Failure on analysing SRA samples
HAMLET crashes on plot_itd_flt3 for a number of SRA samples from a leukemia cell line:
SRR8615628
SRR8616093
SRR8615762
[Tue Dec 17 06:39:01 2019] python /exports/hem-leukemia/production/deps/rose-dt-plot.py --sample-id SRR8615762 --mode per-event /exports/hem-leukemia/rrvandenberg/cell-lines/output/SRR8615762/itd/SRR8615762.flt3.csv /exports/hem-leukemia/rrvandenberg/cell-lines/output/SRR8615762/itd/SRR8615762.flt3.bg.csv /exports/hem-leukemia/rrvandenberg/cell-lines/output/SRR8615762/itd/SRR8615762.flt3.png
[Tue Dec 17 06:39:01 2019] Activating conda environment /exports/hem-leukemia/aml-downsample/conda-run/3ee6a7e2.
plotting rose events of sample 'SRR8615762' ...
Traceback (most recent call last):
File "/exports/hem-leukemia/production/deps/rose-dt-plot.py", line 433, in <module>
main()
File "/exports/hem-leukemia/aml-downsample/conda-run/3ee6a7e2/lib/python3.6/site-packages/click/core.py", line 722, in __call__
return self.main(*args, **kwargs)
File "/exports/hem-leukemia/aml-downsample/conda-run/3ee6a7e2/lib/python3.6/site-packages/click/core.py", line 697, in main
rv = self.invoke(ctx)
File "/exports/hem-leukemia/aml-downsample/conda-run/3ee6a7e2/lib/python3.6/site-packages/click/core.py", line 895, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/exports/hem-leukemia/aml-downsample/conda-run/3ee6a7e2/lib/python3.6/site-packages/click/core.py", line 535, in invoke
return callback(*args, **kwargs)
File "/exports/hem-leukemia/production/deps/rose-dt-plot.py", line 425, in main
plot_per_event(rose_df, bg_df, output, sample_id, show_pileup)
File "/exports/hem-leukemia/production/deps/rose-dt-plot.py", line 69, in plot_per_event
lowerypad=0.25, upperypad=0.3)
File "/exports/hem-leukemia/production/deps/rose-dt-plot.py", line 44, in calc_limits
xmin = min(bgd["position"])
ValueError: min() arg is an empty sequence
See an example log file for details /exports/hem-leukemia/rrvandenberg/cell-lines/drmaa-logs/hamlet.81.e4594532