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When I run the 'make test' after a successful setup of the environment and pipeline, I get the following error:
(raseenv) analynano@analynano:/media/analynano/Data500GB/ArnieFiles/rase-pipeline$ prophyle decompress "database/spneumoniae-sparc.k18.tar.gz" database
[prophyle] 2019-10-15 16:15:26 Shell command: make -j -s -C /home/analynano/miniconda3/envs/raseenv/lib/python3.7/site-packages/prophyle
prophyle_assembler.cpp:43:10: fatal error: zlib.h: No such file or directory
#include <zlib.h>
^~~~~~~~
compilation terminated.
make[1]: *** [Makefile:13: prophyle_assembler.o] Error 1
make: *** [Makefile:14: compile_assembler] Error 2
[prophyle] 2019-10-15 16:15:26 Unfinished, an error occurred (error code 2, 0.8 MB used): make -j -s -C /home/analynano/miniconda3/e
nvs/raseenv/lib/python3.7/site-packages/prophyle
ProPhyle Error: A command failed, see messages above.

There is a zlib.h in /home/analynano/miniconda3/envs/raseenv/include. And it is referenced in $CFLAGS:

(raseenv) analynano@analynano:/media/analynano/Data500GB/ArnieFiles/rase-pipeline/rase$ echo $CFLAGS
-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/analynano/miniconda3/envs/raseenv/include

What could I be missing?

hi,
I have classified reads wiht prophyle successfully. Afterwards I wanted to use the RASE predict tool.

command:
python3 rase_predict.py /sparc/spneumoniae-sparc.k18/tree.nw /sparc/spneumoniae-sparc.k18.tsv prophyle_read.bam > output.tsv1

error:
Antibiotics in the RASE DB: cro, ery, pen, sxt, tet
datetime reads kbps kkmers ks ls ls_pass ln alt_ln bm bm_serotype bm_ST cro_ss cro_pred cro_bm ery_ss ery_pred ery_bm pen_ss pen_pred pen_bm sxt_ss sxt_pred sxt_bm tet_ss tet_pred tet_bm
2020-03-20 11:25:23 0 0 0 0.000 0 0 NA NA NA NA NA 0.000 R NA (NA) 0.000 R NA (NA) 0.000 R NA (NA) 0.000 R NA (NA)0.000 R NA (NA)
Time t=0h1m: 0 reads and 0 kbps.
Traceback (most recent call last):
File "scripts/rase/rase_predict.py", line 985, in
main()
File "scripts/rase/rase_predict.py", line 979, in main
r.run()
File "scripts/rase/rase_predict.py", line 201, in run
self.stats.update_from_read(read_stats)
File "scripts/rase/rase_predict.py", line 519, in update_from_read
bestmatching_isolates = self._descending_isolates(*nnames)
File "scripts/rase/rase_predict.py", line 450, in _descending_isolates
isolates |= self._descending_isolates_d[nname]
KeyError: '281310'

Like here: https://bioinformatics.stackexchange.com/questions/2913/how-to-specify-resources-for-cluster-in-snakemake

Can differ between timeline and selected plots, based on the stop detection approach (e.g., 15h vs. 17h)