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snerx
Apr 28, 2019, 4:03:34 PM4/28/19
to dDocent User Help Forum
Everything was going fine until I got to the "cat namelist | parallel --no-notice" and I got a whole bunch of error messages--same for forward, reverse and uniq seqs commands. Got no idea what's going on here. Is this a matter of reinstalling these perl modules? See screen outputs below...
Thanks in advance.
snerx
Enter code here...
(ddocent_env) snerx@linux-pze0 my_dDocent_working_dir $
cat namelist | parallel --no-notice -j 8 "zcat {}.F.fq.gz | mawk '$AWK1' | mawk '$AWK2' > {}.forward"
warnings.pm did not return a true value at /home/snerx/miniconda3/envs/ddocent_env/lib/site_perl/5.26.2/Carp.pm line 5.
BEGIN failed--compilation aborted at /home/snerx/miniconda3/envs/ddocent_env/lib/site_perl/5.26.2/Carp.pm line 5.
Compilation failed in require at /home/snerx/miniconda3/envs/ddocent_env/lib/5.26.2/IPC/Open3.pm line 9.
BEGIN failed--compilation aborted at /home/snerx/miniconda3/envs/ddocent_env/lib/5.26.2/IPC/Open3.pm line 9.
Compilation failed in require at /home/snerx/miniconda3/envs/ddocent_env/bin/parallel line 21.
BEGIN failed--compilation aborted at /home/snerx/miniconda3/envs/ddocent_env/bin/parallel line 21.
snerx
Apr 29, 2019, 3:32:31 AM4/29/19
to dDocent User Help Forum
Seems the issue may have been a Linux distro one. The perl problems arose on an old Toshiba laptop on which I'm running OpenSUSE Tumbleweed. This morning I set up dDocent on my main computer, an HP laptop running Ubuntu 18.04 and all is well, it ran the commands without a glitz.
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