summarize does not work by itself

[koadman]

The following command should produce a single chunk summary, but has no effect: phylosift summarize --chunks 1 --chunk_size 2000 --output=results sewage.fq

[gjospin]

Had the summarize step been flagged as completed in the run_info.txt file? If it did, then PS skips that step. Remove the line from run_info.txt. Using -f should clean up the files for the particular chunk and force the step to get flagged as incomplete.

[koadman]

yes. it's listed as complete. thanks for the -f tip. When I add -f I get zillions of these: Use of uninitialized value in concatenation (.) or string at /home/koadman/software/phylosift_20130813/bin/../lib/Phylosift/Summarize.pm line 367. Use of uninitialized value in concatenation (.) or string at /home/koadman/software/phylosift_20130813/bin/../lib/Phylosift/Summarize.pm line 367. Use of uninitialized value in concatenation (.) or string at /home/koadman/software/phylosift_20130813/bin/../lib/Phylosift/Summarize.pm line 367. Use of uninitialized value in concatenation (.) or string at /home/koadman/software/phylosift_20130813/bin/../lib/Phylosift/Summarize.pm line 367. Use of uninitialized value in concatenation (.) or string at /home/koadman/software/phylosift_20130813/bin/../lib/Phylosift/Summarize.pm line 367. Use of uninitialized value in concatenation (.) or string at /home/koadman/software/phylosift_20130813/bin/../lib/Phylosift/Summarize.pm line 367. Use of uninitialized value in concatenation (.) or string at /home/koadman/software/phylosift_20130813/bin/../lib/Phylosift/Summarize.pm line 367. Use of uninitialized value in concatenation (.) or string at /home/koadman/software/phylosift_20130813/bin/../lib/Phylosift/Summarize.pm line 367. Use of uninitialized value in concatenation (.) or string at /home/koadman/software/phylosift_20130813/bin/../lib/Phylosift/Summarize.pm line 367. Use of uninitialized value in concatenation (.) or string at /home/koadman/software/phylosift_20130813/bin/../lib/Phylosift/Summarize.pm line 367.

renaming bug?

[gjospin]

Interesting. I'll check it out. Thanks.

On Tue, Aug 13, 2013 at 3:39 PM, Aaron Darling notifications@github.comwrote:

yes. it's listed as complete. thanks for the -f tip. When I add -f I get zillions of these: Use of uninitialized value in concatenation (.) or string at /home/koadman/software/phylosift_20130813/bin/../lib/Phylosift/Summarize.pm line 367. Use of uninitialized value in concatenation (.) or string at /home/koadman/software/phylosift_20130813/bin/../lib/Phylosift/Summarize.pm line 367. Use of uninitialized value in concatenation (.) or string at /home/koadman/software/phylosift_20130813/bin/../lib/Phylosift/Summarize.pm line 367. Use of uninitialized value in concatenation (.) or string at /home/koadman/software/phylosift_20130813/bin/../lib/Phylosift/Summarize.pm line 367. Use of uninitialized value in concatenation (.) or string at /home/koadman/software/phylosift_20130813/bin/../lib/Phylosift/Summarize.pm line 367. Use of uninitialized value in concatenation (.) or string at /home/koadman/software/phylosift_20130813/bin/../lib/Phylosift/Summarize.pm line 367. Use of uninitialized value in concatenation (.) or string at /home/koadman/software/phylosift_20130813/bin/../lib/Phylosift/Summarize.pm line 367. Use of uninitialized value in concatenation (.) or string at /home/koadman/software/phylosift_20130813/bin/../lib/Phylosift/Summarize.pm line 367. Use of uninitialized value in concatenation (.) or string at /home/koadman/software/phylosift_20130813/bin/../lib/Phylosift/Summarize.pm line 367. Use of uninitialized value in concatenation (.) or string at /home/koadman/software/phylosift_20130813/bin/../lib/Phylosift/Summarize.pm line 367.

renaming bug?

— Reply to this email directly or view it on GitHubhttps://github.com/gjospin/PhyloSift/issues/433#issuecomment-22603135 .