Closed GoogleCodeExporter closed 9 years ago
This is unfortunately in conflict with an earlier report I’ve received,
please see http://code.google.com/p/cutadapt/issues/detail?id=20 . There the
explicit request was made to send statistics to stdout if -o is used.
The problem was that Galaxy (in the version current at that time) interpreted
it as an error if anything was written to stderr. I guess the correct fix would
have been to introduce a '--report-file' option that determines where to send
the statistics. However, unless you have compelling arguments, I’m reluctant
to change behavior again as this would break existing scripts.
Original comment by marcel.m...@tu-dortmund.de
on 18 Jan 2013 at 12:47
I cannot change this anymore, so closing.
Original comment by marcel.m...@tu-dortmund.de
on 5 Nov 2014 at 12:26
I think this is important, since the output is contaminated with the report, it
would be best to sent to --report_file when stdout is used.
Original comment by oabiogro...@gmail.com
on 1 Jul 2015 at 6:33
Please comment at https://github.com/marcelm/cutadapt/issues/70 instead. The
bugtracker here is not used anymore.
There is no need for a --report-file option since you can always redirect it.
Use either
cutadapt ... -o file.fastq > report.txt
or
cutadapt ... > file.fastq 2> report.txt
Unless you use -o - or -o /dev/stdout, trimmed reads and the report are always
sent to different streams.
Original comment by marcel.m...@tu-dortmund.de
on 1 Jul 2015 at 8:12
Original issue reported on code.google.com by
simon.po...@eaglegenomics.com
on 18 Jan 2013 at 11:10