Hi,
When running shhh.flows in the new V1.23 I get an error at the ‘Finalizing’ stage, which looks like this (I replaced here my endless path names with ‘/file.path/’, for short):
Finalizing…
[ERROR]: Could not open /file.path/RTL2011.08.HaIS_1_arc.fwd.shhh.qual
[ERROR]: Could not open /file.path/RTL2011.08.HaIS_1_arc.fwd.shhh.fasta
[ERROR]: Could not open /file.path/RTL2011.08.HaIS_1_arc.fwd.shhh.names
[ERROR]: Could not open /file.path/RTL2011.08.HaIS_1_arc.fwd.shhh.counts
[ERROR]: Could not open /file.path/RTL2011.08.HaIS_1_arc.fwd.shhh.groups
Total time to process /file.path/RTL2011.08.HaIS_1_arc.fwd.flow: 0 0.49
mothur then moves to the next flow file but at the end of the process I have empty .fasta and .names files.
Looking at the output more closely I notice that the /file.path/ in the Error msg is in fact twice the file path concatenated.
The problem persists on both windows and linux and on different machines.
Running the command on the previous mothur version (V1.22.2) gives no error and the file path at the ‘Finalizing’ step isnt concatenated.
Roey