/share/anaconda3/envs/methylpy/bin/methylpy:4: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html __import__('pkg_resources').run_script('methylpy==1.4.7', 'methylpy') Running RMS tests failed. /share/anaconda3/envs/methylpy/bin/methylpy:4: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html __import__('pkg_resources').run_script('methylpy==1.4.7', 'methylpy') Traceback (most recent call last): File "/share/anaconda3/envs/methylpy/bin/methylpy", line 4, in __import__('pkg_resources').run_script('methylpy==1.4.7', 'methylpy') File "/share/anaconda3/envs/methylpy/lib/python3.10/site-packages/pkg_resources/__init__.py", line 722, in run_script self.require(requires)[0].run_script(script_name, ns) File "/share/anaconda3/envs/methylpy/lib/python3.10/site-packages/pkg_resources/__init__.py", line 1561, in run_script exec(code, namespace, namespace) File "/share/anaconda3/envs/methylpy/lib/python3.10/site-packages/methylpy-1.4.7-py3.10.egg/EGG-INFO/scripts/methylpy", line 5, in parse_args() File "/share/anaconda3/envs/methylpy/lib/python3.10/site-packages/methylpy-1.4.7-py3.10.egg/methylpy/parser.py", line 75, in parse_args merge_DMS_to_DMR(input_rms_file=args.input_rms_file, File "/share/anaconda3/envs/methylpy/lib/python3.10/site-packages/methylpy-1.4.7-py3.10.egg/methylpy/DMRfind.py", line 311, in merge_DMS_to_DMR pvalue_cutoff=histogram_correction_DMRfind(input_rms_file, File "/share/anaconda3/envs/methylpy/lib/python3.10/site-packages/methylpy-1.4.7-py3.10.egg/methylpy/DMRfind.py", line 365, in histogram_correction_DMRfind f = gzip.open(rms_results,'rt') File "/share/anaconda3/envs/methylpy/lib/python3.10/gzip.py", line 58, in open binary_file = GzipFile(filename, gz_mode, compresslevel) File "/share/anaconda3/envs/methylpy/lib/python3.10/gzip.py", line 174, in __init__ fileobj = self.myfileobj = builtins.open(filename, mode or 'rb') FileNotFoundError: [Errno 2] No such file or directory: 'results/DMR_P0_FBvsHT_rms_results.tsv.gz' /share/anaconda3/envs/methylpy/bin/methylpy:4: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html __import__('pkg_resources').run_script('methylpy==1.4.7', 'methylpy') Building a SMALL index Renaming chrL/chrL_f.3.bt2.tmp to chrL/chrL_f.3.bt2 Renaming chrL/chrL_f.4.bt2.tmp to chrL/chrL_f.4.bt2 Renaming chrL/chrL_f.1.bt2.tmp to chrL/chrL_f.1.bt2 Renaming chrL/chrL_f.2.bt2.tmp to chrL/chrL_f.2.bt2 Renaming chrL/chrL_f.rev.1.bt2.tmp to chrL/chrL_f.rev.1.bt2 Renaming chrL/chrL_f.rev.2.bt2.tmp to chrL/chrL_f.rev.2.bt2 Building a SMALL index Renaming chrL/chrL_r.3.bt2.tmp to chrL/chrL_r.3.bt2 Renaming chrL/chrL_r.4.bt2.tmp to chrL/chrL_r.4.bt2 Renaming chrL/chrL_r.1.bt2.tmp to chrL/chrL_r.1.bt2 Renaming chrL/chrL_r.2.bt2.tmp to chrL/chrL_r.2.bt2 Renaming chrL/chrL_r.rev.1.bt2.tmp to chrL/chrL_r.rev.1.bt2 Renaming chrL/chrL_r.rev.2.bt2.tmp to chrL/chrL_r.rev.2.bt2 /share/anaconda3/envs/methylpy/bin/methylpy:4: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html __import__('pkg_resources').run_script('methylpy==1.4.7', 'methylpy') 93996 reads; of these: 93996 (100.00%) were unpaired; of these: 47003 (50.01%) aligned 0 times 46993 (49.99%) aligned exactly 1 time 0 (0.00%) aligned >1 times 49.99% overall alignment rate 93996 reads; of these: 93996 (100.00%) were unpaired; of these: 47008 (50.01%) aligned 0 times 46988 (49.99%) aligned exactly 1 time 0 (0.00%) aligned >1 times 49.99% overall alignment rate [mpileup] 1 samples in 1 input files /share/anaconda3/envs/methylpy/bin/methylpy:4: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html __import__('pkg_resources').run_script('methylpy==1.4.7', 'methylpy') 93996 reads; of these: 93996 (100.00%) were paired; of these: 46989 (49.99%) aligned concordantly 0 times 47007 (50.01%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 50.01% overall alignment rate 93996 reads; of these: 93996 (100.00%) were paired; of these: 47007 (50.01%) aligned concordantly 0 times 46989 (49.99%) aligned concordantly exactly 1 time 0 (0.00%) aligned concordantly >1 times 49.99% overall alignment rate [mpileup] 1 samples in 1 input files /share/anaconda3/envs/methylpy/bin/methylpy:4: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html __import__('pkg_resources').run_script('methylpy==1.4.7', 'methylpy') [W::hts_idx_load3] The index file is older than the data file: results/se_bt2_processed_reads.bam.bai /share/anaconda3/envs/methylpy/bin/methylpy:4: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html __import__('pkg_resources').run_script('methylpy==1.4.7', 'methylpy') [mpileup] 1 samples in 1 input files /share/anaconda3/envs/methylpy/bin/methylpy:4: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html __import__('pkg_resources').run_script('methylpy==1.4.7', 'methylpy') [mpileup] 1 samples in 1 input files /share/anaconda3/envs/methylpy/bin/methylpy:4: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html __import__('pkg_resources').run_script('methylpy==1.4.7', 'methylpy') /share/anaconda3/envs/methylpy/bin/methylpy:4: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html __import__('pkg_resources').run_script('methylpy==1.4.7', 'methylpy')