trim-low-abund.py fails with zero exit status: graph structure is too small

[fungs]

Hi,

I just ran khmer for kmer pruning on > 300 samples in quiet mode. Somewhere in the middle, I got this on stderr (I didn't log stderr, my bad).

**
** ERROR: the graph structure is too small for 
** this data set.  Increase data structure size
** with --max_memory_usage/-M.
**
** Do not use these results!!
**
** (estimated false positive rate of 0.889; max recommended 0.800)
**

When I screen throught the running stats, all jobs have zero exit status. Sorry, this is really ..., basic programming. Now I probably have to redo computations for all files because khmer does not do proper error reporting.

Best, Johannes

[ctb]

Hi Johannes, definitely a bug. What script are you running?

[ctb]

(installed version would also be useful!)

[fungs]

Sorry, I forgot the details:

trim-low-abund.py -C 3 -Z 18 -V -M 4e9 -T $TMPDIR -q -o - $infile | pigz > ${outfile}

[fungs]

I installed the latest version via pip, which is 2.1.2

[fungs]

Please check but I think this might be the same pipe issue as in #1853, sorry about that.

[ctb]

willcheck - again, regardless of where the problem lies, we really appreciate the report!