I've updated to 1.4 now (which removes the earlier problems), but I'm running into new trouble. It seems that necessary output files are not created (see below). Do you have an idea why this is the case?
ERROR: The following critical files could not be used
./Metassembly/QSPAdes.MIRA/QSPAdes.MIRA.delta
./Metassembly/QSPAdes.MIRA/QSPAdes.MIRA.mgaps
./Metassembly/QSPAdes.MIRA/QSPAdes.MIRA.ntref
Check your paths and file permissions and try again
As suggested by nucmer, this typically arises when one of the input files
is not readable or the output is not writable. Could you double check that
the files "./MIRA/MIRA.fa" and "./SPAdes/SPAdes.fa" are readable? I noticed
you set the output directory to './', I am thinking that if you had an
already existent directory and file "./MIRA/MIRA.fa" or "./SPAdes/SPAdes.fa"
this could have been replaced by the file (actually a symbolic link) that
the metassemble script creates in this path, removing the sequence content
and causing nucmer to crash. On the other hand, if that is not the case,
could you check whether the directory "./Metassembly/QSPAdes.MIRA" exists
and is writable?. If this directory doesn't exists then the error may have
arisen earlier in the pipeline.
I've updated to 1.4 now (which removes the earlier problems), but I'm
running into new trouble. It seems that necessary output files are not
created (see below). Do you have an idea why this is the case?
ERROR: The following critical files could not be used
./Metassembly/QSPAdes.MIRA/QSPAdes.MIRA.delta
./Metassembly/QSPAdes.MIRA/QSPAdes.MIRA.mgaps
./Metassembly/QSPAdes.MIRA/QSPAdes.MIRA.ntref
Check your paths and file permissions and try again
I've updated to 1.4 now (which removes the earlier problems), but I'm running into new trouble. It seems that necessary output files are not created (see below). Do you have an idea why this is the case?
Cheers,
Bastian
---------- Run bash command ----------
nucmer ./MIRA/MIRA.fa ./SPAdes/SPAdes.fa:
nucmer --maxmatch -l 50 -c 300 -p ./Metassembly/QSPAdes.MIRA/QSPAdes.MIRA ./MIRA/MIRA.fa ./SPAdes/SPAdes.fa ...
ERROR: The following critical files could not be used
./Metassembly/QSPAdes.MIRA/QSPAdes.MIRA.delta
./Metassembly/QSPAdes.MIRA/QSPAdes.MIRA.mgaps
./Metassembly/QSPAdes.MIRA/QSPAdes.MIRA.ntref
Check your paths and file permissions and try again
---------- Run bash command ----------
delta-filter ./Metassembly/QSPAdes.MIRA/QSPAdes.MIRA.delta:
delta-filter -1 ./Metassembly/QSPAdes.MIRA/QSPAdes.MIRA.delta ...
ERROR: Could not parse delta file, ./Metassembly/QSPAdes.MIRA/QSPAdes.MIRA.delta
error no: 400
---------- Run bash command ----------
show-coords ./Metassembly/QSPAdes.MIRA/QSPAdes.MIRA.1delta:
show-coords -cHlTr ./Metassembly/QSPAdes.MIRA/QSPAdes.MIRA.1delta ...
ERROR: Could not parse delta file, ./Metassembly/QSPAdes.MIRA/QSPAdes.MIRA.1delta
error no: 402
Hi Bastian,
This is an error message raised by nucmer, when trying to run:
nucmer --maxmatch -l 50 -c 300 -p ./Metassembly/QSPAdes.MIRA/QSPAdes.MIRA
./MIRA/MIRA.fa ./SPAdes/SPAdes.fa
As suggested by nucmer, this typically arises when one of the input files
is not readable or the output is not writable. Could you double check that
the files "./MIRA/MIRA.fa" and "./SPAdes/SPAdes.fa" are readable? I noticed
you set the output directory to './', I am thinking that if you had an
already existent directory and file "./MIRA/MIRA.fa" or "./SPAdes/SPAdes.fa"
this could have been replaced by the file (actually a symbolic link) that
the metassemble script creates in this path, removing the sequence content
and causing nucmer to crash. On the other hand, if that is not the case,
could you check whether the directory "./Metassembly/QSPAdes.MIRA" exists
and is writable?. If this directory doesn't exists then the error may have
arisen earlier in the pipeline.
Wences
On Tue, May 5, 2015 at 1:56 AM, Bastian Greshake gedankenstuecke@users.sf.net wrote:
Thanks, I'll have a look into it!
It seems the problem was not setting the output directory, so "./" was used, which messed things up. Now it works. :-)