koadman
commented
5 years ago Hi Xin, can you post the contents of the following files please: /oasis/projects/nsf/csd465/xif033/scripts/DESMAN/work/8d/36dd7b4706010e6adf6e24fc00696f/outputsel_var.csv /oasis/projects/nsf/csd465/xif033/scripts/DESMAN/work/8d/36dd7b4706010e6adf6e24fc00696f/outputtran_df.csv
either here if it is small or somewhere else and then send a link please?
One issue we've seen previously is that the workflow fails with an error when there are no variants in the 37 universal genes. Knowing what's in those files will help tell us whether that's the problem, or if it's something else.
xif033
Hello,
I am running desmanflow automated flow on my dataset. It works on most of my samples, but for a few samples I am getting the following error and I am wondering if you have recommendations to fix it :
ERROR ~ Error executing process > 'estimateStrainCountDesman (19)'
Caused by: Process
estimateStrainCountDesman (19)terminated with an error exit status (1)Command executed:
/home/xif033/tools/DESMAN//bin/desman outputsel_var.csv -e outputtran_df.csv -o cluster_9_2 -r 1000 -i 100 -g 9 -s 2 > cluster_9_2.out cp */fit.txt fit_9_2.txt
Command exit status: 1
Command output: (empty)
Command error: Up and running. Check cluster_9_2/log_file.txt for progress /home/xif033/.local/lib/python3.4/site-packages/desman-2.1.1-py3.4-linux-x86_64.egg/desman/Variant_Filter.py:74: FutureWarning: Method .as_matrix will be removed in a future version. Use .va lues instead. variants_matrix = variants.as_matrix() /home/xif033/.local/lib/python3.4/site-packages/numpy/core/fromnumeric.py:2920: RuntimeWarning: Mean of empty slice. out=out, kwargs) Traceback (most recent call last): File "/home/xif033/tools/DESMAN//bin/desman", line 246, in
main(sys.argv[1:])
File "/home/xif033/tools/DESMAN//bin/desman", line 95, in main
min_coverage=min_coverage, qvalue_cutoff=max_qvalue)
File "/home/xif033/.local/lib/python3.4/site-packages/desman-2.1.1-py3.4-linux-x86_64.egg/desman/Variant_Filter.py", line 81, in init
vs_mean = np.mean(vs_sum,axis=0)
File "/home/xif033/.local/lib/python3.4/site-packages/numpy/core/fromnumeric.py", line 2920, in mean
out=out, kwargs)
File "/home/xif033/.local/lib/python3.4/site-packages/numpy/core/_methods.py", line 78, in _mean
ret, rcount, out=ret, casting='unsafe', subok=False)
ZeroDivisionError: division by zero
Work dir: /oasis/projects/nsf/csd465/xif033/scripts/DESMAN/work/8d/36dd7b4706010e6adf6e24fc00696f
Tip: when you have fixed the problem you can continue the execution appending to the nextflow command line the option
-resume-- Check '.nextflow.log' file for details WARN: Killing pending tasks (24)
I'd really appreciate any suggestions! Best, Xin