
Begin flipping the strand of read 2
Mon Aug 26 08:34:14 2019

Traceback (most recent call last):
  File "/gscratch/srlab/strigg/bin/anaconda3/bin/methylpy", line 4, in <module>
    __import__('pkg_resources').run_script('methylpy==1.3.7', 'methylpy')
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 666, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 1453, in run_script
    exec(code, namespace, namespace)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/EGG-INFO/scripts/methylpy", line 5, in <module>
    parse_args()
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/parser.py", line 221, in parse_args
    min_base_quality=args.min_base_quality)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1343, in call_methylated_sites_pe
    path_to_samtools=path_to_samtools)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1257, in flip_read2_strand
    universal_newlines=True)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/subprocess.py", line 775, in __init__
    restore_signals, start_new_session)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/subprocess.py", line 1522, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'samtools': 'samtools'
Begin flipping the strand of read 2
Mon Aug 26 08:34:14 2019

Traceback (most recent call last):
  File "/gscratch/srlab/strigg/bin/anaconda3/bin/methylpy", line 4, in <module>
    __import__('pkg_resources').run_script('methylpy==1.3.7', 'methylpy')
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 666, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 1453, in run_script
    exec(code, namespace, namespace)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/EGG-INFO/scripts/methylpy", line 5, in <module>
    parse_args()
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/parser.py", line 221, in parse_args
    min_base_quality=args.min_base_quality)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1343, in call_methylated_sites_pe
    path_to_samtools=path_to_samtools)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1257, in flip_read2_strand
    universal_newlines=True)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/subprocess.py", line 775, in __init__
    restore_signals, start_new_session)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/subprocess.py", line 1522, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'samtools': 'samtools'
Begin flipping the strand of read 2
Mon Aug 26 08:34:14 2019

Traceback (most recent call last):
  File "/gscratch/srlab/strigg/bin/anaconda3/bin/methylpy", line 4, in <module>
    __import__('pkg_resources').run_script('methylpy==1.3.7', 'methylpy')
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 666, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 1453, in run_script
    exec(code, namespace, namespace)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/EGG-INFO/scripts/methylpy", line 5, in <module>
    parse_args()
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/parser.py", line 221, in parse_args
    min_base_quality=args.min_base_quality)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1343, in call_methylated_sites_pe
    path_to_samtools=path_to_samtools)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1257, in flip_read2_strand
    universal_newlines=True)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/subprocess.py", line 775, in __init__
    restore_signals, start_new_session)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/subprocess.py", line 1522, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'samtools': 'samtools'
Begin flipping the strand of read 2
Mon Aug 26 08:34:15 2019

Traceback (most recent call last):
  File "/gscratch/srlab/strigg/bin/anaconda3/bin/methylpy", line 4, in <module>
    __import__('pkg_resources').run_script('methylpy==1.3.7', 'methylpy')
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 666, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 1453, in run_script
    exec(code, namespace, namespace)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/EGG-INFO/scripts/methylpy", line 5, in <module>
    parse_args()
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/parser.py", line 221, in parse_args
    min_base_quality=args.min_base_quality)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1343, in call_methylated_sites_pe
    path_to_samtools=path_to_samtools)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1257, in flip_read2_strand
    universal_newlines=True)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/subprocess.py", line 775, in __init__
    restore_signals, start_new_session)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/subprocess.py", line 1522, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'samtools': 'samtools'
Begin flipping the strand of read 2
Mon Aug 26 08:34:15 2019

Traceback (most recent call last):
  File "/gscratch/srlab/strigg/bin/anaconda3/bin/methylpy", line 4, in <module>
    __import__('pkg_resources').run_script('methylpy==1.3.7', 'methylpy')
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 666, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 1453, in run_script
    exec(code, namespace, namespace)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/EGG-INFO/scripts/methylpy", line 5, in <module>
    parse_args()
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/parser.py", line 221, in parse_args
    min_base_quality=args.min_base_quality)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1343, in call_methylated_sites_pe
    path_to_samtools=path_to_samtools)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1257, in flip_read2_strand
    universal_newlines=True)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/subprocess.py", line 775, in __init__
    restore_signals, start_new_session)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/subprocess.py", line 1522, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'samtools': 'samtools'
Begin flipping the strand of read 2
Mon Aug 26 08:34:16 2019

Traceback (most recent call last):
  File "/gscratch/srlab/strigg/bin/anaconda3/bin/methylpy", line 4, in <module>
    __import__('pkg_resources').run_script('methylpy==1.3.7', 'methylpy')
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 666, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 1453, in run_script
    exec(code, namespace, namespace)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/EGG-INFO/scripts/methylpy", line 5, in <module>
    parse_args()
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/parser.py", line 221, in parse_args
    min_base_quality=args.min_base_quality)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1343, in call_methylated_sites_pe
    path_to_samtools=path_to_samtools)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1257, in flip_read2_strand
    universal_newlines=True)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/subprocess.py", line 775, in __init__
    restore_signals, start_new_session)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/subprocess.py", line 1522, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'samtools': 'samtools'
Begin flipping the strand of read 2
Mon Aug 26 08:34:16 2019

Traceback (most recent call last):
  File "/gscratch/srlab/strigg/bin/anaconda3/bin/methylpy", line 4, in <module>
    __import__('pkg_resources').run_script('methylpy==1.3.7', 'methylpy')
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 666, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 1453, in run_script
    exec(code, namespace, namespace)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/EGG-INFO/scripts/methylpy", line 5, in <module>
    parse_args()
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/parser.py", line 221, in parse_args
    min_base_quality=args.min_base_quality)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1343, in call_methylated_sites_pe
    path_to_samtools=path_to_samtools)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1257, in flip_read2_strand
    universal_newlines=True)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/subprocess.py", line 775, in __init__
    restore_signals, start_new_session)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/subprocess.py", line 1522, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'samtools': 'samtools'
Begin flipping the strand of read 2
Mon Aug 26 08:34:16 2019

Traceback (most recent call last):
  File "/gscratch/srlab/strigg/bin/anaconda3/bin/methylpy", line 4, in <module>
    __import__('pkg_resources').run_script('methylpy==1.3.7', 'methylpy')
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 666, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 1453, in run_script
    exec(code, namespace, namespace)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/EGG-INFO/scripts/methylpy", line 5, in <module>
    parse_args()
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/parser.py", line 221, in parse_args
    min_base_quality=args.min_base_quality)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1343, in call_methylated_sites_pe
    path_to_samtools=path_to_samtools)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1257, in flip_read2_strand
    universal_newlines=True)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/subprocess.py", line 775, in __init__
    restore_signals, start_new_session)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/subprocess.py", line 1522, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'samtools': 'samtools'
Begin flipping the strand of read 2
Mon Aug 26 08:34:17 2019

Traceback (most recent call last):
  File "/gscratch/srlab/strigg/bin/anaconda3/bin/methylpy", line 4, in <module>
    __import__('pkg_resources').run_script('methylpy==1.3.7', 'methylpy')
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 666, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 1453, in run_script
    exec(code, namespace, namespace)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/EGG-INFO/scripts/methylpy", line 5, in <module>
    parse_args()
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/parser.py", line 221, in parse_args
    min_base_quality=args.min_base_quality)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1343, in call_methylated_sites_pe
    path_to_samtools=path_to_samtools)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1257, in flip_read2_strand
    universal_newlines=True)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/subprocess.py", line 775, in __init__
    restore_signals, start_new_session)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/subprocess.py", line 1522, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'samtools': 'samtools'
Begin flipping the strand of read 2
Mon Aug 26 08:34:17 2019

Traceback (most recent call last):
  File "/gscratch/srlab/strigg/bin/anaconda3/bin/methylpy", line 4, in <module>
    __import__('pkg_resources').run_script('methylpy==1.3.7', 'methylpy')
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 666, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 1453, in run_script
    exec(code, namespace, namespace)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/EGG-INFO/scripts/methylpy", line 5, in <module>
    parse_args()
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/parser.py", line 221, in parse_args
    min_base_quality=args.min_base_quality)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1343, in call_methylated_sites_pe
    path_to_samtools=path_to_samtools)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1257, in flip_read2_strand
    universal_newlines=True)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/subprocess.py", line 775, in __init__
    restore_signals, start_new_session)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/subprocess.py", line 1522, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'samtools': 'samtools'
Begin flipping the strand of read 2
Mon Aug 26 08:34:18 2019

Traceback (most recent call last):
  File "/gscratch/srlab/strigg/bin/anaconda3/bin/methylpy", line 4, in <module>
    __import__('pkg_resources').run_script('methylpy==1.3.7', 'methylpy')
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 666, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 1453, in run_script
    exec(code, namespace, namespace)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/EGG-INFO/scripts/methylpy", line 5, in <module>
    parse_args()
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/parser.py", line 221, in parse_args
    min_base_quality=args.min_base_quality)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1343, in call_methylated_sites_pe
    path_to_samtools=path_to_samtools)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1257, in flip_read2_strand
    universal_newlines=True)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/subprocess.py", line 775, in __init__
    restore_signals, start_new_session)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/subprocess.py", line 1522, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'samtools': 'samtools'
Begin flipping the strand of read 2
Mon Aug 26 08:34:18 2019

Traceback (most recent call last):
  File "/gscratch/srlab/strigg/bin/anaconda3/bin/methylpy", line 4, in <module>
    __import__('pkg_resources').run_script('methylpy==1.3.7', 'methylpy')
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 666, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 1453, in run_script
    exec(code, namespace, namespace)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/EGG-INFO/scripts/methylpy", line 5, in <module>
    parse_args()
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/parser.py", line 221, in parse_args
    min_base_quality=args.min_base_quality)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1343, in call_methylated_sites_pe
    path_to_samtools=path_to_samtools)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1257, in flip_read2_strand
    universal_newlines=True)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/subprocess.py", line 775, in __init__
    restore_signals, start_new_session)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/subprocess.py", line 1522, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'samtools': 'samtools'
Begin flipping the strand of read 2
Mon Aug 26 08:34:18 2019

Traceback (most recent call last):
  File "/gscratch/srlab/strigg/bin/anaconda3/bin/methylpy", line 4, in <module>
    __import__('pkg_resources').run_script('methylpy==1.3.7', 'methylpy')
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 666, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 1453, in run_script
    exec(code, namespace, namespace)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/EGG-INFO/scripts/methylpy", line 5, in <module>
    parse_args()
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/parser.py", line 221, in parse_args
    min_base_quality=args.min_base_quality)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1343, in call_methylated_sites_pe
    path_to_samtools=path_to_samtools)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1257, in flip_read2_strand
    universal_newlines=True)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/subprocess.py", line 775, in __init__
    restore_signals, start_new_session)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/subprocess.py", line 1522, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'samtools': 'samtools'
Begin flipping the strand of read 2
Mon Aug 26 08:34:19 2019

Traceback (most recent call last):
  File "/gscratch/srlab/strigg/bin/anaconda3/bin/methylpy", line 4, in <module>
    __import__('pkg_resources').run_script('methylpy==1.3.7', 'methylpy')
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 666, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 1453, in run_script
    exec(code, namespace, namespace)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/EGG-INFO/scripts/methylpy", line 5, in <module>
    parse_args()
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/parser.py", line 221, in parse_args
    min_base_quality=args.min_base_quality)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1343, in call_methylated_sites_pe
    path_to_samtools=path_to_samtools)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1257, in flip_read2_strand
    universal_newlines=True)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/subprocess.py", line 775, in __init__
    restore_signals, start_new_session)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/subprocess.py", line 1522, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'samtools': 'samtools'
Begin flipping the strand of read 2
Mon Aug 26 08:34:19 2019

Traceback (most recent call last):
  File "/gscratch/srlab/strigg/bin/anaconda3/bin/methylpy", line 4, in <module>
    __import__('pkg_resources').run_script('methylpy==1.3.7', 'methylpy')
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 666, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 1453, in run_script
    exec(code, namespace, namespace)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/EGG-INFO/scripts/methylpy", line 5, in <module>
    parse_args()
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/parser.py", line 221, in parse_args
    min_base_quality=args.min_base_quality)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1343, in call_methylated_sites_pe
    path_to_samtools=path_to_samtools)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1257, in flip_read2_strand
    universal_newlines=True)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/subprocess.py", line 775, in __init__
    restore_signals, start_new_session)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/subprocess.py", line 1522, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'samtools': 'samtools'
Begin flipping the strand of read 2
Mon Aug 26 08:34:20 2019

Traceback (most recent call last):
  File "/gscratch/srlab/strigg/bin/anaconda3/bin/methylpy", line 4, in <module>
    __import__('pkg_resources').run_script('methylpy==1.3.7', 'methylpy')
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 666, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 1453, in run_script
    exec(code, namespace, namespace)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/EGG-INFO/scripts/methylpy", line 5, in <module>
    parse_args()
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/parser.py", line 221, in parse_args
    min_base_quality=args.min_base_quality)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1343, in call_methylated_sites_pe
    path_to_samtools=path_to_samtools)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/call_mc_pe.py", line 1257, in flip_read2_strand
    universal_newlines=True)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/subprocess.py", line 775, in __init__
    restore_signals, start_new_session)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/subprocess.py", line 1522, in _execute_child
    raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: 'samtools': 'samtools'
/var/spool/slurm/d/job1231397/slurm_script: line 76: fg: no job control
/var/spool/slurm/d/job1231397/slurm_script: line 79: allc_*.tsv.gz: No such file or directory
/var/spool/slurm/d/job1231397/slurm_script: line 94: fg: no job control
Filtering allc files using 8 node(s).
Mon Aug 26 08:34:20 2019

Traceback (most recent call last):
  File "/gscratch/srlab/strigg/bin/anaconda3/bin/methylpy", line 4, in <module>
    __import__('pkg_resources').run_script('methylpy==1.3.7', 'methylpy')
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 666, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 1453, in run_script
    exec(code, namespace, namespace)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/EGG-INFO/scripts/methylpy", line 5, in <module>
    parse_args()
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/parser.py", line 71, in parse_args
    seed=args.seed)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/DMRfind.py", line 166, in DMRfind
    chrom_pointer[sample] = read_allc_index(allc_file)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/utilities.py", line 724, in read_allc_index
    index_allc_file(allc_file,reindex=False)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/utilities.py", line 686, in index_allc_file
    f = open_allc_file(allc_file)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/utilities.py", line 1133, in open_allc_file
    f = open(allc_file,'r')
FileNotFoundError: [Errno 2] No such file or directory: 'amb_AllTimes_DMR250bp_MCmax25_cov5x_filtered_allc_EPI-41.tsv'
/var/spool/slurm/d/job1231397/slurm_script: line 125: fg: no job control
Filtering allc files using 8 node(s).
Mon Aug 26 08:34:21 2019

Traceback (most recent call last):
  File "/gscratch/srlab/strigg/bin/anaconda3/bin/methylpy", line 4, in <module>
    __import__('pkg_resources').run_script('methylpy==1.3.7', 'methylpy')
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 666, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 1453, in run_script
    exec(code, namespace, namespace)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/EGG-INFO/scripts/methylpy", line 5, in <module>
    parse_args()
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/parser.py", line 71, in parse_args
    seed=args.seed)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/DMRfind.py", line 166, in DMRfind
    chrom_pointer[sample] = read_allc_index(allc_file)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/utilities.py", line 724, in read_allc_index
    index_allc_file(allc_file,reindex=False)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/utilities.py", line 686, in index_allc_file
    f = open_allc_file(allc_file)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/utilities.py", line 1133, in open_allc_file
    f = open(allc_file,'r')
FileNotFoundError: [Errno 2] No such file or directory: 'day10_AllpH_DMR250bp_MCmax25_cov5x_filtered_allc_EPI-103.tsv'
/var/spool/slurm/d/job1231397/slurm_script: line 152: fg: no job control
Filtering allc files using 8 node(s).
Mon Aug 26 08:34:22 2019

Traceback (most recent call last):
  File "/gscratch/srlab/strigg/bin/anaconda3/bin/methylpy", line 4, in <module>
    __import__('pkg_resources').run_script('methylpy==1.3.7', 'methylpy')
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 666, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 1453, in run_script
    exec(code, namespace, namespace)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/EGG-INFO/scripts/methylpy", line 5, in <module>
    parse_args()
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/parser.py", line 71, in parse_args
    seed=args.seed)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/DMRfind.py", line 166, in DMRfind
    chrom_pointer[sample] = read_allc_index(allc_file)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/utilities.py", line 724, in read_allc_index
    index_allc_file(allc_file,reindex=False)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/utilities.py", line 686, in index_allc_file
    f = open_allc_file(allc_file)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/utilities.py", line 1133, in open_allc_file
    f = open(allc_file,'r')
FileNotFoundError: [Errno 2] No such file or directory: 'day135_AllpH_DMR250bp_MCmax25_cov5x_filtered_allc_EPI-151.tsv'
/var/spool/slurm/d/job1231397/slurm_script: line 178: fg: no job control
Filtering allc files using 8 node(s).
Mon Aug 26 08:34:22 2019

Traceback (most recent call last):
  File "/gscratch/srlab/strigg/bin/anaconda3/bin/methylpy", line 4, in <module>
    __import__('pkg_resources').run_script('methylpy==1.3.7', 'methylpy')
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 666, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 1453, in run_script
    exec(code, namespace, namespace)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/EGG-INFO/scripts/methylpy", line 5, in <module>
    parse_args()
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/parser.py", line 71, in parse_args
    seed=args.seed)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/DMRfind.py", line 166, in DMRfind
    chrom_pointer[sample] = read_allc_index(allc_file)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/utilities.py", line 724, in read_allc_index
    index_allc_file(allc_file,reindex=False)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/utilities.py", line 686, in index_allc_file
    f = open_allc_file(allc_file)
  File "/gscratch/srlab/strigg/bin/anaconda3/lib/python3.7/site-packages/methylpy-1.3.7-py3.7.egg/methylpy/utilities.py", line 1133, in open_allc_file
    f = open(allc_file,'r')
FileNotFoundError: [Errno 2] No such file or directory: 'day145_AllpH_DMR250bp_MCmax25_cov5x_filtered_allc_EPI-175.tsv'