'LIBNAME.phyloFlash.NTUabundance.csv'-file not generated

[Mathildebd]

Hi,

I have a weird issue, for two of my samples a number of files are not generated. The bbmap.sam file and histogram are made, but then the rest is not, and no report- or log-file is written. For a while I thought the job was cancelled to to time limit, but that doesn't seem to be the case... In this particular case I am only interested in the 'LIBNAME.phyloFlash.NTUabundance.csv'. Is there a command that will generate this summary file for me? (since the bbmap.sam file is there I am thinking this must be pretty simple.... yet I don't know what such a command would look like).

Would greatly appreciate it if someone could help me with this, so I can move on, there seems not to be anything wrong with these two samples, so I don't want to just discard them.

An explanation to what might be causing this is of course also very welcome, in case I experience this again next time.