ddsommer

Yes that is correct it is failing because of the missing CTG files. Is there a amos log file with logging from the casm-layout step? On Sat, Apr 25, 2020 at 12:34 PM Francesco Cicconardi francicco@users.sourceforge.net wrote: Hi, I think consensus fails because layout didn't generate the file. layout also finishes without error messages Thanks a lot F [bugs:#29] https://sourceforge.net/p/amos/bugs/29/ casm-layout ERROR* Status: open Group: v1.x.x Created: Wed Apr 15, 2020 02:37 PM UTC by Francesco...

How are you running "concensus" if the casm-layout program had already failed to produce the CTG bank files? What was the error or log from casm-layout? On Wed, Apr 15, 2020 at 10:37 AM Francesco Cicconardi francicco@users.sourceforge.net wrote: Unfortunately casm-layout: casm-layout -t 1000 -U ${supercontigs}.layout -C ${supercontigs}.conflict -b ${supercontigs}.bnk ${supercontigs}.delta fails to generate the some files, specifically CTG.0.map, CTG.0.0.fix and CTG.0.0.var I get the following error...

The wiki is back up and running at http://amos.sourceforge.net/wiki/index.php/AMOS...

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