search

BSSeeker / BSseeker2

A versatile aligning pipeline for bisulfite sequencing data
http://pellegrini.mcdb.ucla.edu/BS_Seeker2/
MIT License
60 stars 25 forks source link

Error with python subprocess.py #27

Closed kscott94 closed 5 years ago

kscott94 commented 5 years ago

I've never had this error while using BSseeker2 before. Any ideas what could be causing it and how to fix it?

Traceback (most recent call last): File "/bsseeker2/bs_seeker2-align.py", line 412, in options.Output_unmapped_hit File "/bsseeker2/bs_align/bs_single_end.py", line 592, in bs_single_end 'output_file' : CC2T} ]) File "/bsseeker2/bs_utils/utils.py", line 332, in run_in_parallel for i, proc in enumerate([subprocess.Popen(args = shlex.split(cmd), stdout = stdout) for cmd, stdout in commands]): File "/usr/lib/python2.7/subprocess.py", line 394, in init errread, errwrite) File "/usr/lib/python2.7/subprocess.py", line 1047, in _execute_child raise child_exception OSError: [Errno 2] No such file or directory

kscott94 commented 5 years ago

I did not have an aligner installed. Installed bowtie2 and the issue was resolved

guoweilong commented 5 years ago

Thanks for your feedback!